RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3626
(189 letters)
>gnl|CDD|187555 cd05244, BVR-B_like_SDR_a, biliverdin IX beta reductase (BVR-B, aka
flavin reductase)-like proteins; atypical (a) SDRs.
Human BVR-B catalyzes pyridine nucleotide-dependent
production of bilirubin-IX beta during fetal
development; in the adult BVR-B has flavin and ferric
reductase activities. Human BVR-B catalyzes the
reduction of FMN, FAD, and riboflavin. Recognition of
flavin occurs mostly by hydrophobic interactions,
accounting for the broad substrate specificity. Atypical
SDRs are distinct from classical SDRs. BVR-B does not
share the key catalytic triad, or conserved tyrosine
typical of SDRs. The glycine-rich NADP-binding motif of
BVR-B is GXXGXXG, which is similar but not identical to
the pattern seen in extended SDRs. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Atypical SDRs include
biliverdin IX beta reductase (BVR-B,aka flavin
reductase), NMRa (a negative transcriptional regulator
of various fungi), progesterone 5-beta-reductase like
proteins, phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. In addition to the
Rossmann fold core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 207
Score = 148 bits (376), Expect = 2e-45
Identities = 77/196 (39%), Positives = 100/196 (51%), Gaps = 53/196 (27%)
Query: 3 KIAIFGATGMTGLCSLEAALKQGLEVCTLLRDPQRLPSEYHSKVEIIQGDVLKLADVKKA 62
KIAI GATG TG + AL +G EV L+RDP +LP+E
Sbjct: 1 KIAIIGATGRTGSAIVREALARGHEVTALVRDPAKLPAE--------------------- 39
Query: 63 IEGKDGLEVCTLLRDPQRLPSEYHSKVEIIQGDVLKLADVKKAIEGKDGVVVALGTRNDL 122
H K++++QGDVL L DVK+A+EG+D V+ ALGTRNDL
Sbjct: 40 -----------------------HEKLKVVQGDVLDLEDVKEALEGQDAVISALGTRNDL 76
Query: 123 SPTTVMSEGMKNIVTAMKEYNVSVVSVCLSAFLFYEPSKV---------PPMFHNVNDDH 173
SPTT+ SEG +NIV+AMK V + V A + KV PP V +DH
Sbjct: 77 SPTTLHSEGTRNIVSAMKAAGVKRLIVVGGAGSLDDRPKVTLVLDTLLFPPALRRVAEDH 136
Query: 174 QRMYNVLKDSGLNYIA 189
RM VL++SGL++ A
Sbjct: 137 ARMLKVLRESGLDWTA 152
>gnl|CDD|222146 pfam13460, NAD_binding_10, NADH(P)-binding.
Length = 182
Score = 70.0 bits (172), Expect = 2e-15
Identities = 47/190 (24%), Positives = 71/190 (37%), Gaps = 59/190 (31%)
Query: 4 IAIFGATGMTGLCSLEAALKQGLEVCTLLRDPQRLPSEYHSKVEIIQGDVLKLADVKKAI 63
IA+ GATG TG ++ L +G +V L R+P + P
Sbjct: 1 IAVIGATGKTGRRLVKELLARGHQVTALSRNPSKAP------------------------ 36
Query: 64 EGKDGLEVCTLLRDPQRLPSEYHSKVEIIQGDVLKLADVKKAIEGKDGVVVALGTRNDLS 123
V +Q D+ LAD+ +A+ G D VV A G R D S
Sbjct: 37 ----------------------APGVTPVQKDLFDLADLAEALAGVDAVVDAFGARPDDS 74
Query: 124 PTTVMSEGMKNIVTAMKEYNVSVVSVCLSAFLFY--EPSKV----PPMFHNVNDDHQRMY 177
+G+K+++ A V + V +SA Y EP P+F
Sbjct: 75 ------DGVKHLLDAAARAGVRRI-VVVSAAGLYRDEPGTFRLDDAPLFPPYARAKAAAE 127
Query: 178 NVLKDSGLNY 187
+L+ SGL++
Sbjct: 128 ELLRASGLDW 137
>gnl|CDD|187537 cd05226, SDR_e_a, Extended (e) and atypical (a) SDRs. Extended or
atypical short-chain dehydrogenases/reductases (SDRs,
aka tyrosine-dependent oxidoreductases) are distinct
from classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately 100
amino acids. Extended SDRs are a diverse collection of
proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. Atypical SDRs generally
lack the catalytic residues characteristic of the SDRs,
and their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Atypical SDRs include biliverdin IX beta
reductase (BVR-B,aka flavin reductase), NMRa (a negative
transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Complex
(multidomain) SDRs such as ketoreductase domains of
fatty acid synthase have a GGXGXXG NAD(P)-binding motif
and an altered active site motif (YXXXN). Fungal type
ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding
motif.
Length = 176
Score = 59.7 bits (145), Expect = 2e-11
Identities = 44/189 (23%), Positives = 62/189 (32%), Gaps = 48/189 (25%)
Query: 4 IAIFGATGMTGLCSLEAALKQGLEVCTLLRDPQRLPSEYHSKVEIIQGDVLKLADVKKAI 63
I I GATG G L+QG EV TLL
Sbjct: 1 ILILGATGFIGRALARELLEQGHEV-TLLV------------------------------ 29
Query: 64 EGKDGLEVCTLLRDPQRLPSEYHSKVEIIQGDVLKLADVKKAIEGKDGVVVALGTRNDL- 122
R+ +RL E V +++GD+ L + A++G D V+ G D
Sbjct: 30 ------------RNTKRLSKEDQEPVAVVEGDLRDLDSLSDAVQGVDVVIHLAGAPRDTR 77
Query: 123 SPTTVMSEGMKNIVTAMKEYNVSVVSVCLSAFLFYE---PSKVPPMFHNVNDDHQRMYNV 179
V EG +N++ A KE V S Y P + V
Sbjct: 78 DFCEVDVEGTRNVLEAAKEAGVKHFIFISSLG-AYGDLHEETEPSPSSPYLAVKAKTEAV 136
Query: 180 LKDSGLNYI 188
L+++ L Y
Sbjct: 137 LREASLPYT 145
>gnl|CDD|187577 cd05267, SDR_a6, atypical (a) SDRs, subgroup 6. These atypical SDR
family members of unknown function have only a partial
match to a prototypical glycine-rich NAD(P)-binding
motif consensus, GXXG, which conserves part of the motif
of extended SDR. Furthermore, they lack the
characteristic active site residues of the SDRs. This
subgroup is related to phenylcoumaran benzylic ether
reductase, an NADPH-dependent aromatic alcohol
reductase. One member is identified as a putative
NAD-dependent epimerase/dehydratase. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Atypical SDRs include
biliverdin IX beta reductase (BVR-B,aka flavin
reductase), NMRa (a negative transcriptional regulator
of various fungi), progesterone 5-beta-reductase like
proteins, phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. In addition to the
Rossmann fold core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 203
Score = 53.5 bits (129), Expect = 3e-09
Identities = 34/130 (26%), Positives = 59/130 (45%), Gaps = 18/130 (13%)
Query: 66 KDGLEVCTLLRDPQRLPSEYHSKVEIIQGDVLKLADVKKAIEGKDGVVVALGTRNDLSPT 125
+E+ LR+ RL ++V +++GD L D+K A+ G+D V LG +
Sbjct: 23 NSNVELTLFLRNAHRLLHLKSARVTVVEGDALNSDDLKAAMRGQDVVYANLGG----TDL 78
Query: 126 TVMSEGMKNIVTAMKEYNVSVVSVCLSAFLFYEPSKVPPMFHNVNDD--------HQRMY 177
+E N+V AMK V + S ++ E VP F N + +++
Sbjct: 79 DQQAE---NVVQAMKAVGVKRLIWTTSLGIYDE---VPGKFGEWNKEFIGNYLAPYRKSA 132
Query: 178 NVLKDSGLNY 187
V+++S L+Y
Sbjct: 133 AVIENSDLDY 142
Score = 43.9 bits (104), Expect = 1e-05
Identities = 22/70 (31%), Positives = 35/70 (50%), Gaps = 7/70 (10%)
Query: 2 KKIAIFGATGMTGLCSLEAAL----KQGLEVCTLLRDPQRLPSEYHSKVEIIQGDVLKLA 57
KK+ I GA G + EA +E+ LR+ RL ++V +++GD L
Sbjct: 1 KKVLILGANGEI---AREATTMLLENSNVELTLFLRNAHRLLHLKSARVTVVEGDALNSD 57
Query: 58 DVKKAIEGKD 67
D+K A+ G+D
Sbjct: 58 DLKAAMRGQD 67
>gnl|CDD|187554 cd05243, SDR_a5, atypical (a) SDRs, subgroup 5. This subgroup
contains atypical SDRs, some of which are identified as
putative NAD(P)-dependent epimerases, one as a putative
NAD-dependent epimerase/dehydratase. Atypical SDRs are
distinct from classical SDRs. Members of this subgroup
have a glycine-rich NAD(P)-binding motif that is very
similar to the extended SDRs, GXXGXXG, and binds NADP.
Generally, this subgroup has poor conservation of the
active site tetrad; however, individual sequences do
contain matches to the YXXXK active site motif, the
upstream Ser, and there is a highly conserved Asp in
place of the usual active site Asn throughout the
subgroup. Atypical SDRs generally lack the catalytic
residues characteristic of the SDRs, and their
glycine-rich NAD(P)-binding motif is often different
from the forms normally seen in classical or extended
SDRs. Atypical SDRs include biliverdin IX beta reductase
(BVR-B,aka flavin reductase), NMRa (a negative
transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. In addition to the
Rossmann fold core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 203
Score = 51.1 bits (123), Expect = 3e-08
Identities = 33/132 (25%), Positives = 59/132 (44%), Gaps = 5/132 (3%)
Query: 59 VKKAIEGKDGLEVCTLLRDPQRLPSEYHSKVEIIQGDVLKLADVKKAIEGKDGVVVALGT 118
V++ + G +V L+RDP + + E++ GD+ + A+EG D V+ A G+
Sbjct: 16 VRELL--DRGYQVRALVRDPSQAEKLEAAGAEVVVGDLTDAESLAAALEGIDAVISAAGS 73
Query: 119 RN--DLSPTTVMSEGMKNIVTAMKEYNVSVVSVCLSAFLFYEPSKVPPMFHNVNDDHQRM 176
V +G N++ A K+ V V +S+ +PS D ++
Sbjct: 74 GGKGGPRTEAVDYDGNINLIDAAKKAGVKRF-VLVSSIGADKPSHPLEALGPYLDAKRKA 132
Query: 177 YNVLKDSGLNYI 188
+ L+ SGL+Y
Sbjct: 133 EDYLRASGLDYT 144
Score = 51.1 bits (123), Expect = 3e-08
Identities = 20/72 (27%), Positives = 35/72 (48%), Gaps = 1/72 (1%)
Query: 3 KIAIFGATGMTGLCSLEAALKQGLEVCTLLRDPQRLPSEYHSKVEIIQGDVLKLADVKKA 62
K+ + GATG G + L +G +V L+RDP + + E++ GD+ + A
Sbjct: 1 KVLVVGATGKVGRHVVRELLDRGYQVRALVRDPSQAEKLEAAGAEVVVGDLTDAESLAAA 60
Query: 63 IEGKDGLEVCTL 74
+EG D + +
Sbjct: 61 LEGIDAV-ISAA 71
>gnl|CDD|225462 COG2910, COG2910, Putative NADH-flavin reductase [General
function prediction only].
Length = 211
Score = 50.4 bits (121), Expect = 5e-08
Identities = 24/66 (36%), Positives = 36/66 (54%), Gaps = 2/66 (3%)
Query: 2 KKIAIFGATGMTGLCSLEAALKQGLEVCTLLRDPQRLPSEYHSKVEIIQGDVLKLADVKK 61
KIAI GA+G G L+ ALK+G EV ++R+ +L + V I+Q D+ L +
Sbjct: 1 MKIAIIGASGKAGSRILKEALKRGHEVTAIVRNASKLAAR--QGVTILQKDIFDLTSLAS 58
Query: 62 AIEGKD 67
+ G D
Sbjct: 59 DLAGHD 64
>gnl|CDD|235630 PRK05865, PRK05865, hypothetical protein; Provisional.
