RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7029
(125 letters)
>gnl|CDD|226674 COG4221, COG4221, Short-chain alcohol dehydrogenase of unknown
specificity [General function prediction only].
Length = 246
Score = 78.8 bits (195), Expect = 4e-19
Identities = 37/117 (31%), Positives = 54/117 (46%), Gaps = 31/117 (26%)
Query: 2 SKIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVI 61
K+ ++TGAS GIG A RALA G +V+ ARR E ++
Sbjct: 6 GKVALITGASSGIGEATARALAEAGAKVVLAARREERLE--------------------- 44
Query: 62 GFARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGV 118
A+A E +L +DVT A V A + + +FG ID+++NNAG+
Sbjct: 45 ----------ALADEIGAGAALALALDVTDRAAVEAAIEALPEEFGRIDILVNNAGL 91
>gnl|CDD|187632 cd05374, 17beta-HSD-like_SDR_c, 17beta hydroxysteroid
dehydrogenase-like, classical (c) SDRs.
17beta-hydroxysteroid dehydrogenases are a group of
isozymes that catalyze activation and inactivation of
estrogen and androgens. 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 15-hydroxyprostaglandin
dehydrogenase (15-PGDH) numbering). In addition to the
Tyr and Lys, there is often an upstream Ser (Ser-138,
15-PGDH numbering) and/or an Asn (Asn-107, 15-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 ketoacyl
reductases 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 = 248
Score = 75.0 bits (185), Expect = 2e-17
Identities = 35/122 (28%), Positives = 57/122 (46%), Gaps = 32/122 (26%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K++++TG S GIG A+ ALAA+G++VI AR + ++
Sbjct: 1 KVVLITGCSSGIGLALALALAAQGYRVIATARNPDKLE---------------------- 38
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNEFA 122
N + +V L++DVT + + A + +FG IDV++NNAG F
Sbjct: 39 --------SLGELLNDNLEV--LELDVTDEESIKAAVKEVIERFGRIDVLVNNAGYGLFG 88
Query: 123 PV 124
P+
Sbjct: 89 PL 90
>gnl|CDD|187601 cd05343, Mgc4172-like_SDR_c, human Mgc4172-like, classical (c)
SDRs. Human Mgc4172-like proteins, putative SDRs. These
proteins are members of the SDR family, with a canonical
active site tetrad and a typical Gly-rich NAD-binding
motif. 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
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-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 ketoacyl reductases 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 = 250
Score = 71.4 bits (175), Expect = 3e-16
Identities = 33/116 (28%), Positives = 53/116 (45%), Gaps = 28/116 (24%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
++ +VTGASVGIGAA+ RAL G +V+G ARR + I
Sbjct: 7 RVALVTGASVGIGAAVARALVQHGMKVVGCARRVDKI----------------------- 43
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGV 118
E + A + + + D++ + +++ F I + +DV INNAG+
Sbjct: 44 -----EALAAECQSAGYPTLFPYQCDLSNEEQILSMFSAIRTQHQGVDVCINNAGL 94
>gnl|CDD|212491 cd05233, SDR_c, classical (c) SDRs. 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 ketoacyl reductases 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 = 234
Score = 67.7 bits (166), Expect = 6e-15
Identities = 29/120 (24%), Positives = 49/120 (40%), Gaps = 30/120 (25%)
Query: 5 IVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIGFA 64
+VTGAS GIG AI R LA +G +V+ R E
Sbjct: 1 ALVTGASSGIGRAIARRLAREGAKVVLADRNEE--------------------------- 33
Query: 65 RRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNEFAPV 124
+ A+ +++ DV+ + +V + +FG +D+++NNAG+ P+
Sbjct: 34 -ALAELAAIEALGG--NAVAVQADVSDEEDVEALVEEALEEFGRLDILVNNAGIARPGPL 90
>gnl|CDD|223959 COG1028, FabG, Dehydrogenases with different specificities (related
to short-chain alcohol dehydrogenases) [Secondary
metabolites biosynthesis, transport, and catabolism /
General function prediction only].
Length = 251
Score = 67.5 bits (165), Expect = 1e-14
Identities = 41/123 (33%), Positives = 57/123 (46%), Gaps = 27/123 (21%)
Query: 1 MSKIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQV 60
K+ +VTGAS GIG AI RALA +G +V+ ARR+E
Sbjct: 4 SGKVALVTGASSGIGRAIARALAREGARVVVAARRSE----------------------- 40
Query: 61 IGFARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEA-FDWINNKFGHIDVMINNAGVN 119
AE + A KE + ++ DV+ D E VEA +FG ID+++NNAG+
Sbjct: 41 ---EEAAEALAAAIKEAGGGRAAAVAADVSDDEESVEALVAAAEEEFGRIDILVNNAGIA 97
Query: 120 EFA 122
Sbjct: 98 GPD 100
>gnl|CDD|180448 PRK06182, PRK06182, short chain dehydrogenase; Validated.
Length = 273
Score = 67.7 bits (166), Expect = 1e-14
Identities = 41/117 (35%), Positives = 52/117 (44%), Gaps = 37/117 (31%)
Query: 2 SKIIVVTGASVGIGAAILRALAAKGHQVIGFARRAE-MIDFAESLFAFFVDIVAAKGHQV 60
K+ +VTGAS GIG A R LAA+G+ V G ARR + M D A
Sbjct: 3 KKVALVTGASSGIGKATARRLAAQGYTVYGAARRVDKMEDLASL---------------- 46
Query: 61 IGFARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAG 117
VH L +DVT +A + A D I + G IDV++NNAG
Sbjct: 47 --------------------GVHPLSLDVTDEASIKAAVDTIIAEEGRIDVLVNNAG 83
>gnl|CDD|187604 cd05346, SDR_c5, classical (c) SDR, subgroup 5. These proteins are
members of the classical SDR family, with a canonical
active site tetrad and a typical Gly-rich NAD-binding
motif. 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
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-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 ketoacyl reductases 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 = 249
Score = 66.9 bits (164), Expect = 1e-14
Identities = 34/115 (29%), Positives = 52/115 (45%), Gaps = 28/115 (24%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K +++TGAS GIG A R A G ++I RRAE
Sbjct: 1 KTVLITGASSGIGEATARRFAKAGAKLILTGRRAE------------------------- 35
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAG 117
R E+ D + + P KV L++DV+ + A + + +F ID+++NNAG
Sbjct: 36 --RLQELADELGAKFPV-KVLPLQLDVSDRESIEAALENLPEEFRDIDILVNNAG 87
>gnl|CDD|223377 COG0300, DltE, Short-chain dehydrogenases of various substrate
specificities [General function prediction only].
Length = 265
Score = 66.1 bits (162), Expect = 4e-14
Identities = 32/126 (25%), Positives = 51/126 (40%), Gaps = 30/126 (23%)
Query: 1 MSKIIVVTGASVGIGAAILRALAAKGHQVIGFARRAE-MIDFAESLFAFFVDIVAAKGHQ 59
K ++TGAS GIGA + + LA +G+ +I ARR + + A+ L
Sbjct: 5 KGKTALITGASSGIGAELAKQLARRGYNLILVARREDKLEALAKEL---------EDKTG 55
Query: 60 VIGFARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVN 119
V +V + D++ + D + + G IDV++NNAG
Sbjct: 56 V--------------------EVEVIPADLSDPEALERLEDELKERGGPIDVLVNNAGFG 95
Query: 120 EFAPVT 125
F P
Sbjct: 96 TFGPFL 101
>gnl|CDD|235546 PRK05653, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Validated.
Length = 246
Score = 64.8 bits (159), Expect = 8e-14
Identities = 35/124 (28%), Positives = 51/124 (41%), Gaps = 29/124 (23%)
Query: 1 MSKIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQV 60
K +VTGAS GIG AI LAA G +V+ + E AE+L + A G +
Sbjct: 4 QGKTALVTGASRGIGRAIALRLAADGAKVVIYDSNEEA---AEAL----AAELRAAGGEA 56
Query: 61 IGFARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNE 120
L DV+ +A V + FG +D+++NNAG+
Sbjct: 57 RV----------------------LVFDVSDEAAVRALIEAAVEAFGALDILVNNAGITR 94
Query: 121 FAPV 124
A +
Sbjct: 95 DALL 98
>gnl|CDD|187584 cd05323, ADH_SDR_c_like, insect type alcohol dehydrogenase
(ADH)-like, classical (c) SDRs. This subgroup contains
insect type ADH, and 15-hydroxyprostaglandin
dehydrogenase (15-PGDH) type I; these proteins are
classical SDRs. ADH catalyzes the NAD+-dependent
oxidation of alcohols to aldehydes/ketones. This
subgroup is distinct from the zinc-dependent alcohol
dehydrogenases of the medium chain
dehydrogenase/reductase family, and evolved in fruit
flies to allow the digestion of fermenting fruit.
15-PGDH catalyzes the NAD-dependent interconversion of
(5Z,13E)-(15S)-11alpha,15-dihydroxy-9-oxoprost-13-enoate
and (5Z,13E)-11alpha-hydroxy-9,15-dioxoprost-13-enoate,
and has a typical SDR glycine-rich NAD-binding motif,
which is not fully present in ADH. 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
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-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 ketoacyl reductases 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 = 244
Score = 63.9 bits (156), Expect = 2e-13
Identities = 28/118 (23%), Positives = 46/118 (38%), Gaps = 29/118 (24%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K+ ++TG + GIG A + L KG +V ++
Sbjct: 1 KVAIITGGASGIGLATAKLLLKKGAKVA-----------------------------ILD 31
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNE 120
+ NP K ++ DVT ++ AF KFG +D++INNAG+ +
Sbjct: 32 RNENPGAAAELQAINPKVKATFVQCDVTSWEQLAAAFKKAIEKFGRVDILINNAGILD 89
>gnl|CDD|235990 PRK07326, PRK07326, short chain dehydrogenase; Provisional.
Length = 237
Score = 63.9 bits (156), Expect = 2e-13
Identities = 42/125 (33%), Positives = 55/125 (44%), Gaps = 32/125 (25%)
Query: 1 MSKIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQV 60
K+ ++TG S GIG AI AL A+G++V I
Sbjct: 5 KGKVALITGGSKGIGFAIAEALLAEGYKV--------AI--------------------- 35
Query: 61 IGFARRAEMIDAMAKE-NPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVN 119
AR + ++ A E N V L DV +A+V A D I FG +DV+I NAGV
Sbjct: 36 --TARDQKELEEAAAELNNKGNVLGLAADVRDEADVQRAVDAIVAAFGGLDVLIANAGVG 93
Query: 120 EFAPV 124
FAPV
Sbjct: 94 HFAPV 98
>gnl|CDD|181721 PRK09242, PRK09242, tropinone reductase; Provisional.
Length = 257
Score = 64.0 bits (156), Expect = 2e-13
Identities = 33/117 (28%), Positives = 52/117 (44%), Gaps = 27/117 (23%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
+ ++TGAS GIG AI R G V+ AR A+ + A
Sbjct: 10 QTALITGASKGIGLAIAREFLGLGADVLIVARDADALAQAR------------------- 50
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVN 119
D +A+E P+ +VH L DV+ D + DW+ + + + +++NNAG N
Sbjct: 51 --------DELAEEFPEREVHGLAADVSDDEDRRAILDWVEDHWDGLHILVNNAGGN 99
>gnl|CDD|235725 PRK06179, PRK06179, short chain dehydrogenase; Provisional.
Length = 270
Score = 63.8 bits (156), Expect = 3e-13
Identities = 38/123 (30%), Positives = 50/123 (40%), Gaps = 37/123 (30%)
Query: 2 SKIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVI 61
SK+ +VTGAS GIG A LA G++V G +R
Sbjct: 4 SKVALVTGASSGIGRATAEKLARAGYRVFGTSRNP------------------------- 38
Query: 62 GFARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNEF 121
A+ P V L++DVT DA V A D + + G IDV++NNAGV
Sbjct: 39 ------------ARAAPIPGVELLELDVTDDASVQAAVDEVIARAGRIDVLVNNAGVGLA 86
Query: 122 APV 124
Sbjct: 87 GAA 89
>gnl|CDD|235500 PRK05557, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Validated.
Length = 248
Score = 62.5 bits (153), Expect = 6e-13
Identities = 36/116 (31%), Positives = 53/116 (45%), Gaps = 28/116 (24%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K+ +VTGAS GIG AI LAA+G V+ +E AE+L V + A G
Sbjct: 6 KVALVTGASRGIGRAIAERLAAQGANVVINYASSE--AGAEAL----VAEIGALGG---- 55
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGV 118
K +++ DV+ V A D +FG +D+++NNAG+
Sbjct: 56 ------------------KALAVQGDVSDAESVERAVDEAKAEFGGVDILVNNAGI 93
>gnl|CDD|235935 PRK07109, PRK07109, short chain dehydrogenase; Provisional.
Length = 334
Score = 61.9 bits (151), Expect = 2e-12
Identities = 32/123 (26%), Positives = 47/123 (38%), Gaps = 29/123 (23%)
Query: 2 SKIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVI 61
+++V+TGAS G+G A RA A +G +V+ AR E ++ + A G + +
Sbjct: 8 RQVVVITGASAGVGRATARAFARRGAKVVLLARGEEGLEAL-------AAEIRAAGGEAL 60
Query: 62 GFARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNEF 121
DV V A D + G ID +NNA V F
Sbjct: 61 AVV----------------------ADVADAEAVQAAADRAEEELGPIDTWVNNAMVTVF 98
Query: 122 APV 124
P
Sbjct: 99 GPF 101
>gnl|CDD|235794 PRK06398, PRK06398, aldose dehydrogenase; Validated.
Length = 258
Score = 61.4 bits (149), Expect = 2e-12
Identities = 31/122 (25%), Positives = 50/122 (40%), Gaps = 40/122 (32%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K+ +VTG S GIG A++ L +G VI F
Sbjct: 7 KVAIVTGGSQGIGKAVVNRLKEEGSNVINFDI---------------------------- 38
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNEFA 122
KE V KVDV+ +V++ D++ +K+G ID+++NNAG+ +
Sbjct: 39 ------------KEPSYNDVDYFKVDVSNKEQVIKGIDYVISKYGRIDILVNNAGIESYG 86
Query: 123 PV 124
+
Sbjct: 87 AI 88
>gnl|CDD|187594 cd05333, BKR_SDR_c, beta-Keto acyl carrier protein reductase (BKR),
involved in Type II FAS, classical (c) SDRs. This
subgroup includes the Escherichai coli K12 BKR, FabG.
BKR catalyzes the NADPH-dependent reduction of ACP in
the first reductive step of de novo fatty acid synthesis
(FAS). FAS consists of four elongation steps, which are
repeated to extend the fatty acid chain through the
addition of two-carbo units from malonyl acyl-carrier
protein (ACP): condensation, reduction, dehydration, and
a final reduction. Type II FAS, typical of plants and
many bacteria, maintains these activities on discrete
polypeptides, while type I FAS utilizes one or two
multifunctional polypeptides. BKR resembles enoyl
reductase, which catalyzes the second reduction step in
FAS. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with
structurally conserved Rossmann fold (alpha/beta folding
pattern with a central beta-sheet) 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 have a 3-glycine N-terminal NAD(P)(H) binding
pattern: TGxxxGxG in classical SDRs. 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 type ketoacyl reductases 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. A critical catalytic Tyr residue
(Tyr-151, human 15-hydroxyprostaglandin dehydrogenase
(15-PGDH) numbering), is often found in a conserved
YXXXK pattern. In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) or additional
Ser, contributing to the active site. Substrates for
these enzymes include sugars, steroids, alcohols, and
aromatic compounds. The standard reaction mechanism is a
proton relay involving the conserved Tyr-151 and
Lys-155, and well as Asn-111 (or Ser). Some SDR family
members, including 17 beta-hydroxysteroid dehydrogenase
contain an additional helix-turn-helix motif that is not
generally found among SDRs.
Length = 240
Score = 61.0 bits (149), Expect = 2e-12
Identities = 30/116 (25%), Positives = 46/116 (39%), Gaps = 29/116 (25%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K+ +VTGAS GIG AI LAA+G +V R E
Sbjct: 1 KVALVTGASRGIGRAIALRLAAEGAKVAVTDRSEE------------------------- 35
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGV 118
A + +L+ DV+ V + + +FG +D+++NNAG+
Sbjct: 36 ----AAAETVEEIKALGGNAAALEADVSDREAVEALVEKVEAEFGPVDILVNNAGI 87
>gnl|CDD|187605 cd05347, Ga5DH-like_SDR_c, gluconate 5-dehydrogenase (Ga5DH)-like,
classical (c) SDRs. Ga5DH catalyzes the NADP-dependent
conversion of carbon source D-gluconate and
5-keto-D-gluconate. This SDR subgroup has a classical
Gly-rich NAD(P)-binding motif and a conserved active
site tetrad pattern. However, it has been proposed that
Arg104 (Streptococcus suis Ga5DH numbering), as well as
an active site Ca2+, play a critical role in catalysis.
In addition to Ga5DHs this subgroup contains Erwinia
chrysanthemi KduD which is involved in pectin
degradation, and is a putative
2,5-diketo-3-deoxygluconate dehydrogenase. 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
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107,15-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 ketoacyl reductases 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 = 248
Score = 60.8 bits (148), Expect = 3e-12
Identities = 31/123 (25%), Positives = 48/123 (39%), Gaps = 29/123 (23%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K+ +VTGAS GIG I LA G ++ +R E + A+ L
Sbjct: 6 KVALVTGASRGIGFGIASGLAEAGANIVINSRNEEKAEEAQQLI---------------- 49
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNEFA 122
E + + DV+ + + A + I FG ID+++NNAG+
Sbjct: 50 -------------EKEGVEATAFTCDVSDEEAIKAAVEAIEEDFGKIDILVNNAGIIRRH 96
Query: 123 PVT 125
P
Sbjct: 97 PAE 99
>gnl|CDD|233590 TIGR01830, 3oxo_ACP_reduc, 3-oxoacyl-(acyl-carrier-protein)
reductase. This model represents 3-oxoacyl-[ACP]
reductase, also called 3-ketoacyl-acyl carrier protein
reductase, an enzyme of fatty acid biosynthesis [Fatty
acid and phospholipid metabolism, Biosynthesis].
Length = 239
Score = 60.3 bits (147), Expect = 3e-12
Identities = 34/113 (30%), Positives = 51/113 (45%), Gaps = 28/113 (24%)
Query: 6 VVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIGFAR 65
+VTGAS GIG AI LA +G +VI R +E AE + V+ + A G + +G
Sbjct: 2 LVTGASRGIGRAIALKLAKEGAKVIITYRSSEEG--AEEV----VEELKAYGVKALGV-- 53
Query: 66 RAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGV 118
DV+ +V + I + G ID+++NNAG+
Sbjct: 54 --------------------VCDVSDREDVKAVVEEIEEELGPIDILVNNAGI 86
>gnl|CDD|235924 PRK07063, PRK07063, short chain dehydrogenase; Provisional.
Length = 260
Score = 60.1 bits (146), Expect = 7e-12
Identities = 39/120 (32%), Positives = 55/120 (45%), Gaps = 27/120 (22%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K+ +VTGA+ GIGAAI RA A +G V D+ AA +
Sbjct: 8 KVALVTGAAQGIGAAIARAFAREGAAVA------------------LADLDAALAERAA- 48
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNEFA 122
A+A++ +V ++ DVT A V A FG +DV++NNAG+N FA
Sbjct: 49 --------AAIARDVAGARVLAVPADVTDAASVAAAVAAAEEAFGPLDVLVNNAGINVFA 100
>gnl|CDD|180446 PRK06180, PRK06180, short chain dehydrogenase; Provisional.
Length = 277
Score = 59.5 bits (145), Expect = 1e-11
Identities = 30/117 (25%), Positives = 41/117 (35%), Gaps = 32/117 (27%)
Query: 1 MSKIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQV 60
K ++TG S G G RALA A GH+V
Sbjct: 3 SMKTWLITGVSSGFG----RALAQA---------------------------ALAAGHRV 31
Query: 61 IGFARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAG 117
+G R +PD + + +DVT + FG IDV++NNAG
Sbjct: 32 VGTVRSEAARADFEALHPD-RALARLLDVTDFDAIDAVVADAEATFGPIDVLVNNAG 87
>gnl|CDD|235962 PRK07201, PRK07201, short chain dehydrogenase; Provisional.
Length = 657
Score = 60.0 bits (146), Expect = 1e-11
Identities = 32/115 (27%), Positives = 45/115 (39%), Gaps = 29/115 (25%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K++++TGAS GIG A +A G V AR E +D V + AKG
Sbjct: 372 KVVLITGASSGIGRATAIKVAEAGATVFLVARNGEALDEL-------VAEIRAKGGTAHA 424
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAG 117
+ D+T A V I + GH+D ++NNAG
Sbjct: 425 YT----------------------CDLTDSAAVDHTVKDILAEHGHVDYLVNNAG 457
>gnl|CDD|212492 cd05327, retinol-DH_like_SDR_c_like, retinol dehydrogenase
(retinol-DH), Light dependent Protochlorophyllide
(Pchlide) OxidoReductase (LPOR) and related proteins,
classical (c) SDRs. Classical SDR subgroup containing
retinol-DHs, LPORs, and related proteins. Retinol is
processed by a medium chain alcohol dehydrogenase
followed by retinol-DHs. Pchlide reductases act in
chlorophyll biosynthesis. There are distinct enzymes
that catalyze Pchlide reduction in light or dark
conditions. Light-dependent reduction is via an
NADP-dependent SDR, LPOR. Proteins in this subfamily
share the glycine-rich NAD-binding motif of the
classical SDRs, have a partial match to the canonical
active site tetrad, but lack the typical active site
Ser. This subgroup includes the human proteins: retinol
dehydrogenase -12, -13 ,and -14, dehydrogenase/reductase
SDR family member (DHRS)-12 , -13 and -X (a DHRS on
chromosome X), and WWOX (WW domain-containing
oxidoreductase), as well as a Neurospora crassa SDR
encoded by the blue light inducible bli-4 gene. 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
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-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 ketoacyl reductases 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 = 269
Score = 59.2 bits (144), Expect = 1e-11
Identities = 34/118 (28%), Positives = 54/118 (45%), Gaps = 27/118 (22%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K++V+TGA+ GIG R LA +G VI R E KG +
Sbjct: 2 KVVVITGANSGIGKETARELAKRGAHVIIACRNEE------------------KGEEA-- 41
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNE 120
AE+ KE + KV +++D++ A V + + +F +D++INNAG+
Sbjct: 42 ---AAEIK----KETGNAKVEVIQLDLSSLASVRQFAEEFLARFPRLDILINNAGIMA 92
>gnl|CDD|187610 cd05352, MDH-like_SDR_c, mannitol dehydrogenase (MDH)-like,
classical (c) SDRs. NADP-mannitol dehydrogenase
catalyzes the conversion of fructose to mannitol, an
acyclic 6-carbon sugar. MDH is a tetrameric member of
the SDR family. This subgroup also includes various
other tetrameric SDRs, including Pichia stipitis
D-arabinitol dehydrogenase (aka polyol dehydrogenase),
Candida albicans Sou1p, a sorbose reductase, and Candida
parapsilosis (S)-specific carbonyl reductase (SCR, aka
S-specific alcohol dehydrogenase) which catalyzes the
enantioselective reduction of 2-hydroxyacetophenone into
(S)-1-phenyl-1,2-ethanediol. 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 have a 3-glycine N-terminal
NAD(P)(H)-binding pattern (typically, TGxxxGxG in
classical SDRs and TGxxGxxG in extended SDRs), while
substrate binding is in the C-terminal region. A
critical catalytic Tyr residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering), is often found in a conserved YXXXK pattern.
In addition to the Tyr and Lys, there is often an
upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn
(Asn-107, 15-PGDH numbering) or additional Ser,
contributing to the active site. Substrates for these
enzymes include sugars, steroids, alcohols, and aromatic
compounds. The standard reaction mechanism is a proton
relay involving the conserved Tyr and Lys, as well as
Asn (or Ser).
Length = 252
Score = 58.9 bits (143), Expect = 1e-11
Identities = 39/124 (31%), Positives = 50/124 (40%), Gaps = 30/124 (24%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQV-IGFARRAEMIDFAESLFAFFVDIVAAKGHQVI 61
K+ +VTG S GIG AI RALA G V I + + AE L AK + V
Sbjct: 9 KVAIVTGGSRGIGLAIARALAEAGADVAIIYNSAPRAEEKAEEL---------AKKYGV- 58
Query: 62 GFARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNEF 121
K + K DV+ V + F I FG ID++I NAG+
Sbjct: 59 -------------------KTKAYKCDVSSQESVEKTFKQIQKDFGKIDILIANAGITVH 99
Query: 122 APVT 125
P
Sbjct: 100 KPAL 103
>gnl|CDD|183833 PRK12939, PRK12939, short chain dehydrogenase; Provisional.
Length = 250
Score = 57.7 bits (140), Expect = 4e-11
Identities = 32/117 (27%), Positives = 49/117 (41%), Gaps = 29/117 (24%)
Query: 2 SKIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVI 61
K +VTGA+ G+GAA ALA G V F D +AA+ ++
Sbjct: 7 GKRALVTGAARGLGAAFAEALAEAGATVA------------------FNDGLAAEAREL- 47
Query: 62 GFARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGV 118
A ++A + H++ D+ A V FD G +D ++NNAG+
Sbjct: 48 -----AAALEAAGG-----RAHAIAADLADPASVQRFFDAAAAALGGLDGLVNNAGI 94
>gnl|CDD|181508 PRK08628, PRK08628, short chain dehydrogenase; Provisional.
Length = 258
Score = 57.7 bits (140), Expect = 5e-11
Identities = 40/118 (33%), Positives = 56/118 (47%), Gaps = 30/118 (25%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K+++VTG + GIGAAI LA +G + F R A +FAE L
Sbjct: 8 KVVIVTGGASGIGAAISLRLAEEGAIPVIFGRSAPDDEFAEEL----------------- 50
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNE 120
RA A ++VD+T DA+ +A + KFG ID ++NNAGVN+
Sbjct: 51 ---RALQPRA----------EFVQVDLTDDAQCRDAVEQTVAKFGRIDGLVNNAGVND 95
>gnl|CDD|183775 PRK12826, PRK12826, 3-ketoacyl-(acyl-carrier-protein) reductase;
Reviewed.
Length = 251
Score = 57.6 bits (140), Expect = 5e-11
Identities = 32/118 (27%), Positives = 49/118 (41%), Gaps = 29/118 (24%)
Query: 1 MSKIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQV 60
++ +VTGA+ GIG AI LAA G +VI + D A + ++V A G
Sbjct: 5 EGRVALVTGAARGIGRAIAVRLAADGAEVIVVDICGD--DAAAT-----AELVEAAG--- 54
Query: 61 IGFARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGV 118
K + +VDV A + A FG +D+++ NAG+
Sbjct: 55 -------------------GKARARQVDVRDRAALKAAVAAGVEDFGRLDILVANAGI 93
>gnl|CDD|237100 PRK12429, PRK12429, 3-hydroxybutyrate dehydrogenase; Provisional.
Length = 258
Score = 57.6 bits (140), Expect = 5e-11
Identities = 32/122 (26%), Positives = 54/122 (44%), Gaps = 29/122 (23%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K+ +VTGA+ GIG I ALA +G +V+ + D + A + + G + IG
Sbjct: 5 KVALVTGAASGIGLEIALALAKEGAKVV-------IADLNDEAAAAAAEALQKAGGKAIG 57
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNEFA 122
+ +DVT + + D+ FG +D+++NNAG+ A
Sbjct: 58 ----------------------VAMDVTDEEAINAGIDYAVETFGGVDILVNNAGIQHVA 95
Query: 123 PV 124
P+
Sbjct: 96 PI 97
>gnl|CDD|235506 PRK05565, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 247
Score = 57.2 bits (139), Expect = 6e-11
Identities = 37/126 (29%), Positives = 52/126 (41%), Gaps = 30/126 (23%)
Query: 1 MSKIIVVTGASVGIGAAILRALAAKG-HQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQ 59
M K+ +VTGAS GIG AI LA +G VI + E
Sbjct: 4 MGKVAIVTGASGGIGRAIAELLAKEGAKVVIAYDINEE---------------------- 41
Query: 60 VIGFARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVN 119
E I ++K DV+ + +V + I KFG ID+++NNAG++
Sbjct: 42 --AAQELLEEIKEEGG-----DAIAVKADVSSEEDVENLVEQIVEKFGKIDILVNNAGIS 94
Query: 120 EFAPVT 125
F VT
Sbjct: 95 NFGLVT 100
>gnl|CDD|211705 TIGR01963, PHB_DH, 3-hydroxybutyrate dehydrogenase. This model
represents a subfamily of the short chain
dehydrogenases. Characterized members so far as
3-hydroxybutyrate dehydrogenases and are found in
species that accumulate ester polmers called
polyhydroxyalkanoic acids (PHAs) under certain
conditions. Several members of the family are from
species not known to accumulate PHAs, including
Oceanobacillus iheyensis and Bacillus subtilis. However,
polymer formation is not required for there be a role
for 3-hydroxybutyrate dehydrogenase; it may be members
of this family have the same function in those species.
Length = 255
Score = 57.4 bits (139), Expect = 6e-11
Identities = 37/122 (30%), Positives = 52/122 (42%), Gaps = 29/122 (23%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K +VTGA+ GIG AI RALAA G V+ E + A + G VI
Sbjct: 2 KTALVTGAASGIGLAIARALAAAGANVVVNDFGEEGAEAAAKV-------AGDAGGSVIY 54
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNEFA 122
L DVTK+ E+ + +FG +D+++NNAG+ A
Sbjct: 55 ----------------------LPADVTKEDEIADMIAAAAAEFGGLDILVNNAGIQHVA 92
Query: 123 PV 124
P+
Sbjct: 93 PI 94
>gnl|CDD|180744 PRK06914, PRK06914, short chain dehydrogenase; Provisional.
Length = 280
Score = 57.3 bits (139), Expect = 6e-11
Identities = 30/117 (25%), Positives = 46/117 (39%), Gaps = 28/117 (23%)
Query: 1 MSKIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQV 60
KI +VTGAS G G LA KG+ VI R E
Sbjct: 2 NKKIAIVTGASSGFGLLTTLELAKKGYLVIATMRNPE----------------------- 38
Query: 61 IGFARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAG 117
++ ++ + N + ++DVT D + F + + G ID+++NNAG
Sbjct: 39 ----KQENLLSQATQLNLQQNIKVQQLDVT-DQNSIHNFQLVLKEIGRIDLLVNNAG 90
>gnl|CDD|187616 cd05358, GlcDH_SDR_c, glucose 1 dehydrogenase (GlcDH), classical
(c) SDRs. GlcDH, is a tetrameric member of the SDR
family, it catalyzes the NAD(P)-dependent oxidation of
beta-D-glucose to D-glucono-delta-lactone. GlcDH has a
typical NAD-binding site glycine-rich pattern as well as
the canonical active site tetrad (YXXXK motif plus
upstream Ser and Asn). 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 have a 3-glycine N-terminal
NAD(P)(H)-binding pattern (typically, TGxxxGxG in
classical SDRs and TGxxGxxG in extended SDRs), while
substrate binding is in the C-terminal region. A
critical catalytic Tyr residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering), is often found in a conserved YXXXK pattern.
In addition to the Tyr and Lys, there is often an
upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn
(Asn-107, 15-PGDH numbering) or additional Ser,
contributing to the active site. Substrates for these
enzymes include sugars, steroids, alcohols, and aromatic
compounds. The standard reaction mechanism is a proton
relay involving the conserved Tyr and Lys, as well as
Asn (or Ser). Some SDR family members, including 17
beta-hydroxysteroid dehydrogenase contain an additional
helix-turn-helix motif that is not generally found among
SDRs.
Length = 253
Score = 56.6 bits (137), Expect = 1e-10
Identities = 38/122 (31%), Positives = 57/122 (46%), Gaps = 28/122 (22%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K+ +VTGAS GIG AI LA G V+ R E D AE + V+ + A G + I
Sbjct: 4 KVALVTGASSGIGKAIAIRLATAGANVVVNYRSKE--DAAEEV----VEEIKAVGGKAI- 56
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNEFA 122
+++ DV+K+ +VV F +FG +D+++NNAG+ A
Sbjct: 57 ---------------------AVQADVSKEEDVVALFQSAIKEFGTLDILVNNAGLQGDA 95
Query: 123 PV 124
Sbjct: 96 SS 97
>gnl|CDD|187620 cd05362, THN_reductase-like_SDR_c,
tetrahydroxynaphthalene/trihydroxynaphthalene
reductase-like, classical (c) SDRs.
1,3,6,8-tetrahydroxynaphthalene reductase (4HNR) of
Magnaporthe grisea and the related
1,3,8-trihydroxynaphthalene reductase (3HNR) are typical
members of the SDR family containing the canonical
glycine rich NAD(P)-binding site and active site tetrad,
and function in fungal melanin biosynthesis. This
subgroup also includes an SDR from Norway spruce that
may function to protect against both biotic and abitoic
stress. 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
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-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 ketoacyl reductases 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 = 243
Score = 56.5 bits (137), Expect = 1e-10
Identities = 36/124 (29%), Positives = 55/124 (44%), Gaps = 30/124 (24%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQV-IGFARRAEMIDFAESLFAFFVDIVAAKGHQVI 61
K+ +VTGAS GIG AI + LA G V + +A AE + V + A G + I
Sbjct: 4 KVALVTGASRGIGRAIAKRLARDGASVVVNYASSKAA---AEEV----VAEIEAAGGKAI 56
Query: 62 GFARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNEF 121
+++ DV+ ++V FD FG +D+++NNAGV
Sbjct: 57 ----------------------AVQADVSDPSQVARLFDAAEKAFGGVDILVNNAGVMLK 94
Query: 122 APVT 125
P+
Sbjct: 95 KPIA 98
>gnl|CDD|181324 PRK08251, PRK08251, short chain dehydrogenase; Provisional.
Length = 248
Score = 56.1 bits (136), Expect = 1e-10
Identities = 33/124 (26%), Positives = 51/124 (41%), Gaps = 27/124 (21%)
Query: 1 MSKIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQV 60
+ I++TGAS G+GA + R AAKG + ARR +
Sbjct: 1 TRQKILITGASSGLGAGMAREFAAKGRDLALCARRTD----------------------- 37
Query: 61 IGFARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNE 120
R E+ + P KV +DV +V E F ++ G +D +I NAG+ +
Sbjct: 38 ----RLEELKAELLARYPGIKVAVAALDVNDHDQVFEVFAEFRDELGGLDRVIVNAGIGK 93
Query: 121 FAPV 124
A +
Sbjct: 94 GARL 97
>gnl|CDD|187639 cd08934, CAD_SDR_c, clavulanic acid dehydrogenase (CAD), classical
(c) SDR. CAD catalyzes the NADP-dependent reduction of
clavulanate-9-aldehyde to clavulanic acid, a
beta-lactamase inhibitor. 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 15-hydroxyprostaglandin
dehydrogenase (15-PGDH) numbering). In addition to the
Tyr and Lys, there is often an upstream Ser (Ser-138,
15-PGDH numbering) and/or an Asn (Asn-107, 15-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 ketoacyl
reductases 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 = 243
Score = 56.0 bits (135), Expect = 2e-10
Identities = 38/123 (30%), Positives = 54/123 (43%), Gaps = 29/123 (23%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K+ +VTGAS GIG A RALAA+G V ARR + L A ++ A G
Sbjct: 4 KVALVTGASSGIGEATARALAAEGAAVAIAARRVDR------LEALADELEAEGGK---- 53
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNEFA 122
L++DVT + +V A + G +D+++NNAG+
Sbjct: 54 -------------------ALVLELDVTDEQQVDAAVERTVEALGRLDILVNNAGIMLLG 94
Query: 123 PVT 125
PV
Sbjct: 95 PVE 97
>gnl|CDD|235975 PRK07231, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 251
Score = 56.0 bits (136), Expect = 2e-10
Identities = 33/117 (28%), Positives = 49/117 (41%), Gaps = 30/117 (25%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K+ +VTGAS GIG I R AA+G +V+ R E A + I
Sbjct: 6 KVAIVTGASSGIGEGIARRFAAEGARVVVTDRNEEA---------------AERVAAEIL 50
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVN 119
RA ++ DV+ +A+V A +FG +D+++NNAG
Sbjct: 51 AGGRA---------------IAVAADVSDEADVEAAVAAALERFGSVDILVNNAGTT 92
>gnl|CDD|187593 cd05332, 11beta-HSD1_like_SDR_c, 11beta-hydroxysteroid
dehydrogenase type 1 (11beta-HSD1)-like, classical (c)
SDRs. Human 11beta_HSD1 catalyzes the NADP(H)-dependent
interconversion of cortisone and cortisol. This subgroup
also includes human dehydrogenase/reductase SDR family
member 7C (DHRS7C) and DHRS7B. These proteins have the
GxxxGxG nucleotide binding motif and S-Y-K catalytic
triad characteristic of the SDRs, but have an atypical
C-terminal domain that contributes to homodimerization
contacts. 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
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-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 ketoacyl reductases 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 = 257
Score = 56.1 bits (136), Expect = 2e-10
Identities = 28/122 (22%), Positives = 51/122 (41%), Gaps = 28/122 (22%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K++++TGAS GIG + LA G +++ ARR E
Sbjct: 4 KVVIITGASSGIGEELAYHLARLGARLVLSARREE------------------------- 38
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNEFA 122
R E + + E H + +D++ + + + FG +D++INNAG++ +
Sbjct: 39 ---RLEEVKSECLELGAPSPHVVPLDMSDLEDAEQVVEEALKLFGGLDILINNAGISMRS 95
Query: 123 PV 124
Sbjct: 96 LF 97
>gnl|CDD|187634 cd08929, SDR_c4, classical (c) SDR, subgroup 4. This subgroup has
a canonical active site tetrad and a typical Gly-rich
NAD-binding motif. 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 15-hydroxyprostaglandin
dehydrogenase (15-PGDH) numbering). In addition to the
Tyr and Lys, there is often an upstream Ser (Ser-138,
15-PGDH numbering) and/or an Asn (Asn-107, 15-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 ketoacyl
reductases 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 = 226
Score = 55.6 bits (134), Expect = 2e-10
Identities = 39/122 (31%), Positives = 51/122 (41%), Gaps = 32/122 (26%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K +VTGAS GIG A R L A+G++V AR
Sbjct: 1 KAALVTGASRGIGEATARLLHAEGYRVGICARDE-------------------------- 34
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNEFA 122
A + A A+E V L DV +A+V A D + FG +D ++NNAGV
Sbjct: 35 ----ARLAAAAAQELE--GVLGLAGDVRDEADVRRAVDAMEEAFGGLDALVNNAGVGVMK 88
Query: 123 PV 124
PV
Sbjct: 89 PV 90
>gnl|CDD|187598 cd05339, 17beta-HSDXI-like_SDR_c, human 17-beta-hydroxysteroid
dehydrogenase XI-like, classical (c) SDRs.
17-beta-hydroxysteroid dehydrogenases (17betaHSD) are a
group of isozymes that catalyze activation and
inactivation of estrogen and androgens. 17betaHSD type
XI, a classical SDR, preferentially converts
3alpha-adiol to androsterone but not numerous other
tested steroids. This subgroup of classical SDRs also
includes members identified as retinol dehydrogenases,
which convert retinol to retinal, a property that
overlaps with 17betaHSD activity. 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 have a
3-glycine N-terminal NAD(P)(H)-binding pattern
(typically, TGxxxGxG in classical SDRs and TGxxGxxG in
extended SDRs), while substrate binding is in the
C-terminal region. A critical catalytic Tyr residue
(Tyr-151, human 15-hydroxyprostaglandin dehydrogenase
(15-PGDH) numbering), is often found in a conserved
YXXXK pattern. In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) or additional
Ser, contributing to the active site. Substrates for
these enzymes include sugars, steroids, alcohols, and
aromatic compounds. The standard reaction mechanism is a
proton relay involving the conserved Tyr and Lys, as
well as Asn (or Ser). Some SDR family members, including
17 beta-hydroxysteroid dehydrogenase contain an
additional helix-turn-helix motif that is not generally
found among SDRs.
Length = 243
Score = 55.7 bits (135), Expect = 2e-10
Identities = 31/115 (26%), Positives = 46/115 (40%), Gaps = 29/115 (25%)
Query: 4 IIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIGF 63
I+++TG GIG + A +G +V+ +DI +
Sbjct: 1 IVLITGGGSGIGRLLALEFAKRGAKVV------------------ILDINEKGAEE---- 38
Query: 64 ARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGV 118
A + KVH K DV+K EV EA I + G + ++INNAGV
Sbjct: 39 --TANNVRKAGG-----KVHYYKCDVSKREEVYEAAKKIKKEVGDVTILINNAGV 86
>gnl|CDD|235726 PRK06181, PRK06181, short chain dehydrogenase; Provisional.
Length = 263
Score = 55.4 bits (134), Expect = 3e-10
Identities = 29/116 (25%), Positives = 47/116 (40%), Gaps = 29/116 (25%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K++++TGAS GIG A+ LA G Q++ AR + SL +A G + +
Sbjct: 2 KVVIITGASEGIGRALAVRLARAGAQLVLAARNETRLA---SL----AQELADHGGEALV 54
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGV 118
DV+ + +FG ID+++NNAG+
Sbjct: 55 VP----------------------TDVSDAEACERLIEAAVARFGGIDILVNNAGI 88
>gnl|CDD|187585 cd05324, carb_red_PTCR-like_SDR_c, Porcine testicular carbonyl
reductase (PTCR)-like, classical (c) SDRs. PTCR is a
classical SDR which catalyzes the NADPH-dependent
reduction of ketones on steroids and prostaglandins.
Unlike most SDRs, PTCR functions as a monomer. This
subgroup also includes human carbonyl reductase 1 (CBR1)
and CBR3. CBR1 is an NADPH-dependent SDR with broad
substrate specificity and may be responsible for the in
vivo reduction of quinones, prostaglandins, and other
carbonyl-containing compounds. In addition it includes
poppy NADPH-dependent salutaridine reductase which
catalyzes the stereospecific reduction of salutaridine
to 7(S)-salutaridinol in the biosynthesis of morphine,
and Arabidopsis SDR1,a menthone reductase, which
catalyzes the reduction of menthone to neomenthol, a
compound with antimicrobial activity; SDR1 can also
carry out neomenthol oxidation. 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, 15-hydroxyprostaglandin dehydrogenase
(15-PGDH) numbering). In addition to the Tyr and Lys,
there is often an upstream Ser (Ser-138, 15-PGDH
numbering) and/or an Asn (Asn-107, 15-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 ketoacyl
reductases 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 = 225
Score = 54.9 bits (133), Expect = 4e-10
Identities = 40/118 (33%), Positives = 55/118 (46%), Gaps = 32/118 (27%)
Query: 3 KIIVVTGASVGIGAAILRALAAKG-HQVIGFARRAEMIDFA-ESLFAFFVDIVAAKGHQV 60
K+ +VTGA+ GIG I+R LA G VI AR E A E L A +G V
Sbjct: 1 KVALVTGANRGIGFEIVRQLAKSGPGTVILTARDVERGQAAVEKLRA--------EGLSV 52
Query: 61 IGFARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGV 118
+ H L DVT DA + A D++ K+G +D+++NNAG+
Sbjct: 53 --------------------RFHQL--DVTDDASIEAAADFVEEKYGGLDILVNNAGI 88
>gnl|CDD|236241 PRK08324, PRK08324, short chain dehydrogenase; Validated.
Length = 681
Score = 55.6 bits (135), Expect = 4e-10
Identities = 29/116 (25%), Positives = 47/116 (40%), Gaps = 30/116 (25%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K+ +VTGA+ GIG A + LAA+G V+ D+
Sbjct: 423 KVALVTGAAGGIGKATAKRLAAEGACVVL------------------ADLDEEAAEAAA- 463
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGV 118
A+ + + DVT +A V AF+ FG +D++++NAG+
Sbjct: 464 -----------AELGGPDRALGVACDVTDEAAVQAAFEEAALAFGGVDIVVSNAGI 508
>gnl|CDD|187628 cd05370, SDR_c2, classical (c) SDR, subgroup 2. Short-chain
dehydrogenases/reductases (SDRs, aka Tyrosine-dependent
oxidoreductases) 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
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-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 ketoacyl reductases 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 = 228
Score = 54.6 bits (132), Expect = 4e-10
Identities = 27/116 (23%), Positives = 49/116 (42%), Gaps = 33/116 (28%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
+++TG + GIG A+ R G+ VI I
Sbjct: 6 NTVLITGGTSGIGLALARKFLEAGNTVI------------------------------IT 35
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGV 118
RR E + KE P+ +H++ +DV V + + +++ ++D++INNAG+
Sbjct: 36 -GRREERLAEAKKELPN--IHTIVLDVGDAESVEALAEALLSEYPNLDILINNAGI 88
>gnl|CDD|181297 PRK08217, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 253
Score = 54.6 bits (132), Expect = 5e-10
Identities = 34/116 (29%), Positives = 51/116 (43%), Gaps = 29/116 (25%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K+IV+TG + G+G A+ LA KG A+ A +ID + V A G +V G
Sbjct: 6 KVIVITGGAQGLGRAMAEYLAQKG------AKLA-LIDLNQEKLEEAVAECGALGTEVRG 58
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGV 118
+A +VT + +V F I FG ++ +INNAG+
Sbjct: 59 YA----------------------ANVTDEEDVEATFAQIAEDFGQLNGLINNAGI 92
>gnl|CDD|168574 PRK06484, PRK06484, short chain dehydrogenase; Validated.
Length = 520
Score = 55.2 bits (133), Expect = 5e-10
Identities = 34/117 (29%), Positives = 55/117 (47%), Gaps = 32/117 (27%)
Query: 2 SKIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVI 61
S++++VTGA+ GIG A + A G QV+ R V
Sbjct: 5 SRVVLVTGAAGGIGRAACQRFARAGDQVVVADR------------------------NVE 40
Query: 62 GFARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGV 118
RA+ + H+L +DV+ +A++ E F+ ++ +FG IDV++NNAGV
Sbjct: 41 RARERADSLGP--------DHHALAMDVSDEAQIREGFEQLHREFGRIDVLVNNAGV 89
Score = 53.3 bits (128), Expect = 2e-09
Identities = 34/125 (27%), Positives = 55/125 (44%), Gaps = 33/125 (26%)
Query: 2 SKIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVI 61
+++ +TG + GIG A+ AA G +++ R AE
Sbjct: 269 PRVVAITGGARGIGRAVADRFAAAGDRLLIIDRDAE------------------------ 304
Query: 62 GFARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNE- 120
G + AE A+ E+ + D+T +A V AF I ++G +DV++NNAG+ E
Sbjct: 305 GAKKLAE---ALGDEHLSVQA-----DITDEAAVESAFAQIQARWGRLDVLVNNAGIAEV 356
Query: 121 FAPVT 125
F P
Sbjct: 357 FKPSL 361
>gnl|CDD|181491 PRK08589, PRK08589, short chain dehydrogenase; Validated.
