RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11862
(152 letters)
>gnl|CDD|187547 cd05236, FAR-N_SDR_e, fatty acyl CoA reductases (FARs), extended
(e) SDRs. SDRs are Rossmann-fold NAD(P)H-binding
proteins, many of which may function as fatty acyl CoA
reductases (FAR), acting on medium and long chain fatty
acids, and have been reported to be involved in diverse
processes such as biosynthesis of insect pheromones,
plant cuticular wax production, and mammalian wax
biosynthesis. In Arabidopsis thaliana, proteins with
this particular architecture have also been identified
as the MALE STERILITY 2 (MS2) gene product, which is
implicated in male gametogenesis. Mutations in MS2
inhibit the synthesis of exine (sporopollenin),
rendering plants unable to reduce pollen wall fatty
acids to corresponding alcohols. This N-terminal domain
shares the catalytic triad (but not the upstream Asn)
and characteristic NADP-binding motif of the extended
SDR family. 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 = 320
Score = 172 bits (437), Expect = 7e-54
Identities = 67/137 (48%), Positives = 93/137 (67%)
Query: 11 RSVLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFSKLPVFERLRK 70
+SVL+TG TGF+GKVLLEKLLRSCPDIGK+Y+L R K G + + RL E K +F+R R
Sbjct: 1 KSVLITGATGFLGKVLLEKLLRSCPDIGKIYLLIRGKSGQSAEERLRELLKDKLFDRGRN 60
Query: 71 ECPAQLSRLHIIEGDILQANLGIKDSDLLMLQEEVSVVFNGAASLKLEAELKENVAANTR 130
P S++ IEGD+ + NLG+ D DL L EEV+++ + AA++ + L E ++ N
Sbjct: 61 LNPLFESKIVPIEGDLSEPNLGLSDEDLQTLIEEVNIIIHCAATVTFDERLDEALSINVL 120
Query: 131 GTQRLLDIALKMKKLVV 147
GT RLL++A + KKL
Sbjct: 121 GTLRLLELAKRCKKLKA 137
>gnl|CDD|219687 pfam07993, NAD_binding_4, Male sterility protein. This family
represents the C-terminal region of the male sterility
protein in a number of arabidopsis and drosophila. A
sequence-related jojoba acyl CoA reductase is also
included.
Length = 245
Score = 142 bits (360), Expect = 4e-43
Identities = 57/134 (42%), Positives = 80/134 (59%), Gaps = 7/134 (5%)
Query: 15 VTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARL-AEFSKLPVFERLRKECP 73
+TG TGF+GKVLLEKLLRS P++ K+Y L RAK G + RL E K +F+RL+
Sbjct: 1 LTGATGFLGKVLLEKLLRSTPEV-KIYCLVRAKDGESALERLRQELLKYGLFDRLK---- 55
Query: 74 AQLSRLHIIEGDILQANLGIKDSDLLMLQEEVSVVFNGAASLKLEAELKENVAANTRGTQ 133
L R+ + GD+ + NLG+ D D L EEV V+ + AA++ + A N GT+
Sbjct: 56 -ALERIIPVAGDLSEPNLGLSDEDFQELAEEVDVIIHNAATVNFVEPYSDLRATNVLGTR 114
Query: 134 RLLDIALKMKKLVV 147
+L +A +MKKL
Sbjct: 115 EVLRLAKQMKKLPF 128
>gnl|CDD|215279 PLN02503, PLN02503, fatty acyl-CoA reductase 2.
Length = 605
Score = 93.4 bits (232), Expect = 6e-23
Identities = 52/154 (33%), Positives = 86/154 (55%), Gaps = 6/154 (3%)
Query: 4 VARWYAGRSVLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLA-EFSKL 62
+A + G++ L+TG TGF+ KVL+EK+LR+ PD+GK+Y+L +AK RL E
Sbjct: 113 IAEFLRGKNFLITGATGFLAKVLIEKILRTNPDVGKIYLLIKAKDKEAAIERLKNEVIDA 172
Query: 63 PVFERLRKECPAQ-----LSRLHIIEGDILQANLGIKDSDLLMLQEEVSVVFNGAASLKL 117
+F+ L++ LS+L + G++ ++NLG++ + +EV V+ N AA+
Sbjct: 173 ELFKCLQETHGKSYQSFMLSKLVPVVGNVCESNLGLEPDLADEIAKEVDVIINSAANTTF 232
Query: 118 EAELKENVAANTRGTQRLLDIALKMKKLVVSLDI 151
+ + NTRG L+ A K KKL + L +
Sbjct: 233 DERYDVAIDINTRGPCHLMSFAKKCKKLKLFLQV 266
>gnl|CDD|187573 cd05263, MupV_like_SDR_e, Pseudomonas fluorescens MupV-like,
extended (e) SDRs. This subgroup of extended SDR family
domains have the characteristic active site tetrad and a
well-conserved NAD(P)-binding motif. This subgroup is
not well characterized, its members are annotated as
having a variety of putative functions. One
characterized member is Pseudomonas fluorescens MupV a
protein involved in the biosynthesis of Mupirocin, a
polyketide-derived antibiotic. Extended SDRs are
distinct from classical SDRs. In addition to the
Rossmann fold (alpha/beta folding pattern with a central
beta-sheet) core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids. Extended SDRs are a
diverse collection of proteins, and include isomerases,
epimerases, oxidoreductases, and lyases; they typically
have a TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 293
Score = 84.3 bits (209), Expect = 2e-20
Identities = 38/127 (29%), Positives = 63/127 (49%), Gaps = 16/127 (12%)
Query: 13 VLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFSKLPVFERLRKEC 72
V VTGGTGF+G+ L+++LL + KV +L R++ R+ E
Sbjct: 1 VFVTGGTGFLGRHLVKRLL---ENGFKVLVLVRSESLGEAHERIEEAGLEA--------- 48
Query: 73 PAQLSRLHIIEGDILQANLGIKDSDLLMLQEEVSVVFNGAASLKLEAELKENVAANTRGT 132
R+ ++EGD+ Q NLG+ + L +V V + AAS +A ++ N GT
Sbjct: 49 ----DRVRVLEGDLTQPNLGLSAAASRELAGKVDHVIHCAASYDFQAPNEDAWRTNIDGT 104
Query: 133 QRLLDIA 139
+ +L++A
Sbjct: 105 EHVLELA 111
>gnl|CDD|187546 cd05235, SDR_e1, extended (e) SDRs, subgroup 1. This family
consists of an SDR module of multidomain proteins
identified as putative polyketide sythases fatty acid
synthases (FAS), and nonribosomal peptide synthases,
among others. However, unlike the usual ketoreductase
modules of FAS and polyketide synthase, these domains
are related to the extended SDRs, and have canonical
NAD(P)-binding motifs and an active site tetrad.
Extended SDRs are distinct from classical SDRs. In
addition to the Rossmann fold (alpha/beta folding
pattern with a central beta-sheet) core region typical
of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 290
Score = 81.9 bits (203), Expect = 1e-19
Identities = 50/140 (35%), Positives = 73/140 (52%), Gaps = 10/140 (7%)
Query: 12 SVLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFSKLPVFERLRKE 71
+VL+TG TGF+G LL +LL+ ++ K+Y L RAK RL + K L E
Sbjct: 1 TVLLTGATGFLGAYLLRELLK-RKNVSKIYCLVRAKDEEAALERLIDNLKE-YGLNLWDE 58
Query: 72 CPAQLSRLHIIEGDILQANLGIKDSDLLMLQEEVSVVFNGAASLKL---EAELKENVAAN 128
+LSR+ ++ GD+ + NLG+ D D L EEV V+ + A++ ELK AN
Sbjct: 59 --LELSRIKVVVGDLSKPNLGLSDDDYQELAEEVDVIIHNGANVNWVYPYEELK---PAN 113
Query: 129 TRGTQRLLDIALKMKKLVVS 148
GT+ LL +A K +
Sbjct: 114 VLGTKELLKLAATGKLKPLH 133
>gnl|CDD|215538 PLN02996, PLN02996, fatty acyl-CoA reductase.