Length = 854
Score = 42.0 bits (98), Expect = 9e-05
Identities = 22/76 (28%), Positives = 34/76 (44%), Gaps = 3/76 (3%)
Query: 3 KIAIFGATGMTGLCSLEAALKQGLEVCTLLRDPQRLPSEYHSKVEIIQGDVLKLADVKKA 62
+IA+ GA+G+ G L QG EV + R P + S + I D+ V+ A
Sbjct: 2 RIAVTGASGVLGRGLTARLLSQGHEVVGIAR---HRPDSWPSSADFIAADIRDATAVESA 58
Query: 63 IEGKDGLEVCTLLRDP 78
+ G D + C +R
Sbjct: 59 MTGADVVAHCAWVRGR 74
Score = 32.7 bits (74), Expect = 0.095
Identities = 15/63 (23%), Positives = 25/63 (39%), Gaps = 2/63 (3%)
Query: 79 QRLPSEYHSKVEIIQGDVLKLADVKKAIEGKDGVVVALGTRNDLSPTTVMSEGMKNIVTA 138
+ P + S + I D+ V+ A+ G D V R + +G N++ A
Sbjct: 32 RHRPDSWPSSADFIAADIRDATAVESAMTGADVVAHCAWVRGRNDHINI--DGTANVLKA 89
Query: 139 MKE 141
M E
Sbjct: 90 MAE 92
>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 = 41.6 bits (98), Expect = 1e-04
Identities = 21/85 (24%), Positives = 30/85 (35%), Gaps = 2/85 (2%)
Query: 4 IAIFGATGMTGLCSLEAALKQGLEVCTLLRDPQRLPSEYHSKVEIIQGDVLKL-ADVKKA 62
I + GA G G L L V + +R P KVE ++ D+ A
Sbjct: 1 ILVTGAAGGLGR-LLARRLAASPRVIGVDGLDRRRPPGSPPKVEYVRLDIRDPAAADVFR 59
Query: 63 IEGKDGLEVCTLLRDPQRLPSEYHS 87
D + + DP R +E H
Sbjct: 60 EREADAVVHLAFILDPPRDGAERHR 84
Score = 31.6 bits (72), Expect = 0.23
Identities = 22/91 (24%), Positives = 32/91 (35%), Gaps = 9/91 (9%)
Query: 70 EVCTLLRDPQRLPSEYHSKVEIIQGDVLKLADVKKAIEGKDGVVVALGTRNDLSPTTVMS 129
V + +R P KVE ++ D+ A E + VV L L P +
Sbjct: 23 RVIGVDGLDRRRPPGSPPKVEYVRLDIRDPAAADVFREREADAVVHLAF--ILDPPRDGA 80
Query: 130 E-------GMKNIVTAMKEYNVSVVSVCLSA 153
E G +N++ A V V V S
Sbjct: 81 ERHRINVDGTQNVLDACAAAGVPRVVVTSSV 111
>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 = 41.2 bits (97), Expect = 1e-04
Identities = 19/70 (27%), Positives = 30/70 (42%)
Query: 4 IAIFGATGMTGLCSLEAALKQGLEVCTLLRDPQRLPSEYHSKVEIIQGDVLKLADVKKAI 63
I + GATG G L+ G V L+R +R + E++ GD+ A + A+
Sbjct: 1 ILVTGATGRIGSKVATTLLEAGRPVRALVRSDERAAALAARGAEVVVGDLDDPAVLAAAL 60
Query: 64 EGKDGLEVCT 73
G D +
Sbjct: 61 AGVDAVFFLA 70
>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 = 40.7 bits (96), Expect = 2e-04
Identities = 20/60 (33%), Positives = 29/60 (48%)
Query: 8 GATGMTGLCSLEAALKQGLEVCTLLRDPQRLPSEYHSKVEIIQGDVLKLADVKKAIEGKD 67
GATG G + A L QG V L+R VE+++GD+ A + A++G D
Sbjct: 5 GATGFLGSNLVRALLAQGYRVRALVRSGSDAVLLDGLPVEVVEGDLTDAASLAAAMKGCD 64
Score = 30.3 bits (69), Expect = 0.45
Identities = 13/47 (27%), Positives = 21/47 (44%)
Query: 66 KDGLEVCTLLRDPQRLPSEYHSKVEIIQGDVLKLADVKKAIEGKDGV 112
G V L+R VE+++GD+ A + A++G D V
Sbjct: 20 AQGYRVRALVRSGSDAVLLDGLPVEVVEGDLTDAASLAAAMKGCDRV 66
>gnl|CDD|223774 COG0702, COG0702, Predicted nucleoside-diphosphate-sugar
epimerases [Cell envelope biogenesis, outer membrane /
Carbohydrate transport and metabolism].
Length = 275
Score = 40.3 bits (94), Expect = 3e-04
Identities = 22/80 (27%), Positives = 38/80 (47%), Gaps = 3/80 (3%)
Query: 2 KKIAIFGATGMTGLCSLEAALKQGLEVCTLLRDPQRLPSEYHSK-VEIIQGDVLKLADVK 60
KI + GATG G + L +G EV +R+P+ + + VE++ GD+ +
Sbjct: 1 MKILVTGATGFVGGAVVRELLARGHEVRAAVRNPEAAAA--LAGGVEVVLGDLRDPKSLV 58
Query: 61 KAIEGKDGLEVCTLLRDPQR 80
+G DG+ + + L D
Sbjct: 59 AGAKGVDGVLLISGLLDGSD 78
>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 = 39.9 bits (94), Expect = 3e-04
Identities = 22/66 (33%), Positives = 34/66 (51%)
Query: 4 IAIFGATGMTGLCSLEAALKQGLEVCTLLRDPQRLPSEYHSKVEIIQGDVLKLADVKKAI 63
I + GATG G +E L + V L+R+P++ + VE+ QGD +++A
Sbjct: 1 ILVTGATGKLGTAVVELLLAKVASVVALVRNPEKAKAFAADGVEVRQGDYDDPETLERAF 60
Query: 64 EGKDGL 69
EG D L
Sbjct: 61 EGVDRL 66
Score = 31.5 bits (72), Expect = 0.19
Identities = 32/124 (25%), Positives = 53/124 (42%), Gaps = 15/124 (12%)
Query: 66 KDGLEVCTLLRDPQRLPSEYHSKVEIIQGDVLKLADVKKAIEGKDGVVVALGTRNDLSPT 125
V L+R+P++ + VE+ QGD +++A EG D +++ +SP+
Sbjct: 20 AKVASVVALVRNPEKAKAFAADGVEVRQGDYDDPETLERAFEGVDRLLL-------ISPS 72
Query: 126 TV--MSEGMKNIVTAMKEYNVSVVSVCLSAFLFYEPSKVPPMFHNVNDDHQRMYNVLKDS 183
+ + KN + A K+ V + V LSA E S DH L+ S
Sbjct: 73 DLEDRIQQHKNFIDAAKQAGVKHI-VYLSASGADEDSPFLLA-----RDHGATEKYLEAS 126
Query: 184 GLNY 187
G+ Y
Sbjct: 127 GIPY 130
>gnl|CDD|223528 COG0451, WcaG, Nucleoside-diphosphate-sugar epimerases [Cell
envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 314
Score = 39.9 bits (93), Expect = 4e-04
Identities = 18/68 (26%), Positives = 25/68 (36%), Gaps = 5/68 (7%)
Query: 2 KKIAIFGATGMTG--LCSLEAALKQGLEVCTLLRDPQRLPSEYHSKVEIIQGDVLKLADV 59
+I + G G G L E L G +V L R L S VE + D+ V
Sbjct: 1 MRILVTGGAGFIGSHLV--ERLLAAGHDVRGLDRLRDGLD-PLLSGVEFVVLDLTDRDLV 57
Query: 60 KKAIEGKD 67
+ +G
Sbjct: 58 DELAKGVP 65
Score = 31.5 bits (71), Expect = 0.22
Identities = 19/88 (21%), Positives = 30/88 (34%), Gaps = 10/88 (11%)
Query: 66 KDGLEVCTLLRDPQRLPSEYHSKVEIIQGDVLKLADVKKAIEGKDGVVVALG------TR 119
G +V L R L S VE + D+ V + +G V+ L
Sbjct: 22 AAGHDVRGLDRLRDGLD-PLLSGVEFVVLDLTDRDLVDELAKGVPDAVIHLAAQSSVPDS 80
Query: 120 NDLSPTTVMS---EGMKNIVTAMKEYNV 144
N P + +G N++ A + V
Sbjct: 81 NASDPAEFLDVNVDGTLNLLEAARAAGV 108
>gnl|CDD|187556 cd05245, SDR_a2, atypical (a) SDRs, subgroup 2. This subgroup
contains atypical SDRs, one member is identified as
Escherichia coli protein ybjT, function unknown.
Atypical SDRs are distinct from classical SDRs. Members
of this subgroup have a glycine-rich NAD(P)-binding
motif consensus that generally matches the extended
SDRs, TGXXGXXG, but lacks the characteristic active
site residues of the SDRs. This subgroup has basic
residues (HXXXR) in place of the active site motif
YXXXK, these may have a catalytic role. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif
is often different from the forms normally seen in
classical or extended SDRs. Atypical SDRs include
biliverdin IX beta reductase (BVR-B,aka flavin
reductase), NMRa (a negative transcriptional regulator
of various fungi), progesterone 5-beta-reductase like
proteins, phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane
reductase, isoflavone reductases, and others. SDRs are
a functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. In addition to the Rossmann fold
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids, and typically have a TGXXGXXG cofactor
binding motif. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 293
Score = 39.6 bits (93), Expect = 4e-04
Identities = 19/65 (29%), Positives = 37/65 (56%), Gaps = 1/65 (1%)
Query: 4 IAIFGATGMTGLCSLEAALKQGLEVCTLLRDPQRL-PSEYHSKVEIIQGDVLKLADVKKA 62
+ + GATG G + L++G +V L+R P++L + +V +++GD+ ++ A
Sbjct: 1 VLVTGATGYVGGRLVPRLLQEGHQVRALVRSPEKLADRPWSERVTVVRGDLEDPESLRAA 60
Query: 63 IEGKD 67
+EG D
Sbjct: 61 LEGID 65
Score = 32.3 bits (74), Expect = 0.11
Identities = 13/49 (26%), Positives = 28/49 (57%), Gaps = 1/49 (2%)
Query: 66 KDGLEVCTLLRDPQRL-PSEYHSKVEIIQGDVLKLADVKKAIEGKDGVV 113
++G +V L+R P++L + +V +++GD+ ++ A+EG D
Sbjct: 20 QEGHQVRALVRSPEKLADRPWSERVTVVRGDLEDPESLRAALEGIDTAY 68
>gnl|CDD|187651 cd08947, NmrA_TMR_like_SDR_a, NmrA (a transcriptional regulator),
HSCARG (an NADPH sensor), and triphenylmethane reductase
(TMR) like proteins, atypical (a) SDRs. Atypical SDRs
belonging to this subgroup include NmrA, HSCARG, and
TMR, these proteins bind NAD(P) but they lack the usual
catalytic residues of the SDRs. Atypical SDRs are
distinct from classical SDRs. NmrA is a negative
transcriptional regulator of various fungi, involved in
the post-translational modulation of the GATA-type
transcription factor AreA. NmrA lacks the canonical
GXXGXXG NAD-binding motif and has altered residues at
the catalytic triad, including a Met instead of the
critical Tyr residue. NmrA may bind nucleotides but
appears to lack any dehydrogenase activity. HSCARG has
been identified as a putative NADP-sensing molecule, and
redistributes and restructures in response to NADPH/NADP
ratios. Like NmrA, it lacks most of the active site
residues of the SDR family, but has an NAD(P)-binding
motif similar to the extended SDR family, GXXGXXG. TMR,
an NADP-binding protein, lacks the active site residues
of the SDRs but has a glycine rich NAD(P)-binding motif
that matches the extended SDRs. Atypical SDRs include
biliverdin IX beta reductase (BVR-B,aka flavin
reductase), NMRa (a negative transcriptional regulator
of various fungi), progesterone 5-beta-reductase like
proteins, phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. In addition to the
Rossmann fold core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 224
Score = 38.3 bits (89), Expect = 0.001
Identities = 30/165 (18%), Positives = 58/165 (35%), Gaps = 16/165 (9%)
Query: 4 IAIFGATGMTGLCSLEAALKQGL-EVCTLLRDPQRLPSEYHSKVEIIQGDVLKLADVKKA 62
IA+ GATG G + L +G +V ++R+ ++ + VE+ QGD + ++KA
Sbjct: 1 IAVTGATGQQGGSVIRHLLAKGASQVRAVVRNVEKAATLADQGVEVRQGDYNQPELLQKA 60
Query: 63 IEGKDGLEVCTLLRDPQRLPSEYHSKVEIIQGDVLKLADVKKAIEGKDGVVVALGTRNDL 122
G L + T Y + +EI QG + A + + G
Sbjct: 61 FAGASKLFIIT--------GPHYDNTLEIKQGKNV----ADAARRAGVKHIYSTGYAFAE 108
Query: 123 SPTTVMSEGMKNIVTAMKEYNVSVVSV---CLSAFLFYEPSKVPP 164
++ + A++ + + + E
Sbjct: 109 ESAIPLAHVKLAVEYAIRTTGIPYTFLRNGLYTENFVSEGLPAAD 153
Score = 27.1 bits (60), Expect = 5.9
Identities = 21/112 (18%), Positives = 41/112 (36%), Gaps = 10/112 (8%)
Query: 76 RDPQRLPSEYHSKVEIIQGDVLKLADVKKAIEGKDGVVVALGTRNDLSPTTVMSEGMKNI 135
R+ ++ + VE+ QGD + ++KA G + + G D + KN+
Sbjct: 31 RNVEKAATLADQGVEVRQGDYNQPELLQKAFAGASKLFIITGPHYDNTLEIKQG---KNV 87
Query: 136 VTAMKEYNVSVVSVCLSAFLFYEPSKVPPMFHNVNDDHQRMYNVLKDSGLNY 187
A + V + AF P+ H + ++ +G+ Y
Sbjct: 88 ADAARRAGVKHIYSTGYAFAEES---AIPLAHV----KLAVEYAIRTTGIPY 132
>gnl|CDD|191263 pfam05368, NmrA, NmrA-like family. NmrA is a negative
transcriptional regulator involved in the
post-translational modification of the transcription
factor AreA. NmrA is part of a system controlling
nitrogen metabolite repression in fungi. This family
only contains a few sequences as iteration results in
significant matches to other Rossmann fold families.
