RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13412
(137 letters)
>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 = 74.0 bits (182), Expect = 8e-17
Identities = 37/102 (36%), Positives = 52/102 (50%), Gaps = 10/102 (9%)
Query: 46 DANLQTPTNH---YCK----NVLFHPPGANI---TNVNTYAVHPGVVDTELSRHFDSIIP 95
D N + N YC+ NVLF A T V A+HPGVV TEL RH
Sbjct: 149 DLNSEKSYNTGFAYCQSKLANVLFTRELARRLQGTGVTVNALHPGVVRTELGRHTGIHHL 208
Query: 96 GTAWLYQRVGGLFIKSPLQGAQTTLYCALDKKCERETGLYYA 137
+ L + F+K+P +GAQT++Y AL ++ E +G Y++
Sbjct: 209 FLSTLLNPLFWPFVKTPREGAQTSIYLALAEELEGVSGKYFS 250
>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 = 64.9 bits (159), Expect = 2e-13
Identities = 29/71 (40%), Positives = 39/71 (54%), Gaps = 6/71 (8%)
Query: 68 NITNVNTYAVHPGVVDTELSRHFDSIIPGTAWLYQRVGGLFIK-SPLQGAQTTLYCALDK 126
T V A+HPGVV TEL R G+ +L ++ F+K SP QGAQT LY A
Sbjct: 183 EGTGVTVNALHPGVVRTELLRRN-----GSFFLLYKLLRPFLKKSPEQGAQTALYAATSP 237
Query: 127 KCERETGLYYA 137
+ E +G Y++
Sbjct: 238 ELEGVSGKYFS 248
>gnl|CDD|235737 PRK06197, PRK06197, short chain dehydrogenase; Provisional.
Length = 306
Score = 41.2 bits (97), Expect = 4e-05
Identities = 23/62 (37%), Positives = 28/62 (45%), Gaps = 8/62 (12%)
Query: 65 PGANITNVNTYAVHPGVVDTELSRHFDSII-PGTAWLYQRVGGLFIKSPLQGAQTTLYCA 123
GA V A HPGV +TEL+R+ + P L L +SP GA TL A
Sbjct: 199 AGATTIAV---AAHPGVSNTELARNLPRALRPVATVL----APLLAQSPEMGALPTLRAA 251
Query: 124 LD 125
D
Sbjct: 252 TD 253
>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 = 40.3 bits (94), Expect = 1e-04
Identities = 21/69 (30%), Positives = 37/69 (53%), Gaps = 12/69 (17%)
Query: 72 VNTYAVHPG-VVDTELSRHFDSIIPGTAWLYQRVGGL---FIKSPLQGAQTTLYCALDKK 127
+ + ++HPG ++ + + R++ W+Y + L F KS QGA TT+YCA +
Sbjct: 193 ITSNSLHPGNMMYSSIHRNW--------WVYTLLFTLARPFTKSMQQGAATTVYCATAPE 244
Query: 128 CERETGLYY 136
E G+Y+
Sbjct: 245 LEGLGGMYF 253
>gnl|CDD|235736 PRK06196, PRK06196, oxidoreductase; Provisional.
Length = 315
Score = 37.7 bits (88), Expect = 8e-04
Identities = 21/69 (30%), Positives = 32/69 (46%), Gaps = 7/69 (10%)
Query: 72 VNTYAVHPGVVDTELSRHF---DSIIPGTAWLYQ--RVGGLFIKSPLQGAQTTLYCALDK 126
V ++VHPG + T L RH + + G W+ + K+P QGA T ++ A
Sbjct: 204 VRAFSVHPGGILTPLQRHLPREEQVALG--WVDEHGNPIDPGFKTPAQGAATQVWAATSP 261
Query: 127 KCERETGLY 135
+ GLY
Sbjct: 262 QLAGMGGLY 270
>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 = 31.8 bits (73), Expect = 0.063
Identities = 16/56 (28%), Positives = 23/56 (41%), Gaps = 17/56 (30%)
Query: 70 TNVNTYAVHPGVVDTELSRHFDSIIPGTAWLYQRVGGLFIKSPLQGAQTTLYCALD 125
T + A PG V T++ G A K+P +GA+T +Y AL
Sbjct: 168 TGIKVNACCPGWVKTDMG-------GGKAP----------KTPEEGAETPVYLALL 206
>gnl|CDD|163175 TIGR03178, allantoinase, allantoinase. This enzyme carries out
the first step in the degradation of allantoin, a
ring-opening hydrolysis. The seed members of this model
are all in the vicinity of other genes involved in the
processes of xanthine/urate/allantoin catabolism.