Length = 491
Score = 75.9 bits (187), Expect = 8e-17
Identities = 46/142 (32%), Positives = 79/142 (55%), Gaps = 7/142 (4%)
Query: 11 RSVLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARL-AEFSKLPVFERLR 69
+++LVTG TGF+ K+ +EK+LR P++ K+Y+L RA + RL E +F+ LR
Sbjct: 12 KTILVTGATGFLAKIFVEKILRVQPNVKKLYLLLRASDAKSATQRLHDEVIGKDLFKVLR 71
Query: 70 KECPAQLS-----RLHIIEGDILQANLGIKDSDLL-MLQEEVSVVFNGAASLKLEAELKE 123
++ L+ ++ + GDI +LG+KDS+L + +E+ +V N AA+ +
Sbjct: 72 EKLGENLNSLISEKVTPVPGDISYDDLGVKDSNLREEMWKEIDIVVNLAATTNFDERYDV 131
Query: 124 NVAANTRGTQRLLDIALKMKKL 145
+ NT G +L+ A K K+
Sbjct: 132 ALGINTLGALNVLNFAKKCVKV 153
>gnl|CDD|235962 PRK07201, PRK07201, short chain dehydrogenase; Provisional.
Length = 657
Score = 68.1 bits (167), Expect = 4e-14
Identities = 36/130 (27%), Positives = 64/130 (49%), Gaps = 17/130 (13%)
Query: 14 LVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFSKLPVFERLRKECP 73
VTGGTGF+G+ L+ +LL + V++L R L E L
Sbjct: 4 FVTGGTGFIGRRLVSRLLDRRRE-ATVHVLVRR-------------QSLSRLEALAAYWG 49
Query: 74 AQLSRLHIIEGDILQANLGIKDSDLLMLQEEVSVVFNGAASLKLEAELKENVAANTRGTQ 133
A R+ + GD+ + LG+ ++D+ L ++ V + AA L A+ + AAN GT+
Sbjct: 50 AD--RVVPLVGDLTEPGLGLSEADIAELG-DIDHVVHLAAIYDLTADEEAQRAANVDGTR 106
Query: 134 RLLDIALKMK 143
++++A +++
Sbjct: 107 NVVELAERLQ 116
>gnl|CDD|233557 TIGR01746, Thioester-redct, thioester reductase domain. This model
includes the terminal domain from the fungal alpha
aminoadipate reductase enzyme (also known as
aminoadipate semialdehyde dehydrogenase) which is
involved in the biosynthesis of lysine , as well as the
reductase-containing component of the myxochelin
biosynthetic gene cluster, MxcG. The mechanism of
reduction involves activation of the substrate by
adenylation and transfer to a covalently-linked
pantetheine cofactor as a thioester. This thioester is
then reduced to give an aldehyde (thus releasing the
product) and a regenerated pantetheine thiol. (In
myxochelin biosynthesis this aldehyde is further reduced
to an alcohol or converted to an amine by an
aminotransferase.) This is a fundamentally different
reaction than beta-ketoreductase domains of polyketide
synthases which act at a carbonyl two carbons removed
from the thioester and forms an alcohol as a product.
This domain is invariably found at the C-terminus of the
proteins which contain it (presumably because it results
in the release of the product). The majority of hits to
this model are non-ribosomal peptide synthetases in
which this domain is similarly located proximal to a
thiolation domain (pfam00550). In some cases this domain
is found at the end of a polyketide synthetase enzyme,
but is unlike ketoreductase domains which are found
before the thiolase domains. Exceptions to this observed
relationship with the thiolase domain include three
proteins which consist of stand-alone reductase domains
(GP|466833 from M. leprae, GP|435954 from Anabaena and
OMNI|NTL02SC1199 from Strep. coelicolor) and one protein
(OMNI|NTL01NS2636 from Nostoc) which contains N-terminal
homology with a small group of hypothetical proteins but
no evidence of a thiolation domain next to the putative
reductase domain. Below the noise cutoff to this model
are proteins containing more distantly related
ketoreductase and dehydratase/epimerase domains. It has
been suggested that a NADP-binding motif can be found in
the N-terminal portion of this domain that may form a
Rossman-type fold.
Length = 367
Score = 65.5 bits (160), Expect = 2e-13
Identities = 40/136 (29%), Positives = 63/136 (46%), Gaps = 21/136 (15%)
Query: 12 SVLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFSKLPVFERLRKE 71
+VL+TG TGF+G LLE+LLR KV L RA + + + ERLR+
Sbjct: 1 TVLLTGATGFLGAYLLEELLRRSTQA-KVICLVRAA---SEEHAM---------ERLREA 47
Query: 72 CPAQL--------SRLHIIEGDILQANLGIKDSDLLMLQEEVSVVFNGAASLKLEAELKE 123
+ R+ ++ GD+ + LG+ D++ L E V + + A + E
Sbjct: 48 LRSYRLWHEDLARERIEVVAGDLSEPRLGLSDAEWERLAENVDTIVHNGALVNWVYPYSE 107
Query: 124 NVAANTRGTQRLLDIA 139
AN GT+ +L +A
Sbjct: 108 LRGANVLGTREVLRLA 123
>gnl|CDD|225857 COG3320, COG3320, Putative dehydrogenase domain of multifunctional
non-ribosomal peptide synthetases and related enzymes
[Secondary metabolites biosynthesis, transport, and
catabolism].
Length = 382
Score = 61.6 bits (150), Expect = 6e-12
Identities = 41/143 (28%), Positives = 62/143 (43%), Gaps = 27/143 (18%)
Query: 11 RSVLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFSKLPVFERLRK 70
R+VL+TG TGF+G LL +LL KV L RA+ S RL K
Sbjct: 1 RNVLLTGATGFLGAYLLLELLDRSD--AKVICLVRAQ------------SDEAALARLEK 46
Query: 71 ECPAQL-------SRLHIIEGDILQANLGIKDSDLLMLQEEVSVVFNGAA---SLKLEAE 120
R+ ++ GD+ + +LG+ + L E V ++ + AA + +E
Sbjct: 47 TFDLYRHWDELSADRVEVVAGDLAEPDLGLSERTWQELAENVDLIIHNAALVNHVFPYSE 106
Query: 121 LKENVAANTRGTQRLLDIALKMK 143
L+ AN GT +L +A K
Sbjct: 107 LRG---ANVLGTAEVLRLAATGK 126
>gnl|CDD|234212 TIGR03443, alpha_am_amid, L-aminoadipate-semialdehyde dehydrogenase.
Members of this protein family are
L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31),
product of the LYS2 gene. It is also called
alpha-aminoadipate reductase. In fungi, lysine is
synthesized via aminoadipate. Currently, all members of
this family are fungal.