Length = 232
Score = 37.2 bits (87), Expect = 0.002
Identities = 23/67 (34%), Positives = 38/67 (56%), Gaps = 2/67 (2%)
Query: 4 IAIFGATGMTGLCSLEAALKQGLEVCTLLRDPQRLPSEYHSK--VEIIQGDVLKLADVKK 61
I +FGATG G + A+LK G V L+RDP+ ++ VE+++GD+ + +
Sbjct: 1 ILVFGATGYQGGSVVRASLKAGHPVRALVRDPKSELAKSLKAAGVELVEGDLDDHESLVE 60
Query: 62 AIEGKDG 68
A++G D
Sbjct: 61 ALKGVDV 67
>gnl|CDD|187560 cd05250, CC3_like_SDR_a, CC3(TIP30)-like, atypical (a) SDRs.
Atypical SDRs in this subgroup include CC3 (also known
as TIP30) which is implicated in tumor suppression.
Atypical SDRs are distinct from classical SDRs. Members
of this subgroup have a glycine rich NAD(P)-binding
motif that resembles the extended SDRs, and have an
active site triad of the SDRs (YXXXK and upstream Ser),
although the upstream Asn of the usual SDR active site
is substituted with Asp. For CC3, the Tyr of the triad
is displaced compared to the usual SDRs and the protein
is monomeric, both these observations suggest that the
usual SDR catalytic activity is not present. NADP
appears to serve an important role as a ligand, and may
be important in the interaction with other
macromolecules. 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 = 214
Score = 36.9 bits (86), Expect = 0.002
Identities = 18/69 (26%), Positives = 28/69 (40%), Gaps = 5/69 (7%)
Query: 2 KKIAIFGATGMTGLCSLEAALKQGL--EVCTLLRDPQRLPSEY-HSKVEIIQGDVLKLAD 58
K + GATG+ G L LK +V ++R L K+ I D +L +
Sbjct: 1 KTALVLGATGLVGKHLLRELLKSPYYSKVTAIVRRK--LTFPEAKEKLVQIVVDFERLDE 58
Query: 59 VKKAIEGKD 67
+A + D
Sbjct: 59 YLEAFQNPD 67
>gnl|CDD|187540 cd05229, SDR_a3, atypical (a) SDRs, subgroup 3. These atypical
SDR family members of unknown function have a
glycine-rich NAD(P)-binding motif consensus that is
very similar to the extended SDRs, GXXGXXG. Generally,
this group has poor conservation of the active site
tetrad, However, individual sequences do contain
matches to the YXXXK active site motif, and generally
Tyr or Asn in place of the upstream Ser found in most
SDRs. Atypical SDRs generally lack the catalytic
residues characteristic of the SDRs, and their
glycine-rich NAD(P)-binding motif is often different
from the forms normally seen in classical or extended
SDRs. Atypical SDRs include biliverdin IX beta
reductase (BVR-B,aka flavin reductase), NMRa (a
negative transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane
reductase, isoflavone reductases, and others. SDRs are
a functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. In addition to the Rossmann fold
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids, and typically have a TGXXGXXG cofactor
binding motif. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 302
Score = 36.5 bits (85), Expect = 0.005
Identities = 16/65 (24%), Positives = 27/65 (41%), Gaps = 2/65 (3%)
Query: 3 KIAIFGATGMTGLCSLEAALKQGLEVCTLLRDPQRLPSEYHSKVEIIQGDVLKLADVKKA 62
+ GA+G G ++G +V + R +L + VEI+ D + + V A
Sbjct: 1 TAHVLGASGPIGREVARELRRRGWDVRLVSRSGSKL--AWLPGVEIVAADAMDASSVIAA 58
Query: 63 IEGKD 67
G D
Sbjct: 59 ARGAD 63
Score = 31.1 bits (71), Expect = 0.29
Identities = 17/83 (20%), Positives = 30/83 (36%), Gaps = 3/83 (3%)
Query: 65 GKDGLEVCTLLRDPQRLPSEYHSKVEIIQGDVLKLADVKKAIEGKDGVVVALGTRNDLSP 124
+ G +V + R +L + VEI+ D + + V A G D +
Sbjct: 20 RRRGWDVRLVSRSGSKL--AWLPGVEIVAADAMDASSVIAAARGADVIYHCANPAYTRWE 77
Query: 125 TTVMSEGMKNIVTAMKEYNVSVV 147
M+N+V A + +V
Sbjct: 78 ELFPPL-MENVVAAAEANGAKLV 99
>gnl|CDD|187561 cd05251, NmrA_like_SDR_a, NmrA (a transcriptional regulator) and
HSCARG (an NADPH sensor) like proteins, atypical (a)
SDRs. NmrA and HSCARG like proteins. NmrA is a
negative transcriptional regulator of various fungi,
involved in the post-translational modulation of the
GATA-type transcription factor AreA. NmrA lacks the
canonical GXXGXXG NAD-binding motif and has altered
residues at the catalytic triad, including a Met
instead of the critical Tyr residue. NmrA may bind
nucleotides but appears to lack any dehydrogenase
activity. HSCARG has been identified as a putative
NADP-sensing molecule, and redistributes and
restructures in response to NADPH/NADP ratios. Like
NmrA, it lacks most of the active site residues of the
SDR family, but has an NAD(P)-binding motif similar to
the extended SDR family, GXXGXXG. SDRs are a
functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Atypical
SDRs are distinct from classical SDRs. Classical SDRs
have an TGXXX[AG]XG cofactor binding motif and a YXXXK
active site motif, with the Tyr residue of the active
site motif serving as a critical catalytic residue
(Tyr-151, human 15-hydroxyprostaglandin dehydrogenase
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser and/or an Asn, contributing to
the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. In addition to the Rossmann fold core
region typical of all SDRs, extended SDRs have a less
conserved C-terminal extension of approximately 100
amino acids, and typically have a TGXXGXXG cofactor
binding motif. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 242
Score = 36.1 bits (84), Expect = 0.006
Identities = 26/80 (32%), Positives = 37/80 (46%), Gaps = 25/80 (31%)
Query: 4 IAIFGATGMTGLCSLEAALKQGLEVC-TLLRDPQ-------RLPSEYHSK------VEII 49
I +FGATG KQG V LL+DP R PS +K VE++
Sbjct: 1 ILVFGATG-----------KQGGSVVRALLKDPGFKVRALTRDPSSPAAKALAAPGVEVV 49
Query: 50 QGDVLKLADVKKAIEGKDGL 69
QGD+ ++ A++G G+
Sbjct: 50 QGDLDDPESLEAALKGVYGV 69
>gnl|CDD|224015 COG1090, COG1090, Predicted nucleoside-diphosphate sugar
epimerase [General function prediction only].
Length = 297
Score = 35.7 bits (83), Expect = 0.008
Identities = 18/50 (36%), Positives = 24/50 (48%), Gaps = 2/50 (4%)
Query: 4 IAIFGATGMTGLCSLEAAL-KQGLEVCTLLRDPQRLPSEYHSKVEIIQGD 52
I I G TG+ G +L A L K G +V L R P + H V + +G
Sbjct: 1 ILITGGTGLIG-RALTARLRKGGHQVTILTRRPPKASQNLHPNVTLWEGL 49
>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 = 35.4 bits (82), Expect = 0.010
Identities = 22/98 (22%), Positives = 42/98 (42%), Gaps = 9/98 (9%)
Query: 59 VKKAIEGKDGLEVCTLLRDPQRLPSEYHSKVEI---IQGDVLKLADVKKAIEGKDGVVVA 115
V+ + + EV E SK+++ I+GDV D+++A++G D V+
Sbjct: 14 VRLLLREGELQEVRVFDLRFSPELLEDFSKLQVITYIEGDVTDKQDLRRALQGSDVVIHT 73
Query: 116 LG---TRNDLSPTTVMS---EGMKNIVTAMKEYNVSVV 147
T+M +G +N++ A + V V+
Sbjct: 74 AAIIDVFGKAYRDTIMKVNVKGTQNVLDACVKAGVRVL 111
Score = 31.2 bits (71), Expect = 0.26
Identities = 17/68 (25%), Positives = 29/68 (42%), Gaps = 5/68 (7%)
Query: 5 AIFGATGMTG--LCSLEAALKQGLEVCTLLRDPQRLPSEYHSKVEI---IQGDVLKLADV 59
+ G G G + L + EV E SK+++ I+GDV D+
Sbjct: 1 LVTGGGGFLGRHIVRLLLREGELQEVRVFDLRFSPELLEDFSKLQVITYIEGDVTDKQDL 60
Query: 60 KKAIEGKD 67
++A++G D
Sbjct: 61 RRALQGSD 68
>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 = 35.0 bits (81), Expect = 0.012
Identities = 17/64 (26%), Positives = 31/64 (48%), Gaps = 3/64 (4%)
Query: 4 IAIFGATGMTGLCSLEAALKQGLEVCTLLRDPQR---LPSEYHSKVEIIQGDVLKLADVK 60
I G G +E + +G +V L R ++ L +++ V ++GDV LAD +
Sbjct: 7 ALITGGGSGLGRALVERFVAEGAKVAVLDRSAEKVAELRADFGDAVVGVEGDVRSLADNE 66
Query: 61 KAIE 64
+A+
Sbjct: 67 RAVA 70
Score = 30.8 bits (70), Expect = 0.31
Identities = 16/57 (28%), Positives = 31/57 (54%), Gaps = 5/57 (8%)
Query: 54 LKLADVKKAIEGKDGLEVCTLLRDPQR---LPSEYHSKVEIIQGDVLKLADVKKAIE 107
L A V++ + +G +V L R ++ L +++ V ++GDV LAD ++A+
Sbjct: 16 LGRALVERFVA--EGAKVAVLDRSAEKVAELRADFGDAVVGVEGDVRSLADNERAVA 70
>gnl|CDD|163279 TIGR03466, HpnA, hopanoid-associated sugar epimerase. The
sequences in this family are members of the pfam01370
superfamily of NAD-dependent epimerases and
dehydratases typically acting on nucleotide-sugar
substrates. The genes of the family modeled here are
generally in the same locus with genes involved in the
biosynthesis and elaboration of hopene, the cyclization
product of the polyisoprenoid squalene. This gene and
its association with hopene biosynthesis in Zymomonas
mobilis has been noted in the literature where the gene
symbol hpnA was assigned. Hopanoids are known to be
components of the plasma membrane and to have polar
sugar head groups in Z. mobilis and other species.
Length = 328
Score = 35.0 bits (81), Expect = 0.013
Identities = 22/64 (34%), Positives = 34/64 (53%)
Query: 2 KKIAIFGATGMTGLCSLEAALKQGLEVCTLLRDPQRLPSEYHSKVEIIQGDVLKLADVKK 61
K+ + GATG G + L+QG EV L+R + VEI++GD+ A ++K
Sbjct: 1 MKVLVTGATGFVGSAVVRLLLEQGEEVRVLVRPTSDRRNLEGLDVEIVEGDLRDPASLRK 60
Query: 62 AIEG 65
A+ G
Sbjct: 61 AVAG 64
>gnl|CDD|180983 PRK07453, PRK07453, protochlorophyllide oxidoreductase; Validated.
Length = 322
Score = 35.0 bits (81), Expect = 0.014
Identities = 36/143 (25%), Positives = 57/143 (39%), Gaps = 38/143 (26%)
Query: 6 IFGATGMTGLCSLEAALKQGLEVCTLLRDPQR---------LPSE-YHSKVEIIQGDVLK 55
I GA+ GL + +A K+G V R+ ++ +P + Y II D+
Sbjct: 11 ITGASSGVGLYAAKALAKRGWHVIMACRNLKKAEAAAQELGIPPDSYT----IIHIDLGD 66
Query: 56 LADVKKAIEGKDGLE------VCT------LLRDPQRLPSEYHSKVE--------IIQGD 95
L V++ ++ L VC LL++P R P Y + +
Sbjct: 67 LDSVRRFVDDFRALGKPLDALVCNAAVYMPLLKEPLRSPQGYELSMATNHLGHFLLCN-- 124
Query: 96 VLKLADVKKAIEGKDGVVVALGT 118
L L D+KK+ D +V LGT
Sbjct: 125 -LLLEDLKKS-PAPDPRLVILGT 145
>gnl|CDD|235739 PRK06200, PRK06200, 2,3-dihydroxy-2,3-dihydrophenylpropionate
dehydrogenase; Provisional.