Although not included in the seed, many eukaryotic
homologs of this family are included above the trusted
cutoff. Below the noise cutoff are related
hydantoinases.
Length = 443
Score = 30.8 bits (70), Expect = 0.19
Identities = 15/37 (40%), Positives = 18/37 (48%), Gaps = 5/37 (13%)
Query: 64 PPGANITNVNTYAVHPGVVDTELSRHFDSIIPG-TAW 99
P A I + V PGVVDT + H + PG T W
Sbjct: 36 GPAAKIIDAGGLVVFPGVVDTHV--HINE--PGRTEW 68
>gnl|CDD|235975 PRK07231, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 251
Score = 29.8 bits (68), Expect = 0.37
Identities = 10/19 (52%), Positives = 11/19 (57%), Gaps = 2/19 (10%)
Query: 72 VNTYAVHPGVVDTELSRHF 90
VN AV P VV+T L F
Sbjct: 179 VN--AVAPVVVETGLLEAF 195
>gnl|CDD|181335 PRK08264, PRK08264, short chain dehydrogenase; Validated.
Length = 238
Score = 29.5 bits (67), Expect = 0.52
Identities = 7/16 (43%), Positives = 11/16 (68%)
Query: 76 AVHPGVVDTELSRHFD 91
VHPG +DT+++ D
Sbjct: 173 GVHPGPIDTDMAAGLD 188
>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 = 28.9 bits (65), Expect = 0.63
Identities = 6/21 (28%), Positives = 10/21 (47%)
Query: 71 NVNTYAVHPGVVDTELSRHFD 91
+VHPG +DT ++
Sbjct: 169 GTLVLSVHPGPIDTRMAAGAG 189
>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 = 28.8 bits (65), Expect = 0.78
Identities = 15/68 (22%), Positives = 25/68 (36%), Gaps = 5/68 (7%)
Query: 66 GANITNVNTYAVHPGVVDTELSRHFDSIIPGTAWLYQRVGGLFIKSPLQGAQTTLYCALD 125
I VN AV PG+VDT + L + + +P + A+ ++
Sbjct: 166 PYGIR-VN--AVAPGLVDTPMLAKLGP-EEAEKELAAAIPLGRLGTPEEVAEAVVF-LAS 220
Query: 126 KKCERETG 133
+ TG
Sbjct: 221 DEASYITG 228
>gnl|CDD|181609 PRK09009, PRK09009, C factor cell-cell signaling protein;
Provisional.
Length = 235
Score = 28.5 bits (64), Expect = 1.0
Identities = 10/29 (34%), Positives = 16/29 (55%)
Query: 68 NITNVNTYAVHPGVVDTELSRHFDSIIPG 96
++ + A+HPG DT LS+ F +P
Sbjct: 169 SLKHGVVLALHPGTTDTALSKPFQQNVPK 197
>gnl|CDD|235925 PRK07067, PRK07067, sorbitol dehydrogenase; Provisional.
Length = 257
Score = 28.5 bits (64), Expect = 1.1
Identities = 11/22 (50%), Positives = 14/22 (63%), Gaps = 2/22 (9%)
Query: 71 NVNTYAVHPGVVDTELSRHFDS 92
NVN A+ PGVVDT + D+
Sbjct: 177 NVN--AIAPGVVDTPMWDQVDA 196
>gnl|CDD|187668 cd09808, DHRS-12_like_SDR_c-like, human dehydrogenase/reductase SDR
family member (DHRS)-12/FLJ13639-like, classical
(c)-like SDRs. Classical SDR-like subgroup containing
human DHRS-12/FLJ13639, the 36K protein of zebrafish CNS
myelin, and related proteins. DHRS-12/FLJ13639 is
expressed in neurons and oligodendrocytes in the human
cerebral cortex. Proteins in this subgroup share the
glycine-rich NAD-binding motif of the classical SDRs,
have a partial match to the canonical active site
tetrad, but lack the typical active site Ser. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold (alpha/beta folding pattern with a central
beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRs are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes catalyze a
wide range of activities including the metabolism of
steroids, cofactors, carbohydrates, lipids, aromatic
compounds, and amino acids, and act in redox sensing.