Length = 1389
Score = 58.5 bits (142), Expect = 7e-11
Identities = 35/111 (31%), Positives = 48/111 (43%), Gaps = 21/111 (18%)
Query: 11 RSVLVTGGTGFMGKVLLEKLL-RSCPDIGKVYILCRAKRGLTPKARLAEFSKLPVFERLR 69
+V +TG TGF+G +L LL R KV+ RAK S+ ERLR
Sbjct: 972 ITVFLTGATGFLGSFILRDLLTRRSNSNFKVFAHVRAK------------SEEAGLERLR 1019
Query: 70 KECPAQ-------LSRLHIIEGDILQANLGIKDSDLLMLQEEVSVVF-NGA 112
K SR+ ++ GD+ + G+ D L EV V+ NGA
Sbjct: 1020 KTGTTYGIWDEEWASRIEVVLGDLSKEKFGLSDEKWSDLTNEVDVIIHNGA 1070
>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 = 49.7 bits (119), Expect = 8e-08
Identities = 38/139 (27%), Positives = 55/139 (39%), Gaps = 29/139 (20%)
Query: 12 SVLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFSKLPVFERLRKE 71
SVLVTGG+GF G+ L+++LL + G Y+ R F P E L
Sbjct: 1 SVLVTGGSGFFGERLVKQLL----ERGGTYV------------RS--FDIAPPGEALSAW 42
Query: 72 CPAQLSRLHIIEGDILQANLGIKDSDLLMLQEEVSVVFNGAASLKLEAELKENVAANTRG 131
+ ++GDI N D+ VF+ AA + L N G
Sbjct: 43 QHPNIE---FLKGDITDRN------DVEQALSGADCVFHTAAIVPLAGPRDLYWEVNVGG 93
Query: 132 TQRLLDI--ALKMKKLVVS 148
TQ +LD ++K V +
Sbjct: 94 TQNVLDACQRCGVQKFVYT 112
>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 = 47.9 bits (114), Expect = 4e-07
Identities = 36/131 (27%), Positives = 55/131 (41%), Gaps = 29/131 (22%)
Query: 12 SVLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKAR-LAEFSKLPVFERLRK 70
LVTGG GF+G+ ++ LL ++ ++ +L +A P+ E S+
Sbjct: 1 VCLVTGGGGFLGQHIIRLLLERKEELKEIRVLDKA---FGPELIEHFEKSQGKT------ 51
Query: 71 ECPAQLSRLHIIEGDILQANLGIKDSDLLMLQEEVSVVFNGAASLKLEA----ELKENVA 126
+ IEGDI S L + VSVV + AA + + E E V
Sbjct: 52 -------YVTDIEGDIKDL------SFLFRACQGVSVVIHTAAIVDVFGPPNYEELEEV- 97
Query: 127 ANTRGTQRLLD 137
N GTQ +L+
Sbjct: 98 -NVNGTQAVLE 107
>gnl|CDD|187548 cd05237, UDP_invert_4-6DH_SDR_e, UDP-Glcnac (UDP-linked
N-acetylglucosamine) inverting 4,6-dehydratase, extended
(e) SDRs. UDP-Glcnac inverting 4,6-dehydratase was
identified in Helicobacter pylori as the hexameric flaA1
gene product (FlaA1). FlaA1 is hexameric, possesses
UDP-GlcNAc-inverting 4,6-dehydratase activity, and
catalyzes the first step in the creation of a
pseudaminic acid derivative in protein glycosylation.
Although this subgroup has the NADP-binding motif
characteristic of extended SDRs, its members tend to
have a Met substituted for the active site Tyr found in
most SDR families. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately 100
amino acids. Extended SDRs are a diverse collection of
proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 287
Score = 46.8 bits (112), Expect = 6e-07
Identities = 34/142 (23%), Positives = 64/142 (45%), Gaps = 34/142 (23%)
Query: 9 AGRSVLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFSKLPVFERL 68
G+++LVTGG G +G L+ ++L+ K+ + R + L L
Sbjct: 1 KGKTILVTGGAGSIGSELVRQILKF--GPKKLIVFDRDENKL---------------HEL 43
Query: 69 RKECPAQ--LSRLHIIEGDILQANLGIKDSDLL---MLQEEVSVVFNGAASLK----LEA 119
+E ++ +L I GD ++D + L + +VF+ AA+LK +E
Sbjct: 44 VRELRSRFPHDKLRFIIGD-------VRDKERLRRAFKERGPDIVFH-AAALKHVPSMED 95
Query: 120 ELKENVAANTRGTQRLLDIALK 141
+E + N GT+ ++D A++
Sbjct: 96 NPEEAIKTNVLGTKNVIDAAIE 117
>gnl|CDD|223528 COG0451, WcaG, Nucleoside-diphosphate-sugar epimerases [Cell
envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 314
Score = 44.9 bits (106), Expect = 3e-06
Identities = 34/142 (23%), Positives = 53/142 (37%), Gaps = 36/142 (25%)
Query: 13 VLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFSKLPVFERLRKEC 72
+LVTGG GF+G L+E+LL + D V L R + GL
Sbjct: 3 ILVTGGAGFIGSHLVERLLAAGHD---VRGLDRLRDGL---------------------- 37
Query: 73 PAQLSRLHIIEGDILQANLGIKDSDLLMLQEEVSVVFNGAA----SLKLEAELKENVAAN 128
LS + + D+ D + + V + AA ++ E + N
Sbjct: 38 DPLLSGVEFVVLDLTDR-----DLVDELAKGVPDAVIHLAAQSSVPDSNASDPAEFLDVN 92
Query: 129 TRGTQRLLDIALK--MKKLVVS 148
GT LL+ A +K+ V +
Sbjct: 93 VDGTLNLLEAARAAGVKRFVFA 114
>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 = 44.2 bits (105), Expect = 7e-06
Identities = 39/142 (27%), Positives = 56/142 (39%), Gaps = 43/142 (30%)
Query: 13 VLVTGGTGFMGKVLLEKLLRSCPDIG-KVYILCRAKRGLTPKARLAEFSKLPVFERLRKE 71
+LVTG TGF+G L+ LL G +V L R + LPV
Sbjct: 1 ILVTGATGFLGSNLVRALLAQ----GYRVRALVR------SGSDAVLLDGLPV------- 43
Query: 72 CPAQLSRLHIIEGDILQANLGIKDSDLLMLQEEVSVVFNGAA----SLKLEAELKE-NVA 126
++EGD+ A L + VF+ AA K EL NV
Sbjct: 44 --------EVVEGDLTDAAS------LAAAMKGCDRVFHLAAFTSLWAKDRKELYRTNVE 89
Query: 127 ANTRGTQRLLDIALK--MKKLV 146
GT+ +LD AL+ ++++V
Sbjct: 90 ----GTRNVLDAALEAGVRRVV 107
>gnl|CDD|217199 pfam02719, Polysacc_synt_2, Polysaccharide biosynthesis protein.
This is a family of diverse bacterial polysaccharide
biosynthesis proteins including the CapD protein, WalL
protein mannosyl-transferase and several putative
epimerases (e.g. WbiI).
