RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12454
(113 letters)
>gnl|CDD|235546 PRK05653, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Validated.
Length = 246
Score = 111 bits (281), Expect = 6e-32
Identities = 47/119 (39%), Positives = 59/119 (49%), Gaps = 10/119 (8%)
Query: 3 MDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIY 62
M L+GK ALVTG + GIGRA L GAKV I D N+ E LA + R G A
Sbjct: 1 MSLQGKTALVTGASRGIGRAIALRLAADGAKVVIYDSNEEAAEALAAELRAAGG--EARV 58
Query: 63 CPCDVTDYPQFEEAFQITLQKLGGLDIVINNAGIFND-RFWELE-------VDVNLVGT 113
DV+D + ++ G LDI++NNAGI D + +DVNL GT
Sbjct: 59 LVFDVSDEAAVRALIEAAVEAFGALDILVNNAGITRDALLPRMSEEDWDRVIDVNLTGT 117
>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 = 110 bits (278), Expect = 2e-31
Identities = 48/116 (41%), Positives = 69/116 (59%), Gaps = 12/116 (10%)
Query: 8 KVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPCDV 67
KVA++TGGA+GIG A + LLK GAKV+I D N++ G A + + +A + CDV
Sbjct: 1 KVAIITGGASGIGLATAKLLLKKGAKVAILDRNENPGA--AAELQAINPKVKATFVQCDV 58
Query: 68 TDYPQFEEAFQITLQKLGGLDIVINNAGIFNDRF----------WELEVDVNLVGT 113
T + Q AF+ ++K G +DI+INNAGI +++ WE +DVNL G
Sbjct: 59 TSWEQLAAAFKKAIEKFGRVDILINNAGILDEKSYLFAGKLPPPWEKTIDVNLTGV 114
>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 = 104 bits (262), Expect = 4e-29
Identities = 48/114 (42%), Positives = 64/114 (56%), Gaps = 11/114 (9%)
Query: 7 GKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPCD 66
GKVALVTGGA+GIG A + L GA V + DI+ + E +AE G RA+ CD
Sbjct: 1 GKVALVTGGASGIGLAIAKRLAAEGAAVVVADIDPEIAEKVAEA---AQGGPRALGVQCD 57
Query: 67 VTDYPQFEEAFQITLQKLGGLDIVINNAGIF--------NDRFWELEVDVNLVG 112
VT Q + AF+ + + GGLDIV++NAGI + W +D+NL G
Sbjct: 58 VTSEAQVQSAFEQAVLEFGGLDIVVSNAGIATSSPIAETSLEDWNRSMDINLTG 111
>gnl|CDD|183775 PRK12826, PRK12826, 3-ketoacyl-(acyl-carrier-protein) reductase;
Reviewed.
Length = 251
Score = 103 bits (260), Expect = 9e-29
Identities = 47/118 (39%), Positives = 59/118 (50%), Gaps = 10/118 (8%)
Query: 4 DLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYC 63
DL+G+VALVTG A GIGRA L GA+V + DI AE G RA
Sbjct: 3 DLEGRVALVTGAARGIGRAIAVRLAADGAEVIVVDICGDDAAATAELVEAAGGKARAR-- 60
Query: 64 PCDVTDYPQFEEAFQITLQKLGGLDIVINNAGIFND-RFWELE-------VDVNLVGT 113
DV D + A ++ G LDI++ NAGIF F E++ +DVNL GT
Sbjct: 61 QVDVRDRAALKAAVAAGVEDFGRLDILVANAGIFPLTPFAEMDDEQWERVIDVNLTGT 118
>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 = 100 bits (250), Expect = 3e-27
Identities = 41/122 (33%), Positives = 59/122 (48%), Gaps = 11/122 (9%)
Query: 3 MDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSI-CDINDSVGEDLAEQWRTKYGPNRAI 61
MDL GKVALVTG ++GIGRA L + GA+V + ++ + + G RA
Sbjct: 1 MDLSGKVALVTGASSGIGRAIARALAREGARVVVAARRSEEEAAEALAAAIKEAGGGRAA 60
Query: 62 YCPCDVTDYP-QFEEAFQITLQKLGGLDIVINNAGIFNDR---------FWELEVDVNLV 111
DV+D E ++ G +DI++NNAGI W+ +DVNL+
Sbjct: 61 AVAADVSDDEESVEALVAAAEEEFGRIDILVNNAGIAGPDAPLEELTEEDWDRVIDVNLL 120
Query: 112 GT 113
G
Sbjct: 121 GA 122
>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 = 98.5 bits (246), Expect = 1e-26
Identities = 46/122 (37%), Positives = 65/122 (53%), Gaps = 20/122 (16%)
Query: 6 KGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPC 65
KG VA+VTGGA+G+G A E LL GAKV I D+ +S GE +A+ + + P
Sbjct: 1 KGLVAVVTGGASGLGLATVERLLAQGAKVVILDLPNSPGETVAK------LGDNCRFVPV 54
Query: 66 DVTDYPQFEEAFQITLQKLGGLDIVINNAGI------FNDR--------FWELEVDVNLV 111
DVT + A + K G LDIV+N AGI +N + ++ ++VNL+
Sbjct: 55 DVTSEKDVKAALALAKAKFGRLDIVVNCAGIAVAAKTYNKKGQQPHSLELFQRVINVNLI 114
Query: 112 GT 113
GT
Sbjct: 115 GT 116
>gnl|CDD|235975 PRK07231, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 251
Score = 98.0 bits (245), Expect = 2e-26
Identities = 38/119 (31%), Positives = 57/119 (47%), Gaps = 12/119 (10%)
Query: 3 MDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIY 62
M L+GKVA+VTG ++GIG GA+V + D N+ E +A + RAI
Sbjct: 1 MRLEGKVAIVTGASSGIGEGIARRFAAEGARVVVTDRNEEAAERVAAEIL---AGGRAIA 57
Query: 63 CPCDVTDYPQFEEAFQITLQKLGGLDIVINNAGIF--NDRFWELE-------VDVNLVG 112
DV+D E A L++ G +DI++NNAG N +++ VN+
Sbjct: 58 VAADVSDEADVEAAVAAALERFGSVDILVNNAGTTHRNGPLLDVDEAEFDRIFAVNVKS 116
>gnl|CDD|236241 PRK08324, PRK08324, short chain dehydrogenase; Validated.
Length = 681
Score = 101 bits (254), Expect = 2e-26
Identities = 47/116 (40%), Positives = 62/116 (53%), Gaps = 11/116 (9%)
Query: 5 LKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCP 64
L GKVALVTG A GIG+A + L GA V + D+++ E A + GP+RA+
Sbjct: 420 LAGKVALVTGAAGGIGKATAKRLAAEGACVVLADLDEEAAEAAAAELG---GPDRALGVA 476
Query: 65 CDVTDYPQFEEAFQITLQKLGGLDIVINNAGIF--------NDRFWELEVDVNLVG 112
CDVTD + AF+ GG+DIV++NAGI +D W DVN G
Sbjct: 477 CDVTDEAAVQAAFEEAALAFGGVDIVVSNAGIAISGPIEETSDEDWRRSFDVNATG 532
>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 = 96.2 bits (240), Expect = 6e-26
Identities = 42/112 (37%), Positives = 57/112 (50%), Gaps = 11/112 (9%)
Query: 10 ALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPCDVTD 69
ALVTG ++GIGRA L + GAKV + D N+ E LAE + A+ DV+D
Sbjct: 1 ALVTGASSGIGRAIARRLAREGAKVVLADRNE---EALAELAAIEALGGNAVAVQADVSD 57
Query: 70 YPQFEEAFQITLQKLGGLDIVINNAGIFNDRF--------WELEVDVNLVGT 113
E + L++ G LDI++NNAGI W+ +DVNL G
Sbjct: 58 EEDVEALVEEALEEFGRLDILVNNAGIARPGPLEELTDEDWDRVLDVNLTGV 109
>gnl|CDD|237100 PRK12429, PRK12429, 3-hydroxybutyrate dehydrogenase; Provisional.
Length = 258
Score = 93.8 bits (234), Expect = 9e-25
Identities = 47/116 (40%), Positives = 58/116 (50%), Gaps = 10/116 (8%)
Query: 5 LKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCP 64
LKGKVALVTG A+GIG L K GAKV I D+ND AE K G +AI
Sbjct: 2 LKGKVALVTGAASGIGLEIALALAKEGAKVVIADLNDEAAAAAAEA-LQKAGG-KAIGVA 59
Query: 65 CDVTDYPQFEEAFQITLQKLGGLDIVINNAGI--------FNDRFWELEVDVNLVG 112
DVTD ++ GG+DI++NNAGI F W+ + + L G
Sbjct: 60 MDVTDEEAINAGIDYAVETFGGVDILVNNAGIQHVAPIEDFPTEKWKKMIAIMLDG 115
>gnl|CDD|237218 PRK12825, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 249
Score = 93.4 bits (233), Expect = 1e-24
Identities = 44/120 (36%), Positives = 61/120 (50%), Gaps = 11/120 (9%)
Query: 3 MDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSI-CDINDSVGEDLAEQWRTKYGPNRAI 61
L G+VALVTG A G+GRA L + GA V + ++ E+L E G RA
Sbjct: 2 GSLMGRVALVTGAARGLGRAIALRLARAGADVVVHYRSDEEAAEELVEAVEA-LGR-RAQ 59
Query: 62 YCPCDVTDYPQFEEAFQITLQKLGGLDIVINNAGIFNDR-FWELE-------VDVNLVGT 113
DVTD E A +++ G +DI++NNAGIF D+ ++ +DVNL G
Sbjct: 60 AVQADVTDKAALEAAVAAAVERFGRIDILVNNAGIFEDKPLADMSDDEWDEVIDVNLSGV 119
>gnl|CDD|235990 PRK07326, PRK07326, short chain dehydrogenase; Provisional.
Length = 237
Score = 91.6 bits (228), Expect = 4e-24
Identities = 43/118 (36%), Positives = 56/118 (47%), Gaps = 11/118 (9%)
Query: 3 MDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIY 62
M LKGKVAL+TGG+ GIG A E LL G KV+I + E+ A + K +
Sbjct: 2 MSLKGKVALITGGSKGIGFAIAEALLAEGYKVAITARDQKELEEAAAELNNK---GNVLG 58
Query: 63 CPCDVTDYPQFEEAFQITLQKLGGLDIVINNAGI--------FNDRFWELEVDVNLVG 112
DV D + A + GGLD++I NAG+ W L +D NL G
Sbjct: 59 LAADVRDEADVQRAVDAIVAAFGGLDVLIANAGVGHFAPVEELTPEEWRLVIDTNLTG 116
>gnl|CDD|235506 PRK05565, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 247
Score = 91.4 bits (228), Expect = 5e-24
Identities = 50/119 (42%), Positives = 67/119 (56%), Gaps = 11/119 (9%)
Query: 3 MDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSI-CDINDSVGEDLAEQWRTKYGPNRAI 61
M L GKVA+VTG + GIGRA E L K GAKV I DIN+ ++L E+ + + G AI
Sbjct: 1 MKLMGKVAIVTGASGGIGRAIAELLAKEGAKVVIAYDINEEAAQELLEEIKEEGG--DAI 58
Query: 62 YCPCDVTDYPQFEEAFQITLQKLGGLDIVINNAGIFN--------DRFWELEVDVNLVG 112
DV+ E + ++K G +DI++NNAGI N D W+ +DVNL G
Sbjct: 59 AVKADVSSEEDVENLVEQIVEKFGKIDILVNNAGISNFGLVTDMTDEEWDRVIDVNLTG 117
>gnl|CDD|235500 PRK05557, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Validated.
Length = 248
Score = 91.0 bits (227), Expect = 7e-24
Identities = 44/119 (36%), Positives = 57/119 (47%), Gaps = 9/119 (7%)
Query: 3 MDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIY 62
M L+GKVALVTG + GIGRA E L GA V I + G + G +A+
Sbjct: 1 MSLEGKVALVTGASRGIGRAIAERLAAQGANVVINYASSEAGAEALVAEIGALG-GKALA 59
Query: 63 CPCDVTDYPQFEEAFQITLQKLGGLDIVINNAGIFNDR--------FWELEVDVNLVGT 113
DV+D E A + GG+DI++NNAGI D W+ +D NL G
Sbjct: 60 VQGDVSDAESVERAVDEAKAEFGGVDILVNNAGITRDNLLMRMKEEDWDRVIDTNLTGV 118
>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 = 90.5 bits (225), Expect = 1e-23
Identities = 42/118 (35%), Positives = 57/118 (48%), Gaps = 13/118 (11%)
Query: 4 DLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYC 63
LKGKVA+VTGGA G+G A+ L+ GAKV + DI D G+ A + A +
Sbjct: 2 RLKGKVAIVTGGARGLGLAHARLLVAEGAKVVLSDILDEEGQAAAAELGD-----AARFF 56
Query: 64 PCDVTDYPQFEEAFQITLQKLGGLDIVINNAGIFNDRF--------WELEVDVNLVGT 113
DVTD + + G LD+++NNAGI W +D+NL G
Sbjct: 57 HLDVTDEDGWTAVVDTAREAFGRLDVLVNNAGILTGGTVETTTLEEWRRLLDINLTGV 114
>gnl|CDD|183778 PRK12829, PRK12829, short chain dehydrogenase; Provisional.
Length = 264
Score = 89.7 bits (223), Expect = 3e-23
Identities = 41/122 (33%), Positives = 58/122 (47%), Gaps = 13/122 (10%)
Query: 1 MVMDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRA 60
++ L G LVTGGA+GIGRA E + GA+V +CD++ E + +
Sbjct: 5 LLKPLDGLRVLVTGGASGIGRAIAEAFAEAGARVHVCDVS----EAALAATAARLPGAKV 60
Query: 61 IYCPCDVTDYPQFEEAFQITLQKLGGLDIVINNAGIFNDRF---------WELEVDVNLV 111
DV D Q E F +++ GGLD+++NNAGI WE + VNL
Sbjct: 61 TATVADVADPAQVERVFDTAVERFGGLDVLVNNAGIAGPTGGIDEITPEQWEQTLAVNLN 120
Query: 112 GT 113
G
Sbjct: 121 GQ 122
>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 = 88.9 bits (221), Expect = 6e-23
Identities = 44/118 (37%), Positives = 60/118 (50%), Gaps = 9/118 (7%)
Query: 4 DLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYC 63
LKGKVA+VTGG+ GIG A L + GA V+I + E+ AE+ KYG +
Sbjct: 5 SLKGKVAIVTGGSRGIGLAIARALAEAGADVAIIYNSAPRAEEKAEELAKKYG-VKTKAY 63
Query: 64 PCDVTDYPQFEEAFQITLQKLGGLDIVINNAGI--------FNDRFWELEVDVNLVGT 113
CDV+ E+ F+ + G +DI+I NAGI + W +DVNL G
Sbjct: 64 KCDVSSQESVEKTFKQIQKDFGKIDILIANAGITVHKPALDYTYEQWNKVIDVNLNGV 121
>gnl|CDD|183833 PRK12939, PRK12939, short chain dehydrogenase; Provisional.
Length = 250
Score = 88.1 bits (219), Expect = 1e-22
Identities = 42/121 (34%), Positives = 58/121 (47%), Gaps = 10/121 (8%)
Query: 1 MVMDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRA 60
M +L GK ALVTG A G+G A+ E L + GA V+ D + +LA G RA
Sbjct: 1 MASNLAGKRALVTGAARGLGAAFAEALAEAGATVAFNDGLAAEARELAAALEAAGG--RA 58
Query: 61 IYCPCDVTDYPQFEEAFQITLQKLGGLDIVINNAGI--------FNDRFWELEVDVNLVG 112
D+ D + F LGGLD ++NNAGI + W+ ++VN+ G
Sbjct: 59 HAIAADLADPASVQRFFDAAAAALGGLDGLVNNAGITNSKSATELDIDTWDAVMNVNVRG 118
Query: 113 T 113
T
Sbjct: 119 T 119
>gnl|CDD|236209 PRK08265, PRK08265, short chain dehydrogenase; Provisional.
Length = 261
Score = 87.4 bits (217), Expect = 2e-22
Identities = 41/116 (35%), Positives = 56/116 (48%), Gaps = 12/116 (10%)
Query: 4 DLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYC 63
L GKVA+VTGGA IG A L+ GA+V+I DI+ G +A RA +
Sbjct: 3 GLAGKVAIVTGGATLIGAAVARALVAAGARVAIVDIDADNGAAVAASL-----GERARFI 57
Query: 64 PCDVTDYPQFEEAFQITLQKLGGLDIVINNAGIFNDRF-------WELEVDVNLVG 112
D+TD E A + + G +DI++N A + D W +DVNLV
Sbjct: 58 ATDITDDAAIERAVATVVARFGRVDILVNLACTYLDDGLASSRADWLAALDVNLVS 113
>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 = 86.9 bits (216), Expect = 3e-22
Identities = 44/117 (37%), Positives = 60/117 (51%), Gaps = 9/117 (7%)
Query: 5 LKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCP 64
LKGKVA +TGG GIG+A + + GA V+I V E AE+ RA
Sbjct: 1 LKGKVAFITGGGTGIGKAIAKAFAELGASVAIAGRKPEVLEAAAEEIS-SATGGRAHPIQ 59
Query: 65 CDVTDYPQFEEAFQITLQKLGGLDIVINNA-GIF-------NDRFWELEVDVNLVGT 113
CDV D E A TL++ G +DI+INNA G F + ++ +D++L GT
Sbjct: 60 CDVRDPEAVEAAVDETLKEFGKIDILINNAAGNFLAPAESLSPNGFKTVIDIDLNGT 116
>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 = 86.8 bits (216), Expect = 3e-22
Identities = 39/114 (34%), Positives = 55/114 (48%), Gaps = 10/114 (8%)
Query: 8 KVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPCDV 67
KVALVTG + GIGRA L GAKV++ D ++ + E+ K A DV
Sbjct: 1 KVALVTGASRGIGRAIALRLAAEGAKVAVTDRSEEAAAETVEE--IKALGGNAAALEADV 58
Query: 68 TDYPQFEEAFQITLQKLGGLDIVINNAGIFNDRF--------WELEVDVNLVGT 113
+D E + + G +DI++NNAGI D W+ ++VNL G
Sbjct: 59 SDREAVEALVEKVEAEFGPVDILVNNAGITRDNLLMRMSEEDWDAVINVNLTGV 112
>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 = 86.5 bits (215), Expect = 4e-22
Identities = 39/113 (34%), Positives = 59/113 (52%), Gaps = 11/113 (9%)
Query: 10 ALVTGGAAGIGRAYCEELLKFGAKVSICDIN-DSVGEDLAEQWRTKYGPNRAIYCPCDVT 68
ALVTG + GIGRA +L K GAKV I + + E++ E+ + +A+ CDV+
Sbjct: 1 ALVTGASRGIGRAIALKLAKEGAKVIITYRSSEEGAEEVVEELKAYGV--KALGVVCDVS 58
Query: 69 DYPQFEEAFQITLQKLGGLDIVINNAGIFNDRF--------WELEVDVNLVGT 113
D + + ++LG +DI++NNAGI D W+ +D NL G
Sbjct: 59 DREDVKAVVEEIEEELGPIDILVNNAGITRDNLLMRMKEEDWDAVIDTNLTGV 111
>gnl|CDD|235545 PRK05650, PRK05650, short chain dehydrogenase; Provisional.
Length = 270
Score = 85.5 bits (212), Expect = 1e-21
Identities = 35/110 (31%), Positives = 60/110 (54%), Gaps = 10/110 (9%)
Query: 11 LVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPCDVTDY 70
++TG A+G+GRA + G ++++ D+N+ GE+ + R G Y CDV DY
Sbjct: 4 MITGAASGLGRAIALRWAREGWRLALADVNEEGGEETLKLLREAGG--DGFYQRCDVRDY 61
Query: 71 PQFEEAFQITLQKLGGLDIVINNAGIFNDRF--------WELEVDVNLVG 112
Q Q +K GG+D+++NNAG+ + F W+ ++ +NL+G
Sbjct: 62 SQLTALAQACEEKWGGIDVIVNNAGVASGGFFEELSLEDWDWQIAINLMG 111
>gnl|CDD|235925 PRK07067, PRK07067, sorbitol dehydrogenase; Provisional.
Length = 257
Score = 84.7 bits (210), Expect = 2e-21
Identities = 38/95 (40%), Positives = 50/95 (52%), Gaps = 5/95 (5%)
Query: 3 MDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIY 62
M L+GKVAL+TG A+GIG A E L GA+V I DI A + GP AI
Sbjct: 2 MRLQGKVALLTGAASGIGEAVAERYLAEGARVVIADIK----PARARLAALEIGPA-AIA 56
Query: 63 CPCDVTDYPQFEEAFQITLQKLGGLDIVINNAGIF 97
DVT + +++ GG+DI+ NNA +F
Sbjct: 57 VSLDVTRQDSIDRIVAAAVERFGGIDILFNNAALF 91
>gnl|CDD|180439 PRK06171, PRK06171, sorbitol-6-phosphate 2-dehydrogenase;
Provisional.
Length = 266
Score = 84.7 bits (210), Expect = 3e-21
Identities = 34/128 (26%), Positives = 57/128 (44%), Gaps = 28/128 (21%)
Query: 3 MDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIY 62
++L+GK+ +VTGG++GIG A +ELL GA V DI+ G+ +
Sbjct: 5 LNLQGKIIIVTGGSSGIGLAIVKELLANGANVVNADIHGGDGQH-----------ENYQF 53
Query: 63 CPCDVTDYPQFEEAFQITLQKLGGLDIVINNAGI-----------------FNDRFWELE 105
P DV+ + ++K G +D ++NNAGI N+ ++
Sbjct: 54 VPTDVSSAEEVNHTVAEIIEKFGRIDGLVNNAGINIPRLLVDEKDPAGKYELNEAAFDKM 113
Query: 106 VDVNLVGT 113
++N G
Sbjct: 114 FNINQKGV 121
>gnl|CDD|235924 PRK07063, PRK07063, short chain dehydrogenase; Provisional.
Length = 260
Score = 83.6 bits (207), Expect = 7e-21
Identities = 36/96 (37%), Positives = 49/96 (51%)
Query: 1 MVMDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRA 60
M+ L GKVALVTG A GIG A + GA V++ D++ ++ E A R
Sbjct: 1 MMNRLAGKVALVTGAAQGIGAAIARAFAREGAAVALADLDAALAERAAAAIARDVAGARV 60
Query: 61 IYCPCDVTDYPQFEEAFQITLQKLGGLDIVINNAGI 96
+ P DVTD A + G LD+++NNAGI
Sbjct: 61 LAVPADVTDAASVAAAVAAAEEAFGPLDVLVNNAGI 96
>gnl|CDD|181297 PRK08217, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 253
Score = 83.1 bits (206), Expect = 8e-21
Identities = 42/128 (32%), Positives = 59/128 (46%), Gaps = 19/128 (14%)
Query: 3 MDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIY 62
MDLK KV ++TGGA G+GRA E L + GAK+++ D+N E+ + R
Sbjct: 1 MDLKDKVIVITGGAQGLGRAMAEYLAQKGAKLALIDLNQEKLEEAVAECGALGTEVRGY- 59
Query: 63 CPCDVTDYPQFEEAFQITLQKLGGLDIVINNAGIFNDRF-----------------WELE 105
+VTD E F + G L+ +INNAGI D ++
Sbjct: 60 -AANVTDEEDVEATFAQIAEDFGQLNGLINNAGILRDGLLVKAKDGKVTSKMSLEQFQSV 118
Query: 106 VDVNLVGT 113
+DVNL G
Sbjct: 119 IDVNLTGV 126
>gnl|CDD|235633 PRK05872, PRK05872, short chain dehydrogenase; Provisional.
Length = 296
Score = 83.1 bits (206), Expect = 1e-20
Identities = 38/117 (32%), Positives = 59/117 (50%), Gaps = 11/117 (9%)
Query: 4 DLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYC 63
L GKV +VTG A GIG L GAK+++ D+ ++ LA + G +R +
Sbjct: 6 SLAGKVVVVTGAARGIGAELARRLHARGAKLALVDLEEAELAALAAEL---GGDDRVLTV 62
Query: 64 PCDVTDYPQFEEAFQITLQKLGGLDIVINNAGI-----FND---RFWELEVDVNLVG 112
DVTD + A + +++ GG+D+V+ NAGI + +DVNL+G
Sbjct: 63 VADVTDLAAMQAAAEEAVERFGGIDVVVANAGIASGGSVAQVDPDAFRRVIDVNLLG 119
>gnl|CDD|236074 PRK07666, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 239
Score = 82.0 bits (203), Expect = 2e-20
Identities = 43/121 (35%), Positives = 61/121 (50%), Gaps = 10/121 (8%)
Query: 1 MVMDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRA 60
M L+GK AL+TG GIGRA L K G V + + + +AE+ YG +
Sbjct: 1 MAQSLQGKNALITGAGRGIGRAVAIALAKEGVNVGLLARTEENLKAVAEEVE-AYGV-KV 58
Query: 61 IYCPCDVTDYPQFEEAFQITLQKLGGLDIVINNAGI-----FND---RFWELEVDVNLVG 112
+ DV+DY + A + +LG +DI+INNAGI F + WE + VNL+G
Sbjct: 59 VIATADVSDYEEVTAAIEQLKNELGSIDILINNAGISKFGKFLELDPAEWEKIIQVNLMG 118
Query: 113 T 113
Sbjct: 119 V 119
>gnl|CDD|135765 PRK06113, PRK06113, 7-alpha-hydroxysteroid dehydrogenase;
Validated.
Length = 255
Score = 81.4 bits (201), Expect = 4e-20
Identities = 32/91 (35%), Positives = 46/91 (50%), Gaps = 2/91 (2%)
Query: 5 LKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCP 64
L GK A++TG AGIG+ GA V + DIN + ++ + G +A C
Sbjct: 9 LDGKCAIITGAGAGIGKEIAITFATAGASVVVSDINADAANHVVDEIQQLGG--QAFACR 66
Query: 65 CDVTDYPQFEEAFQITLQKLGGLDIVINNAG 95
CD+T + L KLG +DI++NNAG
Sbjct: 67 CDITSEQELSALADFALSKLGKVDILVNNAG 97
>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 = 80.7 bits (200), Expect = 5e-20
Identities = 35/93 (37%), Positives = 52/93 (55%), Gaps = 2/93 (2%)
Query: 9 VALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPCDVT 68
+ L+TGG +GIGR E K GAKV I DIN+ E+ A R G + Y CDV+
Sbjct: 1 IVLITGGGSGIGRLLALEFAKRGAKVVILDINEKGAEETANNVRKAGG--KVHYYKCDVS 58
Query: 69 DYPQFEEAFQITLQKLGGLDIVINNAGIFNDRF 101
+ EA + +++G + I+INNAG+ + +
Sbjct: 59 KREEVYEAAKKIKKEVGDVTILINNAGVVSGKK 91
>gnl|CDD|177895 PLN02253, PLN02253, xanthoxin dehydrogenase.
Length = 280
Score = 81.4 bits (201), Expect = 6e-20
Identities = 46/119 (38%), Positives = 59/119 (49%), Gaps = 13/119 (10%)
Query: 5 LKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCP 64
L GKVALVTGGA GIG + K GAKV I D+ D +G+++ + + +
Sbjct: 16 LLGKVALVTGGATGIGESIVRLFHKHGAKVCIVDLQDDLGQNVCDSLGGEPN---VCFFH 72
Query: 65 CDVTDYPQFEEAFQITLQKLGGLDIVINNAG--------IFNDRFWELE--VDVNLVGT 113
CDVT A T+ K G LDI++NNAG I N E E DVN+ G
Sbjct: 73 CDVTVEDDVSRAVDFTVDKFGTLDIMVNNAGLTGPPCPDIRNVELSEFEKVFDVNVKGV 131
>gnl|CDD|181136 PRK07825, PRK07825, short chain dehydrogenase; Provisional.
Length = 273
Score = 81.1 bits (201), Expect = 7e-20
Identities = 41/118 (34%), Positives = 58/118 (49%), Gaps = 14/118 (11%)
Query: 3 MDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIY 62
DL+GKV +TGGA GIG A L GA+V+I D++ E LA++ + G +
Sbjct: 1 DDLRGKVVAITGGARGIGLATARALAALGARVAIGDLD----EALAKETAAELG--LVVG 54
Query: 63 CPCDVTDYPQFEEAFQITLQKLGGLDIVINNAGIF--------NDRFWELEVDVNLVG 112
P DVTD F LG +D+++NNAG+ D +DVN+ G
Sbjct: 55 GPLDVTDPASFAAFLDAVEADLGPIDVLVNNAGVMPVGPFLDEPDAVTRRILDVNVYG 112
>gnl|CDD|131680 TIGR02632, RhaD_aldol-ADH, rhamnulose-1-phosphate aldolase/alcohol
dehydrogenase.
Length = 676
Score = 82.6 bits (204), Expect = 9e-20
Identities = 43/116 (37%), Positives = 58/116 (50%), Gaps = 8/116 (6%)
Query: 5 LKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCP 64
L +VA VTGGA GIGR L GA V + D+N E +A + ++G RA+
Sbjct: 412 LARRVAFVTGGAGGIGRETARRLAAEGAHVVLADLNLEAAEAVAAEINGQFGAGRAVALK 471
Query: 65 CDVTDYPQFEEAFQITLQKLGGLDIVINNAGIF--------NDRFWELEVDVNLVG 112
DVTD + AF GG+DIV+NNAGI + W+L +D+ G
Sbjct: 472 MDVTDEQAVKAAFADVALAYGGVDIVVNNAGIATSSPFEETTLQEWQLNLDILATG 527
>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 = 80.2 bits (198), Expect = 1e-19
Identities = 42/118 (35%), Positives = 59/118 (50%), Gaps = 14/118 (11%)
Query: 5 LKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCP 64
L GKVA++TGGA+GIG A K GA+V I DI+D G+ +A + G +
Sbjct: 2 LDGKVAIITGGASGIGEATARLFAKHGARVVIADIDDDAGQAVAAE----LGDPDISFVH 57
Query: 65 CDVTDYPQFEEAFQITLQKLGGLDIVINNAGI----------FNDRFWELEVDVNLVG 112
CDVT A + + G LDI+ NNAG+ + +E +DVN+ G
Sbjct: 58 CDVTVEADVRAAVDTAVARFGRLDIMFNNAGVLGAPCYSILETSLEEFERVLDVNVYG 115
>gnl|CDD|180818 PRK07062, PRK07062, short chain dehydrogenase; Provisional.
Length = 265
Score = 80.1 bits (198), Expect = 2e-19
Identities = 35/95 (36%), Positives = 53/95 (55%)
Query: 1 MVMDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRA 60
M + L+G+VA+VTGG++GIG A E LL+ GA V+IC ++ + R K+ R
Sbjct: 2 MQIQLEGRVAVVTGGSSGIGLATVELLLEAGASVAICGRDEERLASAEARLREKFPGARL 61
Query: 61 IYCPCDVTDYPQFEEAFQITLQKLGGLDIVINNAG 95
+ CDV D + GG+D+++NNAG
Sbjct: 62 LAARCDVLDEADVAAFAAAVEARFGGVDMLVNNAG 96
>gnl|CDD|236094 PRK07774, PRK07774, short chain dehydrogenase; Provisional.
Length = 250
Score = 78.6 bits (194), Expect = 5e-19
Identities = 37/95 (38%), Positives = 50/95 (52%), Gaps = 2/95 (2%)
Query: 3 MDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIY 62
KVA+VTG A GIG+AY E L + GA V + DIN E +A+Q G AI
Sbjct: 2 GRFDDKVAIVTGAAGGIGQAYAEALAREGASVVVADINAEGAERVAKQIVADGG--TAIA 59
Query: 63 CPCDVTDYPQFEEAFQITLQKLGGLDIVINNAGIF 97
DV+D + T+ GG+D ++NNA I+
Sbjct: 60 VQVDVSDPDSAKAMADATVSAFGGIDYLVNNAAIY 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 = 77.8 bits (192), Expect = 1e-18
Identities = 33/90 (36%), Positives = 46/90 (51%), Gaps = 1/90 (1%)
Query: 7 GKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPCD 66
KVA++TG A GIGRA E L G + + D+N Q ++ G N A+ D
Sbjct: 2 SKVAIITGAAQGIGRAIAERLAADGFNIVLADLNLEEAAKSTIQEISEAGYN-AVAVGAD 60
Query: 67 VTDYPQFEEAFQITLQKLGGLDIVINNAGI 96
VTD E ++K G D+++NNAGI
Sbjct: 61 VTDKDDVEALIDQAVEKFGSFDVMVNNAGI 90
>gnl|CDD|183489 PRK12384, PRK12384, sorbitol-6-phosphate dehydrogenase;
Provisional.
Length = 259
Score = 77.0 bits (190), Expect = 2e-18
Identities = 31/115 (26%), Positives = 52/115 (45%), Gaps = 8/115 (6%)
Query: 6 KGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPC 65
+VA+V GG +G C L + G +V++ DIN ++A++ +YG A
Sbjct: 1 MNQVAVVIGGGQTLGAFLCHGLAEEGYRVAVADINSEKAANVAQEINAEYGEGMAYGFGA 60
Query: 66 DVTDYPQFEEAFQITLQKLGGLDIVINNAGI--------FNDRFWELEVDVNLVG 112
D T + + G +D+++ NAGI F ++ + VNLVG
Sbjct: 61 DATSEQSVLALSRGVDEIFGRVDLLVYNAGIAKAAFITDFQLGDFDRSLQVNLVG 115
>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 = 76.6 bits (189), Expect = 2e-18
Identities = 44/118 (37%), Positives = 58/118 (49%), Gaps = 10/118 (8%)
Query: 4 DLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYC 63
LKGKVALVTG + GIG L + GA + I N+ E A+Q K G A
Sbjct: 2 SLKGKVALVTGASRGIGFGIASGLAEAGANIVINSRNEEKAE-EAQQLIEKEG-VEATAF 59
Query: 64 PCDVTDYPQFEEAFQITLQKLGGLDIVINNAGI--------FNDRFWELEVDVNLVGT 113
CDV+D + A + + G +DI++NNAGI F + W +DVNL G
Sbjct: 60 TCDVSDEEAIKAAVEAIEEDFGKIDILVNNAGIIRRHPAEEFPEAEWRDVIDVNLNGV 117
>gnl|CDD|226674 COG4221, COG4221, Short-chain alcohol dehydrogenase of unknown
specificity [General function prediction only].
Length = 246
Score = 76.5 bits (189), Expect = 3e-18
Identities = 41/117 (35%), Positives = 60/117 (51%), Gaps = 12/117 (10%)
Query: 5 LKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCP 64
LKGKVAL+TG ++GIG A L + GAKV + + E LA++ G A+
Sbjct: 4 LKGKVALITGASSGIGEATARALAEAGAKVVLAARREERLEALADE----IGAGAALALA 59
Query: 65 CDVTDYPQFEEAFQITLQKLGGLDIVINNAGIF-NDRFWELE-------VDVNLVGT 113
DVTD E A + ++ G +DI++NNAG+ D E + +D N+ G
Sbjct: 60 LDVTDRAAVEAAIEALPEEFGRIDILVNNAGLALGDPLDEADLDDWDRMIDTNVKGL 116
>gnl|CDD|180723 PRK06841, PRK06841, short chain dehydrogenase; Provisional.
Length = 255
Score = 76.6 bits (189), Expect = 3e-18
Identities = 41/118 (34%), Positives = 62/118 (52%), Gaps = 13/118 (11%)
Query: 4 DLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYC 63
DL GKVA+VTGGA+GIG A E GA+V++ D ++ V E A+ A
Sbjct: 12 DLSGKVAVVTGGASGIGHAIAELFAAKGARVALLDRSEDVAEVAAQL-----LGGNAKGL 66
Query: 64 PCDVTDYPQFEEAFQITLQKLGGLDIVINNAGI--------FNDRFWELEVDVNLVGT 113
CDV+D E A + G +DI++N+AG+ ++ W+ +D+NL G+
Sbjct: 67 VCDVSDSQSVEAAVAAVISAFGRIDILVNSAGVALLAPAEDVSEEDWDKTIDINLKGS 124
>gnl|CDD|236110 PRK07831, PRK07831, short chain dehydrogenase; Provisional.
Length = 262
Score = 76.6 bits (189), Expect = 3e-18
Identities = 42/118 (35%), Positives = 59/118 (50%), Gaps = 9/118 (7%)
Query: 5 LKGKVALVTGGA-AGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYC 63
L GKV LVT A GIG A L+ GA+V I DI++ + A++ + G R
Sbjct: 15 LAGKVVLVTAAAGTGIGSATARRALEEGARVVISDIHERRLGETADELAAELGLGRVEAV 74
Query: 64 PCDVTDYPQFEEAFQITLQKLGGLDIVINNAGI--------FNDRFWELEVDVNLVGT 113
CDVT Q + +++LG LD+++NNAG+ D W +DV L GT
Sbjct: 75 VCDVTSEAQVDALIDAAVERLGRLDVLVNNAGLGGQTPVVDMTDDEWSRVLDVTLTGT 132
>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 = 76.5 bits (189), Expect = 3e-18
Identities = 36/115 (31%), Positives = 51/115 (44%), Gaps = 10/115 (8%)
Query: 7 GKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPCD 66
GKVALVT ++GIG A L + GA+V+IC N E A + R G + D
Sbjct: 1 GKVALVTAASSGIGLAIARALAREGARVAICARNRENLERAASELRA--GGAGVLAVVAD 58
Query: 67 VTDYPQFEEAFQITLQKLGGLDIVINNAG------IFN--DRFWELEVDVNLVGT 113
+TD + + G +DI++NNAG D W D+ L+
Sbjct: 59 LTDPEDIDRLVEKAGDAFGRVDILVNNAGGPPPGPFAELTDEDWLEAFDLKLLSV 113
>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 = 76.3 bits (188), Expect = 3e-18
Identities = 40/114 (35%), Positives = 51/114 (44%), Gaps = 10/114 (8%)
Query: 7 GKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPCD 66
GK ALVTG A+GIG A L GA V + D + E A+ G IY P D
Sbjct: 1 GKTALVTGAASGIGLAIARALAAAGANVVVNDFGEEGAEAAAKVAGDAGG--SVIYLPAD 58
Query: 67 VTDYPQFEEAFQITLQKLGGLDIVINNAGI--------FNDRFWELEVDVNLVG 112
VT + + + GGLDI++NNAGI F W+ + V L
Sbjct: 59 VTKEDEIADMIAAAAAEFGGLDILVNNAGIQHVAPIEEFPPEDWDRIIAVMLTS 112
>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 = 76.3 bits (188), Expect = 4e-18
Identities = 37/97 (38%), Positives = 48/97 (49%), Gaps = 11/97 (11%)
Query: 5 LKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTK----YGPNRA 60
L+GK ALVTGG GIG A EEL GA+V C N ++ +WR K G
Sbjct: 4 LEGKTALVTGGTKGIGYAIVEELAGLGAEVYTCARNQKELDECLTEWREKGFKVEGS--- 60
Query: 61 IYCPCDVTDYPQFEEAFQITLQKLGG-LDIVINNAGI 96
CDV+ + +E GG L+I++NNAG
Sbjct: 61 ---VCDVSSRSERQELMDTVASHFGGKLNILVNNAGT 94
>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 = 75.9 bits (187), Expect = 4e-18
Identities = 37/94 (39%), Positives = 46/94 (48%), Gaps = 5/94 (5%)
Query: 3 MDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIY 62
M L+GKVA+VTG +G G + GA+V I DIN E +A AI
Sbjct: 1 MRLEGKVAIVTGAGSGFGEGIARRFAQEGARVVIADINADGAERVAAD-----IGEAAIA 55
Query: 63 CPCDVTDYPQFEEAFQITLQKLGGLDIVINNAGI 96
DVT E + L K G LDI++NNAGI
Sbjct: 56 IQADVTKRADVEAMVEAALSKFGRLDILVNNAGI 89
>gnl|CDD|180440 PRK06172, PRK06172, short chain dehydrogenase; Provisional.