Length = 272
Score = 54.0 bits (130), Expect = 1e-09
Identities = 36/118 (30%), Positives = 57/118 (48%), Gaps = 30/118 (25%)
Query: 2 SKIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVI 61
+K+ V+TGAS GIG A ALA +G V+ +D AE++
Sbjct: 6 NKVAVITGASTGIGQASAIALAQEGAYVL-------AVDIAEAV---------------- 42
Query: 62 GFARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVN 119
+E +D + K N K + VD++ + +V + I +FG +DV+ NNAGV+
Sbjct: 43 -----SETVDKI-KSNGG-KAKAYHVDISDEQQVKDFASEIKEQFGRVDVLFNNAGVD 93
>gnl|CDD|180439 PRK06171, PRK06171, sorbitol-6-phosphate 2-dehydrogenase;
Provisional.
Length = 266
Score = 53.9 bits (130), Expect = 1e-09
Identities = 32/117 (27%), Positives = 42/117 (35%), Gaps = 38/117 (32%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
KII+VTG S GIG AI++ L A G V+
Sbjct: 10 KIIIVTGGSSGIGLAIVKELLANGANVV-------------------------------- 37
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVN 119
D + + DV+ EV I KFG ID ++NNAG+N
Sbjct: 38 ------NADIHGGDGQHENYQFVPTDVSSAEEVNHTVAEIIEKFGRIDGLVNNAGIN 88
>gnl|CDD|183489 PRK12384, PRK12384, sorbitol-6-phosphate dehydrogenase;
Provisional.
Length = 259
Score = 53.5 bits (129), Expect = 1e-09
Identities = 28/125 (22%), Positives = 51/125 (40%), Gaps = 27/125 (21%)
Query: 1 MSKIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQV 60
M+++ VV G +GA + LA +G++V DI + K V
Sbjct: 1 MNQVAVVIGGGQTLGAFLCHGLAEEGYRVA------------------VADINSEKAANV 42
Query: 61 IGFARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNE 120
A+ I E + + D T + V+ ++ FG +D+++ NAG+ +
Sbjct: 43 ------AQEI---NAEYGEGMAYGFGADATSEQSVLALSRGVDEIFGRVDLLVYNAGIAK 93
Query: 121 FAPVT 125
A +T
Sbjct: 94 AAFIT 98
>gnl|CDD|235737 PRK06197, PRK06197, short chain dehydrogenase; Provisional.
Length = 306
Score = 53.5 bits (129), Expect = 1e-09
Identities = 33/116 (28%), Positives = 47/116 (40%), Gaps = 27/116 (23%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
++ VVTGA+ G+G ALAAKG V+ R + KG
Sbjct: 17 RVAVVTGANTGLGYETAAALAAKGAHVVLAVRNLD------------------KGKAAA- 57
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGV 118
+ P V ++D+T A V A D + + ID++INNAGV
Sbjct: 58 --------ARITAATPGADVTLQELDLTSLASVRAAADALRAAYPRIDLLINNAGV 105
>gnl|CDD|182531 PRK10538, PRK10538, malonic semialdehyde reductase; Provisional.
Length = 248
Score = 53.2 bits (128), Expect = 2e-09
Identities = 29/115 (25%), Positives = 49/115 (42%), Gaps = 32/115 (27%)
Query: 4 IIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIGF 63
I++VTGA+ G G I R +GH+VI RR E +
Sbjct: 2 IVLVTGATAGFGECITRRFIQQGHKVIATGRRQERLQ----------------------- 38
Query: 64 ARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGV 118
+ E+ D ++ ++DV A + E + ++ +IDV++NNAG+
Sbjct: 39 ELKDELGDN---------LYIAQLDVRNRAAIEEMLASLPAEWRNIDVLVNNAGL 84
>gnl|CDD|187618 cd05360, SDR_c3, classical (c) SDR, subgroup 3. These proteins are
members of the classical SDR family, with a canonical
active site triad (and also active site Asn) and a
typical Gly-rich NAD-binding motif. 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 have a
3-glycine N-terminal NAD(P)(H)-binding pattern
(typically, TGxxxGxG in classical SDRs and TGxxGxxG in
extended SDRs), while substrate binding is in the
C-terminal region. A critical catalytic Tyr residue
(Tyr-151, human 15-hydroxyprostaglandin dehydrogenase
(15-PGDH) numbering), is often found in a conserved
YXXXK pattern. In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) or additional
Ser, contributing to the active site. Substrates for
these enzymes include sugars, steroids, alcohols, and
aromatic compounds. The standard reaction mechanism is a
proton relay involving the conserved Tyr and Lys, as
well as Asn (or Ser). Some SDR family members, including
17 beta-hydroxysteroid dehydrogenase contain an
additional helix-turn-helix motif that is not generally
found among SDRs.
Length = 233
Score = 53.2 bits (128), Expect = 2e-09
Identities = 36/118 (30%), Positives = 49/118 (41%), Gaps = 29/118 (24%)
Query: 4 IIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIGF 63
++V+TGAS GIG A A A +G +V+ AR AE + V G + I
Sbjct: 2 VVVITGASSGIGRATALAFAERGAKVVLAARSAEALHEL-------AREVRELGGEAI-- 52
Query: 64 ARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNEF 121
++ DV A+V A D +FG ID +NNAGV F
Sbjct: 53 --------------------AVVADVADAAQVERAADTAVERFGRIDTWVNNAGVAVF 90
>gnl|CDD|235631 PRK05866, PRK05866, short chain dehydrogenase; Provisional.
Length = 293
Score = 53.6 bits (129), Expect = 2e-09
Identities = 34/115 (29%), Positives = 49/115 (42%), Gaps = 29/115 (25%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K I++TGAS GIG A A +G V+ ARR +++D A I A G
Sbjct: 41 KRILLTGASSGIGEAAAEQFARRGATVVAVARREDLLD------AVADRITRAGG----- 89
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAG 117
DAMA + D++ V + + G +D++INNAG
Sbjct: 90 --------DAMA----------VPCDLSDLDAVDALVADVEKRIGGVDILINNAG 126
>gnl|CDD|187631 cd05373, SDR_c10, classical (c) SDR, subgroup 10. This subgroup
resembles the classical SDRs, but has an incomplete
match to the canonical glycine rich NAD-binding motif
and lacks the typical active site tetrad (instead of the
critical active site Tyr, it has Phe, but contains the
nearby Lys). 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
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-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 ketoacyl reductases 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 = 238
Score = 52.8 bits (127), Expect = 2e-09
Identities = 35/122 (28%), Positives = 48/122 (39%), Gaps = 28/122 (22%)
Query: 4 IIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIGF 63
+ V GA G+GAAI R AA+G V ARR L A VDI+ G
Sbjct: 1 VAAVVGAGDGLGAAIARRFAAEGFSVALAARR------EAKLEALLVDIIRDAGGSAKAV 54
Query: 64 ARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNEFAP 123
D + EV+ FD I + G ++V++ NAG N + P
Sbjct: 55 P----------------------TDARDEDEVIALFDLIEEEIGPLEVLVYNAGANVWFP 92
Query: 124 VT 125
+
Sbjct: 93 IL 94
>gnl|CDD|187624 cd05366, meso-BDH-like_SDR_c, meso-2,3-butanediol
dehydrogenase-like, classical (c) SDRs. 2,3-butanediol
dehydrogenases (BDHs) catalyze the NAD+ dependent
conversion of 2,3-butanediol to acetonin; BDHs are
classified into types according to their
stereospecificity as to substrates and products.
Included in this subgroup are Klebsiella pneumonia
meso-BDH which catalyzes meso-2,3-butanediol to
D(-)-acetonin, and Corynebacterium glutamicum L-BDH
which catalyzes lX+)-2,3-butanediol to L(+)-acetonin.
This subgroup is comprised of classical SDRs with the
characteristic catalytic triad and NAD-binding motif.
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
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-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 ketoacyl reductases 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 = 257
Score = 52.4 bits (126), Expect = 3e-09
Identities = 38/125 (30%), Positives = 51/125 (40%), Gaps = 31/125 (24%)
Query: 1 MSKIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQV 60
MSK+ ++TGA+ GIG AI LAA G F L ++ A Q
Sbjct: 1 MSKVAIITGAAQGIGRAIAERLAADG--------------FNIVLADLNLEEAAKSTIQE 46
Query: 61 IGFARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNE 120
I + ++ DVT +V D KFG DVM+NNAG+
Sbjct: 47 I--------------SEAGYNAVAVGADVTDKDDVEALIDQAVEKFGSFDVMVNNAGI-- 90
Query: 121 FAPVT 125
AP+T
Sbjct: 91 -APIT 94
>gnl|CDD|213929 TIGR04316, dhbA_paeA, 2,3-dihydro-2,3-dihydroxybenzoate
dehydrogenase. Members of this family are
2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase (EC
1.3.1.28), the third enzyme in the biosynthesis of
2,3-dihydroxybenzoic acid (DHB) from chorismate. The
first two enzymes are isochorismate synthase (EC
5.4.4.2) and isochorismatase (EC 3.3.2.1). Synthesis is
often followed by adenylation by the enzyme DHBA-AMP
ligase (EC 2.7.7.58) to activate (DHB) for a
non-ribosomal peptide synthetase.
Length = 250
Score = 51.9 bits (125), Expect = 6e-09
Identities = 31/119 (26%), Positives = 45/119 (37%), Gaps = 29/119 (24%)
Query: 7 VTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIGFARR 66
VTGA+ GIG A+ RALA G +V R E V + G+ +
Sbjct: 3 VTGAAQGIGYAVARALAEAGARVAAVDRNFE-------QLLELVADLRRYGYPFATY--- 52
Query: 67 AEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNEFAPVT 125
K+DV A V E + ++G IDV++N AG+ +
Sbjct: 53 -------------------KLDVADSAAVDEVVQRLEREYGPIDVLVNVAGILRLGAID 92
>gnl|CDD|237218 PRK12825, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 249
Score = 51.0 bits (123), Expect = 9e-09
Identities = 29/126 (23%), Positives = 50/126 (39%), Gaps = 32/126 (25%)
Query: 1 MSKIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQV 60
M ++ +VTGA+ G+G AI LA G V
Sbjct: 5 MGRVALVTGAARGLGRAIALRLARAGA------------------------------DVV 34
Query: 61 IGFARRAEMIDAMAKENPDW--KVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGV 118
+ + E + + + + +++ DVT A + A +FG ID+++NNAG+
Sbjct: 35 VHYRSDEEAAEELVEAVEALGRRAQAVQADVTDKAALEAAVAAAVERFGRIDILVNNAGI 94
Query: 119 NEFAPV 124
E P+
Sbjct: 95 FEDKPL 100
>gnl|CDD|181518 PRK08643, PRK08643, acetoin reductase; Validated.
Length = 256
Score = 51.3 bits (123), Expect = 9e-09
Identities = 38/125 (30%), Positives = 56/125 (44%), Gaps = 32/125 (25%)
Query: 1 MSKIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQV 60
MSK+ +VTGA GIG AI + L G +V ++D+ E A K +
Sbjct: 1 MSKVALVTGAGQGIGFAIAKRLVEDGFKV-------AIVDYNEET----AQAAADKLSKD 49
Query: 61 IGFARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNE 120
G A+A +K DV+ +V A + + FG ++V++NNAGV
Sbjct: 50 GG--------KAIA----------VKADVSDRDQVFAAVRQVVDTFGDLNVVVNNAGV-- 89
Query: 121 FAPVT 125
AP T
Sbjct: 90 -APTT 93
>gnl|CDD|215720 pfam00106, adh_short, short chain dehydrogenase. This family
contains a wide variety of dehydrogenases.
Length = 167
Score = 50.2 bits (121), Expect = 1e-08
Identities = 26/123 (21%), Positives = 45/123 (36%), Gaps = 26/123 (21%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
+++TG + G+G A+ R LAA+G + + R A L
Sbjct: 1 GTVLITGGTGGLGLALARWLAAEGARHLVLVSRRGPAPGAAEL----------------- 43
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNEFA 122
AE+ A +V DV + + G +D +++NAGV +
Sbjct: 44 ---VAELEALGA------EVTVAACDVADRDALAALLAALPAALGPLDGVVHNAGVLDDG 94
Query: 123 PVT 125
P+
Sbjct: 95 PLE 97
>gnl|CDD|171821 PRK12937, PRK12937, short chain dehydrogenase; Provisional.
Length = 245
Score = 50.9 bits (122), Expect = 1e-08
Identities = 43/124 (34%), Positives = 57/124 (45%), Gaps = 30/124 (24%)
Query: 2 SKIIVVTGASVGIGAAILRALAAKGHQV-IGFARRAEMIDFAESLFAFFVDIVAAKGHQV 60
+K+ +VTGAS GIGAAI R LAA G V + +A A A+ L A +I AA G
Sbjct: 5 NKVAIVTGASRGIGAAIARRLAADGFAVAVNYAGSAAA---ADELVA---EIEAAGG--- 55
Query: 61 IGFARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNE 120
+ +++ DV A V FD FG IDV++NNAGV
Sbjct: 56 --------------------RAIAVQADVADAAAVTRLFDAAETAFGRIDVLVNNAGVMP 95
Query: 121 FAPV 124
+
Sbjct: 96 LGTI 99
>gnl|CDD|183778 PRK12829, PRK12829, short chain dehydrogenase; Provisional.
Length = 264
Score = 51.2 bits (123), Expect = 1e-08
Identities = 33/118 (27%), Positives = 46/118 (38%), Gaps = 31/118 (26%)
Query: 1 MSKIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQV 60
++VTG + GIG AI A A G +V V
Sbjct: 10 DGLRVLVTGGASGIGRAIAEAFAEAGARVH-----------------------------V 40
Query: 61 IGFARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGV 118
+ A + A A P KV + DV A+V FD +FG +DV++NNAG+
Sbjct: 41 CDVSEAA--LAATAARLPGAKVTATVADVADPAQVERVFDTAVERFGGLDVLVNNAGI 96
>gnl|CDD|181136 PRK07825, PRK07825, short chain dehydrogenase; Provisional.
Length = 273
Score = 51.1 bits (123), Expect = 1e-08
Identities = 38/118 (32%), Positives = 49/118 (41%), Gaps = 37/118 (31%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQV-IGFARRAEMIDFAESLFAFFVDIVAAKGHQVI 61
K++ +TG + GIG A RALAA G +V IG D +D AK
Sbjct: 6 KVVAITGGARGIGLATARALAALGARVAIG--------D---------LDEALAK----- 43
Query: 62 GFARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAF-DWINNKFGHIDVMINNAGV 118
A + V +DVT D AF D + G IDV++NNAGV
Sbjct: 44 ---ETAAELGL---------VVGGPLDVT-DPASFAAFLDAVEADLGPIDVLVNNAGV 88
>gnl|CDD|180723 PRK06841, PRK06841, short chain dehydrogenase; Provisional.
Length = 255
Score = 50.4 bits (121), Expect = 2e-08
Identities = 35/121 (28%), Positives = 48/121 (39%), Gaps = 32/121 (26%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K+ VVTG + GIG AI AAKG +V R ++ + A L AKG
Sbjct: 16 KVAVVTGGASGIGHAIAELFAAKGARVALLDRSEDVAEVAAQLLG-----GNAKGLV--- 67
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNEFA 122
DV+ V A + + FG ID+++N+AGV A
Sbjct: 68 ------------------------CDVSDSQSVEAAVAAVISAFGRIDILVNSAGVALLA 103
Query: 123 P 123
P
Sbjct: 104 P 104
>gnl|CDD|187644 cd08940, HBDH_SDR_c, d-3-hydroxybutyrate dehydrogenase (HBDH),
classical (c) SDRs. DHBDH, an NAD+ -dependent enzyme,
catalyzes the interconversion of D-3-hydroxybutyrate and
acetoacetate. It is a classical SDR, with the canonical
NAD-binding motif and active site tetrad. 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
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-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 ketoacyl reductases 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 = 258
Score = 50.5 bits (121), Expect = 2e-08
Identities = 35/127 (27%), Positives = 54/127 (42%), Gaps = 31/127 (24%)
Query: 1 MSKIIVVTGASVGIGAAILRALAAKGHQVI--GFARRAEMIDFAESLFAFFVDIVAAKGH 58
K+ +VTG++ GIG I RALAA G ++ GF AE+
Sbjct: 1 KGKVALVTGSTSGIGLGIARALAAAGANIVLNGFGDAAEI-------------------- 40
Query: 59 QVIGFARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGV 118
A AK KV D++K A + + + +FG +D+++NNAG+
Sbjct: 41 -------EAVRAGLAAKHG--VKVLYHGADLSKPAAIEDMVAYAQRQFGGVDILVNNAGI 91
Query: 119 NEFAPVT 125
AP+
Sbjct: 92 QHVAPIE 98
>gnl|CDD|187627 cd05369, TER_DECR_SDR_a, Trans-2-enoyl-CoA reductase (TER) and
2,4-dienoyl-CoA reductase (DECR), atypical (a) SDR.
TTER is a peroxisomal protein with a proposed role in
fatty acid elongation. Fatty acid synthesis is known to
occur in the both endoplasmic reticulum and
mitochondria; peroxisomal TER has been proposed as an
additional fatty acid elongation system, it reduces the
double bond at C-2 as the last step of elongation. This
system resembles the mitochondrial system in that
acetyl-CoA is used as a carbon donor. TER may also
function in phytol metabolism, reducting phytenoyl-CoA
to phytanoyl-CoA in peroxisomes. DECR processes double
bonds in fatty acids to increase their utility in fatty
acid metabolism; it reduces 2,4-dienoyl-CoA to an
enoyl-CoA. DECR is active in mitochondria and
peroxisomes. This subgroup has the Gly-rich NAD-binding
motif of the classical SDR family, but does not display
strong identity to the canonical active site tetrad, and
lacks the characteristic Tyr at the usual position. 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 have a
3-glycine N-terminal NAD(P)(H)-binding pattern
(typically, TGxxxGxG in classical SDRs and TGxxGxxG in
extended SDRs), while substrate binding is in the
C-terminal region. A critical catalytic Tyr residue
(Tyr-151, human 15-hydroxyprostaglandin dehydrogenase
(15-PGDH) numbering), is often found in a conserved
YXXXK pattern. In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) or additional
Ser, contributing to the active site. Substrates for
these enzymes include sugars, steroids, alcohols, and
aromatic compounds. The standard reaction mechanism is a
proton relay involving the conserved Tyr and Lys, as
well as Asn (or Ser). Some SDR family members, including
17 beta-hydroxysteroid dehydrogenase contain an
additional helix-turn-helix motif that is not generally
found among SDRs.
Length = 249
Score = 50.3 bits (121), Expect = 2e-08
Identities = 34/121 (28%), Positives = 47/121 (38%), Gaps = 28/121 (23%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K+ +TG GIG AI +A A G V R+ E+++ AA+
Sbjct: 4 KVAFITGGGTGIGKAIAKAFAELGASVAIAGRKPEVLE------------AAAEEISSAT 51
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNEFA 122
R H ++ DV V A D +FG ID++INNA N A
Sbjct: 52 GGR----------------AHPIQCDVRDPEAVEAAVDETLKEFGKIDILINNAAGNFLA 95
Query: 123 P 123
P
Sbjct: 96 P 96
>gnl|CDD|181298 PRK08219, PRK08219, short chain dehydrogenase; Provisional.
Length = 227
Score = 49.9 bits (120), Expect = 2e-08
Identities = 34/124 (27%), Positives = 49/124 (39%), Gaps = 38/124 (30%)
Query: 1 MSKIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQV 60
++TGAS GIGAAI R LA H +
Sbjct: 2 ERPTALITGASRGIGAAIARELA--------------------------------PTHTL 29
Query: 61 IGFARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNE 120
+ R AE +D +A E P VD+T + A + + G +DV+++NAGV +
Sbjct: 30 LLGGRPAERLDELAAELPG--ATPFPVDLTDPEAIAAAVE----QLGRLDVLVHNAGVAD 83
Query: 121 FAPV 124
PV
Sbjct: 84 LGPV 87
>gnl|CDD|181517 PRK08642, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 253
Score = 50.1 bits (120), Expect = 2e-08
Identities = 31/120 (25%), Positives = 50/120 (41%), Gaps = 32/120 (26%)
Query: 1 MSKIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQV 60
+ ++VTG S G+GAAI RA A +G +V V
Sbjct: 4 SEQTVLVTGGSRGLGAAIARAFAREGARV------------------------------V 33
Query: 61 IGFARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGH-IDVMINNAGVN 119
+ + + + +A+A E D + +L+ DVT +V F FG I ++NNA +
Sbjct: 34 VNYHQSEDAAEALADELGD-RAIALQADVTDREQVQAMFATATEHFGKPITTVVNNALAD 92
>gnl|CDD|187597 cd05338, DHRS1_HSDL2-like_SDR_c, human dehydrogenase/reductase (SDR
family) member 1 (DHRS1) and human hydroxysteroid
dehydrogenase-like protein 2 (HSDL2), classical (c)
SDRs. This subgroup includes human DHRS1 and human
HSDL2 and related proteins. These are members of the
classical SDR family, with a canonical Gly-rich
NAD-binding motif and the typical YXXXK active site
motif. However, the rest of the catalytic tetrad is not
strongly conserved. DHRS1 mRNA has been detected in many
tissues, liver, heart, skeletal muscle, kidney and
pancreas; a longer transcript is predominantly expressed
in the liver , a shorter one in the heart. HSDL2 may
play a part in fatty acid metabolism, as it is found in
peroxisomes. 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 have a 3-glycine N-terminal NAD(P)(H)-binding
pattern (typically, TGxxxGxG in classical SDRs and
TGxxGxxG in extended SDRs), while substrate binding is
in the C-terminal region. A critical catalytic Tyr
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase (15-PGDH) numbering), is often found in a
conserved YXXXK pattern. In addition to the Tyr and Lys,
there is often an upstream Ser (Ser-138, 15-PGDH
numbering) and/or an Asn (Asn-107, 15-PGDH numbering) or
additional Ser, contributing to the active site.
Substrates for these enzymes include sugars, steroids,
alcohols, and aromatic compounds. The standard reaction
mechanism is a proton relay involving the conserved Tyr
and Lys, as well as Asn (or Ser). Some SDR family
members, including 17 beta-hydroxysteroid dehydrogenase
contain an additional helix-turn-helix motif that is not
generally found among SDRs.
Length = 246
Score = 50.1 bits (120), Expect = 2e-08
Identities = 36/122 (29%), Positives = 52/122 (42%), Gaps = 17/122 (13%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K+ VTGAS GIG AI LA G V+ A+ A D A I
Sbjct: 4 KVAFVTGASRGIGRAIALRLAKAGATVVVAAKTASEGDNGS----------AKSLPGTIE 53
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNEFA 122
AE I+A + + VDV + +V + ++FG +D+++NNAG +
Sbjct: 54 --ETAEEIEAAGG-----QALPIVVDVRDEDQVRALVEATVDQFGRLDILVNNAGAIWLS 106
Query: 123 PV 124
V
Sbjct: 107 LV 108
>gnl|CDD|236372 PRK09072, PRK09072, short chain dehydrogenase; Provisional.
Length = 263
Score = 49.9 bits (120), Expect = 2e-08
Identities = 35/123 (28%), Positives = 50/123 (40%), Gaps = 35/123 (28%)
Query: 2 SKIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMID--FAESLFAFFVDIVAAKGHQ 59
K +++TGAS GIG A+ ALAA G +++ R AE ++ A + V A
Sbjct: 5 DKRVLLTGASGGIGQALAEALAAAGARLLLVGRNAEKLEALAARLPYPGRHRWVVAD--- 61
Query: 60 VIGFARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVN 119
+ E + A A+E I+V+INNAGVN
Sbjct: 62 -LTSEAGREAVLARAREMGG-----------------------------INVLINNAGVN 91
Query: 120 EFA 122
FA
Sbjct: 92 HFA 94
>gnl|CDD|187647 cd08943, R1PA_ADH_SDR_c, rhamnulose-1-phosphate aldolase/alcohol
dehydrogenase, classical (c) SDRs. This family has
bifunctional proteins with an N-terminal aldolase and a
C-terminal classical SDR domain. One member is
identified as a rhamnulose-1-phosphate aldolase/alcohol
dehydrogenase. The SDR domain has a canonical SDR
glycine-rich NAD(P) binding motif and a match to the
characteristic active site triad. However, it lacks an
upstream active site Asn typical of SDRs. 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
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-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 ketoacyl reductases 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 = 250
Score = 50.1 bits (120), Expect = 3e-08
Identities = 32/116 (27%), Positives = 53/116 (45%), Gaps = 30/116 (25%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K+ +VTG + GIG AI + LAA+G V+ DI +V
Sbjct: 2 KVALVTGGASGIGLAIAKRLAAEGAAVVV------------------ADIDPEIAEKV-- 41
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGV 118
A A + + ++ DVT +A+V AF+ +FG +D++++NAG+
Sbjct: 42 ---------AEAAQGGP-RALGVQCDVTSEAQVQSAFEQAVLEFGGLDIVVSNAGI 87
>gnl|CDD|236145 PRK08063, PRK08063, enoyl-(acyl carrier protein) reductase;
Provisional.
Length = 250
Score = 50.1 bits (120), Expect = 3e-08
Identities = 36/122 (29%), Positives = 54/122 (44%), Gaps = 32/122 (26%)
Query: 1 MSKIIVVTGASVGIGAAILRALAAKG-HQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQ 59
K+ +VTG+S GIG AI LA +G + +AR AE
Sbjct: 3 SGKVALVTGSSRGIGKAIALRLAEEGYDIAVNYARSR---KAAEET-------------- 45
Query: 60 VIGFARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNA--G 117
AE I+A+ + K ++K +V ++ E F I+ +FG +DV +NNA G
Sbjct: 46 -------AEEIEALGR-----KALAVKANVGDVEKIKEMFAQIDEEFGRLDVFVNNAASG 93
Query: 118 VN 119
V
Sbjct: 94 VL 95
>gnl|CDD|187643 cd08939, KDSR-like_SDR_c, 3-ketodihydrosphingosine reductase (KDSR)
and related proteins, classical (c) SDR. These proteins
include members identified as KDSR, ribitol type
dehydrogenase, and others. The group shows strong
conservation of the active site tetrad and glycine rich
NAD-binding motif of the classical SDRs. 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
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-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 ketoacyl reductases 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 = 239
Score = 49.9 bits (120), Expect = 3e-08
Identities = 30/123 (24%), Positives = 48/123 (39%), Gaps = 25/123 (20%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K +++TG S GIG A+ + L +G VI AR ++ A +I A
Sbjct: 2 KHVLITGGSSGIGKALAKELVKEGANVIIVARSESKLEEAV------EEIEAEAN----- 50
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNEFA 122
KV + D++ EV +AF K G D+++N AG++
Sbjct: 51 --------------ASGQKVSYISADLSDYEEVEQAFAQAVEKGGPPDLVVNCAGISIPG 96
Query: 123 PVT 125
Sbjct: 97 LFE 99
>gnl|CDD|180984 PRK07454, PRK07454, short chain dehydrogenase; Provisional.
Length = 241
Score = 49.6 bits (119), Expect = 3e-08
Identities = 27/118 (22%), Positives = 44/118 (37%), Gaps = 29/118 (24%)
Query: 1 MSKIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQV 60
++TGAS GIG A A A G + AR + + E+L + + G
Sbjct: 5 SMPRALITGASSGIGKATALAFAKAGWDLALVARSQDAL---EAL----AAELRSTGV-- 55
Query: 61 IGFARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGV 118
K + +D++ + + +FG DV+INNAG+
Sbjct: 56 --------------------KAAAYSIDLSNPEAIAPGIAELLEQFGCPDVLINNAGM 93
>gnl|CDD|187603 cd05345, BKR_3_SDR_c, putative beta-ketoacyl acyl carrier protein
[ACP] reductase (BKR), subgroup 3, classical (c) SDR.
This subgroup includes the putative Brucella melitensis
biovar Abortus 2308 BKR, FabG, Mesorhizobium loti
MAFF303099 FabG, and other classical SDRs. BKR, a member
of the SDR family, catalyzes the NADPH-dependent
reduction of acyl carrier protein in the first reductive
step of de novo fatty acid synthesis (FAS). FAS
consists of 4 elongation steps, which are repeated to
extend the fatty acid chain thru the addition of
two-carbo units from malonyl acyl-carrier protein (ACP):
condensation, reduction, dehydration, and final
reduction. Type II FAS, typical of plants and many
bacteria, maintains these activities on discrete
polypeptides, while type I Fas utilizes one or 2
multifunctional polypeptides. BKR resembles enoyl
reductase, which catalyzes the second reduction step in
FAS. 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 have a 3-glycine N-terminal NAD(P)(H)-binding
pattern (typically, TGxxxGxG in classical SDRs and
TGxxGxxG in extended SDRs), while substrate binding is
in the C-terminal region. A critical catalytic Tyr
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase (15-PGDH) numbering), is often found in a
conserved YXXXK pattern. In addition to the Tyr and Lys,
there is often an upstream Ser (Ser-138, 15-PGDH
numbering) and/or an Asn (Asn-107, 15-PGDH numbering) or
additional Ser, contributing to the active site.
Substrates for these enzymes include sugars, steroids,
alcohols, and aromatic compounds. The standard reaction
mechanism is a proton relay involving the conserved Tyr
and Lys, as well as Asn (or Ser). Some SDR family
members, including 17 beta-hydroxysteroid dehydrogenase
contain an additional helix-turn-helix motif that is not
generally found among SDRs.
Length = 248
Score = 49.7 bits (119), Expect = 3e-08
Identities = 30/118 (25%), Positives = 50/118 (42%), Gaps = 32/118 (27%)
Query: 1 MSKIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQV 60
K+ +VTGA G G I R A +G +V+ DI A
Sbjct: 4 EGKVAIVTGAGSGFGEGIARRFAQEGARVV------------------IADINADGA--- 42
Query: 61 IGFARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGV 118
+ +A + + +++ DVTK A+V + +KFG +D+++NNAG+
Sbjct: 43 ----------ERVAADIGE-AAIAIQADVTKRADVEAMVEAALSKFGRLDILVNNAGI 89
>gnl|CDD|236074 PRK07666, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 239
Score = 49.3 bits (118), Expect = 4e-08
Identities = 37/124 (29%), Positives = 54/124 (43%), Gaps = 31/124 (25%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMID-FAESLFAFFVDIVAAKGHQVI 61
K ++TGA GIG A+ ALA +G V AR E + AE + A+ V +V A
Sbjct: 8 KNALITGAGRGIGRAVAIALAKEGVNVGLLARTEENLKAVAEEVEAYGVKVVIAT----- 62
Query: 62 GFARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNEF 121
DV+ EV A + + N+ G ID++INNAG+++F
Sbjct: 63 -------------------------ADVSDYEEVTAAIEQLKNELGSIDILINNAGISKF 97
Query: 122 APVT 125
Sbjct: 98 GKFL 101
>gnl|CDD|187607 cd05349, BKR_2_SDR_c, putative beta-ketoacyl acyl carrier protein
[ACP]reductase (BKR), subgroup 2, classical (c) SDR.
This subgroup includes Rhizobium sp. NGR234 FabG1. The
Escherichai coli K12 BKR, FabG, belongs to a different
subgroup. BKR catalyzes the NADPH-dependent reduction of
ACP in the first reductive step of de novo fatty acid
synthesis (FAS). FAS consists of four elongation steps,
which are repeated to extend the fatty acid chain
through the addition of two-carbo units from malonyl
acyl-carrier protein (ACP): condensation, reduction,
dehydration, and a final reduction. Type II FAS, typical
of plants and many bacteria, maintains these activities
on discrete polypeptides, while type I FAS utilizes one
or two multifunctional polypeptides. BKR resembles enoyl
reductase, which catalyzes the second reduction step in
FAS. 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 have a 3-glycine N-terminal NAD(P)(H)-binding
pattern (typically, TGxxxGxG in classical SDRs and
TGxxGxxG in extended SDRs), while substrate binding is
in the C-terminal region. A critical catalytic Tyr
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase (15-PGDH) numbering), is often found in a
conserved YXXXK pattern. In addition to the Tyr and Lys,
there is often an upstream Ser (Ser-138, 15-PGDH
numbering) and/or an Asn (Asn-107, 15-PGDH numbering) or
additional Ser, contributing to the active site.
Substrates for these enzymes include sugars, steroids,
alcohols, and aromatic compounds. The standard reaction
mechanism is a proton relay involving the conserved Tyr
and Lys, as well as Asn (or Ser). Some SDR family
members, including 17 beta-hydroxysteroid dehydrogenase
contain an additional helix-turn-helix motif that is not
generally found among SDRs.
Length = 246
Score = 49.4 bits (118), Expect = 4e-08
Identities = 30/114 (26%), Positives = 52/114 (45%), Gaps = 31/114 (27%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
++++VTGAS G+GAAI R+ A +G +V V+
Sbjct: 1 QVVLVTGASRGLGAAIARSFAREGARV------------------------------VVN 30
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNA 116
+ R E +A+A E + + +++ DV +V + N FG +D ++NNA
Sbjct: 31 YYRSTESAEAVAAEAGE-RAIAIQADVRDRDQVQAMIEEAKNHFGPVDTIVNNA 83
>gnl|CDD|187602 cd05344, BKR_like_SDR_like, putative beta-ketoacyl acyl carrier
protein [ACP] reductase (BKR)-like, SDR. This subgroup
resembles the SDR family, but does not have a perfect
match to the NAD-binding motif or the catalytic tetrad
characteristic of the SDRs. It includes the SDRs, Q9HYA2
from Pseudomonas aeruginosa PAO1 and APE0912 from
Aeropyrum pernix K1. BKR catalyzes the NADPH-dependent
reduction of ACP in the first reductive step of de novo
fatty acid synthesis (FAS). FAS consists of four
elongation steps, which are repeated to extend the fatty
acid chain through the addition of two-carbo units from
malonyl acyl-carrier protein (ACP): condensation,
reduction, dehydration, and a final reduction. Type II
FAS, typical of plants and many bacteria, maintains
these activities on discrete polypeptides, while type I
FAS utilizes one or two multifunctional polypeptides.
BKR resembles enoyl reductase, which catalyzes the
second reduction step in FAS. 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 have a 3-glycine N-terminal
NAD(P)(H)-binding pattern (typically, TGxxxGxG in
classical SDRs and TGxxGxxG in extended SDRs), while
substrate binding is in the C-terminal region. A
critical catalytic Tyr residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering), is often found in a conserved YXXXK pattern.
In addition to the Tyr and Lys, there is often an
upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn
(Asn-107, 15-PGDH numbering) or additional Ser,
contributing to the active site. Substrates for these
enzymes include sugars, steroids, alcohols, and aromatic
compounds. The standard reaction mechanism is a proton
relay involving the conserved Tyr and Lys, as well as
Asn (or Ser). Some SDR family members, including 17
beta-hydroxysteroid dehydrogenase contain an additional
helix-turn-helix motif that is not generally found among
SDRs.
Length = 253
Score = 49.2 bits (118), Expect = 5e-08
Identities = 36/115 (31%), Positives = 49/115 (42%), Gaps = 29/115 (25%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K+ +VT AS GIG AI RALA +G +V AR E ++ A S A V+
Sbjct: 2 KVALVTAASSGIGLAIARALAREGARVAICARNRENLERAASELRAGG----AGVLAVVA 57
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAG 117
E ID + V+ DA FG +D+++NNAG
Sbjct: 58 DLTDPEDIDRL-------------VEKAGDA------------FGRVDILVNNAG 87
>gnl|CDD|187587 cd05326, secoisolariciresinol-DH_like_SDR_c, secoisolariciresinol
dehydrogenase (secoisolariciresinol-DH)-like, classical
(c) SDRs. Podophyllum secoisolariciresinol-DH is a homo
tetrameric, classical SDR that catalyzes the
NAD-dependent conversion of (-)-secoisolariciresinol to
(-)-matairesinol via a (-)-lactol intermediate.
(-)-Matairesinol is an intermediate to various
8'-lignans, including the cancer-preventive mammalian
lignan, and those involved in vascular plant defense.
This subgroup also includes rice momilactone A synthase
which catalyzes the conversion of
3beta-hydroxy-9betaH-pimara-7,15-dien-19,6beta-olide
into momilactone A, Arabidopsis ABA2 which during
abscisic acid (ABA) biosynthesis, catalyzes the
conversion of xanthoxin to abscisic aldehyde and, maize
Tasselseed2 which participate in the maize sex
determination pathway. 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, 15-hydroxyprostaglandin dehydrogenase
(15-PGDH) numbering). In addition to the Tyr and Lys,
there is often an upstream Ser (Ser-138, 15-PGDH
numbering) and/or an Asn (Asn-107, 15-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 ketoacyl
reductases 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 = 249
Score = 49.0 bits (117), Expect = 6e-08
Identities = 34/116 (29%), Positives = 48/116 (41%), Gaps = 31/116 (26%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K+ ++TG + GIG A R A G +V+ DI G
Sbjct: 5 KVAIITGGASGIGEATARLFAKHGARVV------------------IADIDDDAGQ---- 42
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGV 118
A+A E D + + DVT +A+V A D +FG +D+M NNAGV
Sbjct: 43 ---------AVAAELGDPDISFVHCDVTVEADVRAAVDTAVARFGRLDIMFNNAGV 89
>gnl|CDD|235633 PRK05872, PRK05872, short chain dehydrogenase; Provisional.
Length = 296
Score = 48.8 bits (117), Expect = 6e-08
Identities = 35/122 (28%), Positives = 54/122 (44%), Gaps = 30/122 (24%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K++VVTGA+ GIGA + R L A+G ++ VD+
Sbjct: 10 KVVVVTGAARGIGAELARRLHARGAKLA------------------LVDL---------- 41
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNEFA 122
AE+ A+ D +V ++ DVT A + A + +FG IDV++ NAG+
Sbjct: 42 --EEAELAALAAELGGDDRVLTVVADVTDLAAMQAAAEEAVERFGGIDVVVANAGIASGG 99
Query: 123 PV 124
V
Sbjct: 100 SV 101
>gnl|CDD|187625 cd05367, SPR-like_SDR_c, sepiapterin reductase (SPR)-like,
classical (c) SDRs. Human SPR, a member of the SDR
family, catalyzes the NADP-dependent reduction of
sepiaptern to 7,8-dihydrobiopterin (BH2). In addition to
SPRs, this subgroup also contains Bacillus cereus yueD,
a benzil reductase, which catalyzes the stereospecific
reduction of benzil to (S)-benzoin. 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
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-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 ketoacyl reductases 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 = 241
Score = 48.8 bits (117), Expect = 7e-08
Identities = 29/118 (24%), Positives = 48/118 (40%), Gaps = 36/118 (30%)
Query: 5 IVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIGFA 64
I++TGAS GIG A+ L +G + V+ A
Sbjct: 2 IILTGASRGIGRALAEELLKRGSPSV-----------------------------VVLLA 32
Query: 65 RRAEMI-DAMAKENPDWKVHSLKVDVTKDA---EVVEAFDWINNKFGHIDVMINNAGV 118
R E + + + P +V ++K D++ A +++EA G D++INNAG
Sbjct: 33 RSEEPLQELKEELRPGLRVTTVKADLSDAAGVEQLLEAIRK---LDGERDLLINNAGS 87
>gnl|CDD|212493 cd08932, HetN_like_SDR_c, HetN oxidoreductase-like, classical (c)
SDR. This subgroup includes Anabaena sp. strain PCC
7120 HetN, a putative oxidoreductase involved in
heterocyst differentiation, and related proteins. 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
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-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 ketoacyl reductases 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 = 223
Score = 48.5 bits (116), Expect = 7e-08
Identities = 34/117 (29%), Positives = 48/117 (41%), Gaps = 35/117 (29%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K+ +VTGAS GIG I RALA G++V R E +
Sbjct: 1 KVALVTGASRGIGIEIARALARDGYRVSLGLRNPEDLA---------------------- 38
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAF-DWINNKFGHIDVMINNAGV 118
A A V ++ D D E A D + ++FG IDV+++NAG+
Sbjct: 39 -ALSAS----------GGDVEAVPYDAR-DPEDARALVDALRDRFGRIDVLVHNAGI 83
>gnl|CDD|236040 PRK07523, PRK07523, gluconate 5-dehydrogenase; Provisional.
Length = 255
Score = 48.6 bits (116), Expect = 7e-08
Identities = 31/122 (25%), Positives = 45/122 (36%), Gaps = 29/122 (23%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
+ +VTG+S GIG A+ LA G +VI R + A
Sbjct: 11 RRALVTGSSQGIGYALAEGLAQAGAEVILNGRDPAKLAAAAESL---------------- 54
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNEFA 122
+ H+L DVT V A D + G ID+++NNAG+
Sbjct: 55 -------------KGQGLSAHALAFDVTDHDAVRAAIDAFEAEIGPIDILVNNAGMQFRT 101
Query: 123 PV 124
P+
Sbjct: 102 PL 103
>gnl|CDD|237189 PRK12748, PRK12748, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 256
Score = 48.1 bits (115), Expect = 1e-07
Identities = 30/118 (25%), Positives = 50/118 (42%), Gaps = 20/118 (16%)
Query: 1 MSKIIVVTGAS--VGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGH 58
M KI +VTGAS GIGAA+ R LAAKG + F + + H
Sbjct: 4 MKKIALVTGASRLNGIGAAVCRRLAAKGIDI-----------FFTYWSPYDKTM-PWGMH 51
Query: 59 QVIGFARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNA 116
+ E+ E+ + +++D+++ F ++ + G ++INNA
Sbjct: 52 DKEPVLLKEEI------ESYGVRCEHMEIDLSQPYAPNRVFYAVSERLGDPSILINNA 103
>gnl|CDD|187629 cd05371, HSD10-like_SDR_c, 17hydroxysteroid dehydrogenase type 10
(HSD10)-like, classical (c) SDRs. HSD10, also known as
amyloid-peptide-binding alcohol dehydrogenase (ABAD),
was previously identified as a L-3-hydroxyacyl-CoA
dehydrogenase, HADH2. In fatty acid metabolism, HADH2
catalyzes the third step of beta-oxidation, the
conversion of a hydroxyl to a keto group in the
NAD-dependent oxidation of L-3-hydroxyacyl CoA. In
addition to alcohol dehydrogenase and HADH2 activites,
HSD10 has steroid dehydrogenase activity. Although the
mechanism is unclear, HSD10 is implicated in the
formation of amyloid beta-petide in the brain (which is
linked to the development of Alzheimer's disease).
Although HSD10 is normally concentrated in the
mitochondria, in the presence of amyloid beta-peptide it
translocates into the plasma membrane, where it's action
may generate cytotoxic aldehydes and may lower estrogen
levels through its use of 17-beta-estradiol as a
substrate. HSD10 is a member of the SRD family, but
differs from other SDRs by the presence of two
insertions of unknown function. 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 15-hydroxyprostaglandin
dehydrogenase (15-PGDH) numbering). In addition to the
Tyr and Lys, there is often an upstream Ser (Ser-138,
15-PGDH numbering) and/or an Asn (Asn-107, 15-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 ketoacyl
reductases 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 = 252
Score = 48.1 bits (115), Expect = 1e-07
Identities = 29/116 (25%), Positives = 48/116 (41%), Gaps = 33/116 (28%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
+ VVTG + G+G A + L A+G +V +D+ + G V
Sbjct: 3 LVAVVTGGASGLGLATVERLLAQGAKV------------------VILDLPNSPGETV-- 42
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGV 118
A++ D + VDVT + +V A KFG +D+++N AG+
Sbjct: 43 ----AKLGD---------NCRFVPVDVTSEKDVKAALALAKAKFGRLDIVVNCAGI 85
>gnl|CDD|187635 cd08930, SDR_c8, classical (c) SDR, subgroup 8. This subgroup has
a fairly well conserved active site tetrad and domain
size of the classical SDRs, but has an atypical
NAD-binding motif ([ST]G[GA]XGXXG). 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
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-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 ketoacyl reductases 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 = 250
Score = 48.1 bits (115), Expect = 1e-07
Identities = 31/121 (25%), Positives = 49/121 (40%), Gaps = 28/121 (23%)
Query: 1 MSKIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQV 60
KII++TGA+ IG A +AL + G ++I DI A
Sbjct: 1 EDKIILITGAAGLIGKAFCKALLSAGARLIL------------------ADINAP----- 37
Query: 61 IGFARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNE 120
E + +V +L++D+T + E + KFG ID++INNA +
Sbjct: 38 -----ALEQLKEELTNLYKNRVIALELDITSKESIKELIESYLEKFGRIDILINNAYPSP 92
Query: 121 F 121
Sbjct: 93 K 93
>gnl|CDD|187649 cd08945, PKR_SDR_c, Polyketide ketoreductase, classical (c) SDR.
Polyketide ketoreductase (KR) is a classical SDR with a
characteristic NAD-binding pattern and active site
tetrad. Aromatic polyketides include various aromatic
compounds of pharmaceutical interest. Polyketide KR,
part of the type II polyketide synthase (PKS) complex,
is comprised of stand-alone domains that resemble the
domains found in fatty acid synthase and multidomain
type I PKS. 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 have a 3-glycine N-terminal NAD(P)(H)-binding
pattern (typically, TGxxxGxG in classical SDRs and
TGxxGxxG in extended SDRs), while substrate binding is
in the C-terminal region. A critical catalytic Tyr
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase (15-PGDH) numbering), is often found in a
conserved YXXXK pattern. In addition to the Tyr and Lys,
there is often an upstream Ser (Ser-138, 15-PGDH
numbering) and/or an Asn (Asn-107, 15-PGDH numbering) or
additional Ser, contributing to the active site.
Substrates for these enzymes include sugars, steroids,
alcohols, and aromatic compounds. The standard reaction
mechanism is a proton relay involving the conserved Tyr
and Lys, as well as Asn (or Ser). Some SDR family
members, including 17 beta-hydroxysteroid dehydrogenase
contain an additional helix-turn-helix motif that is not
generally found among SDRs.
Length = 258
Score = 47.9 bits (114), Expect = 1e-07
Identities = 29/116 (25%), Positives = 44/116 (37%), Gaps = 29/116 (25%)
Query: 2 SKIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVI 61
S++ +VTGA+ GIG AI R L +G +V AR E
Sbjct: 3 SEVALVTGATSGIGLAIARRLGKEGLRVFVCARGEE------------------------ 38
Query: 62 GFARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAG 117
A + + + + DV E+ ++G IDV++NNAG
Sbjct: 39 ---GLATTVKELREAGV--EADGRTCDVRSVPEIEALVAAAVARYGPIDVLVNNAG 89
>gnl|CDD|235545 PRK05650, PRK05650, short chain dehydrogenase; Provisional.
Length = 270
Score = 48.1 bits (115), Expect = 1e-07
Identities = 25/114 (21%), Positives = 43/114 (37%), Gaps = 29/114 (25%)
Query: 5 IVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIGFA 64
+++TGA+ G+G AI A +G ++ D+ G + +
Sbjct: 3 VMITGAASGLGRAIALRWAREGWRLA------------------LADVNEEGGEETLKLL 44
Query: 65 RRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGV 118
R A + DV +++ K+G IDV++NNAGV
Sbjct: 45 REAGG-----------DGFYQRCDVRDYSQLTALAQACEEKWGGIDVIVNNAGV 87
>gnl|CDD|181334 PRK08263, PRK08263, short chain dehydrogenase; Provisional.