Length = 280
Score = 43.2 bits (103), Expect = 1e-05
Identities = 38/138 (27%), Positives = 60/138 (43%), Gaps = 30/138 (21%)
Query: 13 VLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFSKLPVFERLRKEC 72
VLVTGG G +G L ++L+ + K+ + R EF + + LR+E
Sbjct: 1 VLVTGGGGSIGSELCRQILKF--NPKKIILFSR-----------DEFKLYEIRQELRQEY 47
Query: 73 PAQLSRLHIIEGDILQANLGIKDSDLL---MLQEEVSVVFNGAASLK----LEAELKENV 125
R I GD ++D + L M Q V VF+ AA+LK +E E +
Sbjct: 48 NDPKLRFFI--GD-------VRDRERLERAMEQHGVDTVFH-AAALKHVPLVEYNPMEAI 97
Query: 126 AANTRGTQRLLDIALKMK 143
N GT+ + + A++
Sbjct: 98 KTNVLGTENVAEAAIENG 115
>gnl|CDD|187557 cd05246, dTDP_GD_SDR_e, dTDP-D-glucose 4,6-dehydratase, extended
(e) SDRs. This subgroup contains dTDP-D-glucose
4,6-dehydratase and related proteins, members of the
extended-SDR family, with the characteristic Rossmann
fold core region, active site tetrad and NAD(P)-binding
motif. dTDP-D-glucose 4,6-dehydratase is closely related
to other sugar epimerases of the SDR family.
dTDP-D-dlucose 4,6,-dehydratase catalyzes the second of
four steps in the dTDP-L-rhamnose pathway (the
dehydration of dTDP-D-glucose to
dTDP-4-keto-6-deoxy-D-glucose) in the synthesis of
L-rhamnose, a cell wall component of some pathogenic
bacteria. In many gram negative bacteria, L-rhamnose is
an important constituent of lipopoylsaccharide
O-antigen. The larger N-terminal portion of
dTDP-D-Glucose 4,6-dehydratase forms a Rossmann fold
NAD-binding domain, while the C-terminus binds the sugar
substrate. 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 = 315
Score = 41.4 bits (98), Expect = 5e-05
Identities = 41/149 (27%), Positives = 58/149 (38%), Gaps = 32/149 (21%)
Query: 11 RSVLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFSKLPVFERLRK 70
+LVTGG GF+G + LL PD I+ K LT L +
Sbjct: 1 MKILVTGGAGFIGSNFVRYLLNKYPD---YKIINLDK--LTYAGNLENLEDV-------- 47
Query: 71 ECPAQLSRLHIIEGDILQANLGIKDSDLLMLQEEVSVVFNGAA------SLKLEAELKEN 124
+ R ++GDI A L D L +E++ V + AA S+
Sbjct: 48 ---SSSPRYRFVKGDICDAEL----VDRLFEEEKIDAVIHFAAESHVDRSISDPEPFIRT 100
Query: 125 VAANTRGTQRLLDIALK--MKKLV-VSLD 150
N GT LL+ A K +K+ V +S D
Sbjct: 101 ---NVLGTYTLLEAARKYGVKRFVHISTD 126
>gnl|CDD|224013 COG1088, RfbB, dTDP-D-glucose 4,6-dehydratase [Cell envelope
biogenesis, outer membrane].
Length = 340
Score = 41.4 bits (98), Expect = 6e-05
Identities = 34/137 (24%), Positives = 51/137 (37%), Gaps = 29/137 (21%)
Query: 11 RSVLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFSKLPVFERLRK 70
+LVTGG GF+G + +L PD +++ K LT L + +
Sbjct: 1 MKILVTGGAGFIGSNFVRYILNKHPD---DHVVNLDK--LTYAGNLENLADV-------- 47
Query: 71 ECPAQLSRLHIIEGDILQANLGIKDSDLLMLQEEVSVVFNGAA------SLKLEAELKEN 124
R ++GDI L D L + + V + AA S+ A +
Sbjct: 48 ---EDSPRYRFVQGDICDREL----VDRLFKEYQPDAVVHFAAESHVDRSIDGPAPFIQT 100
Query: 125 VAANTRGTQRLLDIALK 141
N GT LL+ A K
Sbjct: 101 ---NVVGTYTLLEAARK 114
>gnl|CDD|216461 pfam01370, Epimerase, NAD dependent epimerase/dehydratase family.
This family of proteins utilise NAD as a cofactor. The
proteins in this family use nucleotide-sugar substrates
for a variety of chemical reactions.
Length = 233
Score = 39.6 bits (93), Expect = 2e-04
Identities = 34/142 (23%), Positives = 57/142 (40%), Gaps = 40/142 (28%)
Query: 13 VLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFSKLPVFERLRKEC 72
+LVTGGTGF+G L+ +LL+ ++ + R R+
Sbjct: 1 ILVTGGTGFIGSHLVRRLLQEGYEVIVLG-------------------------RRRRSE 35
Query: 73 PAQLSRLHIIEGDILQANLGIKDSDLLMLQEEVSVVFNGAA------SLKLEAELKENVA 126
R+ EGD+ + + L+ + + V + AA S + A+ +
Sbjct: 36 SLNTGRIRFHEGDLTDPDALER----LLAEVQPDAVIHLAAQSGVGASFEDPADF---IR 88
Query: 127 ANTRGTQRLLDIALKM--KKLV 146
AN GT RLL+ A + K+ V
Sbjct: 89 ANVLGTLRLLEAARRAGVKRFV 110
>gnl|CDD|130249 TIGR01181, dTDP_gluc_dehyt, dTDP-glucose 4,6-dehydratase. This
protein is related to UDP-glucose 4-epimerase (GalE) and
likewise has an NAD cofactor [Cell envelope,
Biosynthesis and degradation of surface polysaccharides
and lipopolysaccharides].
Length = 317
Score = 38.9 bits (91), Expect = 4e-04
Identities = 33/133 (24%), Positives = 49/133 (36%), Gaps = 23/133 (17%)
Query: 12 SVLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFSKLPVFERLRKE 71
+LVTGG GF+G + +L PD +V +L LT L + L
Sbjct: 1 RILVTGGAGFIGSNFVRYILNEHPDA-EVIVL----DKLTYAGNLENLADL--------- 46
Query: 72 CPAQLSRLHIIEGDILQANLGIKDSDLLMLQEEVSVVFNGAASLKLEAELKENVA---AN 128
R ++GDI L L + + V + AA ++ + A N
Sbjct: 47 --EDNPRYRFVKGDIGDREL----VSRLFTEHQPDAVVHFAAESHVDRSISGPAAFIETN 100
Query: 129 TRGTQRLLDIALK 141
GT LL+ K
Sbjct: 101 VVGTYTLLEAVRK 113
>gnl|CDD|187566 cd05256, UDP_AE_SDR_e, UDP-N-acetylglucosamine 4-epimerase,
extended (e) SDRs. This subgroup contains
UDP-N-acetylglucosamine 4-epimerase of Pseudomonas
aeruginosa, WbpP, an extended SDR, that catalyzes the
NAD+ dependent conversion of UDP-GlcNAc and UDPGalNA to
UDP-Glc and UDP-Gal. This subgroup has the
characteristic active site tetrad and NAD-binding motif
of the extended SDRs. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately 100
amino acids. Extended SDRs are a diverse collection of
proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 304
Score = 38.0 bits (89), Expect = 7e-04
Identities = 38/142 (26%), Positives = 61/142 (42%), Gaps = 34/142 (23%)
Query: 13 VLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFSKLPVFERLRKEC 72
VLVTGG GF+G L+E+LL ++ + L K+ P+ +
Sbjct: 2 VLVTGGAGFIGSHLVERLLERGHEVIVLDNLSTGKKENLPEVK----------------- 44
Query: 73 PAQLSRLHIIEGDILQANLGIKDSDLL-MLQEEVSVVFNGAASLKLEAELKENVA---AN 128
+ IEGD I+D +L+ E V VF+ AA + +++ + N
Sbjct: 45 ----PNVKFIEGD-------IRDDELVEFAFEGVDYVFHQAAQASVPRSIEDPIKDHEVN 93