Classical SDRs have an TGXXX[AG]XG cofactor binding
motif and a YXXXK active site motif, with the Tyr
residue of the active site motif serving as a critical
catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 255
Score = 28.3 bits (63), Expect = 1.2
Identities = 17/67 (25%), Positives = 30/67 (44%), Gaps = 8/67 (11%)
Query: 71 NVNTYAVHPGVVDTELSRHFDSIIPGTAWLYQRVGGLFIKSPLQGAQTTLYCALDKKC-E 129
++ +HPG DT R + +P + R ++S QGA T ++ AL +
Sbjct: 183 EIHFSVMHPGWADTPAVR---NSMPD---FHARFKDR-LRSEEQGADTVVWLALSSAAAK 235
Query: 130 RETGLYY 136
+G +Y
Sbjct: 236 APSGRFY 242
>gnl|CDD|220365 pfam09726, Macoilin, Transmembrane protein. This entry is a highly
conserved protein present in eukaryotes.
Length = 680
Score = 28.0 bits (62), Expect = 2.2
Identities = 10/48 (20%), Positives = 24/48 (50%)
Query: 28 KEILGRTKRFSNPTILLCDANLQTPTNHYCKNVLFHPPGANITNVNTY 75
EI+ + ++ ++ ++ +++ T HY N L PP ++ + Y
Sbjct: 630 AEIVDLKSKIADILAVMPESRIRSVTPHYSANFLEKPPLVRLSPTSEY 677
>gnl|CDD|237218 PRK12825, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 249
Score = 27.1 bits (61), Expect = 2.7
Identities = 9/25 (36%), Positives = 12/25 (48%), Gaps = 4/25 (16%)
Query: 68 NITNVNTYAVHPGVVDTE-LSRHFD 91
IT VN V PG +DT+ +
Sbjct: 178 GIT-VN--MVAPGDIDTDMKEATIE 199
>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 = 27.1 bits (60), Expect = 2.7
Identities = 7/23 (30%), Positives = 12/23 (52%)
Query: 70 TNVNTYAVHPGVVDTELSRHFDS 92
+ AV PG +DT ++ +S
Sbjct: 177 RGIRVNAVAPGYIDTPMTAALES 199
>gnl|CDD|183775 PRK12826, PRK12826, 3-ketoacyl-(acyl-carrier-protein) reductase;
Reviewed.
Length = 251
Score = 27.2 bits (61), Expect = 2.9
Identities = 12/18 (66%), Positives = 13/18 (72%), Gaps = 3/18 (16%)
Query: 68 NITNVNTYAVHPGVVDTE 85
NIT VN +VHPG VDT
Sbjct: 178 NIT-VN--SVHPGGVDTP 192
>gnl|CDD|219780 pfam08286, Spc24, Spc24 subunit of Ndc80. Spc24 is a component of
the evolutionarily conserved kinetochore-associated
Ndc80 complex and is involved in chromosome segregation.
Length = 117
Score = 26.5 bits (59), Expect = 3.0
Identities = 8/22 (36%), Positives = 10/22 (45%)
Query: 69 ITNVNTYAVHPGVVDTELSRHF 90
I N N V +D +LS F
Sbjct: 87 IRNDNKGDVQVLNLDNKLSPFF 108
>gnl|CDD|237894 PRK15064, PRK15064, ABC transporter ATP-binding protein;
Provisional.
Length = 530
Score = 27.2 bits (61), Expect = 3.1
Identities = 11/19 (57%), Positives = 12/19 (63%), Gaps = 4/19 (21%)
Query: 37 FSNPTILLCDANLQTPTNH 55
FSNP ILL D PTN+
Sbjct: 171 FSNPDILLLD----EPTNN 185
>gnl|CDD|235546 PRK05653, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Validated.
Length = 246
Score = 26.7 bits (60), Expect = 3.7
Identities = 10/21 (47%), Positives = 14/21 (66%), Gaps = 3/21 (14%)
Query: 68 NITNVNTYAVHPGVVDTELSR 88
IT VN AV PG +DT+++
Sbjct: 176 GIT-VN--AVAPGFIDTDMTE 193
>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 = 26.9 bits (60), Expect = 3.7
Identities = 10/20 (50%), Positives = 12/20 (60%), Gaps = 2/20 (10%)
Query: 71 NVNTYAVHPGVVDTELSRHF 90
VN V PGV+DT+ HF
Sbjct: 172 RVNA--VSPGVIDTDALAHF 189
>gnl|CDD|172740 PRK14252, PRK14252, phosphate ABC transporter ATP-binding protein;
Provisional.
Length = 265
Score = 26.5 bits (58), Expect = 4.6
Identities = 18/60 (30%), Positives = 26/60 (43%), Gaps = 4/60 (6%)
Query: 52 PTNHYCKNVLFHPPGANITNVNTYAVHPGVVDTELSRHFDSIIPGTAWLYQRVG-GLFIK 110
P NHY ++ HP NI + V P V +S F P +++ V GL I+
Sbjct: 70 PGNHYEGEIILHPDNVNIL---SPEVDPIEVRMRISMVFQKPNPFPKSIFENVAYGLRIR 126
>gnl|CDD|224640 COG1726, NqrA, Na+-transporting NADH:ubiquinone oxidoreductase,
subunit NqrA [Energy production and conversion].