Length = 263
Score = 33.4 bits (77), Expect = 0.041
Identities = 17/65 (26%), Positives = 27/65 (41%), Gaps = 3/65 (4%)
Query: 2 KKIAIFGATGMTGLCSLEAALKQGLEVCTLLRDP---QRLPSEYHSKVEIIQGDVLKLAD 58
+ I G G +E L +G V L R L + V +++GDV AD
Sbjct: 7 QVALITGGGSGIGRALVERFLAEGARVAVLERSAEKLASLRQRFGDHVLVVEGDVTSYAD 66
Query: 59 VKKAI 63
++A+
Sbjct: 67 NQRAV 71
Score = 29.2 bits (66), Expect = 1.3
Identities = 14/56 (25%), Positives = 26/56 (46%), Gaps = 5/56 (8%)
Query: 54 LKLADVKKAIEGKDGLEVCTLLRDP---QRLPSEYHSKVEIIQGDVLKLADVKKAI 106
+ A V++ + +G V L R L + V +++GDV AD ++A+
Sbjct: 18 IGRALVERFLA--EGARVAVLERSAEKLASLRQRFGDHVLVVEGDVTSYADNQRAV 71
>gnl|CDD|185103 PRK15181, PRK15181, Vi polysaccharide biosynthesis protein TviC;
Provisional.
Length = 348
Score = 33.5 bits (76), Expect = 0.050
Identities = 23/89 (25%), Positives = 46/89 (51%), Gaps = 7/89 (7%)
Query: 84 EYHSKVEIIQGDVLKLADVKKAIEGKDGVV--VALGT-----RNDLSPTTVMSEGMKNIV 136
E S+ IQGD+ K D +KA + D V+ ALG+ ++ ++ + +G N++
Sbjct: 66 EQWSRFIFIQGDIRKFTDCQKACKNVDYVLHQAALGSVPRSLKDPIATNSANIDGFLNML 125
Query: 137 TAMKEYNVSVVSVCLSAFLFYEPSKVPPM 165
TA ++ +VS + S+ + + +P +
Sbjct: 126 TAARDAHVSSFTYAASSSTYGDHPDLPKI 154
>gnl|CDD|187569 cd05259, PCBER_SDR_a, phenylcoumaran benzylic ether reductase
(PCBER) like, atypical (a) SDRs. PCBER and
pinoresinol-lariciresinol reductases are NADPH-dependent
aromatic alcohol reductases, and are atypical members of
the SDR family. Other proteins in this subgroup are
identified as eugenol synthase. These proteins contain
an N-terminus characteristic of NAD(P)-binding proteins
and a small C-terminal domain presumed to be involved in
substrate binding, but they do not have the conserved
active site Tyr residue typically found in SDRs.
Numerous other members have unknown functions. The
glycine rich NADP-binding motif in this subgroup is of 2
forms: GXGXXG and G[GA]XGXXG; it tends to be atypical
compared with the forms generally seen in classical or
extended SDRs. The usual SDR active site tetrad is not
present, but a critical active site Lys at the usual SDR
position has been identified in various members, though
other charged and polar residues are found at this
position in this subgroup. Atypical SDR-related proteins
retain the Rossmann fold of the SDRs, but have limited
sequence identity and generally lack the catalytic
properties of the archetypical members. Atypical SDRs
include biliverdin IX beta reductase (BVR-B,aka flavin
reductase), NMRa (a negative transcriptional regulator
of various fungi), progesterone 5-beta-reductase like
proteins, phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. In addition to the
Rossmann fold core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 282
Score = 32.7 bits (75), Expect = 0.075
Identities = 32/135 (23%), Positives = 53/135 (39%), Gaps = 25/135 (18%)
Query: 3 KIAIFGATGMTGLCSLEAALKQ-GLEVCTLLRDPQRLPSEYH-SKVEIIQGDVLKLADVK 60
KIAI GATG G + A L G V L R +E+ S V+++ D +
Sbjct: 1 KIAIAGATGTLGGPIVSALLASPGFTVTVLTRPSSTSSNEFQPSGVKVVPVDYASHESLV 60
Query: 61 KAIEGKDGLEVCTLLRDP----------------QR-LPSEYHSKVEII----QGDVLKL 99
A++G D + + L +R +PSE+ + I D+
Sbjct: 61 AALKGVDAV-ISALGGAAIGDQLKLIDAAIAAGVKRFIPSEFGVDYDRIGALPLLDLFDE 119
Query: 100 -ADVKKAIEGKDGVV 113
DV++ + K+ +
Sbjct: 120 KRDVRRYLRAKNAGL 134
>gnl|CDD|187552 cd05241, 3b-HSD-like_SDR_e, 3beta-hydroxysteroid dehydrogenases
(3b-HSD)-like, extended (e) SDRs. Extended SDR family
domains belonging to this subgroup have the
characteristic active site tetrad and a fairly
well-conserved NAD(P)-binding motif. 3b-HSD catalyzes
the NAD-dependent conversion of various steroids, such
as pregnenolone to progesterone, or androstenediol to
testosterone. This subgroup includes an unusual
bifunctional 3b-HSD/C-4 decarboxylase from Arabidopsis
thaliana, and Saccharomyces cerevisiae ERG26, a
3b-HSD/C-4 decarboxylase, involved in the synthesis of
ergosterol, the major sterol of yeast. It also includes
human 3 beta-HSD/HSD3B1 and C(27) 3beta-HSD/
[3beta-hydroxy-delta(5)-C(27)-steroid oxidoreductase;
HSD3B7]. C(27) 3beta-HSD/HSD3B7 is a membrane-bound
enzyme of the endoplasmic reticulum, that catalyzes the
isomerization and oxidation of 7alpha-hydroxylated
sterol intermediates, an early step in bile acid
biosynthesis. Mutations in the human NSDHL (NAD(P)H
steroid dehydrogenase-like protein) cause CHILD
syndrome (congenital hemidysplasia with ichthyosiform
nevus and limb defects), an X-linked dominant,
male-lethal trait. Mutations in the human gene encoding
C(27) 3beta-HSD underlie a rare autosomal recessive
form of neonatal cholestasis. 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 sythase 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 = 331
Score = 32.0 bits (73), Expect = 0.14
Identities = 16/65 (24%), Positives = 32/65 (49%), Gaps = 3/65 (4%)
Query: 6 IFGATGMTGLCSLEAALKQGLEVCTL--LRDP-QRLPSEYHSKVEIIQGDVLKLADVKKA 62
+ G +G G ++ L++G + P + L + H +E ++GD+ DV++A
Sbjct: 4 VTGGSGFFGERLVKQLLERGGTYVRSFDIAPPGEALSAWQHPNIEFLKGDITDRNDVEQA 63
Query: 63 IEGKD 67
+ G D
Sbjct: 64 LSGAD 68
Score = 31.6 bits (72), Expect = 0.22
Identities = 11/36 (30%), Positives = 20/36 (55%)
Query: 78 PQRLPSEYHSKVEIIQGDVLKLADVKKAIEGKDGVV 113
+ L + H +E ++GD+ DV++A+ G D V
Sbjct: 36 GEALSAWQHPNIEFLKGDITDRNDVEQALSGADCVF 71
>gnl|CDD|200431 TIGR04180, EDH_00030, NAD dependent epimerase/dehydratase,
LLPSF_EDH_00030 family. This clade within the NAD
dependent epimerase/dehydratase superfamily (pfam01370)
is characterized by inclusion of its members within a
cassette of seven distinctive enzymes. These include
four genes homologous to the elements of the neuraminic
(sialic) acid biosynthesis cluster (NeuABCD), an
aminotransferase and a nucleotidyltransferase in
addition to the epimerase/dehydratase. Together it is
very likely that these enzymes direct the biosynthesis
of a nine-carbon sugar analagous to CMP-neuraminic
acid. These seven genes form the core of the cassette,
although they are often accompanied by additional genes
that may further modify the product sugar. Although
this cassette is widely distributed in bacteria, the
family nomenclature arises from the instance in
Leptospira interrogans serovar Lai, str. 56601, where
it appears as the 30th gene in the 91-gene
lipopolysaccharide biosynthesis cluster.
Length = 297
Score = 31.9 bits (73), Expect = 0.15
Identities = 22/70 (31%), Positives = 33/70 (47%), Gaps = 12/70 (17%)
Query: 8 GATGMTGLCSLEAALKQGLEVCTLLR----------DPQRLPSEYHSKVEIIQGDVLKLA 57
GA G G +EA ++QG EV + D P E K+E++ GD+
Sbjct: 5 GADGFIGSHLVEALVRQGYEVRAFVLYNSFNSWGWLD--TSPPEVKDKIEVVTGDIRDPD 62
Query: 58 DVKKAIEGKD 67
V+KA++G D
Sbjct: 63 SVRKAMKGCD 72
Score = 30.7 bits (70), Expect = 0.34
Identities = 12/33 (36%), Positives = 19/33 (57%)
Query: 80 RLPSEYHSKVEIIQGDVLKLADVKKAIEGKDGV 112
P E K+E++ GD+ V+KA++G D V
Sbjct: 42 TSPPEVKDKIEVVTGDIRDPDSVRKAMKGCDVV 74
>gnl|CDD|188239 TIGR02650, RNase_Z_T_toga, ribonuclease Z, Thermotoga type.
Members of this protein family are ribonuclease Z as
found in the genus Thermotoga, where the enzyme cleaves
after the CCA, in contrast to the activities
characterized for other enzymes also designated
ribonuclease Z. In other systems, cleavage occurs
5-prime to the location of the CCA sequence, and CCA is
added subsequently. A species may lack ribonuclease Z if
all tRNA genes encode the CCA sequence, or if the CCA is
exposed by exonuclease activity rather than endonuclease
activity. Note that members of this sequence family
differ considerably from the majority of RNase Z
sequences [Transcription, RNA processing].
Length = 277
Score = 31.9 bits (72), Expect = 0.17
Identities = 30/89 (33%), Positives = 46/89 (51%), Gaps = 10/89 (11%)
Query: 24 QGL---EVCTLLRDPQR--LPSEYHSKVEIIQGDVLKLADVKKAIEGKDGL-EVCTLLRD 77
QGL E+ L+++ R + EYH K+ I GD L L + IEG + L CT L D
Sbjct: 156 QGLDSKEIARLVKEKGRDFVTEEYHKKILTISGDSLALD--PEEIEGTELLIHECTFL-D 212
Query: 78 PQRLPSEYHSKVEIIQGDVLKLADVKKAI 106
+ + H+ ++ + + +K A VKK I
Sbjct: 213 ARDRRYKNHAAIDEVM-ESVKAAGVKKVI 240
>gnl|CDD|187575 cd05265, SDR_a1, atypical (a) SDRs, subgroup 1. Atypical SDRs in
this subgroup are poorly defined and have been
identified putatively as isoflavones reductase, sugar
dehydratase, mRNA binding protein etc. Atypical SDRs
are distinct from classical SDRs. Members of this
subgroup retain the canonical active site triad (though
not the upstream Asn found in most SDRs) but have an
unusual putative glycine-rich NAD(P)-binding motif,
GGXXXXG, in the usual location. Atypical SDRs generally
lack the catalytic residues characteristic of the SDRs,
and their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Atypical SDRs include biliverdin IX beta
reductase (BVR-B,aka flavin reductase), NMRa (a
negative transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane
reductase, isoflavone reductases, and others. SDRs are
a functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. In addition to the Rossmann fold
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids, and typically have a TGXXGXXG cofactor
binding motif. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 250
Score = 31.1 bits (71), Expect = 0.29
Identities = 19/66 (28%), Positives = 27/66 (40%), Gaps = 2/66 (3%)
Query: 2 KKIAIFGATGMTGLCSLEAALKQGLEVCTLLRDPQRLPSEYHSKVEIIQGDVLKLADVKK 61
KI I G T G +E L G +V R R + VE I GD +++
Sbjct: 1 MKILIIGGTRFIGKALVEELLAAGHDVTVFNRG--RTKPDLPEGVEHIVGDRNDRDALEE 58
Query: 62 AIEGKD 67
+ G+D
Sbjct: 59 LLGGED 64
>gnl|CDD|234188 TIGR03371, cellulose_yhjQ, cellulose synthase operon protein
YhjQ. Members of this family are the YhjQ protein,
found immediately upsteam of bacterial cellulose
synthase (bcs) genes in a broad range of bacteria,
including both copies of the bcs locus in Klebsiella
pneumoniae. In several species it is seen clearly as
part of the bcs operon. It is identified as a probable
component of the bacterial cellulose metabolic process
not only by gene location, but also by partial
phylogenetic profiling, or Haft-Selengut algorithm
(PMID:16930487), based on a bacterial cellulose
biosynthesis genome property profile. Cellulose plays
an important role in biofilm formation and structural
integrity in some bacteria. Mutants in yhjQ in
Escherichia coli, show altered morphology an growth,
but the function of YhjQ has not yet been determined
[Cell envelope, Biosynthesis and degradation of surface
polysaccharides and lipopolysaccharides].