Query: 129 TRGTQRLLDIALK--MKKLVVS 148
GT LL+ A K +K+ V +
Sbjct: 94 VLGTLNLLEAARKAGVKRFVYA 115
>gnl|CDD|224011 COG1086, COG1086, Predicted nucleoside-diphosphate sugar epimerases
[Cell envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 588
Score = 38.0 bits (89), Expect = 0.001
Identities = 36/145 (24%), Positives = 66/145 (45%), Gaps = 30/145 (20%)
Query: 4 VARWYAGRSVLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFSKLP 63
+ G++VLVTGG G +G L ++L+ + ++ + R E+
Sbjct: 244 IGAMLTGKTVLVTGGGGSIGSELCRQILKF--NPKEIILFSR-----------DEYKLYL 290
Query: 64 VFERLRKECPAQLSRLHIIEGDILQANLGIKDSDLL---MLQEEVSVVFNGAASLK---- 116
+ LR++ P +L GD ++D D + M +V +VF+ AA+LK
Sbjct: 291 IDMELREKFPE--LKLRFYIGD-------VRDRDRVERAMEGHKVDIVFH-AAALKHVPL 340
Query: 117 LEAELKENVAANTRGTQRLLDIALK 141
+E +E + N GT+ + + A+K
Sbjct: 341 VEYNPEEAIKTNVLGTENVAEAAIK 365
>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 = 37.7 bits (88), Expect = 0.001
Identities = 32/138 (23%), Positives = 51/138 (36%), Gaps = 32/138 (23%)
Query: 13 VLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFSKLPVFERLRKEC 72
+LVTG G +G++L +L S P + V L R + +P E+ +L + R
Sbjct: 1 ILVTGAAGGLGRLLARRLAAS-PRVIGVDGLDRRRPPGSPPK--VEYVRLDI----RDPA 53
Query: 73 PAQLSRLHIIEGDILQANLGIKDSDLLMLQEEVSVVFNGAASLKLEAELKENVAANTRGT 132
A + R E V + A L + E N GT
Sbjct: 54 AADVFRER-----------------------EADAVVHLAFILDPPRDGAERHRINVDGT 90
Query: 133 QRLLDIALK--MKKLVVS 148
Q +LD + ++VV+
Sbjct: 91 QNVLDACAAAGVPRVVVT 108
>gnl|CDD|187628 cd05370, SDR_c2, classical (c) SDR, subgroup 2. Short-chain
dehydrogenases/reductases (SDRs, aka Tyrosine-dependent
oxidoreductases) are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold (alpha/beta folding
pattern with a central beta-sheet), an NAD(P)(H)-binding
region, and a structurally diverse C-terminal region.
Classical SDRs are typically about 250 residues long,
while extended SDRs are approximately 350 residues.
Sequence identity between different SDR enzymes are
typically in the 15-30% range, but the enzymes share the
Rossmann fold NAD-binding motif and characteristic
NAD-binding and catalytic sequence patterns. These
enzymes catalyze a wide range of activities including
the metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 228
Score = 36.9 bits (86), Expect = 0.001
Identities = 34/152 (22%), Positives = 52/152 (34%), Gaps = 34/152 (22%)
Query: 9 AGRSVLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFSKLPVFERL 68
G +VL+TGGT +G L K L + G I+ G RLAE K +
Sbjct: 4 TGNTVLITGGTSGIGLALARKFL----EAGNTVIIT----GRRE-ERLAEAKKE-LPNIH 53
Query: 69 RKECPAQLSRLHIIEG------------DILQANLGIKDSDLLMLQEEVSVVFNGAASL- 115
+ +E DIL N GI ++ + A+ L
Sbjct: 54 TIVL--DVGDAESVEALAEALLSEYPNLDILINNAGI------QRPIDLR---DPASDLD 102
Query: 116 KLEAELKENVAANTRGTQRLLDIALKMKKLVV 147
K + E+ N+ R + L K + +
Sbjct: 103 KADTEIDTNLIGPIRLIKAFLPHLKKQPEATI 134
>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 = 36.5 bits (85), Expect = 0.002
Identities = 32/110 (29%), Positives = 40/110 (36%), Gaps = 41/110 (37%)
Query: 12 SVLVTGGTGFMGKVLLEKLLRSCPDIG-KVYILC----RAKRGLTPKARLAEFSKLPVFE 66
+VLVTG GF+G L E+LLR G +V L GL A F
Sbjct: 1 NVLVTGADGFIGSHLTERLLRE----GHEVRALDIYNSFNSWGLLDNAVHDRF------- 49
Query: 67 RLRKECPAQLSRLHIIEGDILQANLG---IKDSDLLMLQEEVSVVFNGAA 113
H I GD+ A+ +K D VVF+ AA
Sbjct: 50 -------------HFISGDVRDASEVEYLVKKCD---------VVFHLAA 77
>gnl|CDD|212494 cd08946, SDR_e, extended (e) SDRs. Extended SDRs are distinct
from classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids. Extended SDRs are a diverse collection
of proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and
their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 200
Score = 36.1 bits (84), Expect = 0.003
Identities = 11/25 (44%), Positives = 17/25 (68%)
Query: 13 VLVTGGTGFMGKVLLEKLLRSCPDI 37
+LVTGG GF+G L+ +LL ++
Sbjct: 1 ILVTGGAGFIGSHLVRRLLERGHEV 25
>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 = 33.8 bits (78), Expect = 0.018
Identities = 36/130 (27%), Positives = 57/130 (43%), Gaps = 27/130 (20%)
Query: 14 LVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFSKLPVFERLRKECP 73
LVTGG GF+G+ ++ LLR G++ + +P+ L +FSKL V
Sbjct: 1 LVTGGGGFLGRHIVRLLLR----EGELQEVRVFDLRFSPEL-LEDFSKLQV--------- 46
Query: 74 AQLSRLHIIEGDILQANLGIKDSDLLMLQEEVSVVFNGAASLKLEAELKENV--AANTRG 131
+ IEGD+ DL + VV + AA + + + + N +G
Sbjct: 47 -----ITYIEGDVTDK------QDLRRALQGSDVVIHTAAIIDVFGKAYRDTIMKVNVKG 95
Query: 132 TQRLLDIALK 141
TQ +LD +K
Sbjct: 96 TQNVLDACVK 105
>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 = 33.8 bits (78), Expect = 0.020
Identities = 16/35 (45%), Positives = 22/35 (62%), Gaps = 1/35 (2%)
Query: 11 RSVLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCR 45
++ LV G TG +GK LL +LL+S P KV + R
Sbjct: 1 KTALVLGATGLVGKHLLRELLKS-PYYSKVTAIVR 34
>gnl|CDD|224012 COG1087, GalE, UDP-glucose 4-epimerase [Cell envelope biogenesis,
outer membrane].
Length = 329
Score = 33.7 bits (78), Expect = 0.022
Identities = 36/155 (23%), Positives = 54/155 (34%), Gaps = 58/155 (37%)
Query: 12 SVLVTGGTGFMG----KVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFSKLPVFER 67
VLVTGG G++G + LL+ G V +
Sbjct: 2 KVLVTGGAGYIGSHTVRQLLKT-------------------GHEVV----------VLDN 32
Query: 68 LRKECPAQLSRLHI--IEGDILQANLGIKDSDLL---MLQEEVSVVFNGAASLKLEAELK 122
L L +L EGD+L D LL + ++ V + AAS +
Sbjct: 33 LSNGHKIALLKLQFKFYEGDLL-------DRALLTAVFEENKIDAVVHFAAS----ISVG 81
Query: 123 ENVA-------ANTRGTQRLLDIALK--MKKLVVS 148
E+V N GT L++ L+ +KK + S
Sbjct: 82 ESVQNPLKYYDNNVVGTLNLIEAMLQTGVKKFIFS 116
>gnl|CDD|182639 PRK10675, PRK10675, UDP-galactose-4-epimerase; Provisional.