Length = 275
Score = 48.1 bits (115), Expect = 1e-07
Identities = 31/124 (25%), Positives = 51/124 (41%), Gaps = 32/124 (25%)
Query: 1 MSKIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQV 60
M K+ +TGAS G G A + E+ +G +V
Sbjct: 2 MEKVWFITGASRGFGRA-----------------------WTEAALE--------RGDRV 30
Query: 61 IGFARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNE 120
+ AR + +A++ D ++ L +DVT A V A + FG +D+++NNAG
Sbjct: 31 VATARDTATLADLAEKYGD-RLLPLALDVTDRAAVFAAVETAVEHFGRLDIVVNNAGYGL 89
Query: 121 FAPV 124
F +
Sbjct: 90 FGMI 93
>gnl|CDD|184025 PRK13394, PRK13394, 3-hydroxybutyrate dehydrogenase; Provisional.
Length = 262
Score = 48.0 bits (114), Expect = 2e-07
Identities = 32/122 (26%), Positives = 48/122 (39%), Gaps = 29/122 (23%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K VVTGA+ GIG I LA G V + D + D + G + IG
Sbjct: 8 KTAVVTGAASGIGKEIALELARAGAAVA-------IADLNQDGANAVADEINKAGGKAIG 60
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNEFA 122
A +DVT + V D + +FG +D++++NAG+
Sbjct: 61 VA----------------------MDVTNEDAVNAGIDKVAERFGSVDILVSNAGIQIVN 98
Query: 123 PV 124
P+
Sbjct: 99 PI 100
>gnl|CDD|180411 PRK06123, PRK06123, short chain dehydrogenase; Provisional.
Length = 248
Score = 47.9 bits (114), Expect = 2e-07
Identities = 33/121 (27%), Positives = 58/121 (47%), Gaps = 30/121 (24%)
Query: 1 MSKIIVVTGASVGIGAAILRALAAKGHQV-IGFARRAEMIDFAESLFAFFVDIVAAKGHQ 59
M K++++TGAS GIGAA A +G+ V + + R D AE++ V + +G +
Sbjct: 1 MRKVMIITGASRGIGAATALLAAERGYAVCLNYLRNR---DAAEAV----VQAIRRQGGE 53
Query: 60 VIGFARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVN 119
+ A DV +A+V+ F+ ++ + G +D ++NNAG+
Sbjct: 54 ALAVA----------------------ADVADEADVLRLFEAVDRELGRLDALVNNAGIL 91
Query: 120 E 120
E
Sbjct: 92 E 92
>gnl|CDD|180802 PRK07035, PRK07035, short chain dehydrogenase; Provisional.
Length = 252
Score = 47.3 bits (113), Expect = 2e-07
Identities = 37/117 (31%), Positives = 55/117 (47%), Gaps = 29/117 (24%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
KI +VTGAS GIG AI + LA +G VI +R+ + A IVAA G
Sbjct: 9 KIALVTGASRGIGEAIAKLLAQQGAHVIVSSRKLD------GCQAVADAIVAAGG----- 57
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVN 119
+AE A+A H +++ ++ F I + G +D+++NNA N
Sbjct: 58 ---KAE---ALA-------CHIGEME-----QIDALFAHIRERHGRLDILVNNAAAN 96
>gnl|CDD|181295 PRK08213, PRK08213, gluconate 5-dehydrogenase; Provisional.
Length = 259
Score = 47.6 bits (114), Expect = 2e-07
Identities = 35/122 (28%), Positives = 53/122 (43%), Gaps = 29/122 (23%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K +VTG S G+G I AL G +V+ AR+AE ++ A H
Sbjct: 13 KTALVTGGSRGLGLQIAEALGEAGARVVLSARKAE-------------ELEEAAAHL--- 56
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNEFA 122
A IDA+ + DV +A++ + +FGH+D+++NNAG A
Sbjct: 57 ---EALGIDALW----------IAADVADEADIERLAEETLERFGHVDILVNNAGATWGA 103
Query: 123 PV 124
P
Sbjct: 104 PA 105
>gnl|CDD|236110 PRK07831, PRK07831, short chain dehydrogenase; Provisional.
Length = 262
Score = 47.3 bits (113), Expect = 2e-07
Identities = 35/124 (28%), Positives = 54/124 (43%), Gaps = 30/124 (24%)
Query: 3 KIIVVTGAS-VGIGAAILRALAAKGHQVIGFARRAEMI-DFAESLFAFFVDIVAAKGHQV 60
K+++VT A+ GIG+A R +G +V +I D E
Sbjct: 18 KVVLVTAAAGTGIGSATARRALEEGARV--------VISDIHER---------------- 53
Query: 61 IGFARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNE 120
R E D +A E +V ++ DVT +A+V D + G +DV++NNAG+
Sbjct: 54 ----RLGETADELAAELGLGRVEAVVCDVTSEAQVDALIDAAVERLGRLDVLVNNAGLGG 109
Query: 121 FAPV 124
PV
Sbjct: 110 QTPV 113
>gnl|CDD|236190 PRK08220, PRK08220, 2,3-dihydroxybenzoate-2,3-dehydrogenase;
Validated.
Length = 252
Score = 47.2 bits (113), Expect = 2e-07
Identities = 27/116 (23%), Positives = 42/116 (36%), Gaps = 38/116 (32%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K + VTGA+ GIG A+ A G +VIGF
Sbjct: 9 KTVWVTGAAQGIGYAVALAFVEAGAKVIGF------------------------------ 38
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGV 118
D D+ + +DV+ A V + + + G +DV++N AG+
Sbjct: 39 --------DQAFLTQEDYPFATFVLDVSDAAAVAQVCQRLLAETGPLDVLVNAAGI 86
>gnl|CDD|236209 PRK08265, PRK08265, short chain dehydrogenase; Provisional.
Length = 261
Score = 47.3 bits (113), Expect = 3e-07
Identities = 32/114 (28%), Positives = 47/114 (41%), Gaps = 32/114 (28%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K+ +VTG + IGAA+ RAL A G +V VDI A G V
Sbjct: 7 KVAIVTGGATLIGAAVARALVAAGARV------------------AIVDIDADNGAAV-- 46
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNA 116
A + A + D+T DA + A + +FG +D+++N A
Sbjct: 47 ----AASLGERA--------RFIATDITDDAAIERAVATVVARFGRVDILVNLA 88
>gnl|CDD|235933 PRK07097, PRK07097, gluconate 5-dehydrogenase; Provisional.
Length = 265
Score = 47.0 bits (112), Expect = 3e-07
Identities = 33/116 (28%), Positives = 48/116 (41%), Gaps = 29/116 (25%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
KI ++TGAS GIG AI +A A G ++ E++D +
Sbjct: 11 KIALITGASYGIGFAIAKAYAKAGATIVFNDINQELVDKGLA------------------ 52
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGV 118
A R I+A H DVT + V I + G ID+++NNAG+
Sbjct: 53 -AYRELGIEA----------HGYVCDVTDEDGVQAMVSQIEKEVGVIDILVNNAGI 97
>gnl|CDD|236116 PRK07856, PRK07856, short chain dehydrogenase; Provisional.
Length = 252
Score = 46.9 bits (112), Expect = 3e-07
Identities = 33/121 (27%), Positives = 48/121 (39%), Gaps = 37/121 (30%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
++++VTG + GIGA I RA A G V+ RRA + + A F AA
Sbjct: 7 RVVLVTGGTRGIGAGIARAFLAAGATVVVCGRRAP--ETVDGRPAEF---HAA------- 54
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNEFA 122
DV +V D I + G +DV++NNAG + +A
Sbjct: 55 -------------------------DVRDPDQVAALVDAIVERHGRLDVLVNNAGGSPYA 89
Query: 123 P 123
Sbjct: 90 L 90
>gnl|CDD|187586 cd05325, carb_red_sniffer_like_SDR_c, carbonyl reductase
sniffer-like, classical (c) SDRs. Sniffer is an
NADPH-dependent carbonyl reductase of the classical SDR
family. Studies in Drosophila melanogaster implicate
Sniffer in the prevention of neurodegeneration due to
aging and oxidative-stress. This subgroup also includes
Rhodococcus sp. AD45 IsoH, which is an NAD-dependent
1-hydroxy-2-glutathionyl-2-methyl-3-butene dehydrogenase
involved in isoprene metabolism, Aspergillus nidulans
StcE encoded by a gene which is part of a proposed
sterigmatocystin biosynthesis gene cluster, Bacillus
circulans SANK 72073 BtrF encoded by a gene found in the
butirosin biosynthesis gene cluster, and Aspergillus
parasiticus nor-1 involved in the biosynthesis of
aflatoxins. 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
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-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 ketoacyl reductases 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 = 233
Score = 46.9 bits (112), Expect = 3e-07
Identities = 29/117 (24%), Positives = 50/117 (42%), Gaps = 35/117 (29%)
Query: 5 IVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIGFA 64
+++TGAS GIG ++R L A+G+ + VI
Sbjct: 1 VLITGASRGIGLELVRQLLARGN------------------------------NTVIATC 30
Query: 65 RRAEMIDAMAKENP-DWKVHSLKVDVTKDAEVVEAFDWINNKFG--HIDVMINNAGV 118
R +A ++H L++DVT + E+ + + + G +DV+INNAG+
Sbjct: 31 RDPSAATELAALGASHSRLHILELDVTDEIA--ESAEAVAERLGDAGLDVLINNAGI 85
>gnl|CDD|236207 PRK08261, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 450
Score = 46.8 bits (112), Expect = 4e-07
Identities = 29/116 (25%), Positives = 47/116 (40%), Gaps = 32/116 (27%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K+ +VTGA+ GIGAAI LA G V+ +D+ AA
Sbjct: 211 KVALVTGAARGIGAAIAEVLARDGAHVVC------------------LDVPAAGEA---- 248
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGV 118
A A + A L +D+T + + + G +D++++NAG+
Sbjct: 249 LAAVANRVGGTA----------LALDITAPDAPARIAEHLAERHGGLDIVVHNAGI 294
>gnl|CDD|187600 cd05341, 3beta-17beta-HSD_like_SDR_c, 3beta17beta hydroxysteroid
dehydrogenase-like, classical (c) SDRs. This subgroup
includes members identified as 3beta17beta
hydroxysteroid dehydrogenase, 20beta hydroxysteroid
dehydrogenase, and R-alcohol dehydrogenase. These
proteins exhibit the canonical active site tetrad and
glycine rich NAD(P)-binding motif of the classical SDRs.
17beta-dehydrogenases are a group of isozymes that
catalyze activation and inactivation of estrogen and
androgens, and include members of the SDR family. 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 have a
3-glycine N-terminal NAD(P)(H)-binding pattern
(typically, TGxxxGxG in classical SDRs and TGxxGxxG in
extended SDRs), while substrate binding is in the
C-terminal region. A critical catalytic Tyr residue
(Tyr-151, human 15-hydroxyprostaglandin dehydrogenase
(15-PGDH) numbering), is often found in a conserved
YXXXK pattern. In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) or additional
Ser, contributing to the active site. Substrates for
these enzymes include sugars, steroids, alcohols, and
aromatic compounds. The standard reaction mechanism is a
proton relay involving the conserved Tyr and Lys, as
well as Asn (or Ser). Some SDR family members, including
17 beta-hydroxysteroid dehydrogenase contain an
additional helix-turn-helix motif that is not generally
found among SDRs.
Length = 247
Score = 46.6 bits (111), Expect = 4e-07
Identities = 30/116 (25%), Positives = 45/116 (38%), Gaps = 32/116 (27%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K+ +VTG + G+G A R L A+G +V+ DI+ +G
Sbjct: 6 KVAIVTGGARGLGLAHARLLVAEGAKVV------------------LSDILDEEGQAA-- 45
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGV 118
A E D +DVT + D FG +DV++NNAG+
Sbjct: 46 -----------AAELGD-AARFFHLDVTDEDGWTAVVDTAREAFGRLDVLVNNAGI 89
>gnl|CDD|187608 cd05350, SDR_c6, classical (c) SDR, subgroup 6. These proteins are
members of the classical SDR family, with a canonical
active site tetrad and a fairly well conserved typical
Gly-rich NAD-binding motif. 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 have a 3-glycine N-terminal
NAD(P)(H)-binding pattern (typically, TGxxxGxG in
classical SDRs and TGxxGxxG in extended SDRs), while
substrate binding is in the C-terminal region. A
critical catalytic Tyr residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering), is often found in a conserved YXXXK pattern.
In addition to the Tyr and Lys, there is often an
upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn
(Asn-107, 15-PGDH numbering) or additional Ser,
contributing to the active site. Substrates for these
enzymes include sugars, steroids, alcohols, and aromatic
compounds. The standard reaction mechanism is a proton
relay involving the conserved Tyr and Lys, as well as
Asn (or Ser). Some SDR family members, including 17
beta-hydroxysteroid dehydrogenase contain an additional
helix-turn-helix motif that is not generally found among
SDRs.
Length = 239
Score = 46.6 bits (111), Expect = 4e-07
Identities = 31/114 (27%), Positives = 49/114 (42%), Gaps = 29/114 (25%)
Query: 5 IVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIGFA 64
+++TGAS GIG A+ R A G+ V ARR + +D
Sbjct: 1 VLITGASSGIGRALAREFAKAGYNVALAARRTDRLD-----------------------E 37
Query: 65 RRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGV 118
+AE++ NP+ V +DVT + + + G +D++I NAGV
Sbjct: 38 LKAELL------NPNPSVEVEILDVTDEERNQLVIAELEAELGGLDLVIINAGV 85
>gnl|CDD|235628 PRK05855, PRK05855, short chain dehydrogenase; Validated.
Length = 582
Score = 46.9 bits (112), Expect = 4e-07
Identities = 37/117 (31%), Positives = 55/117 (47%), Gaps = 31/117 (26%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K++VVTGA GIG A A +G +V+ DI A
Sbjct: 316 KLVVVTGAGSGIGRETALAFAREGAEVV------------------ASDIDEA------A 351
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAF-DWINNKFGHIDVMINNAGV 118
R AE+I A H+ +VDV+ DA+ +EAF +W+ + G D+++NNAG+
Sbjct: 352 AERTAELIRAAGAV-----AHAYRVDVS-DADAMEAFAEWVRAEHGVPDIVVNNAGI 402
>gnl|CDD|237188 PRK12745, PRK12745, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 256
Score = 46.5 bits (111), Expect = 4e-07
Identities = 29/118 (24%), Positives = 41/118 (34%), Gaps = 28/118 (23%)
Query: 1 MSKIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQV 60
M + +VTG GIG I RALAA G + R + + +AA ++
Sbjct: 1 MRPVALVTGGRRGIGLGIARALAAAGFDLAINDRPDD-------------EELAATQQEL 47
Query: 61 IGFARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGV 118
V DV + D +G ID ++NNAGV
Sbjct: 48 RALGVE---------------VIFFPADVADLSAHEAMLDAAQAAWGRIDCLVNNAGV 90
>gnl|CDD|181305 PRK08226, PRK08226, short chain dehydrogenase; Provisional.
Length = 263
Score = 46.7 bits (111), Expect = 4e-07
Identities = 31/121 (25%), Positives = 43/121 (35%), Gaps = 30/121 (24%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K ++TGA GIG I R A G +I E+ A+ L +GH+
Sbjct: 7 KTALITGALQGIGEGIARVFARHGANLILLDISPEIEKLADEL--------CGRGHRCT- 57
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNEFA 122
++ DV A V A K G ID+++NNAGV
Sbjct: 58 ---------------------AVVADVRDPASVAAAIKRAKEKEGRIDILVNNAGVCRLG 96
Query: 123 P 123
Sbjct: 97 S 97
>gnl|CDD|187590 cd05329, TR_SDR_c, tropinone reductase-I and II (TR-1, and
TR-II)-like, classical (c) SDRs. This subgroup includes
TR-I and TR-II; these proteins are members of the SDR
family. TRs catalyze the NADPH-dependent reductions of
the 3-carbonyl group of tropinone, to a beta-hydroxyl
group. TR-I and TR-II produce different stereoisomers
from tropinone, TR-I produces tropine
(3alpha-hydroxytropane), and TR-II, produces
pseudotropine (sigma-tropine, 3beta-hydroxytropane).
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
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-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 ketoacyl reductases 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 = 251
Score = 46.7 bits (111), Expect = 4e-07
Identities = 32/118 (27%), Positives = 49/118 (41%), Gaps = 30/118 (25%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K +VTG + GIG AI+ LA G +V AR + +D + KG +V G
Sbjct: 7 KTALVTGGTKGIGYAIVEELAGLGAEVYTCARNQKELD-------ECLTEWREKGFKVEG 59
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKF-GHIDVMINNAGVN 119
DV+ +E E D + + F G +++++NNAG N
Sbjct: 60 SV----------------------CDVSSRSERQELMDTVASHFGGKLNILVNNAGTN 95
>gnl|CDD|180771 PRK06947, PRK06947, glucose-1-dehydrogenase; Provisional.
Length = 248
Score = 46.3 bits (110), Expect = 5e-07
Identities = 33/120 (27%), Positives = 50/120 (41%), Gaps = 32/120 (26%)
Query: 1 MSKIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQV 60
M K++++TGAS GIG A AA+G V
Sbjct: 1 MRKVVLITGASRGIGRATAVLAAARGWSV------------------------------G 30
Query: 61 IGFARRAEMIDAMAKENPDWKVHSLKV--DVTKDAEVVEAFDWINNKFGHIDVMINNAGV 118
I +AR A + A + V DV +A+V+ FD + + FG +D ++NNAG+
Sbjct: 31 INYARDAAAAEETADAVRAAGGRACVVAGDVANEADVIAMFDAVQSAFGRLDALVNNAGI 90
>gnl|CDD|181225 PRK08085, PRK08085, gluconate 5-dehydrogenase; Provisional.
Length = 254
Score = 46.3 bits (110), Expect = 5e-07
Identities = 35/123 (28%), Positives = 48/123 (39%), Gaps = 29/123 (23%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K I++TG++ GIG + LA G ++I AE
Sbjct: 10 KNILITGSAQGIGFLLATGLAEYGAEIIINDITAE------------------------- 44
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNEFA 122
RAE+ K H+ +VT EV A + I G IDV+INNAG+
Sbjct: 45 ---RAELA-VAKLRQEGIKAHAAPFNVTHKQEVEAAIEHIEKDIGPIDVLINNAGIQRRH 100
Query: 123 PVT 125
P T
Sbjct: 101 PFT 103
>gnl|CDD|181044 PRK07577, PRK07577, short chain dehydrogenase; Provisional.
Length = 234
Score = 46.3 bits (110), Expect = 5e-07
Identities = 25/46 (54%), Positives = 30/46 (65%), Gaps = 1/46 (2%)
Query: 2 SKIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFA 47
S+ ++VTGA+ GIG A+ LA GHQVIG AR A DF LFA
Sbjct: 3 SRTVLVTGATKGIGLALSLRLANLGHQVIGIARSAID-DFPGELFA 47
>gnl|CDD|181585 PRK08936, PRK08936, glucose-1-dehydrogenase; Provisional.
Length = 261
Score = 46.3 bits (110), Expect = 5e-07
Identities = 33/123 (26%), Positives = 51/123 (41%), Gaps = 32/123 (26%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVI--GFARRAEMIDFAESLFAFFVDIVAAKGHQV 60
K++V+TG S G+G A+ + +V+ + E D AE +I A G +
Sbjct: 8 KVVVITGGSTGLGRAMAVRFGKEKAKVVINYRSDEEEANDVAE-------EIKKAGGEAI 60
Query: 61 IGFARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNE 120
+K DVT +++VV +FG +DVMINNAG+
Sbjct: 61 A-----------------------VKGDVTVESDVVNLIQTAVKEFGTLDVMINNAGIEN 97
Query: 121 FAP 123
P
Sbjct: 98 AVP 100
>gnl|CDD|180818 PRK07062, PRK07062, short chain dehydrogenase; Provisional.
Length = 265
Score = 46.2 bits (110), Expect = 6e-07
Identities = 30/116 (25%), Positives = 46/116 (39%), Gaps = 29/116 (25%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
++ VVTG S GIG A + L G V R E
Sbjct: 9 RVAVVTGGSSGIGLATVELLLEAGASVAICGRDEE------------------------- 43
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAF-DWINNKFGHIDVMINNAG 117
R A + ++ P ++ + + DV D V AF + +FG +D+++NNAG
Sbjct: 44 --RLASAEARLREKFPGARLLAARCDVL-DEADVAAFAAAVEARFGGVDMLVNNAG 96
>gnl|CDD|183772 PRK12823, benD, 1,6-dihydroxycyclohexa-2,4-diene-1-carboxylate
dehydrogenase; Provisional.
Length = 260
Score = 46.1 bits (110), Expect = 7e-07
Identities = 34/115 (29%), Positives = 49/115 (42%), Gaps = 30/115 (26%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K++VVTGA+ GIG + AA+G +V+ ++D +E V VA
Sbjct: 9 KVVVVTGAAQGIGRGVALRAAAEGARVV-------LVDRSE-----LVHEVA-------- 48
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAG 117
AE+ A + +L D+ A A FG IDV+INN G
Sbjct: 49 ----AELRAAGG------EALALTADLETYAGAQAAMAAAVEAFGRIDVLINNVG 93
>gnl|CDD|187622 cd05364, SDR_c11, classical (c) SDR, subgroup 11. 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
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-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 ketoacyl reductases 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 = 253
Score = 45.5 bits (108), Expect = 9e-07
Identities = 24/117 (20%), Positives = 44/117 (37%), Gaps = 26/117 (22%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K+ ++TG+S GIGA A G ++ R AE ++ +
Sbjct: 4 KVAIITGSSSGIGAGTAILFARLGARLALTGRDAERLE--------------ETRQSCLQ 49
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVN 119
+ K+ + D+T++ KFG +D+++NNAG+
Sbjct: 50 AGVSEK------------KILLVVADLTEEEGQDRIISTTLAKFGRLDILVNNAGIL 94
>gnl|CDD|181762 PRK09291, PRK09291, short chain dehydrogenase; Provisional.
Length = 257
Score = 45.4 bits (108), Expect = 1e-06
Identities = 34/125 (27%), Positives = 49/125 (39%), Gaps = 35/125 (28%)
Query: 1 MSKIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQV 60
MSK I++TGA G G + LA KGH VI + A +
Sbjct: 1 MSKTILITGAGSGFGREVALRLARKGHNVIAGVQIAPQV--------------------- 39
Query: 61 IGFARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNE 120
A RAE + K+D+T + +A +W +DV++NNAG+ E
Sbjct: 40 --TALRAEAARR------GLALRVEKLDLTDAIDRAQAAEW------DVDVLLNNAGIGE 85
Query: 121 FAPVT 125
V
Sbjct: 86 AGAVV 90
>gnl|CDD|188170 TIGR01832, kduD, 2-deoxy-D-gluconate 3-dehydrogenase. This model
describes 2-deoxy-D-gluconate 3-dehydrogenase (also
called 2-keto-3-deoxygluconate oxidoreductase), a member
of the family of short-chain-alcohol dehydrogenases
(pfam00106). This protein has been characterized in
Erwinia chrysanthemi as an enzyme of pectin degradation
[Energy metabolism, Biosynthesis and degradation of
polysaccharides].
Length = 248
Score = 45.5 bits (108), Expect = 1e-06
Identities = 30/116 (25%), Positives = 48/116 (41%), Gaps = 31/116 (26%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K+ +VTGA+ G+G I LA G ++G R + +E+ V A G
Sbjct: 6 KVALVTGANTGLGQGIAVGLAEAGADIVGAGRS----EPSETQ-----QQVEALGR---- 52
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGV 118
+ SL D++ + D +FGHID+++NNAG+
Sbjct: 53 ------------------RFLSLTADLSDIEAIKALVDSAVEEFGHIDILVNNAGI 90
>gnl|CDD|187617 cd05359, ChcA_like_SDR_c, 1-cyclohexenylcarbonyl_coenzyme
A_reductase (ChcA)_like, classical (c) SDRs. This
subgroup contains classical SDR proteins, including
members identified as 1-cyclohexenylcarbonyl coenzyme A
reductase. ChcA of Streptomyces collinus is implicated
in the final reduction step of shikimic acid to
ansatrienin. ChcA shows sequence similarity to the SDR
family of NAD-binding proteins, but it lacks the
conserved Tyr of the characteristic catalytic site. This
subgroup also contains the NADH-dependent
enoyl-[acyl-carrier-protein(ACP)] reductase FabL from
Bacillus subtilis. This enzyme participates in bacterial
fatty acid synthesis, in type II fatty-acid synthases
and catalyzes the last step in each elongation cycle.
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 have a 3-glycine N-terminal NAD(P)(H)-binding
pattern (typically, TGxxxGxG in classical SDRs and
TGxxGxxG in extended SDRs), while substrate binding is
in the C-terminal region. A critical catalytic Tyr
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase (15-PGDH) numbering), is often found in a
conserved YXXXK pattern. In addition to the Tyr and Lys,
there is often an upstream Ser (Ser-138, 15-PGDH
numbering) and/or an Asn (Asn-107, 15-PGDH numbering) or
additional Ser, contributing to the active site.
Substrates for these enzymes include sugars, steroids,
alcohols, and aromatic compounds. The standard reaction
mechanism is a proton relay involving the conserved Tyr
and Lys, as well as Asn (or Ser). Some SDR family
members, including 17 beta-hydroxysteroid dehydrogenase
contain an additional helix-turn-helix motif that is not
generally found among SDRs.
Length = 242
Score = 45.4 bits (108), Expect = 1e-06
Identities = 32/119 (26%), Positives = 50/119 (42%), Gaps = 30/119 (25%)
Query: 7 VTGASVGIGAAILRALAAKG-HQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIGFAR 65
VTG S GIG AI LA +G VI + + + AA
Sbjct: 3 VTGGSRGIGKAIALRLAERGADVVINYRKSKD----------------AAAE-------- 38
Query: 66 RAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNEFAPV 124
A I+ + K ++ DV++ +V E F + +FG +DV+++NA F P+
Sbjct: 39 VAAEIEELGG-----KAVVVRADVSQPQDVEEMFAAVKERFGRLDVLVSNAAAGAFRPL 92
>gnl|CDD|131680 TIGR02632, RhaD_aldol-ADH, rhamnulose-1-phosphate aldolase/alcohol
dehydrogenase.
Length = 676
Score = 45.6 bits (108), Expect = 1e-06
Identities = 28/122 (22%), Positives = 49/122 (40%), Gaps = 27/122 (22%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
++ VTG + GIG R LAA+G V+ D+
Sbjct: 415 RVAFVTGGAGGIGRETARRLAAEGAHVV------------------LADLNL-------- 448
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNEFA 122
+ + + + +LK+DVT + V AF + +G +D+++NNAG+ +
Sbjct: 449 -EAAEAVAAEINGQFGAGRAVALKMDVTDEQAVKAAFADVALAYGGVDIVVNNAGIATSS 507
Query: 123 PV 124
P
Sbjct: 508 PF 509
>gnl|CDD|187640 cd08935, mannonate_red_SDR_c, putative D-mannonate oxidoreductase,
classical (c) SDR. D-mannonate oxidoreductase catalyzes
the NAD-dependent interconversion of D-mannonate and
D-fructuronate. This subgroup includes Bacillus
subtitils UxuB/YjmF, a putative D-mannonate
oxidoreductase; the B. subtilis UxuB gene is part of a
putative ten-gene operon (the Yjm operon) involved in
hexuronate catabolism. Escherichia coli UxuB does not
belong to this subgroup. This subgroup has a canonical
active site tetrad and a typical Gly-rich NAD-binding
motif. 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
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-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 ketoacyl reductases 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 = 271
Score = 45.5 bits (108), Expect = 1e-06
Identities = 33/123 (26%), Positives = 47/123 (38%), Gaps = 29/123 (23%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K+ V+TG + +G A+ RALA G +V R E D + A G + I
Sbjct: 6 KVAVITGGTGVLGGAMARALAQAGAKVAALGRNQEKGDKV-------AKEITALGGRAIA 58
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNEFA 122
A DV A + A + I +FG +D++IN AG N
Sbjct: 59 LA----------------------ADVLDRASLERAREEIVAQFGTVDILINGAGGNHPD 96
Query: 123 PVT 125
T
Sbjct: 97 ATT 99
>gnl|CDD|187612 cd05354, SDR_c7, classical (c) SDR, subgroup 7. These proteins are
members of the classical SDR family, with a canonical
active site triad (and also an active site Asn) and a
typical Gly-rich NAD-binding motif. 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 have a
3-glycine N-terminal NAD(P)(H)-binding pattern
(typically, TGxxxGxG in classical SDRs and TGxxGxxG in
extended SDRs), while substrate binding is in the
C-terminal region. A critical catalytic Tyr residue
(Tyr-151, human 15-hydroxyprostaglandin dehydrogenase
(15-PGDH) numbering), is often found in a conserved
YXXXK pattern. In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) or additional
Ser, contributing to the active site. Substrates for
these enzymes include sugars, steroids, alcohols, and
aromatic compounds. The standard reaction mechanism is a
proton relay involving the conserved Tyr and Lys, as
well as Asn (or Ser). Some SDR family members, including
17 beta-hydroxysteroid dehydrogenase contain an
additional helix-turn-helix motif that is not generally
found among SDRs.
Length = 235
Score = 45.1 bits (107), Expect = 1e-06
Identities = 35/120 (29%), Positives = 50/120 (41%), Gaps = 35/120 (29%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K ++VTGA+ GIG A + +L A G A K V
Sbjct: 4 KTVLVTGANRGIGKAFVESLLAHG---------------------------AKK---VYA 33
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNEFA 122
R + + D KV L++DVT D E ++A + +DV+INNAGV + A
Sbjct: 34 AVRDPGSAAHLVAKYGD-KVVPLRLDVT-DPESIKAA---AAQAKDVDVVINNAGVLKPA 88
>gnl|CDD|180617 PRK06550, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 235
Score = 44.6 bits (106), Expect = 2e-06
Identities = 30/118 (25%), Positives = 47/118 (39%), Gaps = 44/118 (37%)
Query: 1 MSKIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQV 60
M+K +++TGA+ GIG A RA A+G QV G
Sbjct: 4 MTKTVLITGAASGIGLAQARAFLAQGAQVYG----------------------------- 34
Query: 61 IGFARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGV 118
+D K + H L++D++ D E FDW+ +D++ N AG+
Sbjct: 35 ---------VDKQDKPDLSGNFHFLQLDLSDDLE--PLFDWV----PSVDILCNTAGI 77
>gnl|CDD|180576 PRK06463, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 255
Score = 44.8 bits (106), Expect = 2e-06
Identities = 27/117 (23%), Positives = 50/117 (42%), Gaps = 34/117 (29%)
Query: 2 SKIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVI 61
K+ ++TG + GIG AI A +G +V + + +
Sbjct: 7 GKVALITGGTRGIGRAIAEAFLREGAKVA--------VLYNSA----------------- 41
Query: 62 GFARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGV 118
+ AKE + V ++K DV +V ++ + + +FG +DV++NNAG+
Sbjct: 42 ---------ENEAKELREKGVFTIKCDVGNRDQVKKSKEVVEKEFGRVDVLVNNAGI 89
>gnl|CDD|237219 PRK12827, PRK12827, short chain dehydrogenase; Provisional.
Length = 249
Score = 44.3 bits (105), Expect = 2e-06
Identities = 34/123 (27%), Positives = 45/123 (36%), Gaps = 25/123 (20%)
Query: 1 MSKIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQV 60
S+ +++TG S G+G AI LAA G VI A I AA G
Sbjct: 5 DSRRVLITGGSGGLGRAIAVRLAADGADVIVLDIHPMRGR--AEADAVAAGIEAAGG--- 59
Query: 61 IGFARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNE 120
K L DV A A D +FG +D+++NNAG+
Sbjct: 60 --------------------KALGLAFDVRDFAATRAALDAGVEEFGRLDILVNNAGIAT 99
Query: 121 FAP 123
A
Sbjct: 100 DAA 102
>gnl|CDD|187664 cd09763, DHRS1-like_SDR_c, human dehydrogenase/reductase (SDR
family) member 1 (DHRS1) -like, classical (c) SDRs.
This subgroup includes human DHRS1 and related proteins.
These are members of the classical SDR family, with a
canonical Gly-rich NAD-binding motif and the typical
YXXXK active site motif. However, the rest of the
catalytic tetrad is not strongly conserved. DHRS1 mRNA
has been detected in many tissues, liver, heart,
skeletal muscle, kidney and pancreas; a longer
transcript is predominantly expressed in the liver , a
shorter one in the heart. 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 have a 3-glycine N-terminal
NAD(P)(H)-binding pattern (typically, TGxxxGxG in
classical SDRs and TGxxGxxG in extended SDRs), while
substrate binding is in the C-terminal region. A
critical catalytic Tyr residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering), is often found in a conserved YXXXK pattern.
In addition to the Tyr and Lys, there is often an
upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn
(Asn-107, 15-PGDH numbering) or additional Ser,
contributing to the active site. Substrates for these
enzymes include sugars, steroids, alcohols, and aromatic
compounds. The standard reaction mechanism is a proton
relay involving the conserved Tyr and Lys, as well as
Asn (or Ser). Some SDR family members, including 17
beta-hydroxysteroid dehydrogenase contain an additional
helix-turn-helix motif that is not generally found among
SDRs.
Length = 265
Score = 44.4 bits (105), Expect = 3e-06
Identities = 30/116 (25%), Positives = 43/116 (37%), Gaps = 29/116 (25%)
Query: 2 SKIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVI 61
KI +VTGAS GIG I L G V R +
Sbjct: 3 GKIALVTGASRGIGRGIALQLGEAGATVYITGR-----------------------TILP 39
Query: 62 GFARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKF-GHIDVMINNA 116
AE I+A K ++ D + D EV F+ + + G +D+++NNA
Sbjct: 40 QLPGTAEEIEARGG-----KCIPVRCDHSDDDEVEALFERVAREQQGRLDILVNNA 90
>gnl|CDD|183773 PRK12824, PRK12824, acetoacetyl-CoA reductase; Provisional.
Length = 245
Score = 44.0 bits (104), Expect = 3e-06
Identities = 35/118 (29%), Positives = 50/118 (42%), Gaps = 28/118 (23%)
Query: 1 MSKIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQV 60
M KI +VTGA GIG+AI R L G++VI F+ + A D G
Sbjct: 1 MKKIALVTGAKRGIGSAIARELLNDGYRVI-------ATYFSGNDCA--KDWFEEYGFTE 51
Query: 61 IGFARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGV 118
+V ++DVT E EA I + G +D+++NNAG+
Sbjct: 52 D-------------------QVRLKELDVTDTEECAEALAEIEEEEGPVDILVNNAGI 90
>gnl|CDD|236216 PRK08277, PRK08277, D-mannonate oxidoreductase; Provisional.
Length = 278
Score = 44.1 bits (105), Expect = 3e-06
Identities = 32/117 (27%), Positives = 47/117 (40%), Gaps = 29/117 (24%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K+ V+TG +G A+ + LA G +V R E + A +I AA G
Sbjct: 11 KVAVITGGGGVLGGAMAKELARAGAKVAILDRNQEKAE------AVVAEIKAAGG----- 59
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVN 119
+A+A +K DV + +A I FG D++IN AG N
Sbjct: 60 --------EALA----------VKADVLDKESLEQARQQILEDFGPCDILINGAGGN 98
>gnl|CDD|226476 COG3967, DltE, Short-chain dehydrogenase involved in D-alanine
esterification of lipoteichoic acid and wall teichoic
acid (D-alanine transfer protein) [Cell envelope
biogenesis, outer membrane].
Length = 245
Score = 44.0 bits (104), Expect = 3e-06
Identities = 28/115 (24%), Positives = 49/115 (42%), Gaps = 35/115 (30%)
Query: 5 IVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIGFA 64
I++TG + GIG ALA + ++ G+ VI
Sbjct: 8 ILITGGASGIG----LALAKRFLEL---------------------------GNTVIICG 36
Query: 65 RRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAF-DWINNKFGHIDVMINNAGV 118
R E + ENP+ +H+ DV D + +W+ ++ +++V+INNAG+
Sbjct: 37 RNEERLAEAKAENPE--IHTEVCDV-ADRDSRRELVEWLKKEYPNLNVLINNAGI 88
>gnl|CDD|180817 PRK07060, PRK07060, short chain dehydrogenase; Provisional.
Length = 245
Score = 43.9 bits (104), Expect = 4e-06
Identities = 35/122 (28%), Positives = 47/122 (38%), Gaps = 38/122 (31%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K ++VTGAS GIG A ALA +G +V VAA
Sbjct: 10 KSVLVTGASSGIGRACAVALAQRGARV-----------------------VAA------- 39
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNEFA 122
AR A +D +A E L++DV DA + A G D ++N AG+
Sbjct: 40 -ARNAAALDRLAGETGC---EPLRLDVGDDAAIRAALA----AAGAFDGLVNCAGIASLE 91
Query: 123 PV 124
Sbjct: 92 SA 93
>gnl|CDD|235627 PRK05854, PRK05854, short chain dehydrogenase; Provisional.
Length = 313
Score = 43.5 bits (103), Expect = 5e-06
Identities = 34/113 (30%), Positives = 47/113 (41%), Gaps = 27/113 (23%)
Query: 6 VVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIGFAR 65
VVTGAS G+G + R LAA G +VI R AKG + R
Sbjct: 18 VVTGASDGLGLGLARRLAAAGAEVILPVRN------------------RAKGEAAVAAIR 59
Query: 66 RAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGV 118
A PD K+ +D++ A V + + + I ++INNAGV
Sbjct: 60 TA---------VPDAKLSLRALDLSSLASVAALGEQLRAEGRPIHLLINNAGV 103
>gnl|CDD|181349 PRK08278, PRK08278, short chain dehydrogenase; Provisional.
Length = 273
Score = 43.4 bits (103), Expect = 5e-06
Identities = 32/116 (27%), Positives = 46/116 (39%), Gaps = 24/116 (20%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAE-MIDFAESLFAFFVDIVAAKGHQVI 61
K + +TGAS GIG AI A G ++ A+ AE ++ +I AA G
Sbjct: 7 KTLFITGASRGIGLAIALRAARDGANIVIAAKTAEPHPKLPGTIHTAAEEIEAAGGQ--- 63
Query: 62 GFARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAG 117
A+ L DV + +V A +FG ID+ +NNA
Sbjct: 64 ----------ALP----------LVGDVRDEDQVAAAVAKAVERFGGIDICVNNAS 99
>gnl|CDD|181077 PRK07677, PRK07677, short chain dehydrogenase; Provisional.
Length = 252
Score = 43.1 bits (102), Expect = 6e-06
Identities = 31/121 (25%), Positives = 53/121 (43%), Gaps = 29/121 (23%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K++++TG S G+G A+ + A +G V+ R E ++ A+ +I G
Sbjct: 2 KVVIITGGSSGMGKAMAKRFAEEGANVVITGRTKEKLEEAKL------EIEQFPGQ---- 51
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNEFA 122
V ++++DV +V + + I+ KFG ID +INNA N
Sbjct: 52 -------------------VLTVQMDVRNPEDVQKMVEQIDEKFGRIDALINNAAGNFIC 92
Query: 123 P 123
P
Sbjct: 93 P 93
>gnl|CDD|180343 PRK05993, PRK05993, short chain dehydrogenase; Provisional.
Length = 277
Score = 43.1 bits (102), Expect = 6e-06
Identities = 22/53 (41%), Positives = 30/53 (56%), Gaps = 2/53 (3%)
Query: 1 MSKIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDF--AESLFAFFVD 51
M + I++TG S GIGA RAL + G +V R+ E + AE L AF +D
Sbjct: 3 MKRSILITGCSSGIGAYCARALQSDGWRVFATCRKEEDVAALEAEGLEAFQLD 55
>gnl|CDD|131468 TIGR02415, 23BDH, acetoin reductases. One member of this family,
as characterized in Klebsiella terrigena, is described
as able to interconvert acetoin + NADH with
meso-2,3-butanediol + NAD(+). It is also called capable
of irreversible reduction of diacetyl with NADH to
acetoin. Blomqvist, et al. decline to specify either EC
1.1.1.4 which is (R,R)-butanediol dehydrogenase, or EC
1.1.1.5, which is acetoin dehydrogenase without a
specified stereochemistry, for this enzyme. This enzyme
is a homotetramer in the family of short chain
dehydrogenases (pfam00106). Another member of this
family, from Corynebacterium glutamicum, is called
L-2,3-butanediol dehydrogenase (PMID:11577733) [Energy
metabolism, Fermentation].
Length = 254
Score = 43.2 bits (102), Expect = 6e-06
Identities = 33/122 (27%), Positives = 46/122 (37%), Gaps = 29/122 (23%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K+ +VTG + GIG I LA G V + D E + G + +
Sbjct: 1 KVALVTGGAQGIGKGIAERLAKDGFAVA-------VADLNEETAKETAKEINQAGGKAVA 53
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNEFA 122
+ K+DV+ +V A D KFG DVM+NNAGV
Sbjct: 54 Y----------------------KLDVSDKDQVFSAIDQAAEKFGGFDVMVNNAGVAPIT 91
Query: 123 PV 124
P+
Sbjct: 92 PI 93
>gnl|CDD|188169 TIGR01829, AcAcCoA_reduct, acetoacetyl-CoA reductase. This model
represent acetoacetyl-CoA reductase, a member of the
family short-chain-alcohol dehydrogenases. Note that,
despite the precision implied by the enzyme name, the
reaction of EC 1.1.1.36 is defined more generally as
(R)-3-hydroxyacyl-CoA + NADP+ = 3-oxoacyl-CoA + NADPH.
Members of this family may act in the biosynthesis of
poly-beta-hydroxybutyrate (e.g. Rhizobium meliloti) and
related poly-beta-hydroxyalkanoates. Note that the
member of this family from Azospirillum brasilense,
designated NodG, appears to lack acetoacetyl-CoA
reductase activity and to act instead in the production
of nodulation factor. This family is downgraded to
subfamily for this NodG. Other proteins designated NodG,
as from Rhizobium, belong to related but distinct
protein families.
Length = 242
Score = 43.2 bits (102), Expect = 7e-06
Identities = 28/116 (24%), Positives = 44/116 (37%), Gaps = 28/116 (24%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
+I +VTG GIG AI + LA G++V E
Sbjct: 1 RIALVTGGMGGIGTAICQRLAKDGYRVAANCGPNE------------------------- 35
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGV 118
R + D++V ++ DV+ A + + G IDV++NNAG+
Sbjct: 36 -ERAEAWLQEQGALGFDFRV--VEGDVSSFESCKAAVAKVEAELGPIDVLVNNAGI 88
>gnl|CDD|168186 PRK05693, PRK05693, short chain dehydrogenase; Provisional.
Length = 274
Score = 42.9 bits (101), Expect = 9e-06
Identities = 31/122 (25%), Positives = 51/122 (41%), Gaps = 35/122 (28%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
++++TG S GIG A+ A A G++V AR+AE D +AA G
Sbjct: 2 PVVLITGCSSGIGRALADAFKAAGYEVWATARKAE--DVEA---------LAAAGFT--- 47
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNEFA 122
++++DV A + + + + G +DV+INNAG
Sbjct: 48 ---------------------AVQLDVNDGAALARLAEELEAEHGGLDVLINNAGYGAMG 86
Query: 123 PV 124
P+
Sbjct: 87 PL 88
>gnl|CDD|180761 PRK06935, PRK06935, 2-deoxy-D-gluconate 3-dehydrogenase;
Provisional.
Length = 258
Score = 42.4 bits (100), Expect = 1e-05
Identities = 28/123 (22%), Positives = 46/123 (37%), Gaps = 30/123 (24%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K+ +VTG + G+G ALA G +I + ++ +G
Sbjct: 16 KVAIVTGGNTGLGQGYAVALAKAGADIIITTHGTNWDETRR--------LIEKEGR---- 63
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNEFA 122
KV ++VD+TK + +FG ID+++NNAG A
Sbjct: 64 ------------------KVTFVQVDLTKPESAEKVVKEALEEFGKIDILVNNAGTIRRA 105
Query: 123 PVT 125
P+
Sbjct: 106 PLL 108
>gnl|CDD|177895 PLN02253, PLN02253, xanthoxin dehydrogenase.
Length = 280
Score = 42.5 bits (100), Expect = 1e-05
Identities = 33/118 (27%), Positives = 51/118 (43%), Gaps = 30/118 (25%)
Query: 1 MSKIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQV 60
+ K+ +VTG + GIG +I+R G +V VD+ G V
Sbjct: 17 LGKVALVTGGATGIGESIVRLFHKHGAKVC------------------IVDLQDDLGQNV 58
Query: 61 IGFARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGV 118
D++ E H DVT + +V A D+ +KFG +D+M+NNAG+
Sbjct: 59 C---------DSLGGEPNVCFFHC---DVTVEDDVSRAVDFTVDKFGTLDIMVNNAGL 104
>gnl|CDD|187583 cd05322, SDH_SDR_c_like, Sorbitol 6-phosphate dehydrogenase (SDH),
classical (c) SDRs. Sorbitol 6-phosphate dehydrogenase
(SDH, aka glucitol 6-phosphate dehydrogenase) catalyzes
the NAD-dependent interconversion of D-fructose
6-phosphate to D-sorbitol 6-phosphate. SDH is a member
of the classical SDRs, with the characteristic catalytic
tetrad, but without a complete match to the typical
NAD-binding motif. 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 15-hydroxyprostaglandin
dehydrogenase (15-PGDH) numbering). In addition to the
Tyr and Lys, there is often an upstream Ser (Ser-138,
15-PGDH numbering) and/or an Asn (Asn-107, 15-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 ketoacyl
reductases 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 = 257
Score = 42.5 bits (100), Expect = 1e-05
Identities = 25/125 (20%), Positives = 47/125 (37%), Gaps = 28/125 (22%)
Query: 1 MSKIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQV 60
M+++ VV G +G + LA G+ V DI + +V
Sbjct: 1 MNQVAVVIGGGQTLGEFLCHGLAEAGYDVA------------------VADINSENAEKV 42
Query: 61 IGFARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNE 120
A+ I+A E D T + V+ ++ F +D+++ +AG+ +
Sbjct: 43 ------ADEINAEYGEKAYG----FGADATNEQSVIALSKGVDEIFKRVDLLVYSAGIAK 92
Query: 121 FAPVT 125
A +T
Sbjct: 93 SAKIT 97
>gnl|CDD|187609 cd05351, XR_like_SDR_c, xylulose reductase-like, classical (c)
SDRs. Members of this subgroup include proteins
identified as L-xylulose reductase (XR) and carbonyl
reductase; they are members of the SDR family. XR,
catalyzes the NADP-dependent reduction of L-xyulose and
other sugars. Tetrameric mouse carbonyl reductase is
involved in the metabolism of biogenic and xenobiotic
carbonyl compounds. This subgroup also includes
tetrameric chicken liver D-erythrulose reductase, which
catalyzes the reduction of D-erythrulose to D-threitol.
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 have a 3-glycine N-terminal NAD(P)(H)-binding
pattern (typically, TGxxxGxG in classical SDRs and
TGxxGxxG in extended SDRs), while substrate binding is
in the C-terminal region. A critical catalytic Tyr
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase (15-PGDH) numbering), is often found in a
conserved YXXXK pattern. In addition to the Tyr and Lys,
there is often an upstream Ser (Ser-138, 15-PGDH
numbering) and/or an Asn (Asn-107, 15-PGDH numbering) or
additional Ser, contributing to the active site.
Substrates for these enzymes include sugars, steroids,
alcohols, and aromatic compounds. The standard reaction
mechanism is a proton relay involving the conserved Tyr
and Lys, as well as Asn (or Ser).