Length = 253
Score = 75.9 bits (187), Expect = 4e-18
Identities = 41/96 (42%), Positives = 52/96 (54%), Gaps = 2/96 (2%)
Query: 1 MVMDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRA 60
M M GKVALVTGGAAGIGRA + GAKV + D + + GE+ R G A
Sbjct: 1 MSMTFSGKVALVTGGAAGIGRATALAFAREGAKVVVADRDAAGGEETVALIREAGG--EA 58
Query: 61 IYCPCDVTDYPQFEEAFQITLQKLGGLDIVINNAGI 96
++ CDVT + + + T+ G LD NNAGI
Sbjct: 59 LFVACDVTRDAEVKALVEQTIAAYGRLDYAFNNAGI 94
>gnl|CDD|235726 PRK06181, PRK06181, short chain dehydrogenase; Provisional.
Length = 263
Score = 76.2 bits (188), Expect = 5e-18
Identities = 32/90 (35%), Positives = 51/90 (56%), Gaps = 2/90 (2%)
Query: 7 GKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPCD 66
GKV ++TG + GIGRA L + GA++ + N++ LA++ G A+ P D
Sbjct: 1 GKVVIITGASEGIGRALAVRLARAGAQLVLAARNETRLASLAQELADHGGE--ALVVPTD 58
Query: 67 VTDYPQFEEAFQITLQKLGGLDIVINNAGI 96
V+D E + + + GG+DI++NNAGI
Sbjct: 59 VSDAEACERLIEAAVARFGGIDILVNNAGI 88
>gnl|CDD|180371 PRK06057, PRK06057, short chain dehydrogenase; Provisional.
Length = 255
Score = 75.9 bits (187), Expect = 5e-18
Identities = 33/96 (34%), Positives = 47/96 (48%), Gaps = 7/96 (7%)
Query: 1 MVMDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRA 60
+ L G+VA++TGG +GIG A L GA V + DI+ G+ A++
Sbjct: 1 LSQRLAGRVAVITGGGSGIGLATARRLAAEGATVVVGDIDPEAGKAAADEV-------GG 53
Query: 61 IYCPCDVTDYPQFEEAFQITLQKLGGLDIVINNAGI 96
++ P DVTD F + G +DI NNAGI
Sbjct: 54 LFVPTDVTDEDAVNALFDTAAETYGSVDIAFNNAGI 89
>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 = 76.0 bits (187), Expect = 5e-18
Identities = 35/89 (39%), Positives = 52/89 (58%), Gaps = 2/89 (2%)
Query: 8 KVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPCDV 67
KVALVTGGA GIG+ E L K G V++ D+N+ ++ A++ G +A+ DV
Sbjct: 1 KVALVTGGAQGIGKGIAERLAKDGFAVAVADLNEETAKETAKEINQAGG--KAVAYKLDV 58
Query: 68 TDYPQFEEAFQITLQKLGGLDIVINNAGI 96
+D Q A +K GG D+++NNAG+
Sbjct: 59 SDKDQVFSAIDQAAEKFGGFDVMVNNAGV 87
>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 = 75.7 bits (187), Expect = 8e-18
Identities = 36/112 (32%), Positives = 54/112 (48%), Gaps = 6/112 (5%)
Query: 7 GKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPCD 66
GKV ++TG +GIG+ EL K GA V I N+ GE+ A + + + G + D
Sbjct: 1 GKVVVITGANSGIGKETARELAKRGAHVIIACRNEEKGEEAAAEIKKETGNAKVEVIQLD 60
Query: 67 VTDYPQFEEAFQITLQKLGGLDIVINNAGIFNDRFW------ELEVDVNLVG 112
++ + + L + LDI+INNAGI EL+ VN +G
Sbjct: 61 LSSLASVRQFAEEFLARFPRLDILINNAGIMAPPRRLTKDGFELQFAVNYLG 112
>gnl|CDD|181120 PRK07792, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 306
Score = 76.0 bits (187), Expect = 9e-18
Identities = 44/121 (36%), Positives = 63/121 (52%), Gaps = 12/121 (9%)
Query: 1 MVMDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSV-GEDLAEQWRTKYGPNR 59
DL GKVA+VTG AAG+GRA L + GA V + D+ ++ D+ ++ R +
Sbjct: 6 NTTDLSGKVAVVTGAAAGLGRAEALGLARLGATVVVNDVASALDASDVLDEIRAAGA--K 63
Query: 60 AIYCPCDVTDYPQFEEAFQITLQKLGGLDIVINNAGIFNDRF--------WELEVDVNLV 111
A+ D++ +E T LGGLDIV+NNAGI DR W+ + V+L
Sbjct: 64 AVAVAGDISQRATADELVA-TAVGLGGLDIVVNNAGITRDRMLFNMSDEEWDAVIAVHLR 122
Query: 112 G 112
G
Sbjct: 123 G 123
>gnl|CDD|180576 PRK06463, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 255
Score = 75.2 bits (185), Expect = 1e-17
Identities = 40/121 (33%), Positives = 65/121 (53%), Gaps = 15/121 (12%)
Query: 1 MVMDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRA 60
M KGKVAL+TGG GIGRA E L+ GAKV+ + + E+ A++ R K
Sbjct: 1 YSMRFKGKVALITGGTRGIGRAIAEAFLREGAKVA---VLYNSAENEAKELREKGV---- 53
Query: 61 IYCPCDVTDYPQFEEAFQITLQKLGGLDIVINNAGI--------FNDRFWELEVDVNLVG 112
CDV + Q +++ ++ ++ G +D+++NNAGI F++ + + +NL G
Sbjct: 54 FTIKCDVGNRDQVKKSKEVVEKEFGRVDVLVNNAGIMYLMPFEEFDEEKYNKMIKINLNG 113
Query: 113 T 113
Sbjct: 114 A 114
>gnl|CDD|236216 PRK08277, PRK08277, D-mannonate oxidoreductase; Provisional.
Length = 278
Score = 75.3 bits (186), Expect = 1e-17
Identities = 37/92 (40%), Positives = 50/92 (54%), Gaps = 2/92 (2%)
Query: 4 DLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYC 63
LKGKVA++TGG +G A +EL + GAKV+I D N E + + + G A+
Sbjct: 7 SLKGKVAVITGGGGVLGGAMAKELARAGAKVAILDRNQEKAEAVVAEIKAAGG--EALAV 64
Query: 64 PCDVTDYPQFEEAFQITLQKLGGLDIVINNAG 95
DV D E+A Q L+ G DI+IN AG
Sbjct: 65 KADVLDKESLEQARQQILEDFGPCDILINGAG 96
>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 = 75.1 bits (185), Expect = 1e-17
Identities = 41/118 (34%), Positives = 59/118 (50%), Gaps = 11/118 (9%)
Query: 5 LKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDIND-SVGEDLAEQWRTKYGPNRAIYC 63
LKGKVALVTG ++GIG+A L GA V + + E++ E+ + G A+
Sbjct: 1 LKGKVALVTGASSGIGKAIAIRLATAGANVVVNYRSKEDAAEEVVEEIKAVGGKAIAVQ- 59
Query: 64 PCDVTDYPQFEEAFQITLQKLGGLDIVINNAGIFNDRF--------WELEVDVNLVGT 113
DV+ FQ +++ G LDI++NNAG+ D W +DVNL G
Sbjct: 60 -ADVSKEEDVVALFQSAIKEFGTLDILVNNAGLQGDASSHEMTLEDWNKVIDVNLTGQ 116
>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 = 74.3 bits (183), Expect = 2e-17
Identities = 41/119 (34%), Positives = 59/119 (49%), Gaps = 12/119 (10%)
Query: 6 KGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPC 65
+ K+ L+TG A IG+A+C+ LL GA++ + DIN E L E+ Y NR I
Sbjct: 1 EDKIILITGAAGLIGKAFCKALLSAGARLILADINAPALEQLKEELTNLYK-NRVIALEL 59
Query: 66 DVTDYPQFEEAFQITLQKLGGLDIVINNAGI-----------FNDRFWELEVDVNLVGT 113
D+T +E + L+K G +DI+INNA F W ++VNL G
Sbjct: 60 DITSKESIKELIESYLEKFGRIDILINNAYPSPKVWGSRFEEFPYEQWNEVLNVNLGGA 118
>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 = 73.8 bits (181), Expect = 4e-17
Identities = 45/118 (38%), Positives = 61/118 (51%), Gaps = 14/118 (11%)
Query: 5 LKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCP 64
LK K A+VTGG GIG A C + GAKV++ D+N E +A R K G +A
Sbjct: 1 LKDKTAIVTGGGGGIGGATCRRFAEEGAKVAVFDLNREAAEKVAADIRAKGGNAQAF--A 58
Query: 65 CDVTDYPQFEEAFQITLQKLGGLDIVINNAGIFNDRF----------WELEVDVNLVG 112
CD+TD + A Q LG +D+++NNAG D+F WE + +NL G
Sbjct: 59 CDITDRDSVDTAVAAAEQALGPVDVLVNNAGW--DKFGPFTKTEPPLWERLIAINLTG 114
>gnl|CDD|181518 PRK08643, PRK08643, acetoin reductase; Validated.
Length = 256
Score = 73.2 bits (180), Expect = 6e-17
Identities = 34/91 (37%), Positives = 50/91 (54%), Gaps = 2/91 (2%)
Query: 6 KGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPC 65
KVALVTG GIG A + L++ G KV+I D N+ + A++ G +AI
Sbjct: 1 MSKVALVTGAGQGIGFAIAKRLVEDGFKVAIVDYNEETAQAAADKLSKDGG--KAIAVKA 58
Query: 66 DVTDYPQFEEAFQITLQKLGGLDIVINNAGI 96
DV+D Q A + + G L++V+NNAG+
Sbjct: 59 DVSDRDQVFAAVRQVVDTFGDLNVVVNNAGV 89
>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 = 73.0 bits (179), Expect = 6e-17
Identities = 45/116 (38%), Positives = 63/116 (54%), Gaps = 10/116 (8%)
Query: 5 LKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCP 64
L+GKVALVTG ++GIG A L GA V+I E LA++ + G +A+
Sbjct: 1 LQGKVALVTGASSGIGEATARALAAEGAAVAIAARRVDRLEALADELEAEGG--KALVLE 58
Query: 65 CDVTDYPQFEEAFQITLQKLGGLDIVINNAGIF--------NDRFWELEVDVNLVG 112
DVTD Q + A + T++ LG LDI++NNAGI + W +D NL+G
Sbjct: 59 LDVTDEQQVDAAVERTVEALGRLDILVNNAGIMLLGPVEDADTTDWTRMIDTNLLG 114
>gnl|CDD|181305 PRK08226, PRK08226, short chain dehydrogenase; Provisional.
Length = 263
Score = 72.9 bits (179), Expect = 8e-17
Identities = 34/116 (29%), Positives = 55/116 (47%), Gaps = 11/116 (9%)
Query: 5 LKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCP 64
L GK AL+TG GIG + GA + + DI+ + E LA++ + +R
Sbjct: 4 LTGKTALITGALQGIGEGIARVFARHGANLILLDISPEI-EKLADELCGR--GHRCTAVV 60
Query: 65 CDVTDYPQFEEAFQITLQKLGGLDIVINNAGI--------FNDRFWELEVDVNLVG 112
DV D A + +K G +DI++NNAG+ +D + +D+N+ G
Sbjct: 61 ADVRDPASVAAAIKRAKEKEGRIDILVNNAGVCRLGSFLDMSDEDRDFHIDINIKG 116
>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 = 71.8 bits (176), Expect = 1e-16
Identities = 35/92 (38%), Positives = 51/92 (55%), Gaps = 5/92 (5%)
Query: 5 LKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCP 64
L+GKVA+VTG AGIG A L + GA+V + DI+ + + Q A+
Sbjct: 1 LEGKVAIVTGAGAGIGAACAARLAREGARVVVADIDGGAAQAVVAQI-----AGGALALR 55
Query: 65 CDVTDYPQFEEAFQITLQKLGGLDIVINNAGI 96
DVTD Q F+ +++ GGLD+++NNAG
Sbjct: 56 VDVTDEQQVAALFERAVEEFGGLDLLVNNAGA 87
>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 = 71.1 bits (174), Expect = 3e-16
Identities = 35/94 (37%), Positives = 51/94 (54%), Gaps = 5/94 (5%)
Query: 5 LKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCP 64
L GK AL+TG A GIGRA+ + ++ GA+V+I DIN A + GP A
Sbjct: 1 LDGKTALITGSARGIGRAFAQAYVREGARVAIADINLEAARATAAE----IGPA-ACAIS 55
Query: 65 CDVTDYPQFEEAFQITLQKLGGLDIVINNAGIFN 98
DVTD + + + G +DI++NNA +F+
Sbjct: 56 LDVTDQASIDRCVAALVDRWGSIDILVNNAALFD 89
>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 = 70.8 bits (174), Expect = 3e-16
Identities = 38/127 (29%), Positives = 59/127 (46%), Gaps = 22/127 (17%)
Query: 4 DLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDI---------NDSVGEDLAEQWRTK 54
G+V LVTG G+GRAY + GAKV + D+ + S + + ++ +
Sbjct: 2 RFDGRVVLVTGAGGGLGRAYALAFAERGAKVVVNDLGGDRKGSGKSSSAADKVVDEIKAA 61
Query: 55 YGPNRAIYCPCDVTDYPQFEEAFQITLQKLGGLDIVINNAGIFNDRF--------WELEV 106
G A Y V D E+ + + G +DI++NNAGI DR W+L +
Sbjct: 62 GGKAVANY--DSVEDG---EKIVKTAIDAFGRVDILVNNAGILRDRSFAKMSEEDWDLVM 116
Query: 107 DVNLVGT 113
V+L G+
Sbjct: 117 RVHLKGS 123
>gnl|CDD|184025 PRK13394, PRK13394, 3-hydroxybutyrate dehydrogenase; Provisional.
Length = 262
Score = 71.1 bits (174), Expect = 4e-16
Identities = 34/96 (35%), Positives = 53/96 (55%), Gaps = 2/96 (2%)
Query: 1 MVMDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRA 60
M+ +L GK A+VTG A+GIG+ EL + GA V+I D+N +A++ G +A
Sbjct: 1 MMSNLNGKTAVVTGAASGIGKEIALELARAGAAVAIADLNQDGANAVADEINKAGG--KA 58
Query: 61 IYCPCDVTDYPQFEEAFQITLQKLGGLDIVINNAGI 96
I DVT+ ++ G +DI+++NAGI
Sbjct: 59 IGVAMDVTNEDAVNAGIDKVAERFGSVDILVSNAGI 94
>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 = 71.0 bits (174), Expect = 4e-16
Identities = 32/90 (35%), Positives = 49/90 (54%), Gaps = 1/90 (1%)
Query: 6 KGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPC 65
KV +VTGG+ GIGR ++ GAKV C ++ G+ L E + GP + PC
Sbjct: 8 ADKVVIVTGGSRGIGRGIVRAFVENGAKVVFCARGEAAGQAL-ESELNRAGPGSCKFVPC 66
Query: 66 DVTDYPQFEEAFQITLQKLGGLDIVINNAG 95
DVT + +T+++ G +D ++NNAG
Sbjct: 67 DVTKEEDIKTLISVTVERFGRIDCLVNNAG 96
>gnl|CDD|215720 pfam00106, adh_short, short chain dehydrogenase. This family
contains a wide variety of dehydrogenases.
Length = 167
Score = 69.1 bits (170), Expect = 4e-16
Identities = 27/98 (27%), Positives = 35/98 (35%), Gaps = 3/98 (3%)
Query: 8 KVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWR--TKYGPNRAIYCPC 65
L+TGG G+G A L GA+ + AE G C
Sbjct: 1 GTVLITGGTGGLGLALARWLAAEGARHLVLVSRRGPAPGAAELVAELEALGA-EVTVAAC 59
Query: 66 DVTDYPQFEEAFQITLQKLGGLDIVINNAGIFNDRFWE 103
DV D LG LD V++NAG+ +D E
Sbjct: 60 DVADRDALAALLAALPAALGPLDGVVHNAGVLDDGPLE 97
>gnl|CDD|235739 PRK06200, PRK06200, 2,3-dihydroxy-2,3-dihydrophenylpropionate
dehydrogenase; Provisional.
Length = 263
Score = 70.8 bits (174), Expect = 5e-16
Identities = 33/95 (34%), Positives = 50/95 (52%), Gaps = 5/95 (5%)
Query: 3 MDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIY 62
L G+VAL+TGG +GIGRA E L GA+V++ + + + R ++G + +
Sbjct: 2 GWLHGQVALITGGGSGIGRALVERFLAEGARVAVLERS----AEKLASLRQRFGDHVLVV 57
Query: 63 CPCDVTDYPQFEEAFQITLQKLGGLDIVINNAGIF 97
DVT Y + A T+ G LD + NAGI+
Sbjct: 58 EG-DVTSYADNQRAVDQTVDAFGKLDCFVGNAGIW 91
>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 = 70.0 bits (172), Expect = 6e-16
Identities = 42/121 (34%), Positives = 53/121 (43%), Gaps = 16/121 (13%)
Query: 3 MDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIY 62
M L G L+TGG +GIG A + L+ G V I + LAE K PN
Sbjct: 1 MKLTGNTVLITGGTSGIGLALARKFLEAGNTVIITGRREER---LAEA--KKELPNIHTI 55
Query: 63 CPCDVTDYPQFEEAFQITLQKLGGLDIVINNAGI-----FNDRFWEL-----EVDVNLVG 112
DV D E + L + LDI+INNAGI D +L E+D NL+G
Sbjct: 56 V-LDVGDAESVEALAEALLSEYPNLDILINNAGIQRPIDLRDPASDLDKADTEIDTNLIG 114
Query: 113 T 113
Sbjct: 115 P 115
>gnl|CDD|236399 PRK09186, PRK09186, flagellin modification protein A; Provisional.
Length = 256
Score = 70.4 bits (173), Expect = 6e-16
Identities = 30/107 (28%), Positives = 49/107 (45%), Gaps = 4/107 (3%)
Query: 5 LKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCP 64
LKGK L+TG IG A + +L+ G V DI+ +L E ++ +
Sbjct: 2 LKGKTILITGAGGLIGSALVKAILEAGGIVIAADIDKEALNELLESLGKEFKSKKLSLVE 61
Query: 65 CDVTDYPQFEEAFQITLQKLGGLDIVINNAGIFND----RFWELEVD 107
D+TD EE + +K G +D +N A N +F+++ +D
Sbjct: 62 LDITDQESLEEFLSKSAEKYGKIDGAVNCAYPRNKDYGKKFFDVSLD 108
>gnl|CDD|223377 COG0300, DltE, Short-chain dehydrogenases of various substrate
specificities [General function prediction only].
Length = 265
Score = 70.4 bits (173), Expect = 7e-16
Identities = 30/119 (25%), Positives = 56/119 (47%), Gaps = 9/119 (7%)
Query: 3 MDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIY 62
+KGK AL+TG ++GIG ++L + G + + + E LA++ K G
Sbjct: 2 GPMKGKTALITGASSGIGAELAKQLARRGYNLILVARREDKLEALAKELEDKTG-VEVEV 60
Query: 63 CPCDVTDYPQFEEAFQITLQKLGGLDIVINNAGI-----FNDRFWELE---VDVNLVGT 113
P D++D E ++ G +D+++NNAG F + + E + +N++
Sbjct: 61 IPADLSDPEALERLEDELKERGGPIDVLVNNAGFGTFGPFLELSLDEEEEMIQLNILAL 119
>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 = 69.9 bits (172), Expect = 9e-16
Identities = 33/105 (31%), Positives = 54/105 (51%), Gaps = 2/105 (1%)
Query: 5 LKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCP 64
L+GKV ++TG ++GIG L + GA++ + + E++ + P P
Sbjct: 1 LQGKVVIITGASSGIGEELAYHLARLGARLVLSARREERLEEVKSECLELGAP-SPHVVP 59
Query: 65 CDVTDYPQFEEAFQITLQKLGGLDIVINNAGIFN-DRFWELEVDV 108
D++D E+ + L+ GGLDI+INNAGI F + +DV
Sbjct: 60 LDMSDLEDAEQVVEEALKLFGGLDILINNAGISMRSLFHDTSIDV 104
>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 = 69.7 bits (171), Expect = 1e-15
Identities = 32/111 (28%), Positives = 49/111 (44%), Gaps = 10/111 (9%)
Query: 10 ALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPCDVTD 69
L+TG ++GIGRA E K G V++ ++L + DVTD
Sbjct: 1 VLITGASSGIGRALAREFAKAGYNVALAARRTDRLDELKAE--LLNPNPSVEVEILDVTD 58
Query: 70 YPQFEEAFQITLQKLGGLDIVINNAGI-----FNDRFWELE---VDVNLVG 112
+ + +LGGLD+VI NAG+ D ++ +D NL+G
Sbjct: 59 EERNQLVIAELEAELGGLDLVIINAGVGKGTSLGDLSFKAFRETIDTNLLG 109
>gnl|CDD|237220 PRK12828, PRK12828, short chain dehydrogenase; Provisional.
Length = 239
Score = 69.1 bits (169), Expect = 2e-15
Identities = 32/121 (26%), Positives = 47/121 (38%), Gaps = 12/121 (9%)
Query: 1 MVMDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRA 60
M L+GKV +TGG G+GRA L GA+V++ G Q +
Sbjct: 1 MEHSLQGKVVAITGGFGGLGRATAAWLAARGARVALIGR----GAAPLSQTLPGVPADAL 56
Query: 61 IYCPCDVTDYPQFEEAFQITLQKLGGLDIVINNAGIF--------NDRFWELEVDVNLVG 112
D+ D A ++ G LD ++N AG F + W+ VN+
Sbjct: 57 RIGGIDLVDPQAARRAVDEVNRQFGRLDALVNIAGAFVWGTIADGDADTWDRMYGVNVKT 116
Query: 113 T 113
T
Sbjct: 117 T 117
>gnl|CDD|180822 PRK07069, PRK07069, short chain dehydrogenase; Validated.
Length = 251
Score = 69.0 bits (169), Expect = 2e-15
Identities = 33/88 (37%), Positives = 48/88 (54%), Gaps = 1/88 (1%)
Query: 10 ALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGED-LAEQWRTKYGPNRAIYCPCDVT 68
A +TG A G+GRA + + GAKV + DIND+ G D A + +G A DVT
Sbjct: 2 AFITGAAGGLGRAIARRMAEQGAKVFLTDINDAAGLDAFAAEINAAHGEGVAFAAVQDVT 61
Query: 69 DYPQFEEAFQITLQKLGGLDIVINNAGI 96
D Q++ +GGL +++NNAG+
Sbjct: 62 DEAQWQALLAQAADAMGGLSVLVNNAGV 89
>gnl|CDD|236116 PRK07856, PRK07856, short chain dehydrogenase; Provisional.
Length = 252
Score = 68.4 bits (168), Expect = 3e-15
Identities = 29/93 (31%), Positives = 40/93 (43%), Gaps = 10/93 (10%)
Query: 3 MDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIY 62
+DL G+V LVTGG GIG L GA V +C + A +
Sbjct: 2 LDLTGRVVLVTGGTRGIGAGIARAFLAAGATVVVC----------GRRAPETVDGRPAEF 51
Query: 63 CPCDVTDYPQFEEAFQITLQKLGGLDIVINNAG 95
DV D Q +++ G LD+++NNAG
Sbjct: 52 HAADVRDPDQVAALVDAIVERHGRLDVLVNNAG 84
>gnl|CDD|168574 PRK06484, PRK06484, short chain dehydrogenase; Validated.
Length = 520
Score = 69.5 bits (170), Expect = 3e-15
Identities = 33/108 (30%), Positives = 53/108 (49%), Gaps = 6/108 (5%)
Query: 3 MDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIY 62
+ +V LVTG A GIGRA C+ + G +V + D N + A+ + A+
Sbjct: 1 SKAQSRVVLVTGAAGGIGRAACQRFARAGDQVVVADRNVERARERADSLGP---DHHAL- 56
Query: 63 CPCDVTDYPQFEEAFQITLQKLGGLDIVINNAGIFNDRFWELEVDVNL 110
DV+D Q E F+ ++ G +D+++NNAG+ D +D L
Sbjct: 57 -AMDVSDEAQIREGFEQLHREFGRIDVLVNNAGV-TDPTMTATLDTTL 102
Score = 57.2 bits (138), Expect = 8e-11
Identities = 37/117 (31%), Positives = 53/117 (45%), Gaps = 16/117 (13%)
Query: 7 GKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPCD 66
+V +TGGA GIGRA + G ++ I D + + LAE ++ +A D
Sbjct: 269 PRVVAITGGARGIGRAVADRFAAAGDRLLIIDRDAEGAKKLAEALGDEHLSVQA-----D 323
Query: 67 VTDYPQFEEAFQITLQKLGGLDIVINNAGIFNDRFWELE----------VDVNLVGT 113
+TD E AF + G LD+++NNAGI + F DVNL G
Sbjct: 324 ITDEAAVESAFAQIQARWGRLDVLVNNAGI-AEVFKPSLEQSAEDFTRVYDVNLSGA 379
>gnl|CDD|237219 PRK12827, PRK12827, short chain dehydrogenase; Provisional.
Length = 249
Score = 68.2 bits (167), Expect = 3e-15
Identities = 38/119 (31%), Positives = 55/119 (46%), Gaps = 10/119 (8%)
Query: 5 LKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPN--RAIY 62
L + L+TGG+ G+GRA L GA V + DI+ G A+ +A+
Sbjct: 4 LDSRRVLITGGSGGLGRAIAVRLAADGADVIVLDIHPMRGRAEADAVAAGIEAAGGKALG 63
Query: 63 CPCDVTDYPQFEEAFQITLQKLGGLDIVINNAGIFND--------RFWELEVDVNLVGT 113
DV D+ A +++ G LDI++NNAGI D W+ +DVNL G
Sbjct: 64 LAFDVRDFAATRAALDAGVEEFGRLDILVNNAGIATDAAFAELSIEEWDDVIDVNLDGF 122
>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 = 68.0 bits (167), Expect = 4e-15
Identities = 30/114 (26%), Positives = 47/114 (41%), Gaps = 13/114 (11%)
Query: 8 KVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPCDV 67
KV L+TG ++GIG A L G +V N E L E + DV
Sbjct: 1 KVVLITGCSSGIGLALALALAAQGYRVIATARNPDKLESLGELL-----NDNLEVLELDV 55
Query: 68 TDYPQFEEAFQITLQKLGGLDIVINNAGI--------FNDRFWELEVDVNLVGT 113
TD + A + +++ G +D+++NNAG + +VN+ G
Sbjct: 56 TDEESIKAAVKEVIERFGRIDVLVNNAGYGLFGPLEETSIEEVRELFEVNVFGP 109
>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 = 68.0 bits (166), Expect = 4e-15
Identities = 36/87 (41%), Positives = 49/87 (56%), Gaps = 2/87 (2%)
Query: 9 VALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPCDVT 68
VA+VTGGAAGIG+A L K GA V I D+ E +A + G +AI C+VT
Sbjct: 1 VAIVTGGAAGIGKAIAGTLAKAGASVVIADLKSEGAEAVAAAIQQAGG--QAIGLECNVT 58
Query: 69 DYPQFEEAFQITLQKLGGLDIVINNAG 95
E + T+ + GG+ I++NNAG
Sbjct: 59 SEQDLEAVVKATVSQFGGITILVNNAG 85
>gnl|CDD|181508 PRK08628, PRK08628, short chain dehydrogenase; Provisional.
Length = 258
Score = 68.4 bits (168), Expect = 4e-15
Identities = 38/100 (38%), Positives = 53/100 (53%), Gaps = 4/100 (4%)
Query: 1 MVMDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRA 60
M ++LK KV +VTGGA+GIG A L + GA I + E E P RA
Sbjct: 1 MDLNLKDKVVIVTGGASGIGAAISLRLAEEGAIPVIFGRSAPDDEFAEEL--RALQP-RA 57
Query: 61 IYCPCDVTDYPQFEEAFQITLQKLGGLDIVINNAGIFNDR 100
+ D+TD Q +A + T+ K G +D ++NNAG+ ND
Sbjct: 58 EFVQVDLTDDAQCRDAVEQTVAKFGRIDGLVNNAGV-NDG 96
>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 = 67.5 bits (165), Expect = 4e-15
Identities = 35/113 (30%), Positives = 45/113 (39%), Gaps = 13/113 (11%)
Query: 8 KVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPCDV 67
K ALVTG + GIG A L G +V IC +++ A Q DV
Sbjct: 1 KAALVTGASRGIGEATARLLHAEGYRVGICARDEARLAAAAAQELEGVLG-----LAGDV 55
Query: 68 TDYPQFEEAFQITLQKLGGLDIVINNAGI--------FNDRFWELEVDVNLVG 112
D A + GGLD ++NNAG+ W L +D NL G
Sbjct: 56 RDEADVRRAVDAMEEAFGGLDALVNNAGVGVMKPVEELTPEEWRLVLDTNLTG 108
>gnl|CDD|183773 PRK12824, PRK12824, acetoacetyl-CoA reductase; Provisional.
Length = 245
Score = 67.5 bits (165), Expect = 5e-15
Identities = 39/113 (34%), Positives = 53/113 (46%), Gaps = 13/113 (11%)
Query: 8 KVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYG--PNRAIYCPC 65
K+ALVTG GIG A ELL G +V G D A+ W +YG ++
Sbjct: 3 KIALVTGAKRGIGSAIARELLNDGYRVIA---TYFSGNDCAKDWFEEYGFTEDQVRLKEL 59
Query: 66 DVTDYPQFEEAFQITLQKLGGLDIVINNAGIFNDRF--------WELEVDVNL 110
DVTD + EA ++ G +DI++NNAGI D W ++ NL
Sbjct: 60 DVTDTEECAEALAEIEEEEGPVDILVNNAGITRDSVFKRMSHQEWNDVINTNL 112
>gnl|CDD|235853 PRK06701, PRK06701, short chain dehydrogenase; Provisional.
Length = 290
Score = 68.1 bits (167), Expect = 6e-15
Identities = 38/93 (40%), Positives = 58/93 (62%), Gaps = 5/93 (5%)
Query: 5 LKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAE-QWRTKYGPNRAIYC 63
LKGKVAL+TGG +GIGRA K GA ++I +++ ED E + R + + +
Sbjct: 44 LKGKVALITGGDSGIGRAVAVLFAKEGADIAIVYLDEH--EDANETKQRVEKEGVKCLLI 101
Query: 64 PCDVTDYPQF-EEAFQITLQKLGGLDIVINNAG 95
P DV+D F ++A + T+++LG LDI++NNA
Sbjct: 102 PGDVSD-EAFCKDAVEETVRELGRLDILVNNAA 133
>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 = 67.3 bits (165), Expect = 8e-15
Identities = 41/118 (34%), Positives = 64/118 (54%), Gaps = 12/118 (10%)
Query: 7 GKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPN--RAIYCP 64
GK L+TGG++GIG+A +EL+K GA V I ++S E+ E+ + + + Y
Sbjct: 1 GKHVLITGGSSGIGKALAKELVKEGANVIIVARSESKLEEAVEEIEAEANASGQKVSYIS 60
Query: 65 CDVTDYPQFEEAFQITLQKLGGL-DIVINNAGIFNDRFWE------LE--VDVNLVGT 113
D++DY + E+AF + GG D+V+N AGI +E E +DVN G+
Sbjct: 61 ADLSDYEEVEQAFA-QAVEKGGPPDLVVNCAGISIPGLFEDLTAEEFERGMDVNYFGS 117
>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 = 66.8 bits (163), Expect = 1e-14
Identities = 40/128 (31%), Positives = 58/128 (45%), Gaps = 19/128 (14%)
Query: 5 LKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVG----------EDLAEQWRTK 54
L+GKVA +TG A G GRA+ L GA + D+ + EDL E R
Sbjct: 1 LEGKVAFITGAARGQGRAHAVRLAAEGADIIAIDLCAPLSDYPTYPLATREDLDETARLV 60
Query: 55 YGPNR-AIYCPCDVTDYPQFEEAFQITLQKLGGLDIVINNAGIFN-DRFWELE------- 105
R + DV D + + +++ G LD+V+ NAG+ + R WEL
Sbjct: 61 EALGRKVLARKADVRDLAEVRAVVEDGVEQFGRLDVVVANAGVLSYGRSWELSEEQWDTV 120
Query: 106 VDVNLVGT 113
+D+NL G
Sbjct: 121 LDINLTGV 128
>gnl|CDD|235935 PRK07109, PRK07109, short chain dehydrogenase; Provisional.
Length = 334
Score = 67.6 bits (166), Expect = 1e-14
Identities = 29/96 (30%), Positives = 47/96 (48%), Gaps = 2/96 (2%)
Query: 1 MVMDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRA 60
M+ + +V ++TG +AG+GRA + GAKV + + E LA + R G A
Sbjct: 2 MLKPIGRQVVVITGASAGVGRATARAFARRGAKVVLLARGEEGLEALAAEIRAAGG--EA 59
Query: 61 IYCPCDVTDYPQFEEAFQITLQKLGGLDIVINNAGI 96
+ DV D + A ++LG +D +NNA +
Sbjct: 60 LAVVADVADAEAVQAAADRAEEELGPIDTWVNNAMV 95
>gnl|CDD|235933 PRK07097, PRK07097, gluconate 5-dehydrogenase; Provisional.
Length = 265
Score = 67.0 bits (164), Expect = 1e-14
Identities = 34/93 (36%), Positives = 49/93 (52%), Gaps = 2/93 (2%)
Query: 4 DLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYC 63
LKGK+AL+TG + GIG A + K GA + DIN + + +R G Y
Sbjct: 7 SLKGKIALITGASYGIGFAIAKAYAKAGATIVFNDINQELVDKGLAAYREL-GIEAHGYV 65
Query: 64 PCDVTDYPQFEEAFQITLQKLGGLDIVINNAGI 96
CDVTD + +++G +DI++NNAGI
Sbjct: 66 -CDVTDEDGVQAMVSQIEKEVGVIDILVNNAGI 97
>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 = 66.3 bits (162), Expect = 2e-14
Identities = 32/93 (34%), Positives = 48/93 (51%), Gaps = 4/93 (4%)
Query: 6 KGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWR--TKYGPNRAIYC 63
KGKVALVTG +GIG L GA + + D+ E A + K+G + +Y
Sbjct: 1 KGKVALVTGSTSGIGLGIARALAAAGANIVLNGFGDA-AEIEAVRAGLAAKHG-VKVLYH 58
Query: 64 PCDVTDYPQFEEAFQITLQKLGGLDIVINNAGI 96
D++ E+ ++ GG+DI++NNAGI
Sbjct: 59 GADLSKPAAIEDMVAYAQRQFGGVDILVNNAGI 91
>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 = 66.1 bits (161), Expect = 2e-14
Identities = 41/114 (35%), Positives = 57/114 (50%), Gaps = 13/114 (11%)
Query: 7 GKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPCD 66
GKVA+VTGG GIG+ C + L+ G KV DI++ G D AE GPN + D
Sbjct: 1 GKVAIVTGGGHGIGKQICLDFLEAGDKVVFADIDEERGADFAEA----EGPN-LFFVHGD 55
Query: 67 VTDYPQFEEAFQITLQKLGGLDIVINNAGIFNDRF--------WELEVDVNLVG 112
V D + L+KLG +D+++NNA + W+ + VNL G
Sbjct: 56 VADETLVKFVVYAMLEKLGRIDVLVNNAARGSKGILSSLLLEEWDRILSVNLTG 109
>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 = 65.8 bits (161), Expect = 3e-14
Identities = 35/93 (37%), Positives = 50/93 (53%), Gaps = 3/93 (3%)
Query: 5 LKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVG-EDLAEQWRTKYGPNRAIYC 63
L GKVALVTG + GIGRA + L + GA V + + E++ + G +AI
Sbjct: 1 LAGKVALVTGASRGIGRAIAKRLARDGASVVVNYASSKAAAEEVVAEIEAAGG--KAIAV 58
Query: 64 PCDVTDYPQFEEAFQITLQKLGGLDIVINNAGI 96
DV+D Q F + GG+DI++NNAG+
Sbjct: 59 QADVSDPSQVARLFDAAEKAFGGVDILVNNAGV 91
>gnl|CDD|236210 PRK08267, PRK08267, short chain dehydrogenase; Provisional.
Length = 260
Score = 65.7 bits (161), Expect = 3e-14
Identities = 34/111 (30%), Positives = 49/111 (44%), Gaps = 13/111 (11%)
Query: 11 LVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPCDVTDY 70
+TG A+GIGRA G +V DIN++ LA + G A DVTD
Sbjct: 5 FITGAASGIGRATALLFAAEGWRVGAYDINEAGLAALAAEL----GAGNAWTGALDVTDR 60
Query: 71 PQFEEAF-QITLQKLGGLDIVINNAGIFND-RFWELE-------VDVNLVG 112
++ A G LD++ NNAGI F ++ +D+N+ G
Sbjct: 61 AAWDAALADFAAATGGRLDVLFNNAGILRGGPFEDIPLEAHDRVIDINVKG 111
>gnl|CDD|237188 PRK12745, PRK12745, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 256
Score = 65.8 bits (161), Expect = 3e-14
Identities = 31/90 (34%), Positives = 40/90 (44%), Gaps = 3/90 (3%)
Query: 8 KVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAE-QWRTKYGPNRAIYCPCD 66
VALVTGG GIG L G ++I D D E+LA Q + I+ P D
Sbjct: 3 PVALVTGGRRGIGLGIARALAAAGFDLAINDRPDD--EELAATQQELRALGVEVIFFPAD 60
Query: 67 VTDYPQFEEAFQITLQKLGGLDIVINNAGI 96
V D E G +D ++NNAG+
Sbjct: 61 VADLSAHEAMLDAAQAAWGRIDCLVNNAGV 90
>gnl|CDD|180408 PRK06114, PRK06114, short chain dehydrogenase; Provisional.