Length = 447
Score = 26.6 bits (59), Expect = 4.8
Identities = 22/78 (28%), Positives = 29/78 (37%), Gaps = 17/78 (21%)
Query: 55 HYCKNVLFHPPGANITNVNTYAV---HP-GVVDTELSRHFDSIIPGTA----WL--YQRV 104
H CK PP ++N + + HP G+ T H I P A W YQ V
Sbjct: 190 HVCKAAGTLPPQELLSNAHLHEFSGPHPAGLPGT----HIHFIAPVGATKVVWTINYQDV 245
Query: 105 ---GGLFIKSPLQGAQTT 119
G LF+ L +
Sbjct: 246 IAIGKLFLTGELLTERVV 263
>gnl|CDD|185752 cd08961, GH64-TLP-SF, glycoside hydrolase family 64
(beta-1,3-glucanases which produce specific
pentasaccharide oligomers) and thaumatin-like proteins.
This superfamily includes glycoside hydrolases of
family 64 (GH64), these are mostly bacterial
beta-1,3-glucanases which cleave long-chain
polysaccharide beta-1,3-glucans, into specific
pentasaccharide oligomers and are implicated in fungal
cell wall degradation. Also included in this
superfamily are thaumatin, the sweet-tasting protein
from the African berry Thaumatococcus daniellii, and
thaumatin-like proteins (TLPs) which are involved in
host defense and a wide range of developmental
processes in fungi, plants, and animals. Like GH64s,
some TLPs also hydrolyze the beta-1,3-glucans of the
type commonly found in fungal walls. Plant TLPs are
classified as pathogenesis-related (PR) protein family
5 (PR5), their expression is induced by environmental
stresses such as pathogen/pest attack, drought and
cold. Several members of the plant TLP family have been
reported as food allergens from fruits, and pollen
allergens from conifers. Streptomyces matensis
laminaripentaose-producing, beta-1,3-glucanase
(GH64-LPHase), and TLPs have in common, a core
N-terminal barrel domain (domain I) composed of 10
beta-strands, two coming from the C-terminal region of
the protein. In TLPs, this core domain is flanked by
two shorter domains (domains II and III). Small TLPs,
such as Triticum aestivum thaumatin-like xylanase
inhibitor, have a deletion in the third domain (domain
II). GH64-LPHase has a second C-terminal domain which
corresponds positional to, but is much larger than,
domain III of TLP. GH64-LPHase and TLPs are described
as crescent-fold structures. Critical functional
residues, common to GH64-LPHase and TLPs are a Glu and
an Asp residue. LPHase has an electronegative,
substrate-binding cleft and the afore mentioned
conserved Glu and Asp residues are the catalytic
residues essential for beta-1,3-glucan cleavage. In
TLPs, these residues are two of the four conserved
residues which contribute to the strong electronegative
character of the cleft which is associated with the
antifungal activity of TLPs.
Length = 153
Score = 26.0 bits (57), Expect = 5.4
Identities = 13/30 (43%), Positives = 15/30 (50%)
Query: 69 ITNVNTYAVHPGVVDTELSRHFDSIIPGTA 98
ITN Y V + TELS D+ PG A
Sbjct: 3 ITNNCGYQVWIYNLGTELSSAPDASGPGLA 32
>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 = 26.1 bits (58), Expect = 7.4
Identities = 4/26 (15%), Positives = 10/26 (38%)
Query: 67 ANITNVNTYAVHPGVVDTELSRHFDS 92
+ T V P ++T + + +
Sbjct: 169 YGKPGIKTTLVCPYFINTGMFQGVKT 194
>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 = 25.7 bits (57), Expect = 8.5
Identities = 5/14 (35%), Positives = 9/14 (64%)
Query: 75 YAVHPGVVDTELSR 88
++HPG V T++
Sbjct: 177 VSLHPGWVRTDMGG 190
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
0.323 0.139 0.459
Gapped
Lambda K H
0.267 0.0762 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,922,065
Number of extensions: 583594
Number of successful extensions: 471
Number of sequences better than 10.0: 1
Number of HSP's gapped: 467
Number of HSP's successfully gapped: 31
Length of query: 137
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 50
Effective length of database: 7,078,804
Effective search space: 353940200
Effective search space used: 353940200
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 54 (24.5 bits)