Length = 338
Score = 33.6 bits (77), Expect = 0.026
Identities = 27/75 (36%), Positives = 38/75 (50%), Gaps = 17/75 (22%)
Query: 12 SVLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFSKLPVFERLRKE 71
VLVTGG+G++G +LL++ D+ + LC +KR S LPV ERL +
Sbjct: 2 RVLVTGGSGYIGSHTCVQLLQNGHDVVILDNLCNSKR-----------SVLPVIERLGGK 50
Query: 72 CPAQLSRLHIIEGDI 86
P +EGDI
Sbjct: 51 HPT------FVEGDI 59
>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 = 33.5 bits (77), Expect = 0.030
Identities = 38/140 (27%), Positives = 58/140 (41%), Gaps = 35/140 (25%)
Query: 12 SVLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFSKLPVFERLRKE 71
S LV GG+GF+G+ L+E+LLR RG + F P FE
Sbjct: 1 SCLVVGGSGFLGRHLVEQLLR---------------RG---NPTVHVFDIRPTFELDPSS 42
Query: 72 CPAQLSRLHIIEGDILQANLGIKDSDLL--MLQEEVSVVFNGAA-SLKLEAELKENVAAN 128
R+ GD+ DL ++ +VVF+ A+ +L V N
Sbjct: 43 SG----RVQFHTGDL------TDPQDLEKAFNEKGPNVVFHTASPDHGSNDDLYYKV--N 90
Query: 129 TRGTQRLLDIALK--MKKLV 146
+GT+ +++ K +KKLV
Sbjct: 91 VQGTRNVIEACRKCGVKKLV 110
>gnl|CDD|215146 PLN02260, PLN02260, probable rhamnose biosynthetic enzyme.
Length = 668
Score = 32.8 bits (75), Expect = 0.063
Identities = 33/141 (23%), Positives = 56/141 (39%), Gaps = 39/141 (27%)
Query: 8 YAGRSVLVTGGTGFMGKVLLEKLLRSCPDIGKVYIL-----CRAKRGLTPKARLAEFSKL 62
Y +++L+TG GF+ + +L+R+ PD K+ +L C + L P F
Sbjct: 4 YEPKNILITGAAGFIASHVANRLIRNYPDY-KIVVLDKLDYCSNLKNLNPSKSSPNFK-- 60
Query: 63 PVFERLRKECPAQLSRLHIIEGDILQANLGIKDSDLLMLQEEVSVVFNGAA------SLK 116
++GDI A+L + L++ E + + + AA S
Sbjct: 61 ------------------FVKGDIASADL----VNYLLITEGIDTIMHFAAQTHVDNSFG 98
Query: 117 LEAELKENVAANTRGTQRLLD 137
E +N N GT LL+
Sbjct: 99 NSFEFTKN---NIYGTHVLLE 116
>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 = 32.3 bits (74), Expect = 0.067
Identities = 11/21 (52%), Positives = 16/21 (76%)
Query: 11 RSVLVTGGTGFMGKVLLEKLL 31
+L+ GGT F+GK L+E+LL
Sbjct: 1 MKILIIGGTRFIGKALVEELL 21
>gnl|CDD|187652 cd08948, 5beta-POR_like_SDR_a, progesterone 5-beta-reductase-like
proteins (5beta-POR), atypical (a) SDRs. 5beta-POR
catalyzes the reduction of progesterone to
5beta-pregnane-3,20-dione in Digitalis plants. This
subgroup of atypical-extended SDRs, shares the
structure of an extended SDR, but has a different
glycine-rich nucleotide binding motif (GXXGXXG) and
lacks the YXXXK active site motif of classical and
extended SDRs. Tyr-179 and Lys 147 are present in the
active site, but not in the usual SDR configuration.
Given these differences, it has been proposed that this
subfamily represents a new SDR class. Other atypical
SDRs include biliverdin IX beta reductase (BVR-B,aka
flavin reductase), NMRa (a negative transcriptional
regulator of various fungi), phenylcoumaran benzylic
ether and pinoresinol-lariciresinol reductases,
phenylpropene synthases, eugenol synthase,
triphenylmethane reductase, isoflavone reductases, and
others. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving
as a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton
relay involving the conserved Tyr and Lys, a water
molecule stabilized by Asn, and nicotinamide. In
addition to the Rossmann fold core region typical of
all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids,
and typically have a TGXXGXXG cofactor binding motif.
Complex (multidomain) SDRs such as ketoreductase
domains of fatty acid synthase have a GGXGXXG
NAD(P)-binding motif and an altered active site motif
(YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 308
Score = 32.2 bits (74), Expect = 0.070
Identities = 18/49 (36%), Positives = 19/49 (38%)
Query: 12 SVLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFS 60
LV G TG G L+E LL KVY L R RL E
Sbjct: 1 VALVVGATGISGWALVEHLLSDPGTWWKVYGLSRRPLPTEDDPRLVEHI 49
>gnl|CDD|187538 cd05227, AR_SDR_e, aldehyde reductase, extended (e) SDRs. This
subgroup contains aldehyde reductase of the extended
SDR-type and related proteins. Aldehyde reductase I
(aka carbonyl reductase) is an NADP-binding SDR; it has
an NADP-binding motif consensus that is slightly
different from the canonical SDR form and lacks the Asn
of the extended SDR active site tetrad. Aldehyde
reductase I catalyzes the NADP-dependent reduction of
ethyl 4-chloro-3-oxobutanoate to ethyl
(R)-4-chloro-3-hydroxybutanoate. Extended SDRs are
distinct from classical SDRs. In addition to the
Rossmann fold (alpha/beta folding pattern with a
central beta-sheet) core region typical of all SDRs,
extended SDRs have a less conserved C-terminal
extension of approximately 100 amino acids. Extended
SDRs are a diverse collection of proteins, and include
isomerases, epimerases, oxidoreductases, and lyases;
they typically have a TGXXGXXG cofactor binding motif.
SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving
as a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton
relay involving the conserved Tyr and Lys, a water
molecule stabilized by Asn, and nicotinamide. Atypical
SDRs generally lack the catalytic residues
characteristic of the SDRs, and their glycine-rich
NAD(P)-binding motif is often different from the forms
normally seen in classical or extended SDRs. Complex
(multidomain) SDRs such as ketoreductase domains of
fatty acid synthase have a GGXGXXG NAD(P)-binding motif
and an altered active site motif (YXXXN). Fungal type
ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding
motif.