Length = 254
Score = 65.6 bits (160), Expect = 4e-14
Identities = 39/117 (33%), Positives = 54/117 (46%), Gaps = 9/117 (7%)
Query: 4 DLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYC 63
DL G+VA VTG +GIG+ L + GA V++ D+ G + G RAI
Sbjct: 5 DLDGQVAFVTGAGSGIGQRIAIGLAQAGADVALFDLRTDDGLAETAEHIEAAG-RRAIQI 63
Query: 64 PCDVTDYPQFEEAFQITLQKLGGLDIVINNAGIFN--------DRFWELEVDVNLVG 112
DVT A T +LG L + +N AGI N + W+ +D+NL G
Sbjct: 64 AADVTSKADLRAAVARTEAELGALTLAVNAAGIANANPAEEMEEEQWQTVMDINLTG 120
>gnl|CDD|235962 PRK07201, PRK07201, short chain dehydrogenase; Provisional.
Length = 657
Score = 65.4 bits (160), Expect = 8e-14
Identities = 43/122 (35%), Positives = 61/122 (50%), Gaps = 18/122 (14%)
Query: 5 LKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAE---QWRTKYGPNRAI 61
L GKV L+TG ++GIGRA ++ + GA V + N GE L E + R K G A
Sbjct: 369 LVGKVVLITGASSGIGRATAIKVAEAGATVFLVARN---GEALDELVAEIRAKGG--TAH 423
Query: 62 YCPCDVTDYPQFEEAFQITLQKLGGLDIVINNAG------IFN--DRFWELE--VDVNLV 111
CD+TD + + L + G +D ++NNAG + N DRF + E + VN
Sbjct: 424 AYTCDLTDSAAVDHTVKDILAEHGHVDYLVNNAGRSIRRSVENSTDRFHDYERTMAVNYF 483
Query: 112 GT 113
G
Sbjct: 484 GA 485
Score = 26.1 bits (58), Expect = 5.0
Identities = 27/91 (29%), Positives = 41/91 (45%), Gaps = 10/91 (10%)
Query: 11 LVTGGAAGIGRAYCEELL--KFGAKVSICDINDSVG--EDLAEQWRTKYGPNRAIYCPCD 66
VTGG IGR LL + A V + S+ E LA W G +R + D
Sbjct: 4 FVTGGTGFIGRRLVSRLLDRRREATVHVLVRRQSLSRLEALAAYW----GADRVVPLVGD 59
Query: 67 VTDYPQFEEAFQITLQKLGGLDIVINNAGIF 97
+T+ P + + +LG +D V++ A I+
Sbjct: 60 LTE-PGLGLSEA-DIAELGDIDHVVHLAAIY 88
>gnl|CDD|235794 PRK06398, PRK06398, aldose dehydrogenase; Validated.
Length = 258
Score = 64.5 bits (157), Expect = 1e-13
Identities = 36/117 (30%), Positives = 54/117 (46%), Gaps = 21/117 (17%)
Query: 4 DLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYC 63
LK KVA+VTGG+ GIG+A L + G+ V DI + N Y
Sbjct: 3 GLKDKVAIVTGGSQGIGKAVVNRLKEEGSNVINFDIKEP-------------SYNDVDYF 49
Query: 64 PCDVTDYPQFEEAFQITLQKLGGLDIVINNAGI--------FNDRFWELEVDVNLVG 112
DV++ Q + + K G +DI++NNAGI + W+ ++VN+ G
Sbjct: 50 KVDVSNKEQVIKGIDYVISKYGRIDILVNNAGIESYGAIHAVEEDEWDRIINVNVNG 106
>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 = 64.1 bits (156), Expect = 1e-13
Identities = 36/117 (30%), Positives = 54/117 (46%), Gaps = 9/117 (7%)
Query: 5 LKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCP 64
+G+VALVTG + GIG A L++ G KV C E LA + ++ P Y
Sbjct: 4 WRGRVALVTGASVGIGAAVARALVQHGMKVVGCARRVDKIEALAAECQSAGYPTLFPY-Q 62
Query: 65 CDVTDYPQFEEAFQITLQKLGGLDIVINNAGIFNDRF--------WELEVDVNLVGT 113
CD+++ Q F + G+D+ INNAG+ W+ DVN++
Sbjct: 63 CDLSNEEQILSMFSAIRTQHQGVDVCINNAGLARPEPLLSGKTEGWKEMFDVNVLAL 119
>gnl|CDD|180761 PRK06935, PRK06935, 2-deoxy-D-gluconate 3-dehydrogenase;
Provisional.
Length = 258
Score = 64.0 bits (156), Expect = 2e-13
Identities = 36/117 (30%), Positives = 55/117 (47%), Gaps = 15/117 (12%)
Query: 4 DLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGE--DLAEQWRTKYGPNRAI 61
L GKVA+VTGG G+G+ Y L K GA + I + E L E+ +
Sbjct: 12 SLDGKVAIVTGGNTGLGQGYAVALAKAGADIIITTHGTNWDETRRLIEK-----EGRKVT 66
Query: 62 YCPCDVTDYPQFEEAFQITLQKLGGLDIVINNAGI--------FNDRFWELEVDVNL 110
+ D+T E+ + L++ G +DI++NNAG + D W +D+NL
Sbjct: 67 FVQVDLTKPESAEKVVKEALEEFGKIDILVNNAGTIRRAPLLEYKDEDWNAVMDINL 123
>gnl|CDD|181295 PRK08213, PRK08213, gluconate 5-dehydrogenase; Provisional.
Length = 259
Score = 63.8 bits (156), Expect = 2e-13
Identities = 34/93 (36%), Positives = 49/93 (52%), Gaps = 4/93 (4%)
Query: 4 DLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAE-QWRTKYGPNRAIY 62
DL GK ALVTGG+ G+G E L + GA+V + E+L E + A++
Sbjct: 9 DLSGKTALVTGGSRGLGLQIAEALGEAGARVVLS---ARKAEELEEAAAHLEALGIDALW 65
Query: 63 CPCDVTDYPQFEEAFQITLQKLGGLDIVINNAG 95
DV D E + TL++ G +DI++NNAG
Sbjct: 66 IAADVADEADIERLAEETLERFGHVDILVNNAG 98
>gnl|CDD|183832 PRK12935, PRK12935, acetoacetyl-CoA reductase; Provisional.
Length = 247
Score = 63.9 bits (155), Expect = 2e-13
Identities = 42/116 (36%), Positives = 56/116 (48%), Gaps = 13/116 (11%)
Query: 5 LKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPN--RAIY 62
L GKVA+VTGGA GIG+A L + GAKV IN + ++ AE + G
Sbjct: 4 LNGKVAIVTGGAKGIGKAITVALAQEGAKVV---INYNSSKEAAENLVNELGKEGHDVYA 60
Query: 63 CPCDVTDYPQFEEAFQITLQKLGGLDIVINNAGIFNDRF--------WELEVDVNL 110
DV+ + + G +DI++NNAGI DR WE +DVNL
Sbjct: 61 VQADVSKVEDANRLVEEAVNHFGKVDILVNNAGITRDRTFKKLNREDWERVIDVNL 116
>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 = 63.2 bits (154), Expect = 3e-13
Identities = 28/93 (30%), Positives = 46/93 (49%), Gaps = 1/93 (1%)
Query: 5 LKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYC- 63
L GKVA++TG ++GIG + GA++++ + E+ + + I
Sbjct: 1 LSGKVAIITGSSSGIGAGTAILFARLGARLALTGRDAERLEETRQSCLQAGVSEKKILLV 60
Query: 64 PCDVTDYPQFEEAFQITLQKLGGLDIVINNAGI 96
D+T+ + TL K G LDI++NNAGI
Sbjct: 61 VADLTEEEGQDRIISTTLAKFGRLDILVNNAGI 93
>gnl|CDD|236207 PRK08261, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 450
Score = 63.7 bits (156), Expect = 3e-13
Identities = 45/118 (38%), Positives = 57/118 (48%), Gaps = 21/118 (17%)
Query: 5 LKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCP 64
L GKVALVTG A GIG A E L + GA V D+ + GE LA G A+
Sbjct: 208 LAGKVALVTGAARGIGAAIAEVLARDGAHVVCLDV-PAAGEALAAVANRVGG--TAL--A 262
Query: 65 CDVTDYPQFEEAFQITLQKL----GGLDIVINNAGIFNDR--------FWELEVDVNL 110
D+T +A + L GGLDIV++NAGI D+ W+ + VNL
Sbjct: 263 LDITA----PDAPARIAEHLAERHGGLDIVVHNAGITRDKTLANMDEARWDSVLAVNL 316
>gnl|CDD|235628 PRK05855, PRK05855, short chain dehydrogenase; Validated.
Length = 582
Score = 63.8 bits (156), Expect = 3e-13
Identities = 43/115 (37%), Positives = 57/115 (49%), Gaps = 12/115 (10%)
Query: 7 GKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPCD 66
GK+ +VTG +GIGR + GA+V DI+++ E AE R G Y D
Sbjct: 315 GKLVVVTGAGSGIGRETALAFAREGAEVVASDIDEAAAERTAELIR-AAGAVAHAY-RVD 372
Query: 67 VTDYPQFEEAFQITLQK-LGGLDIVINNAGI-----FND---RFWELEVDVNLVG 112
V+D EAF ++ G DIV+NNAGI F D W+ +DVNL G
Sbjct: 373 VSD-ADAMEAFAEWVRAEHGVPDIVVNNAGIGMAGGFLDTSAEDWDRVLDVNLWG 426
>gnl|CDD|181585 PRK08936, PRK08936, glucose-1-dehydrogenase; Provisional.
Length = 261
Score = 62.8 bits (153), Expect = 5e-13
Identities = 43/122 (35%), Positives = 59/122 (48%), Gaps = 11/122 (9%)
Query: 1 MVMDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVG-EDLAEQWRTKYGPNR 59
M DL+GKV ++TGG+ G+GRA K AKV I +D D+AE+ + G
Sbjct: 1 MYSDLEGKVVVITGGSTGLGRAMAVRFGKEKAKVVINYRSDEEEANDVAEEIKKAGG--E 58
Query: 60 AIYCPCDVTDYPQFEEAFQITLQKLGGLDIVINNAGIFND--------RFWELEVDVNLV 111
AI DVT Q +++ G LD++INNAGI N W ++ NL
Sbjct: 59 AIAVKGDVTVESDVVNLIQTAVKEFGTLDVMINNAGIENAVPSHEMSLEDWNKVINTNLT 118
Query: 112 GT 113
G
Sbjct: 119 GA 120
>gnl|CDD|235631 PRK05866, PRK05866, short chain dehydrogenase; Provisional.
Length = 293
Score = 62.8 bits (153), Expect = 5e-13
Identities = 31/92 (33%), Positives = 51/92 (55%), Gaps = 2/92 (2%)
Query: 4 DLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYC 63
DL GK L+TG ++GIG A E+ + GA V + + + +A++ G A+
Sbjct: 37 DLTGKRILLTGASSGIGEAAAEQFARRGATVVAVARREDLLDAVADRITRAGGDAMAV-- 94
Query: 64 PCDVTDYPQFEEAFQITLQKLGGLDIVINNAG 95
PCD++D + +++GG+DI+INNAG
Sbjct: 95 PCDLSDLDAVDALVADVEKRIGGVDILINNAG 126
>gnl|CDD|171821 PRK12937, PRK12937, short chain dehydrogenase; Provisional.
Length = 245
Score = 62.5 bits (152), Expect = 5e-13
Identities = 34/120 (28%), Positives = 52/120 (43%), Gaps = 11/120 (9%)
Query: 3 MDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDI-NDSVGEDLAEQWRTKYGPNRAI 61
M L KVA+VTG + GIG A L G V++ + + ++L + G RAI
Sbjct: 1 MTLSNKVAIVTGASRGIGAAIARRLAADGFAVAVNYAGSAAAADELVAEIEAAGG--RAI 58
Query: 62 YCPCDVTDYPQFEEAFQITLQKLGGLDIVINNAGI--------FNDRFWELEVDVNLVGT 113
DV D F G +D+++NNAG+ F+ ++ + NL G
Sbjct: 59 AVQADVADAAAVTRLFDAAETAFGRIDVLVNNAGVMPLGTIADFDLEDFDRTIATNLRGA 118
>gnl|CDD|180993 PRK07478, PRK07478, short chain dehydrogenase; Provisional.
Length = 254
Score = 62.6 bits (153), Expect = 5e-13
Identities = 33/94 (35%), Positives = 50/94 (53%), Gaps = 2/94 (2%)
Query: 3 MDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIY 62
M L GKVA++TG ++GIGRA + + GAKV + + + L + R + G A+
Sbjct: 2 MRLNGKVAIITGASSGIGRAAAKLFAREGAKVVVGARRQAELDQLVAEIRAEGG--EAVA 59
Query: 63 CPCDVTDYPQFEEAFQITLQKLGGLDIVINNAGI 96
DV D + + +++ GGLDI NNAG
Sbjct: 60 LAGDVRDEAYAKALVALAVERFGGLDIAFNNAGT 93
>gnl|CDD|235712 PRK06138, PRK06138, short chain dehydrogenase; Provisional.
Length = 252
Score = 62.5 bits (152), Expect = 5e-13
Identities = 36/121 (29%), Positives = 52/121 (42%), Gaps = 15/121 (12%)
Query: 3 MDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIY 62
M L G+VA+VTG +GIGRA + + GA+V + D + E +A RA
Sbjct: 1 MRLAGRVAIVTGAGSGIGRATAKLFAREGARVVVADRDAEAAERVAAAIA---AGGRAFA 57
Query: 63 CPCDVTDYPQFEEAFQITLQKLGGLDIVINNAGIF----------NDRFWELEVDVNLVG 112
DV E + G LD+++NNAG D W+ + VN+ G
Sbjct: 58 RQGDVGSAEAVEALVDFVAARWGRLDVLVNNAGFGCGGTVVTTDEAD--WDAVMRVNVGG 115
Query: 113 T 113
Sbjct: 116 V 116
>gnl|CDD|181225 PRK08085, PRK08085, gluconate 5-dehydrogenase; Provisional.
Length = 254
Score = 62.5 bits (152), Expect = 5e-13
Identities = 36/113 (31%), Positives = 55/113 (48%), Gaps = 10/113 (8%)
Query: 5 LKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCP 64
L GK L+TG A GIG L ++GA++ I DI E + R + +A P
Sbjct: 7 LAGKNILITGSAQGIGFLLATGLAEYGAEIIINDITAERAELAVAKLRQE--GIKAHAAP 64
Query: 65 CDVTDYPQFEEAFQITLQKLGGLDIVINNAGI--------FNDRFWELEVDVN 109
+VT + E A + + +G +D++INNAGI F ++ W + VN
Sbjct: 65 FNVTHKQEVEAAIEHIEKDIGPIDVLINNAGIQRRHPFTEFPEQEWNDVIAVN 117
>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 = 62.5 bits (152), Expect = 5e-13
Identities = 34/115 (29%), Positives = 49/115 (42%), Gaps = 11/115 (9%)
Query: 9 VALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPCDVT 68
VA+VTG + GIGRA EL G ++I D+ D G RAIY D+
Sbjct: 3 VAIVTGASRGIGRAIATELAARGFDIAINDLPDDDQATEVVAEVLAAG-RRAIYFQADIG 61
Query: 69 DYPQFEEAFQITLQKLGGLDIVINNAGI----------FNDRFWELEVDVNLVGT 113
+ E + G LD ++NNAGI + ++ + +NL G
Sbjct: 62 ELSDHEALLDQAWEDFGRLDCLVNNAGIAVRPRGDLLDLTEDSFDRLIAINLRGP 116
>gnl|CDD|181721 PRK09242, PRK09242, tropinone reductase; Provisional.
Length = 257
Score = 62.5 bits (152), Expect = 5e-13
Identities = 26/92 (28%), Positives = 37/92 (40%)
Query: 5 LKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCP 64
L G+ AL+TG + GIG A E L GA V I + ++ ++
Sbjct: 7 LDGQTALITGASKGIGLAIAREFLGLGADVLIVARDADALAQARDELAEEFPEREVHGLA 66
Query: 65 CDVTDYPQFEEAFQITLQKLGGLDIVINNAGI 96
DV+D GL I++NNAG
Sbjct: 67 ADVSDDEDRRAILDWVEDHWDGLHILVNNAGG 98
>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 = 61.6 bits (150), Expect = 1e-12
Identities = 33/95 (34%), Positives = 50/95 (52%), Gaps = 5/95 (5%)
Query: 4 DLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYC 63
LKG+VAL+TGG +G+GRA E + GAKV++ D + + + R +G +
Sbjct: 1 WLKGEVALITGGGSGLGRALVERFVAEGAKVAVLDRS----AEKVAELRADFGDA-VVGV 55
Query: 64 PCDVTDYPQFEEAFQITLQKLGGLDIVINNAGIFN 98
DV E A +++ G LD I NAGI++
Sbjct: 56 EGDVRSLADNERAVARCVERFGKLDCFIGNAGIWD 90
>gnl|CDD|180458 PRK06194, PRK06194, hypothetical protein; Provisional.
Length = 287
Score = 62.0 bits (151), Expect = 1e-12
Identities = 35/120 (29%), Positives = 55/120 (45%), Gaps = 16/120 (13%)
Query: 4 DLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDIN-DSVGEDLAEQWRTKYGPNRAIY 62
D GKVA++TG A+G G A+ G K+ + D+ D++ +AE + +
Sbjct: 3 DFAGKVAVITGAASGFGLAFARIGAALGMKLVLADVQQDALDRAVAE---LRAQGAEVLG 59
Query: 63 CPCDVTDYPQFEEAFQITLQKLGGLDIVINNAGI----------FNDRFWELEVDVNLVG 112
DV+D Q E L++ G + ++ NNAG+ D WE + VNL G
Sbjct: 60 VRTDVSDAAQVEALADAALERFGAVHLLFNNAGVGAGGLVWENSLAD--WEWVLGVNLWG 117
>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 = 61.3 bits (149), Expect = 1e-12
Identities = 36/113 (31%), Positives = 51/113 (45%), Gaps = 13/113 (11%)
Query: 8 KVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQW--RTKYGPNRAIYCPC 65
++ALVTGG GIG A C+ L K G +V+ N E+ AE W
Sbjct: 1 RIALVTGGMGGIGTAICQRLAKDGYRVA---ANCGPNEERAEAWLQEQGALGFDFRVVEG 57
Query: 66 DVTDYPQFEEAFQITLQKLGGLDIVINNAGIFNDRF--------WELEVDVNL 110
DV+ + + A +LG +D+++NNAGI D W +D NL
Sbjct: 58 DVSSFESCKAAVAKVEAELGPIDVLVNNAGITRDATFKKMTYEQWSAVIDTNL 110
>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 = 61.3 bits (149), Expect = 1e-12
Identities = 45/129 (34%), Positives = 58/129 (44%), Gaps = 22/129 (17%)
Query: 5 LKGKVALVTGGAAGIGRAYCEELLKFGAKVSI------CDINDSVG------EDLAEQWR 52
L GKVA VTG + GIGRA L K GA V + N S E+ AE+
Sbjct: 1 LSGKVAFVTGASRGIGRAIALRLAKAGATVVVAAKTASEGDNGSAKSLPGTIEETAEEIE 60
Query: 53 TKYGPNRAIYCPCDVTDYPQFEEAFQITLQKLGGLDIVINNAG-IFNDRFWE-------L 104
G +A+ DV D Q + T+ + G LDI++NNAG I+ + L
Sbjct: 61 AAGG--QALPIVVDVRDEDQVRALVEATVDQFGRLDILVNNAGAIWLSLVEDTPAKRFDL 118
Query: 105 EVDVNLVGT 113
VNL GT
Sbjct: 119 MQRVNLRGT 127
>gnl|CDD|181139 PRK07832, PRK07832, short chain dehydrogenase; Provisional.
Length = 272
Score = 61.2 bits (149), Expect = 2e-12
Identities = 33/113 (29%), Positives = 45/113 (39%), Gaps = 9/113 (7%)
Query: 8 KVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPCDV 67
K VTG A+GIGRA L GA++ + D + R G + D+
Sbjct: 1 KRCFVTGAASGIGRATALRLAAQGAELFLTDRDADGLAQTVADARAL-GGTVPEHRALDI 59
Query: 68 TDYPQFEEAFQITLQKLGGLDIVINNAGI--------FNDRFWELEVDVNLVG 112
+DY G +D+V+N AGI W VDVNL+G
Sbjct: 60 SDYDAVAAFAADIHAAHGSMDVVMNIAGISAWGTVDRLTHEQWRRMVDVNLMG 112
>gnl|CDD|183772 PRK12823, benD, 1,6-dihydroxycyclohexa-2,4-diene-1-carboxylate
dehydrogenase; Provisional.
Length = 260
Score = 61.1 bits (149), Expect = 2e-12
Identities = 33/104 (31%), Positives = 48/104 (46%), Gaps = 5/104 (4%)
Query: 6 KGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPC 65
GKV +VTG A GIGR GA+V + D ++ V E AE A+
Sbjct: 7 AGKVVVVTGAAQGIGRGVALRAAAEGARVVLVDRSELVHEVAAELRAAG---GEALALTA 63
Query: 66 DVTDYPQFEEAFQITLQKLGGLDIVINNAG--IFNDRFWELEVD 107
D+ Y + A ++ G +D++INN G I+ F E E +
Sbjct: 64 DLETYAGAQAAMAAAVEAFGRIDVLINNVGGTIWAKPFEEYEEE 107
>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 = 61.2 bits (149), Expect = 2e-12
Identities = 33/94 (35%), Positives = 51/94 (54%), Gaps = 6/94 (6%)
Query: 5 LKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAE---QWRTKYGPNRAI 61
LKGK AL+TGG +GIGRA + GA V+I + + ED AE + + G + +
Sbjct: 24 LKGKKALITGGDSGIGRAVAIAFAREGADVAINYLPEE--EDDAEETKKLIEEEG-RKCL 80
Query: 62 YCPCDVTDYPQFEEAFQITLQKLGGLDIVINNAG 95
P D+ D + + +++ G LDI++NNA
Sbjct: 81 LIPGDLGDESFCRDLVKEVVKEFGKLDILVNNAA 114
>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 = 61.0 bits (148), Expect = 2e-12
Identities = 31/91 (34%), Positives = 47/91 (51%), Gaps = 3/91 (3%)
Query: 5 LKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCP 64
+GKV +VTG A GIGR E L GA+V + D ++ V E LAE + A
Sbjct: 2 FEGKVVVVTGAAQGIGRGVAERLAGEGARVLLVDRSELVHEVLAE---ILAAGDAAHVHT 58
Query: 65 CDVTDYPQFEEAFQITLQKLGGLDIVINNAG 95
D+ Y + + +++ G +D++INN G
Sbjct: 59 ADLETYAGAQGVVRAAVERFGRVDVLINNVG 89
>gnl|CDD|236190 PRK08220, PRK08220, 2,3-dihydroxybenzoate-2,3-dehydrogenase;
Validated.
Length = 252
Score = 60.3 bits (147), Expect = 3e-12
Identities = 33/96 (34%), Positives = 43/96 (44%), Gaps = 11/96 (11%)
Query: 1 MVMDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRA 60
MD GK VTG A GIG A ++ GAKV +G D A + Y P
Sbjct: 2 NAMDFSGKTVWVTGAAQGIGYAVALAFVEAGAKV--------IGFDQAFLTQEDY-PFAT 52
Query: 61 IYCPCDVTDYPQFEEAFQITLQKLGGLDIVINNAGI 96
DV+D + Q L + G LD+++N AGI
Sbjct: 53 F--VLDVSDAAAVAQVCQRLLAETGPLDVLVNAAGI 86
>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 = 60.6 bits (147), Expect = 3e-12
Identities = 30/115 (26%), Positives = 51/115 (44%), Gaps = 9/115 (7%)
Query: 6 KGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPC 65
+VA+V GG +G C L + G V++ DIN E +A++ +YG A
Sbjct: 1 MNQVAVVIGGGQTLGEFLCHGLAEAGYDVAVADINSENAEKVADEINAEYGEK-AYGFGA 59
Query: 66 DVTDYPQFEEAFQITLQKLGGLDIVINNAGI--------FNDRFWELEVDVNLVG 112
D T+ + + +D+++ +AGI F ++ + VNLVG
Sbjct: 60 DATNEQSVIALSKGVDEIFKRVDLLVYSAGIAKSAKITDFELGDFDRSLQVNLVG 114
>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 = 60.8 bits (148), Expect = 4e-12
Identities = 31/103 (30%), Positives = 46/103 (44%), Gaps = 10/103 (9%)
Query: 6 KGKVALVTGGAAGIGRAYCEELLK-FGAKVSICDINDSVGEDLAEQWRT------KYGPN 58
G V LVTGGA GIGRA L + +GA++ + E+W+ +
Sbjct: 204 PGGVYLVTGGAGGIGRALARALARRYGARLVLLG---RSPLPPEEEWKAQTLAALEALGA 260
Query: 59 RAIYCPCDVTDYPQFEEAFQITLQKLGGLDIVINNAGIFNDRF 101
R +Y DVTD + ++ G +D VI+ AG+ D
Sbjct: 261 RVLYISADVTDAAAVRRLLEKVRERYGAIDGVIHAAGVLRDAL 303
>gnl|CDD|181335 PRK08264, PRK08264, short chain dehydrogenase; Validated.
Length = 238
Score = 59.9 bits (146), Expect = 4e-12
Identities = 44/123 (35%), Positives = 56/123 (45%), Gaps = 27/123 (21%)
Query: 3 MDLKGKVALVTGGAAGIGRAYCEELLKFGA-KVSICDIN-DSVGEDLAEQWRTKYGPNRA 60
MD+KGKV LVTG GIGRA+ E+LL GA KV + +SV T GP R
Sbjct: 2 MDIKGKVVLVTGANRGIGRAFVEQLLARGAAKVYAAARDPESV---------TDLGP-RV 51
Query: 61 IYCPCDVTDYPQFEEAFQITLQKLGGLDIVINNAGIFN----------DRFWELEVDVNL 110
+ DVTD A + + I++NNAGIF D E++ N
Sbjct: 52 VPLQLDVTDPASVAAAAEA----ASDVTILVNNAGIFRTGSLLLEGDEDAL-RAEMETNY 106
Query: 111 VGT 113
G
Sbjct: 107 FGP 109
>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 = 59.4 bits (144), Expect = 7e-12
Identities = 33/121 (27%), Positives = 50/121 (41%), Gaps = 16/121 (13%)
Query: 3 MDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIY 62
M G L+TGGA+GIG A + L+ G V IC N+ + + +
Sbjct: 1 MKTTGNTILITGGASGIGLALAKRFLELGNTVIICGRNEERLAEAKAENPEIHTE----- 55
Query: 63 CPCDVTDYPQFEEAFQITLQKLGGLDIVINNAGIFND----------RFWELEVDVNLVG 112
CDV D E + ++ L+++INNAGI + E E+ NL+
Sbjct: 56 -VCDVADRDSRRELVEWLKKEYPNLNVLINNAGIQRNEDLTGAEDLLDDAEQEIATNLLA 114
Query: 113 T 113
Sbjct: 115 P 115
>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 = 58.3 bits (141), Expect = 2e-11
Identities = 39/118 (33%), Positives = 58/118 (49%), Gaps = 11/118 (9%)
Query: 5 LKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAI-YC 63
K KV L+TGG +G+G A L K GAK+S+ D+N+ E A+ + P+ +
Sbjct: 1 FKDKVVLITGGGSGLGLATAVRLAKEGAKLSLVDLNEEGLEA-AKAALLEIAPDAEVLLI 59
Query: 64 PCDVTDYPQFEEAFQITLQKLGGLDIVINNAGI---------FNDRFWELEVDVNLVG 112
DV+D Q E T+++ G +D NNAGI F ++ V +NL G
Sbjct: 60 KADVSDEAQVEAYVDATVEQFGRIDGFFNNAGIEGKQNLTEDFGADEFDKVVSINLRG 117
>gnl|CDD|236099 PRK07791, PRK07791, short chain dehydrogenase; Provisional.
Length = 286
Score = 58.1 bits (141), Expect = 2e-11
Identities = 37/125 (29%), Positives = 55/125 (44%), Gaps = 19/125 (15%)
Query: 5 LKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDI-----NDSVGEDLAEQ----WRTKY 55
L G+V +VTG GIGRA+ GA+V + DI + G A+
Sbjct: 4 LDGRVVIVTGAGGGIGRAHALAFAAEGARVVVNDIGVGLDGSASGGSAAQAVVDEIVAAG 63
Query: 56 GPNRAIYCPCDVTDYPQFEEAFQITLQKLGGLDIVINNAGIFNDRF--------WELEVD 107
G A+ D+ D+ ++ GGLD+++NNAGI DR W+ +
Sbjct: 64 G--EAVANGDDIADWDGAANLVDAAVETFGGLDVLVNNAGILRDRMIANMSEEEWDAVIA 121
Query: 108 VNLVG 112
V+L G
Sbjct: 122 VHLKG 126
>gnl|CDD|180817 PRK07060, PRK07060, short chain dehydrogenase; Provisional.
Length = 245
Score = 57.8 bits (140), Expect = 2e-11
Identities = 34/96 (35%), Positives = 45/96 (46%), Gaps = 11/96 (11%)
Query: 1 MVMDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRA 60
M D GK LVTG ++GIGRA L + GA+V N + + LA + T P R
Sbjct: 3 MAFDFSGKSVLVTGASSGIGRACAVALAQRGARVVAAARNAAALDRLAGE--TGCEPLRL 60
Query: 61 IYCPCDVTDYPQFEEAFQITLQKLGGLDIVINNAGI 96
DV D + A + L G D ++N AGI
Sbjct: 61 -----DVGD----DAAIRAALAAAGAFDGLVNCAGI 87
>gnl|CDD|180669 PRK06720, PRK06720, hypothetical protein; Provisional.
Length = 169
Score = 56.9 bits (137), Expect = 3e-11
Identities = 35/97 (36%), Positives = 50/97 (51%), Gaps = 2/97 (2%)
Query: 1 MVMDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRA 60
M M L GKVA+VTGG GIGR L K GAKV + DI+ G+ E+ G A
Sbjct: 10 MKMKLAGKVAIVTGGGIGIGRNTALLLAKQGAKVIVTDIDQESGQATVEEITNLGG--EA 67
Query: 61 IYCPCDVTDYPQFEEAFQITLQKLGGLDIVINNAGIF 97
++ D+ ++ ITL +D++ NAG++
Sbjct: 68 LFVSYDMEKQGDWQRVISITLNAFSRIDMLFQNAGLY 104
>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 = 57.7 bits (140), Expect = 3e-11
Identities = 34/112 (30%), Positives = 47/112 (41%), Gaps = 10/112 (8%)
Query: 10 ALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPCDVTD 69
LVTG A GIG A L + GA+V+ D N +L R P DV D
Sbjct: 1 VLVTGAAQGIGYAVARALAEAGARVAAVDRNFEQLLELVADLRRYGYPFATY--KLDVAD 58
Query: 70 YPQFEEAFQITLQKLGGLDIVINNAGI--------FNDRFWELEVDVNLVGT 113
+E Q ++ G +D+++N AGI +D W+ VN G
Sbjct: 59 SAAVDEVVQRLEREYGPIDVLVNVAGILRLGAIDSLSDEDWQATFAVNTFGV 110
>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 = 57.2 bits (139), Expect = 3e-11
Identities = 39/116 (33%), Positives = 49/116 (42%), Gaps = 12/116 (10%)
Query: 8 KVALVTGGAAGIGRAYCEELLKFGA-KVSICDINDSVGEDLAEQWRTKYGPNRAIYCPCD 66
KVALVTG GIG +L K G V + + G+ E+ R + R D
Sbjct: 1 KVALVTGANRGIGFEIVRQLAKSGPGTVILTARDVERGQAAVEKLRAEGLSVRFHQL--D 58
Query: 67 VTDYPQFEEAFQITLQKLGGLDIVINNAGIFNDRF---------WELEVDVNLVGT 113
VTD E A +K GGLDI++NNAGI F + N GT
Sbjct: 59 VTDDASIEAAADFVEEKYGGLDILVNNAGIAFKGFDDSTPTREQARETMKTNFFGT 114
>gnl|CDD|180446 PRK06180, PRK06180, short chain dehydrogenase; Provisional.
Length = 277
Score = 57.6 bits (140), Expect = 4e-11
Identities = 25/90 (27%), Positives = 41/90 (45%), Gaps = 5/90 (5%)
Query: 7 GKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPCD 66
K L+TG ++G GRA + L G +V +++ D P+RA+ D
Sbjct: 4 MKTWLITGVSSGFGRALAQAALAAGHRVVGTVRSEAARADFEAL-----HPDRALARLLD 58
Query: 67 VTDYPQFEEAFQITLQKLGGLDIVINNAGI 96
VTD+ + G +D+++NNAG
Sbjct: 59 VTDFDAIDAVVADAEATFGPIDVLVNNAGY 88
>gnl|CDD|180462 PRK06198, PRK06198, short chain dehydrogenase; Provisional.
Length = 260
Score = 57.3 bits (139), Expect = 4e-11
Identities = 30/94 (31%), Positives = 43/94 (45%), Gaps = 3/94 (3%)
Query: 4 DLKGKVALVTGGAAGIGRAYCEELLKFGAK-VSICDINDSVGEDLAEQWRTKYGPNRAIY 62
L GKVALVTGG G+G A + GA + IC N GE A + +A++
Sbjct: 3 RLDGKVALVTGGTQGLGAAIARAFAERGAAGLVICGRNAEKGEAQAAELEA--LGAKAVF 60
Query: 63 CPCDVTDYPQFEEAFQITLQKLGGLDIVINNAGI 96
D++D + G LD ++N AG+
Sbjct: 61 VQADLSDVEDCRRVVAAADEAFGRLDALVNAAGL 94
>gnl|CDD|181131 PRK07814, PRK07814, short chain dehydrogenase; Provisional.
Length = 263
Score = 57.1 bits (138), Expect = 4e-11
Identities = 31/98 (31%), Positives = 45/98 (45%), Gaps = 5/98 (5%)
Query: 1 MVMD---LKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGP 57
M++D L +VA+VTG G+G A + GA V I +S +++AEQ R
Sbjct: 1 MILDRFRLDDQVAVVTGAGRGLGAAIALAFAEAGADVLIAARTESQLDEVAEQIRAA--G 58
Query: 58 NRAIYCPCDVTDYPQFEEAFQITLQKLGGLDIVINNAG 95
RA D+ ++ G LDIV+NN G
Sbjct: 59 RRAHVVAADLAHPEATAGLAGQAVEAFGRLDIVVNNVG 96
>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 = 57.1 bits (138), Expect = 5e-11
Identities = 41/127 (32%), Positives = 56/127 (44%), Gaps = 26/127 (20%)
Query: 5 LKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWR------TKYGPN 58
L GK+ALVTG + GIGR +L + GA V I G + Q G
Sbjct: 1 LSGKIALVTGASRGIGRGIALQLGEAGATVYI------TGRTILPQLPGTAEEIEARG-G 53
Query: 59 RAIYCPCDVTDYPQFEEAF-QITLQKLGGLDIVINNA-----GIFNDR---FWELEV--- 106
+ I CD +D + E F ++ ++ G LDI++NNA I FWE
Sbjct: 54 KCIPVRCDHSDDDEVEALFERVAREQQGRLDILVNNAYAAVQLILVGVAKPFWEEPPTIW 113
Query: 107 -DVNLVG 112
D+N VG
Sbjct: 114 DDINNVG 120
>gnl|CDD|235693 PRK06077, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 252
Score = 56.7 bits (137), Expect = 7e-11
Identities = 33/120 (27%), Positives = 53/120 (44%), Gaps = 15/120 (12%)
Query: 2 VMDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVG-EDLAEQWRT--KYGPN 58
+ LK KV +VTG GIGRA L K G+ V +N E++ E + + G
Sbjct: 1 MYSLKDKVVVVTGSGRGIGRAIAVRLAKEGSLVV---VNAKKRAEEMNETLKMVKENGGE 57
Query: 59 RAIYCPCDVTDYPQFEEAFQITLQKLGGLDIVINNAGI--------FNDRFWELEVDVNL 110
I DV+ E + T+ + G DI++NNAG+ +D+ + + +
Sbjct: 58 -GIGVLADVSTREGCETLAKATIDRYGVADILVNNAGLGLFSPFLNVDDKLIDKHISTDF 116
>gnl|CDD|181491 PRK08589, PRK08589, short chain dehydrogenase; Validated.
Length = 272
Score = 56.7 bits (137), Expect = 7e-11
Identities = 34/106 (32%), Positives = 59/106 (55%), Gaps = 5/106 (4%)
Query: 5 LKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCP 64
L+ KVA++TG + GIG+A L + GA V DI ++V + ++ ++ G +A +
Sbjct: 4 LENKVAVITGASTGIGQASAIALAQEGAYVLAVDIAEAV-SETVDKIKSNGGKAKAYH-- 60
Query: 65 CDVTDYPQFEEAFQITLQKLGGLDIVINNAGIFND--RFWELEVDV 108
D++D Q ++ ++ G +D++ NNAG+ N R E VDV
Sbjct: 61 VDISDEQQVKDFASEIKEQFGRVDVLFNNAGVDNAAGRIHEYPVDV 106
>gnl|CDD|180604 PRK06523, PRK06523, short chain dehydrogenase; Provisional.
Length = 260
Score = 56.5 bits (137), Expect = 8e-11
Identities = 35/118 (29%), Positives = 53/118 (44%), Gaps = 23/118 (19%)
Query: 4 DLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYC 63
+L GK ALVTGG GIG A LL+ GA+V + R P +
Sbjct: 6 ELAGKRALVTGGTKGIGAATVARLLEAGARVVT-----------TARSRPDDLPEGVEFV 54
Query: 64 PCDVTDYPQFEEAF-QITLQKLGGLDIVINNAG----------IFNDRFWELEVDVNL 110
D+T + A + L++LGG+DI+++ G D W+ E+++NL
Sbjct: 55 AADLTT-AEGCAAVARAVLERLGGVDILVHVLGGSSAPAGGFAALTDEEWQDELNLNL 111
>gnl|CDD|180802 PRK07035, PRK07035, short chain dehydrogenase; Provisional.