Length = 246
Score = 30.8 bits (70), Expect = 0.36
Identities = 16/43 (37%), Positives = 19/43 (44%), Gaps = 5/43 (11%)
Query: 1 MKKIAIFGATGMTGLCSLEAALKQGLEV---CTLLRD--PQRL 38
MK IAI G G +L A L L++ L D PQ L
Sbjct: 1 MKVIAIVSVRGGVGKTTLTANLASALKLLGEPVLAIDLDPQNL 43
>gnl|CDD|109787 pfam00743, FMO-like, Flavin-binding monooxygenase-like. This
family includes FMO proteins, cyclohexanone
mono-oxygenase and a number of different
mono-oxygenases.
Length = 532
Score = 30.5 bits (69), Expect = 0.44
Identities = 14/29 (48%), Positives = 22/29 (75%), Gaps = 2/29 (6%)
Query: 2 KKIAIFGATGMTGLCSLEAALKQGLE-VC 29
KK+A+ GA G++GL S++ L++GLE C
Sbjct: 2 KKVAVIGA-GVSGLSSIKCCLEEGLEPTC 29
>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 = 30.3 bits (69), Expect = 0.49
Identities = 22/68 (32%), Positives = 27/68 (39%), Gaps = 8/68 (11%)
Query: 3 KIAIFGATGMTGLCSLEAAL-KQGLEVCTLLRDPQRLPSEYHSKVEIIQGDVLKLADVKK 61
KI I G TG G +L L G EV L R P + E+I D L L
Sbjct: 1 KIVITGGTGFIGR-ALTRRLTAAGHEVVVLSRRPGKAE----GLAEVITWDGLSLGP--W 53
Query: 62 AIEGKDGL 69
+ G D +
Sbjct: 54 ELPGADAV 61
>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 = 30.2 bits (69), Expect = 0.53
Identities = 18/75 (24%), Positives = 28/75 (37%), Gaps = 13/75 (17%)
Query: 68 GLEVCTLLRDPQRLP-------SEYHSKVEIIQGDVLKLADVKKAIE------GKDGVVV 114
G V R P+ L S + IQ DV V+ A++ GK +++
Sbjct: 27 GASVAIAGRKPEVLEAAAEEISSATGGRAHPIQCDVRDPEAVEAAVDETLKEFGKIDILI 86
Query: 115 ALGTRNDLSPTTVMS 129
N L+P +S
Sbjct: 87 NNAAGNFLAPAESLS 101
Score = 29.9 bits (68), Expect = 0.64
Identities = 19/71 (26%), Positives = 28/71 (39%), Gaps = 10/71 (14%)
Query: 3 KIAIF--GATGMTGLCSLEAALKQGLEVCTLLRDPQRLP-------SEYHSKVEIIQGDV 53
K+A G TG+ G +A + G V R P+ L S + IQ DV
Sbjct: 4 KVAFITGGGTGI-GKAIAKAFAELGASVAIAGRKPEVLEAAAEEISSATGGRAHPIQCDV 62
Query: 54 LKLADVKKAIE 64
V+ A++
Sbjct: 63 RDPEAVEAAVD 73
>gnl|CDD|235010 PRK02186, PRK02186, argininosuccinate lyase; Provisional.
Length = 887
Score = 30.6 bits (69), Expect = 0.60
Identities = 15/55 (27%), Positives = 21/55 (38%), Gaps = 4/55 (7%)
Query: 1 MKKIAIFGATGMTG---LCSLEAALKQGLEVCTLLRDPQRLPSEYHSKVEIIQGD 52
M I +F + TG L L AL +G L + + P +V I D
Sbjct: 1 MTGIFVFIESNTTGTGELL-LRKALLRGFTPYFLTANRGKYPFLDAIRVVTISAD 54
>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 = 29.9 bits (68), Expect = 0.60
Identities = 17/62 (27%), Positives = 28/62 (45%), Gaps = 3/62 (4%)
Query: 6 IFGATGMTGLCSLEAALKQGLEVCTLLRDPQRLPSE---YHSKVEIIQGDVLKLADVKKA 62
I G + GL A QG V R+P +L S + +E+++ DV +K A
Sbjct: 5 ITGCSSGIGLALALALAAQGYRVIATARNPDKLESLGELLNDNLEVLELDVTDEESIKAA 64
Query: 63 IE 64
++
Sbjct: 65 VK 66
>gnl|CDD|187672 cd09812, 3b-HSD_like_1_SDR_e, 3beta-hydroxysteroid dehydrogenase
(3b-HSD)-like, subgroup1, extended (e) SDRs. An
uncharacterized subgroup of the 3b-HSD-like
extended-SDR family. Proteins in this subgroup have the
characteristic active site tetrad and NAD(P)-binding
motif of extended-SDRs. 3 beta-HSD catalyzes the
oxidative conversion of delta 5-3 beta-hydroxysteroids
to the delta 4-3-keto configuration; this activity is
essential for the biosynthesis of all classes of
hormonal steroids. 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 sythase 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 = 339
Score = 30.2 bits (68), Expect = 0.63
Identities = 20/67 (29%), Positives = 26/67 (38%), Gaps = 6/67 (8%)
Query: 3 KIAIFGATGMTGLCSLEAALKQGLEVCTLLRDP--QRLPSEYHSKVEIIQGDVLKLADVK 60
+ I G G G A K G+ V Q LP IQ DV L+ ++
Sbjct: 1 SVLITGGGGYFGFRLGCALAKSGVHVILFDIRRPQQELPEGIK----FIQADVRDLSQLE 56
Query: 61 KAIEGKD 67
KA+ G D
Sbjct: 57 KAVAGVD 63
Score = 27.9 bits (62), Expect = 3.6
Identities = 16/49 (32%), Positives = 21/49 (42%), Gaps = 6/49 (12%)
Query: 66 KDGLEVCTLLRDP--QRLPSEYHSKVEIIQGDVLKLADVKKAIEGKDGV 112
K G+ V Q LP IQ DV L+ ++KA+ G D V
Sbjct: 21 KSGVHVILFDIRRPQQELPEGIK----FIQADVRDLSQLEKAVAGVDCV 65
>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 = 29.9 bits (68), Expect = 0.63
Identities = 18/66 (27%), Positives = 25/66 (37%), Gaps = 10/66 (15%)
Query: 4 IAIFGATGMTG--LCSLEAALKQGLEVCTLLRDPQRLPSEYHSKVEIIQGDVLKLADVKK 61
I I G TG G L + K+G EV L R P + +G +
Sbjct: 1 ILITGGTGFIGRALT--QRLTKRGHEVTILTRSPPPGANTKW------EGYKPWAGEDAD 52
Query: 62 AIEGKD 67
++EG D
Sbjct: 53 SLEGAD 58
>gnl|CDD|176225 cd08264, Zn_ADH_like2, Alcohol dehydrogenases of the MDR family.
This group resembles the zinc-dependent alcohol
dehydrogenases of the medium chain dehydrogenase family.
However, this subgroup does not contain the
characteristic catalytic zinc site. Also, it contains an
atypical structural zinc-binding pattern:
DxxCxxCxxxxxxxC. NAD(P)(H)-dependent oxidoreductases are
the major enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which has a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES. These
proteins typically form dimers (typically higher plants,
mammals) or tetramers (yeast, bacteria), and have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site and a structural zinc in a lobe of
the catalytic domain. NAD(H)-binding occurs in the cleft
between the catalytic and coenzyme-binding domains at
the active site, and coenzyme binding induces a
conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
In human ADH catalysis, the zinc ion helps coordinate
the alcohol, followed by deprotonation of a histidine,
the ribose of NAD, a serine, then the alcohol, which
allows the transfer of a hydride to NAD+, creating NADH
and a zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 325
Score = 30.0 bits (68), Expect = 0.68
Identities = 10/27 (37%), Positives = 18/27 (66%)
Query: 2 KKIAIFGATGMTGLCSLEAALKQGLEV 28
+ + +FGA+G TG+ +++ A G EV
Sbjct: 164 ETVVVFGASGNTGIFAVQLAKMMGAEV 190
>gnl|CDD|223081 COG0002, ArgC, Acetylglutamate semialdehyde dehydrogenase [Amino
acid transport and metabolism].
Length = 349
Score = 29.9 bits (68), Expect = 0.78
Identities = 9/15 (60%), Positives = 11/15 (73%)
Query: 1 MKKIAIFGATGMTGL 15
M K+ I GA+G TGL
Sbjct: 2 MIKVGIVGASGYTGL 16
>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 = 29.5 bits (67), Expect = 0.81
Identities = 18/70 (25%), Positives = 30/70 (42%), Gaps = 4/70 (5%)
Query: 2 KKIAIFGATGMTGLCSLEAALKQGLEVCTLLRDPQ----RLPSEYHSKVEIIQGDVLKLA 57
+ +FGATG G + K+G +V R L +V ++ D+
Sbjct: 1 MVVTVFGATGFIGRYVVNRLAKRGSQVIVPYRCEAYARRLLVMGDLGQVLFVEFDLRDDE 60
Query: 58 DVKKAIEGKD 67
++KA+EG D
Sbjct: 61 SIRKALEGSD 70
>gnl|CDD|132407 TIGR03364, HpnW_proposed, FAD dependent oxidoreductase TIGR03364.
This clade of FAD dependent oxidoreductases (members
of the pfam01266 family) is syntenically associated
with a family of proposed phosphonatase-like enzymes
(TIGR03351) and is also found (less frequently) in
association with phosphonate transporter components. A
likely role for this enzyme involves the oxidative
deamination of an aminophosphonate differring slightly
from 2-aminoethylphosphonate, possibly
1-hydroxy-2-aminoethylphosphonate (see the comments for
TIGR03351). Many members of the larger FAD dependent
oxidoreductase family act as amino acid oxidative
deaminases.
Length = 365
Score = 30.0 bits (68), Expect = 0.82
Identities = 12/33 (36%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 4 IAIFGATGMTGLCSLEAALKQGLEVCTLLRDPQ 36
+ I GA G+ GL AA ++GL V + R +
Sbjct: 3 LIIVGA-GILGLAHAYAAARRGLSVTVIERSSR 34
>gnl|CDD|200085 TIGR01214, rmlD, dTDP-4-dehydrorhamnose reductase. This enzyme
catalyzes the last of 4 steps in making dTDP-rhamnose,
a precursor of LPS core antigen, O-antigen, etc [Cell
envelope, Biosynthesis and degradation of surface
polysaccharides and lipopolysaccharides].
Length = 287
Score = 29.7 bits (67), Expect = 0.83
Identities = 13/42 (30%), Positives = 18/42 (42%), Gaps = 6/42 (14%)
Query: 3 KIAIFGATGMTGLCSLEAALKQGLEVCTL------LRDPQRL 38
+I I GA G G ++ +G V L L DP+ L
Sbjct: 1 RILITGANGQLGRELVQQLSPEGRVVVALTRSQLDLTDPEAL 42
>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 = 29.6 bits (67), Expect = 0.85
Identities = 19/72 (26%), Positives = 30/72 (41%), Gaps = 9/72 (12%)
Query: 3 KIAIFGATGMTG--LCSLEAALKQGLEVCTL-----LRDPQRLPSEYHSKVEIIQGDVLK 55
+ + GA G G L E L++G EV L L + H + I GDV
Sbjct: 1 NVLVTGADGFIGSHLT--ERLLREGHEVRALDIYNSFNSWGLLDNAVHDRFHFISGDVRD 58
Query: 56 LADVKKAIEGKD 67
++V+ ++ D
Sbjct: 59 ASEVEYLVKKCD 70
>gnl|CDD|218026 pfam04321, RmlD_sub_bind, RmlD substrate binding domain.
L-rhamnose is a saccharide required for the virulence
of some bacteria. Its precursor, dTDP-L-rhamnose, is
synthesised by four different enzymes the final one of
which is RmlD. The RmlD substrate binding domain is
responsible for binding a sugar nucleotide.
Length = 284
Score = 29.5 bits (67), Expect = 0.99
Identities = 12/61 (19%), Positives = 19/61 (31%), Gaps = 15/61 (24%)
Query: 4 IAIFGATGMTGLCSLEAALKQGLEVCTLLRDPQRLPSEYHSKVEIIQGDVLKLADVKKAI 63
I + GA G G ++G+EV L R + D+ V +
Sbjct: 1 ILVTGANGQLGRELTRLLAERGVEVVALDRP---------------ELDLTDPEAVAALV 45
Query: 64 E 64
Sbjct: 46 R 46
>gnl|CDD|224803 COG1891, COG1891, Uncharacterized protein conserved in archaea
[Function unknown].