Length = 301
Score = 32.2 bits (74), Expect = 0.077
Identities = 11/20 (55%), Positives = 16/20 (80%)
Query: 13 VLVTGGTGFMGKVLLEKLLR 32
VLVTG TGF+ ++E+LL+
Sbjct: 2 VLVTGATGFIASHIVEQLLK 21
>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 = 32.2 bits (74), Expect = 0.077
Identities = 8/21 (38%), Positives = 14/21 (66%)
Query: 13 VLVTGGTGFMGKVLLEKLLRS 33
V V G TGF+G+ ++ +L +
Sbjct: 3 VTVFGATGFIGRYVVNRLAKR 23
>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 = 31.8 bits (73), Expect = 0.10
Identities = 14/37 (37%), Positives = 23/37 (62%), Gaps = 3/37 (8%)
Query: 13 VLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRG 49
+L+TGGTGF+G+ L ++L + + V IL R+
Sbjct: 1 ILITGGTGFIGRALTQRLTKRGHE---VTILTRSPPP 34
>gnl|CDD|187541 cd05230, UGD_SDR_e, UDP-glucuronate decarboxylase (UGD) and
related proteins, extended (e) SDRs. UGD catalyzes the
formation of UDP-xylose from UDP-glucuronate; it is an
extended-SDR, and has the characteristic glycine-rich
NAD-binding pattern, TGXXGXXG, and active site tetrad.
Extended SDRs are distinct from classical SDRs. In
addition to the Rossmann fold (alpha/beta folding
pattern with a central beta-sheet) core region typical
of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving
as a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton
relay involving the conserved Tyr and Lys, a water
molecule stabilized by Asn, and nicotinamide. Atypical
SDRs generally lack the catalytic residues
characteristic of the SDRs, and their glycine-rich
NAD(P)-binding motif is often different from the forms
normally seen in classical or extended SDRs. Complex
(multidomain) SDRs such as ketoreductase domains of
fatty acid synthase have a GGXGXXG NAD(P)-binding motif
and an altered active site motif (YXXXN). Fungal type
ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding
motif.
Length = 305
Score = 31.8 bits (73), Expect = 0.10
Identities = 10/20 (50%), Positives = 15/20 (75%)
Query: 13 VLVTGGTGFMGKVLLEKLLR 32
+L+TGG GF+G L ++LL
Sbjct: 3 ILITGGAGFLGSHLCDRLLE 22
>gnl|CDD|187570 cd05260, GDP_MD_SDR_e, GDP-mannose 4,6 dehydratase, extended (e)
SDRs. GDP-mannose 4,6 dehydratase, a homodimeric SDR,
catalyzes the NADP(H)-dependent conversion of
GDP-(D)-mannose to GDP-4-keto, 6-deoxy-(D)-mannose in
the fucose biosynthesis pathway. These proteins have the
canonical active site triad and NAD-binding pattern,
however the active site Asn is often missing and may be
substituted with Asp. A Glu residue has been identified
as an important active site base. Extended SDRs are
distinct from classical SDRs. In addition to the
Rossmann fold (alpha/beta folding pattern with a central
beta-sheet) core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids. Extended SDRs are a
diverse collection of proteins, and include isomerases,
epimerases, oxidoreductases, and lyases; they typically
have a TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 316
Score = 31.8 bits (73), Expect = 0.11
Identities = 34/142 (23%), Positives = 54/142 (38%), Gaps = 37/142 (26%)
Query: 13 VLVTGGTGFMGKVLLEKLLRSCPDIG-KVYILCRAKRGLTPKARLAEFSKLPVFERLRKE 71
L+TG TG G L E LL + G +V+ + R R + F+ + L
Sbjct: 2 ALITGITGQDGSYLAEFLL----EKGYEVHGIVR---------RSSSFN-TDRIDHLYIN 47
Query: 72 CPAQLSRLHIIEGDILQANLGIKDSDLLMLQEEVS--VVFNGAA------SLKLEAELKE 123
R+ + GD+ + S L E+V +++ AA S E
Sbjct: 48 KD----RITLHYGDLTDS------SSLRRAIEKVRPDEIYHLAAQSHVKVSFDDPEYTAE 97
Query: 124 NVAANTRGTQRLLDIALKMKKL 145
N GT LL+ A+++ L
Sbjct: 98 ---VNAVGTLNLLE-AIRILGL 115
>gnl|CDD|212492 cd05327, retinol-DH_like_SDR_c_like, retinol dehydrogenase
(retinol-DH), Light dependent Protochlorophyllide
(Pchlide) OxidoReductase (LPOR) and related proteins,
classical (c) SDRs. Classical SDR subgroup containing
retinol-DHs, LPORs, and related proteins. Retinol is
processed by a medium chain alcohol dehydrogenase
followed by retinol-DHs. Pchlide reductases act in
chlorophyll biosynthesis. There are distinct enzymes
that catalyze Pchlide reduction in light or dark
conditions. Light-dependent reduction is via an
NADP-dependent SDR, LPOR. Proteins in this subfamily
share the glycine-rich NAD-binding motif of the
classical SDRs, have a partial match to the canonical
active site tetrad, but lack the typical active site
Ser. This subgroup includes the human proteins: retinol
dehydrogenase -12, -13 ,and -14,
dehydrogenase/reductase SDR family member (DHRS)-12 ,
-13 and -X (a DHRS on chromosome X), and WWOX (WW
domain-containing oxidoreductase), as well as a
Neurospora crassa SDR encoded by the blue light
inducible bli-4 gene. SDRs are a functionally diverse
family of oxidoreductases that have a single domain
with a structurally conserved Rossmann fold (alpha/beta
folding pattern with a central beta-sheet), an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRs are
approximately 350 residues. Sequence identity between
different SDR enzymes are typically in the 15-30%
range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes catalyze a
wide range of activities including the metabolism of
steroids, cofactors, carbohydrates, lipids, aromatic
compounds, and amino acids, and act in redox sensing.
Classical SDRs have an TGXXX[AG]XG cofactor binding
motif and a YXXXK active site motif, with the Tyr
residue of the active site motif serving as a critical
catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 269
Score = 31.4 bits (72), Expect = 0.13
Identities = 13/53 (24%), Positives = 24/53 (45%), Gaps = 4/53 (7%)
Query: 10 GRSVLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCR-AKRGLTPKARLAEFSK 61
G+ V++TG +GK +L + V I CR ++G A + + +
Sbjct: 1 GKVVVITGANSGIGKETARELAKRG---AHVIIACRNEEKGEEAAAEIKKETG 50
>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 = 30.7 bits (70), Expect = 0.21
Identities = 24/101 (23%), Positives = 42/101 (41%), Gaps = 22/101 (21%)
Query: 13 VLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFSKLPVFERLRKEC 72
VLVTG GF+G L+E L+R +G +A ++ + L
Sbjct: 1 VLVTGADGFIGSHLVEALVR---------------QGYEVRA-FVLYNSFNSWGWLDTSP 44
Query: 73 PAQLSRLHIIEGDILQANLGIKDSDLLMLQEEVSVVFNGAA 113
P ++ ++ GDI + ++ + + VVF+ AA
Sbjct: 45 PEVKDKIEVVTGDIRDPD-SVRKA-----MKGCDVVFHLAA 79
>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 = 30.4 bits (69), Expect = 0.24
Identities = 27/129 (20%), Positives = 51/129 (39%), Gaps = 34/129 (26%)
Query: 13 VLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFSKLPVFERLRKEC 72
+L+ G TGF+G+ L +LL +V +L R + RL++ + PV
Sbjct: 1 ILILGATGFIGRALARELLE---QGHEVTLLVRNTK------RLSKEDQEPV-------- 43
Query: 73 PAQLSRLHIIEGDILQANLGIKDSDLLMLQEEVSVVFNGAASLKLEAELKENVAANTRGT 132
++EGD+ + +Q V+ A + ++ + GT
Sbjct: 44 -------AVVEGDLRDLDSLSDA-----VQGVDVVIHLAGAPR----DTRDFCEVDVEGT 87
Query: 133 QRLLDIALK 141
+ +L+ A K
Sbjct: 88 RNVLE-AAK 95
>gnl|CDD|223774 COG0702, COG0702, Predicted nucleoside-diphosphate-sugar
epimerases [Cell envelope biogenesis, outer membrane /
Carbohydrate transport and metabolism].