Length = 252
Score = 55.8 bits (135), Expect = 1e-10
Identities = 37/119 (31%), Positives = 56/119 (47%), Gaps = 13/119 (10%)
Query: 4 DLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYC 63
DL GK+ALVTG + GIG A + L + GA V + + +A+ G A+
Sbjct: 5 DLTGKIALVTGASRGIGEAIAKLLAQQGAHVIVSSRKLDGCQAVADAIVAAGGKAEAL-- 62
Query: 64 PCDVTDYPQFEEAFQITLQKLGGLDIVINNAGIFNDRF----------WELEVDVNLVG 112
C + + Q + F ++ G LDI++NNA N F ++ VDVN+ G
Sbjct: 63 ACHIGEMEQIDALFAHIRERHGRLDILVNNAAA-NPYFGHILDTDLGAFQKTVDVNIRG 120
>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 = 55.9 bits (135), Expect = 1e-10
Identities = 33/92 (35%), Positives = 47/92 (51%), Gaps = 2/92 (2%)
Query: 4 DLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYC 63
LK KVA++TGG +G A L + GAKV+ N G+ +A++ RAI
Sbjct: 2 SLKNKVAVITGGTGVLGGAMARALAQAGAKVAALGRNQEKGDKVAKE--ITALGGRAIAL 59
Query: 64 PCDVTDYPQFEEAFQITLQKLGGLDIVINNAG 95
DV D E A + + + G +DI+IN AG
Sbjct: 60 AADVLDRASLERAREEIVAQFGTVDILINGAG 91
>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 = 55.6 bits (134), Expect = 2e-10
Identities = 33/96 (34%), Positives = 50/96 (52%), Gaps = 11/96 (11%)
Query: 4 DLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYC 63
+ GK+ LVTGG+ GIGR + L+ GA+V I D AE+ + YG AI
Sbjct: 3 SVAGKIVLVTGGSRGIGRMIAQGFLEAGARVIISARKAEACADAAEEL-SAYGECIAI-- 59
Query: 64 PCDVTDYPQFEEAFQITLQKLGG----LDIVINNAG 95
P D++ EE + + ++ LD+++NNAG
Sbjct: 60 PADLSS----EEGIEALVARVAERSDRLDVLVNNAG 91
>gnl|CDD|181349 PRK08278, PRK08278, short chain dehydrogenase; Provisional.
Length = 273
Score = 54.9 bits (133), Expect = 3e-10
Identities = 37/127 (29%), Positives = 52/127 (40%), Gaps = 19/127 (14%)
Query: 3 MDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDL-------AEQWRTKY 55
M L GK +TG + GIG A + GA + I L AE+
Sbjct: 2 MSLSGKTLFITGASRGIGLAIALRAARDGANIVIAAKTAEPHPKLPGTIHTAAEEIEAAG 61
Query: 56 GPNRAIYCPCDVTDYPQFEEAFQITLQKLGGLDIVINNAGIFN---------DRFWELEV 106
G +A+ DV D Q A +++ GG+DI +NNA N RF +L
Sbjct: 62 G--QALPLVGDVRDEDQVAAAVAKAVERFGGIDICVNNASAINLTGTEDTPMKRF-DLMQ 118
Query: 107 DVNLVGT 113
+N+ GT
Sbjct: 119 QINVRGT 125
>gnl|CDD|235702 PRK06124, PRK06124, gluconate 5-dehydrogenase; Provisional.
Length = 256
Score = 54.7 bits (132), Expect = 4e-10
Identities = 32/97 (32%), Positives = 41/97 (42%), Gaps = 2/97 (2%)
Query: 4 DLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYC 63
L G+VALVTG A G+G L GA V + N + E R G A
Sbjct: 8 SLAGQVALVTGSARGLGFEIARALAGAGAHVLVNGRNAATLEAAVAALRAAGG--AAEAL 65
Query: 64 PCDVTDYPQFEEAFQITLQKLGGLDIVINNAGIFNDR 100
D+ D AF + G LDI++NN G + R
Sbjct: 66 AFDIADEEAVAAAFARIDAEHGRLDILVNNVGARDRR 102
>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 = 54.4 bits (131), Expect = 4e-10
Identities = 36/112 (32%), Positives = 49/112 (43%), Gaps = 19/112 (16%)
Query: 6 KGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPC 65
GKVAL+T A GIGRA + GA V DIN+ E L E R R +
Sbjct: 1 DGKVALITAAAQGIGRAIALAFAREGANVIATDINE---EKLKELERGPGITTRVL---- 53
Query: 66 DVTDYPQFEEAFQITLQKLGGLDIVINNAGIF--------NDRFWELEVDVN 109
DVTD Q ++ G +D++ N AG D W+ +++N
Sbjct: 54 DVTDKEQVAALA----KEEGRIDVLFNCAGFVHHGSILDCEDDDWDFAMNLN 101
>gnl|CDD|181334 PRK08263, PRK08263, short chain dehydrogenase; Provisional.
Length = 275
Score = 54.3 bits (131), Expect = 5e-10
Identities = 34/90 (37%), Positives = 47/90 (52%), Gaps = 5/90 (5%)
Query: 7 GKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPCD 66
KV +TG + G GRA+ E L+ G +V + + DLAE KYG +R + D
Sbjct: 3 EKVWFITGASRGFGRAWTEAALERGDRVVATARDTATLADLAE----KYG-DRLLPLALD 57
Query: 67 VTDYPQFEEAFQITLQKLGGLDIVINNAGI 96
VTD A + ++ G LDIV+NNAG
Sbjct: 58 VTDRAAVFAAVETAVEHFGRLDIVVNNAGY 87
>gnl|CDD|180823 PRK07074, PRK07074, short chain dehydrogenase; Provisional.
Length = 257
Score = 54.0 bits (130), Expect = 6e-10
Identities = 28/88 (31%), Positives = 41/88 (46%), Gaps = 4/88 (4%)
Query: 8 KVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPCDV 67
+ ALVTG A GIG+A L G +V DI+ + A+ G R + CD+
Sbjct: 3 RTALVTGAAGGIGQALARRFLAAGDRVLALDIDAAALAAFAD----ALGDARFVPVACDL 58
Query: 68 TDYPQFEEAFQITLQKLGGLDIVINNAG 95
TD A + G +D+++ NAG
Sbjct: 59 TDAASLAAALANAAAERGPVDVLVANAG 86
>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 = 53.9 bits (130), Expect = 6e-10
Identities = 30/88 (34%), Positives = 45/88 (51%), Gaps = 2/88 (2%)
Query: 9 VALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPCDVT 68
V ++TG ++GIGRA + GAKV + + +LA + R G AI DV
Sbjct: 2 VVVITGASSGIGRATALAFAERGAKVVLAARSAEALHELAREVRELGG--EAIAVVADVA 59
Query: 69 DYPQFEEAFQITLQKLGGLDIVINNAGI 96
D Q E A +++ G +D +NNAG+
Sbjct: 60 DAAQVERAADTAVERFGRIDTWVNNAGV 87
>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 = 53.8 bits (130), Expect = 8e-10
Identities = 36/119 (30%), Positives = 55/119 (46%), Gaps = 16/119 (13%)
Query: 7 GKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPCD 66
G A+VTG GIG+AY EEL K G V + + +A++ KYG
Sbjct: 1 GTWAVVTGATDGIGKAYAEELAKRGFNVILISRTQEKLDAVAKEIEEKYGVETKTI---- 56
Query: 67 VTDYPQFEEAFQITLQKLGGLDI--VINNAGIFNDR---FWELEVD-------VNLVGT 113
D+ ++ ++ ++L GLDI ++NN GI + F E D VN++ T
Sbjct: 57 AADFSAGDDIYERIEKELEGLDIGILVNNVGISHSIPEYFLETPEDELQDIINVNVMAT 115
>gnl|CDD|181517 PRK08642, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 253
Score = 53.6 bits (129), Expect = 1e-09
Identities = 32/93 (34%), Positives = 44/93 (47%), Gaps = 5/93 (5%)
Query: 3 MDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIY 62
M + + LVTGG+ G+G A + GA+V +N ED AE + G RAI
Sbjct: 1 MQISEQTVLVTGGSRGLGAAIARAFAREGARVV---VNYHQSEDAAEALADELGD-RAIA 56
Query: 63 CPCDVTDYPQFEEAFQITLQKLG-GLDIVINNA 94
DVTD Q + F + G + V+NNA
Sbjct: 57 LQADVTDREQVQAMFATATEHFGKPITTVVNNA 89
>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 = 53.4 bits (129), Expect = 1e-09
Identities = 33/116 (28%), Positives = 55/116 (47%), Gaps = 14/116 (12%)
Query: 8 KVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPCDV 67
K L+TG ++GIG A K GAK+ + ++LA++ K+ P + + DV
Sbjct: 1 KTVLITGASSGIGEATARRFAKAGAKLILTGRRAERLQELADELGAKF-PVKVLPLQLDV 59
Query: 68 TDYPQFEEAFQITLQKLGGLDIVINNAGI-----------FNDRFWELEVDVNLVG 112
+D E A + ++ +DI++NNAG+ D WE +D N+ G
Sbjct: 60 SDRESIEAALENLPEEFRDIDILVNNAGLALGLDPAQEADLED--WETMIDTNVKG 113
>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 = 53.3 bits (128), Expect = 1e-09
Identities = 31/96 (32%), Positives = 51/96 (53%), Gaps = 5/96 (5%)
Query: 3 MDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIY 62
M LKG+V LVTGGA+G+GRA + + GA+V++ D + ++ +G + +
Sbjct: 1 MRLKGEVVLVTGGASGLGRAIVDRFVAEGARVAVLDKS----AAGLQELEAAHG-DAVVG 55
Query: 63 CPCDVTDYPQFEEAFQITLQKLGGLDIVINNAGIFN 98
DV +EA + G +D +I NAGI++
Sbjct: 56 VEGDVRSLDDHKEAVARCVAAFGKIDCLIPNAGIWD 91
>gnl|CDD|235736 PRK06196, PRK06196, oxidoreductase; Provisional.
Length = 315
Score = 53.1 bits (128), Expect = 2e-09
Identities = 27/93 (29%), Positives = 39/93 (41%), Gaps = 6/93 (6%)
Query: 4 DLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYC 63
DL GK A+VTGG +G+G L + GA V + V + G +
Sbjct: 23 DLSGKTAIVTGGYSGLGLETTRALAQAGAHVIVPARRPDVAREALA------GIDGVEVV 76
Query: 64 PCDVTDYPQFEEAFQITLQKLGGLDIVINNAGI 96
D+ D + L +DI+INNAG+
Sbjct: 77 MLDLADLESVRAFAERFLDSGRRIDILINNAGV 109
>gnl|CDD|236372 PRK09072, PRK09072, short chain dehydrogenase; Provisional.
Length = 263
Score = 52.6 bits (127), Expect = 2e-09
Identities = 38/124 (30%), Positives = 57/124 (45%), Gaps = 22/124 (17%)
Query: 3 MDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVG---EDLAEQWRTKYGPNR 59
MDLK K L+TG + GIG+A E L GA++ + VG E L P R
Sbjct: 1 MDLKDKRVLLTGASGGIGQALAEALAAAGARLLL------VGRNAEKLEALAARLPYPGR 54
Query: 60 AIYCPCDVTDYPQFEEAFQITLQKLGGLDIVINNAGIFNDRFWELE----------VDVN 109
+ D+T EA +++GG++++INNAG+ + F LE + +N
Sbjct: 55 HRWVVADLTS-EAGREAVLARAREMGGINVLINNAGV--NHFALLEDQDPEAIERLLALN 111
Query: 110 LVGT 113
L
Sbjct: 112 LTAP 115
>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 = 52.4 bits (126), Expect = 2e-09
Identities = 40/121 (33%), Positives = 55/121 (45%), Gaps = 23/121 (19%)
Query: 5 LKGKVALVTGGAAGIGRAYCEELLKFGAK---VSICDINDSVGEDLAEQWRTKYGPNRAI 61
+K K LVTG GIG+A+ E LL GAK ++ D S L ++ K P R
Sbjct: 1 IKDKTVLVTGANRGIGKAFVESLLAHGAKKVYAAVRDP-GSA-AHLVAKYGDKVVPLRL- 57
Query: 62 YCPCDVTDYPQFEEAFQITLQKLGGLDIVINNAGIFN------DRFWE---LEVDVNLVG 112
DVTD + A + +D+VINNAG+ + E E+DVN+ G
Sbjct: 58 ----DVTDPESIKAA----AAQAKDVDVVINNAGVLKPATLLEEGALEALKQEMDVNVFG 109
Query: 113 T 113
Sbjct: 110 L 110
>gnl|CDD|236389 PRK09134, PRK09134, short chain dehydrogenase; Provisional.
Length = 258
Score = 52.6 bits (127), Expect = 2e-09
Identities = 31/112 (27%), Positives = 48/112 (42%), Gaps = 11/112 (9%)
Query: 8 KVALVTGGAAGIGRAYCEELLKFGAKVSI-CDINDSVGEDLAEQWRTKYGPNRAIYCPCD 66
+ ALVTG A IGRA +L G V++ + + E LA + R RA+ D
Sbjct: 10 RAALVTGAARRIGRAIALDLAAHGFDVAVHYNRSRDEAEALAAEIRALGR--RAVALQAD 67
Query: 67 VTDYPQFEEAFQITLQKLGGLDIVINNAGIFN-DRF-------WELEVDVNL 110
+ D + LG + +++NNA +F D W+ + NL
Sbjct: 68 LADEAEVRALVARASAALGPITLLVNNASLFEYDSAASFTRASWDRHMATNL 119
>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 = 52.5 bits (126), Expect = 2e-09
Identities = 27/87 (31%), Positives = 40/87 (45%), Gaps = 4/87 (4%)
Query: 8 KVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPCDV 67
+V LVTG + G+G A + GA+V +N + AE + G RAI DV
Sbjct: 1 QVVLVTGASRGLGAAIARSFAREGARVV---VNYYRSTESAEAVAAEAG-ERAIAIQADV 56
Query: 68 TDYPQFEEAFQITLQKLGGLDIVINNA 94
D Q + + G +D ++NNA
Sbjct: 57 RDRDQVQAMIEEAKNHFGPVDTIVNNA 83
>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 = 52.0 bits (125), Expect = 3e-09
Identities = 31/113 (27%), Positives = 46/113 (40%), Gaps = 14/113 (12%)
Query: 8 KVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPCDV 67
KVALVTG + GIG L + G +VS+ N EDLA + P D
Sbjct: 1 KVALVTGASRGIGIEIARALARDGYRVSLGLRN---PEDLAALSASGG---DVEAVPYDA 54
Query: 68 TDYPQFEEAFQITLQKLGGLDIVINNAGI--------FNDRFWELEVDVNLVG 112
D + G +D++++NAGI +D E +N++
Sbjct: 55 RDPEDARALVDALRDRFGRIDVLVHNAGIGRPTTLREGSDAELEAHFSINVIA 107
>gnl|CDD|135631 PRK05867, PRK05867, short chain dehydrogenase; Provisional.
Length = 253
Score = 52.3 bits (125), Expect = 3e-09
Identities = 31/95 (32%), Positives = 49/95 (51%), Gaps = 2/95 (2%)
Query: 2 VMDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAI 61
+ DL GK AL+TG + GIG+ ++ GA+V+I + E LA++ + +
Sbjct: 4 LFDLHGKRALITGASTGIGKRVALAYVEAGAQVAIAARHLDALEKLADE--IGTSGGKVV 61
Query: 62 YCPCDVTDYPQFEEAFQITLQKLGGLDIVINNAGI 96
CDV+ + Q +LGG+DI + NAGI
Sbjct: 62 PVCCDVSQHQQVTSMLDQVTAELGGIDIAVCNAGI 96
>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 = 52.1 bits (125), Expect = 3e-09
Identities = 34/102 (33%), Positives = 49/102 (48%), Gaps = 22/102 (21%)
Query: 1 MVMDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRA 60
M +D GK ALVTG GIGRA + L K GA+V + + L +
Sbjct: 1 MELDFAGKRALVTGAGKGIGRATVKALAKAGARVVAVSRTQADLDSLVRE---------- 50
Query: 61 IYCP-----C-DVTDYPQFEEAFQITLQKLGGLDIVINNAGI 96
CP C D++D+ EEA L +G +D+++NNA +
Sbjct: 51 --CPGIEPVCVDLSDWDATEEA----LGSVGPVDLLVNNAAV 86
>gnl|CDD|237187 PRK12743, PRK12743, oxidoreductase; Provisional.
Length = 256
Score = 52.0 bits (125), Expect = 3e-09
Identities = 33/102 (32%), Positives = 57/102 (55%), Gaps = 4/102 (3%)
Query: 8 KVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVG-EDLAEQWRTKYGPNRAIYCPCD 66
+VA+VT +GIG+A L + G + I +D G ++ AE+ R +G RA D
Sbjct: 3 QVAIVTASDSGIGKACALLLAQQGFDIGITWHSDEEGAKETAEEVR-SHG-VRAEIRQLD 60
Query: 67 VTDYPQFEEAFQITLQKLGGLDIVINNAGI-FNDRFWELEVD 107
++D P+ +A +Q+LG +D+++NNAG F +++ D
Sbjct: 61 LSDLPEGAQALDKLIQRLGRIDVLVNNAGAMTKAPFLDMDFD 102
>gnl|CDD|187548 cd05237, UDP_invert_4-6DH_SDR_e, UDP-Glcnac (UDP-linked
N-acetylglucosamine) inverting 4,6-dehydratase, extended
(e) SDRs. UDP-Glcnac inverting 4,6-dehydratase was
identified in Helicobacter pylori as the hexameric flaA1
gene product (FlaA1). FlaA1 is hexameric, possesses
UDP-GlcNAc-inverting 4,6-dehydratase activity, and
catalyzes the first step in the creation of a
pseudaminic acid derivative in protein glycosylation.
Although this subgroup has the NADP-binding motif
characteristic of extended SDRs, its members tend to
have a Met substituted for the active site Tyr found in
most SDR families. 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 = 287
Score = 52.2 bits (126), Expect = 3e-09
Identities = 35/116 (30%), Positives = 56/116 (48%), Gaps = 16/116 (13%)
Query: 6 KGKVALVTGGAAGIGRAYCEELLKFGAK-VSICDINDSVGEDLAEQWRTKYGPNRAIYCP 64
KGK LVTGGA IG ++LKFG K + + D +++ +L + R+++ ++ +
Sbjct: 1 KGKTILVTGGAGSIGSELVRQILKFGPKKLIVFDRDENKLHELVRELRSRFPHDKLRFII 60
Query: 65 CDVTDYPQFEEAFQITLQKLGGLDIVINNAGI-------FNDRFWELEVDVNLVGT 113
DV D + AF K G DIV + A + N E + N++GT
Sbjct: 61 GDVRDKERLRRAF-----KERGPDIVFHAAALKHVPSMEDN---PEEAIKTNVLGT 108
>gnl|CDD|236145 PRK08063, PRK08063, enoyl-(acyl carrier protein) reductase;
Provisional.
Length = 250
Score = 52.0 bits (125), Expect = 3e-09
Identities = 28/91 (30%), Positives = 45/91 (49%), Gaps = 3/91 (3%)
Query: 5 LKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDS-VGEDLAEQWRTKYGPNRAIYC 63
GKVALVTG + GIG+A L + G +++ E+ AE+ +A+
Sbjct: 2 FSGKVALVTGSSRGIGKAIALRLAEEGYDIAVNYARSRKAAEETAEEIEAL--GRKALAV 59
Query: 64 PCDVTDYPQFEEAFQITLQKLGGLDIVINNA 94
+V D + +E F ++ G LD+ +NNA
Sbjct: 60 KANVGDVEKIKEMFAQIDEEFGRLDVFVNNA 90
>gnl|CDD|236040 PRK07523, PRK07523, gluconate 5-dehydrogenase; Provisional.
Length = 255
Score = 52.1 bits (125), Expect = 3e-09
Identities = 32/93 (34%), Positives = 49/93 (52%), Gaps = 2/93 (2%)
Query: 4 DLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYC 63
DL G+ ALVTG + GIG A E L + GA+V + + + AE + + A+
Sbjct: 7 DLTGRRALVTGSSQGIGYALAEGLAQAGAEVILNGRDPAKLAAAAESLKGQGLSAHAL-- 64
Query: 64 PCDVTDYPQFEEAFQITLQKLGGLDIVINNAGI 96
DVTD+ A ++G +DI++NNAG+
Sbjct: 65 AFDVTDHDAVRAAIDAFEAEIGPIDILVNNAGM 97
>gnl|CDD|235725 PRK06179, PRK06179, short chain dehydrogenase; Provisional.
Length = 270
Score = 51.4 bits (124), Expect = 6e-09
Identities = 29/101 (28%), Positives = 44/101 (43%), Gaps = 30/101 (29%)
Query: 6 KGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAI---- 61
KVALVTG ++GIGRA E+L + G +V +G +R
Sbjct: 3 NSKVALVTGASSGIGRATAEKLARAGYRV--------------------FGTSRNPARAA 42
Query: 62 ------YCPCDVTDYPQFEEAFQITLQKLGGLDIVINNAGI 96
DVTD + A + + G +D+++NNAG+
Sbjct: 43 PIPGVELLELDVTDDASVQAAVDEVIARAGRIDVLVNNAGV 83
>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 = 51.3 bits (123), Expect = 6e-09
Identities = 29/113 (25%), Positives = 49/113 (43%), Gaps = 8/113 (7%)
Query: 7 GKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYC-PC 65
GK ++TG GIG+ EL + GA+V + + + E+ A + R N +
Sbjct: 1 GKTVIITGANTGIGKETARELARRGARVIMACRDMAKCEEAAAEIRRDTL-NHEVIVRHL 59
Query: 66 DVTDYPQFEEAFQITLQKLGGLDIVINNAGIFNDRFW------ELEVDVNLVG 112
D+ L + LD++INNAG+ + E++ VN +G
Sbjct: 60 DLASLKSIRAFAAEFLAEEDRLDVLINNAGVMRCPYSKTEDGFEMQFGVNHLG 112
>gnl|CDD|180300 PRK05875, PRK05875, short chain dehydrogenase; Provisional.
Length = 276
Score = 51.3 bits (123), Expect = 7e-09
Identities = 37/122 (30%), Positives = 49/122 (40%), Gaps = 9/122 (7%)
Query: 1 MVMDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRA 60
M + + + LVTGG +GIG+ L+ GA V I N AE+ G
Sbjct: 1 MQLSFQDRTYLVTGGGSGIGKGVAAGLVAAGAAVMIVGRNPDKLAAAAEEIEALKGAGAV 60
Query: 61 IYCPCDVTDYPQFEEAFQITLQKLGGLDIVINNAG---------IFNDRFWELEVDVNLV 111
Y P DVTD Q A G L V++ AG + W VD+N+
Sbjct: 61 RYEPADVTDEDQVARAVDAATAWHGRLHGVVHCAGGSETIGPITQIDSDAWRRTVDLNVN 120
Query: 112 GT 113
GT
Sbjct: 121 GT 122
>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 = 50.9 bits (122), Expect = 8e-09
Identities = 34/115 (29%), Positives = 47/115 (40%), Gaps = 13/115 (11%)
Query: 8 KVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPCDV 67
K +TG A+GIGR + G V + DI++ LA + G + DV
Sbjct: 1 KAIFITGAASGIGRETALLFARNGWFVGLYDIDEDGLAALAAE----LGAENVVAGALDV 56
Query: 68 TDYPQFEEAFQITLQKLGG-LDIVINNAGI-----FNDRFWE---LEVDVNLVGT 113
TD + A GG LD + NNAG+ F D VD+N+ G
Sbjct: 57 TDRAAWAAALADFAAATGGRLDALFNNAGVGRGGPFEDVPLAAHDRMVDINVKGV 111
>gnl|CDD|135637 PRK05876, PRK05876, short chain dehydrogenase; Provisional.
Length = 275
Score = 51.1 bits (122), Expect = 9e-09
Identities = 35/119 (29%), Positives = 56/119 (47%), Gaps = 18/119 (15%)
Query: 7 GKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPCD 66
G+ A++TGGA+GIG A E + GA+V + D++ R + + CD
Sbjct: 6 GRGAVITGGASGIGLATGTEFARRGARVVLGDVDKPGLRQAVNHLRAEGFDVHGVM--CD 63
Query: 67 VTDYPQF----EEAFQITLQKLGGLDIVINNAGI--------FNDRFWELEVDVNLVGT 113
V + +EAF++ LG +D+V +NAGI W +DV+L G+
Sbjct: 64 VRHREEVTHLADEAFRL----LGHVDVVFSNAGIVVGGPIVEMTHDDWRWVIDVDLWGS 118
>gnl|CDD|181668 PRK09135, PRK09135, pteridine reductase; Provisional.
Length = 249
Score = 50.3 bits (121), Expect = 1e-08
Identities = 31/100 (31%), Positives = 42/100 (42%), Gaps = 8/100 (8%)
Query: 2 VMDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSI-CDINDSVGEDLA---EQWRTKYGP 57
+M KVAL+TGGA IG A L G +V+I + + + LA R P
Sbjct: 1 MMTDSAKVALITGGARRIGAAIARTLHAAGYRVAIHYHRSAAEADALAAELNALR----P 56
Query: 58 NRAIYCPCDVTDYPQFEEAFQITLQKLGGLDIVINNAGIF 97
A D+ D E + G LD ++NNA F
Sbjct: 57 GSAAALQADLLDPDALPELVAACVAAFGRLDALVNNASSF 96
>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 = 50.0 bits (120), Expect = 1e-08
Identities = 31/112 (27%), Positives = 52/112 (46%), Gaps = 11/112 (9%)
Query: 10 ALVTGGAAGIGRAYCEELLKFGAKVSICDINDS-VGEDLAEQWRTKYGPNRAIYCPCDVT 68
ALVTGG+ GIG+A L + GA V I ++A + G +A+ DV+
Sbjct: 1 ALVTGGSRGIGKAIALRLAERGADVVINYRKSKDAAAEVAAEIEELGG--KAVVVRADVS 58
Query: 69 DYPQFEEAFQITLQKLGGLDIVINNAGI-----FND---RFWELEVDVNLVG 112
EE F ++ G LD++++NA ++ W+ +++ NL
Sbjct: 59 QPQDVEEMFAAVKERFGRLDVLVSNAAAGAFRPLSELTPAHWDAKMNTNLKA 110
>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 = 50.2 bits (120), Expect = 2e-08
Identities = 34/111 (30%), Positives = 46/111 (41%), Gaps = 17/111 (15%)
Query: 10 ALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPCDVTD 69
+VTG A GIGRA LL+ GA V + DL +YG + P DV D
Sbjct: 1 VIVTGAAQGIGRAVARHLLQAGATV--------IALDLPFVLLLEYGDPLRLT-PLDVAD 51
Query: 70 YPQFEEAFQITLQKLGGLDIVINNAGIF--------NDRFWELEVDVNLVG 112
E L + G +D ++N AG+ + WE VN+ G
Sbjct: 52 AAAVREVCSRLLAEHGPIDALVNCAGVLRPGATDPLSTEDWEQTFAVNVTG 102
>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 = 49.8 bits (119), Expect = 2e-08
Identities = 37/115 (32%), Positives = 51/115 (44%), Gaps = 14/115 (12%)
Query: 8 KVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWR--TKYGPNRAIYCPC 65
+VALVTG +GIG A L K G +V +C E LA + + G A C
Sbjct: 4 EVALVTGATSGIGLAIARRLGKEGLRVFVCARG---EEGLATTVKELREAGVE-ADGRTC 59
Query: 66 DVTDYPQFEEAFQITLQKLGGLDIVINNAG--------IFNDRFWELEVDVNLVG 112
DV P+ E + + G +D+++NNAG D W V+ NL G
Sbjct: 60 DVRSVPEIEALVAAAVARYGPIDVLVNNAGRSGGGATAELADELWLDVVETNLTG 114
>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 = 49.2 bits (118), Expect = 3e-08
Identities = 28/90 (31%), Positives = 40/90 (44%), Gaps = 1/90 (1%)
Query: 8 KVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPCDV 67
VALVTG A IGRA E L G +V + N S E + N A+ D+
Sbjct: 1 AVALVTGAAKRIGRAIAEALAAEGYRV-VVHYNRSEAEAQRLKDELNALRNSAVLVQADL 59
Query: 68 TDYPQFEEAFQITLQKLGGLDIVINNAGIF 97
+D+ + + G D+++NNA F
Sbjct: 60 SDFAACADLVAAAFRAFGRCDVLVNNASAF 89
>gnl|CDD|180949 PRK07370, PRK07370, enoyl-(acyl carrier protein) reductase;
Validated.
Length = 258
Score = 48.9 bits (117), Expect = 5e-08
Identities = 33/91 (36%), Positives = 46/91 (50%), Gaps = 2/91 (2%)
Query: 3 MDLKGKVALVTGGA--AGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRA 60
+DL GK ALVTG A I ++L GA++ I + D G + N +
Sbjct: 2 LDLTGKKALVTGIANNRSIAWGIAQQLHAAGAELGITYLPDEKGRFEKKVRELTEPLNPS 61
Query: 61 IYCPCDVTDYPQFEEAFQITLQKLGGLDIVI 91
++ PCDV D Q EE F+ QK G LDI++
Sbjct: 62 LFLPCDVQDDAQIEETFETIKQKWGKLDILV 92
>gnl|CDD|171820 PRK12936, PRK12936, 3-ketoacyl-(acyl-carrier-protein) reductase
NodG; Reviewed.
Length = 245
Score = 48.8 bits (116), Expect = 5e-08
Identities = 38/120 (31%), Positives = 56/120 (46%), Gaps = 13/120 (10%)
Query: 2 VMDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAI 61
+ DL G+ ALVTG + GIG L GA V + E LA + G I
Sbjct: 1 MFDLSGRKALVTGASGGIGEEIARLLHAQGAIVGLHGTRVEKLEALA----AELGERVKI 56
Query: 62 YCPCDVTDYPQFEEAFQITLQKLGGLDIVINNAGI--------FNDRFWELEVDVNLVGT 113
+ P +++D + + Q L G+DI++NNAGI +D W+ ++VNL T
Sbjct: 57 F-PANLSDRDEVKALGQKAEADLEGVDILVNNAGITKDGLFVRMSDEDWDSVLEVNLTAT 115
>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 = 48.6 bits (116), Expect = 6e-08
Identities = 31/97 (31%), Positives = 46/97 (47%), Gaps = 9/97 (9%)
Query: 5 LKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDL-------AEQWRTKYGP 57
L GK +TG + GIG+A + + GA V I L AE+ G
Sbjct: 1 LAGKTLFITGASRGIGKAIALKAARDGANVVIAAKTAEPHPKLPGTIYTAAEEIEAAGG- 59
Query: 58 NRAIYCPCDVTDYPQFEEAFQITLQKLGGLDIVINNA 94
+A+ C D+ D Q A + ++K GG+DI++NNA
Sbjct: 60 -KALPCIVDIRDEDQVRAAVEKAVEKFGGIDILVNNA 95
>gnl|CDD|181159 PRK07890, PRK07890, short chain dehydrogenase; Provisional.
Length = 258
Score = 48.4 bits (116), Expect = 7e-08
Identities = 33/120 (27%), Positives = 57/120 (47%), Gaps = 11/120 (9%)
Query: 3 MDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIY 62
M LKGKV +V+G G+GR + GA V + +++A + RA+
Sbjct: 1 MLLKGKVVVVSGVGPGLGRTLAVRAARAGADVVLAARTAERLDEVAAEIDDLGR--RALA 58
Query: 63 CPCDVTDYPQFEEAFQITLQKLGGLDIVINNA-------GIFNDRF--WELEVDVNLVGT 113
P D+TD Q + L++ G +D ++NNA + + F W +++N++GT
Sbjct: 59 VPTDITDEDQCANLVALALERFGRVDALVNNAFRVPSMKPLADADFAHWRAVIELNVLGT 118
>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 = 47.5 bits (114), Expect = 7e-08
Identities = 25/95 (26%), Positives = 33/95 (34%), Gaps = 6/95 (6%)
Query: 11 LVTGGAAGIGRAYCEELLKFGAK----VSICDINDSVGEDLAEQWRTKYGPNRAIYCPCD 66
LVTGG G+G L + GA+ +S D E L + G CD
Sbjct: 4 LVTGGLGGLGLELARWLAERGARHLVLLSRSGAPDPEAEALLAELE-ARG-AEVTVVACD 61
Query: 67 VTDYPQFEEAFQITLQKLGGLDIVINNAGIFNDRF 101
V+D L VI+ AG+ D
Sbjct: 62 VSDRDAVRALLAEIRADGPPLRGVIHAAGVLRDAL 96
>gnl|CDD|235713 PRK06139, PRK06139, short chain dehydrogenase; Provisional.
Length = 330
Score = 48.2 bits (115), Expect = 8e-08
Identities = 27/96 (28%), Positives = 48/96 (50%), Gaps = 2/96 (2%)
Query: 1 MVMDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRA 60
M+ L G V ++TG ++GIG+A E + GA++ + ++ + +AE+ R
Sbjct: 1 MMGPLHGAVVVITGASSGIGQATAEAFARRGARLVLAARDEEALQAVAEECRALGA--EV 58
Query: 61 IYCPCDVTDYPQFEEAFQITLQKLGGLDIVINNAGI 96
+ P DVTD Q + G +D+ +NN G+
Sbjct: 59 LVVPTDVTDADQVKALATQAASFGGRIDVWVNNVGV 94
>gnl|CDD|181077 PRK07677, PRK07677, short chain dehydrogenase; Provisional.
Length = 252
Score = 48.1 bits (115), Expect = 8e-08
Identities = 23/88 (26%), Positives = 42/88 (47%), Gaps = 2/88 (2%)
Query: 7 GKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPCD 66
KV ++TGG++G+G+A + + GA V I E+ + G + + D
Sbjct: 1 EKVVIITGGSSGMGKAMAKRFAEEGANVVITGRTKEKLEEAKLEIEQFPG--QVLTVQMD 58
Query: 67 VTDYPQFEEAFQITLQKLGGLDIVINNA 94
V + ++ + +K G +D +INNA
Sbjct: 59 VRNPEDVQKMVEQIDEKFGRIDALINNA 86
>gnl|CDD|180773 PRK06949, PRK06949, short chain dehydrogenase; Provisional.
Length = 258
Score = 47.8 bits (114), Expect = 1e-07
Identities = 30/94 (31%), Positives = 52/94 (55%), Gaps = 2/94 (2%)
Query: 3 MDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIY 62
++L+GKVALVTG ++G+G + + L + GAKV + ++L + + G +
Sbjct: 5 INLEGKVALVTGASSGLGARFAQVLAQAGAKVVLASRRVERLKELRAEIEAEGGAAHVV- 63
Query: 63 CPCDVTDYPQFEEAFQITLQKLGGLDIVINNAGI 96
DVTDY + A + G +DI++NN+G+
Sbjct: 64 -SLDVTDYQSIKAAVAHAETEAGTIDILVNNSGV 96
>gnl|CDD|235816 PRK06500, PRK06500, short chain dehydrogenase; Provisional.
Length = 249
Score = 47.6 bits (114), Expect = 1e-07
Identities = 32/116 (27%), Positives = 52/116 (44%), Gaps = 13/116 (11%)
Query: 5 LKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCP 64
L+GK AL+TGG +GIG + L GA+V+I + E R + G + A+
Sbjct: 4 LQGKTALITGGTSGIGLETARQFLAEGARVAITGRD----PASLEAARAELGES-ALVIR 58
Query: 65 CDVTDYPQFEEAFQITLQKLGGLDIVINNAGI--------FNDRFWELEVDVNLVG 112
D D + Q + G LD V NAG+ +++ ++ + N+ G
Sbjct: 59 ADAGDVAAQKALAQALAEAFGRLDAVFINAGVAKFAPLEDWDEAMFDRSFNTNVKG 114
>gnl|CDD|180984 PRK07454, PRK07454, short chain dehydrogenase; Provisional.
Length = 241
Score = 47.3 bits (113), Expect = 2e-07
Identities = 24/89 (26%), Positives = 43/89 (48%), Gaps = 2/89 (2%)
Query: 8 KVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPCDV 67
AL+TG ++GIG+A K G +++ + E LA + R+ +A D+
Sbjct: 7 PRALITGASSGIGKATALAFAKAGWDLALVARSQDALEALAAELRSTGV--KAAAYSIDL 64
Query: 68 TDYPQFEEAFQITLQKLGGLDIVINNAGI 96
++ L++ G D++INNAG+
Sbjct: 65 SNPEAIAPGIAELLEQFGCPDVLINNAGM 93
>gnl|CDD|180413 PRK06128, PRK06128, oxidoreductase; Provisional.
Length = 300
Score = 46.8 bits (111), Expect = 3e-07
Identities = 30/92 (32%), Positives = 51/92 (55%), Gaps = 2/92 (2%)
Query: 5 LKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNR-AIYC 63
L+G+ AL+TG +GIGRA + GA +++ + + +D AE + R A+
Sbjct: 53 LQGRKALITGADSGIGRATAIAFAREGADIALNYLPEE-EQDAAEVVQLIQAEGRKAVAL 111
Query: 64 PCDVTDYPQFEEAFQITLQKLGGLDIVINNAG 95
P D+ D + + +++LGGLDI++N AG
Sbjct: 112 PGDLKDEAFCRQLVERAVKELGGLDILVNIAG 143
>gnl|CDD|180448 PRK06182, PRK06182, short chain dehydrogenase; Validated.