Length = 235
Score = 29.4 bits (66), Expect = 1.0
Identities = 33/115 (28%), Positives = 51/115 (44%), Gaps = 12/115 (10%)
Query: 58 DVKKAIEGKDGLEVCTLLRDPQRLPSEYHSKVEIIQGDV------LKLADVKKAIEGKDG 111
DVK EG G ++R+ + + E +V GDV LA + A+ G D
Sbjct: 25 DVKNPAEGSLGANFPWVIREIREVVPEDQ-EVSATVGDVPYKPGTASLAALGAAVAGADY 83
Query: 112 VVVAL-GTRNDLSPTTVMSEGMKNIVTAMKEYNVSVVSVCLSAFLFYEPSKVPPM 165
+ V L GT+N+ VM KN+V A+K+++ S V + V P+
Sbjct: 84 IKVGLYGTKNEEEALEVM----KNVVRAVKDFDPSKKVVAAGYADAHRVGSVSPL 134
>gnl|CDD|187673 cd09813, 3b-HSD-NSDHL-like_SDR_e, human NSDHL (NAD(P)H steroid
dehydrogenase-like protein)-like, extended (e) SDRs.
This subgroup includes human NSDHL and related proteins.
These proteins have the characteristic active site
tetrad of extended SDRs, and also have a close match to
their NAD(P)-binding motif. Human NSDHL is a
3beta-hydroxysteroid dehydrogenase (3 beta-HSD) which
functions in the cholesterol biosynthetic pathway. 3
beta-HSD catalyzes the oxidative conversion of delta 5-3
beta-hydroxysteroids to the delta 4-3-keto
configuration; this activity is essential for the
biosynthesis of all classes of hormonal steroids.
Mutations in the gene encoding NSDHL cause CHILD
syndrome (congenital hemidysplasia with ichthyosiform
nevus and limb defects), an X-linked dominant,
male-lethal trait. This subgroup also includes an
unusual bifunctional [3beta-hydroxysteroid dehydrogenase
(3b-HSD)/C-4 decarboxylase from Arabidopsis thaliana,
and Saccharomyces cerevisiae ERG26, a 3b-HSD/C-4
decarboxylase, involved in the synthesis of ergosterol,
the major sterol of yeast. 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 sythase 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 = 335
Score = 29.2 bits (66), Expect = 1.1
Identities = 28/119 (23%), Positives = 47/119 (39%), Gaps = 17/119 (14%)
Query: 75 LRDPQRLPSEYHSKVEIIQGDVLKLADVKKAIEGKDGVVV------ALGTRNDLSPTTVM 128
+R L +V+ GD+ D++KA K VV G+ +DL V
Sbjct: 32 IRPTFELDPSSSGRVQFHTGDLTDPQDLEKAFNEKGPNVVFHTASPDHGSNDDLY-YKVN 90
Query: 129 SEGMKNIVTAMKEYNVSVVSVCLSAFLFYEPSKVPPMFHNVN------DDHQRMYNVLK 181
+G +N++ A ++ V + SA + + + N + D HQ YN K
Sbjct: 91 VQGTRNVIEACRKCGVKKLVYTSSASVVFNGQDI----INGDESLPYPDKHQDAYNETK 145
>gnl|CDD|187671 cd09811, 3b-HSD_HSDB1_like_SDR_e, human 3beta-HSD (hydroxysteroid
dehydrogenase) and HSD3B1(delta 5-delta
4-isomerase)-like, extended (e) SDRs. This extended-SDR
subgroup includes human 3 beta-HSD/HSD3B1 and C(27)
3beta-HSD/ [3beta-hydroxy-delta(5)-C(27)-steroid
oxidoreductase; HSD3B7], and related proteins. These
proteins have the characteristic active site tetrad and
NAD(P)-binding motif of extended SDRs. 3 beta-HSD
catalyzes the oxidative conversion of delta 5-3
beta-hydroxysteroids to the delta 4-3-keto
configuration; this activity is essential for the
biosynthesis of all classes of hormonal steroids. C(27)
3beta-HSD is a membrane-bound enzyme of the endoplasmic
reticulum, it catalyzes the isomerization and oxidation
of 7alpha-hydroxylated sterol intermediates, an early
step in bile acid biosynthesis. Mutations in the human
gene encoding C(27) 3beta-HSD underlie a rare autosomal
recessive form of neonatal cholestasis. 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 sythase 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 = 354
Score = 29.4 bits (66), Expect = 1.2
Identities = 21/97 (21%), Positives = 37/97 (38%), Gaps = 18/97 (18%)
Query: 87 SKVEIIQGDVLKLADVKKAIEGKDGVVVALGTRNDLSPTT------VMSEGMKNIVTAMK 140
+ V I+GD+ L+ + +A +G V+ + P V G + ++ A
Sbjct: 51 TYVTDIEGDIKDLSFLFRACQGVSVVIHTAAIVDVFGPPNYEELEEVNVNGTQAVLEACV 110
Query: 141 EYNV------SVVSVCLSAFLFYEPSKVPPMFHNVND 171
+ NV S + V K P+F+ V D
Sbjct: 111 QNNVKRLVYTSSIEVA------GPNFKGRPIFNGVED 141
>gnl|CDD|235990 PRK07326, PRK07326, short chain dehydrogenase; Provisional.
Length = 237
Score = 28.8 bits (65), Expect = 1.4
Identities = 20/70 (28%), Positives = 30/70 (42%), Gaps = 6/70 (8%)
Query: 1 MKKIA-IFGATGMTGLCSLEAALKQGLEVCTLLRDPQRLPS-----EYHSKVEIIQGDVL 54
K+A I G + G EA L +G +V RD + L V + DV
Sbjct: 5 KGKVALITGGSKGIGFAIAEALLAEGYKVAITARDQKELEEAAAELNNKGNVLGLAADVR 64
Query: 55 KLADVKKAIE 64
ADV++A++
Sbjct: 65 DEADVQRAVD 74
>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 = 29.2 bits (66), Expect = 1.4
Identities = 21/67 (31%), Positives = 33/67 (49%), Gaps = 5/67 (7%)
Query: 3 KIAIFGATGMTGLCSLEAALKQGLEVCTLLR--DPQRLPSEYHSKVEIIQGDVLKLADVK 60
++ I G G G ++A L++G +V R P LP V+ I+GD AD++
Sbjct: 1 RVLIVGGNGFIGSHLVDALLEEGPQVRVFDRSIPPYELPLGG---VDYIKGDYENRADLE 57
Query: 61 KAIEGKD 67
A+ G D
Sbjct: 58 SALVGID 64
>gnl|CDD|187564 cd05254, dTDP_HR_like_SDR_e, dTDP-6-deoxy-L-lyxo-4-hexulose
reductase and related proteins, extended (e) SDRs.
dTDP-6-deoxy-L-lyxo-4-hexulose reductase, an extended
SDR, synthesizes dTDP-L-rhamnose from
alpha-D-glucose-1-phosphate, providing the precursor
of L-rhamnose, an essential cell wall component of many
pathogenic bacteria. This subgroup has the
characteristic active site tetrad and NADP-binding
motif. This subgroup also contains human MAT2B, the
regulatory subunit of methionine adenosyltransferase
(MAT); MAT catalyzes S-adenosylmethionine synthesis.
The human gene encoding MAT2B encodes two major
splicing variants which are induced in human cell liver
cancer and regulate HuR, an mRNA-binding protein which
stabilizes the mRNA of several cyclins, to affect cell
proliferation. Both MAT2B variants include this
extended SDR domain. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids. Extended SDRs are a diverse collection
of proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and
their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 280
Score = 28.7 bits (65), Expect = 1.4
Identities = 17/61 (27%), Positives = 26/61 (42%), Gaps = 10/61 (16%)
Query: 3 KIAIFGATGMTGLCSLEAALKQGLEVCTLLRDPQRLPSEYHSKVEIIQGDVLKLADVKKA 62
KI I GATGM G + ++G EV S+ + + D+ V++A
Sbjct: 1 KILITGATGMLGRALVRLLKERGYEVIGT----------GRSRASLFKLDLTDPDAVEEA 50
Query: 63 I 63
I
Sbjct: 51 I 51
>gnl|CDD|224016 COG1091, RfbD, dTDP-4-dehydrorhamnose reductase [Cell envelope
biogenesis, outer membrane].
Length = 281
Score = 28.8 bits (65), Expect = 1.5
Identities = 13/31 (41%), Positives = 13/31 (41%), Gaps = 1/31 (3%)
Query: 3 KIAIFGATGMTGLCSLEAALKQGLEVCTLLR 33
KI I GA G G L AL EV R
Sbjct: 2 KILITGANGQLGT-ELRRALPGEFEVIATDR 31
>gnl|CDD|214863 smart00859, Semialdhyde_dh, Semialdehyde dehydrogenase, NAD
binding domain. The semialdehyde dehydrogenase family
is found in N-acetyl-glutamine semialdehyde
dehydrogenase (AgrC), which is involved in arginine
biosynthesis, and aspartate-semialdehyde dehydrogenase,
an enzyme involved in the biosynthesis of various amino
acids from aspartate. This family is also found in
yeast and fungal Arg5,6 protein, which is cleaved into
the enzymes N-acety-gamma-glutamyl-phosphate reductase
and acetylglutamate kinase. These are also involved in
arginine biosynthesis. All proteins in this entry
contain a NAD binding region of semialdehyde
dehydrogenase.
Length = 123
Score = 27.9 bits (63), Expect = 1.5
Identities = 8/13 (61%), Positives = 9/13 (69%)
Query: 3 KIAIFGATGMTGL 15
K+AI GATG G
Sbjct: 1 KVAIVGATGYVGQ 13
>gnl|CDD|113252 pfam04476, DUF556, Protein of unknown function (DUF556). Family of
uncharacterized, hypothetical prokaryotic proteins.
Length = 235
Score = 28.6 bits (64), Expect = 1.5
Identities = 37/134 (27%), Positives = 57/134 (42%), Gaps = 13/134 (9%)
Query: 39 PSEYHSKVEIIQGDVLKLADVKKAIEGKDGLEVCTLLRDPQRLPSEYHSKVEIIQGDV-- 96
P +E I+G + DVK EG G ++R+ + L + V GDV
Sbjct: 7 PISVEEALEAIEGG-ADIIDVKNPAEGSLGANFPWVIREIRELTPKD-KLVSATVGDVPY 64
Query: 97 ----LKLADVKKAIEGKDGVVVAL-GTRNDLSPTTVMSEGMKNIVTAMKEYNVSVVSVCL 151
+ LA + A+ G D + V L G +N VM KN+V A+K+++ S + V
Sbjct: 65 KPGTVSLAALGAAVSGADYIKVGLYGVKNYDEAVEVM----KNVVRAVKDFDSSKIVVAA 120
Query: 152 SAFLFYEPSKVPPM 165
Y V P+
Sbjct: 121 GYADAYRIGAVEPL 134
>gnl|CDD|220067 pfam08907, DUF1853, Domain of unknown function (DUF1853). This
family of proteins are functionally uncharacterized.
Length = 277
Score = 28.8 bits (65), Expect = 1.7
Identities = 8/41 (19%), Positives = 16/41 (39%), Gaps = 2/41 (4%)
Query: 137 TAMKEYNVSVVS--VCLSAFLFYEPSKVPPMFHNVNDDHQR 175
A+ + + + + + LFY + +N DH R
Sbjct: 161 AALPKLGIEPLQQQLLMKGRLFYPWPPSVCLPQEINPDHLR 201
>gnl|CDD|235608 PRK05786, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 238
Score = 28.6 bits (64), Expect = 1.7
Identities = 19/68 (27%), Positives = 29/68 (42%), Gaps = 5/68 (7%)
Query: 2 KKIAIFGATGMTGLCSLEAALKQGLEVCTLLRDPQRLPS-----EYHSKVEIIQGDVLKL 56
KK+AI G + G ALK+G +VC R+ +L + + + GDV
Sbjct: 6 KKVAIIGVSEGLGYAVAYFALKEGAQVCINSRNENKLKRMKKTLSKYGNIHYVVGDVSST 65
Query: 57 ADVKKAIE 64
+ IE
Sbjct: 66 ESARNVIE 73
>gnl|CDD|235935 PRK07109, PRK07109, short chain dehydrogenase; Provisional.