Length = 244
Score = 42.1 bits (99), Expect = 2e-05
Identities = 28/116 (24%), Positives = 46/116 (39%), Gaps = 37/116 (31%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K +VTGA GIG A ++AL A G +V+
Sbjct: 8 KRALVTGAGKGIGRATVKAL-------------------------------AKAGARVVA 36
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGV 118
+R +D++ +E P + + VD++ EA G +D+++NNA V
Sbjct: 37 VSRTQADLDSLVRECP--GIEPVCVDLSDWDATEEAL----GSVGPVDLLVNNAAV 86
>gnl|CDD|187614 cd05356, 17beta-HSD1_like_SDR_c, 17-beta-hydroxysteroid
dehydrogenases (17beta-HSDs) types -1, -3, and -12,
-like, classical (c) SDRs. This subgroup includes
various 17-beta-hydroxysteroid dehydrogenases and
3-ketoacyl-CoA reductase, these are members of the SDR
family, and contain the canonical active site tetrad and
glycine-rich NAD-binding motif of the classical SDRs.
3-ketoacyl-CoA reductase (KAR, aka 17beta-HSD type 12,
encoded by HSD17B12) acts in fatty acid elongation;
17beta- hydroxysteroid dehydrogenases are isozymes that
catalyze activation and inactivation of estrogen and
androgens, and include members of the SDR family.
17beta-estradiol dehydrogenase (aka 17beta-HSD type 1,
encoded by HSD17B1) converts estrone to estradiol.
Estradiol is the predominant female sex hormone.
17beta-HSD type 3 (aka testosterone
17-beta-dehydrogenase 3, encoded by HSD17B3) catalyses
the reduction of androstenedione to testosterone, it
also accepts estrogens as substrates. This subgroup also
contains a putative steroid dehydrogenase let-767 from
Caenorhabditis elegans, mutation in which results in
hypersensitivity to cholesterol limitation. 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 have a
3-glycine N-terminal NAD(P)(H)-binding pattern
(typically, TGxxxGxG in classical SDRs and TGxxGxxG in
extended SDRs), while substrate binding is in the
C-terminal region. A critical catalytic Tyr residue
(Tyr-151, human 15-hydroxyprostaglandin dehydrogenase
(15-PGDH) numbering), is often found in a conserved
YXXXK pattern. In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) or additional
Ser, contributing to the active site. Substrates for
these enzymes include sugars, steroids, alcohols, and
aromatic compounds. The standard reaction mechanism is a
proton relay involving the conserved Tyr and Lys, as
well as Asn (or Ser). Some SDR family members, including
17 beta-hydroxysteroid dehydrogenase contain an
additional helix-turn-helix motif that is not generally
found among SDRs.
Length = 239
Score = 41.8 bits (99), Expect = 2e-05
Identities = 29/117 (24%), Positives = 46/117 (39%), Gaps = 37/117 (31%)
Query: 6 VVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIGFAR 65
VVTGA+ GIG A +AE L A +G VI +R
Sbjct: 5 VVTGATDGIGKA-----------------------YAEEL--------AKRGFNVILISR 33
Query: 66 RAEMIDAMAKE---NPDWKVHSLKVDVTKDAEVVEA-FDWINNKFGHIDVMINNAGV 118
E +DA+AKE + ++ D + ++ E + I +++NN G+
Sbjct: 34 TQEKLDAVAKEIEEKYGVETKTIAADFSAGDDIYERIEKELEGL--DIGILVNNVGI 88
>gnl|CDD|183832 PRK12935, PRK12935, acetoacetyl-CoA reductase; Provisional.
Length = 247
Score = 41.5 bits (97), Expect = 3e-05
Identities = 32/116 (27%), Positives = 56/116 (48%), Gaps = 28/116 (24%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K+ +VTG + GIG AI ALA +G +V+ ++ + AE+L V+ + +GH V
Sbjct: 7 KVAIVTGGAKGIGKAITVALAQEGAKVVINYNSSK--EAAENL----VNELGKEGHDVY- 59
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGV 118
+++ DV+K + + N FG +D+++NNAG+
Sbjct: 60 ---------------------AVQADVSKVEDANRLVEEAVNHFGKVDILVNNAGI 94
>gnl|CDD|223528 COG0451, WcaG, Nucleoside-diphosphate-sugar epimerases [Cell
envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 314
Score = 41.5 bits (97), Expect = 3e-05
Identities = 23/81 (28%), Positives = 36/81 (44%), Gaps = 11/81 (13%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
I+VTG + IG+ ++ L A GH V G R + +D S F V +
Sbjct: 1 MRILVTGGAGFIGSHLVERLLAAGHDVRGLDRLRDGLDPLLSGVEFVVLDL--------- 51
Query: 63 FARRAEMIDAMAKENPDWKVH 83
+++D +AK PD +H
Sbjct: 52 --TDRDLVDELAKGVPDAVIH 70
>gnl|CDD|235925 PRK07067, PRK07067, sorbitol dehydrogenase; Provisional.
Length = 257
Score = 41.6 bits (98), Expect = 3e-05
Identities = 29/123 (23%), Positives = 49/123 (39%), Gaps = 32/123 (26%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K+ ++TGA+ GIG A+ A+G +V+ DI A+
Sbjct: 7 KVALLTGAASGIGEAVAERYLAEGARVV------------------IADIKPARARLA-- 46
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNEFA 122
A I A ++ +DVT+ + +FG ID++ NNA + + A
Sbjct: 47 ----ALEIGPAAI--------AVSLDVTRQDSIDRIVAAAVERFGGIDILFNNAALFDMA 94
Query: 123 PVT 125
P+
Sbjct: 95 PIL 97
>gnl|CDD|237187 PRK12743, PRK12743, oxidoreductase; Provisional.
Length = 256
Score = 41.2 bits (97), Expect = 3e-05
Identities = 32/127 (25%), Positives = 51/127 (40%), Gaps = 34/127 (26%)
Query: 1 MSKIIVVTGASVGIGAAILRALAAKGHQV-IGFARRAEMIDFAESLFAFFVDIVAAKG-- 57
M+++ +VT + GIG A LA +G + I + E AK
Sbjct: 1 MAQVAIVTASDSGIGKACALLLAQQGFDIGITWHSDEE----------------GAKETA 44
Query: 58 HQVIGFARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAG 117
+V RAE+ ++D++ E +A D + + G IDV++NNAG
Sbjct: 45 EEVRSHGVRAEIR---------------QLDLSDLPEGAQALDKLIQRLGRIDVLVNNAG 89
Query: 118 VNEFAPV 124
AP
Sbjct: 90 AMTKAPF 96
>gnl|CDD|187638 cd08933, RDH_SDR_c, retinal dehydrogenase-like, classical (c) SDR.
These classical SDRs includes members identified as
retinol dehydrogenases, which convert retinol to
retinal, a property that overlaps with 17betaHSD
activity. 17beta-dehydrogenases are a group of isozymes
that catalyze activation and inactivation of estrogen
and androgens, and include members of the short-chain
dehydrogenases/reductase family. 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 15-hydroxyprostaglandin
dehydrogenase (15-PGDH) numbering). In addition to the
Tyr and Lys, there is often an upstream Ser (Ser-138,
15-PGDH numbering) and/or an Asn (Asn-107, 15-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 ketoacyl
reductases 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 = 261
Score = 41.0 bits (96), Expect = 4e-05
Identities = 31/115 (26%), Positives = 47/115 (40%), Gaps = 28/115 (24%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K+++VTG S GIG I+RA G +V+ AR G
Sbjct: 10 KVVIVTGGSRGIGRGIVRAFVENGAKVVFCARGEAA-----------------------G 46
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAG 117
A +E + + P + DVTK+ ++ +FG ID ++NNAG
Sbjct: 47 QALESE----LNRAGPGSCKF-VPCDVTKEEDIKTLISVTVERFGRIDCLVNNAG 96
>gnl|CDD|180993 PRK07478, PRK07478, short chain dehydrogenase; Provisional.
Length = 254
Score = 41.1 bits (97), Expect = 4e-05
Identities = 36/124 (29%), Positives = 52/124 (41%), Gaps = 30/124 (24%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K+ ++TGAS GIG A + A +G +V+ ARR +D L A +I A G V
Sbjct: 7 KVAIITGASSGIGRAAAKLFAREGAKVVVGARRQAELD---QLVA---EIRAEGGEAV-- 58
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVN-EF 121
A+A + D V + + +FG +D+ NNAG E
Sbjct: 59 ---------ALAGDVRDEAYAKALVALAVE------------RFGGLDIAFNNAGTLGEM 97
Query: 122 APVT 125
PV
Sbjct: 98 GPVA 101
>gnl|CDD|187642 cd08937, DHB_DH-like_SDR_c,
1,6-dihydroxycyclohexa-2,4-diene-1-carboxylate
dehydrogenase (DHB DH)-like, classical (c) SDR. DHB DH
(aka 1,2-dihydroxycyclohexa-3,5-diene-1-carboxylate
dehydrogenase) catalyzes the NAD-dependent conversion of
1,2-dihydroxycyclohexa-3,4-diene carboxylate to a
catechol. This subgroup also contains Pseudomonas putida
F1 CmtB, 2,3-dihydroxy-2,3-dihydro-p-cumate
dehydrogenase, the second enzyme in the pathway for
catabolism of p-cumate catabolism. This subgroup shares
the glycine-rich NAD-binding motif of the classical SDRs
and shares the same catalytic triad; however, the
upstream Asn implicated in cofactor binding or catalysis
in other SDRs is generally substituted by a Ser. 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
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-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 ketoacyl reductases 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 = 256
Score = 41.0 bits (96), Expect = 4e-05
Identities = 29/115 (25%), Positives = 46/115 (40%), Gaps = 30/115 (26%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K++VVTGA+ GIG + LA +G +V+ ++D +E + +I+AA
Sbjct: 5 KVVVVTGAAQGIGRGVAERLAGEGARVL-------LVDRSELVHEVLAEILAAGDA---- 53
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAG 117
H D+ A +FG +DV+INN G
Sbjct: 54 -------------------AHVHTADLETYAGAQGVVRAAVERFGRVDVLINNVG 89
>gnl|CDD|180371 PRK06057, PRK06057, short chain dehydrogenase; Provisional.
Length = 255
Score = 40.9 bits (96), Expect = 5e-05
Identities = 29/116 (25%), Positives = 43/116 (37%), Gaps = 34/116 (29%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
++ V+TG GIG A R LAA+G V+ DI G
Sbjct: 8 RVAVITGGGSGIGLATARRLAAEGATVV------------------VGDIDPEAGKAA-- 47
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGV 118
A+ + + + DVT + V FD +G +D+ NNAG+
Sbjct: 48 ----ADEVGGLF----------VPTDVTDEDAVNALFDTAAETYGSVDIAFNNAGI 89
>gnl|CDD|180753 PRK06924, PRK06924, short chain dehydrogenase; Provisional.
Length = 251
Score = 40.8 bits (96), Expect = 5e-05
Identities = 16/43 (37%), Positives = 23/43 (53%), Gaps = 2/43 (4%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRA--EMIDFAE 43
+ +++TG S G+G AI L KG VI +R E+ AE
Sbjct: 2 RYVIITGTSQGLGEAIANQLLEKGTHVISISRTENKELTKLAE 44
>gnl|CDD|181126 PRK07806, PRK07806, short chain dehydrogenase; Provisional.
Length = 248
Score = 40.5 bits (95), Expect = 6e-05
Identities = 30/116 (25%), Positives = 47/116 (40%), Gaps = 30/116 (25%)
Query: 2 SKIIVVTGASVGIGAAILRALAAKG-HQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQV 60
K +VTG+S GIGA + LA G H V+ + ++A A + A +I AA G
Sbjct: 6 GKTALVTGSSRGIGADTAKILAGAGAHVVVNYRQKAPR---ANKVVA---EIEAAGGRAS 59
Query: 61 IGFARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNA 116
++ D+T + V D +FG +D ++ NA
Sbjct: 60 -----------------------AVGADLTDEESVAALMDTAREEFGGLDALVLNA 92
>gnl|CDD|187591 cd05330, cyclohexanol_reductase_SDR_c, cyclohexanol reductases,
including levodione reductase, classical (c) SDRs.
Cyloclohexanol reductases,including
(6R)-2,2,6-trimethyl-1,4-cyclohexanedione (levodione)
reductase of Corynebacterium aquaticum, catalyze the
reversible oxidoreduction of hydroxycyclohexanone
derivatives. 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
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-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 ketoacyl reductases 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 = 257
Score = 40.2 bits (94), Expect = 7e-05
Identities = 30/116 (25%), Positives = 51/116 (43%), Gaps = 27/116 (23%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K++++TG G+G A LA +G ++ ++D E
Sbjct: 4 KVVLITGGGSGLGLATAVRLAKEGAKLS-------LVDLNEEGLE--------------- 41
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGV 118
A +A +++ PD +V +K DV+ +A+V D +FG ID NNAG+
Sbjct: 42 -AAKAALLEI----APDAEVLLIKADVSDEAQVEAYVDATVEQFGRIDGFFNNAGI 92
>gnl|CDD|180408 PRK06114, PRK06114, short chain dehydrogenase; Provisional.
Length = 254
Score = 40.2 bits (94), Expect = 7e-05
Identities = 30/116 (25%), Positives = 42/116 (36%), Gaps = 28/116 (24%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
++ VTGA GIG I LA G V F R + D +A +
Sbjct: 9 QVAFVTGAGSGIGQRIAIGLAQAGADVALFDLRTD-------------DGLAETAEHIEA 55
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGV 118
RRA I A DVT A++ A + G + + +N AG+
Sbjct: 56 AGRRAIQIAA---------------DVTSKADLRAAVARTEAELGALTLAVNAAGI 96
>gnl|CDD|235702 PRK06124, PRK06124, gluconate 5-dehydrogenase; Provisional.
Length = 256
Score = 40.1 bits (94), Expect = 7e-05
Identities = 29/115 (25%), Positives = 48/115 (41%), Gaps = 29/115 (25%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
++ +VTG++ G+G I RALA G V+ R A ++ A V + A G
Sbjct: 12 QVALVTGSARGLGFEIARALAGAGAHVLVNGRNAATLEAA-------VAALRAAG----- 59
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAG 117
+L D+ + V AF I+ + G +D+++NN G
Sbjct: 60 -----------------GAAEALAFDIADEEAVAAAFARIDAEHGRLDILVNNVG 97
>gnl|CDD|235813 PRK06482, PRK06482, short chain dehydrogenase; Provisional.
Length = 276
Score = 40.1 bits (94), Expect = 7e-05
Identities = 34/123 (27%), Positives = 48/123 (39%), Gaps = 32/123 (26%)
Query: 1 MSKIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQV 60
MSK +TGAS G G + L A+G +V RR + +D D+ A G ++
Sbjct: 1 MSKTWFITGASSGFGRGMTERLLARGDRVAATVRRPDALD----------DLKARYGDRL 50
Query: 61 IGFARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNE 120
L++DVT A V D G IDV+++NAG
Sbjct: 51 ----------------------WVLQLDVTDSAAVRAVVDRAFAALGRIDVVVSNAGYGL 88
Query: 121 FAP 123
F
Sbjct: 89 FGA 91
>gnl|CDD|235910 PRK07024, PRK07024, short chain dehydrogenase; Provisional.
Length = 257
Score = 40.3 bits (95), Expect = 8e-05
Identities = 34/120 (28%), Positives = 45/120 (37%), Gaps = 34/120 (28%)
Query: 1 MSKIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQV 60
M + +TGAS GIG A+ R A +G +G
Sbjct: 1 MPLKVFITGASSGIGQALAREYARQG-ATLGLV--------------------------- 32
Query: 61 IGFARRAEMIDAMAKENP-DWKVHSLKVDVTK-DAEVVEAFDWINNKFGHIDVMINNAGV 118
ARR + + A A P +V DV DA A D+I G DV+I NAG+
Sbjct: 33 ---ARRTDALQAFAARLPKAARVSVYAADVRDADALAAAAADFIA-AHGLPDVVIANAGI 88
>gnl|CDD|187623 cd05365, 7_alpha_HSDH_SDR_c, 7 alpha-hydroxysteroid dehydrogenase
(7 alpha-HSDH), classical (c) SDRs. This bacterial
subgroup contains 7 alpha-HSDHs, including Escherichia
coli 7 alpha-HSDH. 7 alpha-HSDH, a member of the SDR
family, catalyzes the NAD+ -dependent dehydrogenation of
a hydroxyl group at position 7 of the steroid skeleton
of bile acids. In humans the two primary bile acids are
cholic and chenodeoxycholic acids, these are formed from
cholesterol in the liver. Escherichia coli 7 alpha-HSDH
dehydroxylates these bile acids in the human intestine.
Mammalian 7 alpha-HSDH activity has been found in
livers. 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 have a 3-glycine N-terminal NAD(P)(H)-binding
pattern (typically, TGxxxGxG in classical SDRs and
TGxxGxxG in extended SDRs), while substrate binding is
in the C-terminal region. A critical catalytic Tyr
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase (15-PGDH) numbering), is often found in a
conserved YXXXK pattern. In addition to the Tyr and Lys,
there is often an upstream Ser (Ser-138, 15-PGDH
numbering) and/or an Asn (Asn-107, 15-PGDH numbering) or
additional Ser, contributing to the active site.
Substrates for these enzymes include sugars, steroids,
alcohols, and aromatic compounds. The standard reaction
mechanism is a proton relay involving the conserved Tyr
and Lys, as well as Asn (or Ser). Some SDR family
members, including 17 beta-hydroxysteroid dehydrogenase
contain an additional helix-turn-helix motif that is not
generally found among SDRs.
Length = 242
Score = 39.5 bits (92), Expect = 1e-04
Identities = 25/114 (21%), Positives = 44/114 (38%), Gaps = 29/114 (25%)
Query: 4 IIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIGF 63
+ +VTG + GIG AI LA G V+ D+ + V
Sbjct: 1 VAIVTGGAAGIGKAIAGTLAKAGASVV------------------IADLKSEGAEAVA-- 40
Query: 64 ARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAG 117
A+ + + L+ +VT + ++ ++FG I +++NNAG
Sbjct: 41 -------AAIQQAGG--QAIGLECNVTSEQDLEAVVKATVSQFGGITILVNNAG 85
>gnl|CDD|180822 PRK07069, PRK07069, short chain dehydrogenase; Validated.
Length = 251
Score = 39.3 bits (92), Expect = 2e-04
Identities = 32/118 (27%), Positives = 48/118 (40%), Gaps = 26/118 (22%)
Query: 7 VTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIGFARR 66
+TGA+ G+G AI R +A +G +V F DI A G
Sbjct: 4 ITGAAGGLGRAIARRMAEQGAKV------------------FLTDINDAAG-----LDAF 40
Query: 67 AEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNEFAPV 124
A I+A E + + DVT +A+ + G + V++NNAGV F +
Sbjct: 41 AAEINAAHGEGVAF---AAVQDVTDEAQWQALLAQAADAMGGLSVLVNNAGVGSFGAI 95
>gnl|CDD|176183 cd05280, MDR_yhdh_yhfp, Yhdh and yhfp-like putative quinone
oxidoreductases. Yhdh and yhfp-like putative quinone
oxidoreductases (QOR). QOR catalyzes the conversion of a
quinone + NAD(P)H to a hydroquinone + NAD(P)+. Quinones
are cyclic diones derived from aromatic compounds.
Membrane bound QOR actin the respiratory chains of
bacteria and mitochondria, while soluble QOR acts to
protect from toxic quinones (e.g. DT-diaphorase) or as a
soluble eye-lens protein in some vertebrates (e.g.
zeta-crystalin). QOR reduces quinones through a
semi-quinone intermediate via a NAD(P)H-dependent single
electron transfer. QOR is a member of the medium chain
dehydrogenase/reductase family, but lacks the
zinc-binding sites of the prototypical alcohol
dehydrogenases of this group. NAD(P)(H)-dependent
oxidoreductases are the major enzymes in the
interconversion of alcohols and aldehydes, or ketones.
Alcohol dehydrogenase in the liver converts ethanol and
NAD+ to acetaldehyde and NADH, while in yeast and some
other microorganisms ADH catalyzes the conversion
acetaldehyde to ethanol in alcoholic fermentation. ADH
is a member of the medium chain alcohol dehydrogenase
family (MDR), which has a NAD(P)(H)-binding domain in a
Rossmann fold of a beta-alpha form. The NAD(H)-binding
region is comprised of 2 structurally similar halves,
each of which contacts a mononucleotide. A GxGxxG motif
after the first mononucleotide contact half allows the
close contact of the coenzyme with the ADH backbone.
The N-terminal catalytic domain has a distant homology
to GroES. These proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and have 2 tightly bound zinc atoms per
subunit, a catalytic zinc at the active site and a
structural zinc in a lobe of the catalytic domain.
NAD(H) binding occurs in the cleft between the catalytic
and coenzyme-binding domains at the active site, and
coenzyme binding induces a conformational closing of
this cleft. Coenzyme binding typically precedes and
contributes to substrate binding. In human ADH
catalysis, the zinc ion helps coordinate the alcohol,
followed by deprotonation of a histidine, the ribose of
NAD, a serine, then the alcohol, which allows the
transfer of a hydride to NAD+, creating NADH and a
zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 325
Score = 39.4 bits (93), Expect = 2e-04
Identities = 16/46 (34%), Positives = 27/46 (58%)
Query: 5 IVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFV 50
++VTGA+ G+G+ + LA G+ V+ + E D+ +SL A V
Sbjct: 150 VLVTGATGGVGSIAVAILAKLGYTVVALTGKEEQADYLKSLGASEV 195
>gnl|CDD|187589 cd05328, 3alpha_HSD_SDR_c, alpha hydroxysteroid dehydrogenase
(3alpha_HSD), classical (c) SDRs. Bacterial
3-alpha_HSD, which catalyzes the NAD-dependent
oxidoreduction of hydroxysteroids, is a dimeric member
of the classical SDR family. 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
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-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 ketoacyl reductases 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 = 250
Score = 39.0 bits (91), Expect = 2e-04
Identities = 17/32 (53%), Positives = 19/32 (59%)
Query: 4 IIVVTGASVGIGAAILRALAAKGHQVIGFARR 35
IV+TGA+ GIGAA L GH VIG R
Sbjct: 1 TIVITGAASGIGAATAELLEDAGHTVIGIDLR 32
>gnl|CDD|180823 PRK07074, PRK07074, short chain dehydrogenase; Provisional.
Length = 257
Score = 39.0 bits (91), Expect = 2e-04
Identities = 29/117 (24%), Positives = 44/117 (37%), Gaps = 31/117 (26%)
Query: 1 MSKIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQV 60
+ +VTGA+ GIG A+ R A G +V +DI AA
Sbjct: 1 TKRTALVTGAAGGIGQALARRFLAAGDRV------------------LALDIDAAA---- 38
Query: 61 IGFARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAG 117
+ A A D + + D+T A + A + G +DV++ NAG
Sbjct: 39 ---------LAAFADALGDARFVPVACDLTDAASLAAALANAAAERGPVDVLVANAG 86
>gnl|CDD|180796 PRK07023, PRK07023, short chain dehydrogenase; Provisional.
Length = 243
Score = 38.8 bits (91), Expect = 2e-04
Identities = 14/31 (45%), Positives = 18/31 (58%)
Query: 6 VVTGASVGIGAAILRALAAKGHQVIGFARRA 36
+VTG S G+GAA+ L G V+G AR
Sbjct: 5 IVTGHSRGLGAALAEQLLQPGIAVLGVARSR 35
>gnl|CDD|187599 cd05340, Ycik_SDR_c, Escherichia coli K-12 YCIK-like, classical (c)
SDRs. Escherichia coli K-12 YCIK and related proteins
have a canonical classical SDR nucleotide-binding motif
and active site tetrad. They are predicted oxoacyl-(acyl
carrier protein/ACP) reductases. 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 have a 3-glycine N-terminal
NAD(P)(H)-binding pattern (typically, TGxxxGxG in
classical SDRs and TGxxGxxG in extended SDRs), while
substrate binding is in the C-terminal region. A
critical catalytic Tyr residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering), is often found in a conserved YXXXK pattern.
In addition to the Tyr and Lys, there is often an
upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn
(Asn-107, 15-PGDH numbering) or additional Ser,
contributing to the active site. Substrates for these
enzymes include sugars, steroids, alcohols, and aromatic
compounds. The standard reaction mechanism is a proton
relay involving the conserved Tyr and Lys, as well as
Asn (or Ser). Some SDR family members, including 17
beta-hydroxysteroid dehydrogenase contain an additional
helix-turn-helix motif that is not generally found among
SDRs.
Length = 236
Score = 39.1 bits (91), Expect = 2e-04
Identities = 28/117 (23%), Positives = 43/117 (36%), Gaps = 28/117 (23%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
+II+VTGAS GIG A G VI R E +
Sbjct: 5 RIILVTGASDGIGREAALTYARYGATVILLGRNEEKL----------------------- 41
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAF-DWINNKFGHIDVMINNAGV 118
+ A+ I+ P W + L T +E + I + +D +++NAG+
Sbjct: 42 -RQVADHINEEGGRQPQWFILDLL---TCTSENCQQLAQRIAVNYPRLDGVLHNAGL 94
>gnl|CDD|236399 PRK09186, PRK09186, flagellin modification protein A; Provisional.
Length = 256
Score = 38.8 bits (91), Expect = 2e-04
Identities = 29/115 (25%), Positives = 44/115 (38%), Gaps = 29/115 (25%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K I++TGA IG+A+++A+ G VI A +D A
Sbjct: 5 KTILITGAGGLIGSALVKAILEAGGIVI----------------AADIDKEALN------ 42
Query: 63 FARRAEMIDAMAKENPDWKVHSL-KVDVTKDAEVVEAFDWINNKFGHIDVMINNA 116
E + K K SL ++D+T + E K+G ID +N A
Sbjct: 43 --ELLESLGKEFKS----KKLSLVELDITDQESLEEFLSKSAEKYGKIDGAVNCA 91
>gnl|CDD|235703 PRK06125, PRK06125, short chain dehydrogenase; Provisional.
Length = 259
Score = 38.9 bits (91), Expect = 2e-04
Identities = 36/116 (31%), Positives = 51/116 (43%), Gaps = 32/116 (27%)
Query: 2 SKIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVI 61
K +++TGAS GIGAA A AA+G + AR A++L A D+ AA G V
Sbjct: 7 GKRVLITGASKGIGAAAAEAFAAEGCHLHLVARD------ADALEALAADLRAAHGVDV- 59
Query: 62 GFARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAG 117
VH+L + + E + A G ID+++NNAG
Sbjct: 60 -------------------AVHALDLSSPEAREQLAAE------AGDIDILVNNAG 90
>gnl|CDD|180773 PRK06949, PRK06949, short chain dehydrogenase; Provisional.
Length = 258
Score = 38.6 bits (90), Expect = 2e-04
Identities = 32/116 (27%), Positives = 49/116 (42%), Gaps = 29/116 (25%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K+ +VTGAS G+GA + LA G +V+ +RR E +
Sbjct: 10 KVALVTGASSGLGARFAQVLAQAGAKVVLASRRVERLK---------------------- 47
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGV 118
RAE+ E H + +DVT + A + G ID+++NN+GV
Sbjct: 48 -ELRAEI------EAEGGAAHVVSLDVTDYQSIKAAVAHAETEAGTIDILVNNSGV 96
>gnl|CDD|180440 PRK06172, PRK06172, short chain dehydrogenase; Provisional.
Length = 253
Score = 38.6 bits (90), Expect = 2e-04
Identities = 30/116 (25%), Positives = 43/116 (37%), Gaps = 29/116 (25%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K+ +VTG + GIG A A A +G +V+ R A G
Sbjct: 8 KVALVTGGAAGIGRATALAFAREGAKVVVADRDAA------------------------G 43
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGV 118
+I E + DVT+DAEV + +G +D NNAG+
Sbjct: 44 GEETVALIREAGGE-----ALFVACDVTRDAEVKALVEQTIAAYGRLDYAFNNAGI 94
>gnl|CDD|235739 PRK06200, PRK06200, 2,3-dihydroxy-2,3-dihydrophenylpropionate
dehydrogenase; Provisional.
Length = 263
Score = 38.8 bits (91), Expect = 3e-04
Identities = 28/119 (23%), Positives = 49/119 (41%), Gaps = 32/119 (26%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
++ ++TG GIG A++ A+G AR A +
Sbjct: 7 QVALITGGGSGIGRALVERFLAEG------ARVAVL------------------------ 36
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNEF 121
R AE + ++ + D V ++ DVT A+ A D + FG +D + NAG+ ++
Sbjct: 37 -ERSAEKLASLRQRFGD-HVLVVEGDVTSYADNQRAVDQTVDAFGKLDCFVGNAGIWDY 93
>gnl|CDD|132250 TIGR03206, benzo_BadH, 2-hydroxycyclohexanecarboxyl-CoA
dehydrogenase. Members of this protein family are the
enzyme 2-hydroxycyclohexanecarboxyl-CoA dehydrogenase.
The enzymatic properties were confirmed experimentally
in Rhodopseudomonas palustris; the enzyme is
homotetrameric, and not sensitive to oxygen. This enzyme
is part of proposed pathway for degradation of
benzoyl-CoA to 3-hydroxypimeloyl-CoA that differs from
the analogous in Thauera aromatica. It also may occur in
degradation of the non-aromatic compound
cyclohexane-1-carboxylate.
Length = 250
Score = 38.7 bits (90), Expect = 3e-04
Identities = 35/123 (28%), Positives = 46/123 (37%), Gaps = 29/123 (23%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K +VTG GIG A R A +G +V F E AE + + AKG
Sbjct: 4 KTAIVTGGGGGIGGATCRRFAEEGAKVAVFDLNREA---AEKV----AADIRAKGGNAQA 56
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNEFA 122
FA D+T V A G +DV++NNAG ++F
Sbjct: 57 FA----------------------CDITDRDSVDTAVAAAEQALGPVDVLVNNAGWDKFG 94
Query: 123 PVT 125
P T
Sbjct: 95 PFT 97
>gnl|CDD|187662 cd09761, A3DFK9-like_SDR_c, Clostridium thermocellum A3DFK9-like, a
putative carbohydrate or polyalcohol metabolizing SDR,
classical (c) SDRs. This subgroup includes a putative
carbohydrate or polyalcohol metabolizing SDR (A3DFK9)
from Clostridium thermocellum. Its members have a
TGXXXGXG classical-SDR glycine-rich NAD-binding motif,
and some have a canonical SDR active site tetrad (A3DFK9
lacks the upstream Asn). 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 15-hydroxyprostaglandin
dehydrogenase (15-PGDH) numbering). In addition to the
Tyr and Lys, there is often an upstream Ser (Ser-138,
15-PGDH numbering) and/or an Asn (Asn-107, 15-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 ketoacyl
reductases 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 = 242
Score = 38.7 bits (90), Expect = 3e-04
Identities = 34/117 (29%), Positives = 44/117 (37%), Gaps = 34/117 (29%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K+ +VTG GIG I G +V+ F DI +G
Sbjct: 2 KVAIVTGGGHGIGKQICLDFLEAGDKVV------------------FADIDEERG----- 38
Query: 63 FARRAEMIDAMAKENPD-WKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGV 118
A AE E P+ + VH D T VV A + K G IDV++NNA
Sbjct: 39 -ADFAEA------EGPNLFFVHGDVADETLVKFVVYA---MLEKLGRIDVLVNNAAR 85
>gnl|CDD|187654 cd08951, DR_C-13_KR_SDR_c_like, daunorubicin C-13 ketoreductase
(KR), classical (c)-like SDRs. Daunorubicin is a
clinically important therapeutic compound used in some
cancer treatments. Daunorubicin C-13 ketoreductase is
member of the classical SDR family with a canonical
glycine-rich NAD(P)-binding motif, but lacking a
complete match to the active site tetrad characteristic
of this group. The critical Tyr, plus the Lys and
upstream Asn are present, but the catalytic Ser is
replaced, generally by Gln. 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 = 260
Score = 38.6 bits (90), Expect = 3e-04
Identities = 31/114 (27%), Positives = 45/114 (39%), Gaps = 33/114 (28%)
Query: 5 IVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIGFA 64
I +TG+S G+G A R L +GH+V+ AR
Sbjct: 10 IFITGSSDGLGLAAARTLLHQGHEVVLHARS----------------------------Q 41
Query: 65 RRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGV 118
+RA A AK L D++ AE + D + N G D +I+NAG+
Sbjct: 42 KRA----ADAKAACPGAAGVLIGDLSSLAETRKLADQV-NAIGRFDAVIHNAGI 90
>gnl|CDD|169556 PRK08703, PRK08703, short chain dehydrogenase; Provisional.
Length = 239
Score = 38.4 bits (89), Expect = 3e-04
Identities = 26/74 (35%), Positives = 38/74 (51%), Gaps = 8/74 (10%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K I+VTGAS G+G + +A AA G VI AR + ++ + IV A +
Sbjct: 7 KTILVTGASQGLGEQVAKAYAAAGATVILVARHQKKLE------KVYDAIVEAGHPE--P 58
Query: 63 FARRAEMIDAMAKE 76
FA R +++ A KE
Sbjct: 59 FAIRFDLMSAEEKE 72
>gnl|CDD|187572 cd05262, SDR_a7, atypical (a) SDRs, subgroup 7. This subgroup
contains atypical SDRs of unknown function. Members of
this subgroup have a glycine-rich NAD(P)-binding motif
consensus that matches the extended SDRs, TGXXGXXG, but
lacks the characteristic active site residues of the
SDRs. This subgroup has basic residues (HXXXR) in place
of the active site motif YXXXK, these may have a
catalytic role. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and
their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Atypical SDRs include biliverdin IX beta
reductase (BVR-B,aka flavin reductase), NMRa (a
negative transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane
reductase, isoflavone reductases, and others. SDRs are
a functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they 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 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
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. In addition to the Rossmann fold
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids, 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 ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 291
Score = 38.5 bits (90), Expect = 3e-04
Identities = 16/30 (53%), Positives = 23/30 (76%)
Query: 5 IVVTGASVGIGAAILRALAAKGHQVIGFAR 34
+ VTGA+ IG+A++R L A GH+V+G AR
Sbjct: 3 VFVTGATGFIGSAVVRELVAAGHEVVGLAR 32
>gnl|CDD|187592 cd05331, DH-DHB-DH_SDR_c, 2,3 dihydro-2,3 dihydrozybenzoate
dehydrogenases, classical (c) SDRs. 2,3 dihydro-2,3
dihydrozybenzoate dehydrogenase shares the
characteristics of the classical SDRs. This subgroup
includes Escherichai coli EntA which catalyzes the
NAD+-dependent oxidation of
2,3-dihydro-2,3-dihydroxybenzoate to
2,3-dihydroxybenzoate during biosynthesis of the
siderophore Enterobactin. 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 15-hydroxyprostaglandin
dehydrogenase (15-PGDH) numbering). In addition to the
Tyr and Lys, there is often an upstream Ser (Ser-138,
15-PGDH numbering) and/or an Asn (Asn-107, 15-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 ketoacyl
reductases 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 = 244
Score = 38.2 bits (89), Expect = 3e-04
Identities = 25/114 (21%), Positives = 36/114 (31%), Gaps = 36/114 (31%)
Query: 5 IVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIGFA 64
++VTGA+ GIG A+ R L G VI ++
Sbjct: 1 VIVTGAAQGIGRAVARHLLQAGATVIALDLPFVLLLEYGDPLRLT--------------- 45
Query: 65 RRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGV 118
+DV A V E + + G ID ++N AGV
Sbjct: 46 ---------------------PLDVADAAAVREVCSRLLAEHGPIDALVNCAGV 78
>gnl|CDD|187626 cd05368, DHRS6_like_SDR_c, human DHRS6-like, classical (c) SDRs.
Human DHRS6, and similar proteins. These proteins are
classical SDRs, with a canonical active site tetrad and
a close match to the typical Gly-rich NAD-binding motif.
Human DHRS6 is a cytosolic type 2 (R)-hydroxybutyrate
dehydrogenase, which catalyses the conversion of
(R)-hydroxybutyrate to acetoacetate. Also included in
this subgroup is Escherichia coli UcpA (upstream cys P).
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
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-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 ketoacyl reductases 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. Note: removed :
needed to make this chiodl smaller when drew final
trees: rmeoved text form description: Other proteins in
this subgroup include Thermoplasma acidophilum
aldohexose dehydrogenase, which has high dehydrogenase
activity against D-mannose, Bacillus subtilis BacC
involved in the biosynthesis of the dipeptide bacilysin
and its antibiotic moiety anticapsin, Sphingomonas
paucimobilis strain B90 LinC, involved in the
degradation of hexachlorocyclohexane isomers...... P).
Length = 241
Score = 38.2 bits (89), Expect = 3e-04
Identities = 27/116 (23%), Positives = 39/116 (33%), Gaps = 38/116 (32%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K+ ++T A+ GIG AI A A +G VI D E +G
Sbjct: 3 KVALITAAAQGIGRAIALAFAREGANVIA-------TDINEEKLK-----ELERGP---- 46
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGV 118
+ + +DVT +V + G IDV+ N AG
Sbjct: 47 ------------------GITTRVLDVTDKEQVAALA----KEEGRIDVLFNCAGF 80
>gnl|CDD|222146 pfam13460, NAD_binding_10, NADH(P)-binding.
Length = 182
Score = 38.1 bits (89), Expect = 3e-04
Identities = 12/36 (33%), Positives = 18/36 (50%)
Query: 5 IVVTGASVGIGAAILRALAAKGHQVIGFARRAEMID 40
I V GA+ G +++ L A+GHQV +R
Sbjct: 1 IAVIGATGKTGRRLVKELLARGHQVTALSRNPSKAP 36
>gnl|CDD|180462 PRK06198, PRK06198, short chain dehydrogenase; Provisional.
Length = 260
Score = 38.1 bits (89), Expect = 4e-04
Identities = 29/118 (24%), Positives = 47/118 (39%), Gaps = 32/118 (27%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K+ +VTG + G+GAAI RA A +G A G ++
Sbjct: 7 KVALVTGGTQGLGAAIARAFAERG----------------------------AAG--LVI 36
Query: 63 FARRAEMIDAMAKE--NPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGV 118
R AE +A A E K ++ D++ + + FG +D ++N AG+
Sbjct: 37 CGRNAEKGEAQAAELEALGAKAVFVQADLSDVEDCRRVVAAADEAFGRLDALVNAAGL 94
>gnl|CDD|181335 PRK08264, PRK08264, short chain dehydrogenase; Validated.
Length = 238
Score = 37.9 bits (89), Expect = 4e-04
Identities = 31/117 (26%), Positives = 49/117 (41%), Gaps = 39/117 (33%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K+++VTGA+ GIG A + L A+G AAK V
Sbjct: 7 KVVLVTGANRGIGRAFVEQLLARG---------------------------AAK---VYA 36
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVN 119
AR +++ P +V L++DVT A V A + + +++NNAG+
Sbjct: 37 AARD---PESVTDLGP--RVVPLQLDVTDPASVAAAAE----AASDVTILVNNAGIF 84
>gnl|CDD|182051 PRK09730, PRK09730, putative NAD(P)-binding oxidoreductase;
Provisional.
Length = 247
Score = 37.9 bits (88), Expect = 5e-04
Identities = 28/117 (23%), Positives = 47/117 (40%), Gaps = 30/117 (25%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQV-IGFARRAEMIDFAESLFAFFVDIVAAKGHQVI 61
I +VTG S GIG A LA +G+ V + + + + A+ + I A G
Sbjct: 2 AIALVTGGSRGIGRATALLLAQEGYTVAVNYQQN---LHAAQEVVN---LITQAGG---- 51
Query: 62 GFARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGV 118
K L+ D++ + +VV F I+ + ++NNAG+
Sbjct: 52 -------------------KAFVLQADISDENQVVAMFTAIDQHDEPLAALVNNAGI 89
>gnl|CDD|181139 PRK07832, PRK07832, short chain dehydrogenase; Provisional.
Length = 272
Score = 37.7 bits (88), Expect = 5e-04
Identities = 30/122 (24%), Positives = 48/122 (39%), Gaps = 28/122 (22%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K VTGA+ GIG A LAA+G ++ F D A G
Sbjct: 1 KRCFVTGAASGIGRATALRLAAQGAEL------------------FLTDRDAD------G 36
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNEFA 122
A+ A+ P+ + +D++ V I+ G +DV++N AG++ +
Sbjct: 37 LAQTVADARALGGTVPEHRA----LDISDYDAVAAFAADIHAAHGSMDVVMNIAGISAWG 92
Query: 123 PV 124
V
Sbjct: 93 TV 94
>gnl|CDD|187615 cd05357, PR_SDR_c, pteridine reductase (PR), classical (c) SDRs.
Pteridine reductases (PRs), members of the SDR family,
catalyzes the NAD-dependent reduction of folic acid,
dihydrofolate and related compounds. In Leishmania,
pteridine reductase (PTR1) acts to circumvent the
anti-protozoan drugs that attack dihydrofolate reductase
activity. Proteins in this subgroup have an N-terminal
NAD-binding motif and a YxxxK active site motif, but
have an Asp instead of the usual upstream catalytic Ser.
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 have a 3-glycine N-terminal NAD(P)(H)-binding
pattern (typically, TGxxxGxG in classical SDRs and
TGxxGxxG in extended SDRs), while substrate binding is
in the C-terminal region. A critical catalytic Tyr
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase (15-PGDH) numbering), is often found in a
conserved YXXXK pattern. In addition to the Tyr and Lys,
there is often an upstream Ser (Ser-138, 15-PGDH
numbering) and/or an Asn (Asn-107, 15-PGDH numbering) or
additional Ser, contributing to the active site.
Substrates for these enzymes include sugars, steroids,
alcohols, and aromatic compounds. The standard reaction
mechanism is a proton relay involving the conserved Tyr
and Lys, as well as Asn (or Ser). Some SDR family
members, including 17 beta-hydroxysteroid dehydrogenase
contain an additional helix-turn-helix motif that is not
generally found among SDRs.
Length = 234
Score = 37.3 bits (87), Expect = 7e-04
Identities = 32/116 (27%), Positives = 50/116 (43%), Gaps = 28/116 (24%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
+ +VTGA+ IG AI ALAA+G++V+ R+E A+ L D + A + +
Sbjct: 1 AVALVTGAAKRIGRAIAEALAAEGYRVVVHYNRSE--AEAQRL----KDELNALRNSAVL 54
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGV 118
+A++ D A D+ A FG DV++NNA
Sbjct: 55 V--QADLSDFAACA-----------DLVAAAFRA---------FGRCDVLVNNASA 88
>gnl|CDD|187648 cd08944, SDR_c12, classical (c) SDR, subgroup 12. These are
classical SDRs, with the canonical active site tetrad
and glycine-rich NAD-binding motif. 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
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-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 ketoacyl reductases 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 = 246
Score = 37.5 bits (87), Expect = 7e-04
Identities = 31/121 (25%), Positives = 48/121 (39%), Gaps = 32/121 (26%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K+ +VTGA GIGAA LA +G +V+ + A G +
Sbjct: 4 KVAIVTGAGAGIGAACAARLAREGARVVVADIDGGAAQAVVAQIA---------GGAL-- 52
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNEFA 122
+L+VDVT + +V F+ +FG +D+++NNAG
Sbjct: 53 ---------------------ALRVDVTDEQQVAALFERAVEEFGGLDLLVNNAGAMHLT 91
Query: 123 P 123
P
Sbjct: 92 P 92
>gnl|CDD|236210 PRK08267, PRK08267, short chain dehydrogenase; Provisional.
Length = 260
Score = 37.2 bits (87), Expect = 7e-04
Identities = 32/122 (26%), Positives = 45/122 (36%), Gaps = 32/122 (26%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K I +TGA+ GIG A AA+G +V + DI
Sbjct: 2 KSIFITGAASGIGRATALLFAAEGWRVGAY------------------DI---------- 33
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAF-DWINNKFGHIDVMINNAGVNEF 121
+ A+A E + +DVT A A D+ G +DV+ NNAG+
Sbjct: 34 ---NEAGLAALAAELGAGNAWTGALDVTDRAAWDAALADFAAATGGRLDVLFNNAGILRG 90
Query: 122 AP 123
P
Sbjct: 91 GP 92
>gnl|CDD|183797 PRK12859, PRK12859, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 256
Score = 37.5 bits (87), Expect = 7e-04
Identities = 29/116 (25%), Positives = 48/116 (41%), Gaps = 20/116 (17%)
Query: 3 KIIVVTGASV--GIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQV 60
K+ VVTG S GIGAAI + LA G + FF A
Sbjct: 7 KVAVVTGVSRLDGIGAAICKELAEAGADI------------------FFTYWTAYDKEMP 48
Query: 61 IGFARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNA 116
G + ++ KV S+++D+T++ E + + + G+ +++NNA
Sbjct: 49 WGVDQDEQIQLQEELLKNGVKVSSMELDLTQNDAPKELLNKVTEQLGYPHILVNNA 104
>gnl|CDD|223774 COG0702, COG0702, Predicted nucleoside-diphosphate-sugar
epimerases [Cell envelope biogenesis, outer membrane /
Carbohydrate transport and metabolism].
Length = 275
Score = 37.2 bits (86), Expect = 8e-04
Identities = 15/33 (45%), Positives = 22/33 (66%)
Query: 5 IVVTGASVGIGAAILRALAAKGHQVIGFARRAE 37
I+VTGA+ +G A++R L A+GH+V R E
Sbjct: 3 ILVTGATGFVGGAVVRELLARGHEVRAAVRNPE 35
>gnl|CDD|180458 PRK06194, PRK06194, hypothetical protein; Provisional.
Length = 287
Score = 37.3 bits (87), Expect = 8e-04
Identities = 33/117 (28%), Positives = 51/117 (43%), Gaps = 31/117 (26%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K+ V+TGA+ G G A R AA G +++ + D + V + A+G +V+G
Sbjct: 7 KVAVITGAASGFGLAFARIGAALGMKLV-------LADVQQDALDRAVAELRAQGAEVLG 59
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAF-DWINNKFGHIDVMINNAGV 118
+ DV+ DA VEA D +FG + ++ NNAGV
Sbjct: 60 V----------------------RTDVS-DAAQVEALADAALERFGAVHLLFNNAGV 93
>gnl|CDD|187645 cd08941, 3KS_SDR_c, 3-keto steroid reductase, classical (c) SDRs.
3-keto steroid reductase (in concert with other enzymes)
catalyzes NADP-dependent sterol C-4 demethylation, as
part of steroid biosynthesis. 3-keto reductase is a
classical SDR, with a well conserved canonical active
site tetrad and fairly well conserved characteristic
NAD-binding motif. 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 15-hydroxyprostaglandin
dehydrogenase (15-PGDH) numbering). In addition to the
Tyr and Lys, there is often an upstream Ser (Ser-138,
15-PGDH numbering) and/or an Asn (Asn-107, 15-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 ketoacyl
reductases 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 = 290
Score = 37.4 bits (87), Expect = 8e-04
Identities = 30/125 (24%), Positives = 49/125 (39%), Gaps = 38/125 (30%)
Query: 2 SKIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVD------IVAA 55
K+++VTGA+ G+G AI E L A + I+A
Sbjct: 1 RKVVLVTGANSGLGLAI-----------------------CERLLAEDDENPELTLILAC 37
Query: 56 KGHQVIGFARRAE-MIDAMAKENPDWKVHS--LKVDVTKDAEVVEAFDWINNKFGHIDVM 112
+ Q RAE A+ +PD +V + VD++ V A + ++ +D +
Sbjct: 38 RNLQ------RAEAACRALLASHPDARVVFDYVLVDLSNMVSVFAAAKELKKRYPRLDYL 91
Query: 113 INNAG 117
NAG
Sbjct: 92 YLNAG 96
>gnl|CDD|234422 TIGR03971, SDR_subfam_1, oxidoreductase, SDR family. Members of
this protein subfamily are putative oxidoreductases
belonging to the larger SDR family. Members of the
present subfamily may occur several to a genome and are
largely restricted to genomes that contain members of
families TIGR03962, TIGR03967, and TIGR03969. Many
members have been annotated by homology as carveol
dehydrogenases.