Length = 273
Score = 46.5 bits (111), Expect = 3e-07
Identities = 30/88 (34%), Positives = 40/88 (45%), Gaps = 8/88 (9%)
Query: 8 KVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPCDV 67
KVALVTG ++GIG+A L G V EDLA G DV
Sbjct: 4 KVALVTGASSGIGKATARRLAAQGYTVYGAARRVDKMEDLAS-----LG---VHPLSLDV 55
Query: 68 TDYPQFEEAFQITLQKLGGLDIVINNAG 95
TD + A + + G +D+++NNAG
Sbjct: 56 TDEASIKAAVDTIIAEEGRIDVLVNNAG 83
>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 = 46.6 bits (111), Expect = 4e-07
Identities = 25/91 (27%), Positives = 32/91 (35%), Gaps = 4/91 (4%)
Query: 11 LVTGGAAGIGRAYCEELLKFGAK--VSICDINDSVGEDLAEQWRTKYGPNRAIYCPCDVT 68
L+TGG G+G L GA+ V + + G R CDVT
Sbjct: 154 LITGGLGGLGLLVARWLAARGARHLVLLSRRGPAPRAAARAALLRAGGA-RVSVVRCDVT 212
Query: 69 DYPQFEEAFQITLQKLGGLDIVINNAGIFND 99
D L G L VI+ AG+ D
Sbjct: 213 DPAALAALLAE-LAAGGPLAGVIHAAGVLRD 242
>gnl|CDD|180617 PRK06550, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 235
Score = 46.1 bits (110), Expect = 4e-07
Identities = 28/97 (28%), Positives = 40/97 (41%), Gaps = 17/97 (17%)
Query: 3 MDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIY 62
+ K L+TG A+GIG A L GA+V D D DL+ +
Sbjct: 1 QEFMTKTVLITGAASGIGLAQARAFLAQGAQVYGVDKQDK--PDLSGNFHFLQL------ 52
Query: 63 CPCDVTDYPQFEEAFQITLQKLGGLDIVINNAGIFND 99
D++D E F + +DI+ N AGI +D
Sbjct: 53 ---DLSD--DLEPLF----DWVPSVDILCNTAGILDD 80
>gnl|CDD|237189 PRK12748, PRK12748, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 256
Score = 46.2 bits (110), Expect = 4e-07
Identities = 29/103 (28%), Positives = 39/103 (37%), Gaps = 11/103 (10%)
Query: 3 MDLKGKVALVTGGA--AGIGRAYCEELLKFGAKV-----SICDINDSVGEDLAEQWRTK- 54
+ L K+ALVTG + GIG A C L G + S D G E K
Sbjct: 1 LPLMKKIALVTGASRLNGIGAAVCRRLAAKGIDIFFTYWSPYDKTMPWGMHDKEPVLLKE 60
Query: 55 ---YGPNRAIYCPCDVTDYPQFEEAFQITLQKLGGLDIVINNA 94
R + D++ F ++LG I+INNA
Sbjct: 61 EIESYGVRCEHMEIDLSQPYAPNRVFYAVSERLGDPSILINNA 103
>gnl|CDD|180744 PRK06914, PRK06914, short chain dehydrogenase; Provisional.
Length = 280
Score = 45.8 bits (109), Expect = 7e-07
Identities = 35/117 (29%), Positives = 54/117 (46%), Gaps = 11/117 (9%)
Query: 6 KGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYC-P 64
K+A+VTG ++G G EL K G V N E+L Q T+ + I
Sbjct: 2 NKKIAIVTGASSGFGLLTTLELAKKGYLVIATMRNPEKQENLLSQ-ATQLNLQQNIKVQQ 60
Query: 65 CDVTDYPQFEEAFQITLQKLGGLDIVINNAGIFNDRF--------WELEVDVNLVGT 113
DVTD FQ+ L+++G +D+++NNAG N F + + + N+ G
Sbjct: 61 LDVTDQNSIH-NFQLVLKEIGRIDLLVNNAGYANGGFVEEIPVEEYRKQFETNVFGA 116
>gnl|CDD|181324 PRK08251, PRK08251, short chain dehydrogenase; Provisional.
Length = 248
Score = 45.3 bits (108), Expect = 7e-07
Identities = 28/89 (31%), Positives = 42/89 (47%)
Query: 8 KVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPCDV 67
+ L+TG ++G+G E G +++C E+L + +Y + DV
Sbjct: 3 QKILITGASSGLGAGMAREFAAKGRDLALCARRTDRLEELKAELLARYPGIKVAVAALDV 62
Query: 68 TDYPQFEEAFQITLQKLGGLDIVINNAGI 96
D+ Q E F +LGGLD VI NAGI
Sbjct: 63 NDHDQVFEVFAEFRDELGGLDRVIVNAGI 91
>gnl|CDD|236357 PRK08945, PRK08945, putative oxoacyl-(acyl carrier protein)
reductase; Provisional.
Length = 247
Score = 45.2 bits (108), Expect = 9e-07
Identities = 30/111 (27%), Positives = 51/111 (45%), Gaps = 11/111 (9%)
Query: 5 LKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCP 64
LK ++ LVTG GIGR + GA V + + E + ++ GP AI P
Sbjct: 10 LKDRIILVTGAGDGIGREAALTYARHGATVILLGRTEEKLEAVYDEIEAAGGPQPAII-P 68
Query: 65 CDVT-----DYPQFEEAFQITLQKLGGLDIVINNAGIFNDR--FWELEVDV 108
D+ +Y Q + + ++ G LD V++NAG+ + + + +V
Sbjct: 69 LDLLTATPQNYQQLADTIE---EQFGRLDGVLHNAGLLGELGPMEQQDPEV 116
>gnl|CDD|181020 PRK07533, PRK07533, enoyl-(acyl carrier protein) reductase;
Provisional.
Length = 258
Score = 44.9 bits (107), Expect = 1e-06
Identities = 28/98 (28%), Positives = 42/98 (42%), Gaps = 19/98 (19%)
Query: 3 MDLKGKVALVTGGA------AGIGRAYCEELLKFGAKVSICDINDSVG---EDLAEQWRT 53
+ L GK LV G A G RA+ GA++++ +ND E LAE+
Sbjct: 6 LPLAGKRGLVVGIANEQSIAWGCARAFRA----LGAELAVTYLNDKARPYVEPLAEELDA 61
Query: 54 KYGPNRAIYCPCDVTDYPQFEEAFQITLQKLGGLDIVI 91
I+ P DV + Q E F ++ G LD ++
Sbjct: 62 ------PIFLPLDVREPGQLEAVFARIAEEWGRLDFLL 93
>gnl|CDD|171822 PRK12938, PRK12938, acetyacetyl-CoA reductase; Provisional.
Length = 246
Score = 44.6 bits (105), Expect = 1e-06
Identities = 33/115 (28%), Positives = 51/115 (44%), Gaps = 17/115 (14%)
Query: 8 KVALVTGGAAGIGRAYCEELLKFGAK-VSICDINDSVGEDLAEQWRT---KYGPNRAIYC 63
++A VTGG GIG + C+ L K G K V+ C N E + + +
Sbjct: 4 RIAYVTGGMGGIGTSICQRLHKDGFKVVAGCGPNSPRRVKWLEDQKALGFDFIASEG--- 60
Query: 64 PCDVTDYPQFEEAFQITLQKLGGLDIVINNAGIFNDRF--------WELEVDVNL 110
+V D+ + AF ++G +D+++NNAGI D W +D NL
Sbjct: 61 --NVGDWDSTKAAFDKVKAEVGEIDVLVNNAGITRDVVFRKMTREDWTAVIDTNL 113
>gnl|CDD|168204 PRK05717, PRK05717, oxidoreductase; Validated.
Length = 255
Score = 44.5 bits (105), Expect = 2e-06
Identities = 36/116 (31%), Positives = 50/116 (43%), Gaps = 15/116 (12%)
Query: 7 GKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPCD 66
G+VALVTG A GIG L+ G +V + D++ G +A+ G N A + D
Sbjct: 10 GRVALVTGAARGIGLGIAAWLIAEGWQVVLADLDRERGSKVAK----ALGEN-AWFIAMD 64
Query: 67 VTDYPQFEEAFQITLQKLGGLDIVINNAGIFNDR----------FWELEVDVNLVG 112
V D Q L + G LD ++ NA I + W + VNL G
Sbjct: 65 VADEAQVAAGVAEVLGQFGRLDALVCNAAIADPHNTTLESLSLAHWNRVLAVNLTG 120
>gnl|CDD|181417 PRK08416, PRK08416, 7-alpha-hydroxysteroid dehydrogenase;
Provisional.
Length = 260
Score = 44.4 bits (105), Expect = 2e-06
Identities = 27/98 (27%), Positives = 47/98 (47%), Gaps = 2/98 (2%)
Query: 1 MVMDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSIC-DINDSVGEDLAEQWRTKYGPNR 59
M ++KGK +++GG GIG+A E + G ++ + N +AE KYG
Sbjct: 2 MSNEMKGKTLVISGGTRGIGKAIVYEFAQSGVNIAFTYNSNVEEANKIAEDLEQKYGIKA 61
Query: 60 AIYCPCDVTDYPQFEEAFQITLQKLGGLDIVINNAGIF 97
Y P ++ + ++E F+ + +D I+NA I
Sbjct: 62 KAY-PLNILEPETYKELFKKIDEDFDRVDFFISNAIIS 98
>gnl|CDD|235813 PRK06482, PRK06482, short chain dehydrogenase; Provisional.
Length = 276
Score = 44.3 bits (105), Expect = 2e-06
Identities = 31/115 (26%), Positives = 50/115 (43%), Gaps = 13/115 (11%)
Query: 7 GKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPCD 66
K +TG ++G GR E LL G +V+ +DL ++ +R D
Sbjct: 2 SKTWFITGASSGFGRGMTERLLARGDRVAATVRRPDALDDLKARY-----GDRLWVLQLD 56
Query: 67 VTDYPQFEEAFQITLQKLGGLDIVINNAG--IF------NDRFWELEVDVNLVGT 113
VTD LG +D+V++NAG +F +D ++D NL+G+
Sbjct: 57 VTDSAAVRAVVDRAFAALGRIDVVVSNAGYGLFGAAEELSDAQIRRQIDTNLIGS 111
>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 = 43.8 bits (104), Expect = 2e-06
Identities = 29/91 (31%), Positives = 42/91 (46%), Gaps = 1/91 (1%)
Query: 9 VALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPCDVT 68
V ++TG + GIGRA EELLK G+ + + S E L E R D++
Sbjct: 1 VIILTGASRGIGRALAEELLKRGSPSVVVLLARSE-EPLQELKEELRPGLRVTTVKADLS 59
Query: 69 DYPQFEEAFQITLQKLGGLDIVINNAGIFND 99
D E+ + + G D++INNAG
Sbjct: 60 DAAGVEQLLEAIRKLDGERDLLINNAGSLGP 90
>gnl|CDD|235703 PRK06125, PRK06125, short chain dehydrogenase; Provisional.
Length = 259
Score = 43.9 bits (104), Expect = 3e-06
Identities = 29/95 (30%), Positives = 46/95 (48%), Gaps = 5/95 (5%)
Query: 1 MVMDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRA 60
M + L GK L+TG + GIG A E G + + + E LA R +G + A
Sbjct: 1 MDLHLAGKRVLITGASKGIGAAAAEAFAAEGCHLHLVARDADALEALAADLRAAHGVDVA 60
Query: 61 IYCPCDVTDYPQFEEAFQITLQKLGGLDIVINNAG 95
++ D++ EA + + G +DI++NNAG
Sbjct: 61 VH-ALDLSS----PEAREQLAAEAGDIDILVNNAG 90
>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 = 42.9 bits (102), Expect = 4e-06
Identities = 26/98 (26%), Positives = 36/98 (36%), Gaps = 6/98 (6%)
Query: 8 KVALVTGGAAGIGRAYCEELLKFGAK----VSICDINDSVGEDLAEQWRTKYGPNRAIYC 63
L+TGG G+GRA L + GA+ +S + L + G R
Sbjct: 1 GTYLITGGLGGLGRALARWLAERGARRLVLLSRSGPDAPGAAALLAELE-AAGA-RVTVV 58
Query: 64 PCDVTDYPQFEEAFQITLQKLGGLDIVINNAGIFNDRF 101
CDV D G L VI+ AG+ +D
Sbjct: 59 ACDVADRDALAAVLAAIPAVEGPLTGVIHAAGVLDDGV 96
>gnl|CDD|180753 PRK06924, PRK06924, short chain dehydrogenase; Provisional.
Length = 251
Score = 43.1 bits (102), Expect = 5e-06
Identities = 25/95 (26%), Positives = 42/95 (44%), Gaps = 12/95 (12%)
Query: 8 KVALVTGGAAGIGRAYCEELLKFGAKV-SICDINDSVGEDLAEQWRTKYGPNRAIYCPCD 66
+ ++TG + G+G A +LL+ G V SI + LAEQ+ + + D
Sbjct: 2 RYVIITGTSQGLGEAIANQLLEKGTHVISISRTENKELTKLAEQYNSNL-----TFHSLD 56
Query: 67 VTDYPQFEEAF-----QITLQKLGGLDIVINNAGI 96
+ D + E F I + + + INNAG+
Sbjct: 57 LQDVHELETNFNEILSSIQEDNVSSIHL-INNAGM 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 = 43.1 bits (102), Expect = 5e-06
Identities = 30/91 (32%), Positives = 42/91 (46%), Gaps = 8/91 (8%)
Query: 10 ALVTGGAAGIGRAYCEELLKFG-AKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPCDVT 68
L+TG + GIG +LL G V + S +LA +R DVT
Sbjct: 1 VLITGASRGIGLELVRQLLARGNNTVIATCRDPSAATELAA---LGASHSRLHILELDVT 57
Query: 69 DYPQFEEAFQITLQKLG--GLDIVINNAGIF 97
D E+ + ++LG GLD++INNAGI
Sbjct: 58 DEIA--ESAEAVAERLGDAGLDVLINNAGIL 86
>gnl|CDD|236056 PRK07576, PRK07576, short chain dehydrogenase; Provisional.
Length = 264
Score = 43.0 bits (102), Expect = 5e-06
Identities = 22/93 (23%), Positives = 39/93 (41%), Gaps = 2/93 (2%)
Query: 2 VMDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAI 61
+ D GK +V GG +GI + + GA V++ + + Q + +
Sbjct: 4 MFDFAGKNVVVVGGTSGINLGIAQAFARAGANVAVASRSQEKVDAAVAQLQQAGP--EGL 61
Query: 62 YCPCDVTDYPQFEEAFQITLQKLGGLDIVINNA 94
DV DY E AF + G +D++++ A
Sbjct: 62 GVSADVRDYAAVEAAFAQIADEFGPIDVLVSGA 94
>gnl|CDD|224011 COG1086, COG1086, Predicted nucleoside-diphosphate sugar epimerases
[Cell envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 588
Score = 43.4 bits (103), Expect = 5e-06
Identities = 22/76 (28%), Positives = 35/76 (46%), Gaps = 1/76 (1%)
Query: 4 DLKGKVALVTGGAAGIGRAYCEELLKFGAK-VSICDINDSVGEDLAEQWRTKYGPNRAIY 62
L GK LVTGG IG C ++LKF K + + ++ + + R K+ + +
Sbjct: 247 MLTGKTVLVTGGGGSIGSELCRQILKFNPKEIILFSRDEYKLYLIDMELREKFPELKLRF 306
Query: 63 CPCDVTDYPQFEEAFQ 78
DV D + E A +
Sbjct: 307 YIGDVRDRDRVERAME 322
>gnl|CDD|216283 pfam01073, 3Beta_HSD, 3-beta hydroxysteroid dehydrogenase/isomerase
family. The enzyme 3 beta-hydroxysteroid
dehydrogenase/5-ene-4-ene isomerase (3 beta-HSD)
catalyzes the oxidation and isomerisation of 5-ene-3
beta-hydroxypregnene and 5-ene-hydroxyandrostene steroid
precursors into the corresponding 4-ene-ketosteroids
necessary for the formation of all classes of steroid
hormones.
Length = 280
Score = 43.1 bits (102), Expect = 5e-06
Identities = 32/110 (29%), Positives = 43/110 (39%), Gaps = 21/110 (19%)
Query: 11 LVTGGAAGIGRAYCEELLKFGAK--VSICDINDSVGEDLAEQWRTKYGP-NRAIYCPCDV 67
LVTGG +GR LL+ G V + D+ S + + Y DV
Sbjct: 1 LVTGGGGFLGRHIVRLLLREGELQEVRVFDLRFS------PELLEDFSKLQVITYIEGDV 54
Query: 68 TDYPQFEEAFQITLQKLGGLDIVINNAGIFNDRFWELE----VDVNLVGT 113
TD A Q G D+VI+ A I D F + + VN+ GT
Sbjct: 55 TDKQDLRRALQ-------GSDVVIHTAAI-IDVFGKAYRDTIMKVNVKGT 96
>gnl|CDD|183716 PRK12744, PRK12744, short chain dehydrogenase; Provisional.
Length = 257
Score = 42.8 bits (101), Expect = 6e-06
Identities = 29/94 (30%), Positives = 39/94 (41%), Gaps = 2/94 (2%)
Query: 4 DLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRT--KYGPNRAI 61
LKGKV L+ GGA +G +L GAK N + + AE+ K +A+
Sbjct: 5 SLKGKVVLIAGGAKNLGGLIARDLAAQGAKAVAIHYNSAASKADAEETVAAVKAAGAKAV 64
Query: 62 YCPCDVTDYPQFEEAFQITLQKLGGLDIVINNAG 95
D+T E+ F G DI IN G
Sbjct: 65 AFQADLTTAAAVEKLFDDAKAAFGRPDIAINTVG 98
>gnl|CDD|171531 PRK12481, PRK12481, 2-deoxy-D-gluconate 3-dehydrogenase;
Provisional.
Length = 251
Score = 42.6 bits (100), Expect = 7e-06
Identities = 29/114 (25%), Positives = 52/114 (45%), Gaps = 12/114 (10%)
Query: 4 DLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYC 63
DL GKVA++TG G+G+ L K GA I + + + Q + + +
Sbjct: 5 DLNGKVAIITGCNTGLGQGMAIGLAKAGA--DIVGVGVAEAPETQAQ--VEALGRKFHFI 60
Query: 64 PCDVTDYPQFEEAFQITLQKLGGLDIVINNAGI--------FNDRFWELEVDVN 109
D+ + ++ +G +DI+INNAGI F ++ W+ +++N
Sbjct: 61 TADLIQQKDIDSIVSQAVEVMGHIDILINNAGIIRRQDLLEFGNKDWDDVININ 114
>gnl|CDD|182051 PRK09730, PRK09730, putative NAD(P)-binding oxidoreductase;
Provisional.
Length = 247
Score = 42.5 bits (100), Expect = 7e-06
Identities = 28/90 (31%), Positives = 41/90 (45%), Gaps = 3/90 (3%)
Query: 8 KVALVTGGAAGIGRAYCEELLKFGAKVSICDI-NDSVGEDLAEQWRTKYGPNRAIYCPCD 66
+ALVTGG+ GIGRA L + G V++ N +++ G +A D
Sbjct: 2 AIALVTGGSRGIGRATALLLAQEGYTVAVNYQQNLHAAQEVVNLITQAGG--KAFVLQAD 59
Query: 67 VTDYPQFEEAFQITLQKLGGLDIVINNAGI 96
++D Q F Q L ++NNAGI
Sbjct: 60 ISDENQVVAMFTAIDQHDEPLAALVNNAGI 89
>gnl|CDD|183719 PRK12747, PRK12747, short chain dehydrogenase; Provisional.
Length = 252
Score = 42.4 bits (99), Expect = 8e-06
Identities = 37/104 (35%), Positives = 49/104 (47%), Gaps = 5/104 (4%)
Query: 5 LKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDIN-DSVGEDLAEQWRTKYGPNRAIYC 63
LKGKVALVTG + GIGRA + L GA V+I N E+ + ++ G +I
Sbjct: 2 LKGKVALVTGASRGIGRAIAKRLANDGALVAIHYGNRKEEAEETVYEIQSNGGSAFSIGA 61
Query: 64 PCD-VTDYPQFEEAFQITLQKLGG---LDIVINNAGIFNDRFWE 103
+ + + LQ G DI+INNAGI F E
Sbjct: 62 NLESLHGVEALYSSLDNELQNRTGSTKFDILINNAGIGPGAFIE 105
>gnl|CDD|181188 PRK07985, PRK07985, oxidoreductase; Provisional.
Length = 294
Score = 42.3 bits (99), Expect = 9e-06
Identities = 34/98 (34%), Positives = 50/98 (51%), Gaps = 14/98 (14%)
Query: 5 LKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRT--KYGPNRAIY 62
LK + ALVTGG +GIGRA + GA V+I + E+ A+ + + +A+
Sbjct: 47 LKDRKALVTGGDSGIGRAAAIAYAREGADVAISYLPVE--EEDAQDVKKIIEECGRKAVL 104
Query: 63 CPCDVTDYPQFEEAFQITL-----QKLGGLDIVINNAG 95
P D++D E F +L + LGGLDI+ AG
Sbjct: 105 LPGDLSD-----EKFARSLVHEAHKALGGLDIMALVAG 137
>gnl|CDD|180771 PRK06947, PRK06947, glucose-1-dehydrogenase; Provisional.
Length = 248
Score = 41.7 bits (98), Expect = 1e-05
Identities = 31/90 (34%), Positives = 39/90 (43%), Gaps = 3/90 (3%)
Query: 8 KVALVTGGAAGIGRAYCEELLKFGAKVSICDIND-SVGEDLAEQWRTKYGPNRAIYCPCD 66
KV L+TG + GIGRA G V I D + E+ A+ R G RA D
Sbjct: 3 KVVLITGASRGIGRATAVLAAARGWSVGINYARDAAAAEETADAVRAAGG--RACVVAGD 60
Query: 67 VTDYPQFEEAFQITLQKLGGLDIVINNAGI 96
V + F G LD ++NNAGI
Sbjct: 61 VANEADVIAMFDAVQSAFGRLDALVNNAGI 90
>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 = 41.8 bits (98), Expect = 1e-05
Identities = 27/104 (25%), Positives = 41/104 (39%), Gaps = 7/104 (6%)
Query: 7 GKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPCD 66
GKV ++TG +GIG GA V + N S + ++ R D
Sbjct: 1 GKVIIITGANSGIGFETARSFALHGAHVILACRNMSRASAAVSRILEEWHKARVEAMTLD 60
Query: 67 VT---DYPQFEEAFQITLQKLGGLDIVINNAGIFNDRFWELEVD 107
+ +F EAF+ K L +++ NA +F W L D
Sbjct: 61 LASLRSVQRFAEAFK---AKNSPLHVLVCNAAVFALP-WTLTED 100
>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 = 41.7 bits (98), Expect = 2e-05
Identities = 33/115 (28%), Positives = 57/115 (49%), Gaps = 12/115 (10%)
Query: 4 DLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYC 63
L+GKVALVTG G+G+ L + GA + + S + +Q G R +
Sbjct: 2 SLEGKVALVTGANTGLGQGIAVGLAEAGADI-VG-AGRSEPSETQQQ-VEALG-RRFLSL 57
Query: 64 PCDVTDYPQFEEAFQITLQKLGGLDIVINNAGI--------FNDRFWELEVDVNL 110
D++D + +++ G +DI++NNAGI F+++ W+ ++VNL
Sbjct: 58 TADLSDIEAIKALVDSAVEEFGHIDILVNNAGIIRRADAEEFSEKDWDDVMNVNL 112
>gnl|CDD|181113 PRK07775, PRK07775, short chain dehydrogenase; Provisional.
Length = 274
Score = 41.7 bits (98), Expect = 2e-05
Identities = 33/113 (29%), Positives = 54/113 (47%), Gaps = 12/113 (10%)
Query: 10 ALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPCDVTD 69
ALV G ++GIG A EL G V++ E+L ++ R G A+ P DVTD
Sbjct: 13 ALVAGASSGIGAATAIELAAAGFPVALGARRVEKCEELVDKIRADGG--EAVAFPLDVTD 70
Query: 70 YPQFEEAFQITLQKLGGLDIVINNAG---------IFNDRFWELEVDVNLVGT 113
+ + LG ++++++ AG I ++F E +V ++LVG
Sbjct: 71 PDSVKSFVAQAEEALGEIEVLVSGAGDTYFGKLHEISTEQF-ESQVQIHLVGA 122
>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 = 2e-05
Identities = 31/108 (28%), Positives = 38/108 (35%), Gaps = 20/108 (18%)
Query: 11 LVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPCDVTDY 70
LVTGGA IG E LL G V D G D + D+TD
Sbjct: 4 LVTGGAGFIGSHLVERLLAAGHDVRGLD-RLRDGLDPLLSGVE--------FVVLDLTDR 54
Query: 71 PQFEEAFQITLQKLGGLDIVINNAGIF-----NDRFWELEVDVNLVGT 113
+E + G D VI+ A N +DVN+ GT
Sbjct: 55 DLVDELAK------GVPDAVIHLAAQSSVPDSNASDPAEFLDVNVDGT 96
>gnl|CDD|183797 PRK12859, PRK12859, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 256
Score = 41.3 bits (97), Expect = 2e-05
Identities = 34/106 (32%), Positives = 46/106 (43%), Gaps = 21/106 (19%)
Query: 5 LKGKVALVTGG--AAGIGRAYCEELLKFGAKV-----SICDINDSVGEDLAEQWRTK--- 54
LK KVA+VTG GIG A C+EL + GA + + D G D EQ + +
Sbjct: 4 LKNKVAVVTGVSRLDGIGAAICKELAEAGADIFFTYWTAYDKEMPWGVDQDEQIQLQEEL 63
Query: 55 --YGPNRAIYCPCDVTDYPQFEEAFQITLQK----LGGLDIVINNA 94
G + D Q +A + L K LG I++NNA
Sbjct: 64 LKNG----VKVSSMELDLTQ-NDAPKELLNKVTEQLGYPHILVNNA 104
>gnl|CDD|180411 PRK06123, PRK06123, short chain dehydrogenase; Provisional.
Length = 248
Score = 41.3 bits (97), Expect = 2e-05
Identities = 28/90 (31%), Positives = 43/90 (47%), Gaps = 3/90 (3%)
Query: 8 KVALVTGGAAGIGRAYCEELLKFGAKVSICDI-NDSVGEDLAEQWRTKYGPNRAIYCPCD 66
KV ++TG + GIG A + G V + + N E + + R + G A+ D
Sbjct: 3 KVMIITGASRGIGAATALLAAERGYAVCLNYLRNRDAAEAVVQAIRRQGG--EALAVAAD 60
Query: 67 VTDYPQFEEAFQITLQKLGGLDIVINNAGI 96
V D F+ ++LG LD ++NNAGI
Sbjct: 61 VADEADVLRLFEAVDRELGRLDALVNNAGI 90
>gnl|CDD|168186 PRK05693, PRK05693, short chain dehydrogenase; Provisional.
Length = 274
Score = 40.9 bits (96), Expect = 3e-05
Identities = 27/88 (30%), Positives = 36/88 (40%), Gaps = 8/88 (9%)
Query: 8 KVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPCDV 67
V L+TG ++GIGRA + G +V E LA T DV
Sbjct: 2 PVVLITGCSSGIGRALADAFKAAGYEVWATARKAEDVEALAAAGFTAV--------QLDV 53
Query: 68 TDYPQFEEAFQITLQKLGGLDIVINNAG 95
D + + GGLD++INNAG
Sbjct: 54 NDGAALARLAEELEAEHGGLDVLINNAG 81
>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 = 40.3 bits (94), Expect = 5e-05
Identities = 28/120 (23%), Positives = 49/120 (40%), Gaps = 12/120 (10%)
Query: 5 LKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCP 64
L ++ LVTG + GIGR ++GA V + N+ +A+ + G + +
Sbjct: 2 LNDRIILVTGASDGIGREAALTYARYGATVILLGRNEEKLRQVADHINEEGGR-QPQWFI 60
Query: 65 CDVTD--YPQFEEAFQITLQKLGGLDIVINNAGIF---------NDRFWELEVDVNLVGT 113
D+ ++ Q LD V++NAG+ N + W+ VN+ T
Sbjct: 61 LDLLTCTSENCQQLAQRIAVNYPRLDGVLHNAGLLGDVCPLSEQNPQVWQDVXQVNVNAT 120
>gnl|CDD|183718 PRK12746, PRK12746, short chain dehydrogenase; Provisional.
Length = 254
Score = 40.0 bits (93), Expect = 6e-05
Identities = 33/99 (33%), Positives = 46/99 (46%), Gaps = 7/99 (7%)
Query: 4 DLKGKVALVTGGAAGIGRAYCEELLKFGAKVSI-CDINDSVGEDLAEQWRTKYGPNRAIY 62
+L GKVALVTG + GIGRA L GA V+I N ++ + + G I
Sbjct: 3 NLDGKVALVTGASRGIGRAIAMRLANDGALVAIHYGRNKQAADETIREIESNGGKAFLIE 62
Query: 63 CPCDVTD-----YPQFEEAFQITLQKLGGLDIVINNAGI 96
+ D Q + QI + +DI++NNAGI
Sbjct: 63 ADLNSIDGVKKLVEQLKNELQIRVGT-SEIDILVNNAGI 100
>gnl|CDD|223696 COG0623, FabI, Enoyl-[acyl-carrier-protein].
Length = 259
Score = 39.9 bits (94), Expect = 6e-05
Identities = 24/94 (25%), Positives = 41/94 (43%), Gaps = 11/94 (11%)
Query: 3 MDLKGKVALVTGGAA--GIGRAYCEELLKFGAKVSICDINDSVG---EDLAEQWRTKYGP 57
L+GK L+ G A I + L + GA+++ + + E+LAE+
Sbjct: 2 GLLEGKRILIMGVANNRSIAWGIAKALAEQGAELAFTYQGERLEKRVEELAEEL------ 55
Query: 58 NRAIYCPCDVTDYPQFEEAFQITLQKLGGLDIVI 91
+ PCDVT+ + F +K G LD ++
Sbjct: 56 GSDLVLPCDVTNDESIDALFATIKKKWGKLDGLV 89
>gnl|CDD|181298 PRK08219, PRK08219, short chain dehydrogenase; Provisional.
Length = 227
Score = 39.9 bits (94), Expect = 7e-05
Identities = 29/127 (22%), Positives = 45/127 (35%), Gaps = 47/127 (37%)
Query: 8 KVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYG----------- 56
AL+TG + GIG A + +LA G
Sbjct: 4 PTALITGASRGIGAA--------------------IARELAPTHTLLLGGRPAERLDELA 43
Query: 57 ---PNRAIYCPCDVTDYPQFEEAFQITLQKLGGLDIVINNAGIFND--------RFWELE 105
P A P D+TD A + +LG LD++++NAG+ + W
Sbjct: 44 AELPG-ATPFPVDLTDPEAIAAAVE----QLGRLDVLVHNAGVADLGPVAESTVDEWRAT 98
Query: 106 VDVNLVG 112
++VN+V
Sbjct: 99 LEVNVVA 105
>gnl|CDD|181126 PRK07806, PRK07806, short chain dehydrogenase; Provisional.
Length = 248
Score = 39.7 bits (93), Expect = 8e-05
Identities = 28/92 (30%), Positives = 39/92 (42%), Gaps = 3/92 (3%)
Query: 4 DLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSV-GEDLAEQWRTKYGPNRAIY 62
DL GK ALVTG + GIG + L GA V + + + + G RA
Sbjct: 3 DLPGKTALVTGSSRGIGADTAKILAGAGAHVVVNYRQKAPRANKVVAEIEAAGG--RASA 60
Query: 63 CPCDVTDYPQFEEAFQITLQKLGGLDIVINNA 94
D+TD ++ GGLD ++ NA
Sbjct: 61 VGADLTDEESVAALMDTAREEFGGLDALVLNA 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 = 39.5 bits (92), Expect = 9e-05
Identities = 31/99 (31%), Positives = 52/99 (52%), Gaps = 9/99 (9%)
Query: 7 GKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCP-C 65
G+ L+TG +GIG+A + K G V + N + E+ ++ T+ G N+ I+
Sbjct: 1 GRSFLITGANSGIGKAAALAIAKRGGTVHMVCRNQTRAEEARKEIETESG-NQNIFLHIV 59
Query: 66 DVTDYPQ---FEEAFQITLQKLGGLDIVINNAG-IFNDR 100
D++D Q F E F+ ++ L ++INNAG + N R
Sbjct: 60 DMSDPKQVWEFVEEFK---EEGKKLHVLINNAGCMVNKR 95
>gnl|CDD|133444 cd01075, NAD_bind_Leu_Phe_Val_DH, NAD(P) binding domain of
leucine dehydrogenase, phenylalanine dehydrogenase, and
valine dehydrogenase. Amino acid dehydrogenase (DH) is
a widely distributed family of enzymes that catalyzes
the oxidative deamination of an amino acid to its keto
acid and ammonia with concomitant reduction of NADP+.
For example, leucine DH catalyzes the reversible
oxidative deamination of L-leucine and several other
straight or branched chain amino acids to the
corresponding 2-oxoacid derivative. Amino acid DH -like
NAD(P)-binding domains are members of the Rossmann fold
superfamily and include glutamate, leucine, and
phenylalanine DHs, methylene tetrahydrofolate DH,
methylene-tetrahydromethanopterin DH,
methylene-tetrahydropholate DH/cyclohydrolase,
Shikimate DH-like proteins, malate oxidoreductases, and
glutamyl tRNA reductase. Amino acid DHs catalyze the
deamination of amino acids to keto acids with NAD(P)+
as a cofactor. The NAD(P)-binding Rossmann fold
superfamily includes a wide variety of protein families
including NAD(P)- binding domains of alcohol DHs,
tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate DH, lactate/malate DHs,
formate/glycerate DHs, siroheme synthases,
6-phosphogluconate DH, amino acid DHs, repressor rex,
NAD-binding potassium channel domain, CoA-binding, and
ornithine cyclodeaminase-like domains. These domains
have an alpha-beta-alpha configuration. NAD binding
involves numerous hydrogen and van der Waals contacts.
Length = 200
Score = 39.1 bits (92), Expect = 1e-04
Identities = 22/66 (33%), Positives = 29/66 (43%), Gaps = 4/66 (6%)
Query: 4 DLKGKVALVTG-GAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIY 62
L+GK V G G +G E LL+ GAK+ + DIN+ AE + IY
Sbjct: 25 SLEGKTVAVQGLGK--VGYKLAEHLLEEGAKLIVADINEEAVARAAELFGATVVAPEEIY 82
Query: 63 -CPCDV 67
DV
Sbjct: 83 SVDADV 88
>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 = 39.1 bits (92), Expect = 1e-04
Identities = 26/88 (29%), Positives = 37/88 (42%), Gaps = 12/88 (13%)
Query: 11 LVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPCDVTDY 70
LVTGGA IG E LL+ G +V + D N S G ++ + D+ D
Sbjct: 3 LVTGGAGFIGSHLVERLLERGHEVIVLD-NLSTG----KKENLPEVKPNVKFIEGDIRDD 57
Query: 71 PQFEEAFQITLQKLGGLDIVINNAGIFN 98
E AF+ G+D V + A +
Sbjct: 58 ELVEFAFE-------GVDYVFHQAAQAS 78
>gnl|CDD|181605 PRK08993, PRK08993, 2-deoxy-D-gluconate 3-dehydrogenase; Validated.
Length = 253
Score = 39.1 bits (91), Expect = 2e-04
Identities = 33/125 (26%), Positives = 59/125 (47%), Gaps = 23/125 (18%)
Query: 1 MVMD---LKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTK--- 54
M++D L+GKVA+VTG G+G+ L + G CDI VG ++ E T
Sbjct: 1 MILDAFSLEGKVAVVTGCDTGLGQGMALGLAEAG-----CDI---VGINIVEPTETIEQV 52
Query: 55 -YGPNRAIYCPCDVTDYPQFEEAFQITLQKLGGLDIVINNAGI--------FNDRFWELE 105
R + D+ + + + G +DI++NNAG+ F+++ W+
Sbjct: 53 TALGRRFLSLTADLRKIDGIPALLERAVAEFGHIDILVNNAGLIRREDAIEFSEKDWDDV 112
Query: 106 VDVNL 110
+++N+
Sbjct: 113 MNLNI 117
>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 = 38.4 bits (90), Expect = 2e-04
Identities = 34/118 (28%), Positives = 49/118 (41%), Gaps = 16/118 (13%)
Query: 8 KVALVTGGAAGIGRAYCEELLKFGAKV-SICDINDSVGEDLAEQWRTKYGPNRAIYCPCD 66
K L+TG +G G ++L G V + C + G A++ R R D
Sbjct: 1 KAVLITGCDSGFGNLLAKKLDSLGFTVLAGCLTKNGPG---AKELRRVCSD-RLRTLQLD 56
Query: 67 VTDYPQFEEAFQITLQKLG--GLDIVINNAGI---FNDRFWELE------VDVNLVGT 113
VT Q + A Q + +G GL ++NNAGI D ++VNL GT
Sbjct: 57 VTKPEQIKRAAQWVKEHVGEKGLWGLVNNAGILGFGGDEELLPMDDYRKCMEVNLFGT 114
Score = 25.3 bits (56), Expect = 7.7
Identities = 14/38 (36%), Positives = 17/38 (44%), Gaps = 8/38 (21%)
Query: 7 GKVALVTGGAAGIGRAYCE--------ELLKFGAKVSI 36
G+V GGA +A E EL +G KVSI
Sbjct: 140 GRVPFPAGGAYCASKAAVEAFSDSLRRELQPWGVKVSI 177
>gnl|CDD|177883 PLN02240, PLN02240, UDP-glucose 4-epimerase.
Length = 352
Score = 38.4 bits (90), Expect = 3e-04
Identities = 31/96 (32%), Positives = 44/96 (45%), Gaps = 9/96 (9%)
Query: 3 MDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICD-INDSVGEDLAEQWRTKYGPN--R 59
M L G+ LVTGGA IG +LL G KV + D +++S E L + + G
Sbjct: 1 MSLMGRTILVTGGAGYIGSHTVLQLLLAGYKVVVIDNLDNSSEEAL-RRVKELAGDLGDN 59
Query: 60 AIYCPCDVTDYPQFEEAFQITLQKLGGLDIVINNAG 95
++ D+ D E+ F T D VI+ AG
Sbjct: 60 LVFHKVDLRDKEALEKVFAST-----RFDAVIHFAG 90
>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 = 38.1 bits (89), Expect = 3e-04
Identities = 21/88 (23%), Positives = 34/88 (38%), Gaps = 3/88 (3%)
Query: 9 VALVTGGAAGIGRAYCEELLKFGAKVS-ICDINDSVGEDLAEQWRTKYGPNRAIYCPCDV 67
VA V G G+G A G V+ + L + R A P D
Sbjct: 1 VAAVVGAGDGLGAAIARRFAAEGFSVALAARREAKLEALLVDIIRDA--GGSAKAVPTDA 58
Query: 68 TDYPQFEEAFQITLQKLGGLDIVINNAG 95
D + F + +++G L++++ NAG
Sbjct: 59 RDEDEVIALFDLIEEEIGPLEVLVYNAG 86
>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 = 37.6 bits (88), Expect = 4e-04
Identities = 24/111 (21%), Positives = 34/111 (30%), Gaps = 27/111 (24%)
Query: 10 ALVTGGAAGIGRAYCEELLKFGAKV-----SICDINDSVGEDLAEQWRTKYGPNRAIYCP 64
LVTG +G LL G +V S D G + + G
Sbjct: 1 ILVTGATGFLGSNLVRALLAQGYRVRALVRSGSDAVLLDGLPV--EVV--EG-------- 48
Query: 65 CDVTDYPQFEEAFQITLQKLGGLDIVINNAGIF--NDRFWELEVDVNLVGT 113
D+TD A + G D V + A + + N+ GT
Sbjct: 49 -DLTDAASLAAAMK-------GCDRVFHLAAFTSLWAKDRKELYRTNVEGT 91
>gnl|CDD|235910 PRK07024, PRK07024, short chain dehydrogenase; Provisional.