Length = 334
Score = 28.7 bits (65), Expect = 1.8
Identities = 14/65 (21%), Positives = 25/65 (38%), Gaps = 6/65 (9%)
Query: 4 IAIFGATGMTGLCSLEAALKQGLEVCTLLRDPQRLPS------EYHSKVEIIQGDVLKLA 57
+ I GA+ G + A ++G +V L R + L + + + DV
Sbjct: 11 VVITGASAGVGRATARAFARRGAKVVLLARGEEGLEALAAEIRAAGGEALAVVADVADAE 70
Query: 58 DVKKA 62
V+ A
Sbjct: 71 AVQAA 75
>gnl|CDD|173687 cd05596, STKc_ROCK, Catalytic domain of the Protein
Serine/Threonine Kinase, Rho-associated coiled-coil
containing protein kinase. Serine/Threonine Kinases
(STKs), Rho-associated coiled-coil containing protein
kinase (ROCK) subfamily, catalytic (c) domain. STKs
catalyze the transfer of the gamma-phosphoryl group from
ATP to serine/threonine residues on protein substrates.
The ROCK subfamily is part of a larger superfamily that
includes the catalytic domains of other protein STKs,
protein tyrosine kinases, RIO kinases, aminoglycoside
phosphotransferase, choline kinase, and phosphoinositide
3-kinase. ROCK is also referred to as Rho-associated
kinase or simply as Rho kinase. It contains an
N-terminal extension, a catalytic kinase domain, and a
long C-terminal extension, which contains a coiled-coil
region encompassing a Rho-binding domain (RBD) and a
pleckstrin homology (PH) domain. ROCK is auto-inhibited
by the RBD and PH domain interacting with the catalytic
domain. It is activated via interaction with Rho GTPases
and is involved in many cellular functions including
contraction, adhesion, migration, motility,
proliferation, and apoptosis. The ROCK subfamily
consists of two isoforms, ROCK1 and ROCK2, which may be
functionally redundant in some systems, but exhibit
different tissue distributions. Both isoforms are
ubiquitously expressed in most tissues, but ROCK2 is
more prominent in brain and skeletal muscle while ROCK1
is more pronounced in the liver, testes, and kidney.
Studies in knockout mice result in different phenotypes,
suggesting that the two isoforms do not compensate for
each other during embryonic development.
Length = 370
Score = 28.6 bits (64), Expect = 1.9
Identities = 14/39 (35%), Positives = 23/39 (58%), Gaps = 4/39 (10%)
Query: 97 LKLADVKKAIE-GKDGVVV---ALGTRNDLSPTTVMSEG 131
LKLAD ++ +G+V A+GT + +SP + S+G
Sbjct: 181 LKLADFGTCMKMDANGMVRCDTAVGTPDYISPEVLKSQG 219
>gnl|CDD|224417 COG1500, COG1500, Predicted exosome subunit [Translation, ribosomal
structure and biogenesis].
Length = 234
Score = 28.4 bits (64), Expect = 2.0
Identities = 12/42 (28%), Positives = 19/42 (45%), Gaps = 3/42 (7%)
Query: 37 RLPSEYHSKVEIIQGDVLKLADVKKAIEGKDGLEVCTLLRDP 78
++P EY K G + K ++KK +DG +C L
Sbjct: 169 KIPVEYAGKA---YGLLRKFGEIKKEEWQEDGSWICVLEIPA 207
>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 = 28.1 bits (63), Expect = 2.4
Identities = 17/72 (23%), Positives = 28/72 (38%), Gaps = 5/72 (6%)
Query: 2 KKIAIFGATGMTGLCSLEAALKQGLEVCTLLRDPQRLPSEYHS--KVEIIQ---GDVLKL 56
K + GA+ G+ A + G V LR+P+ L + S VE + D
Sbjct: 1 KVALVTGASRGIGIEIARALARDGYRVSLGLRNPEDLAALSASGGDVEAVPYDARDPEDA 60
Query: 57 ADVKKAIEGKDG 68
+ A+ + G
Sbjct: 61 RALVDALRDRFG 72
>gnl|CDD|201603 pfam01118, Semialdhyde_dh, Semialdehyde dehydrogenase, NAD
binding domain. This Pfam entry contains the following
members: N-acetyl-glutamine semialdehyde dehydrogenase
(AgrC) Aspartate-semialdehyde dehydrogenase.
Length = 121
Score = 27.5 bits (62), Expect = 2.5
Identities = 8/12 (66%), Positives = 9/12 (75%)
Query: 3 KIAIFGATGMTG 14
K+AI GATG G
Sbjct: 1 KVAIVGATGYVG 12
>gnl|CDD|215072 PLN00141, PLN00141, Tic62-NAD(P)-related group II protein;
Provisional.
Length = 251
Score = 28.3 bits (63), Expect = 2.6
Identities = 17/59 (28%), Positives = 30/59 (50%), Gaps = 2/59 (3%)
Query: 2 KKIAIFGATGMTGLCSLEAALKQGLEVCTLLRDPQRLPSEY--HSKVEIIQGDVLKLAD 58
K + + GATG TG +E L +G V +RD + + ++I++ DV + +D
Sbjct: 18 KTVFVAGATGRTGKRIVEQLLAKGFAVKAGVRDVDKAKTSLPQDPSLQIVRADVTEGSD 76
>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 = 27.8 bits (62), Expect = 3.1
Identities = 19/64 (29%), Positives = 30/64 (46%), Gaps = 3/64 (4%)
Query: 1 MKKIAIFGATGMTGLCSLEAALKQGLEVCTLLRDPQRLP---SEYHSKVEIIQGDVLKLA 57
MK+I I G++ GL + L QG EV R +R + ++ GD+ LA
Sbjct: 7 MKRIFITGSSDGLGLAAARTLLHQGHEVVLHARSQKRAADAKAACPGAAGVLIGDLSSLA 66
Query: 58 DVKK 61
+ +K
Sbjct: 67 ETRK 70
>gnl|CDD|235202 PRK04023, PRK04023, DNA polymerase II large subunit; Validated.
Length = 1121
Score = 28.3 bits (64), Expect = 3.2
Identities = 9/20 (45%), Positives = 15/20 (75%)
Query: 94 GDVLKLADVKKAIEGKDGVV 113
GDV+++ DV++A E +D V
Sbjct: 378 GDVVRIDDVEEAKEIRDDVE 397
Score = 27.2 bits (61), Expect = 6.0
Identities = 9/20 (45%), Positives = 16/20 (80%)
Query: 51 GDVLKLADVKKAIEGKDGLE 70
GDV+++ DV++A E +D +E
Sbjct: 378 GDVVRIDDVEEAKEIRDDVE 397
>gnl|CDD|233115 TIGR00755, ksgA, dimethyladenosine transferase. In both E. coli
and Saccharomyces cerevisiae, this protein is
responsible for the dimethylation of two adjacent
adenosine residues in a conserved hairpin of 16S rRNA in
bacteria, 18S rRNA in eukaryotes. This adjacent
dimethylation is the only rRNA modification shared by
bacteria and eukaryotes. A single member of this family
is present in each of the first 20 completed microbial
genomes. This protein is essential in yeast, but not in
E. coli, where its deletion leads to resistance to the
antibiotic kasugamycin. Alternate name:
S-adenosylmethionine--6-N',N'-adenosyl (rRNA)
dimethyltransferase [Protein synthesis, tRNA and rRNA
base modification].
Length = 253
Score = 27.6 bits (62), Expect = 3.3
Identities = 22/63 (34%), Positives = 28/63 (44%), Gaps = 9/63 (14%)
Query: 53 VLKLADVKKAIEGKDGLEVCTLLRDPQRLPSEYHSKVEIIQGDVLKLADVKKAIEGKDGV 112
+LK A AIE D L ++L S Y +EII+GD LK V K
Sbjct: 47 LLKRAKKVTAIE-IDRRLAERL----RKLLSLYE-NLEIIEGDALK---VDLNEFPKQLK 97
Query: 113 VVA 115
VV+
Sbjct: 98 VVS 100
Score = 26.5 bits (59), Expect = 8.1
Identities = 18/50 (36%), Positives = 27/50 (54%), Gaps = 8/50 (16%)
Query: 14 GLCSL-EAALKQGLEVCTLLRDP------QRLPSEYHSKVEIIQGDVLKL 56
GL +L E LK+ +V + D ++L S Y +EII+GD LK+
Sbjct: 39 GLGALTEPLLKRAKKVTAIEIDRRLAERLRKLLSLYE-NLEIIEGDALKV 87
>gnl|CDD|215477 PLN02882, PLN02882, aminoacyl-tRNA ligase.
Length = 1159
Score = 28.2 bits (63), Expect = 3.4
Identities = 13/40 (32%), Positives = 19/40 (47%)
Query: 5 AIFGATGMTGLCSLEAALKQGLEVCTLLRDPQRLPSEYHS 44
F + LCS + L +G+E L RD L SE+ +
Sbjct: 1088 LAFNEDALLALCSGDEELAEGVEAVLLSRDHSNLKSEFQA 1127
>gnl|CDD|234761 PRK00436, argC, N-acetyl-gamma-glutamyl-phosphate reductase;
Validated.
Length = 343
Score = 27.8 bits (63), Expect = 3.5
Identities = 8/15 (53%), Positives = 10/15 (66%)
Query: 1 MKKIAIFGATGMTGL 15
M K+ I GA+G TG
Sbjct: 2 MIKVGIVGASGYTGG 16
>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 = 27.6 bits (62), Expect = 3.5
Identities = 18/59 (30%), Positives = 27/59 (45%), Gaps = 3/59 (5%)
Query: 8 GATGMTGLCSLEAALKQGLEVCTLLR--DPQRLPSEYHSKVEIIQGDVLKLADVKKAIE 64
GA+G+ GL ++E L QG +V L P ++ + DV DVK A+
Sbjct: 10 GASGL-GLATVERLLAQGAKVVILDLPNSPGETVAKLGDNCRFVPVDVTSEKDVKAALA 67
>gnl|CDD|235472 PRK05447, PRK05447, 1-deoxy-D-xylulose 5-phosphate
reductoisomerase; Provisional.
Length = 385
Score = 27.7 bits (63), Expect = 4.3
Identities = 7/11 (63%), Positives = 9/11 (81%)
Query: 1 MKKIAIFGATG 11
MK+I I G+TG
Sbjct: 1 MKRITILGSTG 11
>gnl|CDD|223679 COG0606, COG0606, Predicted ATPase with chaperone activity
[Posttranslational modification, protein turnover,
chaperones].
Length = 490
Score = 27.6 bits (62), Expect = 4.6
Identities = 14/47 (29%), Positives = 17/47 (36%)
Query: 26 LEVCTLLRDPQRLPSEYHSKVEIIQGDVLKLADVKKAIEGKDGLEVC 72
EV L RLP S+V DVK + K LE+
Sbjct: 148 EEVVNFLEGKLRLPIPIPSEVIESFSLAPDFKDVKGQEQAKRALEIA 194
>gnl|CDD|223737 COG0665, DadA, Glycine/D-amino acid oxidases (deaminating) [Amino
acid transport and metabolism].
Length = 387
Score = 27.6 bits (61), Expect = 5.2
Identities = 8/35 (22%), Positives = 14/35 (40%), Gaps = 1/35 (2%)
Query: 1 MKKIAIFGATGMTGLCSLEAALKQGLEVCTLLRDP 35
+ I G G+ GL + ++G +V L
Sbjct: 4 KMDVVIIGG-GIVGLSAAYYLAERGADVTVLEAGE 37
>gnl|CDD|220382 pfam09754, PAC2, PAC2 family. This PAC2 (Proteasome assembly
chaperone) family of proteins is found in bacteria,
archaea and eukaryotes. Proteins in this family are
typically between 247 and 307 amino acids in length.
These proteins function as a chaperone for the 26S
proteasome. The 26S proteasome mediates
ubiquitin-dependent proteolysis in eukaryotic cells. A
number of studies including very recent ones have
revealed that assembly of its 20S catalytic core
particle is an ordered process that involves several
conserved proteasome assembly chaperones (PACs). Two
heterodimeric chaperones, PAC1-PAC2 and PAC3-PAC4,
promote the assembly of rings composed of seven alpha
subunits.
Length = 220
Score = 26.9 bits (60), Expect = 5.2
Identities = 10/41 (24%), Positives = 15/41 (36%), Gaps = 1/41 (2%)
Query: 133 KNIVTAMKEYNVSVVSVCLSAFLFYEPSKVPPMFHNVNDDH 173
+ I+ +E VS V + L P PP+ D
Sbjct: 89 EAILDWAEELGVSEV-ITLGGLPAGVPHTRPPVTGAATDPE 128
>gnl|CDD|223214 COG0136, Asd, Aspartate-semialdehyde dehydrogenase [Amino acid
transport and metabolism].
Length = 334
Score = 27.2 bits (61), Expect = 5.8
Identities = 6/14 (42%), Positives = 8/14 (57%)
Query: 1 MKKIAIFGATGMTG 14
+A+ GATG G
Sbjct: 1 KLNVAVLGATGAVG 14
>gnl|CDD|178567 PLN02986, PLN02986, cinnamyl-alcohol dehydrogenase family
protein.