Length = 265
Score = 37.1 bits (86), Expect = 9e-04
Identities = 34/121 (28%), Positives = 54/121 (44%), Gaps = 16/121 (13%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K+ +TGA+ G G A LAA+G +I A + D+ A D+
Sbjct: 4 KVAFITGAARGQGRAHAVRLAAEGADIIAIDLCAPLSDYPTYPLATREDL---------- 53
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNEFA 122
A +++A+ + KV + K DV AEV + +FG +DV++ NAGV +
Sbjct: 54 -DETARLVEALGR-----KVLARKADVRDLAEVRAVVEDGVEQFGRLDVVVANAGVLSYG 107
Query: 123 P 123
Sbjct: 108 R 108
>gnl|CDD|187663 cd09762, HSDL2_SDR_c, human hydroxysteroid dehydrogenase-like
protein 2 (HSDL2), classical (c) SDRs. This subgroup
includes human HSDL2 and related protens. These are
members of the classical SDR family, with a canonical
Gly-rich NAD-binding motif and the typical YXXXK active
site motif. However, the rest of the catalytic tetrad is
not strongly conserved. HSDL2 may play a part in fatty
acid metabolism, as it is found in peroxisomes. 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 have a
3-glycine N-terminal NAD(P)(H)-binding pattern
(typically, TGxxxGxG in classical SDRs and TGxxGxxG in
extended SDRs), while substrate binding is in the
C-terminal region. A critical catalytic Tyr residue
(Tyr-151, human 15-hydroxyprostaglandin dehydrogenase
(15-PGDH) numbering), is often found in a conserved
YXXXK pattern. In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) or additional
Ser, contributing to the active site. Substrates for
these enzymes include sugars, steroids, alcohols, and
aromatic compounds. The standard reaction mechanism is a
proton relay involving the conserved Tyr and Lys, as
well as Asn (or Ser). Some SDR family members, including
17 beta-hydroxysteroid dehydrogenase contain an
additional helix-turn-helix motif that is not generally
found among SDRs.
Length = 243
Score = 37.0 bits (86), Expect = 9e-04
Identities = 33/115 (28%), Positives = 49/115 (42%), Gaps = 24/115 (20%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAE-MIDFAESLFAFFVDIVAAKGHQVI 61
K + +TGAS GIG AI A G V+ A+ AE +++ +I AA G
Sbjct: 4 KTLFITGASRGIGKAIALKAARDGANVVIAAKTAEPHPKLPGTIYTAAEEIEAAGGK--- 60
Query: 62 GFARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNA 116
A+ VD+ + +V A + KFG ID+++NNA
Sbjct: 61 ----------ALP----------CIVDIRDEDQVRAAVEKAVEKFGGIDILVNNA 95
>gnl|CDD|237220 PRK12828, PRK12828, short chain dehydrogenase; Provisional.
Length = 239
Score = 36.7 bits (85), Expect = 0.001
Identities = 26/116 (22%), Positives = 43/116 (37%), Gaps = 31/116 (26%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K++ +TG G+G A LAA+G +V R A + + V A ++ G
Sbjct: 8 KVVAITGGFGGLGRATAAWLAARGARVALIGRGAAPLSQT-------LPGVPADALRIGG 60
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGV 118
+D+ A D +N +FG +D ++N AG
Sbjct: 61 ------------------------IDLVDPQAARRAVDEVNRQFGRLDALVNIAGA 92
>gnl|CDD|181113 PRK07775, PRK07775, short chain dehydrogenase; Provisional.
Length = 274
Score = 36.7 bits (85), Expect = 0.001
Identities = 35/119 (29%), Positives = 45/119 (37%), Gaps = 29/119 (24%)
Query: 6 VVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIGFAR 65
+V GAS GIGAA LAA G V ARR E E L VD + A G + + F
Sbjct: 14 LVAGASSGIGAATAIELAAAGFPVALGARRVEKC---EEL----VDKIRADGGEAVAFP- 65
Query: 66 RAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNEFAPV 124
+DVT V G I+V+++ AG F +
Sbjct: 66 ---------------------LDVTDPDSVKSFVAQAEEALGEIEVLVSGAGDTYFGKL 103
>gnl|CDD|236056 PRK07576, PRK07576, short chain dehydrogenase; Provisional.
Length = 264
Score = 36.9 bits (86), Expect = 0.001
Identities = 34/122 (27%), Positives = 48/122 (39%), Gaps = 29/122 (23%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K +VV G + GI I +A A G V +R E +D A V + G + +G
Sbjct: 10 KNVVVVGGTSGINLGIAQAFARAGANVAVASRSQEKVDAA-------VAQLQQAGPEGLG 62
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNEFA 122
+ DV A V AF I ++FG IDV+++ A N A
Sbjct: 63 VS----------------------ADVRDYAAVEAAFAQIADEFGPIDVLVSGAAGNFPA 100
Query: 123 PV 124
P
Sbjct: 101 PA 102
>gnl|CDD|187646 cd08942, RhlG_SDR_c, RhlG and related beta-ketoacyl reductases,
classical (c) SDRs. Pseudomonas aeruginosa RhlG is an
SDR-family beta-ketoacyl reductase involved in
Rhamnolipid biosynthesis. RhlG is similar to but
distinct from the FabG family of beta-ketoacyl-acyl
carrier protein (ACP) of type II fatty acid synthesis.
RhlG and related proteins are classical SDRs, with a
canonical active site tetrad and glycine-rich
NAD(P)-binding motif. 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 15-hydroxyprostaglandin
dehydrogenase (15-PGDH) numbering). In addition to the
Tyr and Lys, there is often an upstream Ser (Ser-138,
15-PGDH numbering) and/or an Asn (Asn-107, 15-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 ketoacyl
reductases 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 = 250
Score = 36.7 bits (85), Expect = 0.001
Identities = 31/123 (25%), Positives = 50/123 (40%), Gaps = 32/123 (26%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEM-IDFAESLFAFFVDIVAAKGHQVI 61
KI++VTG S GIG I + G +VI AR+AE D AE L A+
Sbjct: 7 KIVLVTGGSRGIGRMIAQGFLEAGARVIISARKAEACADAAEELSAY------------- 53
Query: 62 GFARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNEF 121
+ ++ D++ + + + + +DV++NNAG
Sbjct: 54 ------------------GECIAIPADLSSEEGIEALVARVAERSDRLDVLVNNAGATWG 95
Query: 122 APV 124
AP+
Sbjct: 96 APL 98
>gnl|CDD|212494 cd08946, SDR_e, extended (e) SDRs. Extended SDRs are distinct
from classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids. Extended SDRs are a diverse collection
of proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they 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 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
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. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and
their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. 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 ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 200
Score = 36.5 bits (85), Expect = 0.001
Identities = 13/38 (34%), Positives = 23/38 (60%)
Query: 5 IVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFA 42
I+VTG + IG+ ++R L +GH+V+ R ++ A
Sbjct: 1 ILVTGGAGFIGSHLVRRLLERGHEVVVIDRLDVVVHLA 38
>gnl|CDD|180604 PRK06523, PRK06523, short chain dehydrogenase; Provisional.
Length = 260
Score = 36.4 bits (85), Expect = 0.001
Identities = 14/34 (41%), Positives = 19/34 (55%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRA 36
K +VTG + GIGAA + L G +V+ AR
Sbjct: 10 KRALVTGGTKGIGAATVARLLEAGARVVTTARSR 43
>gnl|CDD|187666 cd09806, type1_17beta-HSD-like_SDR_c, human estrogenic
17beta-hydroxysteroid dehydrogenase type 1 (type 1
17beta-HSD)-like, classical (c) SDRs.
17beta-hydroxysteroid dehydrogenases are a group of
isozymes that catalyze activation and inactivation of
estrogen and androgens. This classical SDR subgroup
includes human type 1 17beta-HSD, human retinol
dehydrogenase 8, zebrafish photoreceptor associated
retinol dehydrogenase type 2, and a chicken
ovary-specific 17beta-hydroxysteroid dehydrogenase. 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
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-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 ketoacyl reductases 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 = 258
Score = 36.3 bits (84), Expect = 0.002
Identities = 29/125 (23%), Positives = 48/125 (38%), Gaps = 33/125 (26%)
Query: 3 KIIVVTGASVGIG---AAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQ 59
++++TG S GIG A L + +K +V A M D K +
Sbjct: 1 TVVLITGCSSGIGLHLAVRLASDPSKRFKVY-----ATMRDLK-------------KKGR 42
Query: 60 VIGFARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVN 119
+ A A + +L++DV V A + + H+DV++ NAGV
Sbjct: 43 LWE-AAGALAGGTLE---------TLQLDVCDSKSVAAAVERVTE--RHVDVLVCNAGVG 90
Query: 120 EFAPV 124
P+
Sbjct: 91 LLGPL 95
>gnl|CDD|187653 cd08950, KR_fFAS_SDR_c_like, ketoacyl reductase (KR) domain of
fungal-type fatty acid synthase (fFAS), classical
(c)-like SDRs. KR domain of fungal-type fatty acid
synthase (FAS), type I. Fungal-type FAS is a
heterododecameric FAS composed of alpha and beta
multifunctional polypeptide chains. The KR, an SDR
family member, is located centrally in the alpha chain.
KR catalyzes the NADP-dependent reduction of
ketoacyl-ACP to hydroxyacyl-ACP. KR shares the critical
active site Tyr of the Classical SDR and has partial
identity of the active site tetrad, but the upstream
Asn is replaced in KR by Met. As in other SDRs, there
is a glycine rich NAD-binding motif, but the pattern
found in KR does not match the classical SDRs, and is
not strictly conserved within this group. 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 = 259
Score = 36.0 bits (84), Expect = 0.002
Identities = 21/62 (33%), Positives = 29/62 (46%), Gaps = 7/62 (11%)
Query: 3 KIIVVTGASVG-IGAAILRALAAKGHQVIGFARR--AEMIDFAESLFAFFVDIVAAKGHQ 59
K+ +VTGA G IGA ++ L A G VI R E F + L+ AKG +
Sbjct: 8 KVALVTGAGPGSIGAEVVAGLLAGGATVIVTTSRFSHERTAFFQKLYRKH----GAKGSK 63
Query: 60 VI 61
+
Sbjct: 64 LW 65
>gnl|CDD|235713 PRK06139, PRK06139, short chain dehydrogenase; Provisional.
Length = 330
Score = 36.2 bits (84), Expect = 0.002
Identities = 36/117 (30%), Positives = 51/117 (43%), Gaps = 31/117 (26%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
++V+TGAS GIG A A A +G +++ AR E +L A + A G +V+
Sbjct: 8 AVVVITGASSGIGQATAEAFARRGARLVLAARDEE------ALQAV-AEECRALGAEVL- 59
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKF-GHIDVMINNAGV 118
+ DVT DA+ V+A F G IDV +NN GV
Sbjct: 60 ---------------------VVPTDVT-DADQVKALATQAASFGGRIDVWVNNVGV 94
>gnl|CDD|187596 cd05337, BKR_1_SDR_c, putative beta-ketoacyl acyl carrier protein
[ACP] reductase (BKR), subgroup 1, classical (c) SDR.
This subgroup includes Escherichia coli CFT073 FabG. The
Escherichai coli K12 BKR, FabG, belongs to a different
subgroup. BKR catalyzes the NADPH-dependent reduction of
ACP in the first reductive step of de novo fatty acid
synthesis (FAS). FAS consists of four elongation steps,
which are repeated to extend the fatty acid chain
through the addition of two-carbo units from malonyl
acyl-carrier protein (ACP): condensation, reduction,
dehydration, and a final reduction. Type II FAS, typical
of plants and many bacteria, maintains these activities
on discrete polypeptides, while type I FAS utilizes one
or two multifunctional polypeptides. BKR resembles enoyl
reductase, which catalyzes the second reduction step in
FAS. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with
structurally conserved Rossmann fold (alpha/beta folding
pattern with a central beta-sheet) 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 have a 3-glycine N-terminal NAD(P)(H) binding
pattern: TGxxxGxG in classical SDRs. 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 type ketoacyl reductases 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. A critical catalytic Tyr residue
(Tyr-151, human 15-hydroxyprostaglandin dehydrogenase
(15-PGDH) numbering), is often found in a conserved
YXXXK pattern. In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) or additional
Ser, contributing to the active site. Substrates for
these enzymes include sugars, steroids, alcohols, and
aromatic compounds. The standard reaction mechanism is a
proton relay involving the conserved Tyr-151 and
Lys-155, and well as Asn-111 (or Ser). Some SDR family
members, including 17 beta-hydroxysteroid dehydrogenase
contain an additional helix-turn-helix motif that is not
generally found among SDRs.
Length = 255
Score = 35.9 bits (83), Expect = 0.002
Identities = 29/113 (25%), Positives = 43/113 (38%), Gaps = 28/113 (24%)
Query: 6 VVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIGFAR 65
+VTGAS GIG AI LAA+G + + D +V+ R
Sbjct: 5 IVTGASRGIGRAIATELAARGFDIAINDLPDD-------------DQATEVVAEVLAAGR 51
Query: 66 RAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGV 118
RA A D+ + ++ D FG +D ++NNAG+
Sbjct: 52 RAIYFQA---------------DIGELSDHEALLDQAWEDFGRLDCLVNNAGI 89
>gnl|CDD|176178 cd05188, MDR, Medium chain reductase/dehydrogenase
(MDR)/zinc-dependent alcohol dehydrogenase-like family.
The medium chain reductase/dehydrogenases
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH) , quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. ADH-like proteins
typically form dimers (typically higher plants, mammals)
or tetramers (yeast, bacteria), and generally have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site and a structural zinc in a lobe of
the catalytic domain. The active site zinc is
coordinated by a histidine, two cysteines, and a water
molecule. The second zinc seems to play a structural
role, affects subunit interactions, and is typically
coordinated by 4 cysteines. Other MDR members have only
a catalytic zinc, and some contain no coordinated zinc.
Length = 271
Score = 35.8 bits (83), Expect = 0.002
Identities = 15/46 (32%), Positives = 23/46 (50%), Gaps = 1/46 (2%)
Query: 5 IVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFV 50
++V GA G+G + A G +VI R E ++ A+ L A V
Sbjct: 138 VLVLGAG-GVGLLAAQLAKAAGARVIVTDRSDEKLELAKELGADHV 182
>gnl|CDD|236357 PRK08945, PRK08945, putative oxoacyl-(acyl carrier protein)
reductase; Provisional.
Length = 247
Score = 35.6 bits (83), Expect = 0.002
Identities = 32/122 (26%), Positives = 44/122 (36%), Gaps = 38/122 (31%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQ--V 60
+II+VTGA GIG A G VI R E L A + +I AA G Q +
Sbjct: 13 RIILVTGAGDGIGREAALTYARHGATVILLGRT------EEKLEAVYDEIEAAGGPQPAI 66
Query: 61 IGF----ARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNA 116
I A +A I +FG +D +++NA
Sbjct: 67 IPLDLLTATPQNYQQ-LADT-------------------------IEEQFGRLDGVLHNA 100
Query: 117 GV 118
G+
Sbjct: 101 GL 102
>gnl|CDD|212497 cd11731, Lin1944_like_SDR_c, Lin1944 and related proteins,
classical (c) SDRs. Lin1944 protein from Listeria
Innocua is a classical SDR, it contains a glycine-rich
motif similar to the canonical motif of the SDR
NAD(P)-binding site. However, the typical SDR active
site residues are absent in this subgroup of proteins
of undetermined function. 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 ketoacyl
reductases 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 = 198
Score = 35.6 bits (83), Expect = 0.003
Identities = 18/49 (36%), Positives = 27/49 (55%), Gaps = 4/49 (8%)
Query: 5 IVVTGASVGIGAAILRALAAKGHQVI--GFARRAEMIDF--AESLFAFF 49
I+V GA+ IG A+ + L+A GH+VI G + +D S+ A F
Sbjct: 1 IIVIGATGTIGLAVAQLLSAHGHEVITAGRSSGDYQVDITDEASIKALF 49
>gnl|CDD|187537 cd05226, SDR_e_a, Extended (e) and atypical (a) SDRs. Extended
or atypical short-chain dehydrogenases/reductases
(SDRs, aka tyrosine-dependent oxidoreductases) are
distinct from classical SDRs. In addition to the
Rossmann fold (alpha/beta folding pattern with a
central beta-sheet) core region typical of all SDRs,
extended SDRs have a less conserved C-terminal
extension of approximately 100 amino acids. Extended
SDRs are a diverse collection of proteins, and include
isomerases, epimerases, oxidoreductases, and lyases;
they typically have a TGXXGXXG cofactor binding motif.
Atypical SDRs generally lack the catalytic residues
characteristic of the SDRs, and their glycine-rich
NAD(P)-binding motif is often different from the forms
normally seen in classical or extended SDRs. Atypical
SDRs include biliverdin IX beta reductase (BVR-B,aka
flavin reductase), NMRa (a negative transcriptional
regulator of various fungi), progesterone
5-beta-reductase like proteins, phenylcoumaran benzylic
ether and pinoresinol-lariciresinol reductases,
phenylpropene synthases, eugenol synthase,
triphenylmethane reductase, isoflavone reductases, and
others. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
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
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, 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. 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
ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding
motif.
Length = 176
Score = 35.5 bits (82), Expect = 0.003
Identities = 20/99 (20%), Positives = 33/99 (33%), Gaps = 8/99 (8%)
Query: 5 IVVTGASVGIGAAILRALAAKGHQVIGFARRA--------EMIDFAESLFAFFVDIVAAK 56
I++ GA+ IG A+ R L +GH+V R E + E + A
Sbjct: 1 ILILGATGFIGRALARELLEQGHEVTLLVRNTKRLSKEDQEPVAVVEGDLRDLDSLSDAV 60
Query: 57 GHQVIGFARRAEMIDAMAKENPDWKVHSLKVDVTKDAEV 95
+ D D + ++ K+A V
Sbjct: 61 QGVDVVIHLAGAPRDTRDFCEVDVEGTRNVLEAAKEAGV 99
>gnl|CDD|135631 PRK05867, PRK05867, short chain dehydrogenase; Provisional.
Length = 253
Score = 35.8 bits (82), Expect = 0.003
Identities = 27/119 (22%), Positives = 46/119 (38%), Gaps = 29/119 (24%)
Query: 6 VVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIGFAR 65
++TGAS GIG + A G QV AR + ++ D + G +V+
Sbjct: 13 LITGASTGIGKRVALAYVEAGAQVAIAARHLDALEKL-------ADEIGTSGGKVV---- 61
Query: 66 RAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNEFAPV 124
+ DV++ +V D + + G ID+ + NAG+ P+
Sbjct: 62 ------------------PVCCDVSQHQQVTSMLDQVTAELGGIDIAVCNAGIITVTPM 102
>gnl|CDD|187641 cd08936, CR_SDR_c, Porcine peroxisomal carbonyl reductase like,
classical (c) SDR. This subgroup contains porcine
peroxisomal carbonyl reductase and similar proteins. The
porcine enzyme efficiently reduces retinals. This
subgroup also includes human dehydrogenase/reductase
(SDR family) member 4 (DHRS4), and human DHRS4L1. DHRS4
is a peroxisomal enzyme with 3beta-hydroxysteroid
dehydrogenase activity; it catalyzes the reduction of
3-keto-C19/C21-steroids into 3beta-hydroxysteroids more
efficiently than it does the retinal reduction. The
human DHRS4 gene cluster contains DHRS4, DHRS4L2 and
DHRS4L1. DHRS4L2 and DHRS4L1 are paralogs of DHRS4,
DHRS4L2 being the most recent member. 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
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-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 ketoacyl reductases 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 = 256
Score = 35.6 bits (82), Expect = 0.003
Identities = 32/120 (26%), Positives = 50/120 (41%), Gaps = 29/120 (24%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K+ +VT ++ GIG AI R LA G V+ +R+ + +D A V + +G V G
Sbjct: 11 KVALVTASTDGIGLAIARRLAQDGAHVVVSSRKQQNVDRA-------VATLQGEGLSVTG 63
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNEFA 122
V +D E + A N G +D++++NA VN F
Sbjct: 64 TV--------------------CHVGKAEDRERLVAT--AVNLHGGVDILVSNAAVNPFF 101
>gnl|CDD|135765 PRK06113, PRK06113, 7-alpha-hydroxysteroid dehydrogenase;
Validated.
Length = 255
Score = 35.6 bits (82), Expect = 0.003
Identities = 28/115 (24%), Positives = 44/115 (38%), Gaps = 29/115 (25%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K ++TGA GIG I A G V+ A+ A + VD + G Q
Sbjct: 12 KCAIITGAGAGIGKEIAITFATAGASVVVSDINADA---ANHV----VDEIQQLGGQAFA 64
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAG 117
+ D+T + E+ D+ +K G +D+++NNAG
Sbjct: 65 ----------------------CRCDITSEQELSALADFALSKLGKVDILVNNAG 97
>gnl|CDD|181159 PRK07890, PRK07890, short chain dehydrogenase; Provisional.
Length = 258
Score = 35.3 bits (82), Expect = 0.003
Identities = 29/116 (25%), Positives = 46/116 (39%), Gaps = 33/116 (28%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K++VV+ G+G + R LA + A G V+
Sbjct: 6 KVVVVS----GVGPGLGRTLAVR---------------------------AARAGADVVL 34
Query: 63 FARRAEMIDAMAKENPDWKVHSLKV--DVTKDAEVVEAFDWINNKFGHIDVMINNA 116
AR AE +D +A E D +L V D+T + + +FG +D ++NNA
Sbjct: 35 AARTAERLDEVAAEIDDLGRRALAVPTDITDEDQCANLVALALERFGRVDALVNNA 90
>gnl|CDD|181198 PRK08017, PRK08017, oxidoreductase; Provisional.
Length = 256
Score = 35.4 bits (82), Expect = 0.003
Identities = 12/37 (32%), Positives = 21/37 (56%)
Query: 1 MSKIIVVTGASVGIGAAILRALAAKGHQVIGFARRAE 37
M K +++TG S GIG L +G++V+ R+ +
Sbjct: 1 MQKSVLITGCSSGIGLEAALELKRRGYRVLAACRKPD 37
>gnl|CDD|181131 PRK07814, PRK07814, short chain dehydrogenase; Provisional.
Length = 263
Score = 35.5 bits (82), Expect = 0.003
Identities = 31/115 (26%), Positives = 43/115 (37%), Gaps = 29/115 (25%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
++ VVTGA G+GAAI A A G V+ AR + D VA Q+
Sbjct: 11 QVAVVTGAGRGLGAAIALAFAEAGADVLIAARTESQL-----------DEVAE---QIRA 56
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAG 117
RRA H + D+ FG +D+++NN G
Sbjct: 57 AGRRA---------------HVVAADLAHPEATAGLAGQAVEAFGRLDIVVNNVG 96
>gnl|CDD|180586 PRK06483, PRK06483, dihydromonapterin reductase; Provisional.
Length = 236
Score = 35.3 bits (82), Expect = 0.004
Identities = 14/35 (40%), Positives = 18/35 (51%)
Query: 1 MSKIIVVTGASVGIGAAILRALAAKGHQVIGFARR 35
M I++TGA IG A+ L A+G VI R
Sbjct: 1 MPAPILITGAGQRIGLALAWHLLAQGQPVIVSYRT 35
>gnl|CDD|187539 cd05228, AR_FR_like_1_SDR_e, uncharacterized subgroup of aldehyde
reductase and flavonoid reductase related proteins,
extended (e) SDRs. This subgroup contains proteins of
unknown function related to aldehyde reductase and
flavonoid reductase of the extended SDR-type. Aldehyde
reductase I (aka carbonyl reductase) is an NADP-binding
SDR; it has an NADP-binding motif consensus that is
slightly different from the canonical SDR form and
lacks the Asn of the extended SDR active site tetrad.
Aldehyde reductase I catalyzes the NADP-dependent
reduction of ethyl 4-chloro-3-oxobutanoate to ethyl
(R)-4-chloro-3-hydroxybutanoate. The related flavonoid
reductases act in the NADP-dependent reduction of
flavonoids, ketone-containing plant secondary
metabolites. Extended SDRs are distinct from classical
SDRs. In addition to the Rossmann fold (alpha/beta
folding pattern with a central beta-sheet) core region
typical of all SDRs, extended SDRs have a less
conserved C-terminal extension of approximately 100
amino acids. Extended SDRs are a diverse collection of
proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they 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 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
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. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and
their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. 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 ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 318
Score = 35.3 bits (82), Expect = 0.004
Identities = 17/49 (34%), Positives = 28/49 (57%), Gaps = 3/49 (6%)
Query: 5 IVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIV 53
I+VTGA+ +G+ ++RAL A+G++V R A L V++V
Sbjct: 1 ILVTGATGFLGSNLVRALLAQGYRVRALVRSG---SDAVLLDGLPVEVV 46
>gnl|CDD|236094 PRK07774, PRK07774, short chain dehydrogenase; Provisional.
Length = 250
Score = 35.1 bits (81), Expect = 0.005
Identities = 33/117 (28%), Positives = 48/117 (41%), Gaps = 29/117 (24%)
Query: 2 SKIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVI 61
K+ +VTGA+ GIG A ALA +G V+ AE AE + IVA G +
Sbjct: 6 DKVAIVTGAAGGIGQAYAEALAREGASVVVADINAEG---AERVAK---QIVADGGTAI- 58
Query: 62 GFARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGV 118
+++VDV+ D + FG ID ++NNA +
Sbjct: 59 ----------------------AVQVDVSDPDSAKAMADATVSAFGGIDYLVNNAAI 93
>gnl|CDD|181668 PRK09135, PRK09135, pteridine reductase; Provisional.
Length = 249
Score = 34.9 bits (81), Expect = 0.005
Identities = 14/37 (37%), Positives = 22/37 (59%)
Query: 1 MSKIIVVTGASVGIGAAILRALAAKGHQVIGFARRAE 37
+K+ ++TG + IGAAI R L A G++V R+
Sbjct: 5 SAKVALITGGARRIGAAIARTLHAAGYRVAIHYHRSA 41
>gnl|CDD|235693 PRK06077, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 252
Score = 34.7 bits (80), Expect = 0.005
Identities = 34/122 (27%), Positives = 54/122 (44%), Gaps = 30/122 (24%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFA-RRAEMIDFAESLFAFFVDIVAAKGHQVI 61
K++VVTG+ GIG AI LA +G V+ A +RAE + E+L +V G + I
Sbjct: 7 KVVVVTGSGRGIGRAIAVRLAKEGSLVVVNAKKRAE--EMNETL-----KMVKENGGEGI 59
Query: 62 GFARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNEF 121
G + DV+ +++G D+++NNAG+ F
Sbjct: 60 G----------------------VLADVSTREGCETLAKATIDRYGVADILVNNAGLGLF 97
Query: 122 AP 123
+P
Sbjct: 98 SP 99
>gnl|CDD|180774 PRK06953, PRK06953, short chain dehydrogenase; Provisional.
Length = 222
Score = 34.7 bits (80), Expect = 0.006
Identities = 24/75 (32%), Positives = 36/75 (48%), Gaps = 6/75 (8%)
Query: 2 SKIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFA--FFVDIVAAKGHQ 59
K +++ GAS GIG +R A G +VI AR A + ++L A +D+
Sbjct: 1 MKTVLIVGASRGIGREFVRQYRADGWRVIATARDAAALAALQALGAEALALDVADPA--S 58
Query: 60 VIGFARR--AEMIDA 72
V G A + E +DA
Sbjct: 59 VAGLAWKLDGEALDA 73
Score = 29.7 bits (67), Expect = 0.34
Identities = 21/72 (29%), Positives = 28/72 (38%), Gaps = 10/72 (13%)
Query: 49 FVDIVAAKGHQVIGFARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFG- 107
FV A G +VI AR A + A+ +L +DV D V W K
Sbjct: 17 FVRQYRADGWRVIATARDAAALAALQALG----AEALALDVA-DPASVAGLAW---KLDG 68
Query: 108 -HIDVMINNAGV 118
+D + AGV
Sbjct: 69 EALDAAVYVAGV 80
>gnl|CDD|235712 PRK06138, PRK06138, short chain dehydrogenase; Provisional.
Length = 252
Score = 34.4 bits (79), Expect = 0.007
Identities = 29/116 (25%), Positives = 46/116 (39%), Gaps = 30/116 (25%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
++ +VTGA GIG A + A +G +V+ R AE
Sbjct: 6 RVAIVTGAGSGIGRATAKLFAREGARVVVADRDAE------------------------A 41
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGV 118
R A I A + + + DV V D++ ++G +DV++NNAG
Sbjct: 42 AERVAAAIAA------GGRAFARQGDVGSAEAVEALVDFVAARWGRLDVLVNNAGF 91
>gnl|CDD|237079 PRK12367, PRK12367, short chain dehydrogenase; Provisional.
Length = 245
Score = 34.2 bits (79), Expect = 0.008
Identities = 15/30 (50%), Positives = 20/30 (66%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGF 32
K I +TGAS +G A+ +A AKG +VIG
Sbjct: 15 KRIGITGASGALGKALTKAFRAKGAKVIGL 44
>gnl|CDD|187542 cd05231, NmrA_TMR_like_1_SDR_a, NmrA (a transcriptional
regulator) and triphenylmethane reductase (TMR) like
proteins, subgroup 1, atypical (a) SDRs. Atypical SDRs
related to NMRa, TMR, and HSCARG (an NADPH sensor).
This subgroup resembles the SDRs and has a partially
conserved characteristic [ST]GXXGXXG NAD-binding motif,
but lacks the conserved active site residues. NmrA is a
negative transcriptional regulator of various fungi,
involved in the post-translational modulation of the
GATA-type transcription factor AreA. NmrA lacks the
canonical GXXGXXG NAD-binding motif and has altered
residues at the catalytic triad, including a Met
instead of the critical Tyr residue. NmrA may bind
nucleotides but appears to lack any dehydrogenase
activity. HSCARG has been identified as a putative
NADP-sensing molecule, and redistributes and
restructures in response to NADPH/NADP ratios. Like
NmrA, it lacks most of the active site residues of the
SDR family, but has an NAD(P)-binding motif similar to
the extended SDR family, GXXGXXG. SDRs are a
functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Atypical
SDRs are distinct from classical SDRs. 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 15-hydroxyprostaglandin dehydrogenase
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser and/or an Asn, 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. In addition to the Rossmann fold core
region typical of all SDRs, extended SDRs have a less
conserved C-terminal extension of approximately 100
amino acids, 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 ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 259
Score = 34.2 bits (79), Expect = 0.008
Identities = 19/72 (26%), Positives = 29/72 (40%), Gaps = 13/72 (18%)
Query: 5 IVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVI--G 62
I+VTGA+ IG+ + L G V R E +AA+G +V+
Sbjct: 1 ILVTGATGRIGSKVATTLLEAGRPVRALVRSDE-----------RAAALAARGAEVVVGD 49
Query: 63 FARRAEMIDAMA 74
A + A+A
Sbjct: 50 LDDPAVLAAALA 61
>gnl|CDD|171822 PRK12938, PRK12938, acetyacetyl-CoA reductase; Provisional.
Length = 246
Score = 34.2 bits (78), Expect = 0.009
Identities = 34/121 (28%), Positives = 54/121 (44%), Gaps = 38/121 (31%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIG-----FARRAEMIDFAESLFAFFVDIVAAKG 57
+I VTG GIG +I + L G +V+ RR + ++ ++L D +A++G
Sbjct: 4 RIAYVTGGMGGIGTSICQRLHKDGFKVVAGCGPNSPRRVKWLEDQKALG---FDFIASEG 60
Query: 58 HQVIGFARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAG 117
+ +G DW D TK AFD + + G IDV++NNAG
Sbjct: 61 N--VG----------------DW-------DSTK-----AAFDKVKAEVGEIDVLVNNAG 90
Query: 118 V 118
+
Sbjct: 91 I 91
>gnl|CDD|223210 COG0132, BioD, Dethiobiotin synthetase [Coenzyme metabolism].
Length = 223
Score = 33.8 bits (78), Expect = 0.010
Identities = 14/37 (37%), Positives = 20/37 (54%), Gaps = 5/37 (13%)
Query: 1 MSKIIVVTGASVGIG-----AAILRALAAKGHQVIGF 32
M K VTG G+G AA+ +AL +G+ V G+
Sbjct: 1 MMKRFFVTGTDTGVGKTVVSAALAQALKQQGYSVAGY 37
>gnl|CDD|187669 cd09809, human_WWOX_like_SDR_c-like, human WWOX (WW
domain-containing oxidoreductase)-like, classical
(c)-like SDRs. Classical-like SDR domain of human WWOX
and related proteins. Proteins in this subfamily share
the glycine-rich NAD-binding motif of the classical
SDRs, have a partial match to the canonical active site
tetrad, but lack the typical active site Ser. 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
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-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 ketoacyl reductases 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 = 284
Score = 34.1 bits (78), Expect = 0.010
Identities = 25/116 (21%), Positives = 44/116 (37%), Gaps = 27/116 (23%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K+I++TGA+ GIG R+ A G VI A R
Sbjct: 2 KVIIITGANSGIGFETARSFALHGAHVI-LACRNM------------------------- 35
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGV 118
+R + + + +E +V ++ +D+ V + K + V++ NA V
Sbjct: 36 -SRASAAVSRILEEWHKARVEAMTLDLASLRSVQRFAEAFKAKNSPLHVLVCNAAV 90
>gnl|CDD|187554 cd05243, SDR_a5, atypical (a) SDRs, subgroup 5. This subgroup
contains atypical SDRs, some of which are identified as
putative NAD(P)-dependent epimerases, one as a putative
NAD-dependent epimerase/dehydratase. Atypical SDRs are
distinct from classical SDRs. Members of this subgroup
have a glycine-rich NAD(P)-binding motif that is very
similar to the extended SDRs, GXXGXXG, and binds NADP.
Generally, this subgroup has poor conservation of the
active site tetrad; however, individual sequences do
contain matches to the YXXXK active site motif, the
upstream Ser, and there is a highly conserved Asp in
place of the usual active site Asn throughout the
subgroup. Atypical SDRs generally lack the catalytic
residues characteristic of the SDRs, and their
glycine-rich NAD(P)-binding motif is often different
from the forms normally seen in classical or extended
SDRs. Atypical SDRs include biliverdin IX beta
reductase (BVR-B,aka flavin reductase), NMRa (a
negative transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane
reductase, isoflavone reductases, and others. SDRs are
a functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they 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 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
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. In addition to the Rossmann fold
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids, 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 ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 203
Score = 33.7 bits (78), Expect = 0.010
Identities = 15/49 (30%), Positives = 25/49 (51%), Gaps = 3/49 (6%)
Query: 5 IVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIV 53
++V GA+ +G ++R L +G+QV R AE L A ++V
Sbjct: 2 VLVVGATGKVGRHVVRELLDRGYQVRALVRDPS---QAEKLEAAGAEVV 47
>gnl|CDD|187553 cd05242, SDR_a8, atypical (a) SDRs, subgroup 8. This subgroup
contains atypical SDRs of unknown function. Proteins in
this subgroup have a glycine-rich NAD(P)-binding motif
consensus that resembles that of the extended SDRs,
(GXXGXXG or GGXGXXG), but lacks the characteristic
active site residues of the SDRs. A Cys often replaces
the usual Lys of the YXXXK active site motif, while the
upstream Ser is generally present and Arg replaces the
usual Asn. Atypical SDRs generally lack the catalytic
residues characteristic of the SDRs, and their
glycine-rich NAD(P)-binding motif is often different
from the forms normally seen in classical or extended
SDRs. Atypical SDRs include biliverdin IX beta
reductase (BVR-B,aka flavin reductase), NMRa (a
negative transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane
reductase, isoflavone reductases, and others. SDRs are
a functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they 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 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
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. In addition to the Rossmann fold
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids, 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 ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 296
Score = 34.1 bits (79), Expect = 0.011
Identities = 15/32 (46%), Positives = 21/32 (65%)
Query: 5 IVVTGASVGIGAAILRALAAKGHQVIGFARRA 36
IV+TG + IG A+ R L A GH+V+ +RR
Sbjct: 2 IVITGGTGFIGRALTRRLTAAGHEVVVLSRRP 33
>gnl|CDD|187578 cd05269, TMR_SDR_a, triphenylmethane reductase (TMR)-like
proteins, NMRa-like, atypical (a) SDRs. TMR is an
atypical NADP-binding protein of the SDR family. It
lacks the active site residues of the SDRs but has a
glycine rich NAD(P)-binding motif that matches the
extended SDRs. Proteins in this subgroup however, are
more similar in length to the classical SDRs. TMR was
identified as a reducer of triphenylmethane dyes,
important environmental pollutants. This subgroup also
includes Escherichia coli NADPH-dependent quinine
oxidoreductase (QOR2), which catalyzes two-electron
reduction of quinone; but is unlikely to play a major
role in protecting against quinone cytotoxicity.
Atypical SDRs are distinct from classical SDRs.
Atypical SDRs include biliverdin IX beta reductase
(BVR-B,aka flavin reductase), NMRa (a negative
transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane
reductase, isoflavone reductases, and others. SDRs are
a functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they 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 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
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. In addition to the Rossmann fold
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids, 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 ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 272
Score = 33.8 bits (78), Expect = 0.011
Identities = 13/33 (39%), Positives = 19/33 (57%)
Query: 5 IVVTGASVGIGAAILRALAAKGHQVIGFARRAE 37
I+VTGA+ +G A++ L AK V+ R E
Sbjct: 1 ILVTGATGKLGTAVVELLLAKVASVVALVRNPE 33
>gnl|CDD|187551 cd05240, UDP_G4E_3_SDR_e, UDP-glucose 4 epimerase (G4E), subgroup
3, extended (e) SDRs. Members of this bacterial
subgroup are identified as possible sugar epimerases,
such as UDP-glucose 4 epimerase. However, while the
NAD(P)-binding motif is fairly well conserved, not all
members retain the canonical active site tetrad of the
extended SDRs. UDP-glucose 4 epimerase (aka
UDP-galactose-4-epimerase), is a homodimeric extended
SDR. It catalyzes the NAD-dependent conversion of
UDP-galactose to UDP-glucose, the final step in Leloir
galactose synthesis. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids. Extended SDRs are a diverse collection
of proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they 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 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
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. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and
their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. 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 ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 306
Score = 33.9 bits (78), Expect = 0.012
Identities = 15/36 (41%), Positives = 19/36 (52%), Gaps = 2/36 (5%)
Query: 5 IVVTGASVGIGAAILRALAAK--GHQVIGFARRAEM 38
I+VTGA+ G+G + R LAA V G RR
Sbjct: 1 ILVTGAAGGLGRLLARRLAASPRVIGVDGLDRRRPP 36
>gnl|CDD|187579 cd05271, NDUFA9_like_SDR_a, NADH dehydrogenase (ubiquinone) 1
alpha subcomplex, subunit 9, 39 kDa, (NDUFA9) -like,
atypical (a) SDRs. This subgroup of extended SDR-like
proteins are atypical SDRs. They have a glycine-rich
NAD(P)-binding motif similar to the typical SDRs,
GXXGXXG, and have the YXXXK active site motif (though
not the other residues of the SDR tetrad). Members
identified include NDUFA9 (mitochondrial) and putative
nucleoside-diphosphate-sugar epimerase. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif
is often different from the forms normally seen in
classical or extended SDRs. Atypical SDRs include
biliverdin IX beta reductase (BVR-B,aka flavin
reductase), NMRa (a negative transcriptional regulator
of various fungi), progesterone 5-beta-reductase like
proteins, phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane
reductase, isoflavone reductases, and others. SDRs are
a functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they 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 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
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. In addition to the Rossmann fold
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids, 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 ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 273
Score = 33.8 bits (78), Expect = 0.014
Identities = 12/31 (38%), Positives = 17/31 (54%)
Query: 5 IVVTGASVGIGAAILRALAAKGHQVIGFARR 35
+ V GA+ IG ++ LA +G QVI R
Sbjct: 3 VTVFGATGFIGRYVVNRLAKRGSQVIVPYRC 33
>gnl|CDD|235736 PRK06196, PRK06196, oxidoreductase; Provisional.
Length = 315
Score = 33.9 bits (78), Expect = 0.014
Identities = 16/35 (45%), Positives = 19/35 (54%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAE 37
K +VTG G+G RALA G VI ARR +
Sbjct: 27 KTAIVTGGYSGLGLETTRALAQAGAHVIVPARRPD 61
>gnl|CDD|187606 cd05348, BphB-like_SDR_c,
cis-biphenyl-2,3-dihydrodiol-2,3-dehydrogenase
(BphB)-like, classical (c) SDRs.
cis-biphenyl-2,3-dihydrodiol-2,3-dehydrogenase (BphB) is
a classical SDR, it is of particular importance for its
role in the degradation of biphenyl/polychlorinated
biphenyls(PCBs); PCBs are a significant source of
environmental contamination. This subgroup also includes
Pseudomonas putida F1
cis-biphenyl-1,2-dihydrodiol-1,2-dehydrogenase (aka
cis-benzene glycol dehydrogenase, encoded by the bnzE
gene), which participates in benzene metabolism. In
addition it includes Pseudomonas sp. C18 putative
1,2-dihydroxy-1,2-dihydronaphthalene dehydrogenase (aka
dibenzothiophene dihydrodiol dehydrogenase, encoded by
the doxE gene) which participates in an upper
naphthalene catabolic pathway. 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 15-hydroxyprostaglandin
dehydrogenase (15-PGDH) numbering). In addition to the
Tyr and Lys, there is often an upstream Ser (Ser-138,
15-PGDH numbering) and/or an Asn (Asn-107, 15-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 ketoacyl
reductases 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 = 257
Score = 33.5 bits (77), Expect = 0.014
Identities = 25/116 (21%), Positives = 42/116 (36%), Gaps = 32/116 (27%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
++ ++TG G+G A++ A+G +V R AE + + F +V +G
Sbjct: 5 EVALITGGGSGLGRALVERFVAEGAKVAVLDRSAEKVAELRADFG--DAVVGVEG----- 57
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGV 118
DV A+ A +FG +D I NAG+
Sbjct: 58 -------------------------DVRSLADNERAVARCVERFGKLDCFIGNAGI 88
>gnl|CDD|216461 pfam01370, Epimerase, NAD dependent epimerase/dehydratase family.
This family of proteins utilise NAD as a cofactor. The
proteins in this family use nucleotide-sugar substrates
for a variety of chemical reactions.
Length = 233
Score = 33.4 bits (77), Expect = 0.014
Identities = 13/31 (41%), Positives = 21/31 (67%)
Query: 5 IVVTGASVGIGAAILRALAAKGHQVIGFARR 35
I+VTG + IG+ ++R L +G++VI RR
Sbjct: 1 ILVTGGTGFIGSHLVRRLLQEGYEVIVLGRR 31
>gnl|CDD|180300 PRK05875, PRK05875, short chain dehydrogenase; Provisional.
Length = 276
Score = 33.6 bits (77), Expect = 0.016
Identities = 29/124 (23%), Positives = 45/124 (36%), Gaps = 28/124 (22%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
+ +VTG GIG + L A G V+ R + +
Sbjct: 8 RTYLVTGGGSGIGKGVAAGLVAAGAAVMIVGRNPDKL----------------------- 44
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNE-F 121
A AE I+A+ V DVT + +V A D G + +++ AG +E
Sbjct: 45 -AAAAEEIEALK---GAGAVRYEPADVTDEDQVARAVDAATAWHGRLHGVVHCAGGSETI 100
Query: 122 APVT 125
P+T
Sbjct: 101 GPIT 104
>gnl|CDD|218026 pfam04321, RmlD_sub_bind, RmlD substrate binding domain.
L-rhamnose is a saccharide required for the virulence
of some bacteria. Its precursor, dTDP-L-rhamnose, is
synthesised by four different enzymes the final one of
which is RmlD. The RmlD substrate binding domain is
responsible for binding a sugar nucleotide.
Length = 284
Score = 33.4 bits (77), Expect = 0.017
Identities = 14/48 (29%), Positives = 25/48 (52%)
Query: 5 IVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDI 52
I+VTGA+ +G + R LA +G +V+ R + E++ A +
Sbjct: 1 ILVTGANGQLGRELTRLLAERGVEVVALDRPELDLTDPEAVAALVREA 48
>gnl|CDD|233570 TIGR01777, yfcH, TIGR01777 family protein. This model represents
a clade of proteins of unknown function including the
E. coli yfcH protein [Hypothetical proteins,
Conserved].
Length = 291
Score = 33.4 bits (77), Expect = 0.019
Identities = 11/33 (33%), Positives = 18/33 (54%)
Query: 5 IVVTGASVGIGAAILRALAAKGHQVIGFARRAE 37
I++TG + IG A+ + L +GH+V R
Sbjct: 1 ILITGGTGFIGRALTQRLTKRGHEVTILTRSPP 33
>gnl|CDD|187538 cd05227, AR_SDR_e, aldehyde reductase, extended (e) SDRs. This
subgroup contains aldehyde reductase of the extended
SDR-type and related proteins. Aldehyde reductase I
(aka carbonyl reductase) is an NADP-binding SDR; it has
an NADP-binding motif consensus that is slightly
different from the canonical SDR form and lacks the Asn
of the extended SDR active site tetrad. Aldehyde
reductase I catalyzes the NADP-dependent reduction of
ethyl 4-chloro-3-oxobutanoate to ethyl
(R)-4-chloro-3-hydroxybutanoate. Extended SDRs are
distinct from classical SDRs. In addition to the
Rossmann fold (alpha/beta folding pattern with a
central beta-sheet) core region typical of all SDRs,
extended SDRs have a less conserved C-terminal
extension of approximately 100 amino acids. Extended
SDRs are a diverse collection of proteins, and include
isomerases, epimerases, oxidoreductases, and lyases;
they typically have a TGXXGXXG cofactor binding motif.
SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
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
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, 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. Atypical
SDRs generally lack the catalytic residues
characteristic of the SDRs, and their glycine-rich
NAD(P)-binding motif is often different from the forms
normally seen in classical or extended SDRs. 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
ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding
motif.
Length = 301
Score = 33.0 bits (76), Expect = 0.021
Identities = 12/43 (27%), Positives = 21/43 (48%)
Query: 5 IVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFA 47
++VTGA+ I + I+ L G++V G R ++L
Sbjct: 2 VLVTGATGFIASHIVEQLLKAGYKVRGTVRSLSKSAKLKALLK 44
>gnl|CDD|187556 cd05245, SDR_a2, atypical (a) SDRs, subgroup 2. This subgroup
contains atypical SDRs, one member is identified as
Escherichia coli protein ybjT, function unknown.