Length = 257
Score = 37.2 bits (87), Expect = 7e-04
Identities = 23/85 (27%), Positives = 36/85 (42%), Gaps = 3/85 (3%)
Query: 12 VTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPCDVTDYP 71
+TG ++GIG+A E + GA + + + A + ++Y DV D
Sbjct: 7 ITGASSGIGQALAREYARQGATLGLVARRTDALQAFAARLPK--AARVSVY-AADVRDAD 63
Query: 72 QFEEAFQITLQKLGGLDIVINNAGI 96
A + G D+VI NAGI
Sbjct: 64 ALAAAAADFIAAHGLPDVVIANAGI 88
>gnl|CDD|235627 PRK05854, PRK05854, short chain dehydrogenase; Provisional.
Length = 313
Score = 36.6 bits (85), Expect = 0.001
Identities = 29/96 (30%), Positives = 43/96 (44%), Gaps = 2/96 (2%)
Query: 2 VMDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAI 61
V DL GK A+VTG + G+G L GA+V + N + GE RT +
Sbjct: 9 VPDLSGKRAVVTGASDGLGLGLARRLAAAGAEVILPVRNRAKGEAAVAAIRTAVPDAKLS 68
Query: 62 YCPCDVTDYPQFEEAFQITLQKLG-GLDIVINNAGI 96
D++ A L+ G + ++INNAG+
Sbjct: 69 LRALDLSSLASV-AALGEQLRAEGRPIHLLINNAGV 103
>gnl|CDD|180399 PRK06101, PRK06101, short chain dehydrogenase; Provisional.
Length = 240
Score = 36.4 bits (84), Expect = 0.001
Identities = 22/69 (31%), Positives = 33/69 (47%), Gaps = 8/69 (11%)
Query: 9 VALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYC-PCDV 67
L+TG +GIG+ + K G +V C N SV ++L Q + I+ DV
Sbjct: 3 AVLITGATSGIGKQLALDYAKQGWQVIACGRNQSVLDELHTQ-------SANIFTLAFDV 55
Query: 68 TDYPQFEEA 76
TD+P + A
Sbjct: 56 TDHPGTKAA 64
>gnl|CDD|217199 pfam02719, Polysacc_synt_2, Polysaccharide biosynthesis protein.
This is a family of diverse bacterial polysaccharide
biosynthesis proteins including the CapD protein, WalL
protein mannosyl-transferase and several putative
epimerases (e.g. WbiI).
Length = 280
Score = 36.3 bits (85), Expect = 0.001
Identities = 23/85 (27%), Positives = 40/85 (47%), Gaps = 6/85 (7%)
Query: 11 LVTGGAAGIGRAYCEELLKFGAK-VSICDINDSVGEDLAEQWRTKYGPNRAIYCPCDVTD 69
LVTGG IG C ++LKF K + + ++ ++ ++ R +Y + + DV D
Sbjct: 2 LVTGGGGSIGSELCRQILKFNPKKIILFSRDEFKLYEIRQELRQEYNDPKLRFFIGDVRD 61
Query: 70 YPQFEEAFQITLQKLGGLDIVINNA 94
+ E A + G+D V + A
Sbjct: 62 RERLERAMEQH-----GVDTVFHAA 81
>gnl|CDD|236229 PRK08303, PRK08303, short chain dehydrogenase; Provisional.
Length = 305
Score = 36.1 bits (84), Expect = 0.001
Identities = 35/125 (28%), Positives = 48/125 (38%), Gaps = 22/125 (17%)
Query: 1 MVMDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVG----------EDLAEQ 50
M+ L+GKVALV G G GR EL GA V + + E+ AE
Sbjct: 2 MMKPLRGKVALVAGATRGAGRGIAVELGAAGATVYVTGRSTRARRSEYDRPETIEETAEL 61
Query: 51 WRTKYGPNRAIYCPCDVTDYPQFEEAFQITLQKLGGLDIVINNAGI--------FNDRFW 102
T G R I D Q + ++ G LDI++N+ I + W
Sbjct: 62 -VTAAG-GRGIAVQVDHLVPEQVRALVERIDREQGRLDILVND--IWGGEKLFEWGKPVW 117
Query: 103 ELEVD 107
E +D
Sbjct: 118 EHSLD 122
>gnl|CDD|187630 cd05372, ENR_SDR, Enoyl acyl carrier protein (ACP) reductase
(ENR), divergent SDR. This bacterial subgroup of ENRs
includes Escherichia coli ENR. ENR catalyzes the
NAD(P)H-dependent reduction of enoyl-ACP in the last
step of fatty acid biosynthesis. De novo fatty acid
biosynthesis is catalyzed by the fatty acid synthetase
complex, through the serial addition of 2-carbon
subunits. In bacteria and plants,ENR catalyzes one of
six synthetic steps in this process. Oilseed rape ENR,
and also apparently the NADH-specific form of
Escherichia coli ENR, is tetrameric. Although similar
to the classical SDRs, this group does not have the
canonical catalytic tetrad, nor does it have the
typical Gly-rich NAD-binding pattern. Such so-called
divergent SDRs have a GXXXXXSXA NAD-binding motif and a
YXXMXXXK (or YXXXMXXXK) active site 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 = 36.0 bits (84), Expect = 0.002
Identities = 21/87 (24%), Positives = 37/87 (42%), Gaps = 4/87 (4%)
Query: 7 GKVALVTGGA--AGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCP 64
GK L+TG A I + L + GA++ E+ + G + + P
Sbjct: 1 GKRILITGIANDRSIAWGIAKALHEAGAEL-AFTYQPEALRKRVEKLAERLGESALVL-P 58
Query: 65 CDVTDYPQFEEAFQITLQKLGGLDIVI 91
CDV++ + +E F + G LD ++
Sbjct: 59 CDVSNDEEIKELFAEVKKDWGKLDGLV 85
>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 = 0.002
Identities = 33/127 (25%), Positives = 50/127 (39%), Gaps = 29/127 (22%)
Query: 5 LKGKVALVTGGAAGIGRAYCEELLKFGAKVSIC-----DINDSV----GEDLAEQWRTKY 55
L KVALVT GIG A L + GA V + +++ +V GE L+
Sbjct: 8 LANKVALVTASTDGIGLAIARRLAQDGAHVVVSSRKQQNVDRAVATLQGEGLSVTGTV-- 65
Query: 56 GPNRAIYCPCDVTDYPQFEEAFQITLQKLGGLDIVINNAGI---------FNDRFWELEV 106
C V E + GG+DI+++NA + + W+ +
Sbjct: 66 ---------CHVGKAEDRERLVATAVNLHGGVDILVSNAAVNPFFGNILDSTEEVWDKIL 116
Query: 107 DVNLVGT 113
DVN+ T
Sbjct: 117 DVNVKAT 123
>gnl|CDD|236016 PRK07424, PRK07424, bifunctional sterol desaturase/short chain
dehydrogenase; Validated.
Length = 406
Score = 35.8 bits (83), Expect = 0.002
Identities = 15/30 (50%), Positives = 20/30 (66%)
Query: 5 LKGKVALVTGGAAGIGRAYCEELLKFGAKV 34
LKGK VTG + +G+A +EL + GAKV
Sbjct: 176 LKGKTVAVTGASGTLGQALLKELHQQGAKV 205
>gnl|CDD|166421 PLN02780, PLN02780, ketoreductase/ oxidoreductase.
Length = 320
Score = 35.6 bits (82), Expect = 0.003
Identities = 24/92 (26%), Positives = 45/92 (48%), Gaps = 4/92 (4%)
Query: 7 GKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPCD 66
G ALVTG GIG+ + +L + G + + N +D+++ ++KY + D
Sbjct: 53 GSWALVTGPTDGIGKGFAFQLARKGLNLVLVARNPDKLKDVSDSIQSKYSKTQIKTVVVD 112
Query: 67 VTDYPQFEEAFQITLQKLGGLD--IVINNAGI 96
+ +E + + + GLD ++INN G+
Sbjct: 113 FSG--DIDEGVKRIKETIEGLDVGVLINNVGV 142
>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 = 35.3 bits (82), Expect = 0.003
Identities = 26/111 (23%), Positives = 40/111 (36%), Gaps = 27/111 (24%)
Query: 8 KVALVTGGAAGIGRAYCEELLKFGAKVSI---CDINDS---VGEDLAEQWRTKYGPNRAI 61
V V G IGR L K G++V + C+ V DL + +
Sbjct: 1 MVVTVFGATGFIGRYVVNRLAKRGSQVIVPYRCEAYARRLLVMGDLG----------QVL 50
Query: 62 YCPCDVTDYPQFEEAFQITLQKLGGLDIVINNAGIF----NDRFWELEVDV 108
+ D+ D +A + G D+VIN G N F ++ V+
Sbjct: 51 FVEFDLRDDESIRKALE-------GSDVVINLVGRLYETKNFSFEDVHVEG 94
>gnl|CDD|183714 PRK12742, PRK12742, oxidoreductase; Provisional.
Length = 237
Score = 35.1 bits (81), Expect = 0.003
Identities = 29/94 (30%), Positives = 41/94 (43%), Gaps = 10/94 (10%)
Query: 3 MDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIY 62
GK LV GG+ GIG A + GA V + +D AE+ + G A+
Sbjct: 2 GAFTGKKVLVLGGSRGIGAAIVRRFVTDGANVR---FTYAGSKDAAERLAQETG-ATAVQ 57
Query: 63 CPCDVTDYPQFEEAFQITLQKLGGLDIVINNAGI 96
D D + ++K G LDI++ NAGI
Sbjct: 58 --TDSADRDAVID----VVRKSGALDILVVNAGI 85
>gnl|CDD|223247 COG0169, AroE, Shikimate 5-dehydrogenase [Amino acid transport and
metabolism].
Length = 283
Score = 35.3 bits (82), Expect = 0.003
Identities = 24/90 (26%), Positives = 37/90 (41%), Gaps = 17/90 (18%)
Query: 4 DLKGKVALVTGGAAGIGRAYCEELLKFGAK-VSICDINDSVGEDLAEQWRTKYGPNRAIY 62
D+ GK L+ G A G RA L + GAK +++ + E+LA+ + A
Sbjct: 123 DVTGKRVLILG-AGGAARAVAFALAEAGAKRITVVNRTRERAEELADLFGELGAAVEA-- 179
Query: 63 CPCDVTDYPQFEEAFQITLQKLGGLDIVIN 92
+ D EEA D++IN
Sbjct: 180 --AALADLEGLEEA-----------DLLIN 196
>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 = 35.0 bits (81), Expect = 0.003
Identities = 26/107 (24%), Positives = 45/107 (42%), Gaps = 8/107 (7%)
Query: 11 LVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPCDVTDY 70
VTGG +GR + LL+ G KV + ++S+GE +R D+T
Sbjct: 2 FVTGGTGFLGRHLVKRLLENGFKVLVLVRSESLGEAHERIEEAGLEADRVRVLEGDLTQ- 60
Query: 71 PQFEEAFQITLQKLGGLDIVINNAGIFNDRFWELEVD----VNLVGT 113
P + + + G +D VI+ A + ++ + N+ GT
Sbjct: 61 PNLGLSAAASRELAGKVDHVIHCAASY---DFQAPNEDAWRTNIDGT 104
>gnl|CDD|182531 PRK10538, PRK10538, malonic semialdehyde reductase; Provisional.
Length = 248
Score = 34.7 bits (80), Expect = 0.004
Identities = 28/113 (24%), Positives = 46/113 (40%), Gaps = 14/113 (12%)
Query: 9 VALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPCDVT 68
+ LVTG AG G ++ G KV I ++ ++ + + G N I DV
Sbjct: 2 IVLVTGATAGFGECITRRFIQQGHKV----IATGRRQERLQELKDELGDNLYI-AQLDVR 56
Query: 69 DYPQFEEAFQITLQKLGGLDIVINNAGI---------FNDRFWELEVDVNLVG 112
+ EE + +D+++NNAG+ + WE +D N G
Sbjct: 57 NRAAIEEMLASLPAEWRNIDVLVNNAGLALGLEPAHKASVEDWETMIDTNNKG 109
>gnl|CDD|169390 PRK08340, PRK08340, glucose-1-dehydrogenase; Provisional.
Length = 259
Score = 34.8 bits (80), Expect = 0.004
Identities = 28/85 (32%), Positives = 44/85 (51%), Gaps = 3/85 (3%)
Query: 11 LVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPCDVTDY 70
LVT + GIG ELLK GA+V I N+ E ++ + +YG A+ D++D
Sbjct: 4 LVTASSRGIGFNVARELLKKGARVVISSRNEENLEKALKELK-EYGEVYAV--KADLSDK 60
Query: 71 PQFEEAFQITLQKLGGLDIVINNAG 95
+ + + LGG+D ++ NAG
Sbjct: 61 DDLKNLVKEAWELLGGIDALVWNAG 85
>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 = 34.5 bits (79), Expect = 0.005
Identities = 22/93 (23%), Positives = 38/93 (40%), Gaps = 4/93 (4%)
Query: 9 VALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPCDVT 68
A+VTG A IG + L + G +V + + PN A+ C D++
Sbjct: 3 AAVVTGAAKRIGSSIAVALHQEGYRVVLHYHRSAAAASTLAAELNARRPNSAVTCQADLS 62
Query: 69 D----YPQFEEAFQITLQKLGGLDIVINNAGIF 97
+ + + E + G D+++NNA F
Sbjct: 63 NSATLFSRCEAIIDACFRAFGRCDVLVNNASAF 95
>gnl|CDD|235737 PRK06197, PRK06197, short chain dehydrogenase; Provisional.
Length = 306
Score = 34.2 bits (79), Expect = 0.006
Identities = 25/95 (26%), Positives = 37/95 (38%)
Query: 2 VMDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAI 61
+ D G+VA+VTG G+G L GA V + N G+ A +
Sbjct: 11 IPDQSGRVAVVTGANTGLGYETAAALAAKGAHVVLAVRNLDKGKAAAARITAATPGADVT 70
Query: 62 YCPCDVTDYPQFEEAFQITLQKLGGLDIVINNAGI 96
D+T A +D++INNAG+
Sbjct: 71 LQELDLTSLASVRAAADALRAAYPRIDLLINNAGV 105
>gnl|CDD|169556 PRK08703, PRK08703, short chain dehydrogenase; Provisional.
Length = 239
Score = 34.1 bits (78), Expect = 0.006
Identities = 24/96 (25%), Positives = 38/96 (39%), Gaps = 4/96 (4%)
Query: 5 LKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCP 64
L K LVTG + G+G + GA V + + E + + P
Sbjct: 4 LSDKTILVTGASQGLGEQVAKAYAAAGATVILVARHQKKLEKVYDAIVEAGHPEPFA-IR 62
Query: 65 CDV--TDYPQFEE-AFQITLQKLGGLDIVINNAGIF 97
D+ + +FE+ A I G LD +++ AG F
Sbjct: 63 FDLMSAEEKEFEQFAATIAEATQGKLDGIVHCAGYF 98
>gnl|CDD|184511 PRK14106, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
synthetase; Provisional.
Length = 450
Score = 34.2 bits (79), Expect = 0.007
Identities = 20/48 (41%), Positives = 25/48 (52%), Gaps = 3/48 (6%)
Query: 3 MDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQ 50
M+LKGK LV G A G A + L K GAKV + D + + L E
Sbjct: 1 MELKGKKVLVVG-AGVSGLALAKFLKKLGAKVILTDEKEE--DQLKEA 45
>gnl|CDD|184316 PRK13771, PRK13771, putative alcohol dehydrogenase; Provisional.
Length = 334
Score = 34.2 bits (79), Expect = 0.007
Identities = 28/91 (30%), Positives = 36/91 (39%), Gaps = 17/91 (18%)
Query: 6 KGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPC 65
KG+ LVTG G+G + GAKV I + E A+ KY
Sbjct: 162 KGETVLVTGAGGGVGIHAIQVAKALGAKV----IAVTSSESKAKIVS-KYA--------- 207
Query: 66 DVTDYPQFEEAFQITLQKLGGLDIVINNAGI 96
DY F ++K+GG DIVI G
Sbjct: 208 ---DYVIVGSKFSEEVKKIGGADIVIETVGT 235
>gnl|CDD|227315 COG4982, COG4982, 3-oxoacyl-[acyl-carrier protein].
Length = 866
Score = 34.1 bits (78), Expect = 0.010
Identities = 19/53 (35%), Positives = 24/53 (45%), Gaps = 3/53 (5%)
Query: 4 DLKGKVALVTGGAAG-IGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKY 55
KVALVTG + G I A LL GA V + E+ E +R+ Y
Sbjct: 393 TYGDKVALVTGASKGSIAAAVVARLLAGGATVIATTSR--LSEERTEFYRSLY 443
>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 = 33.7 bits (77), Expect = 0.011
Identities = 26/100 (26%), Positives = 41/100 (41%), Gaps = 10/100 (10%)
Query: 9 VALVTGGAAGIGRAYCEELLKF----GAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCP 64
V LVTG + G GR +EL K G+ + + ND L + + R +
Sbjct: 2 VCLVTGASRGFGRTIAQELAKCLKSPGSVLVLSARNDEALRQLKAEIGAERSGLRVVRVS 61
Query: 65 CDVTDYPQFEEAFQITLQKLGGLD-----IVINNAGIFND 99
D+ E+ + L++L ++INNAG D
Sbjct: 62 LDLGAEAGLEQLLKA-LRELPRPKGLQRLLLINNAGTLGD 100
>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 = 0.011
Identities = 26/108 (24%), Positives = 34/108 (31%), Gaps = 18/108 (16%)
Query: 10 ALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPCDVTD 69
LVTGG IG LL+ G +V I R + D+TD
Sbjct: 1 ILVTGGTGFIGSHLVRRLLQEGYEV----IVLGRRRRSES-----LNTGRIRFHEGDLTD 51
Query: 70 YPQFEEAFQITLQKLGGLDIVINNAG-IFNDRFWELEVD---VNLVGT 113
E D VI+ A +E D N++GT
Sbjct: 52 PDALERLLAEVQ-----PDAVIHLAAQSGVGASFEDPADFIRANVLGT 94
>gnl|CDD|181044 PRK07577, PRK07577, short chain dehydrogenase; Provisional.
Length = 234
Score = 33.5 bits (77), Expect = 0.012
Identities = 24/92 (26%), Positives = 35/92 (38%), Gaps = 14/92 (15%)
Query: 5 LKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCP 64
+ + LVTG GIG A L G +V I S +D P ++
Sbjct: 1 MSSRTVLVTGATKGIGLALSLRLANLGHQV--IGIARSAIDDF---------PGE-LFA- 47
Query: 65 CDVTDYPQFEEAFQITLQKLGGLDIVINNAGI 96
CD+ D Q + +D ++NN GI
Sbjct: 48 CDLADIEQTAATLAQINEI-HPVDAIVNNVGI 78
>gnl|CDD|223774 COG0702, COG0702, Predicted nucleoside-diphosphate-sugar
epimerases [Cell envelope biogenesis, outer membrane /
Carbohydrate transport and metabolism].
Length = 275
Score = 33.3 bits (76), Expect = 0.012
Identities = 11/26 (42%), Positives = 13/26 (50%)
Query: 11 LVTGGAAGIGRAYCEELLKFGAKVSI 36
LVTG +G A ELL G +V
Sbjct: 4 LVTGATGFVGGAVVRELLARGHEVRA 29
>gnl|CDD|222222 pfam13561, adh_short_C2, Enoyl-(Acyl carrier protein) reductase.
Length = 239
Score = 33.0 bits (76), Expect = 0.015
Identities = 15/83 (18%), Positives = 33/83 (39%), Gaps = 3/83 (3%)
Query: 14 GGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPCDVTDYPQF 73
I A + + GA+V + ++ ++ + P I P DVT
Sbjct: 3 ADDNSIAWAIAKAAAEEGAEVVLTTWPPALRMGAVDELAKEL-PADVI--PLDVTSDEDI 59
Query: 74 EEAFQITLQKLGGLDIVINNAGI 96
+E F+ + G +D ++++ +
Sbjct: 60 DELFEKVKEDGGKIDFLVHSIAM 82
>gnl|CDD|176210 cd08248, RTN4I1, Human Reticulon 4 Interacting Protein 1. Human
Reticulon 4 Interacting Protein 1 is a member of the
medium chain dehydrogenase/ reductase (MDR) family.
Riticulons are endoplasmic reticulum associated proteins
involved in membrane trafficking and neuroendocrine
secretion. The 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.
Length = 350
Score = 33.0 bits (76), Expect = 0.018
Identities = 24/92 (26%), Positives = 39/92 (42%), Gaps = 17/92 (18%)
Query: 6 KGKVALVTGGAAGIGRAYCEELLKFGAKVS-ICDINDSVGEDLAEQWRTKYGPNRAIYCP 64
GK L+ GG+ G+G + L +GA V+ C + L + G +
Sbjct: 162 AGKRVLILGGSGGVGTFAIQLLKAWGAHVTTTCSTD---AIPLVK----SLGAD------ 208
Query: 65 CDVTDYPQFEEAFQITLQKLGGLDIVINNAGI 96
DV DY E F+ L + G D++++ G
Sbjct: 209 -DVIDYN--NEDFEEELTERGKFDVILDTVGG 237
>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 = 32.5 bits (75), Expect = 0.026
Identities = 16/29 (55%), Positives = 16/29 (55%), Gaps = 1/29 (3%)
Query: 7 GKVALVTGGAAG-IGRAYCEELLKFGAKV 34
GKVALVTG G IG LL GA V
Sbjct: 7 GKVALVTGAGPGSIGAEVVAGLLAGGATV 35
>gnl|CDD|236342 PRK08862, PRK08862, short chain dehydrogenase; Provisional.
Length = 227
Score = 32.4 bits (74), Expect = 0.027
Identities = 22/92 (23%), Positives = 37/92 (40%), Gaps = 3/92 (3%)
Query: 3 MDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIY 62
MD+K + L+T + +GR + GA + +CD + S +D EQ N +
Sbjct: 1 MDIKSSIILITSAGSVLGRTISCHFARLGATLILCDQDQSALKDTYEQCS-ALTDNVYSF 59
Query: 63 CPCDVTDYPQFEEAFQITLQKLG-GLDIVINN 93
D F Q+ D+++NN
Sbjct: 60 QLKD-FSQESIRHLFDAIEQQFNRAPDVLVNN 90
>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 = 32.2 bits (74), Expect = 0.037
Identities = 26/94 (27%), Positives = 35/94 (37%), Gaps = 23/94 (24%)
Query: 10 ALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPCDVTD 69
L+TGG IGRA + L K G +V+I T+ P A
Sbjct: 1 ILITGGTGFIGRALTQRLTKRGHEVTIL---------------TRSPPPGANTKWEGYKP 45
Query: 70 YPQFEEAFQITLQKLGGLDIVINNAG--IFNDRF 101
+ + L G D VIN AG I + R+
Sbjct: 46 WAGEDA------DSLEGADAVINLAGEPIADKRW 73
>gnl|CDD|172654 PRK14166, PRK14166, bifunctional 5,10-methylene-tetrahydrofolate
dehydrogenase/ 5,10-methylene-tetrahydrofolate
cyclohydrolase; Provisional.
Length = 282
Score = 31.9 bits (72), Expect = 0.041
Identities = 16/37 (43%), Positives = 23/37 (62%)
Query: 3 MDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDI 39
+DL+GK A++ G + +GR LL GA VS+C I
Sbjct: 153 IDLEGKDAVIIGASNIVGRPMATMLLNAGATVSVCHI 189
>gnl|CDD|223677 COG0604, Qor, NADPH:quinone reductase and related Zn-dependent
oxidoreductases [Energy production and conversion /
General function prediction only].
Length = 326
Score = 31.9 bits (73), Expect = 0.042
Identities = 21/90 (23%), Positives = 36/90 (40%), Gaps = 11/90 (12%)
Query: 6 KGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPC 65
G+ LV G A G+G A + GA V V + + G + I
Sbjct: 142 PGETVLVHGAAGGVGSAAIQLAKALGATVVA-----VVSSSEKLELLKELGADHVI---- 192
Query: 66 DVTDYPQFEEAFQITLQKLGGLDIVINNAG 95
+ + E+ ++T K G+D+V++ G
Sbjct: 193 NYREEDFVEQVRELTGGK--GVDVVLDTVG 220
>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 = 31.8 bits (72), Expect = 0.052
Identities = 25/90 (27%), Positives = 37/90 (41%), Gaps = 3/90 (3%)
Query: 11 LVTGGAAGIGRAYCEELLKFGAKVSI-CDINDSVGEDLAEQWRTKYGPNRAIYCPCDVTD 69
LVTG + GIGRA L G ++ + S E + + + G R + DV D
Sbjct: 2 LVTGASRGIGRAIANRLAADGFEICVHYHSGRSDAESVVSAIQAQGGNARLL--QFDVAD 59
Query: 70 YPQFEEAFQITLQKLGGLDIVINNAGIFND 99
+ + + G V+ NAGI D
Sbjct: 60 RVACRTLLEADIAEHGAYYGVVLNAGITRD 89
>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 = 31.7 bits (72), Expect = 0.053
Identities = 29/111 (26%), Positives = 40/111 (36%), Gaps = 19/111 (17%)
Query: 10 ALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPCDVTD 69
AL+ G GIGRA L G ++ + + LA R P DV
Sbjct: 1 ALILGATGGIGRALARALAGRGWRLLLSGRD---AGALAGLAAEVGALAR----PADVA- 52
Query: 70 YPQFEEAFQITLQKLGGLDIVINNAGIFNDR--------FWELEVDVNLVG 112
E Q+LG LD+++ AG + W +D NL G
Sbjct: 53 ---AELEVWALAQELGPLDLLVYAAGAILGKPLARTKPAAWRRILDANLTG 100
>gnl|CDD|235608 PRK05786, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 238
Score = 31.7 bits (72), Expect = 0.054
Identities = 25/93 (26%), Positives = 42/93 (45%), Gaps = 3/93 (3%)
Query: 3 MDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIY 62
M LKGK + G + G+G A LK GA+V I N++ + + ++ +KYG Y
Sbjct: 1 MRLKGKKVAIIGVSEGLGYAVAYFALKEGAQVCINSRNENKLKRM-KKTLSKYG--NIHY 57
Query: 63 CPCDVTDYPQFEEAFQITLQKLGGLDIVINNAG 95
DV+ + + L +D ++ G
Sbjct: 58 VVGDVSSTESARNVIEKAAKVLNAIDGLVVTVG 90
>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 = 31.5 bits (72), Expect = 0.055
Identities = 25/113 (22%), Positives = 39/113 (34%), Gaps = 21/113 (18%)
Query: 7 GKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPCD 66
+V LV GG +G A + G + I DLAE + +I
Sbjct: 1 ARVVLVYGGRGALGSAVVQAFKSRGW--WVASI------DLAENEE----ADASIIVLDS 48
Query: 67 VTDYPQFEEAFQITLQKLGGLDIVINNAGIFN------DRF---WELEVDVNL 110
+ Q ++ + G +D +I AG + F W+L NL
Sbjct: 49 DSFTEQAKQVVASVARLSGKVDALICVAGGWAGGSAKSKSFVKNWDLMWKQNL 101
>gnl|CDD|187568 cd05258, CDP_TE_SDR_e, CDP-tyvelose 2-epimerase, extended (e)
SDRs. CDP-tyvelose 2-epimerase is a tetrameric SDR
that catalyzes the conversion of CDP-D-paratose to
CDP-D-tyvelose, the last step in tyvelose biosynthesis.
This subgroup is a member of the extended SDR
subfamily, with a characteristic active site tetrad and
NAD-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 = 337
Score = 31.5 bits (72), Expect = 0.064
Identities = 13/35 (37%), Positives = 15/35 (42%), Gaps = 1/35 (2%)
Query: 8 KVALVTGGAAGIGRAYCEELLKFGAKVSICDINDS 42
L+TGGA IG LK G +V D N
Sbjct: 1 MRVLITGGAGFIGSNLARFFLKQGWEVIGFD-NLM 34
>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 = 31.2 bits (71), Expect = 0.067
Identities = 13/23 (56%), Positives = 15/23 (65%)
Query: 8 KVALVTGGAAGIGRAYCEELLKF 30
KV LVTG +G+G A CE LL
Sbjct: 2 KVVLVTGANSGLGLAICERLLAE 24
>gnl|CDD|188426 TIGR03911, pyrrolys_PylD, pyrrolysine biosynthesis protein PylD.
This protein is PylD, part of a three-gene cassette that
is sufficient to direct the biosynthesis of pyrrolysine,
the twenty-second amino acid, incorporated in some
species at a UAG canonical stop codon [Amino acid
biosynthesis, Other].
Length = 266
Score = 30.9 bits (70), Expect = 0.086
Identities = 18/46 (39%), Positives = 22/46 (47%), Gaps = 1/46 (2%)
Query: 4 DLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAE 49
LK K LV G +GRA L+ G V + D N V E LA+
Sbjct: 142 GLKSKDVLVIG-LGPVGRAAAFHLVDKGFHVYVYDKNLEVSEKLAQ 186
>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 = 30.7 bits (70), Expect = 0.087
Identities = 15/33 (45%), Positives = 18/33 (54%)
Query: 11 LVTGGAAGIGRAYCEELLKFGAKVSICDINDSV 43
LVTGGA IG LL+ G +V + D D V
Sbjct: 2 LVTGGAGFIGSHLVRRLLERGHEVVVIDRLDVV 34
>gnl|CDD|240631 cd12154, FDH_GDH_like, Formate/glycerate dehydrogenases, D-specific
2-hydroxy acid dehydrogenases and related
dehydrogenases. The formate/glycerate dehydrogenase
like family contains a diverse group of enzymes such as
formate dehydrogenase (FDH), glycerate dehydrogenase
(GDH), D-lactate dehydrogenase, L-alanine dehydrogenase,
and S-Adenosylhomocysteine hydrolase, that share a
common 2-domain structure. Despite often low sequence
identity, these proteins typically have a characteristic
arrangement of 2 similar domains of the alpha/beta
Rossmann fold NAD+ binding form. The NAD(P) binding
domain is inserted within the linear sequence of the
mostly N-terminal catalytic domain. Structurally, these
domains are connected by extended alpha helices and
create a cleft in which NAD(P) is bound, primarily to
the C-terminal portion of the 2nd (internal) domain.
While many members of this family are dimeric, alanine
DH is hexameric and phosphoglycerate DH is tetrameric.
2-hydroxyacid dehydrogenases are enzymes that catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate dehydrogenase (FDH) catalyzes the NAD+-dependent
oxidation of formate ion to carbon dioxide with the
concomitant reduction of NAD+ to NADH. FDHs of this
family contain no metal ions or prosthetic groups.
Catalysis occurs though direct transfer of a hydride ion
to NAD+ without the stages of acid-base catalysis
typically found in related dehydrogenases.
Length = 310
Score = 31.0 bits (70), Expect = 0.100
Identities = 17/48 (35%), Positives = 23/48 (47%), Gaps = 1/48 (2%)
Query: 2 VMDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAE 49
D+ GK +V G +G+ + L GA+V I DIN E L E
Sbjct: 155 APDVAGKTVVVVGAGV-VGKEAAQMLRGLGAQVLITDINVEALEQLEE 201
>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 = 30.8 bits (70), Expect = 0.11
Identities = 19/47 (40%), Positives = 23/47 (48%), Gaps = 1/47 (2%)
Query: 11 LVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGP 57
LVTGGA IG +LL+ G +V I D N S G A + P
Sbjct: 3 LVTGGAGYIGSHTVRQLLESGHEVVILD-NLSNGSREALPRGERITP 48
>gnl|CDD|161904 TIGR00507, aroE, shikimate 5-dehydrogenase. This model finds
proteins from prokaryotes and functionally equivalent
domains from larger, multifunctional proteins of fungi
and plants. Below the trusted cutoff of 180, but above
the noise cutoff of 20, are the putative shikimate
dehydrogenases of Thermotoga maritima and Mycobacterium
tuberculosis, and uncharacterized paralogs of shikimate
dehydrogenase from E. coli and H. influenzae. The
related enzyme quinate 5-dehydrogenase scores below the
noise cutoff. A neighbor-joining tree, constructed with
quinate 5-dehydrogenases as the outgroup, shows the
Clamydial homolog as clustering among the shikimate
dehydrogenases, although the sequence is unusual in the
degree of sequence divergence and the presence of an
additional N-terminal domain [Amino acid biosynthesis,
Aromatic amino acid family].
Length = 270
Score = 30.5 bits (69), Expect = 0.12
Identities = 19/54 (35%), Positives = 24/54 (44%), Gaps = 6/54 (11%)
Query: 2 VMDLKGKVALVTG------GAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAE 49
V DL+ + L GA G +A ELLK V I + S E+LAE
Sbjct: 105 VSDLEQLIPLRPNQNVLIIGAGGAAKAVALELLKADCNVIIANRTVSKAEELAE 158
>gnl|CDD|240636 cd12159, 2-Hacid_dh_2, Putative D-isomer specific 2-hydroxyacid
dehydrogenases. 2-Hydroxyacid dehydrogenases catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 303
Score = 30.7 bits (70), Expect = 0.13
Identities = 16/26 (61%), Positives = 17/26 (65%), Gaps = 2/26 (7%)
Query: 9 VALVTGGAAGIGRAYCEELLKFGAKV 34
VA+V GA GIGRA L FGAKV
Sbjct: 128 VAIV--GAGGIGRALIPLLAPFGAKV 151
>gnl|CDD|240644 cd12167, 2-Hacid_dh_8, Putative D-isomer specific 2-hydroxyacid
dehydrogenases. 2-Hydroxyacid dehydrogenases catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 330
Score = 30.6 bits (70), Expect = 0.13
Identities = 13/31 (41%), Positives = 16/31 (51%), Gaps = 2/31 (6%)
Query: 8 KVALVTGGAAGIGRAYCEELLKFGAKVSICD 38
V +V G IGRA E L FG +V + D
Sbjct: 152 TVGIV--GFGRIGRAVVELLRPFGLRVLVYD 180
>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 = 30.7 bits (70), Expect = 0.13
Identities = 13/31 (41%), Positives = 18/31 (58%)
Query: 8 KVALVTGGAAGIGRAYCEELLKFGAKVSICD 38
K L+TGGA +G C+ LL+ G +V D
Sbjct: 1 KRILITGGAGFLGSHLCDRLLEDGHEVICVD 31
>gnl|CDD|235694 PRK06079, PRK06079, enoyl-(acyl carrier protein) reductase;
Provisional.
Length = 252
Score = 30.5 bits (69), Expect = 0.15
Identities = 24/93 (25%), Positives = 37/93 (39%), Gaps = 7/93 (7%)
Query: 1 MVMDLKGKVALVTGGAAGIGRAY-C-EELLKFGAKVSICDINDSVGEDLAEQWRTKYGPN 58
M L GK +V G A A+ C + + GA V ND + + L K
Sbjct: 1 MSGILSGKKIVVMGVANKRSIAWGCAQAIKDQGATVIYTYQNDRMKKSL-----QKLVDE 55
Query: 59 RAIYCPCDVTDYPQFEEAFQITLQKLGGLDIVI 91
+ CDV E AF +++G +D ++
Sbjct: 56 EDLLVECDVASDESIERAFATIKERVGKIDGIV 88
>gnl|CDD|205018 pfam12683, DUF3798, Protein of unknown function (DUF3798). This
family of proteins is functionally uncharacterized. This
family of proteins is found in bacteria. Proteins in
this family are typically between 247 and 417 amino
acids in length. Most of the proteins in this family
have an N-terminal lipoprotein attachment site. These
proteins have distant similarity to periplasmic ligand
binding families such as pfam02608, which suggests that
this family have a similar role.
Length = 275
Score = 30.4 bits (69), Expect = 0.17
Identities = 16/63 (25%), Positives = 25/63 (39%), Gaps = 10/63 (15%)
Query: 24 CEEL-LKFGAKVSICDINDSVGEDLAEQ--------WRTKYGPNRAIYCPCDVTDYPQFE 74
C++L L+F +V+ D G A+Q KYG + A + D P +
Sbjct: 159 CKDLGLEF-VEVTAPDPTSDAGVSGAQQFILEDIPRQIKKYGKDTAFFGTNDAMQEPLIK 217
Query: 75 EAF 77
A
Sbjct: 218 AAL 220
>gnl|CDD|224012 COG1087, GalE, UDP-glucose 4-epimerase [Cell envelope biogenesis,
outer membrane].
Length = 329
Score = 30.2 bits (69), Expect = 0.17
Identities = 14/28 (50%), Positives = 17/28 (60%)
Query: 11 LVTGGAAGIGRAYCEELLKFGAKVSICD 38
LVTGGA IG +LLK G +V + D
Sbjct: 4 LVTGGAGYIGSHTVRQLLKTGHEVVVLD 31
>gnl|CDD|226351 COG3830, COG3830, ACT domain-containing protein [Signal
transduction mechanisms].
Length = 90
Score = 29.2 bits (66), Expect = 0.18
Identities = 9/36 (25%), Positives = 16/36 (44%), Gaps = 1/36 (2%)
Query: 63 CPCDVTDYPQFEEAFQITLQKLGGLDIVINNAGIFN 98
+V D+ + +KLG +D+ + IFN
Sbjct: 51 ISKEVVDFAALRDELAAEGKKLG-VDVRVQREDIFN 85
>gnl|CDD|227299 COG4964, CpaC, Flp pilus assembly protein, secretin CpaC
[Intracellular trafficking and secretion].