Length = 322
Score = 27.3 bits (60), Expect = 5.8
Identities = 21/91 (23%), Positives = 41/91 (45%), Gaps = 13/91 (14%)
Query: 2 KKIAIFGATGMTGLCSLEAALKQGLEVCTLLRDPQRLPSEYH--------SKVEIIQGDV 53
K + + GA+G ++ L +G V +RD H ++++ + D+
Sbjct: 6 KLVCVTGASGYIASWIVKLLLLRGYTVKATVRDLTDRKKTEHLLALDGAKERLKLFKADL 65
Query: 54 LKLADVKKAIEGKDGL-----EVCTLLRDPQ 79
L+ + ++AIEG D + V ++DPQ
Sbjct: 66 LEESSFEQAIEGCDAVFHTASPVFFTVKDPQ 96
>gnl|CDD|168661 PRK06753, PRK06753, hypothetical protein; Provisional.
Length = 373
Score = 27.0 bits (60), Expect = 6.0
Identities = 13/26 (50%), Positives = 16/26 (61%), Gaps = 1/26 (3%)
Query: 3 KIAIFGATGMTGLCSLEAALKQGLEV 28
KIAI GA G+ GL + +QG EV
Sbjct: 2 KIAIIGA-GIGGLTAAALLQEQGHEV 26
>gnl|CDD|235821 PRK06522, PRK06522, 2-dehydropantoate 2-reductase; Reviewed.
Length = 304
Score = 27.1 bits (61), Expect = 6.4
Identities = 13/36 (36%), Positives = 17/36 (47%), Gaps = 1/36 (2%)
Query: 3 KIAIFGATGMTGLCSLEAALKQGLEVCTLLRDPQRL 38
KIAI GA + GL A + G +V + R L
Sbjct: 2 KIAILGAGAIGGLF-GAALAQAGHDVTLVARRGAHL 36
>gnl|CDD|232936 TIGR00355, purH, phosphoribosylaminoimidazolecarboxamide
formyltransferase/IMP cyclohydrolase. PurH is
bifunctional: IMP cyclohydrolase (EC 3.5.4.10);
phosphoribosylaminoimidazolecarboxamide
formyltransferase (EC 2.1.2.3) Involved in purine
ribonucleotide biosynthesis. The IMP cyclohydrolase
activity is in the N-terminal region [Purines,
pyrimidines, nucleosides, and nucleotides, Purine
ribonucleotide biosynthesis].
Length = 511
Score = 27.1 bits (60), Expect = 7.2
Identities = 25/106 (23%), Positives = 40/106 (37%), Gaps = 13/106 (12%)
Query: 16 CSLEA----ALKQGLEVCTLLRDPQRLPSEYHSKVEIIQGDVLKLADVKKAIEGKDGLEV 71
S EA A K+ L V L R+P +V G +L + D + + L+V
Sbjct: 330 YSAEALEILAKKKNLRVLILGIWANRVPELDFKRV---NGGLL-VQDRDDGMVDQSTLKV 385
Query: 72 CTLLRDPQRLPSEYHSKVEIIQGDVLKLADVKKAIEGKDGVVVALG 117
T +R P+E + V K + K+ + V +G
Sbjct: 386 VT-----KRQPTEQELIDLLFAWKVAKHVKSNAIVYAKNNMTVGVG 426
>gnl|CDD|182134 PRK09897, PRK09897, hypothetical protein; Provisional.
Length = 534
Score = 27.0 bits (60), Expect = 7.3
Identities = 13/25 (52%), Positives = 17/25 (68%), Gaps = 1/25 (4%)
Query: 1 MKKIAIFGATGMTGLCSLEAALKQG 25
MKKIAI GA G TG+ + + L+Q
Sbjct: 1 MKKIAIVGA-GPTGIYTFFSLLQQQ 24
>gnl|CDD|220029 pfam08812, YtxC, YtxC-like family. This family includes proteins
similar to B. subtilis YtxC an uncharacterized protein.
Length = 220
Score = 26.7 bits (60), Expect = 7.4
Identities = 8/50 (16%), Positives = 24/50 (48%), Gaps = 2/50 (4%)
Query: 127 VMSEGMKNIVTAMKEYNVSVVSVCLSAFLFYEPSKVPPMFHNVNDDHQRM 176
+ +E ++ ++ E+ ++ + +S + P K+ + H + DH +
Sbjct: 158 ISNEELEELIDEEFEHEINYDDLLISPLITIAPKKI--ILHTDDPDHNKE 205
>gnl|CDD|223109 COG0030, KsgA, Dimethyladenosine transferase (rRNA methylation)
[Translation, ribosomal structure and biogenesis].
Length = 259
Score = 26.8 bits (60), Expect = 7.7
Identities = 13/47 (27%), Positives = 19/47 (40%), Gaps = 6/47 (12%)
Query: 53 VLKLADVKKAIEGKDGLEVCTLLRDPQRLPSEYHSKVEIIQGDVLKL 99
+L+ A AIE D L + + Y + +I GD LK
Sbjct: 48 LLERAARVTAIE-IDRRLAEVL----KERFAPYD-NLTVINGDALKF 88
>gnl|CDD|235546 PRK05653, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Validated.
Length = 246
Score = 26.7 bits (60), Expect = 7.7
Identities = 14/70 (20%), Positives = 25/70 (35%), Gaps = 6/70 (8%)
Query: 1 MKKIAIFGATGMTGLCSLEAALKQGLEVCTLLRDP---QRLPSEYHS---KVEIIQGDVL 54
K + GA+ G G +V + + L +E + + ++ DV
Sbjct: 5 GKTALVTGASRGIGRAIALRLAADGAKVVIYDSNEEAAEALAAELRAAGGEARVLVFDVS 64
Query: 55 KLADVKKAIE 64
A V+ IE
Sbjct: 65 DEAAVRALIE 74
>gnl|CDD|238869 cd01831, Endoglucanase_E_like, Endoglucanase E-like members of the
SGNH hydrolase family; Endoglucanase E catalyzes the
endohydrolysis of 1,4-beta-glucosidic linkages in
cellulose, lichenin and cereal beta-D-glucans.
Length = 169
Score = 26.5 bits (59), Expect = 7.9
Identities = 15/86 (17%), Positives = 28/86 (32%), Gaps = 13/86 (15%)
Query: 108 GKDGVVVALGTRNDLSPTTVMSE-----GMKNIVTAMKEYNVSVVSVCLSAFLFYEPSKV 162
G D VV+ LGT ND S + +++ V + + + P
Sbjct: 55 GPDLVVINLGT-NDFSTGNNPPGEDFTNAYVEFIEELRKRYPDAPIVLMLGPMLFGPY-- 111
Query: 163 PPMFHNVNDDHQRMYNVLKDSGLNYI 188
++ +R+ KD +
Sbjct: 112 -----GTEEEIKRVAEAFKDQKSKKV 132
>gnl|CDD|233597 TIGR01850, argC, N-acetyl-gamma-glutamyl-phosphate reductase,
common form. This model represents the more common of
two related families of
N-acetyl-gamma-glutamyl-phosphate reductase, an enzyme
catalyzing the third step or Arg biosynthesis from Glu.
The two families differ by phylogeny, similarity
clustering, and the gap architecture in a multiple
sequence alignment. Bacterial members of this family
tend to be found within Arg biosynthesis operons [Amino
acid biosynthesis, Glutamate family].
Length = 346
Score = 26.8 bits (60), Expect = 8.3
Identities = 8/13 (61%), Positives = 10/13 (76%)
Query: 2 KKIAIFGATGMTG 14
K+AI GA+G TG
Sbjct: 1 IKVAIVGASGYTG 13
>gnl|CDD|226150 COG3623, SgaU, Putative L-xylulose-5-phosphate 3-epimerase
[Carbohydrate transport and metabolism].
Length = 287
Score = 26.6 bits (59), Expect = 8.6
Identities = 12/35 (34%), Positives = 19/35 (54%), Gaps = 5/35 (14%)
Query: 119 RNDLSPTTVMSEGMKNIVTAMKEYNVSVVSVCLSA 153
R D S ++ +V A++E V + S+CLSA
Sbjct: 48 RLDWSKEERLA-----LVNAIQETGVRIPSMCLSA 77
>gnl|CDD|173666 cd05575, STKc_SGK, Catalytic domain of the Protein Serine/Threonine
Kinase, Serum- and Glucocorticoid-induced Kinase.
Serine/Threonine Kinases (STKs), Serum- and
Glucocorticoid-induced Kinase (SGK) subfamily, catalytic
(c) domain. STKs catalyze the transfer of the
gamma-phosphoryl group from ATP to serine/threonine
residues on protein substrates. The SGK subfamily is
part of a larger superfamily that includes the catalytic
domains of other protein STKs, protein tyrosine kinases,
RIO kinases, aminoglycoside phosphotransferase, choline
kinase, and phosphoinositide 3-kinase. There are three
isoforms of SGK, named SGK1, SGK2, and SGK3 (also called
cytokine-independent survival kinase CISK). SGKs are
activated by insulin and growth factors via
phosphoinositide 3-kinase and PDK1. They activate ion
channels, ion carriers, and the Na-K-ATPase, as well as
regulate the activity of enzymes and transcription
factors. SGKs play important roles in transport, hormone
release, neuroexcitability, cell proliferation, and
apoptosis.
Length = 323
Score = 26.7 bits (59), Expect = 9.0
Identities = 21/79 (26%), Positives = 31/79 (39%), Gaps = 14/79 (17%)
Query: 103 KKAIEGKDGVVVALGTRNDLSPTTVMSEGMKNIVTAMKEYNVSVVSVCLSAFLFYEPSKV 162
K+ IE GT L+P V + Y+ +V CL A L+ +
Sbjct: 144 KEGIEHSKTTSTFCGTPEYLAPE----------VLRKQPYDRTVDWWCLGAVLYEMLYGL 193
Query: 163 PPMFHNVNDDHQRMY-NVL 180
PP + + D MY N+L
Sbjct: 194 PPFY---SRDTAEMYDNIL 209
>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 = 26.5 bits (59), Expect = 9.1
Identities = 13/66 (19%), Positives = 23/66 (34%), Gaps = 5/66 (7%)
Query: 4 IAIFGATGMTGLCSLEAALKQGLEVCTLLRDPQRL-----PSEYHSKVEIIQGDVLKLAD 58
+ GA+ G ++G +V R+ + L +Q DV D
Sbjct: 1 ALVTGASSGIGRAIARRLAREGAKVVLADRNEEALAELAAIEALGGNAVAVQADVSDEED 60
Query: 59 VKKAIE 64
V+ +E
Sbjct: 61 VEALVE 66
>gnl|CDD|216400 pfam01266, DAO, FAD dependent oxidoreductase. This family
includes various FAD dependent oxidoreductases:
Glycerol-3-phosphate dehydrogenase EC:1.1.99.5,
Sarcosine oxidase beta subunit EC:1.5.3.1, D-alanine
oxidase EC:1.4.99.1, D-aspartate oxidase EC:1.4.3.1.
Length = 234
Score = 26.5 bits (59), Expect = 9.5
Identities = 12/39 (30%), Positives = 19/39 (48%), Gaps = 3/39 (7%)
Query: 3 KIAIFGATGMTGLCSLEAALKQGLEVCTLLRDPQRLPSE 41
+ + G G+ GL + ++GL V TLL + L S
Sbjct: 1 DVVVIGG-GIVGLSTAYELARRGLSV-TLL-ERGDLASG 36
>gnl|CDD|189778 pfam00938, Lipoprotein_3, Lipoprotein. This family of lipoproteins
is Mycoplasma specific.
Length = 87
Score = 25.1 bits (55), Expect = 9.5
Identities = 12/41 (29%), Positives = 21/41 (51%), Gaps = 4/41 (9%)
Query: 117 GTRNDLSPTTVMSEGMKNIVTAMKE-YNV---SVVSVCLSA 153
D+S +SEG KN++T++K+ Y ++ L A
Sbjct: 13 AQDYDVSKNIELSEGKKNLITSLKKSYESNPKKTTNLLLDA 53
>gnl|CDD|235245 PRK04183, PRK04183, glutamyl-tRNA(Gln) amidotransferase subunit D;
Validated.
Length = 419
Score = 26.3 bits (59), Expect = 9.9
Identities = 12/23 (52%), Positives = 17/23 (73%), Gaps = 2/23 (8%)
Query: 98 KLAD-VKKAIE-GKDGVVVALGT 118
++A+ V + I+ G DGVVVA GT
Sbjct: 140 EIAEAVYEEIKNGADGVVVAHGT 162
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
0.318 0.135 0.383
Gapped
Lambda K H
0.267 0.0807 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,562,882
Number of extensions: 885187
Number of successful extensions: 1146
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1131
Number of HSP's successfully gapped: 141
Length of query: 189
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 98
Effective length of database: 6,901,388
Effective search space: 676336024
Effective search space used: 676336024
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 56 (25.2 bits)