Atypical SDRs are distinct from classical SDRs. Members
of this subgroup have a glycine-rich NAD(P)-binding
motif consensus that generally matches the extended
SDRs, TGXXGXXG, but lacks the characteristic active
site residues of the SDRs. This subgroup has basic
residues (HXXXR) in place of the active site motif
YXXXK, these may have a catalytic role. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif
is often different from the forms normally seen in
classical or extended SDRs. Atypical SDRs include
biliverdin IX beta reductase (BVR-B,aka flavin
reductase), NMRa (a negative transcriptional regulator
of various fungi), progesterone 5-beta-reductase like
proteins, phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane
reductase, isoflavone reductases, and others. SDRs are
a functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they 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 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
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. In addition to the Rossmann fold
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids, 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 ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 293
Score = 33.1 bits (76), Expect = 0.023
Identities = 12/33 (36%), Positives = 19/33 (57%)
Query: 5 IVVTGASVGIGAAILRALAAKGHQVIGFARRAE 37
++VTGA+ +G ++ L +GHQV R E
Sbjct: 1 VLVTGATGYVGGRLVPRLLQEGHQVRALVRSPE 33
>gnl|CDD|176248 cd08288, MDR_yhdh, Yhdh putative quinone oxidoreductases. Yhdh
putative quinone oxidoreductases (QOR). QOR catalyzes
the conversion of a quinone + NAD(P)H to a hydroquinone
+ NAD(P)+. Quinones are cyclic diones derived from
aromatic compounds. Membrane bound QOR actin the
respiratory chains of bacteria and mitochondria, while
soluble QOR acts to protect from toxic quinones (e.g.
DT-diaphorase) or as a soluble eye-lens protein in some
vertebrates (e.g. zeta-crystalin). QOR reduces quinones
through a semi-quinone intermediate via a
NAD(P)H-dependent single electron transfer. QOR is a
member of the medium chain dehydrogenase/reductase
family, but lacks the zinc-binding sites of the
prototypical alcohol dehydrogenases of this group.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which has a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES. These
proteins typically form dimers (typically higher plants,
mammals) or tetramers (yeast, bacteria), and have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site and a structural zinc in a lobe of
the catalytic domain. NAD(H) binding occurs in the
cleft between the catalytic and coenzyme-binding
domains at the active site, and coenzyme binding induces
a conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
In human ADH catalysis, the zinc ion helps coordinate
the alcohol, followed by deprotonation of a histidine,
the ribose of NAD, a serine, then the alcohol, which
allows the transfer of a hydride to NAD+, creating NADH
and a zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 324
Score = 32.9 bits (76), Expect = 0.025
Identities = 16/43 (37%), Positives = 26/43 (60%)
Query: 5 IVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFA 47
++VTGA+ G+G+ + LA G++V+ R E D+ SL A
Sbjct: 150 VLVTGAAGGVGSVAVALLARLGYEVVASTGRPEEADYLRSLGA 192
>gnl|CDD|225041 COG2130, COG2130, Putative NADP-dependent oxidoreductases [General
function prediction only].
Length = 340
Score = 32.7 bits (75), Expect = 0.031
Identities = 14/46 (30%), Positives = 24/46 (52%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAF 48
+ +VV+ A+ +G+ + + KG +V+G A AE DF F
Sbjct: 152 ETVVVSAAAGAVGSVVGQIAKLKGCRVVGIAGGAEKCDFLTEELGF 197
>gnl|CDD|212496 cd11730, Tthb094_like_SDR_c, Tthb094 and related proteins,
classical (c) SDRs. Tthb094 from Thermus Thermophilus
is a classical SDR which binds NADP. Members of this
subgroup contain the YXXXK active site characteristic
of SDRs. Also, an upstream Asn residue of the canonical
catalytic tetrad is partially conserved in this
subgroup of proteins of undetermined function. 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 ketoacyl
reductases 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 = 206
Score = 32.5 bits (74), Expect = 0.033
Identities = 13/30 (43%), Positives = 20/30 (66%)
Query: 7 VTGASVGIGAAILRALAAKGHQVIGFARRA 36
+ GA+ GIG A+ RALA +G +++ R A
Sbjct: 3 ILGATGGIGRALARALAGRGWRLLLSGRDA 32
>gnl|CDD|181605 PRK08993, PRK08993, 2-deoxy-D-gluconate 3-dehydrogenase; Validated.
Length = 253
Score = 32.5 bits (74), Expect = 0.039
Identities = 28/116 (24%), Positives = 47/116 (40%), Gaps = 31/116 (26%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K+ VVTG G+G + LA G ++G ++IV
Sbjct: 11 KVAVVTGCDTGLGQGMALGLAEAGCDIVG------------------INIVEPT------ 46
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGV 118
E + A+ + + SL D+ K + + +FGHID+++NNAG+
Sbjct: 47 --ETIEQVTALGR-----RFLSLTADLRKIDGIPALLERAVAEFGHIDILVNNAGL 95
>gnl|CDD|223677 COG0604, Qor, NADPH:quinone reductase and related Zn-dependent
oxidoreductases [Energy production and conversion /
General function prediction only].
Length = 326
Score = 32.3 bits (74), Expect = 0.040
Identities = 13/49 (26%), Positives = 26/49 (53%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVD 51
+ ++V GA+ G+G+A ++ A G V+ +E ++ + L A V
Sbjct: 144 ETVLVHGAAGGVGSAAIQLAKALGATVVAVVSSSEKLELLKELGADHVI 192
>gnl|CDD|171531 PRK12481, PRK12481, 2-deoxy-D-gluconate 3-dehydrogenase;
Provisional.
Length = 251
Score = 32.2 bits (73), Expect = 0.042
Identities = 23/116 (19%), Positives = 43/116 (37%), Gaps = 31/116 (26%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K+ ++TG + G+G + LA G ++G G
Sbjct: 9 KVAIITGCNTGLGQGMAIGLAKAGADIVGV------------------------GVA--E 42
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGV 118
++A+ + K H + D+ + ++ GHID++INNAG+
Sbjct: 43 APETQAQVEALGR-----KFHFITADLIQQKDIDSIVSQAVEVMGHIDILINNAGI 93
>gnl|CDD|163279 TIGR03466, HpnA, hopanoid-associated sugar epimerase. The
sequences in this family are members of the pfam01370
superfamily of NAD-dependent epimerases and
dehydratases typically acting on nucleotide-sugar
substrates. The genes of the family modeled here are
generally in the same locus with genes involved in the
biosynthesis and elaboration of hopene, the cyclization
product of the polyisoprenoid squalene. This gene and
its association with hopene biosynthesis in Zymomonas
mobilis has been noted in the literature where the gene
symbol hpnA was assigned. Hopanoids are known to be
components of the plasma membrane and to have polar
sugar head groups in Z. mobilis and other species.
Length = 328
Score = 32.3 bits (74), Expect = 0.046
Identities = 11/28 (39%), Positives = 18/28 (64%)
Query: 7 VTGASVGIGAAILRALAAKGHQVIGFAR 34
VTGA+ +G+A++R L +G +V R
Sbjct: 5 VTGATGFVGSAVVRLLLEQGEEVRVLVR 32
>gnl|CDD|227315 COG4982, COG4982, 3-oxoacyl-[acyl-carrier protein].
Length = 866
Score = 32.1 bits (73), Expect = 0.048
Identities = 21/49 (42%), Positives = 27/49 (55%), Gaps = 3/49 (6%)
Query: 2 SKIIVVTGASVG-IGAAILRALAAKGHQVIGFARR--AEMIDFAESLFA 47
K+ +VTGAS G I AA++ L A G VI R E +F SL+A
Sbjct: 396 DKVALVTGASKGSIAAAVVARLLAGGATVIATTSRLSEERTEFYRSLYA 444
>gnl|CDD|236389 PRK09134, PRK09134, short chain dehydrogenase; Provisional.
Length = 258
Score = 31.8 bits (73), Expect = 0.059
Identities = 34/119 (28%), Positives = 50/119 (42%), Gaps = 28/119 (23%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
+ +VTGA+ IG AI LAA G V R+ D AE+L + A G
Sbjct: 10 RAALVTGAARRIGRAIALDLAAHGFDVAVHYNRSR--DEAEAL----AAEIRALG----- 58
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNEF 121
RRA +L+ D+ +AEV + G I +++NNA + E+
Sbjct: 59 --RRA---------------VALQADLADEAEVRALVARASAALGPITLLVNNASLFEY 100
>gnl|CDD|187665 cd09805, type2_17beta_HSD-like_SDR_c, human 17beta-hydroxysteroid
dehydrogenase type 2 (type 2 17beta-HSD)-like, classical
(c) SDRs. 17beta-hydroxysteroid dehydrogenases are a
group of isozymes that catalyze activation and
inactivation of estrogen and androgens. This
classical-SDR subgroup includes the human proteins: type
2 17beta-HSD, type 6 17beta-HSD, type 2 11beta-HSD,
dehydrogenase/reductase SDR family member 9,
short-chain dehydrogenase/reductase family 9C member 7,
3-hydroxybutyrate dehydrogenase type 1, and retinol
dehydrogenase 5. 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
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-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 ketoacyl reductases 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 = 281
Score = 31.9 bits (73), Expect = 0.064
Identities = 13/41 (31%), Positives = 23/41 (56%), Gaps = 2/41 (4%)
Query: 83 HSLKVDVTKDAEVVEAFDWINNKFGHIDV--MINNAGVNEF 121
+L++DVTK ++ A W+ G + ++NNAG+ F
Sbjct: 51 RTLQLDVTKPEQIKRAAQWVKEHVGEKGLWGLVNNAGILGF 91
>gnl|CDD|187576 cd05266, SDR_a4, atypical (a) SDRs, subgroup 4. Atypical SDRs in
this subgroup are poorly defined, one member is
identified as a putative NAD-dependent
epimerase/dehydratase. Atypical SDRs are distinct from
classical SDRs. Members of this subgroup have a
glycine-rich NAD(P)-binding motif that is related to,
but is different from, the archetypical SDRs, GXGXXG.
This subgroup also lacks most of the characteristic
active site residues of the SDRs; however, the upstream
Ser is present at the usual place, and some potential
catalytic residues are present in place of the usual
YXXXK active site motif. Atypical SDRs generally lack
the catalytic residues characteristic of the SDRs, and
their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Atypical SDRs include biliverdin IX beta
reductase (BVR-B,aka flavin reductase), NMRa (a
negative transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane
reductase, isoflavone reductases, and others. SDRs are
a functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they 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 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
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. In addition to the Rossmann fold
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids, 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 ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 251
Score = 31.5 bits (72), Expect = 0.065
Identities = 11/44 (25%), Positives = 17/44 (38%), Gaps = 2/44 (4%)
Query: 14 IGAAILRALAAKGHQVIGFARRAEMIDF--AESLFAFFVDIVAA 55
+G + R L A+G QV G R E + + D+
Sbjct: 9 LGQRLARQLLAQGWQVTGTTRSPEKLAADRPAGVTPLAADLTQP 52
>gnl|CDD|212495 cd09807, retinol-DH_like_SDR_c, retinol dehydrogenases
(retinol-DHs), classical (c) SDRs. Classical SDR-like
subgroup containing retinol-DHs and related proteins.
Retinol is processed by a medium chain alcohol
dehydrogenase followed by retinol-DHs. Proteins in this
subfamily share the glycine-rich NAD-binding motif of
the classical SDRs, have a partial match to the
canonical active site tetrad, but lack the typical
active site Ser. This subgroup includes the human
proteins: retinol dehydrogenase -12, -13 ,and -14. 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
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-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 ketoacyl reductases 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 = 274
Score = 31.7 bits (72), Expect = 0.072
Identities = 13/28 (46%), Positives = 19/28 (67%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVI 30
K +++TGA+ GIG R LA +G +VI
Sbjct: 2 KTVIITGANTGIGKETARELARRGARVI 29
>gnl|CDD|187555 cd05244, BVR-B_like_SDR_a, biliverdin IX beta reductase (BVR-B,
aka flavin reductase)-like proteins; atypical (a) SDRs.
Human BVR-B catalyzes pyridine nucleotide-dependent
production of bilirubin-IX beta during fetal
development; in the adult BVR-B has flavin and ferric
reductase activities. Human BVR-B catalyzes the
reduction of FMN, FAD, and riboflavin. Recognition of
flavin occurs mostly by hydrophobic interactions,
accounting for the broad substrate specificity.
Atypical SDRs are distinct from classical SDRs. BVR-B
does not share the key catalytic triad, or conserved
tyrosine typical of SDRs. The glycine-rich NADP-binding
motif of BVR-B is GXXGXXG, which is similar but not
identical to the pattern seen in extended SDRs.
Atypical SDRs generally lack the catalytic residues
characteristic of the SDRs, and their glycine-rich
NAD(P)-binding motif is often different from the forms
normally seen in classical or extended SDRs. Atypical
SDRs include biliverdin IX beta reductase (BVR-B,aka
flavin reductase), NMRa (a negative transcriptional
regulator of various fungi), progesterone
5-beta-reductase like proteins, phenylcoumaran benzylic
ether and pinoresinol-lariciresinol reductases,
phenylpropene synthases, eugenol synthase,
triphenylmethane reductase, isoflavone reductases, and
others. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
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
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, 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. In
addition to the Rossmann fold core region typical of
all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids,
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 ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 207
Score = 31.4 bits (72), Expect = 0.075
Identities = 12/33 (36%), Positives = 18/33 (54%)
Query: 5 IVVTGASVGIGAAILRALAAKGHQVIGFARRAE 37
I + GA+ G+AI+R A+GH+V R
Sbjct: 2 IAIIGATGRTGSAIVREALARGHEVTALVRDPA 34
>gnl|CDD|187621 cd05363, SDH_SDR_c, Sorbitol dehydrogenase (SDH), classical (c)
SDR. This bacterial subgroup includes Rhodobacter
sphaeroides SDH, and other SDHs. SDH preferentially
interconverts D-sorbitol (D-glucitol) and D-fructose,
but also interconverts L-iditol/L-sorbose and
galactitol/D-tagatose. SDH is NAD-dependent and is a
dimeric member of the SDR family. 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 have a
3-glycine N-terminal NAD(P)(H)-binding pattern
(typically, TGxxxGxG in classical SDRs and TGxxGxxG in
extended SDRs), while substrate binding is in the
C-terminal region. A critical catalytic Tyr residue
(Tyr-151, human 15-hydroxyprostaglandin dehydrogenase
(15-PGDH) numbering), is often found in a conserved
YXXXK pattern. In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) or additional
Ser, contributing to the active site. Substrates for
these enzymes include sugars, steroids, alcohols, and
aromatic compounds. The standard reaction mechanism is a
proton relay involving the conserved Tyr and Lys, as
well as Asn (or Ser). Some SDR family members, including
17 beta-hydroxysteroid dehydrogenase contain an
additional helix-turn-helix motif that is not generally
found among SDRs.
Length = 254
Score = 31.4 bits (71), Expect = 0.088
Identities = 12/41 (29%), Positives = 26/41 (63%)
Query: 84 SLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNEFAPV 124
++ +DVT A + + +++G ID+++NNA + + AP+
Sbjct: 53 AISLDVTDQASIDRCVAALVDRWGSIDILVNNAALFDLAPI 93
>gnl|CDD|234026 TIGR02823, oxido_YhdH, putative quinone oxidoreductase, YhdH/YhfP
family. This model represents a subfamily of pfam00107
as defined by Pfam, a superfamily in which some members
are zinc-binding medium-chain alcohol dehydrogenases
while others are quinone oxidoreductases with no bound
zinc. This subfamily includes proteins studied
crystallographically for insight into function: YhdH
from Escherichia coli and YhfP from Bacillus subtilis.
Members bind NADPH or NAD, but not zinc [Unknown
function, Enzymes of unknown specificity].
Length = 323
Score = 31.4 bits (72), Expect = 0.091
Identities = 14/43 (32%), Positives = 27/43 (62%)
Query: 5 IVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFA 47
++VTGA+ G+G+ + L+ G++V+ +AE D+ + L A
Sbjct: 149 VLVTGATGGVGSLAVAILSKLGYEVVASTGKAEEEDYLKELGA 191
>gnl|CDD|187543 cd05232, UDP_G4E_4_SDR_e, UDP-glucose 4 epimerase, subgroup 4,
extended (e) SDRs. UDP-glucose 4 epimerase (aka
UDP-galactose-4-epimerase), is a homodimeric extended
SDR. It catalyzes the NAD-dependent conversion of
UDP-galactose to UDP-glucose, the final step in Leloir
galactose synthesis. This subgroup is comprised of
bacterial proteins, and includes the Staphylococcus
aureus capsular polysaccharide Cap5N, which may have a
role in the synthesis of UDP-N-acetyl-d-fucosamine.
This subgroup has the characteristic active site tetrad
and NAD-binding motif of the extended SDRs. Extended
SDRs are distinct from classical SDRs. In addition to
the Rossmann fold (alpha/beta folding pattern with a
central beta-sheet) core region typical of all SDRs,
extended SDRs have a less conserved C-terminal
extension of approximately 100 amino acids. Extended
SDRs are a diverse collection of proteins, and include
isomerases, epimerases, oxidoreductases, and lyases;
they typically have a TGXXGXXG cofactor binding motif.
SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
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
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, 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. Atypical
SDRs generally lack the catalytic residues
characteristic of the SDRs, and their glycine-rich
NAD(P)-binding motif is often different from the forms
normally seen in classical or extended SDRs. 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
ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding
motif.
Length = 303
Score = 31.2 bits (71), Expect = 0.094
Identities = 16/53 (30%), Positives = 27/53 (50%), Gaps = 1/53 (1%)
Query: 5 IVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKG 57
++VTGA+ IG A++ L ++G +V R AE + + L DI +
Sbjct: 2 VLVTGANGFIGRALVDKLLSRGEEVRIAVRNAENAEPSVVLAE-LPDIDSFTD 53
>gnl|CDD|187633 cd08928, KR_fFAS_like_SDR_c_like, ketoacyl reductase (KR) domain
of fungal-type fatty acid synthase (fFAS)-like,
classical (c)-like SDRs. KR domain of FAS, including
the fungal-type multidomain FAS alpha chain, and the
single domain daunorubicin C-13 ketoreductase.
Fungal-type FAS is a heterododecameric FAS composed of
alpha and beta multifunctional polypeptide chains. The
KR, an SDR family member is located centrally in the
alpha chain. KR catalyzes the NADP-dependent reduction
of ketoacyl-ACP to hydroxyacyl-ACP. KR shares the
critical active site Tyr of the classical SDR and has
partial identity of the active site tetrad, but the
upstream Asn is replaced in KR by Met. As in other
SDRs, there is a glycine rich NAD(P)-binding motif, but
the pattern found in KR does not match the classical
SDRs, and is not strictly conserved within this group.
Daunorubicin is a clinically important therapeutic
compound used in some cancer treatments. Single domain
daunorubicin C-13 ketoreductase is member of the
classical SDR family with a canonical glycine-rich
NAD(P)-binding motif, but lacking a complete match to
the active site tetrad characteristic of this group.
The critical Tyr, plus the Lys and upstream Asn are
present, but the catalytic Ser is replaced, generally
by Gln. 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 = 248
Score = 31.1 bits (70), Expect = 0.099
Identities = 18/54 (33%), Positives = 28/54 (51%), Gaps = 6/54 (11%)
Query: 5 IVVTGASVG-IGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKG 57
+++TGA G IGA +L+ L G +V R F+ + ++ DI AA G
Sbjct: 1 VLITGAGDGSIGAEVLQGLLNGGAKVYVTTSR-----FSRQVTKYYQDIYAACG 49
>gnl|CDD|234629 PRK00094, gpsA, NAD(P)H-dependent glycerol-3-phosphate
dehydrogenase; Validated.
Length = 325
Score = 31.2 bits (72), Expect = 0.11
Identities = 17/56 (30%), Positives = 23/56 (41%), Gaps = 8/56 (14%)
Query: 54 AAKGHQVIGFARRAEMIDAMA--KEN----PDWKVHSLKVDVTKD-AEVVEAFDWI 102
A GH V +AR E + +EN P K+ + T D AE + D I
Sbjct: 21 ARNGHDVTLWARDPEQAAEINADRENPRYLPGIKLPD-NLRATTDLAEALADADLI 75
Score = 29.3 bits (67), Expect = 0.42
Identities = 16/40 (40%), Positives = 19/40 (47%), Gaps = 2/40 (5%)
Query: 1 MSKIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMID 40
M KI V+ S G AI+ LA GH V +AR E
Sbjct: 1 MMKIAVLGAGSWGTALAIV--LARNGHDVTLWARDPEQAA 38
>gnl|CDD|235816 PRK06500, PRK06500, short chain dehydrogenase; Provisional.
Length = 249
Score = 31.1 bits (71), Expect = 0.11
Identities = 29/124 (23%), Positives = 47/124 (37%), Gaps = 32/124 (25%)
Query: 1 MSKIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQV 60
K ++TG + GIG R A+G +V R ++ A A G
Sbjct: 5 QGKTALITGGTSGIGLETARQFLAEGARVAITGRDPASLEAAR----------AELGESA 54
Query: 61 IGFARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNE 120
+ RA+ D A++ + +A + FG +D + NAGV +
Sbjct: 55 L--VIRADAGDVAAQK-----------------ALAQA---LAEAFGRLDAVFINAGVAK 92
Query: 121 FAPV 124
FAP+
Sbjct: 93 FAPL 96
>gnl|CDD|187564 cd05254, dTDP_HR_like_SDR_e, dTDP-6-deoxy-L-lyxo-4-hexulose
reductase and related proteins, extended (e) SDRs.
dTDP-6-deoxy-L-lyxo-4-hexulose reductase, an extended
SDR, synthesizes dTDP-L-rhamnose from
alpha-D-glucose-1-phosphate, providing the precursor
of L-rhamnose, an essential cell wall component of many
pathogenic bacteria. This subgroup has the
characteristic active site tetrad and NADP-binding
motif. This subgroup also contains human MAT2B, the
regulatory subunit of methionine adenosyltransferase
(MAT); MAT catalyzes S-adenosylmethionine synthesis.
The human gene encoding MAT2B encodes two major
splicing variants which are induced in human cell liver
cancer and regulate HuR, an mRNA-binding protein which
stabilizes the mRNA of several cyclins, to affect cell
proliferation. Both MAT2B variants include this
extended SDR domain. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids. Extended SDRs are a diverse collection
of proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they 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 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
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. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and
their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. 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 ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 280
Score = 31.1 bits (71), Expect = 0.12
Identities = 13/31 (41%), Positives = 22/31 (70%)
Query: 5 IVVTGASVGIGAAILRALAAKGHQVIGFARR 35
I++TGA+ +G A++R L +G++VIG R
Sbjct: 2 ILITGATGMLGRALVRLLKERGYEVIGTGRS 32
>gnl|CDD|236308 PRK08594, PRK08594, enoyl-(acyl carrier protein) reductase;
Provisional.
Length = 257
Score = 30.9 bits (70), Expect = 0.12
Identities = 12/43 (27%), Positives = 18/43 (41%), Gaps = 4/43 (9%)
Query: 68 EMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHID 110
E+ D + + L DVT D E+ F+ I + G I
Sbjct: 51 ELADTLEGQES----LLLPCDVTSDEEITACFETIKEEVGVIH 89
>gnl|CDD|130890 TIGR01831, fabG_rel, 3-oxoacyl-(acyl-carrier-protein) reductase,
putative. This model represents a small, very well
conserved family of proteins closely related to the
FabG family, TIGR01830, and possibly equal in function.
In all completed genomes with a member of this family,
a FabG in TIGR01830 is also found [Fatty acid and
phospholipid metabolism, Biosynthesis].
Length = 239
Score = 31.0 bits (70), Expect = 0.12
Identities = 14/25 (56%), Positives = 18/25 (72%)
Query: 5 IVVTGASVGIGAAILRALAAKGHQV 29
++VTGAS GIG AI LAA G ++
Sbjct: 1 VLVTGASRGIGRAIANRLAADGFEI 25
>gnl|CDD|235608 PRK05786, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 238
Score = 30.9 bits (70), Expect = 0.13
Identities = 10/35 (28%), Positives = 16/35 (45%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAE 37
K + + G S G+G A+ +G QV +R
Sbjct: 6 KKVAIIGVSEGLGYAVAYFALKEGAQVCINSRNEN 40
>gnl|CDD|235630 PRK05865, PRK05865, hypothetical protein; Provisional.
Length = 854
Score = 30.8 bits (69), Expect = 0.15
Identities = 14/31 (45%), Positives = 20/31 (64%)
Query: 5 IVVTGASVGIGAAILRALAAKGHQVIGFARR 35
I VTGAS +G + L ++GH+V+G AR
Sbjct: 3 IAVTGASGVLGRGLTARLLSQGHEVVGIARH 33
>gnl|CDD|187636 cd08931, SDR_c9, classical (c) SDR, subgroup 9. This subgroup has
the canonical active site tetrad and NAD-binding motif
of the classical SDRs. 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 15-hydroxyprostaglandin
dehydrogenase (15-PGDH) numbering). In addition to the
Tyr and Lys, there is often an upstream Ser (Ser-138,
15-PGDH numbering) and/or an Asn (Asn-107, 15-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 ketoacyl
reductases 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 = 227
Score = 30.5 bits (69), Expect = 0.15
Identities = 32/122 (26%), Positives = 42/122 (34%), Gaps = 32/122 (26%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K I +TGA+ GIG A G V + + G
Sbjct: 1 KAIFITGAASGIGRETALLFARNGWFVGLYDIDED------------------------G 36
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAF-DWINNKFGHIDVMINNAGVNEF 121
A A + A EN V + +DVT A A D+ G +D + NNAGV
Sbjct: 37 LAALAAELGA---EN----VVAGALDVTDRAAWAAALADFAAATGGRLDALFNNAGVGRG 89
Query: 122 AP 123
P
Sbjct: 90 GP 91
>gnl|CDD|225447 COG2894, MinD, Septum formation inhibitor-activating ATPase [Cell
division and chromosome partitioning].
Length = 272
Score = 30.7 bits (70), Expect = 0.15
Identities = 18/46 (39%), Positives = 24/46 (52%), Gaps = 12/46 (26%)
Query: 1 MSKIIVVTGASVGIG-----AAILRALAAKGHQVIGFARRAEMIDF 41
M++IIVVT G+G A I ALA G +V+ +IDF
Sbjct: 1 MARIIVVTSGKGGVGKTTTTANIGTALAQLGKKVV-------LIDF 39
>gnl|CDD|176235 cd08274, MDR9, Medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family.
This group is a member of the medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, but lacks the zinc-binding
sites of the zinc-dependent alcohol dehydrogenases. The
medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P)-binding Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 350
Score = 30.7 bits (70), Expect = 0.16
Identities = 21/72 (29%), Positives = 38/72 (52%), Gaps = 6/72 (8%)
Query: 5 IVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIGFA 64
++VTGAS G+G+A+++ +G VI A A+ E++ A D V + ++ A
Sbjct: 181 VLVTGASGGVGSALVQLAKRRGAIVIAVAGAAK----EEAVRALGADTVILRDAPLLADA 236
Query: 65 RRA--EMIDAMA 74
+ E +D +A
Sbjct: 237 KALGGEPVDVVA 248
>gnl|CDD|176220 cd08259, Zn_ADH5, Alcohol dehydrogenases of the MDR family.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. This group contains proteins that
share the characteristic catalytic and structural
zinc-binding sites of the zinc-dependent alcohol
dehydrogenase family. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which have a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES. These
proteins typically form dimers (typically higher plants,
mammals) or tetramers (yeast, bacteria), and have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site and a structural zinc in a lobe of
the catalytic domain. NAD(H)-binding occurs in the cleft
between the catalytic and coenzyme-binding domains at
the active site, and coenzyme binding induces a
conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
In human ADH catalysis, the zinc ion helps coordinate
the alcohol, followed by deprotonation of a histidine
(His-51), the ribose of NAD, a serine (Ser-48), then the
alcohol, which allows the transfer of a hydride to NAD+,
creating NADH and a zinc-bound aldehyde or ketone. In
yeast and some bacteria, the active site zinc binds an
aldehyde, polarizing it, and leading to the reverse
reaction.
Length = 332
Score = 30.4 bits (69), Expect = 0.19
Identities = 14/45 (31%), Positives = 22/45 (48%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFA 47
++VTGA G+G ++ A G +VI R E + + L A
Sbjct: 164 DTVLVTGAGGGVGIHAIQLAKALGARVIAVTRSPEKLKILKELGA 208
>gnl|CDD|187535 cd02266, SDR, Short-chain dehydrogenases/reductases (SDR). 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 (KR) 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 = 186
Score = 30.2 bits (68), Expect = 0.19
Identities = 13/22 (59%), Positives = 17/22 (77%)
Query: 5 IVVTGASVGIGAAILRALAAKG 26
++VTG S GIG AI R LA++G
Sbjct: 1 VLVTGGSGGIGGAIARWLASRG 22
>gnl|CDD|234625 PRK00090, bioD, dithiobiotin synthetase; Reviewed.
Length = 222
Score = 30.2 bits (69), Expect = 0.19
Identities = 11/34 (32%), Positives = 17/34 (50%), Gaps = 5/34 (14%)
Query: 4 IIVVTGASVGIG-----AAILRALAAKGHQVIGF 32
+ VTG +G AA+ +AL G+ V G+
Sbjct: 1 RLFVTGTDTDVGKTVVTAALAQALREAGYSVAGY 34
>gnl|CDD|236402 PRK09191, PRK09191, two-component response regulator; Provisional.
Length = 261
Score = 30.2 bits (69), Expect = 0.19
Identities = 12/30 (40%), Positives = 16/30 (53%), Gaps = 1/30 (3%)
Query: 51 DIVAAKGHQVIGFAR-RAEMIDAMAKENPD 79
+V + GH+V G AR RAE + K P
Sbjct: 155 QLVESLGHRVTGIARTRAEAVALAKKTRPG 184
>gnl|CDD|236016 PRK07424, PRK07424, bifunctional sterol desaturase/short chain
dehydrogenase; Validated.
Length = 406
Score = 30.4 bits (69), Expect = 0.22
Identities = 13/37 (35%), Positives = 22/37 (59%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMI 39
K + VTGAS +G A+L+ L +G +V+ ++ I
Sbjct: 179 KTVAVTGASGTLGQALLKELHQQGAKVVALTSNSDKI 215
>gnl|CDD|169390 PRK08340, PRK08340, glucose-1-dehydrogenase; Provisional.
Length = 259
Score = 30.2 bits (68), Expect = 0.23
Identities = 14/39 (35%), Positives = 23/39 (58%)
Query: 5 IVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAE 43
++VT +S GIG + R L KG +V+ +R E ++ A
Sbjct: 3 VLVTASSRGIGFNVARELLKKGARVVISSRNEENLEKAL 41
>gnl|CDD|187611 cd05353, hydroxyacyl-CoA-like_DH_SDR_c-like, (3R)-hydroxyacyl-CoA
dehydrogenase-like, classical(c)-like SDRs. Beta
oxidation of fatty acids in eukaryotes occurs by a
four-reaction cycle, that may take place in mitochondria
or in peroxisomes. (3R)-hydroxyacyl-CoA dehydrogenase is
part of rat peroxisomal multifunctional MFE-2, it is a
member of the NAD-dependent SDRs, but contains an
additional small C-terminal domain that completes the
active site pocket and participates in dimerization. The
atypical, additional C-terminal extension allows for
more extensive dimerization contact than other SDRs.
MFE-2 catalyzes the second and third reactions of the
peroxisomal beta oxidation cycle. Proteins in this
subgroup have a typical catalytic triad, but have a His
in place of the usual upstream Asn. This subgroup also
contains members identified as 17-beta-hydroxysteroid
dehydrogenases, including human peroxisomal
17-beta-hydroxysteroid dehydrogenase type 4 (17beta-HSD
type 4, aka MFE-2, encoded by HSD17B4 gene) which is
involved in fatty acid beta-oxidation and steroid
metabolism. This subgroup also includes two SDR domains
of the Neurospora crassa and Saccharomyces cerevisiae
multifunctional beta-oxidation protein (MFP, aka Fox2).
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 have a 3-glycine N-terminal NAD(P)(H)-binding
pattern (typically, TGxxxGxG in classical SDRs and
TGxxGxxG in extended SDRs), while substrate binding is
in the C-terminal region. A critical catalytic Tyr
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase (15-PGDH) numbering), is often found in a
conserved YXXXK pattern. In addition to the Tyr and Lys,
there is often an upstream Ser (Ser-138, 15-PGDH
numbering) and/or an Asn (Asn-107, 15-PGDH numbering) or
additional Ser, contributing to the active site.
Substrates for these enzymes include sugars, steroids,
alcohols, and aromatic compounds. The standard reaction
mechanism is a proton relay involving the conserved Tyr
and Lys, as well as Asn (or Ser). Some SDR family
members, including 17 beta-hydroxysteroid dehydrogenase
contain an additional helix-turn-helix motif that is not
generally found among SDRs.
Length = 250
Score = 30.0 bits (68), Expect = 0.23
Identities = 32/123 (26%), Positives = 51/123 (41%), Gaps = 37/123 (30%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQV----IGFARRAEMIDFAESLFAFFV--DIVAAK 56
++++VTGA G+G A A A +G +V +G R+ S A V +I AA
Sbjct: 6 RVVLVTGAGGGLGRAYALAFAERGAKVVVNDLGGDRKG---SGKSSSAADKVVDEIKAAG 62
Query: 57 GHQVIGFARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVE-AFDWINNKFGHIDVMINN 115
G V + V ++V+ A D FG +D+++NN
Sbjct: 63 GKAVANYD-----------------------SVEDGEKIVKTAID----AFGRVDILVNN 95
Query: 116 AGV 118
AG+
Sbjct: 96 AGI 98
>gnl|CDD|187563 cd05253, UDP_GE_SDE_e, UDP glucuronic acid epimerase, extended
(e) SDRs. This subgroup contains UDP-D-glucuronic acid
4-epimerase, an extended SDR, which catalyzes the
conversion of UDP-alpha-D-glucuronic acid to
UDP-alpha-D-galacturonic acid. This group has the SDR's
canonical catalytic tetrad and the TGxxGxxG NAD-binding
motif of the extended SDRs. Extended SDRs are distinct
from classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids. Extended SDRs are a diverse collection
of proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they 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 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
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. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and
their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. 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 ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 332
Score = 30.0 bits (68), Expect = 0.24
Identities = 11/28 (39%), Positives = 18/28 (64%)
Query: 5 IVVTGASVGIGAAILRALAAKGHQVIGF 32
I+VTGA+ IG + + L +G +V+G
Sbjct: 3 ILVTGAAGFIGFHVAKRLLERGDEVVGI 30
>gnl|CDD|176249 cd08289, MDR_yhfp_like, Yhfp putative quinone oxidoreductases.
yhfp putative quinone oxidoreductases (QOR). QOR
catalyzes the conversion of a quinone + NAD(P)H to a
hydroquinone + NAD(P)+. Quinones are cyclic diones
derived from aromatic compounds. Membrane bound QOR
actin the respiratory chains of bacteria and
mitochondria, while soluble QOR acts to protect from
toxic quinones (e.g. DT-diaphorase) or as a soluble
eye-lens protein in some vertebrates (e.g.
zeta-crystalin). QOR reduces quinones through a
semi-quinone intermediate via a NAD(P)H-dependent single
electron transfer. QOR is a member of the medium chain
dehydrogenase/reductase family, but lacks the
zinc-binding sites of the prototypical alcohol
dehydrogenases of this group. NAD(P)(H)-dependent
oxidoreductases are the major enzymes in the
interconversion of alcohols and aldehydes, or ketones.
Alcohol dehydrogenase in the liver converts ethanol and
NAD+ to acetaldehyde and NADH, while in yeast and some
other microorganisms ADH catalyzes the conversion
acetaldehyde to ethanol in alcoholic fermentation. ADH
is a member of the medium chain alcohol dehydrogenase
family (MDR), which has a NAD(P)(H)-binding domain in a
Rossmann fold of a beta-alpha form. The NAD(H)-binding
region is comprised of 2 structurally similar halves,
each of which contacts a mononucleotide. A GxGxxG motif
after the first mononucleotide contact half allows the
close contact of the coenzyme with the ADH backbone.
The N-terminal catalytic domain has a distant homology
to GroES. These proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and have 2 tightly bound zinc atoms per
subunit, a catalytic zinc at the active site, and a
structural zinc in a lobe of the catalytic domain.
NAD(H) binding occurs in the cleft between the catalytic
and coenzyme-binding domains at the active site, and
coenzyme binding induces a conformational closing of
this cleft. Coenzyme binding typically precedes and
contributes to substrate binding. In human ADH
catalysis, the zinc ion helps coordinate the alcohol,
followed by deprotonation of a histidine, the ribose of
NAD, a serine, then the alcohol, which allows the
transfer of a hydride to NAD+, creating NADH and a
zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 326
Score = 30.0 bits (68), Expect = 0.25
Identities = 14/43 (32%), Positives = 27/43 (62%)
Query: 5 IVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFA 47
++VTGA+ G+G+ + LA G++V+ +A+ D+ + L A
Sbjct: 150 VLVTGATGGVGSLAVSILAKLGYEVVASTGKADAADYLKKLGA 192
>gnl|CDD|187613 cd05355, SDR_c1, classical (c) SDR, subgroup 1. These proteins are
members of the classical SDR family, with a canonical
active site tetrad and a typical Gly-rich NAD-binding
motif. 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
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-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 ketoacyl reductases 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 = 270
Score = 30.0 bits (68), Expect = 0.29
Identities = 27/116 (23%), Positives = 46/116 (39%), Gaps = 29/116 (25%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
K ++TG GIG RA+A I FAR E D A I +
Sbjct: 27 KKALITGGDSGIG----RAVA------IAFAR--EGADVA---------INYLPEEE--D 63
Query: 63 FARR-AEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAG 117
A ++I+ + K + D+ ++ + + +FG +D+++NNA
Sbjct: 64 DAEETKKLIEEEGR-----KCLLIPGDLGDESFCRDLVKEVVKEFGKLDILVNNAA 114
>gnl|CDD|180983 PRK07453, PRK07453, protochlorophyllide oxidoreductase;
Validated.
Length = 322
Score = 30.0 bits (68), Expect = 0.31
Identities = 17/44 (38%), Positives = 25/44 (56%), Gaps = 5/44 (11%)
Query: 5 IVVTGASVGIGAAILRALAAKGHQVIGFAR---RAEMIDFAESL 45
+++TGAS G+G +ALA +G VI R +AE A+ L
Sbjct: 9 VIITGASSGVGLYAAKALAKRGWHVIMACRNLKKAEAA--AQEL 50
>gnl|CDD|187670 cd09810, LPOR_like_SDR_c_like, light-dependent
protochlorophyllide reductase (LPOR)-like, classical
(c)-like SDRs. Classical SDR-like subgroup containing
LPOR and related proteins. Protochlorophyllide
(Pchlide) reductases act in chlorophyll biosynthesis.
There are distinct enzymes that catalyze Pchlide
reduction in light or dark conditions. Light-dependent
reduction is via an NADP-dependent SDR, LPOR. Proteins
in this subfamily share the glycine-rich NAD-binding
motif of the classical SDRs, have a partial match to
the canonical active site tetrad, but lack the typical
active site Ser. 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
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-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 ketoacyl reductases 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 = 311
Score = 29.8 bits (67), Expect = 0.34
Identities = 12/24 (50%), Positives = 17/24 (70%)
Query: 3 KIIVVTGASVGIGAAILRALAAKG 26
+V+TGAS G+G A +ALA +G
Sbjct: 2 GTVVITGASSGLGLAAAKALARRG 25
>gnl|CDD|183714 PRK12742, PRK12742, oxidoreductase; Provisional.
Length = 237
Score = 29.3 bits (66), Expect = 0.38
Identities = 23/74 (31%), Positives = 31/74 (41%), Gaps = 6/74 (8%)
Query: 2 SKIIVVTGASVGIGAAILRALAAKGHQVI----GFARRAEMIDFAESLFAFFVDIVAAKG 57
K ++V G S GIGAAI+R G V G AE + A D +A
Sbjct: 6 GKKVLVLGGSRGIGAAIVRRFVTDGANVRFTYAGSKDAAERLAQETGATAVQTD--SADR 63
Query: 58 HQVIGFARRAEMID 71
VI R++ +D
Sbjct: 64 DAVIDVVRKSGALD 77
>gnl|CDD|236057 PRK07578, PRK07578, short chain dehydrogenase; Provisional.
Length = 199
Score = 29.0 bits (66), Expect = 0.46
Identities = 29/81 (35%), Positives = 43/81 (53%), Gaps = 16/81 (19%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFAR-----RAEMIDFAESLFAFF-----VD- 51
KI+V+ GAS IG A++ L+ + H+VI R + ++ D S+ A F VD
Sbjct: 2 KILVI-GASGTIGRAVVAELSKR-HEVITAGRSSGDVQVDITD-PASIRALFEKVGKVDA 58
Query: 52 IVAAKGHQVIGFARRAEMIDA 72
+V+A G + FA AEM D
Sbjct: 59 VVSAAG--KVHFAPLAEMTDE 77
>gnl|CDD|187550 cd05239, GDP_FS_SDR_e, GDP-fucose synthetase, extended (e) SDRs.
GDP-fucose synthetase (aka 3, 5-epimerase-4-reductase)
acts in the NADP-dependent synthesis of GDP-fucose from
GDP-mannose. Two activities have been proposed for the
same active site: epimerization and reduction. Proteins
in this subgroup are extended SDRs, which have a
characteristic active site tetrad and an NADP-binding
motif, [AT]GXXGXXG, that is a close match to the
archetypical form. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids. Extended SDRs are a diverse collection
of proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they 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 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
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. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and
their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. 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 ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 300
Score = 29.1 bits (66), Expect = 0.46
Identities = 18/47 (38%), Positives = 29/47 (61%), Gaps = 3/47 (6%)
Query: 5 IVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDF--AESLFAFF 49
I+VTG +G+AI+R LA +G++ + F E+ D E++ AFF
Sbjct: 2 ILVTGHRGLVGSAIVRVLARRGYENVVFRTSKEL-DLTDQEAVRAFF 47
>gnl|CDD|178263 PLN02657, PLN02657, 3,8-divinyl protochlorophyllide a 8-vinyl
reductase.
Length = 390
Score = 29.3 bits (66), Expect = 0.48
Identities = 12/36 (33%), Positives = 20/36 (55%)
Query: 5 IVVTGASVGIGAAILRALAAKGHQVIGFARRAEMID 40
++V GA+ IG ++R L +G+ V+ AR I
Sbjct: 63 VLVVGATGYIGKFVVRELVRRGYNVVAVAREKSGIR 98
>gnl|CDD|235914 PRK07041, PRK07041, short chain dehydrogenase; Provisional.
Length = 230
Score = 28.8 bits (65), Expect = 0.52
Identities = 15/37 (40%), Positives = 22/37 (59%)
Query: 6 VVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFA 42
+V G S GIG A+ RA AA+G +V +R + + A
Sbjct: 1 LVVGGSSGIGLALARAFAAEGARVTIASRSRDRLAAA 37
>gnl|CDD|223364 COG0287, TyrA, Prephenate dehydrogenase [Amino acid transport and
metabolism].
Length = 279
Score = 28.8 bits (65), Expect = 0.55
Identities = 29/109 (26%), Positives = 42/109 (38%), Gaps = 12/109 (11%)
Query: 1 MSKIIVVTGASVGIGAAILRALAAKGHQV--IGFARRAEMIDFAESLFAFF-----VDIV 53
S + + G +G ++ RAL G V IG R A + A L
Sbjct: 2 ASMKVGIVGLG-LMGGSLARALKEAGLVVRIIGRDRSAATLKAALELGVIDELTVAGLAE 60
Query: 54 AAKGHQVIGFARRAEMIDAMAKEN-PDWKVHSLKVDVT--KDAEVVEAF 99
AA ++ A E + + KE P K ++ DV K + VVEA
Sbjct: 61 AAAEADLVIVAVPIEATEEVLKELAPHLKKGAIVTDVGSVK-SSVVEAM 108
>gnl|CDD|182756 PRK10818, PRK10818, cell division inhibitor MinD; Provisional.
Length = 270
Score = 29.1 bits (65), Expect = 0.57
Identities = 18/46 (39%), Positives = 24/46 (52%), Gaps = 12/46 (26%)
Query: 1 MSKIIVVTGASVGIG-----AAILRALAAKGHQVIGFARRAEMIDF 41
M++IIVVT G+G AAI LA KG + + +IDF
Sbjct: 1 MARIIVVTSGKGGVGKTTSSAAIATGLAQKGKKTV-------VIDF 39
>gnl|CDD|181609 PRK09009, PRK09009, C factor cell-cell signaling protein;
Provisional.
Length = 235
Score = 28.9 bits (65), Expect = 0.59
Identities = 18/74 (24%), Positives = 32/74 (43%), Gaps = 24/74 (32%)
Query: 61 IGFARRAEMIDAMAKENPDWKVHS----------------LKVDVTKDAEVVEAFDWINN 104
IG A M+ + + PD VH+ +DVT +AE+ + ++
Sbjct: 12 IGKA----MVKQLLERYPDATVHATYRHHKPDFQHDNVQWHALDVTDEAEIKQ----LSE 63
Query: 105 KFGHIDVMINNAGV 118
+F +D +IN G+
Sbjct: 64 QFTQLDWLINCVGM 77
>gnl|CDD|171820 PRK12936, PRK12936, 3-ketoacyl-(acyl-carrier-protein) reductase
NodG; Reviewed.
Length = 245
Score = 28.7 bits (64), Expect = 0.61
Identities = 29/115 (25%), Positives = 46/115 (40%), Gaps = 32/115 (27%)
Query: 6 VVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIGFAR 65
+VTGAS GIG I R L A+G IV G +V
Sbjct: 10 LVTGASGGIGEEIARLLHAQGA------------------------IVGLHGTRV----- 40
Query: 66 RAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNE 120
E ++A+A E + +V +++ EV +D+++NNAG+ +
Sbjct: 41 --EKLEALAAELGE-RVKIFPANLSDRDEVKALGQKAEADLEGVDILVNNAGITK 92
>gnl|CDD|187668 cd09808, DHRS-12_like_SDR_c-like, human dehydrogenase/reductase SDR
family member (DHRS)-12/FLJ13639-like, classical
(c)-like SDRs. Classical SDR-like subgroup containing
human DHRS-12/FLJ13639, the 36K protein of zebrafish CNS
myelin, and related proteins. DHRS-12/FLJ13639 is
expressed in neurons and oligodendrocytes in the human
cerebral cortex. Proteins in this subgroup share the
glycine-rich NAD-binding motif of the classical SDRs,
have a partial match to the canonical active site
tetrad, but lack the typical active site Ser. 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
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-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 ketoacyl reductases 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 = 255
Score = 28.7 bits (64), Expect = 0.63
Identities = 31/122 (25%), Positives = 47/122 (38%), Gaps = 31/122 (25%)
Query: 2 SKIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVI 61
+ ++TGA+ GIG A A+A +G V R + A +I G+Q I
Sbjct: 1 GRSFLITGANSGIGKAAALAIAKRGGTVHMVCRNQTRAEEARK------EIETESGNQNI 54
Query: 62 GFARRAEMIDAMAKENPDWKVHSLKVDVTKDA-EVVEAFDWINNKFGHIDVMINNAG--V 118
+H + + K E VE F + + V+INNAG V
Sbjct: 55 -------------------FLHIVDMSDPKQVWEFVEEF---KEEGKKLHVLINNAGCMV 92
Query: 119 NE 120
N+
Sbjct: 93 NK 94
>gnl|CDD|173942 cd08183, Fe-ADH2, Iron-containing alcohol dehydrogenases-like.