Length = 455
Score = 30.0 bits (68), Expect = 0.19
Identities = 9/65 (13%), Positives = 18/65 (27%), Gaps = 3/65 (4%)
Query: 33 KVSICDINDSVGEDLAEQWRTKYGPNRAIYCPCDVTDYPQFEEAFQITLQKLGGLDIVIN 92
KV + +++ SV + L + G + + G + N
Sbjct: 174 KVRVVEVSRSVLKQLGANLSARGGFSGGPV---SFGALAVLGTGLGLEKGTTFGSLLSDN 230
Query: 93 NAGIF 97
I
Sbjct: 231 GVSID 235
>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 = 29.8 bits (67), Expect = 0.20
Identities = 29/104 (27%), Positives = 41/104 (39%), Gaps = 20/104 (19%)
Query: 11 LVTGGAAGIGRAYCEELLKFGAKVSICDINDS-VGEDLAEQWRTKYGPNRAIYCPCDVTD 69
++TG A+GIG A E L G V D+ ++ V DL T G AI
Sbjct: 3 VITGAASGIGAATAELLEDAGHTVIGIDLREADVIADL----STPEGRAAAIA------- 51
Query: 70 YPQFEEAFQITLQKLGGLDIVINNAGIFNDRFWELEVDVNLVGT 113
+ + G LD ++N AG+ L + VN G
Sbjct: 52 --------DVLARCSGVLDGLVNCAGVGGTTVAGLVLKVNYFGL 87
>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 = 29.5 bits (67), Expect = 0.24
Identities = 19/86 (22%), Positives = 30/86 (34%), Gaps = 23/86 (26%)
Query: 10 ALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPCDVTD 69
+V G IG A + L G +V G + Y D+TD
Sbjct: 1 IIVIGATGTIGLAVAQLLSAHGHEV------------------ITAGRSSGDY-QVDITD 41
Query: 70 YPQFEEAFQITLQKLGGLDIVINNAG 95
+ F +K+G D +++ AG
Sbjct: 42 EASIKALF----EKVGHFDAIVSTAG 63
>gnl|CDD|181162 PRK07904, PRK07904, short chain dehydrogenase; Provisional.
Length = 253
Score = 29.7 bits (67), Expect = 0.28
Identities = 26/94 (27%), Positives = 38/94 (40%), Gaps = 10/94 (10%)
Query: 11 LVTGGAAGIGRAYCEELLKFG-AKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPCDVTD 69
L+ GG + IG A CE LK A+V + + D D A G + D D
Sbjct: 12 LLLGGTSEIGLAICERYLKNAPARVVLAALPDDPRRDAAVAQMKAAGASSVEVIDFDALD 71
Query: 70 ---YPQ-FEEAFQITLQKLGGLDIVINNAGIFND 99
+P+ + AF G +D+ I G+ D
Sbjct: 72 TDSHPKVIDAAFA-----GGDVDVAIVAFGLLGD 100
>gnl|CDD|184555 PRK14183, PRK14183, bifunctional 5,10-methylene-tetrahydrofolate
dehydrogenase/ 5,10-methylene-tetrahydrofolate
cyclohydrolase; Provisional.
Length = 281
Score = 29.4 bits (66), Expect = 0.30
Identities = 16/47 (34%), Positives = 22/47 (46%), Gaps = 3/47 (6%)
Query: 3 MDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAE 49
+D+KGK V G + +G+ LL A V IC I +DL
Sbjct: 153 IDVKGKDVCVVGASNIVGKPMAALLLNANATVDICHI---FTKDLKA 196
>gnl|CDD|239786 cd04253, AAK_UMPK-PyrH-Pf, AAK_UMPK-PyrH-Pf: UMP kinase
(UMPK)-Pf, the mostly archaeal uridine monophosphate
kinase (uridylate kinase) enzymes that catalyze UMP
phosphorylation and play a key role in pyrimidine
nucleotide biosynthesis; regulation of this process is
via feed-back control and via gene repression of
carbamoyl phosphate synthetase (the first enzyme of the
pyrimidine biosynthesis pathway). The UMP kinase of
Pyrococcus furiosus (Pf) is known to function as a
homohexamer, with GTP and UTP being allosteric
effectors. Like other related enzymes (carbamate
kinase, aspartokinase, and N-acetylglutamate kinase)
the E. coli and most bacterial UMPKs have a conserved,
N-terminal, lysine residue proposed to function in the
catalysis of the phosphoryl group transfer, whereas
most archaeal UMPKs (this CD) appear to lack this
residue and the Pyrococcus furiosus structure has an
additional Mg ion bound to the ATP molecule which is
proposed to function as the catalysis instead. Members
of this CD belong to the Amino Acid Kinase Superfamily
(AAK).
Length = 221
Score = 29.1 bits (66), Expect = 0.32
Identities = 12/34 (35%), Positives = 15/34 (44%), Gaps = 1/34 (2%)
Query: 5 LKGKVALVTGGAAGIGRAYCEELLKFGAKVSICD 38
KVA+V GG + R Y K GA + D
Sbjct: 32 DGHKVAVVVGGG-RLAREYISVARKLGASEAFLD 64
>gnl|CDD|187558 cd05247, UDP_G4E_1_SDR_e, UDP-glucose 4 epimerase, subgroup 1,
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 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 = 323
Score = 29.4 bits (67), Expect = 0.34
Identities = 14/28 (50%), Positives = 16/28 (57%)
Query: 11 LVTGGAAGIGRAYCEELLKFGAKVSICD 38
LVTGGA IG ELL+ G V + D
Sbjct: 3 LVTGGAGYIGSHTVVELLEAGYDVVVLD 30
>gnl|CDD|225885 COG3349, COG3349, Uncharacterized conserved protein [Function
unknown].
Length = 485
Score = 29.3 bits (66), Expect = 0.34
Identities = 15/46 (32%), Positives = 22/46 (47%), Gaps = 3/46 (6%)
Query: 8 KVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRT 53
+VA+ G AG+ AY EL G V++ + D +G WR
Sbjct: 2 RVAIAGAGLAGLAAAY--ELADAGYDVTLYEARDRLG-GKVASWRD 44
>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 = 29.2 bits (66), Expect = 0.35
Identities = 13/41 (31%), Positives = 17/41 (41%), Gaps = 1/41 (2%)
Query: 11 LVTGGAAGIGRAYCEELLKFGAKVS-ICDINDSVGEDLAEQ 50
LVTG IG E LL+ G +V + N L +
Sbjct: 3 LVTGADGFIGSHLTERLLREGHEVRALDIYNSFNSWGLLDN 43
>gnl|CDD|184464 PRK14031, PRK14031, glutamate dehydrogenase; Provisional.
Length = 444
Score = 29.1 bits (65), Expect = 0.42
Identities = 15/39 (38%), Positives = 23/39 (58%), Gaps = 1/39 (2%)
Query: 3 MDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDIND 41
DLKGKV LV+ G+ + + E++L+ G KV +D
Sbjct: 224 TDLKGKVCLVS-GSGNVAQYTAEKVLELGGKVVTMSDSD 261
>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 = 28.9 bits (65), Expect = 0.43
Identities = 26/104 (25%), Positives = 37/104 (35%), Gaps = 16/104 (15%)
Query: 11 LVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPCDVTDY 70
LVTG A G+GR L V D D + P + Y D+ D
Sbjct: 2 LVTGAAGGLGRLLARRLAASPR-VIGVDGLDRRRPPGS--------PPKVEYVRLDIRD- 51
Query: 71 PQFEEAFQITLQKLGGLDIVINNAGIFNDRFWELEV-DVNLVGT 113
P + F+ D V++ A I + E +N+ GT
Sbjct: 52 PAAADVFRER-----EADAVVHLAFILDPPRDGAERHRINVDGT 90
>gnl|CDD|184559 PRK14189, PRK14189, bifunctional 5,10-methylene-tetrahydrofolate
dehydrogenase/ 5,10-methylene-tetrahydrofolate
cyclohydrolase; Provisional.
Length = 285
Score = 28.9 bits (65), Expect = 0.45
Identities = 18/50 (36%), Positives = 26/50 (52%), Gaps = 3/50 (6%)
Query: 3 MDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWR 52
+ L+G A+V G + +G+ LL+ GA V+IC S DLA R
Sbjct: 154 IPLRGAHAVVIGRSNIVGKPMAMLLLQAGATVTIC---HSKTRDLAAHTR 200
>gnl|CDD|187657 cd08954, KR_1_FAS_SDR_x, beta-ketoacyl reductase (KR) domain of
fatty acid synthase (FAS), subgroup 1, complex (x) SDRs.
NADP-dependent KR domain of the multidomain type I FAS,
a complex SDR family. This subfamily also includes
proteins identified as polyketide synthase (PKS), a
protein with related modular protein architecture and
similar function. It includes the KR domains of
mammalian and chicken FAS, and Dictyostelium discoideum
putative polyketide synthases (PKSs). These KR domains
contain two subdomains, each of which is related to SDR
Rossmann fold domains. However, while the C-terminal
subdomain has an active site similar to the other SDRs
and a NADP-binding capability, the N-terminal SDR-like
subdomain is truncated and lacks these functions,
serving a supportive structural role. In some instances,
such as porcine FAS, an enoyl reductase (a Rossman fold
NAD-binding domain of the medium-chain
dehydrogenase/reductase, MDR family) module is inserted
between the sub-domains. Fatty acid synthesis occurs via
the stepwise elongation of a chain (which is attached to
acyl carrier protein, ACP) with 2-carbon units.
Eukaryotic systems consists of large, multifunctional
synthases (type I) while bacterial, type II systems, use
single function proteins. Fungal fatty acid synthesis
uses 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-ketoacyl reductase (KR), forming
beta-hydroxyacyl-ACP, which is in turn dehydrated by
dehydratase to a beta-enoyl intermediate, which is
reduced by NADP-dependent beta-enoyl reductase (ER);
this KR and ER are members of the SDR family. This KR
subfamily has an active site tetrad with a similar 3D
orientation compared to archetypical SDRs, but the
active site Lys and Asn residue positions are swapped.
The characteristic NADP-binding is typical of the
multidomain complex SDRs, with a GGXGXXG NADP 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
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 = 452
Score = 29.0 bits (65), Expect = 0.46
Identities = 27/103 (26%), Positives = 47/103 (45%), Gaps = 14/103 (13%)
Query: 7 GKVALVTGGAAGIGRAYCEELLKFGAKVSI------CDINDSVGEDLAEQWRTKYGPNRA 60
GK L+TGG+ G+G + L+K GA +I + E L +W+++ N
Sbjct: 218 GKSYLITGGSGGLGLEILKWLVKRGAVENIIILSRSGMKWEL--ELLIREWKSQ---NIK 272
Query: 61 IYCP-CDVTDYPQFEEAF-QITL-QKLGGLDIVINNAGIFNDR 100
+ DV+D E+A I K+G + + + A + D+
Sbjct: 273 FHFVSVDVSDVSSLEKAINLILNAPKIGPIGGIFHLAFVLIDK 315
>gnl|CDD|179571 PRK03369, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
synthetase; Provisional.
Length = 488
Score = 28.9 bits (65), Expect = 0.49
Identities = 18/47 (38%), Positives = 25/47 (53%), Gaps = 3/47 (6%)
Query: 5 LKGKVALVTGGAAGI-GRAYCEELLKFGAKVSICDINDSVGEDLAEQ 50
L G LV G AG+ GRA L +FGA+ ++CD + AE+
Sbjct: 10 LPGAPVLVAG--AGVTGRAVLAALTRFGARPTVCDDDPDALRPHAER 54
>gnl|CDD|240652 cd12175, 2-Hacid_dh_11, Putative D-isomer specific 2-hydroxyacid
dehydrogenases, NAD-binding and catalytic domains.
2-Hydroxyacid dehydrogenases catalyze the conversion of
a wide variety of D-2-hydroxy acids to their
corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 311
Score = 28.7 bits (65), Expect = 0.51
Identities = 17/55 (30%), Positives = 25/55 (45%), Gaps = 6/55 (10%)
Query: 2 VMDLKGK-VALVTGGAAGIGRAYCEELLKFGAKVSICDI---NDSVGEDLAEQWR 52
+L GK V +V G IGRA L FG +V D ++ +DL ++
Sbjct: 137 SRELSGKTVGIV--GLGNIGRAVARRLRGFGVEVIYYDRFRDPEAEEKDLGVRYV 189
>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 = 28.8 bits (65), Expect = 0.53
Identities = 26/92 (28%), Positives = 37/92 (40%), Gaps = 18/92 (19%)
Query: 6 KGKVALVTGGAAGIGRAYCEELLK-FGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCP 64
KG LVTG G+G + +L K GA+V I + + + +
Sbjct: 162 KGDTVLVTGAGGGVG-IHAIQLAKALGARV----IAVTRSPEKLKILKELGAD------- 209
Query: 65 CDVTDYPQFEEAFQITLQKLGGLDIVINNAGI 96
V D +F E +KLGG D+VI G
Sbjct: 210 -YVIDGSKFSEDV----KKLGGADVVIELVGS 236
>gnl|CDD|172666 PRK14178, PRK14178, bifunctional 5,10-methylene-tetrahydrofolate
dehydrogenase/ 5,10-methylene-tetrahydrofolate
cyclohydrolase; Provisional.
Length = 279
Score = 28.7 bits (64), Expect = 0.65
Identities = 17/50 (34%), Positives = 25/50 (50%), Gaps = 3/50 (6%)
Query: 3 MDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWR 52
+ + GK A+V G + +GR LL A V+IC S E+L + R
Sbjct: 148 ISIAGKRAVVVGRSIDVGRPMAALLLNADATVTIC---HSKTENLKAELR 194
>gnl|CDD|139246 PRK12814, PRK12814, putative NADPH-dependent glutamate synthase
small subunit; Provisional.
Length = 652
Score = 28.5 bits (64), Expect = 0.66
Identities = 16/37 (43%), Positives = 22/37 (59%), Gaps = 2/37 (5%)
Query: 8 KVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVG 44
KVA++ G AG+ AY LL+ G V+I D N+ G
Sbjct: 195 KVAIIGAGPAGLTAAY--YLLRKGHDVTIFDANEQAG 229
>gnl|CDD|224562 COG1648, CysG, Siroheme synthase (precorrin-2
oxidase/ferrochelatase domain) [Coenzyme metabolism].
Length = 210
Score = 28.4 bits (64), Expect = 0.69
Identities = 16/47 (34%), Positives = 25/47 (53%), Gaps = 5/47 (10%)
Query: 4 DLKGKVALVTG-GAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAE 49
DL+GK LV G G+ + +A LLK GA V++ ++ +L
Sbjct: 9 DLEGKKVLVVGGGSVALRKA--RLLLKAGADVTV--VSPEFEPELKA 51
>gnl|CDD|223842 COG0771, MurD, UDP-N-acetylmuramoylalanine-D-glutamate ligase
[Cell envelope biogenesis, outer membrane].
Length = 448
Score = 28.4 bits (64), Expect = 0.70
Identities = 16/40 (40%), Positives = 21/40 (52%), Gaps = 1/40 (2%)
Query: 1 MVMDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDIN 40
M+ D +GK LV G G A LLK GA+V++ D
Sbjct: 1 MMEDFQGKKVLVLGLGKS-GLAAARFLLKLGAEVTVSDDR 39
>gnl|CDD|180596 PRK06505, PRK06505, enoyl-(acyl carrier protein) reductase;
Provisional.
Length = 271
Score = 28.2 bits (63), Expect = 0.73
Identities = 28/105 (26%), Positives = 47/105 (44%), Gaps = 20/105 (19%)
Query: 5 LKGKVALVTGGAA------GIGRAYCEELLKFGAKVSICDINDSVG---EDLAEQWRTKY 55
++GK L+ G A GI + L GA+++ +++G + LAE +
Sbjct: 5 MQGKRGLIMGVANDHSIAWGIAKQ----LAAQGAELAFTYQGEALGKRVKPLAESLGSD- 59
Query: 56 GPNRAIYCPCDVTDYPQFEEAFQITLQKLGGLDIVINNAGIFNDR 100
PCDV D + F+ +K G LD V++ G F+D+
Sbjct: 60 -----FVLPCDVEDIASVDAVFEALEKKWGKLDFVVHAIG-FSDK 98
>gnl|CDD|133443 cd01065, NAD_bind_Shikimate_DH, NAD(P) binding domain of
Shikimate dehydrogenase. Shikimate dehydrogenase (DH)
is an amino acid DH family member. Shikimate pathway
links metabolism of carbohydrates to de novo
biosynthesis of aromatic amino acids, quinones and
folate. It is essential in plants, bacteria, and fungi
but absent in mammals, thus making enzymes involved in
this pathway ideal targets for broad spectrum
antibiotics and herbicides. Shikimate DH catalyzes the
reduction of 3-hydroshikimate to shikimate using the
cofactor NADH. Amino acid DH-like NAD(P)-binding
domains are members of the Rossmann fold superfamily
and include glutamate, leucine, and phenylalanine DHs,
methylene tetrahydrofolate DH,
methylene-tetrahydromethanopterin DH,
methylene-tetrahydropholate DH/cyclohydrolase,
Shikimate DH-like proteins, malate oxidoreductases, and
glutamyl tRNA reductase. Amino acid DHs catalyze the
deamination of amino acids to keto acids with NAD(P)+
as a cofactor. The NAD(P)-binding Rossmann fold
superfamily includes a wide variety of protein families
including NAD(P)- binding domains of alcohol DHs,
tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate DH, lactate/malate DHs,
formate/glycerate DHs, siroheme synthases,
6-phosphogluconate DHs, amino acid DHs, repressor rex,
NAD-binding potassium channel domain, CoA-binding, and
ornithine cyclodeaminase-like domains. These domains
have an alpha-beta-alpha configuration. NAD binding
involves numerous hydrogen and van der Waals contacts.
Length = 155
Score = 28.0 bits (63), Expect = 0.77
Identities = 22/90 (24%), Positives = 33/90 (36%), Gaps = 19/90 (21%)
Query: 4 DLKGKVALVTGGAAGIGRAYCEELLKFGA-KVSICDINDSVGEDLAEQWRTKYGPNRAIY 62
+LKGK L+ G A G RA L + GA K+ I + + LAE++
Sbjct: 16 ELKGKKVLILG-AGGAARAVAYALAELGAAKIVIVNRTLEKAKALAERFGEL-------G 67
Query: 63 CPCDVTDYPQFEEAFQITLQKLGGLDIVIN 92
D + D++IN
Sbjct: 68 IAIAYLDLEELLAEA----------DLIIN 87
>gnl|CDD|235914 PRK07041, PRK07041, short chain dehydrogenase; Provisional.
Length = 230
Score = 28.1 bits (63), Expect = 0.84
Identities = 25/85 (29%), Positives = 34/85 (40%), Gaps = 8/85 (9%)
Query: 11 LVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPCDVTDY 70
LV GG++GIG A GA+V+I + + LA R G D+TD
Sbjct: 1 LVVGGSSGIGLALARAFAAEGARVTIASRSR---DRLAAAARALGGGAPVRTAALDITDE 57
Query: 71 PQFEEAFQITLQKLGGLD-IVINNA 94
+ F G D +VI A
Sbjct: 58 AAVDAFFAEA----GPFDHVVITAA 78
>gnl|CDD|235977 PRK07233, PRK07233, hypothetical protein; Provisional.
Length = 434
Score = 28.3 bits (64), Expect = 0.85
Identities = 15/37 (40%), Positives = 24/37 (64%), Gaps = 2/37 (5%)
Query: 8 KVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVG 44
K+A+V GG AG+ AY L K G +V++ + +D +G
Sbjct: 1 KIAIVGGGIAGLAAAY--RLAKRGHEVTVFEADDQLG 35
>gnl|CDD|180789 PRK06997, PRK06997, enoyl-(acyl carrier protein) reductase;
Provisional.
Length = 260
Score = 28.2 bits (63), Expect = 0.87
Identities = 27/97 (27%), Positives = 45/97 (46%), Gaps = 13/97 (13%)
Query: 5 LKGKVALVTGG------AAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPN 58
L GK L+TG A GI +A E GA+++ + D + + E + ++G +
Sbjct: 4 LAGKRILITGLLSNRSIAYGIAKACKRE----GAELAFTYVGDRFKDRITE-FAAEFGSD 58
Query: 59 RAIYCPCDVTDYPQFEEAFQITLQKLGGLDIVINNAG 95
+ PCDV Q + F Q GLD ++++ G
Sbjct: 59 --LVFPCDVASDEQIDALFASLGQHWDGLDGLVHSIG 93
>gnl|CDD|176215 cd08253, zeta_crystallin, Zeta-crystallin with NADP-dependent
quinone reductase activity (QOR). Zeta-crystallin is a
eye lens protein with NADP-dependent quinone reductase
activity (QOR). It has been cited as a structural
component in mammalian eyes, but also has homology to
quinone reductases in unrelated species. QOR catalyzes
the conversion of a quinone and NAD(P)H to a
hydroquinone and 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.
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.
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 = 27.9 bits (63), Expect = 0.92
Identities = 10/30 (33%), Positives = 15/30 (50%)
Query: 5 LKGKVALVTGGAAGIGRAYCEELLKFGAKV 34
G+ LV GG+ +G A + GA+V
Sbjct: 143 KAGETVLVHGGSGAVGHAAVQLARWAGARV 172
>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 = 28.1 bits (63), Expect = 0.96
Identities = 34/113 (30%), Positives = 45/113 (39%), Gaps = 19/113 (16%)
Query: 11 LVTGGAAGIGRAYCEELLKFGAKV-SICDINDSVGEDLAEQWRTKYG-PNRAIYCPCDVT 68
LVTG A IG + LL+ G +V I ++ND L E G + D+
Sbjct: 4 LVTGAAGFIGFHVAKRLLERGDEVVGIDNLNDYYDVRLKEARLELLGKSGGFKFVKGDLE 63
Query: 69 DYPQFEEAFQITLQKLGGLDIVIN---NAGIFNDRFWELE-----VDVNLVGT 113
D F K D VI+ AG+ R+ LE VD N+VG
Sbjct: 64 DREALRRLF-----KDHEFDAVIHLAAQAGV---RY-SLENPHAYVDSNIVGF 107
>gnl|CDD|182639 PRK10675, PRK10675, UDP-galactose-4-epimerase; Provisional.
Length = 338
Score = 28.2 bits (63), Expect = 0.98
Identities = 14/28 (50%), Positives = 17/28 (60%)
Query: 11 LVTGGAAGIGRAYCEELLKFGAKVSICD 38
LVTGG+ IG C +LL+ G V I D
Sbjct: 4 LVTGGSGYIGSHTCVQLLQNGHDVVILD 31
>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 = 27.8 bits (62), Expect = 1.1
Identities = 12/32 (37%), Positives = 13/32 (40%)
Query: 8 KVALVTGGAAGIGRAYCEELLKFGAKVSICDI 39
+ ALVTG IG E L G V D
Sbjct: 1 QRALVTGAGGFIGSHLAERLKAEGHYVRGADW 32
>gnl|CDD|151953 pfam11516, DUF3220, Protein of unknown function (DUF3120). This
family of proteins with unknown function appears to be
restricted to Bordetella.
Length = 106
Score = 27.1 bits (59), Expect = 1.2
Identities = 15/51 (29%), Positives = 25/51 (49%), Gaps = 5/51 (9%)
Query: 41 DSVGEDLAEQWRTKYG-PNRAIYCPCDVTDYPQFEEAFQITLQKLGGLDIV 90
D++ L QW ++G P A DV PQ++E + ++ GLD +
Sbjct: 60 DALYSHLEAQWAKQHGTPPTA----SDVAGMPQWQEYTAMLRERFAGLDTI 106
>gnl|CDD|206040 pfam13869, NUDIX_2, Nucleotide hydrolase. Nudix hydrolases are
found in all classes of organism and hydrolyse a wide
range of organic pyrophosphates, including nucleoside
di- and triphosphates, di-nucleoside and
diphospho-inositol polyphosphates, nucleotide sugars and
RNA caps, with varying degrees of substrate specificity.
Length = 188
Score = 27.6 bits (62), Expect = 1.3
Identities = 11/41 (26%), Positives = 19/41 (46%)
Query: 43 VGEDLAEQWRTKYGPNRAIYCPCDVTDYPQFEEAFQITLQK 83
VGE L E WR + + Y P +T + + + + L +
Sbjct: 107 VGECLGEWWRPNFETSMYPYLPAHITKPKECIKLYLVQLPE 147
>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 = 27.7 bits (62), Expect = 1.4
Identities = 25/90 (27%), Positives = 38/90 (42%), Gaps = 13/90 (14%)
Query: 6 KGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPC 65
G LV G A G+G + GA+V + D +D E LA++
Sbjct: 134 PGDTVLVLG-AGGVGLLAAQLAKAAGARVIVTDRSDEKLE-LAKELGA-----------D 180
Query: 66 DVTDYPQFEEAFQITLQKLGGLDIVINNAG 95
V DY + + ++ L GG D+VI+ G
Sbjct: 181 HVIDYKEEDLEEELRLTGGGGADVVIDAVG 210
>gnl|CDD|169389 PRK08339, PRK08339, short chain dehydrogenase; Provisional.
Length = 263
Score = 27.5 bits (61), Expect = 1.5
Identities = 13/34 (38%), Positives = 18/34 (52%)
Query: 3 MDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSI 36
+DL GK+A T + GIG L + GA V +
Sbjct: 4 IDLSGKLAFTTASSKGIGFGVARVLARAGADVIL 37
>gnl|CDD|133446 cd01078, NAD_bind_H4MPT_DH, NADP binding domain of methylene
tetrahydromethanopterin dehydrogenase. Methylene
Tetrahydromethanopterin Dehydrogenase (H4MPT DH) NADP
binding domain. NADP-dependent H4MPT DH catalyzes the
dehydrogenation of methylene- H4MPT and
methylene-tetrahydrofolate (H4F) with NADP+ as
cofactor. H4F and H4MPT are both cofactors that carry
the one-carbon units between the formyl and methyl
oxidation level. H4F and H4MPT are structurally
analogous to each other with respect to the pterin
moiety, but each has distinct side chain. H4MPT is
present only in anaerobic methanogenic archaea and
aerobic methylotrophic proteobacteria. H4MPT seems to
have evolved independently from H4F and functions as a
distinct carrier in C1 metabolism. Amino acid DH-like
NAD(P)-binding domains are members of the Rossmann fold
superfamily and include glutamate, leucine, and
phenylalanine DHs, methylene tetrahydrofolate DH,
methylene-tetrahydromethanopterin DH,
methylene-tetrahydropholate DH/cyclohydrolase,
Shikimate DH-like proteins, malate oxidoreductases, and
glutamyl tRNA reductase. Amino acid DHs catalyze the
deamination of amino acids to keto acids with NAD(P)+
as a cofactor. The NAD(P)-binding Rossmann fold
superfamily includes a wide variety of protein families
including NAD(P)- binding domains of alcohol DHs,
tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate DH, lactate/malate DHs,
formate/glycerate DHs, siroheme synthases,
6-phosphogluconate DH, amino acid DHs, repressor rex,
NAD-binding potassium channel domain, CoA-binding, and
ornithine cyclodeaminase-like domains. These domains
have an alpha-beta-alpha configuration. NAD binding
involves numerous hydrogen and van der Waals contacts.
Length = 194
Score = 27.4 bits (61), Expect = 1.5
Identities = 15/37 (40%), Positives = 21/37 (56%)
Query: 1 MVMDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSIC 37
M DLKGK A+V GG +G+ L + GA+V +
Sbjct: 22 MGKDLKGKTAVVLGGTGPVGQRAAVLLAREGARVVLV 58
>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 = 27.5 bits (61), Expect = 1.6
Identities = 23/92 (25%), Positives = 37/92 (40%), Gaps = 8/92 (8%)
Query: 11 LVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPCDVTDY 70
+TG + G+G A LL G +V + + D P A D++
Sbjct: 11 FITGSSDGLGLAAARTLLHQGHEVVLHARSQKRAADAKAA-----CPGAAGVLIGDLSSL 65
Query: 71 PQFEE-AFQITLQKLGGLDIVINNAGIFNDRF 101
+ + A Q+ +G D VI+NAGI +
Sbjct: 66 AETRKLADQV--NAIGRFDAVIHNAGILSGPN 95
>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 = 27.5 bits (61), Expect = 1.7
Identities = 29/119 (24%), Positives = 48/119 (40%), Gaps = 20/119 (16%)
Query: 8 KVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYG--PNRAIYCPC 65
++TG ++G+G A + L + G + D + AEQ + G + C
Sbjct: 2 GTVVITGASSGLGLAAAKALARRGEWHVVMACRDFLK---AEQAAQEVGMPKDSYSVLHC 58
Query: 66 DVTDYP---QFEEAFQITLQKLGGLDIVINNAGI---------FNDRFWELEVDVNLVG 112
D+ QF + F+ T LD ++ NA + F +EL V VN +G
Sbjct: 59 DLASLDSVRQFVDNFRRT---GRPLDALVCNAAVYLPTAKEPRFTADGFELTVGVNHLG 114
>gnl|CDD|224013 COG1088, RfbB, dTDP-D-glucose 4,6-dehydratase [Cell envelope
biogenesis, outer membrane].
Length = 340
Score = 27.2 bits (61), Expect = 1.8
Identities = 9/26 (34%), Positives = 12/26 (46%)
Query: 11 LVTGGAAGIGRAYCEELLKFGAKVSI 36
LVTGGA IG + +L +
Sbjct: 4 LVTGGAGFIGSNFVRYILNKHPDDHV 29
>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 = 27.1 bits (60), Expect = 1.9
Identities = 15/35 (42%), Positives = 18/35 (51%), Gaps = 1/35 (2%)
Query: 10 ALVTGGAAGIGRAYCEELLKFGA-KVSICDINDSV 43
LVTGG+ GIG A L G+ KV + D V
Sbjct: 1 VLVTGGSGGIGGAIARWLASRGSPKVLVVSRRDVV 35
>gnl|CDD|172679 PRK14191, PRK14191, bifunctional 5,10-methylene-tetrahydrofolate
dehydrogenase/ 5,10-methylene-tetrahydrofolate
cyclohydrolase; Provisional.
Length = 285
Score = 27.0 bits (60), Expect = 2.1
Identities = 12/37 (32%), Positives = 22/37 (59%)
Query: 3 MDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDI 39
+++KGK ++ G + +G+ +L GA VS+C I
Sbjct: 153 IEIKGKDVVIIGASNIVGKPLAMLMLNAGASVSVCHI 189
>gnl|CDD|130536 TIGR01470, cysG_Nterm, siroheme synthase, N-terminal domain.
This model represents a subfamily of CysG N-terminal
region-related sequences. All sequences in the seed
alignment for this model are N-terminal regions of
known or predicted siroheme synthases. The C-terminal
region of each is uroporphyrin-III C-methyltransferase
(EC 2.1.1.107), which catalyzes the first step
committed to the biosynthesis of either siroheme or
cobalamin (vitamin B12) rather than protoheme (heme).
The region represented by this model completes the
process of oxidation and iron insertion to yield
siroheme. Siroheme is a cofactor for nitrite and
sulfite reductases, so siroheme synthase is CysG of
cysteine biosynthesis in some organisms [Biosynthesis
of cofactors, prosthetic groups, and carriers, Heme,
porphyrin, and cobalamin].
Length = 205
Score = 27.0 bits (60), Expect = 2.1
Identities = 11/33 (33%), Positives = 17/33 (51%), Gaps = 1/33 (3%)
Query: 4 DLKGKVALVTGGAAGIGRAYCEELLKFGAKVSI 36
+L+G+ LV GG LLK GA++ +
Sbjct: 6 NLEGRAVLVVGGGDV-ALRKARLLLKAGAQLRV 37
>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 = 26.9 bits (60), Expect = 2.1
Identities = 10/23 (43%), Positives = 12/23 (52%)
Query: 12 VTGGAAGIGRAYCEELLKFGAKV 34
VTG IG A EL+ G +V
Sbjct: 5 VTGATGFIGSAVVRELVAAGHEV 27
>gnl|CDD|236760 PRK10792, PRK10792, bifunctional 5,10-methylene-tetrahydrofolate
dehydrogenase/ 5,10-methylene-tetrahydrofolate
cyclohydrolase; Provisional.
Length = 285
Score = 26.8 bits (60), Expect = 2.2
Identities = 13/34 (38%), Positives = 18/34 (52%)
Query: 4 DLKGKVALVTGGAAGIGRAYCEELLKFGAKVSIC 37
D G A+V G + +GR ELL G V++C
Sbjct: 156 DTYGLNAVVVGASNIVGRPMSLELLLAGCTVTVC 189
>gnl|CDD|187652 cd08948, 5beta-POR_like_SDR_a, progesterone 5-beta-reductase-like
proteins (5beta-POR), atypical (a) SDRs. 5beta-POR
catalyzes the reduction of progesterone to
5beta-pregnane-3,20-dione in Digitalis plants. This
subgroup of atypical-extended SDRs, shares the
structure of an extended SDR, but has a different
glycine-rich nucleotide binding motif (GXXGXXG) and
lacks the YXXXK active site motif of classical and
extended SDRs. Tyr-179 and Lys 147 are present in the
active site, but not in the usual SDR configuration.
Given these differences, it has been proposed that this
subfamily represents a new SDR class. Other atypical
SDRs include biliverdin IX beta reductase (BVR-B,aka
flavin reductase), NMRa (a negative transcriptional
regulator of various fungi), 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 = 308
Score = 26.8 bits (60), Expect = 2.2
Identities = 13/22 (59%), Positives = 13/22 (59%), Gaps = 2/22 (9%)
Query: 9 VALVTGGAAGI-GRAYCEELLK 29
VALV G A GI G A E LL
Sbjct: 1 VALVVG-ATGISGWALVEHLLS 21
>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 = 26.9 bits (60), Expect = 2.3
Identities = 10/33 (30%), Positives = 16/33 (48%)
Query: 10 ALVTGGAAGIGRAYCEELLKFGAKVSICDINDS 42
L+ GG IG + LL+ G +V + D +
Sbjct: 2 VLIVGGNGFIGSHLVDALLEEGPQVRVFDRSIP 34
>gnl|CDD|240622 cd05198, formate_dh_like, Formate/glycerate and related
dehydrogenases of the D-specific 2-hydroxy acid
dehydrogenase family. Formate dehydrogenase, D-specific
2-hydroxy acid dehydrogenase, Phosphoglycerate
Dehydrogenase, Lactate dehydrogenase, Thermostable
Phosphite Dehydrogenase, and Hydroxy(phenyl)pyruvate
reductase, among others, share a characteristic
arrangement of 2 similar subdomains of the alpha/beta
Rossmann fold NAD+ binding form. 2-hydroxyacid
dehydrogenases are enzymes that catalyze the conversion
of a wide variety of D-2-hydroxy acids to their
corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
The NAD+ binding domain is inserted within the linear
sequence of the mostly N-terminal catalytic domain,
which has a similar domain structure to the internal NAD
binding domain. Structurally, these domains are
connected by extended alpha helices and create a cleft
in which NAD is bound, primarily to the C-terminal
portion of the 2nd (internal) domain. Some related
proteins have similar structural subdomain but with a
tandem arrangement of the catalytic and NAD-binding
subdomains in the linear sequence. Formate dehydrogenase
(FDH) catalyzes the NAD+-dependent oxidation of formate
ion to carbon dioxide with the concomitant reduction of
NAD+ to NADH. FDHs of this family contain no metal ions
or prosthetic groups. Catalysis occurs though direct
transfer of hydride ion to NAD+ without the stages of
acid-base catalysis typically found in related
dehydrogenases. FDHs are found in all methylotrophic
microorganisms in energy production and in the stress
responses of plants. Formate/glycerate and related
dehydrogenases of the D-specific 2-hydroxyacid
dehydrogenase superfamily include groups such as formate
dehydrogenase, glycerate dehydrogenase, L-alanine
dehydrogenase, and S-Adenosylhomocysteine Hydrolase,
among others. While many members of this family are
dimeric, alanine DH is hexameric and phosphoglycerate DH
is tetrameric.
Length = 302
Score = 26.8 bits (60), Expect = 2.3
Identities = 15/50 (30%), Positives = 21/50 (42%), Gaps = 3/50 (6%)
Query: 4 DLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDS--VGEDLAEQW 51
+L+GK + G IG+ + L FG KV D EDL +
Sbjct: 137 ELEGKTVGIVG-LGRIGQRVAKRLQAFGMKVLYYDRTRKPEPEEDLGFRV 185
>gnl|CDD|178263 PLN02657, PLN02657, 3,8-divinyl protochlorophyllide a 8-vinyl
reductase.
Length = 390
Score = 27.0 bits (60), Expect = 2.5
Identities = 18/75 (24%), Positives = 26/75 (34%), Gaps = 4/75 (5%)
Query: 6 KGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDS--VGEDLAEQWRTKYGPNRAIYC 63
K LV G IG+ EL++ G V S G++ E + + A
Sbjct: 59 KDVTVLVVGATGYIGKFVVRELVRRGYNVVAVAREKSGIRGKNGKEDTKKELPG--AEVV 116
Query: 64 PCDVTDYPQFEEAFQ 78
DVTD +
Sbjct: 117 FGDVTDADSLRKVLF 131
>gnl|CDD|181260 PRK08159, PRK08159, enoyl-(acyl carrier protein) reductase;
Provisional.
Length = 272
Score = 26.6 bits (59), Expect = 2.6
Identities = 14/37 (37%), Positives = 21/37 (56%), Gaps = 1/37 (2%)
Query: 64 PCDVTDYPQFEEAFQITLQKLGGLDIVINNAGIFNDR 100
CDVTD + F+ +K G LD V++ G F+D+
Sbjct: 66 HCDVTDEASIDAVFETLEKKWGKLDFVVHAIG-FSDK 101
>gnl|CDD|240659 cd12183, LDH_like_2, D-Lactate and related Dehydrogenases,
NAD-binding and catalytic domains. D-Lactate
dehydrogenase (LDH) catalyzes the interconversion of
pyruvate and lactate, and is a member of the
2-hydroxyacid dehydrogenase family. LDH is homologous to
D-2-hydroxyisocaproic acid dehydrogenase (D-HicDH) and
shares the 2-domain structure of formate dehydrogenase.
D-2-hydroxyisocaproate dehydrogenase-like (HicDH)
proteins are NAD-dependent members of the
hydroxycarboxylate dehydrogenase family, and share the
Rossmann fold typical of many NAD binding proteins.
HicDH from Lactobacillus casei forms a monomer and
catalyzes the reaction R-CO-COO(-) + NADH + H+ to
R-COH-COO(-) + NAD+. D-HicDH, like the structurally
distinct L-HicDH, exhibits low side-chain R specificity,
accepting a wide range of 2-oxocarboxylic acid side
chains. Formate/glycerate and related dehydrogenases of
the D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain.
Length = 328
Score = 26.6 bits (60), Expect = 2.7
Identities = 15/38 (39%), Positives = 18/38 (47%), Gaps = 3/38 (7%)
Query: 3 MDLKGKVALVTG-GAAGIGRAYCEELLKFGAKVSICDI 39
DL GK V G G IG+A+ L FG +V D
Sbjct: 140 FDLHGKTVGVIGTGK--IGQAFARILKGFGCRVLAYDP 175
>gnl|CDD|222146 pfam13460, NAD_binding_10, NADH(P)-binding.