Iron-containing alcohol dehydrogenases (Fe-ADH).
Alcohol dehydrogenase catalyzes the reduction of
acetaldehyde to alcohol with NADP as cofactor. Its
activity requires iron ions. The protein structure
represents a dehydroquinate synthase-like fold and is a
member of the iron-activated alcohol dehydrogenase-like
family. They are distinct from other alcohol
dehydrogenases which contains different protein domain.
Proteins of this family have not been characterized.
Their specific function is unknown. They are mainly
found in bacteria.
Length = 374
Score = 29.1 bits (66), Expect = 0.63
Identities = 17/61 (27%), Positives = 27/61 (44%), Gaps = 5/61 (8%)
Query: 2 SKIIVVTGASVGIGAAILRALAAKGHQVIGFARRAE----MID-FAESLFAFFVDIVAAK 56
++++VTGAS A ++ AL A G +V E ++D D+V A
Sbjct: 23 RRVLLVTGASSLRAAWLIEALRAAGIEVTHVVVAGEPSVELVDAAVAEARNAGCDVVIAI 82
Query: 57 G 57
G
Sbjct: 83 G 83
>gnl|CDD|181417 PRK08416, PRK08416, 7-alpha-hydroxysteroid dehydrogenase;
Provisional.
Length = 260
Score = 29.0 bits (65), Expect = 0.65
Identities = 23/119 (19%), Positives = 42/119 (35%), Gaps = 33/119 (27%)
Query: 1 MSKIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQV 60
K +V++G + GIG AI+ A G + AF
Sbjct: 7 KGKTLVISGGTRGIGKAIVYEFAQSGVNI-----------------AF------------ 37
Query: 61 IGFARRAEMIDAMAKE---NPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNA 116
+ E + +A++ K + +++ + E F I+ F +D I+NA
Sbjct: 38 -TYNSNVEEANKIAEDLEQKYGIKAKAYPLNILEPETYKELFKKIDEDFDRVDFFISNA 95
>gnl|CDD|235694 PRK06079, PRK06079, enoyl-(acyl carrier protein) reductase;
Provisional.
Length = 252
Score = 28.5 bits (64), Expect = 0.68
Identities = 14/61 (22%), Positives = 27/61 (44%), Gaps = 1/61 (1%)
Query: 53 VAAKGHQVIGFARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVM 112
+ +G VI + M ++ K + + ++ DV D + AF I + G ID +
Sbjct: 29 IKDQGATVIYTYQNDRMKKSLQKLVDE-EDLLVECDVASDESIERAFATIKERVGKIDGI 87
Query: 113 I 113
+
Sbjct: 88 V 88
>gnl|CDD|200089 TIGR01289, LPOR, light-dependent protochlorophyllide reductase.
This model represents the light-dependent,
NADPH-dependent form of protochlorophyllide reductase.
It belongs to the short chain alcohol dehydrogenase
family, in contrast to the nitrogenase-related
light-independent form [Biosynthesis of cofactors,
prosthetic groups, and carriers, Chlorophyll and
bacteriochlorphyll].
Length = 314
Score = 28.7 bits (64), Expect = 0.71
Identities = 11/26 (42%), Positives = 16/26 (61%)
Query: 1 MSKIIVVTGASVGIGAAILRALAAKG 26
+++TGAS G+G +ALAA G
Sbjct: 2 QKPTVIITGASSGLGLYAAKALAATG 27
>gnl|CDD|236953 PRK11677, PRK11677, hypothetical protein; Provisional.
Length = 134
Score = 28.1 bits (63), Expect = 0.72
Identities = 9/14 (64%), Positives = 12/14 (85%)
Query: 63 FARRAEMIDAMAKE 76
FAR AE++D MAK+
Sbjct: 56 FARSAELLDTMAKD 69
>gnl|CDD|213592 TIGR01179, galE, UDP-glucose-4-epimerase GalE. Alternate name:
UDPgalactose 4-epimerase This enzyme interconverts
UDP-glucose and UDP-galactose. A set of related
proteins, some of which are tentatively identified as
UDP-glucose-4-epimerase in Thermotoga maritima,
Bacillus halodurans, and several archaea, but deeply
branched from this set and lacking experimental
evidence, are excluded from This model and described by
a separate model [Energy metabolism, Sugars].
Length = 328
Score = 28.8 bits (65), Expect = 0.74
Identities = 11/26 (42%), Positives = 17/26 (65%)
Query: 5 IVVTGASVGIGAAILRALAAKGHQVI 30
I+VTG + IG+ +R L GH+V+
Sbjct: 2 ILVTGGAGYIGSHTVRQLLESGHEVV 27
>gnl|CDD|224015 COG1090, COG1090, Predicted nucleoside-diphosphate sugar
epimerase [General function prediction only].
Length = 297
Score = 28.8 bits (65), Expect = 0.74
Identities = 13/32 (40%), Positives = 17/32 (53%)
Query: 5 IVVTGASVGIGAAILRALAAKGHQVIGFARRA 36
I++TG + IG A+ L GHQV RR
Sbjct: 1 ILITGGTGLIGRALTARLRKGGHQVTILTRRP 32
Score = 25.7 bits (57), Expect = 7.7
Identities = 14/63 (22%), Positives = 18/63 (28%), Gaps = 17/63 (26%)
Query: 57 GHQVIGFARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNA 116
GHQV RR +H A+ + ID +IN A
Sbjct: 22 GHQVTILTRRPP--------KASQNLHPNVTLWEGLADALT---------LGIDAVINLA 64
Query: 117 GVN 119
G
Sbjct: 65 GEP 67
>gnl|CDD|177654 PLN00015, PLN00015, protochlorophyllide reductase.
Length = 308
Score = 28.5 bits (64), Expect = 0.76
Identities = 11/21 (52%), Positives = 15/21 (71%)
Query: 6 VVTGASVGIGAAILRALAAKG 26
++TGAS G+G A +ALA G
Sbjct: 1 IITGASSGLGLATAKALAETG 21
>gnl|CDD|223970 COG1040, ComFC, Predicted amidophosphoribosyltransferases [General
function prediction only].
Length = 225
Score = 28.5 bits (64), Expect = 0.81
Identities = 11/31 (35%), Positives = 16/31 (51%)
Query: 4 IIVVTGASVGIGAAILRALAAKGHQVIGFAR 34
+ TGA++ A +LR AK V+ AR
Sbjct: 192 DVYTTGATLKEAAKLLREAGAKRVFVLTLAR 222
>gnl|CDD|187574 cd05264, UDP_G4E_5_SDR_e, UDP-glucose 4-epimerase (G4E), subgroup
5, extended (e) SDRs. This subgroup partially
conserves the characteristic active site tetrad and
NAD-binding motif of the extended SDRs, and has been
identified as possible UDP-glucose 4-epimerase (aka
UDP-galactose 4-epimerase), a homodimeric member of the
extended SDR family. UDP-glucose 4-epimerase catalyzes
the NAD-dependent conversion of UDP-galactose to
UDP-glucose, the final step in Leloir galactose
synthesis. Extended SDRs are distinct from classical
SDRs. In addition to the Rossmann fold (alpha/beta
folding pattern with a central beta-sheet) core region
typical of all SDRs, extended SDRs have a less
conserved C-terminal extension of approximately 100
amino acids. Extended SDRs are a diverse collection of
proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they 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 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
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. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and
their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. 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 ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 300
Score = 28.4 bits (64), Expect = 0.82
Identities = 10/31 (32%), Positives = 18/31 (58%)
Query: 5 IVVTGASVGIGAAILRALAAKGHQVIGFARR 35
+++ G + IG+ ++ AL +G QV F R
Sbjct: 2 VLIVGGNGFIGSHLVDALLEEGPQVRVFDRS 32
>gnl|CDD|214833 smart00822, PKS_KR, This enzymatic domain is part of bacterial
polyketide synthases. It catalyses the first step in
the reductive modification of the beta-carbonyl centres
in the growing polyketide chain. It uses NADPH to reduce
the keto group to a hydroxy group.
Length = 180
Score = 28.2 bits (64), Expect = 0.83
Identities = 26/121 (21%), Positives = 42/121 (34%), Gaps = 27/121 (22%)
Query: 6 VVTGASVGIGAAILRALAAKGHQVIGFA-RRAEMIDFAESLFAFFVDIVAAKGHQVIGFA 64
++TG G+G A+ R LA +G + + R A G A
Sbjct: 4 LITGGLGGLGRALARWLAERGARRLVLLSRSGP----------------DAPGAA----A 43
Query: 65 RRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNEFAPV 124
AE+ A A+ V + DV + I G + +I+ AGV + +
Sbjct: 44 LLAELEAAGAR------VTVVACDVADRDALAAVLAAIPAVEGPLTGVIHAAGVLDDGVL 97
Query: 125 T 125
Sbjct: 98 A 98
>gnl|CDD|180669 PRK06720, PRK06720, hypothetical protein; Provisional.
Length = 169
Score = 28.4 bits (63), Expect = 0.85
Identities = 18/56 (32%), Positives = 27/56 (48%), Gaps = 9/56 (16%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVI--------GFARRAEMIDF-AESLFAFF 49
K+ +VTG +GIG LA +G +VI G A E+ + E+LF +
Sbjct: 17 KVAIVTGGGIGIGRNTALLLAKQGAKVIVTDIDQESGQATVEEITNLGGEALFVSY 72
>gnl|CDD|132368 TIGR03325, BphB_TodD, cis-2,3-dihydrobiphenyl-2,3-diol
dehydrogenase. Members of this family occur as the BphD
protein of biphenyl catabolism and as the TodD protein
of toluene catabolism. Members catalyze the second step
in each pathway and proved interchangeable when tested;
the first and fourth enzymes in each pathway confer
metabolic specificity. In the context of biphenyl
degradation, the enzyme acts as
cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase (EC
1.3.1.56), while in toluene degradation it acts as
cis-toluene dihydrodiol dehydrogenase.
Length = 262
Score = 28.6 bits (64), Expect = 0.86
Identities = 27/116 (23%), Positives = 44/116 (37%), Gaps = 32/116 (27%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
++++VTG + G+G AI VD A+G +V
Sbjct: 6 EVVLVTGGASGLGRAI-------------------------------VDRFVAEGARVAV 34
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGV 118
+ A + + + D V ++ DV + EA FG ID +I NAG+
Sbjct: 35 LDKSAAGLQELEAAHGD-AVVGVEGDVRSLDDHKEAVARCVAAFGKIDCLIPNAGI 89
>gnl|CDD|176258 cd08298, CAD2, Cinnamyl alcohol dehydrogenases (CAD). These
alcohol dehydrogenases are related to the cinnamyl
alcohol dehydrogenases (CAD), members of the medium
chain dehydrogenase/reductase family.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. Cinnamyl alcohol dehydrogenases
(CAD) reduce cinnamaldehydes to cinnamyl alcohols in the
last step of monolignal metabolism in plant cells walls.
CAD binds 2 zinc ions and is NADPH- dependent. CAD
family members are also found in non-plant species, e.g.
in yeast where they have an aldehyde reductase activity.
The medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 329
Score = 28.3 bits (64), Expect = 0.90
Identities = 12/41 (29%), Positives = 18/41 (43%), Gaps = 3/41 (7%)
Query: 13 GIGAA---ILRALAAKGHQVIGFARRAEMIDFAESLFAFFV 50
G GA+ L+ +G +V F R E + A L A +
Sbjct: 175 GFGASAHLALQIARYQGAEVFAFTRSGEHQELARELGADWA 215
>gnl|CDD|187582 cd05274, KR_FAS_SDR_x, ketoreductase (KR) and fatty acid synthase
(FAS), complex (x) SDRs. Ketoreductase, a module of the
multidomain polyketide synthase (PKS), has 2 subdomains,
each corresponding to a 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 oligomerize but is composed of 2 subdomains, each
resembling an SDR monomer. The active site resembles
that of typical SDRs, except that the usual positions of
the catalytic Asn and Tyr are swapped, so that the
canonical YXXXK motif changes to YXXXN. Modular PKSs are
multifunctional structures in which the makeup
recapitulates that found in (and may have evolved from)
FAS. In some instances, such as porcine FAS, an enoyl
reductase (ER) 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 consist of large, multifunctional
synthases (type I) while bacterial, type II systems, use
single function proteins. Fungal fatty acid synthase
uses a 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-KR, forming beta-hydroxyacyl-ACP, which is in turn
dehydrated by dehydratase to a beta-enoyl intermediate,
which is reduced by NADP-dependent beta-ER. Polyketide
synthesis 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.
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 = 375
Score = 28.5 bits (64), Expect = 1.00
Identities = 9/25 (36%), Positives = 16/25 (64%)
Query: 6 VVTGASVGIGAAILRALAAKGHQVI 30
++TG G+G + R LAA+G + +
Sbjct: 154 LITGGLGGLGLLVARWLAARGARHL 178
Score = 26.2 bits (58), Expect = 5.8
Identities = 21/112 (18%), Positives = 39/112 (34%), Gaps = 15/112 (13%)
Query: 8 TGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIGFARRA 67
A + + AA+L A A+ G + R AE + D+ A + G R
Sbjct: 30 LAALLALVAALLAAYASTGPPLWLVTRGAEAVSAD--------DVAALAQAALWGLLR-- 79
Query: 68 EMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFD-WINNKFGHIDVMINNAGV 118
+A E+P+ + +D A+ A + G ++ +
Sbjct: 80 ----VLALEHPELWGGLVDLDAADAADEAAALAALLAGAPGEDELALRGGQR 127
>gnl|CDD|233441 TIGR01500, sepiapter_red, sepiapterin reductase. This model
describes sepiapterin reductase, a member of the short
chain dehydrogenase/reductase family. The enzyme
catalyzes the last step in the biosynthesis of
tetrahydrobiopterin. A similar enzyme in Bacillus cereus
was isolated for its ability to convert benzil to
(S)-benzoin, a property sepiapterin reductase also
shares. Cutoff scores for this model are set such that
benzil reductase scores between trusted and noise
cutoffs.
Length = 256
Score = 28.3 bits (63), Expect = 1.0
Identities = 24/115 (20%), Positives = 41/115 (35%), Gaps = 14/115 (12%)
Query: 4 IIVVTGASVGIGAAILRALA----AKGHQVIGFARRAEMI-DFAESLFAFFVDIVAAKGH 58
+ +VTGAS G G I + LA + G ++ AR E + + A + +
Sbjct: 2 VCLVTGASRGFGRTIAQELAKCLKSPGSVLVLSARNDEALRQLKAEIGAERSGLRVVRVS 61
Query: 59 QVIGFARRAEMIDAMAKENPDWKVHSLKV---------DVTKDAEVVEAFDWINN 104
+G E + +E P K + DV+K + + N
Sbjct: 62 LDLGAEAGLEQLLKALRELPRPKGLQRLLLINNAGTLGDVSKGFVDLSDSTQVQN 116
>gnl|CDD|223696 COG0623, FabI, Enoyl-[acyl-carrier-protein].
Length = 259
Score = 28.3 bits (64), Expect = 1.0
Identities = 16/51 (31%), Positives = 25/51 (49%), Gaps = 5/51 (9%)
Query: 73 MAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNEFAP 123
+A+E V L DVT D + F I K+G +D ++++ FAP
Sbjct: 51 LAEELGSDLV--LPCDVTNDESIDALFATIKKKWGKLDGLVHSIA---FAP 96
>gnl|CDD|236582 PRK09599, PRK09599, 6-phosphogluconate dehydrogenase-like
protein; Reviewed.
Length = 301
Score = 28.2 bits (64), Expect = 1.0
Identities = 11/37 (29%), Positives = 17/37 (45%)
Query: 15 GAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVD 51
G + R L GH+V+G+ R E ++ A D
Sbjct: 12 GGNMARRLLRGGHEVVGYDRNPEAVEALAEEGATGAD 48
Score = 27.8 bits (63), Expect = 1.6
Identities = 9/24 (37%), Positives = 17/24 (70%)
Query: 53 VAAKGHQVIGFARRAEMIDAMAKE 76
+ GH+V+G+ R E ++A+A+E
Sbjct: 19 LLRGGHEVVGYDRNPEAVEALAEE 42
>gnl|CDD|187595 cd05334, DHPR_SDR_c_like, dihydropteridine reductase (DHPR),
classical (c) SDRs. Dihydropteridine reductase is an
NAD-binding protein related to the SDRs. It converts
dihydrobiopterin into tetrahydrobiopterin, a cofactor
necessary in catecholamines synthesis. Dihydropteridine
reductase has the YXXXK of these tyrosine-dependent
oxidoreductases, but lacks the typical upstream Asn and
Ser catalytic residues. 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 have a
3-glycine N-terminal NAD(P)(H)-binding pattern
(typically, TGxxxGxG in classical SDRs and TGxxGxxG in
extended SDRs), while substrate binding is in the
C-terminal region. A critical catalytic Tyr residue
(Tyr-151, human 15-hydroxyprostaglandin dehydrogenase
(15-PGDH) numbering), is often found in a conserved
YXXXK pattern. In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) or
additional Ser, contributing to the active site.
Substrates for these enzymes include sugars, steroids,
alcohols, and aromatic compounds. The standard reaction
mechanism is a proton relay involving the conserved Tyr
and Lys, as well as Asn (or Ser). Some SDR family
members, including 17 beta-hydroxysteroid dehydrogenase
contain an additional helix-turn-helix motif that is
not generally found among SDRs.
Length = 221
Score = 28.1 bits (63), Expect = 1.1
Identities = 11/43 (25%), Positives = 24/43 (55%), Gaps = 7/43 (16%)
Query: 2 SKIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAES 44
+++++V G +G+A+++A ++G V ID AE+
Sbjct: 1 ARVVLVYGGRGALGSAVVQAFKSRGWWVAS-------IDLAEN 36
>gnl|CDD|187545 cd05234, UDP_G4E_2_SDR_e, UDP-glucose 4 epimerase, subgroup 2,
extended (e) SDRs. UDP-glucose 4 epimerase (aka
UDP-galactose-4-epimerase), is a homodimeric extended
SDR. It catalyzes the NAD-dependent conversion of
UDP-galactose to UDP-glucose, the final step in Leloir
galactose synthesis. This subgroup is comprised of
archaeal and bacterial proteins, and has the
characteristic active site tetrad and NAD-binding motif
of the extended SDRs. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids. Extended SDRs are a diverse collection
of proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they 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 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
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. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and
their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. 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 ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 305
Score = 28.0 bits (63), Expect = 1.2
Identities = 9/28 (32%), Positives = 18/28 (64%)
Query: 5 IVVTGASVGIGAAILRALAAKGHQVIGF 32
I+VTG + IG+ ++ L +G++V+
Sbjct: 2 ILVTGGAGFIGSHLVDRLLEEGNEVVVV 29
>gnl|CDD|180838 PRK07102, PRK07102, short chain dehydrogenase; Provisional.
Length = 243
Score = 28.0 bits (63), Expect = 1.2
Identities = 23/80 (28%), Positives = 37/80 (46%), Gaps = 3/80 (3%)
Query: 1 MSKIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMID-FAESLFAFFVDIVAAKGHQ 59
M KI+++ GA+ I A R AA G ++ AR E ++ A+ L A V+
Sbjct: 1 MKKILII-GATSDIARACARRYAAAGARLYLAARDVERLERLADDLRARGAVAVSTHELD 59
Query: 60 VIGFARRAEMIDAMAKENPD 79
++ A A +D+ PD
Sbjct: 60 ILDTASHAAFLDS-LPALPD 78
>gnl|CDD|225462 COG2910, COG2910, Putative NADH-flavin reductase [General
function prediction only].
Length = 211
Score = 28.1 bits (63), Expect = 1.2
Identities = 14/48 (29%), Positives = 22/48 (45%)
Query: 5 IVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDI 52
I + GAS G+ IL+ +GH+V R A + + + DI
Sbjct: 3 IAIIGASGKAGSRILKEALKRGHEVTAIVRNASKLAARQGVTILQKDI 50
>gnl|CDD|239383 cd03109, DTBS, Dethiobiotin synthetase (DTBS) is the penultimate
enzyme in the biotin biosynthesis pathway in
Escherichia coli and other microorganisms. The enzyme
catalyzes formation of the ureido ring of dethiobiotin
from (7R,8S)-7,8-diaminononanoic acid (DAPA) and carbon
dioxide. The enzyme utilizes carbon dioxide instead of
hydrogen carbonate as substrate and is dependent on ATP
and divalent metal ions as cofactors.
Length = 134
Score = 27.8 bits (62), Expect = 1.2
Identities = 10/33 (30%), Positives = 15/33 (45%), Gaps = 3/33 (9%)
Query: 3 KIIVVTGASVG---IGAAILRALAAKGHQVIGF 32
+ TG +G A + RAL KG++V
Sbjct: 1 IMGFGTGTDIGKTVATAILARALKEKGYRVAPL 33
>gnl|CDD|236173 PRK08177, PRK08177, short chain dehydrogenase; Provisional.
Length = 225
Score = 28.1 bits (63), Expect = 1.2
Identities = 10/35 (28%), Positives = 18/35 (51%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAE 37
+ ++ GAS G+G ++ L +G QV R +
Sbjct: 2 RTALIIGASRGLGLGLVDRLLERGWQVTATVRGPQ 36
>gnl|CDD|187569 cd05259, PCBER_SDR_a, phenylcoumaran benzylic ether reductase
(PCBER) like, atypical (a) SDRs. PCBER and
pinoresinol-lariciresinol reductases are
NADPH-dependent aromatic alcohol reductases, and are
atypical members of the SDR family. Other proteins in
this subgroup are identified as eugenol synthase. These
proteins contain an N-terminus characteristic of
NAD(P)-binding proteins and a small C-terminal domain
presumed to be involved in substrate binding, but they
do not have the conserved active site Tyr residue
typically found in SDRs. Numerous other members have
unknown functions. The glycine rich NADP-binding motif
in this subgroup is of 2 forms: GXGXXG and G[GA]XGXXG;
it tends to be atypical compared with the forms
generally seen in classical or extended SDRs. The usual
SDR active site tetrad is not present, but a critical
active site Lys at the usual SDR position has been
identified in various members, though other charged and
polar residues are found at this position in this
subgroup. Atypical SDR-related proteins retain the
Rossmann fold of the SDRs, but have limited sequence
identity and generally lack the catalytic properties of
the archetypical members. Atypical SDRs include
biliverdin IX beta reductase (BVR-B,aka flavin
reductase), NMRa (a negative transcriptional regulator
of various fungi), progesterone 5-beta-reductase like
proteins, phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane
reductase, isoflavone reductases, and others. SDRs are
a functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they 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 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
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. In addition to the Rossmann fold
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids, 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 ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 282
Score = 28.0 bits (63), Expect = 1.3
Identities = 11/31 (35%), Positives = 16/31 (51%), Gaps = 1/31 (3%)
Query: 5 IVVTGASVGIGAAILRAL-AAKGHQVIGFAR 34
I + GA+ +G I+ AL A+ G V R
Sbjct: 2 IAIAGATGTLGGPIVSALLASPGFTVTVLTR 32
>gnl|CDD|187656 cd08953, KR_2_SDR_x, ketoreductase (KR), subgroup 2, complex (x)
SDRs. Ketoreductase, a module of the multidomain
polyketide synthase (PKS), has 2 subdomains, each
corresponding to a 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 oligomerize but is composed
of 2 subdomains, each resembling an SDR monomer. The
active site resembles that of typical SDRs, except that
the usual positions of the catalytic Asn and Tyr are
swapped, so that the canonical YXXXK motif changes to
YXXXN. Modular PKSs are multifunctional structures in
which the makeup recapitulates that found in (and may
have evolved from) FAS. Polyketide synthesis 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
both KR domains of the Bacillus subtilis Pks J,-L, and
PksM, and all three KR domains of PksN, components of
the megacomplex bacillaene synthase, which synthesizes
the antibiotic bacillaene. 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 = 436
Score = 28.1 bits (63), Expect = 1.3
Identities = 30/114 (26%), Positives = 48/114 (42%), Gaps = 25/114 (21%)
Query: 6 VVTGASVGIGAAILRALAAK-GHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIGFA 64
+VTG + GIG A+ RALA + G +++ R + E A + + A G +
Sbjct: 209 LVTGGAGGIGRALARALARRYGARLVLLGRSP--LPPEEEWKAQTLAALEALGAR----- 261
Query: 65 RRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGV 118
V + DVT A V + + ++G ID +I+ AGV
Sbjct: 262 -----------------VLYISADVTDAAAVRRLLEKVRERYGAIDGVIHAAGV 298
>gnl|CDD|234896 PRK01077, PRK01077, cobyrinic acid a,c-diamide synthase;
Validated.
Length = 451
Score = 27.8 bits (63), Expect = 1.4
Identities = 9/35 (25%), Positives = 16/35 (45%), Gaps = 5/35 (14%)
Query: 3 KIIVVTGASVGIG-----AAILRALAAKGHQVIGF 32
+V+ + G G ++RAL +G +V F
Sbjct: 4 PALVIAAPASGSGKTTVTLGLMRALRRRGLRVQPF 38
>gnl|CDD|107260 cd01575, PBP1_GntR, Ligand-binding domain of DNA transcription
repressor GntR specific for gluconate, a member of the
LacI-GalR family of bacterial transcription regulators.
This group represents the ligand-binding domain of DNA
transcription repressor GntR specific for gluconate, a
member of the LacI-GalR family of bacterial
transcription regulators. The ligand-binding domain of
GntR is structurally homologous to the periplasmic
sugar-binding domain of ABC-type transporters and both
domains contain the type I periplasmic binding
protein-like fold. The LacI-GalR family repressors are
composed of two functional domains: an N-terminal HTH
(helix-turn-helix) domain, which is responsible for the
DNA-binding specificity, and a C-terminal ligand-binding
domain, which is homologous to the type I periplasmic
binding proteins. As also observed in the periplasmic
binding proteins, the C-terminal domain of the bacterial
transcription repressor undergoes a conformational
change upon ligand binding, which in turn changes the
DNA binding affinity of the repressor.
Length = 268
Score = 27.8 bits (63), Expect = 1.4
Identities = 23/86 (26%), Positives = 34/86 (39%), Gaps = 16/86 (18%)
Query: 9 GASVGI-----GAAILRALAAKGHQVIGFARRAEMIDF-AESLFAFFVDIVAAKG----- 57
+VG G A+ R L A+G++ IGF A M D A+ F + A G
Sbjct: 93 DMAVGFSHAEAGRAMARHLLARGYRRIGFL-GARMDDTRAQQRLEGFRAALRAAGLDPPL 151
Query: 58 ----HQVIGFARRAEMIDAMAKENPD 79
+ FA E++ + PD
Sbjct: 152 VVTTPEPSSFALGRELLAELLARWPD 177
>gnl|CDD|99789 cd06192, DHOD_e_trans_like, FAD/NAD binding domain (electron
transfer subunit) of dihydroorotate dehydrogenase-like
proteins. Dihydroorotate dehydrogenases (DHODs) catalyze
the only redox reaction in pyrimidine de novo
biosynthesis. They catalyze the oxidation of
(S)-dihydroorotate to orotate coupled with the reduction
of NAD+. In L. lactis, DHOD B (encoded by pyrDa) is
co-expressed with pyrK and both gene products are
required for full activity, as well as NAD binding.
NAD(P) binding domain of ferredoxin reductase-like
proteins catalyze electron transfer between an
NAD(P)-binding domain of the alpha/beta class and a
discrete (usually N-terminal) domain which vary in
orientation with respect to the NAD(P) binding domain.
The N-terminal domain may contain a flavin prosthetic
group (as in flavoenzymes) or use flavin as a substrate.
Ferredoxin is reduced in the final stage of photosystem
I. The flavoprotein Ferredoxin-NADP+ reductase transfers
electrons from reduced ferredoxin to FAD (forming FADH2
via a semiquinone intermediate) which then transfers a
hydride ion to convert NADP+ to NADPH.
Length = 243
Score = 27.7 bits (62), Expect = 1.4
Identities = 15/57 (26%), Positives = 25/57 (43%), Gaps = 9/57 (15%)
Query: 3 KIIVVTGASVGIGAA----ILRALAAKGHQVIGFA--RRAEMIDFAESLFAFFVDIV 53
+++V G GIG A I + LAA G++V A ++A+ E +
Sbjct: 99 TVLLVAG---GIGLAPLLPIAKKLAANGNKVTVLAGAKKAKEEFLDEYFELPADVEI 152
>gnl|CDD|168204 PRK05717, PRK05717, oxidoreductase; Validated.
Length = 255
Score = 27.9 bits (62), Expect = 1.4
Identities = 28/116 (24%), Positives = 47/116 (40%), Gaps = 32/116 (27%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIG 62
++ +VTGA+ GIG I L A+G QV+ D+ +G +V
Sbjct: 11 RVALVTGAARGIGLGIAAWLIAEGWQVV------------------LADLDRERGSKV-- 50
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGV 118
A A W + +DV +A+V + +FG +D ++ NA +
Sbjct: 51 ---------AKALGENAWFI---AMDVADEAQVAAGVAEVLGQFGRLDALVCNAAI 94
>gnl|CDD|222792 PHA00435, PHA00435, capsid assembly protein.
Length = 306
Score = 27.9 bits (62), Expect = 1.4
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 53 VAAKGHQVIGFARRAEMIDAMA 74
+V GFA +AEMI AM+
Sbjct: 262 AKPVAPKVEGFASQAEMIKAMS 283
>gnl|CDD|183719 PRK12747, PRK12747, short chain dehydrogenase; Provisional.
Length = 252
Score = 27.7 bits (61), Expect = 1.5
Identities = 18/36 (50%), Positives = 22/36 (61%), Gaps = 1/36 (2%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQV-IGFARRAE 37
K+ +VTGAS GIG AI + LA G V I + R E
Sbjct: 5 KVALVTGASRGIGRAIAKRLANDGALVAIHYGNRKE 40
>gnl|CDD|169389 PRK08339, PRK08339, short chain dehydrogenase; Provisional.
Length = 263
Score = 27.9 bits (62), Expect = 1.6
Identities = 15/42 (35%), Positives = 20/42 (47%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAES 44
K+ T +S GIG + R LA G VI +R E + A
Sbjct: 9 KLAFTTASSKGIGFGVARVLARAGADVILLSRNEENLKKARE 50
>gnl|CDD|223318 COG0240, GpsA, Glycerol-3-phosphate dehydrogenase [Energy
production and conversion].
Length = 329
Score = 27.5 bits (62), Expect = 1.8
Identities = 14/40 (35%), Positives = 21/40 (52%), Gaps = 2/40 (5%)
Query: 1 MSKIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMID 40
M KI V+ S G A+ + LA GH+V + R E++
Sbjct: 1 MMKIAVIGAGS--WGTALAKVLARNGHEVRLWGRDEEIVA 38
>gnl|CDD|222085 pfam13377, Peripla_BP_3, Periplasmic binding protein-like domain.
Thi domain is found in a variety of transcriptional
regulatory proteins. It is related to bacterial
periplasmic binding proteins, although this domain is
unlikely to be found in the periplasm. This domain
likely acts to bind a small molecule ligand that the
DNA-binding domain responds to.
Length = 161
Score = 27.3 bits (61), Expect = 1.9
Identities = 7/45 (15%), Positives = 14/45 (31%)
Query: 19 LRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIGF 63
+ L GH+ I F ++ F + + G +
Sbjct: 1 VDHLLELGHRRIAFIGGDGDDSSSDERERGFREALRELGLPLEVL 45
>gnl|CDD|235821 PRK06522, PRK06522, 2-dehydropantoate 2-reductase; Reviewed.
Length = 304
Score = 27.5 bits (62), Expect = 2.0
Identities = 12/51 (23%), Positives = 20/51 (39%), Gaps = 2/51 (3%)
Query: 54 AAKGHQVIGFARRAEMIDAMAKE--NPDWKVHSLKVDVTKDAEVVEAFDWI 102
A GH V ARR +DA+ + + ++ V D + D +
Sbjct: 20 AQAGHDVTLVARRGAHLDALNENGLRLEDGEITVPVLAADDPAELGPQDLV 70
>gnl|CDD|187651 cd08947, NmrA_TMR_like_SDR_a, NmrA (a transcriptional regulator),
HSCARG (an NADPH sensor), and triphenylmethane
reductase (TMR) like proteins, atypical (a) SDRs.
Atypical SDRs belonging to this subgroup include NmrA,
HSCARG, and TMR, these proteins bind NAD(P) but they
lack the usual catalytic residues of the SDRs. Atypical
SDRs are distinct from classical SDRs. NmrA is a
negative transcriptional regulator of various fungi,
involved in the post-translational modulation of the
GATA-type transcription factor AreA. NmrA lacks the
canonical GXXGXXG NAD-binding motif and has altered
residues at the catalytic triad, including a Met
instead of the critical Tyr residue. NmrA may bind
nucleotides but appears to lack any dehydrogenase
activity. HSCARG has been identified as a putative
NADP-sensing molecule, and redistributes and
restructures in response to NADPH/NADP ratios. Like
NmrA, it lacks most of the active site residues of the
SDR family, but has an NAD(P)-binding motif similar to
the extended SDR family, GXXGXXG. TMR, an NADP-binding
protein, lacks the active site residues of the SDRs but
has a glycine rich NAD(P)-binding motif that matches
the extended SDRs. Atypical SDRs include biliverdin IX
beta reductase (BVR-B,aka flavin reductase), NMRa (a
negative transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane
reductase, isoflavone reductases, and others. SDRs are
a functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they 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 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
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. In addition to the Rossmann fold
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids, 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 ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 224
Score = 27.5 bits (61), Expect = 2.0
Identities = 15/34 (44%), Positives = 19/34 (55%), Gaps = 1/34 (2%)
Query: 5 IVVTGASVGIGAAILRALAAKG-HQVIGFARRAE 37
I VTGA+ G +++R L AKG QV R E
Sbjct: 1 IAVTGATGQQGGSVIRHLLAKGASQVRAVVRNVE 34
>gnl|CDD|216396 pfam01262, AlaDh_PNT_C, Alanine dehydrogenase/PNT, C-terminal
domain. This family now also contains the lysine
2-oxoglutarate reductases.
Length = 150
Score = 27.1 bits (61), Expect = 2.0
Identities = 18/50 (36%), Positives = 24/50 (48%), Gaps = 3/50 (6%)
Query: 3 KIIVVTGASV-GIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVD 51
+VV G V G+GAA G V R E ++ +SLFA FV+
Sbjct: 21 AKVVVIGGGVVGLGAAATAKGL--GAPVTILDVRPERLEQLDSLFAEFVE 68
>gnl|CDD|201664 pfam01210, NAD_Gly3P_dh_N, NAD-dependent glycerol-3-phosphate
dehydrogenase N-terminus. NAD-dependent
glycerol-3-phosphate dehydrogenase (GPDH) catalyzes the
interconversion of dihydroxyacetone phosphate and
L-glycerol-3-phosphate. This family represents the
N-terminal NAD-binding domain.
Length = 157
Score = 27.2 bits (61), Expect = 2.0
Identities = 14/38 (36%), Positives = 20/38 (52%), Gaps = 2/38 (5%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAEMID 40
KI V+ S G A + LA GH+V + R E+I+
Sbjct: 1 KIAVLGAGSWGTALAKV--LARNGHEVRLWGRDEELIE 36
>gnl|CDD|223069 PHA03390, pk1, serine/threonine-protein kinase 1; Provisional.
Length = 267
Score = 27.1 bits (61), Expect = 2.1
Identities = 9/25 (36%), Positives = 14/25 (56%)
Query: 87 VDVTKDAEVVEAFDWINNKFGHIDV 111
V K+ E+V+ I+ KFG + V
Sbjct: 10 VQFLKNCEIVKKLKLIDGKFGKVSV 34
>gnl|CDD|238572 cd01167, bac_FRK, Fructokinases (FRKs) mainly from bacteria and
plants are enzymes with high specificity for fructose,
as are all FRKs, but they catalyzes the conversion of
fructose to fructose-6-phosphate, which is an entry
point into glycolysis via conversion into
glucose-6-phosphate. This is in contrast to FRKs [or
ketohexokinases (KHKs)] from mammalia and halophilic
archaebacteria, which phosphorylate fructose to
fructose-1-phosphate.
Length = 295
Score = 27.2 bits (61), Expect = 2.1
Identities = 11/35 (31%), Positives = 16/35 (45%)
Query: 8 TGASVGIGAAILRALAAKGHQVIGFARRAEMIDFA 42
TGA A +L L ++G + AE + FA
Sbjct: 247 TGAGDAFVAGLLAQLLSRGLLALDEDELAEALRFA 281
>gnl|CDD|222222 pfam13561, adh_short_C2, Enoyl-(Acyl carrier protein) reductase.
Length = 239
Score = 27.2 bits (61), Expect = 2.1
Identities = 19/68 (27%), Positives = 34/68 (50%), Gaps = 7/68 (10%)
Query: 54 AAKGHQVI----GFARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHI 109
A +G +V+ A R +D +AKE P + +DVT D ++ E F+ + G I
Sbjct: 17 AEEGAEVVLTTWPPALRMGAVDELAKELP---ADVIPLDVTSDEDIDELFEKVKEDGGKI 73
Query: 110 DVMINNAG 117
D ++++
Sbjct: 74 DFLVHSIA 81
>gnl|CDD|236099 PRK07791, PRK07791, short chain dehydrogenase; Provisional.
Length = 286
Score = 27.3 bits (61), Expect = 2.2
Identities = 35/122 (28%), Positives = 53/122 (43%), Gaps = 32/122 (26%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVI------GFARRAEMIDFAESLFAFFVDIVAAK 56
++++VTGA GIG A A AA+G +V+ G A A+++ +IVAA
Sbjct: 7 RVVIVTGAGGGIGRAHALAFAAEGARVVVNDIGVGLDGSASGGSAAQAVVD---EIVAAG 63
Query: 57 GHQVIGFARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNA 116
G V A + DW + VD + FG +DV++NNA
Sbjct: 64 GEAV-----------ANGDDIADWDGAANLVDAAVET------------FGGLDVLVNNA 100
Query: 117 GV 118
G+
Sbjct: 101 GI 102
>gnl|CDD|187559 cd05248, ADP_GME_SDR_e, ADP-L-glycero-D-mannoheptose 6-epimerase
(GME), extended (e) SDRs. This subgroup contains
ADP-L-glycero-D-mannoheptose 6-epimerase, an extended
SDR, which catalyzes the NAD-dependent interconversion
of ADP-D-glycero-D-mannoheptose and
ADP-L-glycero-D-mannoheptose. This subgroup has the
canonical active site tetrad and NAD(P)-binding motif.
Extended SDRs are distinct from classical SDRs. In
addition to the Rossmann fold (alpha/beta folding
pattern with a central beta-sheet) core region typical
of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
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
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, 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. Atypical
SDRs generally lack the catalytic residues
characteristic of the SDRs, and their glycine-rich
NAD(P)-binding motif is often different from the forms
normally seen in classical or extended SDRs. 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
ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding
motif.
Length = 317
Score = 27.3 bits (61), Expect = 2.2
Identities = 10/26 (38%), Positives = 17/26 (65%)
Query: 5 IVVTGASVGIGAAILRALAAKGHQVI 30
I+VTG + IG+ +++AL +G I
Sbjct: 2 IIVTGGAGFIGSNLVKALNERGITDI 27
>gnl|CDD|181001 PRK07494, PRK07494, 2-octaprenyl-6-methoxyphenyl hydroxylase;
Provisional.
Length = 388
Score = 27.2 bits (61), Expect = 2.3
Identities = 13/33 (39%), Positives = 15/33 (45%), Gaps = 2/33 (6%)
Query: 4 IIVVTGASVGIGAAILRALAAKGHQVIGFARRA 36
I V+ G G+ AAI ALA G V A
Sbjct: 10 IAVIGGGPAGLAAAI--ALARAGASVALVAPEP 40
>gnl|CDD|187566 cd05256, UDP_AE_SDR_e, UDP-N-acetylglucosamine 4-epimerase,
extended (e) SDRs. This subgroup contains
UDP-N-acetylglucosamine 4-epimerase of Pseudomonas
aeruginosa, WbpP, an extended SDR, that catalyzes the
NAD+ dependent conversion of UDP-GlcNAc and UDPGalNA to
UDP-Glc and UDP-Gal. This subgroup has the
characteristic active site tetrad and NAD-binding motif
of the extended SDRs. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids. Extended SDRs are a diverse collection
of proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they 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 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
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. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and
their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. 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 ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 304
Score = 27.2 bits (61), Expect = 2.4
Identities = 10/27 (37%), Positives = 18/27 (66%)
Query: 5 IVVTGASVGIGAAILRALAAKGHQVIG 31
++VTG + IG+ ++ L +GH+VI
Sbjct: 2 VLVTGGAGFIGSHLVERLLERGHEVIV 28
>gnl|CDD|187567 cd05257, Arna_like_SDR_e, Arna decarboxylase_like, extended (e)
SDRs. Decarboxylase domain of ArnA. ArnA, is an enzyme
involved in the modification of outer membrane protein
lipid A of gram-negative bacteria. It is a bifunctional
enzyme that catalyzes the NAD-dependent decarboxylation
of UDP-glucuronic acid and
N-10-formyltetrahydrofolate-dependent formylation of
UDP-4-amino-4-deoxy-l-arabinose; its NAD-dependent
decaboxylating activity is in the C-terminal 360
residues. This subgroup belongs to the extended SDR
family, however the NAD binding motif is not a perfect
match and the upstream Asn of the canonical active site
tetrad is not conserved. Extended SDRs are distinct
from classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids. Extended SDRs are a diverse collection
of proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they 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 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
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. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and
their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. 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 ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 316
Score = 27.3 bits (61), Expect = 2.4
Identities = 10/29 (34%), Positives = 16/29 (55%)
Query: 5 IVVTGASVGIGAAILRALAAKGHQVIGFA 33
++VTGA IG+ + L +GH+V
Sbjct: 2 VLVTGADGFIGSHLTERLLREGHEVRALD 30
>gnl|CDD|216501 pfam01433, Peptidase_M1, Peptidase family M1. Members of this
family are aminopeptidases. The members differ widely in
specificity, hydrolysing acidic, basic or neutral
N-terminal residues. This family includes leukotriene-A4
hydrolase, this enzyme also has an aminopeptidase
activity.
Length = 390
Score = 27.3 bits (61), Expect = 2.4
Identities = 10/43 (23%), Positives = 20/43 (46%), Gaps = 6/43 (13%)
Query: 60 VIGFARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWI 102
V+ + A +D++ H + V+V +E+ + FD I
Sbjct: 349 VLREVQSALALDSLDS------SHPITVNVNTPSEIDDIFDAI 385
>gnl|CDD|187570 cd05260, GDP_MD_SDR_e, GDP-mannose 4,6 dehydratase, extended (e)
SDRs. GDP-mannose 4,6 dehydratase, a homodimeric SDR,
catalyzes the NADP(H)-dependent conversion of
GDP-(D)-mannose to GDP-4-keto, 6-deoxy-(D)-mannose in
the fucose biosynthesis pathway. These proteins have
the canonical active site triad and NAD-binding
pattern, however the active site Asn is often missing
and may be substituted with Asp. A Glu residue has been
identified as an important active site base. Extended
SDRs are distinct from classical SDRs. In addition to
the Rossmann fold (alpha/beta folding pattern with a
central beta-sheet) core region typical of all SDRs,
extended SDRs have a less conserved C-terminal
extension of approximately 100 amino acids. Extended
SDRs are a diverse collection of proteins, and include
isomerases, epimerases, oxidoreductases, and lyases;
they typically have a TGXXGXXG cofactor binding motif.
SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
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
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, 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. Atypical
SDRs generally lack the catalytic residues
characteristic of the SDRs, and their glycine-rich
NAD(P)-binding motif is often different from the forms
normally seen in classical or extended SDRs. 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
ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding
motif.
Length = 316
Score = 27.2 bits (61), Expect = 2.5
Identities = 10/33 (30%), Positives = 18/33 (54%)
Query: 5 IVVTGASVGIGAAILRALAAKGHQVIGFARRAE 37
++TG + G+ + L KG++V G RR+
Sbjct: 2 ALITGITGQDGSYLAEFLLEKGYEVHGIVRRSS 34
>gnl|CDD|187540 cd05229, SDR_a3, atypical (a) SDRs, subgroup 3. These atypical
SDR family members of unknown function have a
glycine-rich NAD(P)-binding motif consensus that is
very similar to the extended SDRs, GXXGXXG. Generally,
this group has poor conservation of the active site
tetrad, However, individual sequences do contain
matches to the YXXXK active site motif, and generally
Tyr or Asn in place of the upstream Ser found in most
SDRs. Atypical SDRs generally lack the catalytic
residues characteristic of the SDRs, and their
glycine-rich NAD(P)-binding motif is often different
from the forms normally seen in classical or extended
SDRs. Atypical SDRs include biliverdin IX beta
reductase (BVR-B,aka flavin reductase), NMRa (a
negative transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane
reductase, isoflavone reductases, and others. SDRs are
a functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they 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 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
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. In addition to the Rossmann fold
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids, 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 ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 302
Score = 26.9 bits (60), Expect = 2.6
Identities = 11/29 (37%), Positives = 14/29 (48%)
Query: 7 VTGASVGIGAAILRALAAKGHQVIGFARR 35
V GAS IG + R L +G V +R
Sbjct: 4 VLGASGPIGREVARELRRRGWDVRLVSRS 32
>gnl|CDD|183716 PRK12744, PRK12744, short chain dehydrogenase; Provisional.
Length = 257
Score = 27.0 bits (60), Expect = 2.8
Identities = 30/120 (25%), Positives = 47/120 (39%), Gaps = 35/120 (29%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGF-----ARRAEMIDFAESLFAFFVDIVAAKG 57
K++++ G + +G I R LAA+G + + A +A+ AE V V A G
Sbjct: 9 KVVLIAGGAKNLGGLIARDLAAQGAKAVAIHYNSAASKAD----AEET----VAAVKAAG 60
Query: 58 HQVIGFARRAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAG 117
+ + F + D+T A V + FD FG D+ IN G
Sbjct: 61 AKAVAF----------------------QADLTTAAAVEKLFDDAKAAFGRPDIAINTVG 98
>gnl|CDD|191263 pfam05368, NmrA, NmrA-like family. NmrA is a negative
transcriptional regulator involved in the
post-translational modification of the transcription
factor AreA. NmrA is part of a system controlling
nitrogen metabolite repression in fungi. This family
only contains a few sequences as iteration results in
significant matches to other Rossmann fold families.
Length = 232
Score = 26.8 bits (60), Expect = 2.9
Identities = 17/51 (33%), Positives = 27/51 (52%), Gaps = 1/51 (1%)
Query: 5 IVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAA 55
I+V GA+ G +++RA GH V R + + A+SL A V++V
Sbjct: 1 ILVFGATGYQGGSVVRASLKAGHPVRALVRDPKS-ELAKSLKAAGVELVEG 50
>gnl|CDD|219957 pfam08659, KR, KR domain. This enzymatic domain is part of
bacterial polyketide synthases and catalyzes the first
step in the reductive modification of the beta-carbonyl
centres in the growing polyketide chain. It uses NADPH
to reduce the keto group to a hydroxy group.