Length = 182
Score = 26.5 bits (59), Expect = 2.7
Identities = 20/85 (23%), Positives = 27/85 (31%), Gaps = 18/85 (21%)
Query: 11 LVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPCDVTDY 70
V G GR +ELL G +V+ N S K D+ D
Sbjct: 2 AVIGATGKTGRRLVKELLARGHQVTALSRNPSKAPAPGVTPVQK-----------DLFDL 50
Query: 71 PQFEEAFQITLQKLGGLDIVINNAG 95
EA G+D V++ G
Sbjct: 51 ADLAEALA-------GVDAVVDAFG 68
>gnl|CDD|223268 COG0190, FolD, 5,10-methylene-tetrahydrofolate
dehydrogenase/Methenyl tetrahydrofolate cyclohydrolase
[Coenzyme metabolism].
Length = 283
Score = 26.8 bits (60), Expect = 2.9
Identities = 16/46 (34%), Positives = 24/46 (52%), Gaps = 3/46 (6%)
Query: 4 DLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAE 49
DL+GK +V G + +G+ LL A V++C S +DLA
Sbjct: 153 DLRGKNVVVVGRSNIVGKPLALLLLNANATVTVC---HSRTKDLAS 195
>gnl|CDD|217136 pfam02602, HEM4, Uroporphyrinogen-III synthase HemD. This family
consists of uroporphyrinogen-III synthase HemD
EC:4.2.1.75 also known as Hydroxymethylbilane hydrolyase
(cyclizing) from eukaryotes, bacteria and archaea. This
enzyme catalyzes the reaction: Hydroxymethylbilane <=>
uroporphyrinogen-III + H(2)O. Some members of this
family are multi-functional proteins possessing other
enzyme activities related to porphyrin biosynthesis,
such as hemD from Clostridium josui with pfam00590,
however the aligned region corresponds with the
uroporphyrinogen-III synthase EC:4.2.1.75 activity only.
Uroporphyrinogen-III synthase is the fourth enzyme in
the heme pathway. Mutant forms of the
Uroporphyrinogen-III synthase gene cause congenital
erythropoietic porphyria in humans a recessive inborn
error of metabolism also known as Gunther disease.
Length = 230
Score = 26.5 bits (59), Expect = 3.0
Identities = 9/47 (19%), Positives = 15/47 (31%)
Query: 16 AAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIY 62
A +G L + G + E LAE+ + R +
Sbjct: 74 IAAVGPKTARALREAGLTPDFVPSAEGTAEGLAEELAERLAGKRVLL 120
>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 = 26.4 bits (59), Expect = 3.0
Identities = 25/93 (26%), Positives = 32/93 (34%), Gaps = 23/93 (24%)
Query: 11 LVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPCDVTDY 70
++TGG IGRA L G +V + E LAE V +
Sbjct: 3 VITGGTGFIGRALTRRLTAAGHEVVVLSRRPGKAEGLAE-----------------VITW 45
Query: 71 PQFEEAFQITLQKLGGLDIVINNAG--IFNDRF 101
+L G D VIN AG I R+
Sbjct: 46 DGLSLGP----WELPGADAVINLAGEPIACRRW 74
>gnl|CDD|223758 COG0686, Ald, Alanine dehydrogenase [Amino acid transport and
metabolism].
Length = 371
Score = 26.5 bits (59), Expect = 3.1
Identities = 14/37 (37%), Positives = 18/37 (48%), Gaps = 2/37 (5%)
Query: 5 LKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDIND 41
L KV ++ GG G A L GA V+I D+N
Sbjct: 167 LPAKVVVLGGGVVGTNAAKIAIGL--GADVTILDLNI 201
>gnl|CDD|223745 COG0673, MviM, Predicted dehydrogenases and related proteins
[General function prediction only].
Length = 342
Score = 26.7 bits (59), Expect = 3.1
Identities = 13/52 (25%), Positives = 23/52 (44%), Gaps = 6/52 (11%)
Query: 8 KVALVTGGAAGIG-RAYCEELLKFGAK---VSICDINDSVGEDLAEQWRTKY 55
+V ++ GA GI +A+ L G V++ D + E AE++
Sbjct: 5 RVGII--GAGGIAGKAHLPALAALGGGLELVAVVDRDPERAEAFAEEFGIAK 54
>gnl|CDD|198065 smart00997, AdoHcyase_NAD, S-adenosyl-L-homocysteine hydrolase,
NAD binding domain.
Length = 162
Score = 26.3 bits (59), Expect = 3.2
Identities = 12/39 (30%), Positives = 20/39 (51%), Gaps = 3/39 (7%)
Query: 3 MDLKGKVALVTG-GAAGIGRAYCEELLKFGAKVSICDIN 40
+ L GK +V G G +G+ L GA+V + +I+
Sbjct: 19 VLLAGKNVVVAGYGD--VGKGVAARLRGLGARVIVTEID 55
>gnl|CDD|236308 PRK08594, PRK08594, enoyl-(acyl carrier protein) reductase;
Provisional.
Length = 257
Score = 26.6 bits (59), Expect = 3.2
Identities = 22/90 (24%), Positives = 39/90 (43%), Gaps = 3/90 (3%)
Query: 1 MVMDLKGKVALVTGGA--AGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPN 58
M++ L+GK +V G A I L GAK+ + + +++ E T G
Sbjct: 1 MMLSLEGKTYVVMGVANKRSIAWGIARSLHNAGAKLVFTYAGERLEKEVRELADTLEGQE 60
Query: 59 RAIYCPCDVTDYPQFEEAFQITLQKLGGLD 88
+ PCDVT + F+ +++G +
Sbjct: 61 SLLL-PCDVTSDEEITACFETIKEEVGVIH 89
>gnl|CDD|233711 TIGR02076, pyrH_arch, uridylate kinase, putative. This family
consists of the archaeal and spirochete proteins most
closely related to bacterial uridylate kinases
(TIGR02075), an enzyme involved in pyrimidine
biosynthesis. Members are likely, but not known, to be
functionally equivalent to their bacterial
counterparts. However, substantial sequence differences
suggest that regulatory mechanisms may be different;
the bacterial form is allosterically regulated by GTP
[Purines, pyrimidines, nucleosides, and nucleotides,
Nucleotide and nucleoside interconversions].
Length = 221
Score = 26.5 bits (59), Expect = 3.2
Identities = 10/34 (29%), Positives = 14/34 (41%), Gaps = 1/34 (2%)
Query: 5 LKGKVALVTGGAAGIGRAYCEELLKFGAKVSICD 38
+ KV +V GG R Y + GA + D
Sbjct: 31 DEHKVGVVVGGG-KTARRYIGVARELGASETFLD 63
>gnl|CDD|234027 TIGR02824, quinone_pig3, putative NAD(P)H quinone oxidoreductase,
PIG3 family. Members of this family are putative
quinone oxidoreductases that belong to the broader
superfamily (modeled by Pfam pfam00107) of
zinc-dependent alcohol (of medium chain length)
dehydrogenases and quinone oxiooreductases. The
alignment shows no motif of conserved Cys residues as
are found in zinc-binding members of the superfamily,
and members are likely to be quinone oxidoreductases
instead. A member of this family in Homo sapiens, PIG3,
is induced by p53 but is otherwise uncharacterized
[Unknown function, Enzymes of unknown specificity].
Length = 325
Score = 26.5 bits (59), Expect = 3.2
Identities = 17/55 (30%), Positives = 27/55 (49%), Gaps = 7/55 (12%)
Query: 6 KGKVALVTGGAAGIGRAYCEELLKFGAKVSI-------CDINDSVGEDLAEQWRT 53
G+ L+ GGA+GIG + FGA+V C +++G D+A +R
Sbjct: 139 AGETVLIHGGASGIGTTAIQLAKAFGARVFTTAGSDEKCAACEALGADIAINYRE 193
>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 = 26.5 bits (59), Expect = 3.4
Identities = 11/26 (42%), Positives = 12/26 (46%)
Query: 11 LVTGGAAGIGRAYCEELLKFGAKVSI 36
LVTG +G A E LL A V
Sbjct: 2 LVTGATGKLGTAVVELLLAKVASVVA 27
>gnl|CDD|240160 cd05124, AFK, Actin-Fragmin Kinase (AFK); catalytic domain. The AFK
catalytic domain is part of a larger superfamily that
includes the catalytic domains of other kinases such as
the typical serine/threonine/tyrosine protein kinases
(PKs), RIO kinases, aminoglycoside phosphotransferase,
choline kinase, and phosphoinositide 3-kinase (PI3K).
AFK is found in slime molds, ciliates, and flowering
plants. It catalyzes the transfer of the
gamma-phosphoryl group from ATP specifically to
threonine residues in the actin-fragmin complex. The
phosphorylation sites are located at a minor contact
site for DNase I and at an actin-actin contact site.
Fragmin is an actin-binding protein that functions as a
regulator of the microfilament system. It interferes
with the growth of F-actin by severing actin filaments
and capping their ends. The phosphorylation of the
actin-fragmin complex inhibits its nucleation activity
and results in calcium-dependent capping activity. Thus,
AFK plays a role in regulating actin polymerization.
Length = 238
Score = 26.2 bits (58), Expect = 3.4
Identities = 10/26 (38%), Positives = 12/26 (46%), Gaps = 3/26 (11%)
Query: 80 TLQKLG---GLDIVINNAGIFNDRFW 102
L +LG LDI INN+ W
Sbjct: 120 RLIQLGKIIALDIFINNSDRLPLAIW 145
>gnl|CDD|197211 cd09112, PLDc_CLS_2, catalytic domain repeat 2 of bacterial
cardiolipin synthase and similar proteins. This CD
corresponds to the catalytic domain repeat 2 of
bacterial cardiolipin synthase (CL synthase, EC
2.7.8.-) and a few homologs found in eukaryotes and
archea. Bacterial CL synthases catalyze reversible
phosphatidyl group transfer between two
phosphatidylglycerol molecules to form cardiolipin (CL)
and glycerol. The monomer of bacterial CL synthase
consists of two catalytic domains. Each catalytic
domain contains one copy of conserved HKD motifs
(H-X-K-X(4)-D, X represents any amino acid residue)
that are the characteristic of the phospholipase D
(PLD) superfamily. Two HKD motifs from two domains
together form a single active site involving in
phosphatidyl group transfer. Bacterial CL synthases can
be stimulated by phosphate and inhibited by CL, the
product of the reaction, and by phosphatidate.
Phosphate stimulation may be unique to enzymes with CL
synthase activity in PLD superfamily. Like other PLD
enzymes, bacterial CL synthase utilize a common
two-step ping-pong catalytic mechanism involving an
enzyme-substrate intermediate to cleave phosphodiester
bonds. The two histidine residues from the two HKD
motifs play key roles in the catalysis. Upon substrate
binding, a histidine residue from one HKD motif could
function as the nucleophile attacking the
phosphodiester bond to create a covalent
phosphohistidine intermediate, while the other
histidine residue from the second HKD motif could serve
as a general acid stabilizing the leaving group.
Length = 174
Score = 26.3 bits (59), Expect = 3.5
Identities = 9/15 (60%), Positives = 11/15 (73%)
Query: 20 GRAYCEELLKFGAKV 34
R+Y EELLK G K+
Sbjct: 71 SRSYFEELLKAGVKI 85
>gnl|CDD|239152 cd02751, MopB_DMSOR-like, The MopB_DMSOR-like CD contains
dimethylsulfoxide reductase (DMSOR), biotin sulfoxide
reductase (BSOR), trimethylamine N-oxide reductase
(TMAOR) and other related proteins. DMSOR catalyzes the
reduction of DMSO to dimethylsulfide, but its cellular
location and oligomerization state are
organism-dependent. For example, in Rhodobacter
sphaeriodes and Rhodobacter capsulatus, it is an 82-kDa
monomeric soluble protein found in the periplasmic
space; in E. coli, it is membrane-bound and exists as a
heterotrimer. BSOR catalyzes the reduction of biotin
sulfixode to biotin, and is unique among Mo enzymes
because no additional auxiliary proteins or cofactors
are required. TMAOR is similar to DMSOR, but its only
natural substrate is TMAO. Also included in this group
is the pyrogallol-phloroglucinol transhydroxylase from
Pelobacter acidigallici. Members of the MopB_DMSOR-like
CD belong to the molybdopterin_binding (MopB)
superfamily of proteins.
Length = 609
Score = 26.4 bits (59), Expect = 3.9
Identities = 8/39 (20%), Positives = 13/39 (33%), Gaps = 1/39 (2%)
Query: 14 GGAAGIGRAYCEELLKFGAK-VSICDINDSVGEDLAEQW 51
GG Y ++ G + + I LA +W
Sbjct: 189 GGPDHGSYYYLKQAKDAGVRFICIDPRYTDTAAVLAAEW 227
>gnl|CDD|200381 TIGR04130, FnlA, UDP-N-acetylglucosamine
4,6-dehydratase/5-epimerase. The FnlA enzyme is the
first step in the biosynthesis of UDP-FucNAc from
UDP-GlcNAc in E. coli (along with FnlB and FnlC). The
proteins identified by this model include FnlA homologs
in the O-antigen clusters of O4, O25, O26, O29
(Shigella D11), O118, O145 and O172 serotype strains,
all of which produce O-antigens containing FucNAc (or
the further modified FucNAm). A homolog from
Pseudomonas aerugiosa serotype O11, WbjB, also involved
in the biosynthesis of UDP-FucNAc has been
characterized and is now believed to carry out both the
initial 4,6-dehydratase reaction and the subsequent
epimerization of the resulting methyl group at C-5. A
phylogenetic tree of related sequences shows a distinct
clade of enzymes involved in the biosynthesis of
UDP-QuiNAc (Qui=qinovosamine). This clade appears to be
descendant from the common ancestor of the Pseudomonas
and E. coli fucose-biosynthesis enzymes. It has been
hypothesized that the first step in the biosynthesis of
these two compounds may be the same, and thus that
these enzymes all have the same function. At present,
lacking sufficient confirmation of this, the current
model trusted cutoff only covers the tree segment
surrounding the E. coli genes. The clades containing
the Pseudomonas and QuiNAc biosynthesis enzymes score
above the noise cutoff. Immediately below the noise
cutoff are enzymes involved in the biosynthesis of
UDP-RhaNAc (Rha=rhamnose), which again may or may not
produce the same product.
Length = 337
Score = 26.5 bits (58), Expect = 4.0
Identities = 19/67 (28%), Positives = 29/67 (43%), Gaps = 5/67 (7%)
Query: 5 LKGKVALVTGGAAGIGRAYCEELLKFGAK-VSICDINDSVGEDLAEQWRTKYGPNRAIYC 63
K K+ L+TGG G A L K + I ++ +D+ R KY ++ +
Sbjct: 2 FKDKILLITGGTGSFGNAVLRRFLDTDIKEIRIFSRDEKKQDDM----RKKYNNSKLKFY 57
Query: 64 PCDVTDY 70
DV DY
Sbjct: 58 IGDVRDY 64
>gnl|CDD|235864 PRK06807, PRK06807, DNA polymerase III subunit epsilon; Validated.
Length = 313
Score = 26.3 bits (58), Expect = 4.3
Identities = 18/46 (39%), Positives = 26/46 (56%), Gaps = 3/46 (6%)
Query: 67 VTDYPQFEEAFQITLQKLGGLDIVINNAGIFNDRFWELEVDVNLVG 112
V+D P EE + L L IV +NA F+ RF L+ +VN++G
Sbjct: 69 VSDAPTIEEVLPLFLAFLHTNVIVAHNAS-FDMRF--LKSNVNMLG 111
>gnl|CDD|183738 PRK12775, PRK12775, putative trifunctional 2-polyprenylphenol
hydroxylase/glutamate synthase subunit beta/ferritin
domain-containing protein; Provisional.
Length = 1006
Score = 26.4 bits (58), Expect = 4.5
Identities = 12/30 (40%), Positives = 19/30 (63%), Gaps = 2/30 (6%)
Query: 7 GKVALVTGGAAGIGRAYCEELLKFGAKVSI 36
GKVA+ G AG+ A +L+K+G V++
Sbjct: 431 GKVAICGSGPAGLAAA--ADLVKYGVDVTV 458
>gnl|CDD|222002 pfam13241, NAD_binding_7, Putative NAD(P)-binding. This domain
is found in fungi, plants, archaea and bacteria.
Length = 104
Score = 25.5 bits (57), Expect = 4.5
Identities = 15/35 (42%), Positives = 21/35 (60%), Gaps = 3/35 (8%)
Query: 3 MDLKGKVALVTG-GAAGIGRAYCEELLKFGAKVSI 36
+DLKGK LV G G + + LL+ GAKV++
Sbjct: 3 LDLKGKRVLVVGGGEVALRKI--RALLEAGAKVTV 35
>gnl|CDD|223411 COG0334, GdhA, Glutamate dehydrogenase/leucine dehydrogenase [Amino
acid transport and metabolism].
Length = 411
Score = 26.0 bits (58), Expect = 4.7
Identities = 25/109 (22%), Positives = 35/109 (32%), Gaps = 29/109 (26%)
Query: 3 MDLKGKVALVTG-GAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAI 61
DL+G V G G G E+L + GAKV DS I
Sbjct: 203 DDLEGARVAVQGFGNVGQ--YAAEKLHELGAKVVAVS--DS---------------KGGI 243
Query: 62 YCP--CDVTDYPQFEEAFQITLQKLGGLDIVINNAGIFNDRFWELEVDV 108
Y DV + +E + G I N+ E++ D+
Sbjct: 244 YDEDGLDVEALLELKERRGSVAEYAGAEYIT-------NEELLEVDCDI 285
>gnl|CDD|233259 TIGR01070, mutS1, DNA mismatch repair protein MutS. [DNA
metabolism, DNA replication, recombination, and
repair].
Length = 840
Score = 26.3 bits (58), Expect = 4.8
Identities = 9/17 (52%), Positives = 13/17 (76%)
Query: 22 AYCEELLKFGAKVSICD 38
AY E+L+K G V+IC+
Sbjct: 69 AYLEKLVKQGESVAICE 85
>gnl|CDD|133448 cd01080, NAD_bind_m-THF_DH_Cyclohyd, NADP binding domain of
methylene-tetrahydrofolate
dehydrogenase/cyclohydrolase. NADP binding domain of
the Methylene-Tetrahydrofolate
Dehydrogenase/cyclohydrolase (m-THF DH/cyclohydrolase)
bifunctional enzyme. Tetrahydrofolate is a versatile
carrier of activated one-carbon units. The major
one-carbon folate donors are N-5
methyltetrahydrofolate, N5,N10-m-THF, and
N10-formayltetrahydrofolate. The oxidation of metabolic
intermediate m-THF to m-THF requires the enzyme m-THF
DH. In addition, most DHs also have an associated
cyclohydrolase activity which catalyzes its hydrolysis
to N10-formyltetrahydrofolate. m-THF DH is typically
found as part of a multifunctional protein in
eukaryotes. NADP-dependent m-THF DH in mammals, birds
and yeast are components of a trifunctional enzyme with
DH, cyclohydrolase, and synthetase activities. Certain
eukaryotic cells also contain homodimeric bifunctional
DH/cyclodrolase form. In bacteria, monofucntional DH,
as well as bifunctional m-THF m-THF DHm-THF
DHDH/cyclodrolase are found. In addition, yeast (S.
cerevisiae) also express an monofunctional DH. This
family contains the bifunctional DH/cyclohydrolase.
M-THF DH, like other amino acid DH-like NAD(P)-binding
domains, is a member of the Rossmann fold superfamily
which includes glutamate, leucine, and phenylalanine
DHs, m-THF DH, methylene-tetrahydromethanopterin DH,
m-THF DH/cyclohydrolase, Shikimate DH-like proteins,
malate oxidoreductases, and glutamyl tRNA reductase.
Amino acid DHs catalyze the deamination of amino acids
to keto acids with NAD(P)+ as a cofactor. The
NAD(P)-binding Rossmann fold superfamily includes a
wide variety of protein families including NAD(P)-
binding domains of alcohol DHs, tyrosine-dependent
oxidoreductases, glyceraldehyde-3-phosphate DH,
lactate/malate DHs, formate/glycerate DHs, siroheme
synthases, 6-phosphogluconate DH, amino acid DHs,
repressor rex, NAD-binding potassium channel domain,
CoA-binding, and ornithine cyclodeaminase-like domains.
Length = 168
Score = 26.0 bits (58), Expect = 4.8
Identities = 12/37 (32%), Positives = 18/37 (48%)
Query: 4 DLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDIN 40
DL GK +V G + +G+ LL A V++C
Sbjct: 41 DLAGKKVVVVGRSNIVGKPLAALLLNRNATVTVCHSK 77
>gnl|CDD|237117 PRK12493, PRK12493, magnesium chelatase subunit H; Provisional.
Length = 1310
Score = 26.1 bits (58), Expect = 5.4
Identities = 11/25 (44%), Positives = 17/25 (68%), Gaps = 2/25 (8%)
Query: 79 ITLQKLGG--LDIVINNAGIFNDRF 101
I L++LG +D+V+ +GIF D F
Sbjct: 1000 IPLEELGRPRIDVVVTCSGIFRDLF 1024
>gnl|CDD|218769 pfam05833, FbpA, Fibronectin-binding protein A N-terminus (FbpA).
This family consists of the N-terminal region of the
prokaryotic fibronectin-binding protein. Fibronectin
binding is considered to be an important virulence
factor in streptococcal infections. Fibronectin is a
dimeric glycoprotein that is present in a soluble form
in plasma and extracellular fluids; it is also present
in a fibrillar form on cell surfaces. Both the soluble
and cellular forms of fibronectin may be incorporated
into the extracellular tissue matrix. While fibronectin
has critical roles in eukaryotic cellular processes,
such as adhesion, migration and differentiation, it is
also a substrate for the attachment of bacteria. The
binding of pathogenic Streptococcus pyogenes and
Staphylococcus aureus to epithelial cells via
fibronectin facilitates their internalisation and
systemic spread within the host.
Length = 447
Score = 26.1 bits (58), Expect = 5.5
Identities = 8/39 (20%), Positives = 16/39 (41%), Gaps = 3/39 (7%)
Query: 18 GIGRAYCEEL---LKFGAKVSICDINDSVGEDLAEQWRT 53
G+ EEL + + +++D E L E ++
Sbjct: 197 GLSPLLAEELCYRAGLDKETPVEELSDEDWERLYEAFKE 235
>gnl|CDD|214685 smart00479, EXOIII, exonuclease domain in DNA-polymerase alpha and
epsilon chain, ribonuclease T and other exonucleases.
Length = 169
Score = 25.7 bits (57), Expect = 5.5
Identities = 14/38 (36%), Positives = 20/38 (52%)
Query: 64 PCDVTDYPQFEEAFQITLQKLGGLDIVINNAGIFNDRF 101
P + D P FEE + L+ L G +V N+ F+ RF
Sbjct: 58 PEMLDDAPTFEEVLEELLEFLRGRILVAGNSAHFDLRF 95
>gnl|CDD|233690 TIGR02025, BchH, magnesium chelatase, H subunit. This model
represents the H subunit of the magnesium chelatase
complex responsible for magnesium insertion into the
protoporphyrin IX ring in the biosynthesis of both
chlorophyll and bacteriochlorophyll. In
chlorophyll-utilizing species, this gene is known as
ChlH, while in bacteriochlorophyll-utilizing spoecies it
is called BchH. Subunit H is the largest (~140kDa) of
the three subunits (the others being BchD/ChlD and
BchI/ChlI), and is known to bind protoporphyrin IX.
Subunit H is homologous to the CobN subunit of
cobaltochelatase and by anology with that enzyme,
subunit H is believed to also bind the magnesium ion
which is inserted into the ring. In conjunction with the
hydrolysis of ATP by subunits I and D, a conformation
change is believed to happen in subunit H causing the
magnesium ion insertion into the distorted
protoporphyrin ring [Biosynthesis of cofactors,
prosthetic groups, and carriers, Chlorophyll and
bacteriochlorphyll].
Length = 1224
Score = 25.9 bits (57), Expect = 5.6
Identities = 12/25 (48%), Positives = 17/25 (68%), Gaps = 2/25 (8%)
Query: 79 ITLQKLGG--LDIVINNAGIFNDRF 101
I L+KLG +D+V+ +GIF D F
Sbjct: 916 IPLEKLGRPRIDVVVTLSGIFRDLF 940
>gnl|CDD|215557 PLN03069, PLN03069, magnesiumprotoporphyrin-IX chelatase subunit H;
Provisional.
Length = 1220
Score = 25.9 bits (57), Expect = 6.0
Identities = 10/25 (40%), Positives = 19/25 (76%), Gaps = 2/25 (8%)
Query: 79 ITLQKLGG--LDIVINNAGIFNDRF 101
++L++LG +D+V+N +G+F D F
Sbjct: 1015 VSLEELGRPRIDVVVNCSGVFRDLF 1039
>gnl|CDD|180796 PRK07023, PRK07023, short chain dehydrogenase; Provisional.
Length = 243
Score = 25.7 bits (57), Expect = 6.1
Identities = 12/25 (48%), Positives = 17/25 (68%)
Query: 10 ALVTGGAAGIGRAYCEELLKFGAKV 34
A+VTG + G+G A E+LL+ G V
Sbjct: 4 AIVTGHSRGLGAALAEQLLQPGIAV 28
>gnl|CDD|180983 PRK07453, PRK07453, protochlorophyllide oxidoreductase;
Validated.
Length = 322
Score = 25.7 bits (57), Expect = 6.6
Identities = 13/34 (38%), Positives = 19/34 (55%), Gaps = 1/34 (2%)
Query: 1 MVMDLKGKVALVTGGAAGIGRAYCEELLKFGAKV 34
M D KG V ++TG ++G+G + L K G V
Sbjct: 1 MSQDAKGTV-IITGASSGVGLYAAKALAKRGWHV 33
>gnl|CDD|240258 PTZ00075, PTZ00075, Adenosylhomocysteinase; Provisional.
Length = 476
Score = 25.8 bits (57), Expect = 6.6
Identities = 13/38 (34%), Positives = 21/38 (55%), Gaps = 2/38 (5%)
Query: 2 VMDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDI 39
VM + GK +V G +G+ + L FGA+V + +I
Sbjct: 250 VM-IAGKTVVVCG-YGDVGKGCAQALRGFGARVVVTEI 285
>gnl|CDD|133451 cd05212, NAD_bind_m-THF_DH_Cyclohyd_like, NAD(P) binding domain
of methylene-tetrahydrofolate dehydrogenase and
methylene-tetrahydrofolate
dehydrogenase/cyclohydrolase. NAD(P) binding domains
of methylene-tetrahydrofolate dehydrogenase (m-THF DH)
and m-THF DH/cyclohydrolase bifunctional enzymes
(m-THF DH/cyclohydrolase). M-THF is a versatile carrier
of activated one-carbon units. The major one-carbon
folate donors are N-5 methyltetrahydrofolate,
N5,N10-m-THF, and N10-formayltetrahydrofolate. The
oxidation of metabolic intermediate m-THF to m-THF
requires the enzyme m-THF DH. In addition, most DHs
also have an associated cyclohydrolase activity which
catalyzes its hydrolysis to N10-formyltetrahydrofolate.
m-THF DH is typically found as part of a
multifunctional protein in eukaryotes. NADP-dependent
m-THF DH in mammals, birds and yeast are components of
a trifunctional enzyme with DH, cyclohydrolase, and
synthetase activities. Certain eukaryotic cells also
contain homodimeric bifunctional DH/cyclodrolase form.
In bacteria, mono-functional DH, as well as
bifunctional DH/cyclodrolase are found. In addition,
yeast (S. cerevisiae) also express a monofunctional DH.
M-THF DH, like other amino acid DH-like NAD(P)-binding
domains, is a member of the Rossmann fold superfamily
which includes glutamate, leucine, and phenylalanine
DHs, m-THF DH, methylene-tetrahydromethanopterin DH,
m-THF DH/cyclohydrolase, Shikimate DH-like proteins,
malate oxidoreductases, and glutamyl tRNA reductase.
Amino acid DHs catalyze the deamination of amino acids
to keto acids with NAD(P)+ as a cofactor. The
NAD(P)-binding Rossmann fold superfamily includes a
wide variety of protein families including NAD(P)-
binding domains of alcohol DHs, tyrosine-dependent
oxidoreductases, glyceraldehyde-3-phosphate DH,
lactate/malate DHs, formate/glycerate DHs, siroheme
synthases, 6-phosphogluconate DH, amino acid DHs,
repressor rex, NAD-binding potassium channel domain,
CoA-binding, and ornithine cyclodeaminase-like domains.
These domains have an alpha-beta-alpha configuration.
NAD binding involves numerous hydrogen and van der
Waals contacts.
Length = 140
Score = 25.2 bits (55), Expect = 6.6
Identities = 13/37 (35%), Positives = 16/37 (43%)
Query: 4 DLKGKVALVTGGAAGIGRAYCEELLKFGAKVSICDIN 40
L GK LV G + +G L + GA V CD
Sbjct: 25 RLDGKKVLVVGRSGIVGAPLQCLLQRDGATVYSCDWK 61
>gnl|CDD|216949 pfam02254, TrkA_N, TrkA-N domain. This domain is found in a wide
variety of proteins. These protein include potassium
channels, phosphoesterases, and various other
transporters. This domain binds to NAD.
Length = 116
Score = 25.2 bits (56), Expect = 6.7
Identities = 11/32 (34%), Positives = 18/32 (56%)
Query: 19 IGRAYCEELLKFGAKVSICDINDSVGEDLAEQ 50
+GR+ EEL + G V + D + E+L E+
Sbjct: 9 VGRSLAEELREGGPDVVVIDKDPERVEELREE 40
>gnl|CDD|233266 TIGR01087, murD, UDP-N-acetylmuramoylalanine--D-glutamate ligase.
[Cell envelope, Biosynthesis and degradation of murein
sacculus and peptidoglycan].
Length = 433
Score = 25.8 bits (57), Expect = 7.0
Identities = 16/77 (20%), Positives = 28/77 (36%), Gaps = 15/77 (19%)
Query: 20 GRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPCDVTDYPQFEEAFQI 79
GRA L K GA+V++ D+ E+ ++ +
Sbjct: 11 GRAVARFLHKKGAEVTVTDL------KPNEE------LEPSMGQLRLNEGSVLHT---GL 55
Query: 80 TLQKLGGLDIVINNAGI 96
L+ L D+V+ + GI
Sbjct: 56 HLEDLNNADLVVKSPGI 72
>gnl|CDD|135642 PRK05884, PRK05884, short chain dehydrogenase; Provisional.
Length = 223
Score = 25.5 bits (56), Expect = 7.0
Identities = 25/82 (30%), Positives = 33/82 (40%), Gaps = 10/82 (12%)
Query: 11 LVTGGAAGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPCDVTDY 70
LVTGG +GR E G KV++ E A++ AI CD TD
Sbjct: 4 LVTGGDTDLGRTIAEGFRNDGHKVTLVGARRDDLEVAAKELDVD-----AIV--CDNTDP 56
Query: 71 PQFEEAFQITLQKLGGLDIVIN 92
EEA + LD ++N
Sbjct: 57 ASLEEARGLFPHH---LDTIVN 75
>gnl|CDD|234372 TIGR03843, TIGR03843, conserved hypothetical protein. This model
represents a protein family largely restricted to the
Actinobacteria (high-GC Gram-positives), although it is
also found in the Chloroflexi. Distant similarity to the
phosphatidylinositol 3- and 4-kinase is suggested by the
matching of some members to pfam00454.
Length = 253
Score = 25.3 bits (56), Expect = 7.3
Identities = 8/26 (30%), Positives = 13/26 (50%), Gaps = 4/26 (15%)
Query: 75 EAFQITLQKLGGLDIVINNAGIFNDR 100
A L+++ D ++NNA DR
Sbjct: 129 HADHPQLRRMAVFDALVNNA----DR 150
>gnl|CDD|184561 PRK14192, PRK14192, bifunctional 5,10-methylene-tetrahydrofolate
dehydrogenase/ 5,10-methylene-tetrahydrofolate
cyclohydrolase; Provisional.
Length = 283
Score = 25.6 bits (56), Expect = 7.5
Identities = 14/35 (40%), Positives = 21/35 (60%)
Query: 3 MDLKGKVALVTGGAAGIGRAYCEELLKFGAKVSIC 37
++L GK A+V G +A +G+ LL A V+IC
Sbjct: 155 IELAGKHAVVVGRSAILGKPMAMMLLNANATVTIC 189
>gnl|CDD|237724 PRK14481, PRK14481, dihydroxyacetone kinase subunit DhaK;
Provisional.
Length = 331
Score = 25.5 bits (57), Expect = 7.8
Identities = 9/13 (69%), Positives = 11/13 (84%)
Query: 6 KGKVALVTGGAAG 18
GKVALV+GG +G
Sbjct: 43 PGKVALVSGGGSG 55
>gnl|CDD|100107 cd02440, AdoMet_MTases, S-adenosylmethionine-dependent
methyltransferases (SAM or AdoMet-MTase), class I;
AdoMet-MTases are enzymes that use
S-adenosyl-L-methionine (SAM or AdoMet) as a substrate
for methyltransfer, creating the product
S-adenosyl-L-homocysteine (AdoHcy). There are at least
five structurally distinct families of AdoMet-MTases,
class I being the largest and most diverse. Within this
class enzymes can be classified by different substrate
specificities (small molecules, lipids, nucleic acids,
etc.) and different target atoms for methylation
(nitrogen, oxygen, carbon, sulfur, etc.).
Length = 107
Score = 24.7 bits (54), Expect = 8.0
Identities = 11/59 (18%), Positives = 19/59 (32%), Gaps = 1/59 (1%)
Query: 17 AGIGRAYCEELLKFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIYCPCDVTDYPQFEE 75
G G GA+V+ DI+ +LA + + D + P +
Sbjct: 7 CGTGALALALASGPGARVTGVDISPVA-LELARKAAAALLADNVEVLKGDAEELPPEAD 64
>gnl|CDD|223916 COG0847, DnaQ, DNA polymerase III, epsilon subunit and related
3'-5' exonucleases [DNA replication, recombination, and
repair].
Length = 243
Score = 25.2 bits (55), Expect = 8.7
Identities = 8/26 (30%), Positives = 14/26 (53%)
Query: 66 DVTDYPQFEEAFQITLQKLGGLDIVI 91
+ D P+F E L +GGL +++
Sbjct: 74 MLADAPKFAEVLPEFLDFIGGLRLLV 99
>gnl|CDD|176191 cd05289, MDR_like_2, alcohol dehydrogenase and quinone
reductase-like medium chain degydrogenases/reductases.
Members identified as zinc-dependent alcohol
dehydrogenases and quinone oxidoreductase. 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 = 309
Score = 25.2 bits (56), Expect = 8.8
Identities = 9/29 (31%), Positives = 14/29 (48%)
Query: 6 KGKVALVTGGAAGIGRAYCEELLKFGAKV 34
G+ L+ G A G+G + GA+V
Sbjct: 144 AGQTVLIHGAAGGVGSFAVQLAKARGARV 172
>gnl|CDD|237723 PRK14479, PRK14479, dihydroxyacetone kinase; Provisional.
Length = 568
Score = 25.2 bits (56), Expect = 8.8
Identities = 8/13 (61%), Positives = 12/13 (92%)
Query: 6 KGKVALVTGGAAG 18
+GKVA+V+GG +G
Sbjct: 42 EGKVAVVSGGGSG 54
>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 = 25.0 bits (55), Expect = 9.3
Identities = 10/24 (41%), Positives = 11/24 (45%)
Query: 11 LVTGGAAGIGRAYCEELLKFGAKV 34
LVTG IG LL+ G V
Sbjct: 2 LVTGATGRIGSKVATTLLEAGRPV 25
>gnl|CDD|181609 PRK09009, PRK09009, C factor cell-cell signaling protein;
Provisional.
Length = 235
Score = 25.0 bits (55), Expect = 9.4
Identities = 9/18 (50%), Positives = 14/18 (77%)
Query: 11 LVTGGAAGIGRAYCEELL 28
L+ GG+ GIG+A ++LL
Sbjct: 4 LIVGGSGGIGKAMVKQLL 21
>gnl|CDD|215268 PLN02487, PLN02487, zeta-carotene desaturase.
Length = 569
Score = 25.1 bits (55), Expect = 9.4
Identities = 15/39 (38%), Positives = 21/39 (53%), Gaps = 2/39 (5%)
Query: 6 KGKVALVTGGAAGIGRAYCEELLKFGAKVSICDINDSVG 44
K KVA++ G AG+ A ELL G +V I + +G
Sbjct: 75 KLKVAIIGAGLAGMSTAV--ELLDQGHEVDIYESRPFIG 111
>gnl|CDD|178331 PLN02730, PLN02730, enoyl-[acyl-carrier-protein] reductase.
Length = 303
Score = 25.1 bits (55), Expect = 9.4
Identities = 13/36 (36%), Positives = 20/36 (55%), Gaps = 2/36 (5%)
Query: 3 MDLKGKVALVTGGA--AGIGRAYCEELLKFGAKVSI 36
+DL+GK A + G A G G A + L GA++ +
Sbjct: 5 IDLRGKRAFIAGVADDNGYGWAIAKALAAAGAEILV 40
>gnl|CDD|132628 TIGR03589, PseB, UDP-N-acetylglucosamine 4,6-dehydratase. This
enzyme catalyzes the first step in the biosynthesis of
pseudaminic acid, the conversion of
UDP-N-acetylglucosamine to
UDP-4-keto-6-deoxy-N-acetylglucosamine. These sequences
are members of the broader pfam01073 (3-beta
hydroxysteroid dehydrogenase/isomerase family) family.
Length = 324
Score = 25.1 bits (55), Expect = 9.9
Identities = 22/94 (23%), Positives = 37/94 (39%), Gaps = 11/94 (11%)
Query: 4 DLKGKVALVTGGAAGIGRAYCEELL-KFGAKVSICDINDSVGEDLAEQWRTKYGPNRAIY 62
K L+TGG G+A+ LL + K I D + + +Q K+ +
Sbjct: 1 MFNNKSILITGGTGSFGKAFISRLLENYNPKKIIIYSRDELKQWEMQQ---KFPAPCLRF 57
Query: 63 CPCDVTDYPQFEEAFQITLQKLGGLDIVINNAGI 96
DV D + A + G+D V++ A +
Sbjct: 58 FIGDVRDKERLTRALR-------GVDYVVHAAAL 84
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
0.321 0.141 0.438
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: 5,857,450
Number of extensions: 503287
Number of successful extensions: 1269
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1042
Number of HSP's successfully gapped: 425
Length of query: 113
Length of database: 10,937,602
Length adjustment: 77
Effective length of query: 36
Effective length of database: 7,522,344
Effective search space: 270804384
Effective search space used: 270804384
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (24.0 bits)