Length = 181
Score = 26.7 bits (60), Expect = 3.1
Identities = 21/119 (17%), Positives = 36/119 (30%), Gaps = 25/119 (21%)
Query: 6 VVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIGFAR 65
+VTG G+G + R LA +G AR +
Sbjct: 4 LVTGGLGGLGLELARWLAERG------ARH-----------------LVLLSRSGAPDPE 40
Query: 66 RAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNEFAPV 124
++ + +V + DV+ V I + +I+ AGV A +
Sbjct: 41 AEALLAELEARGA--EVTVVACDVSDRDAVRALLAEIRADGPPLRGVIHAAGVLRDALL 97
>gnl|CDD|237083 PRK12374, PRK12374, putative dithiobiotin synthetase;
Provisional.
Length = 231
Score = 26.7 bits (59), Expect = 3.3
Identities = 13/37 (35%), Positives = 20/37 (54%), Gaps = 5/37 (13%)
Query: 1 MSKIIVVTGASVGIGA-----AILRALAAKGHQVIGF 32
M K +TG +G A+L+ALA++G V G+
Sbjct: 1 MLKRFFITGTDTSVGKTVVSRALLQALASQGKTVAGY 37
>gnl|CDD|161703 TIGR00091, TIGR00091, tRNA (guanine-N(7)-)-methyltransferase.
This predicted S-adenosylmethionine-dependent
methyltransferase is found in a single copy in most
Bacteria. It is also found, with a short amino-terminal
extension in eukaryotes. Its function is unknown. In E.
coli, this protein flanks the DNA repair protein MutY,
also called micA [Protein synthesis, tRNA and rRNA base
modification].
Length = 194
Score = 26.6 bits (59), Expect = 3.4
Identities = 10/20 (50%), Positives = 13/20 (65%), Gaps = 1/20 (5%)
Query: 61 IGFARRAEMIDAMAKENPDW 80
IG + +ID MAK+NPD
Sbjct: 23 IGCGKGRFLID-MAKQNPDK 41
>gnl|CDD|177837 PLN02182, PLN02182, cytidine deaminase.
Length = 339
Score = 26.9 bits (59), Expect = 3.5
Identities = 22/63 (34%), Positives = 32/63 (50%), Gaps = 6/63 (9%)
Query: 35 RAEMIDF-AESLFAFFVDIVAA----KGHQVIGFARRAEMI-DAMAKENPDWKVHSLKVD 88
+A ++DF A S F IV A K + ++ R A++I D +A N D+KV VD
Sbjct: 254 QAALVDFVARSRGKMFNKIVQAVLVEKNNAIVSQERTAKIILDTIAAPNCDFKVFHCSVD 313
Query: 89 VTK 91
K
Sbjct: 314 CAK 316
>gnl|CDD|178298 PLN02695, PLN02695, GDP-D-mannose-3',5'-epimerase.
Length = 370
Score = 26.7 bits (59), Expect = 3.5
Identities = 12/27 (44%), Positives = 16/27 (59%)
Query: 5 IVVTGASVGIGAAILRALAAKGHQVIG 31
I +TGA I + I R L A+GH +I
Sbjct: 24 ICITGAGGFIASHIARRLKAEGHYIIA 50
>gnl|CDD|240010 cd04639, CBS_pair_26, The CBS domain, named after human CBS, is a
small domain originally identified in cystathionine
beta-synthase and is subsequently found in a wide range
of different proteins. CBS domains usually occur in
tandem repeats. They associate to form a so-called
Bateman domain or a CBS pair based on crystallographic
studies in bacteria. The CBS pair was used as a basis
for this cd hierarchy since the human CBS proteins can
adopt the typical core structure and form an
intramolecular CBS pair. The interface between the two
CBS domains forms a cleft that is a potential ligand
binding site. The CBS pair coexists with a variety of
other functional domains and this has been used to help
in its classification here. It has been proposed that
the CBS domain may play a regulatory role, although its
exact function is unknown. Mutations of conserved
residues within this domain are associated with a
variety of human hereditary diseases, including
congenital myotonia, idiopathic generalized epilepsy,
hypercalciuric nephrolithiasis, and classic Bartter
syndrome (CLC chloride channel family members),
Wolff-Parkinson-White syndrome (gamma 2 subunit of
AMP-activated protein kinase), retinitis pigmentosa
(IMP dehydrogenase-1), and homocystinuria
(cystathionine beta-synthase).
Length = 111
Score = 26.1 bits (58), Expect = 3.8
Identities = 11/31 (35%), Positives = 18/31 (58%), Gaps = 1/31 (3%)
Query: 52 IVAAKGHQVIGFARRAEMIDAMAKENPDWKV 82
+V GH ++G R ++I A+A+ PD V
Sbjct: 29 VVDGDGH-LVGLLTRDDLIRALAEGGPDAPV 58
>gnl|CDD|189008 cd09601, M1_APN_2, Peptidase M1 Aminopeptidase N family incudes
tricorn interacting factor F3, Endoplasmic reticulum
aminopeptidase 1 (ERAP1), Aminopeptidase Q (APQ). This
M1 peptidase family includes eukaryotic and bacterial
members: aminopeptidase N (APN), aminopeptidase Q (APQ,
laeverin), endoplasmic reticulum aminopeptidase 1
(ERAP1) as well as tricorn interacting factor F3.
Aminopeptidase N (APN; CD13; Alanyl aminopeptidase; EC
3.4.11.2), a Type II integral membrane protease,
consists of a small N-terminal cytoplasmic domain, a
single transmembrane domain and a large extracellular
ectodomain that contains the active site. It
preferentially cleaves neutral amino acids from the
N-terminus of oligopeptides and is present in a variety
of human tissues and cell types (leukocyte, fibroblast,
endothelial and epithelial cells). APN expression is
dysregulated in inflammatory diseases such as chronic
pain, rheumatoid arthritis, multiple sclerosis, systemic
sclerosis, systemic lupus erythematosus,
polymyositis/dermatomyosytis and pulmonary sarcoidosis,
and is enhanced in tumor cells such as melanoma, renal,
prostate, pancreas, colon, gastric and thyroid cancers.
It is considered a marker of differentiation since it is
predominantly expressed on stem cells and on cells of
the granulocytic and monocytic lineages at distinct
stages of differentiation. Thus, APN inhibition may lead
to the development of anti-cancer and anti-inflammatory
drugs. ERAP1 also known as endoplasmic reticulum
aminopeptidase associated with antigen processing
(ERAAP), adipocyte derived leucine aminopeptidase
(A-LAP) or aminopeptidase regulating tumor necrosis
factor receptor I (THFRI) shedding (ARTS-1), associates
with the closely related ER aminopeptidase ERAP2, for
the final trimming of peptides within the ER for
presentation by MHC class I molecules. ERAP1 is
associated with ankylosing spondylitis (AS), an
inflammatory arthritis that predominantly affects the
spine. ERAP1 also aids in the shedding of membrane-bound
cytokine receptors. The tricorn interacting factor F3,
together with factors F1 and F2, degrades the tricorn
protease products, producing free amino acids, thus
completing the proteasomal degradation pathway. F3 is
homologous to F2, but not F1, and shows a strong
preference for glutamate in the P1' position. APQ, also
known as laeverin, is specifically expressed in human
embryo-derived extravillous trophoblasts (EVTs) that
invade the uterus during early placentation. It cleaves
the N-terminal amino acid of various peptides such as
angiotensin III, endokinin C, and kisspeptin-10, all
expressed in the placenta in large quantities. APN is a
receptor for coronaviruses, although the virus receptor
interaction site seems to be distinct from the enzymatic
site and aminopeptidase activity is not necessary for
viral infection. APNs are also putative Cry toxin
receptors. Cry1 proteins are pore-forming toxins that
bind to the midgut epithelial cell membrane of
susceptible insect larvae, causing extensive damage.
Several different toxins, including Cry1Aa, Cry1Ab,
Cry1Ac, Cry1Ba, Cry1Ca and Cry1Fa, have been shown to
bind to APNs; however, a direct role of APN in
cytotoxicity has been yet to be firmly established.
Length = 446
Score = 26.8 bits (60), Expect = 3.8
Identities = 14/62 (22%), Positives = 20/62 (32%), Gaps = 22/62 (35%)
Query: 62 GFARRAEMIDAMAKENPDWKV---------------------HSLKVDVTKDAEVVEAFD 100
GFA E + + P+W + H + V V E+ E FD
Sbjct: 316 GFATYMEYL-GVDHLEPEWNMWDQFVLDDLQSALALDSLASSHPISVPVETPDEISEIFD 374
Query: 101 WI 102
I
Sbjct: 375 AI 376
>gnl|CDD|234649 PRK00121, trmB, tRNA (guanine-N(7)-)-methyltransferase; Reviewed.
Length = 202
Score = 26.3 bits (59), Expect = 3.8
Identities = 10/20 (50%), Positives = 12/20 (60%), Gaps = 1/20 (5%)
Query: 61 IGFARRAEMIDAMAKENPDW 80
IGF + E + MAK NPD
Sbjct: 47 IGFGK-GEFLVEMAKANPDI 65
>gnl|CDD|183718 PRK12746, PRK12746, short chain dehydrogenase; Provisional.
Length = 254
Score = 26.5 bits (58), Expect = 3.8
Identities = 18/39 (46%), Positives = 22/39 (56%), Gaps = 1/39 (2%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQV-IGFARRAEMID 40
K+ +VTGAS GIG AI LA G V I + R + D
Sbjct: 7 KVALVTGASRGIGRAIAMRLANDGALVAIHYGRNKQAAD 45
>gnl|CDD|236075 PRK07683, PRK07683, aminotransferase A; Validated.
Length = 387
Score = 26.6 bits (59), Expect = 3.9
Identities = 13/29 (44%), Positives = 16/29 (55%), Gaps = 1/29 (3%)
Query: 2 SKIIVVTGASVGIGAAILRALAAKGHQVI 30
S+IIV GAS I A R + G +VI
Sbjct: 90 SEIIVTIGASEAIDIA-FRTILEPGTEVI 117
>gnl|CDD|187561 cd05251, NmrA_like_SDR_a, NmrA (a transcriptional regulator) and
HSCARG (an NADPH sensor) like proteins, atypical (a)
SDRs. NmrA and HSCARG like proteins. NmrA is a
negative transcriptional regulator of various fungi,
involved in the post-translational modulation of the
GATA-type transcription factor AreA. NmrA lacks the
canonical GXXGXXG NAD-binding motif and has altered
residues at the catalytic triad, including a Met
instead of the critical Tyr residue. NmrA may bind
nucleotides but appears to lack any dehydrogenase
activity. HSCARG has been identified as a putative
NADP-sensing molecule, and redistributes and
restructures in response to NADPH/NADP ratios. Like
NmrA, it lacks most of the active site residues of the
SDR family, but has an NAD(P)-binding motif similar to
the extended SDR family, GXXGXXG. SDRs are a
functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Atypical
SDRs are distinct from classical SDRs. 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 15-hydroxyprostaglandin dehydrogenase
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser and/or an Asn, 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. In addition to the Rossmann fold core
region typical of all SDRs, extended SDRs have a less
conserved C-terminal extension of approximately 100
amino acids, 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 ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 242
Score = 26.5 bits (59), Expect = 4.0
Identities = 11/31 (35%), Positives = 17/31 (54%), Gaps = 1/31 (3%)
Query: 5 IVVTGASVGIGAAILRALAAK-GHQVIGFAR 34
I+V GA+ G +++RAL G +V R
Sbjct: 1 ILVFGATGKQGGSVVRALLKDPGFKVRALTR 31
>gnl|CDD|224710 COG1797, CobB, Cobyrinic acid a,c-diamide synthase [Coenzyme
metabolism].
Length = 451
Score = 26.4 bits (59), Expect = 4.0
Identities = 11/33 (33%), Positives = 17/33 (51%), Gaps = 5/33 (15%)
Query: 5 IVVTGASVGIG-----AAILRALAAKGHQVIGF 32
+V+ G S G G ++RAL +G +V F
Sbjct: 3 VVIAGTSSGSGKTTVTLGLMRALRRRGLKVQPF 35
>gnl|CDD|214966 smart01002, AlaDh_PNT_C, Alanine dehydrogenase/PNT, C-terminal
domain. Alanine dehydrogenase catalyzes the
NAD-dependent reversible reductive amination of
pyruvate into alanine.
Length = 149
Score = 25.9 bits (58), Expect = 4.2
Identities = 16/67 (23%), Positives = 28/67 (41%), Gaps = 3/67 (4%)
Query: 5 IVVTGA-SVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIGF 63
+VV GA VG+GAA G +V R + ESL + ++ +
Sbjct: 23 VVVIGAGVVGLGAA--ATAKGLGAEVTVLDVRPARLRQLESLLGARFTTLYSQAELLEEA 80
Query: 64 ARRAEMI 70
+ A+++
Sbjct: 81 VKEADLV 87
>gnl|CDD|224732 COG1819, COG1819, Glycosyl transferases, related to
UDP-glucuronosyltransferase [Carbohydrate transport and
metabolism / Signal transduction mechanisms].
Length = 406
Score = 26.6 bits (59), Expect = 4.2
Identities = 16/74 (21%), Positives = 27/74 (36%), Gaps = 8/74 (10%)
Query: 1 MSKIIVVTGASVGI---GAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKG 57
KI+ V + G A+ + L +GH+V+ FA + +F E+ FV
Sbjct: 1 RMKILFVVCGAYGHVNPCLALGKELRRRGHEVV-FASTGKFKEFVEAAGLAFVAY----P 55
Query: 58 HQVIGFARRAEMID 71
+ A
Sbjct: 56 IRDSELATEDGKFA 69
>gnl|CDD|138873 PRK12320, PRK12320, hypothetical protein; Provisional.
Length = 699
Score = 26.5 bits (58), Expect = 4.2
Identities = 13/29 (44%), Positives = 18/29 (62%)
Query: 5 IVVTGASVGIGAAILRALAAKGHQVIGFA 33
I+VT A+ +G ++ R L A GH V G A
Sbjct: 3 ILVTDATGAVGRSVTRQLIAAGHTVSGIA 31
>gnl|CDD|176180 cd05276, p53_inducible_oxidoreductase, PIG3 p53-inducible quinone
oxidoreductase. PIG3 p53-inducible quinone
oxidoreductase, a medium chain dehydrogenase/reductase
family member, acts in the apoptotic pathway. PIG3
reduces ortho-quinones, but its apoptotic activity has
been attributed to oxidative stress generation, since
overexpression of PIG3 accumulates reactive oxygen
species. PIG3 resembles the MDR family member quinone
reductases, which catalyze the reduction of quinone to
hydroxyquinone. NAD(P)(H)-dependent oxidoreductases are
the major enzymes in the interconversion of alcohols and
aldehydes or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which has a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES.
These proteins typically form dimers (typically higher
plants, mammals) or tetramers (yeast, bacteria), and
have 2 tightly bound zinc atoms per subunit, a catalytic
zinc at the active site, and a structural zinc in a lobe
of the catalytic domain. NAD(H) binding occurs in the
cleft between the catalytic and coenzyme-binding domains
at the active site, and coenzyme binding induces a
conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
In human ADH catalysis, the zinc ion helps coordinate
the alcohol, followed by deprotonation of a histidine,
the ribose of NAD, a serine, then the alcohol, which
allows the transfer of a hydride to NAD+, creating NADH
and a zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 323
Score = 26.3 bits (59), Expect = 4.5
Identities = 15/42 (35%), Positives = 22/42 (52%), Gaps = 2/42 (4%)
Query: 7 VTGASVGIG-AAILRALAAKGHQVIGFARRAEMIDFAESLFA 47
+ G + G+G AAI A A G +VI A E ++ +L A
Sbjct: 145 IHGGASGVGTAAIQLAKAL-GARVIATAGSEEKLEACRALGA 185
>gnl|CDD|176206 cd08244, MDR_enoyl_red, Possible enoyl reductase. Member
identified as possible enoyl reductase of the MDR
family. 2-enoyl thioester reductase (ETR) catalyzes the
NADPH-dependent dependent conversion of trans-2-enoyl
acyl carrier protein/coenzyme A (ACP/CoA) to
acyl-(ACP/CoA) in fatty acid synthesis. 2-enoyl
thioester reductase activity has been linked in Candida
tropicalis as essential in maintaining mitiochondrial
respiratory function. This ETR family is a part of the
medium chain dehydrogenase/reductase family, but lack
the zinc coordination sites characteristic of the
alcohol dehydrogenases in this family.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which has a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. The N-terminal catalytic domain has a
distant homology to GroES. These proteins typically
form dimers (typically higher plants, mammals) or
tetramers (yeast, bacteria), and have 2 tightly bound
zinc atoms per subunit, a catalytic zinc at the active
site, and a structural zinc in a lobe of the catalytic
domain. NAD(H) binding occurs in the cleft between the
catalytic and coenzyme-binding domains at the active
site, and coenzyme binding induces a conformational
closing of this cleft. Coenzyme binding typically
precedes and contributes to substrate binding. Candida
tropicalis enoyl thioester reductase (Etr1p) catalyzes
the NADPH-dependent reduction of trans-2-enoyl
thioesters in mitochondrial fatty acid synthesis. Etr1p
forms homodimers, with each subunit containing a
nucleotide-binding Rossmann fold domain and a catalytic
domain.
Length = 324
Score = 26.6 bits (59), Expect = 4.5
Identities = 12/43 (27%), Positives = 22/43 (51%)
Query: 5 IVVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFA 47
++VT A+ G+G+ +++ A G V+G A +L A
Sbjct: 146 VLVTAAAGGLGSLLVQLAKAAGATVVGAAGGPAKTALVRALGA 188
>gnl|CDD|187575 cd05265, SDR_a1, atypical (a) SDRs, subgroup 1. Atypical SDRs in
this subgroup are poorly defined and have been
identified putatively as isoflavones reductase, sugar
dehydratase, mRNA binding protein etc. Atypical SDRs
are distinct from classical SDRs. Members of this
subgroup retain the canonical active site triad (though
not the upstream Asn found in most SDRs) but have an
unusual putative glycine-rich NAD(P)-binding motif,
GGXXXXG, in the usual location. Atypical SDRs generally
lack the catalytic residues characteristic of the SDRs,
and their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Atypical SDRs include biliverdin IX beta
reductase (BVR-B,aka flavin reductase), NMRa (a
negative transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane
reductase, isoflavone reductases, and others. SDRs are
a functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they 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 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
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. In addition to the Rossmann fold
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids, 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 ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 250
Score = 26.5 bits (59), Expect = 4.6
Identities = 12/30 (40%), Positives = 17/30 (56%)
Query: 5 IVVTGASVGIGAAILRALAAKGHQVIGFAR 34
I++ G + IG A++ L A GH V F R
Sbjct: 3 ILIIGGTRFIGKALVEELLAAGHDVTVFNR 32
>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 = 26.3 bits (59), Expect = 4.6
Identities = 12/33 (36%), Positives = 18/33 (54%)
Query: 14 IGAAILRALAAKGHQVIGFARRAEMIDFAESLF 46
+GAA+ R LAA G V G++R + I+
Sbjct: 143 LGAAVARRLAALGFPVSGWSRSPKDIEGVTCFH 175
>gnl|CDD|187573 cd05263, MupV_like_SDR_e, Pseudomonas fluorescens MupV-like,
extended (e) SDRs. This subgroup of extended SDR
family domains have the characteristic active site
tetrad and a well-conserved NAD(P)-binding motif. This
subgroup is not well characterized, its members are
annotated as having a variety of putative functions.
One characterized member is Pseudomonas fluorescens
MupV a protein involved in the biosynthesis of
Mupirocin, a polyketide-derived antibiotic. Extended
SDRs are distinct from classical SDRs. In addition to
the Rossmann fold (alpha/beta folding pattern with a
central beta-sheet) core region typical of all SDRs,
extended SDRs have a less conserved C-terminal
extension of approximately 100 amino acids. Extended
SDRs are a diverse collection of proteins, and include
isomerases, epimerases, oxidoreductases, and lyases;
they typically have a TGXXGXXG cofactor binding motif.
SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
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
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, 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. Atypical
SDRs generally lack the catalytic residues
characteristic of the SDRs, and their glycine-rich
NAD(P)-binding motif is often different from the forms
normally seen in classical or extended SDRs. 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
ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding
motif.
Length = 293
Score = 26.2 bits (58), Expect = 4.8
Identities = 11/54 (20%), Positives = 21/54 (38%), Gaps = 6/54 (11%)
Query: 5 IVVTGASVGIGAAILRALAAKGHQVIGFAR------RAEMIDFAESLFAFFVDI 52
+ VTG + +G +++ L G +V+ R E I+ A +
Sbjct: 1 VFVTGGTGFLGRHLVKRLLENGFKVLVLVRSESLGEAHERIEEAGLEADRVRVL 54
>gnl|CDD|135637 PRK05876, PRK05876, short chain dehydrogenase; Provisional.
Length = 275
Score = 26.5 bits (58), Expect = 4.8
Identities = 29/119 (24%), Positives = 46/119 (38%), Gaps = 29/119 (24%)
Query: 6 VVTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIGFAR 65
V+TG + GIG A A +G +V+ + D + V+ + A+G
Sbjct: 10 VITGGASGIGLATGTEFARRGARVV-------LGDVDKPGLRQAVNHLRAEG-------- 54
Query: 66 RAEMIDAMAKENPDWKVHSLKVDVTKDAEVVEAFDWINNKFGHIDVMINNAGVNEFAPV 124
+ VH + DV EV D GH+DV+ +NAG+ P+
Sbjct: 55 --------------FDVHGVMCDVRHREEVTHLADEAFRLLGHVDVVFSNAGIVVGGPI 99
>gnl|CDD|176203 cd08241, QOR1, Quinone oxidoreductase (QOR). QOR catalyzes the
conversion of a quinone + NAD(P)H to a hydroquinone +
NAD(P)+. Quinones are cyclic diones derived from
aromatic compounds. Membrane bound QOR acts in the
respiratory chains of bacteria and mitochondria, while
soluble QOR acts to protect from toxic quinones (e.g.
DT-diaphorase) or as a soluble eye-lens protein in some
vertebrates (e.g. zeta-crystalin). QOR reduces quinones
through a semi-quinone intermediate via a
NAD(P)H-dependent single electron transfer. QOR is a
member of the medium chain dehydrogenase/reductase
family, but lacks the zinc-binding sites of the
prototypical alcohol dehydrogenases of this group.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which has a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES. These
proteins typically form dimers (typically higher plants,
mammals) or tetramers (yeast, bacteria), and have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site, and a structural zinc in a lobe of
the catalytic domain. NAD(H)-binding occurs in the
cleft between the catalytic and coenzyme-binding domains
at the active site, and coenzyme binding induces a
conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
In human ADH catalysis, the zinc ion helps coordinate
the alcohol, followed by deprotonation of a histidine,
the ribose of NAD, a serine, then the alcohol, which
allows the transfer of a hydride to NAD+, creating NADH
and a zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 323
Score = 26.3 bits (59), Expect = 4.9
Identities = 16/45 (35%), Positives = 24/45 (53%), Gaps = 6/45 (13%)
Query: 6 VVTGASVGIGAA---ILRALAAKGHQVIGFARRAEMIDFAESLFA 47
+V GA+ G+G A + +AL A+ VI A E + A +L A
Sbjct: 144 LVLGAAGGVGLAAVQLAKALGAR---VIAAASSEEKLALARALGA 185
>gnl|CDD|235824 PRK06545, PRK06545, prephenate dehydrogenase; Validated.
Length = 359
Score = 26.4 bits (59), Expect = 5.0
Identities = 13/59 (22%), Positives = 23/59 (38%), Gaps = 7/59 (11%)
Query: 14 IGAAILRALAAKGHQV--IGFARRAEMIDFAESLFAFFVDIVAAKGHQVIGFARRAEMI 70
IG ++ A+ A G V IG+ A + A ++ + A A++I
Sbjct: 11 IGGSLALAIKAAGPDVFIIGYDPSAAQLARALGF-----GVIDELAADLQRAAAEADLI 64
>gnl|CDD|182998 PRK11150, rfaD, ADP-L-glycero-D-mannoheptose-6-epimerase;
Provisional.
Length = 308
Score = 26.2 bits (58), Expect = 5.1
Identities = 12/27 (44%), Positives = 18/27 (66%)
Query: 4 IIVVTGASVGIGAAILRALAAKGHQVI 30
+I+VTG + IG+ I++AL KG I
Sbjct: 1 MIIVTGGAGFIGSNIVKALNDKGITDI 27
>gnl|CDD|236178 PRK08187, PRK08187, pyruvate kinase; Validated.
Length = 493
Score = 26.1 bits (58), Expect = 5.2
Identities = 30/82 (36%), Positives = 37/82 (45%), Gaps = 19/82 (23%)
Query: 4 IIVVTGASVGIGAAILRA-LAAKGHQVIGFARRAEMIDFAESLF---AFFVDIVAAKGHQ 59
+IV G I R LA + IGF R AEM + E L+ A V ++ A Q
Sbjct: 375 LIVQAAGRQPFGVMIARGDLAVE----IGFERLAEMQE--EILWLCEAAHVPVIWAT--Q 426
Query: 60 VI------GFARRAEMIDA-MA 74
V+ G RAEM DA MA
Sbjct: 427 VLEGLVKKGLPSRAEMTDAAMA 448
>gnl|CDD|237093 PRK12409, PRK12409, D-amino acid dehydrogenase small subunit;
Provisional.
Length = 410
Score = 26.1 bits (58), Expect = 5.3
Identities = 14/35 (40%), Positives = 18/35 (51%), Gaps = 2/35 (5%)
Query: 1 MSKIIVVTGASVGIGAAILRALAAKGHQVIGFARR 35
MS I V+ G+ A ALA +G+QV F R
Sbjct: 1 MSHIAVIGAGITGVTTAY--ALAQRGYQVTVFDRH 33
>gnl|CDD|180399 PRK06101, PRK06101, short chain dehydrogenase; Provisional.
Length = 240
Score = 26.0 bits (57), Expect = 5.3
Identities = 13/36 (36%), Positives = 21/36 (58%)
Query: 5 IVVTGASVGIGAAILRALAAKGHQVIGFARRAEMID 40
+++TGA+ GIG + A +G QVI R ++D
Sbjct: 4 VLITGATSGIGKQLALDYAKQGWQVIACGRNQSVLD 39
>gnl|CDD|215029 PLN00016, PLN00016, RNA-binding protein; Provisional.
Length = 378
Score = 26.2 bits (58), Expect = 5.4
Identities = 14/54 (25%), Positives = 17/54 (31%), Gaps = 15/54 (27%)
Query: 26 GHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIGFARRAEMIDAMAKENPD 79
GH IGF + + GH+V F R E M KE
Sbjct: 64 GHAFIGF---------------YLAKELVKAGHEVTLFTRGKEPSQKMKKEPFS 102
>gnl|CDD|238506 cd01034, EriC_like, ClC chloride channel family. These protein
sequences, closely related to the ClC Eric family, are
putative halogen ion (Cl-, Br- and I-) transport
proteins found in eubacteria. They belong to the ClC
superfamily of chloride ion channels, which share a
unique double-barreled architecture and
voltage-dependent gating mechanism. This superfamily
lacks any structural or sequence similarity to other
known ion channels and exhibit unique properties of ion
permeation and gating. The voltage-dependent gating is
conferred by the permeating anion itself, acting as the
gating charge.
Length = 390
Score = 26.0 bits (58), Expect = 5.4
Identities = 12/37 (32%), Positives = 20/37 (54%), Gaps = 7/37 (18%)
Query: 6 VVTGASVG-------IGAAILRALAAKGHQVIGFARR 35
++ GASVG IGAA++ A+ + + G + R
Sbjct: 91 LLGGASVGREGPSVQIGAAVMLAIGRRLPKWGGLSER 127
>gnl|CDD|180949 PRK07370, PRK07370, enoyl-(acyl carrier protein) reductase;
Validated.
Length = 258
Score = 26.2 bits (58), Expect = 5.5
Identities = 11/29 (37%), Positives = 19/29 (65%)
Query: 85 LKVDVTKDAEVVEAFDWINNKFGHIDVMI 113
L DV DA++ E F+ I K+G +D+++
Sbjct: 64 LPCDVQDDAQIEETFETIKQKWGKLDILV 92
>gnl|CDD|224014 COG1089, Gmd, GDP-D-mannose dehydratase [Cell envelope
biogenesis, outer membrane].
Length = 345
Score = 26.2 bits (58), Expect = 5.6
Identities = 12/36 (33%), Positives = 21/36 (58%)
Query: 1 MSKIIVVTGASVGIGAAILRALAAKGHQVIGFARRA 36
M K+ ++TG + G+ + L KG++V G RR+
Sbjct: 1 MGKVALITGITGQDGSYLAELLLEKGYEVHGIKRRS 36
>gnl|CDD|187581 cd05273, GME-like_SDR_e, Arabidopsis thaliana
GDP-mannose-3',5'-epimerase (GME)-like, extended (e)
SDRs. This subgroup of NDP-sugar
epimerase/dehydratases are extended SDRs; they have the
characteristic active site tetrad, and an NAD-binding
motif: TGXXGXX[AG], which is a close match to the
canonical NAD-binding motif. Members include
Arabidopsis thaliana GDP-mannose-3',5'-epimerase (GME)
which catalyzes the epimerization of two positions of
GDP-alpha-D-mannose to form GDP-beta-L-galactose.
Extended SDRs are distinct from classical SDRs. In
addition to the Rossmann fold (alpha/beta folding
pattern with a central beta-sheet) core region typical
of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
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
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, 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. Atypical
SDRs generally lack the catalytic residues
characteristic of the SDRs, and their glycine-rich
NAD(P)-binding motif is often different from the forms
normally seen in classical or extended SDRs. 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
ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding
motif.
Length = 328
Score = 26.3 bits (58), Expect = 5.6
Identities = 12/27 (44%), Positives = 16/27 (59%)
Query: 5 IVVTGASVGIGAAILRALAAKGHQVIG 31
+VTGA IG+ + L A+GH V G
Sbjct: 3 ALVTGAGGFIGSHLAERLKAEGHYVRG 29
>gnl|CDD|234436 TIGR03997, mycofact_OYE_2, mycofactocin system FadH/OYE family
oxidoreductase 2. The yeast protein called old yellow
enzyme and FadH from Escherichia coli (2,4-dienoyl CoA
reductase) are enzymes with 4Fe-4S, FMN, and FAD
prosthetic groups, and interact with NADPH as well as
substrate. Members of this related protein family occur
in the vicinity of the putative mycofactocin
biosynthesis operon in a number of Actinobacteria such
as Frankia sp. and Rhodococcus sp., in Pelotomaculum
thermopropionicum SI (Firmicutes), and in Geobacter
uraniireducens Rf4 (Deltaproteobacteria). The function
of this oxidoreductase is unknown.
Length = 645
Score = 26.2 bits (58), Expect = 6.0
Identities = 12/35 (34%), Positives = 18/35 (51%), Gaps = 2/35 (5%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAE 37
+++VV G G+ AA A +GH+V F R
Sbjct: 381 RVLVVGGGPAGLEAA--ATAARRGHRVTLFEREDR 413
>gnl|CDD|235225 PRK04143, PRK04143, hypothetical protein; Provisional.
Length = 264
Score = 26.1 bits (58), Expect = 6.0
Identities = 8/29 (27%), Positives = 13/29 (44%)
Query: 63 FARRAEMIDAMAKENPDWKVHSLKVDVTK 91
AR +I+ + KE V L D+ +
Sbjct: 5 KARLEYLINYLQKEQLTSDVLPLPNDLEE 33
>gnl|CDD|181580 PRK08912, PRK08912, hypothetical protein; Provisional.
Length = 387
Score = 26.1 bits (58), Expect = 6.3
Identities = 13/33 (39%), Positives = 16/33 (48%), Gaps = 2/33 (6%)
Query: 3 KIIVVTGASVG--IGAAILRALAAKGHQVIGFA 33
KI +TG VG A L + AK HQ + F
Sbjct: 232 KIFSLTGWKVGFVCAAPPLLRVLAKAHQFLTFT 264
>gnl|CDD|131732 TIGR02685, pter_reduc_Leis, pteridine reductase. Pteridine
reductase is an enzyme used by trypanosomatids
(including Trypanosoma cruzi and Leishmania major) to
obtain reduced pteridines by salvage rather than
biosynthetic pathways. Enzymes in T. cruzi described as
pteridine reductase 1 (PTR1) and pteridine reductase 2
(PTR2) have different activity profiles. PTR1 is more
active with with fully oxidized biopterin and folate
than with reduced forms, while PTR2 reduces
dihydrobiopterin and dihydrofolate but not oxidized
pteridines. T. cruzi PTR1 and PTR2 are more similar to
each other in sequence than either is to the pteridine
reductase of Leishmania major, and all are included in
this family.
Length = 267
Score = 26.0 bits (57), Expect = 6.7
Identities = 13/32 (40%), Positives = 21/32 (65%)
Query: 6 VVTGASVGIGAAILRALAAKGHQVIGFARRAE 37
VVTGA+ IG++I AL +G++V+ R+
Sbjct: 5 VVTGAAKRIGSSIAVALHQEGYRVVLHYHRSA 36
>gnl|CDD|189010 cd09603, M1_APN_4, Peptidase M1 family Aminopeptidase N. This
family contains mostly bacterial and some archaeal
aminopeptidase N (APN; CD13; Alanyl aminopeptidase; EC
3.4.11.2), a Type II integral membrane protease
belonging to the M1 gluzincin family. APN consists of a
small N-terminal cytoplasmic domain, a single
transmembrane domain and a large extracellular
ectodomain that contains the active site. It
preferentially cleaves neutral amino acids from the
N-terminus of oligopeptides and, in higher eukaryotes,
is present in a variety of human tissues and cell types
(leukocyte, fibroblast, endothelial and epithelial
cells). APN expression is dysregulated in inflammatory
diseases such as chronic pain, rheumatoid arthritis,
multiple sclerosis, systemic sclerosis, systemic lupus
erythematosus, polymyositis/dermatomyosytis and
pulmonary sarcoidosis, and is enhanced in tumor cells
such as melanoma, renal, prostate, pancreas, colon,
gastric and thyroid cancers. It is predominantly
expressed on stem cells and on cells of the granulocytic
and monocytic lineages at distinct stages of
differentiation, thus considered a marker of
differentiation. Thus, APN inhibition may lead to the
development of anti-cancer and anti-inflammatory drugs.
APNs are also present in many pathogenic bacteria and
represent potential drug targets, Some APNs have been
used commercially, such as one from Lactococcus lactis
used in the food industry. APN also serves as a receptor
for coronaviruses, although the virus receptor
interaction site seems to be distinct from the enzymatic
site and aminopeptidase activity is not necessary for
viral infection. APNs have also been extensively studied
as putative Cry toxin receptors. Cry1 proteins are
pore-forming toxins that bind to the midgut epithelial
cell membrane of susceptible insect larvae, causing
extensive damage. Several different toxins, including
Cry1Aa, Cry1Ab, Cry1Ac, Cry1Ba, Cry1Ca and Cry1Fa, have
been shown to bind to APNs; however, a direct role of
APN in cytotoxicity has been yet to be firmly
established.
Length = 415
Score = 26.0 bits (58), Expect = 6.7
Identities = 15/40 (37%), Positives = 19/40 (47%), Gaps = 2/40 (5%)
Query: 7 VTGASVGIGAAILRALAAKGHQVIGFARRAEMIDFAESLF 46
T V + + LAA + FAR EM+DF E LF
Sbjct: 188 TTAGGVPVVYYVPPGLAADARRA--FARTPEMLDFFEELF 225
>gnl|CDD|234094 TIGR03026, NDP-sugDHase, nucleotide sugar dehydrogenase. Enzymes
in this family catalyze the NAD-dependent
alcohol-to-acid oxidation of nucleotide-linked sugars.
Examples include UDP-glucose 6-dehydrogenase (1.1.1.22)
, GDP-mannose 6-dehydrogenase (1.1.1.132) ,
UDP-N-acetylglucosamine 6-dehydrogenase (1.1.1.136),
UDP-N-acetyl-D-galactosaminuronic acid dehydrogenase
and UDP-N-acetyl-D-mannosaminuronic acid dehydrogenase.
These enzymes are most often involved in the
biosynthesis of polysaccharides and are often found in
operons devoted to that purpose. All of these enzymes
contain three Pfam domains, pfam03721, pfam00984, and
pfam03720 for the N-terminal, central, and C-terminal
regions respectively.
Length = 409
Score = 26.0 bits (58), Expect = 6.9
Identities = 13/31 (41%), Positives = 15/31 (48%), Gaps = 2/31 (6%)
Query: 2 SKIIVVTGASVGIGAAILRALAAKGHQVIGF 32
KI V+ VG+ A L LA GH V G
Sbjct: 1 MKIAVIGLGYVGLPLAAL--LADLGHDVTGV 29
>gnl|CDD|187541 cd05230, UGD_SDR_e, UDP-glucuronate decarboxylase (UGD) and
related proteins, extended (e) SDRs. UGD catalyzes the
formation of UDP-xylose from UDP-glucuronate; it is an
extended-SDR, and has the characteristic glycine-rich
NAD-binding pattern, TGXXGXXG, and active site tetrad.
Extended SDRs are distinct from classical SDRs. In
addition to the Rossmann fold (alpha/beta folding
pattern with a central beta-sheet) core region typical
of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
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
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, 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. Atypical
SDRs generally lack the catalytic residues
characteristic of the SDRs, and their glycine-rich
NAD(P)-binding motif is often different from the forms
normally seen in classical or extended SDRs. 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
ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding
motif.
Length = 305
Score = 25.7 bits (57), Expect = 7.1
Identities = 10/29 (34%), Positives = 17/29 (58%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIG 31
K I++TG + +G+ + L GH+VI
Sbjct: 1 KRILITGGAGFLGSHLCDRLLEDGHEVIC 29
>gnl|CDD|99975 cd03802, GT1_AviGT4_like, This family is most closely related to
the GT1 family of glycosyltransferases. aviGT4 in
Streptomyces viridochromogenes has been shown to be
involved in biosynthesis of oligosaccharide antibiotic
avilamycin A. Inactivation of aviGT4 resulted in a
mutant that accumulated a novel avilamycin derivative
lacking the terminal eurekanate residue.
Length = 335
Score = 25.6 bits (57), Expect = 7.5
Identities = 16/64 (25%), Positives = 23/64 (35%), Gaps = 8/64 (12%)
Query: 16 AAILRALAAKGHQVIGFA--------RRAEMIDFAESLFAFFVDIVAAKGHQVIGFARRA 67
AA+ L A+GH+V FA ++ L A D A+ + A A
Sbjct: 26 AALTEGLVARGHEVTLFASGDSKTAAPLVPVVPEPLRLDAPGRDRAEAEALALAERALAA 85
Query: 68 EMID 71
D
Sbjct: 86 GDFD 89
>gnl|CDD|218851 pfam06007, PhnJ, Phosphonate metabolism protein PhnJ. This
family consists of several bacterial phosphonate
metabolism (PhnJ) sequences. The exact role that PhnJ
plays in phosphonate utilisation is unknown.
Length = 279
Score = 25.7 bits (57), Expect = 7.6
Identities = 12/22 (54%), Positives = 16/22 (72%), Gaps = 2/22 (9%)
Query: 17 AILRALAAKGHQVIGFARRAEM 38
A+L+A+A G+QV FA R EM
Sbjct: 21 ALLKAVAIPGYQV-PFASR-EM 40
>gnl|CDD|202773 pfam03807, F420_oxidored, NADP oxidoreductase coenzyme
F420-dependent.
Length = 93
Score = 24.9 bits (55), Expect = 8.1
Identities = 15/57 (26%), Positives = 24/57 (42%), Gaps = 4/57 (7%)
Query: 14 IGAAILRALAAKGHQVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIGFARRAEMI 70
+G A+ R LAA GH+V+ R + A +L V A A+++
Sbjct: 10 MGEALARGLAAAGHEVVIANSRNP--EKAAALAEELG--VKATAVSNEEAVEEADVV 62
>gnl|CDD|235756 PRK06259, PRK06259, succinate dehydrogenase/fumarate reductase
iron-sulfur subunit; Provisional.
Length = 486
Score = 25.7 bits (57), Expect = 8.3
Identities = 7/24 (29%), Positives = 14/24 (58%)
Query: 84 SLKVDVTKDAEVVEAFDWINNKFG 107
S +V V + V++A ++IN +
Sbjct: 22 SYEVPVKEGMTVLDALEYINKTYD 45
>gnl|CDD|187619 cd05361, haloalcohol_DH_SDR_c-like, haloalcohol dehalogenase,
classical (c) SDRs. Dehalogenases cleave
carbon-halogen bonds. Haloalcohol dehalogenase show low
sequence similarity to short-chain
dehydrogenases/reductases (SDRs). Like the SDRs,
haloalcohol dehalogenases have a conserved catalytic
triad (Ser-Tyr-Lys/Arg), and form a Rossmann fold.
However, the normal classical SDR NAD(P)-binding motif
(TGXXGXG) and NAD-binding function is replaced with a
halide binding site, allowing the enzyme to catalyze a
dehalogenation reaction. 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
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-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 ketoacyl reductases 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 = 242
Score = 25.6 bits (56), Expect = 8.3
Identities = 15/44 (34%), Positives = 18/44 (40%), Gaps = 4/44 (9%)
Query: 4 IIVVTGASVGIGAAILRALAAKGHQVIG----FARRAEMIDFAE 43
I +VT A G A AL G+ V+ FA AE F
Sbjct: 3 IALVTHARHFAGPASAEALTEDGYTVVCHDASFADAAERQAFES 46
>gnl|CDD|224012 COG1087, GalE, UDP-glucose 4-epimerase [Cell envelope biogenesis,
outer membrane].
Length = 329
Score = 25.6 bits (57), Expect = 8.3
Identities = 10/26 (38%), Positives = 17/26 (65%)
Query: 5 IVVTGASVGIGAAILRALAAKGHQVI 30
++VTG + IG+ +R L GH+V+
Sbjct: 3 VLVTGGAGYIGSHTVRQLLKTGHEVV 28
>gnl|CDD|237526 PRK13837, PRK13837, two-component VirA-like sensor kinase;
Provisional.
Length = 828
Score = 25.8 bits (57), Expect = 8.4
Identities = 8/25 (32%), Positives = 16/25 (64%)
Query: 51 DIVAAKGHQVIGFARRAEMIDAMAK 75
+ +AA G++ +GF+ A I ++K
Sbjct: 715 EKLAALGYEPVGFSTLAAAIAWISK 739
>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 = 25.6 bits (57), Expect = 8.4
Identities = 11/24 (45%), Positives = 12/24 (50%)
Query: 13 GIGAAILRALAAKGHQVIGFARRA 36
IG AI R LA +V AR A
Sbjct: 142 SIGRAIERRLAPFEVRVTRVARTA 165
>gnl|CDD|153353 cd07669, BAR_SNX33, The Bin/Amphiphysin/Rvs (BAR) domain of Sorting
Nexin 33. BAR domains are dimerization, lipid binding
and curvature sensing modules found in many different
proteins with diverse functions. Sorting nexins (SNXs)
are Phox homology (PX) domain containing proteins that
are involved in regulating membrane traffic and protein
sorting in the endosomal system. SNXs differ from each
other in their lipid-binding specificity, subcellular
localization and specific function in the endocytic
pathway. A subset of SNXs also contain BAR domains. The
PX-BAR structural unit determines the specific membrane
targeting of SNXs. SNX33 interacts with Wiskott-Aldrich
syndrome protein (WASP) and plays a role in the
maintenance of cell shape and cell cycle progression. It
modulates the shedding and endocytosis of cellular prion
protein (PrP(c)) and amyloid precursor protein (APP).
BAR domains form dimers that bind to membranes, induce
membrane bending and curvature, and may also be involved
in protein-protein interactions.
Length = 207
Score = 25.3 bits (55), Expect = 8.6
Identities = 13/39 (33%), Positives = 20/39 (51%)
Query: 28 QVIGFARRAEMIDFAESLFAFFVDIVAAKGHQVIGFARR 66
+V+GFA +AEM F + F ++ Q I F +R
Sbjct: 157 RVVGFALQAEMNHFHQRRELDFKQMMQHYLRQQIIFYQR 195
>gnl|CDD|187661 cd08958, FR_SDR_e, flavonoid reductase (FR), extended (e) SDRs.
This subgroup contains FRs of the extended SDR-type and
related proteins. These FRs act in the NADP-dependent
reduction of flavonoids, ketone-containing plant
secondary metabolites; they have the characteristic
active site triad of the SDRs (though not the upstream
active site Asn) and a NADP-binding motif that is very
similar to the typical extended SDR motif. Extended
SDRs are distinct from classical SDRs. In addition to
the Rossmann fold (alpha/beta folding pattern with a
central beta-sheet) core region typical of all SDRs,
extended SDRs have a less conserved C-terminal
extension of approximately 100 amino acids. Extended
SDRs are a diverse collection of proteins, and include
isomerases, epimerases, oxidoreductases, and lyases;
they typically have a TGXXGXXG cofactor binding motif.
SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
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
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, 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. Atypical
SDRs generally lack the catalytic residues
characteristic of the SDRs, and their glycine-rich
NAD(P)-binding motif is often different from the forms
normally seen in classical or extended SDRs. 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
ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding
motif.
Length = 293
Score = 25.6 bits (57), Expect = 8.6
Identities = 11/28 (39%), Positives = 17/28 (60%)
Query: 7 VTGASVGIGAAILRALAAKGHQVIGFAR 34
VTGAS IG+ +++ L +G+ V R
Sbjct: 3 VTGASGFIGSWLVKRLLQRGYTVRATVR 30
>gnl|CDD|221804 pfam12847, Methyltransf_18, Methyltransferase domain. Protein in
this family function as methyltransferases.
Length = 104
Score = 25.0 bits (55), Expect = 9.4
Identities = 9/52 (17%), Positives = 18/52 (34%), Gaps = 3/52 (5%)
Query: 54 AAKGHQVIGFARRAEMIDAMAKENPDWKVHSLKV---DVTKDAEVVEAFDWI 102
G +V G EM++ + + D +++E FD +
Sbjct: 22 LFPGARVTGVDLSPEMLELARENAKLALGPRITFVQGDAPDALDLLEGFDAV 73
>gnl|CDD|224996 COG2085, COG2085, Predicted dinucleotide-binding enzymes [General
function prediction only].
Length = 211
Score = 25.4 bits (56), Expect = 9.9
Identities = 13/35 (37%), Positives = 18/35 (51%), Gaps = 1/35 (2%)
Query: 3 KIIVVTGASVGIGAAILRALAAKGHQVIGFARRAE 37
II + G IG+A+ LA GH+VI + R
Sbjct: 2 MIIAIIGTG-NIGSALALRLAKAGHEVIIGSSRGP 35
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
0.324 0.136 0.396
Gapped
Lambda K H
0.267 0.0831 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,794,115
Number of extensions: 634123
Number of successful extensions: 2273
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2105
Number of HSP's successfully gapped: 573
Length of query: 125
Length of database: 10,937,602
Length adjustment: 85
Effective length of query: 40
Effective length of database: 7,167,512
Effective search space: 286700480
Effective search space used: 286700480
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (24.0 bits)