Length = 275
Score = 30.6 bits (69), Expect = 0.28
Identities = 14/47 (29%), Positives = 20/47 (42%), Gaps = 3/47 (6%)
Query: 13 VLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEF 59
+LVTG TGF+G ++ +LL +V R A E
Sbjct: 3 ILVTGATGFVGGAVVRELLA---RGHEVRAAVRNPEAAAALAGGVEV 46
>gnl|CDD|187562 cd05252, CDP_GD_SDR_e, CDP-D-glucose 4,6-dehydratase, extended
(e) SDRs. This subgroup contains CDP-D-glucose
4,6-dehydratase, an extended SDR, which catalyzes the
conversion of CDP-D-glucose to
CDP-4-keto-6-deoxy-D-glucose. This subgroup has the
characteristic active site tetrad and NAD-binding motif
of the extended SDRs. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids. Extended SDRs are a diverse collection
of proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and
their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 336
Score = 30.4 bits (69), Expect = 0.31
Identities = 10/16 (62%), Positives = 12/16 (75%)
Query: 8 YAGRSVLVTGGTGFMG 23
+ G+ VLVTG TGF G
Sbjct: 2 WQGKRVLVTGHTGFKG 17
>gnl|CDD|236116 PRK07856, PRK07856, short chain dehydrogenase; Provisional.
Length = 252
Score = 29.9 bits (68), Expect = 0.39
Identities = 18/52 (34%), Positives = 24/52 (46%), Gaps = 4/52 (7%)
Query: 8 YAGRSVLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEF 59
GR VLVTGGT +G + L + G ++C + T R AEF
Sbjct: 4 LTGRVVLVTGGTRGIGAGIARAFLAA----GATVVVCGRRAPETVDGRPAEF 51
>gnl|CDD|233954 TIGR02622, CDP_4_6_dhtase, CDP-glucose 4,6-dehydratase. Members
of this protein family are CDP-glucose 4,6-dehydratase
from a variety of Gram-negative and Gram-positive
bacteria. Members typically are encoded next to a gene
that encodes a glucose-1-phosphate
cytidylyltransferase, which produces the substrate,
CDP-D-glucose, used by this enzyme to produce
CDP-4-keto-6-deoxyglucose [Cell envelope, Biosynthesis
and degradation of surface polysaccharides and
lipopolysaccharides].
Length = 349
Score = 30.0 bits (68), Expect = 0.47
Identities = 10/16 (62%), Positives = 12/16 (75%)
Query: 8 YAGRSVLVTGGTGFMG 23
+ G+ VLVTG TGF G
Sbjct: 2 WQGKKVLVTGHTGFKG 17
>gnl|CDD|132628 TIGR03589, PseB, UDP-N-acetylglucosamine 4,6-dehydratase. This
enzyme catalyzes the first step in the biosynthesis of
pseudaminic acid, the conversion of
UDP-N-acetylglucosamine to
UDP-4-keto-6-deoxy-N-acetylglucosamine. These sequences
are members of the broader pfam01073 (3-beta
hydroxysteroid dehydrogenase/isomerase family) family.
Length = 324
Score = 29.7 bits (67), Expect = 0.49
Identities = 11/22 (50%), Positives = 16/22 (72%)
Query: 10 GRSVLVTGGTGFMGKVLLEKLL 31
+S+L+TGGTG GK + +LL
Sbjct: 4 NKSILITGGTGSFGKAFISRLL 25
>gnl|CDD|187545 cd05234, UDP_G4E_2_SDR_e, UDP-glucose 4 epimerase, subgroup 2,
extended (e) SDRs. UDP-glucose 4 epimerase (aka
UDP-galactose-4-epimerase), is a homodimeric extended
SDR. It catalyzes the NAD-dependent conversion of
UDP-galactose to UDP-glucose, the final step in Leloir
galactose synthesis. This subgroup is comprised of
archaeal and bacterial proteins, and has the
characteristic active site tetrad and NAD-binding motif
of the extended SDRs. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids. Extended SDRs are a diverse collection
of proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and
their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 305
Score = 29.6 bits (67), Expect = 0.51
Identities = 11/20 (55%), Positives = 16/20 (80%)
Query: 13 VLVTGGTGFMGKVLLEKLLR 32
+LVTGG GF+G L+++LL
Sbjct: 2 ILVTGGAGFIGSHLVDRLLE 21
>gnl|CDD|236035 PRK07508, PRK07508, aminodeoxychorismate synthase; Provisional.
Length = 378
Score = 29.6 bits (67), Expect = 0.52
Identities = 23/88 (26%), Positives = 29/88 (32%), Gaps = 28/88 (31%)
Query: 23 GKVLLEKLLRSCPDIGKVYILC------------RAKRGLTPKARLAEFSK-------LP 63
G +L KL P+ + +LC R ARL +
Sbjct: 57 GYLLEPKLAPLMPEGRETPLLCFGVFDAPSPEAPAPARPSENAARLRDPVARWDFADYAQ 116
Query: 64 VFERLRKECPAQLSRLHIIEGDILQANL 91
FERL + HI GD QANL
Sbjct: 117 RFERLHR---------HIRAGDCYQANL 135
>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 = 29.6 bits (67), Expect = 0.55
Identities = 38/132 (28%), Positives = 54/132 (40%), Gaps = 35/132 (26%)
Query: 13 VLVTGGTGFMGKVLLEKLL-RSCPDIGKVYILCRAKRGLTPKARLAEFSKLPVFERLRKE 71
VLVTG TGF+G ++ LL + +V +L R P + L V
Sbjct: 3 VLVTGATGFVGSAVVRLLLEQGE----EVRVLVR------PTSDRRNLEGLDV------- 45
Query: 72 CPAQLSRLHIIEGDILQANLGIKDSDLLMLQ-EEVSVVFNGAASLKLEAELKENV-AANT 129
I+EGD ++D L +F+ AA +L A E + AAN
Sbjct: 46 --------EIVEGD-------LRDPASLRKAVAGCRALFHVAADYRLWAPDPEEMYAANV 90
Query: 130 RGTQRLLDIALK 141
GT+ LL AL+
Sbjct: 91 EGTRNLLRAALE 102
>gnl|CDD|182313 PRK10217, PRK10217, dTDP-glucose 4,6-dehydratase; Provisional.
Length = 355
Score = 29.6 bits (66), Expect = 0.55
Identities = 10/26 (38%), Positives = 16/26 (61%)
Query: 11 RSVLVTGGTGFMGKVLLEKLLRSCPD 36
R +L+TGG GF+G L+ ++ D
Sbjct: 2 RKILITGGAGFIGSALVRYIINETSD 27
>gnl|CDD|183778 PRK12829, PRK12829, short chain dehydrogenase; Provisional.
Length = 264
Score = 29.6 bits (67), Expect = 0.57
Identities = 25/94 (26%), Positives = 38/94 (40%), Gaps = 14/94 (14%)
Query: 8 YAGRSVLVTGGTGFMGKVLLEKLLRSCPDIG-KVYILCRAKRGL-TPKARLAEFSKLPVF 65
G VLVTGG +G+ + E G +V++ ++ L ARL
Sbjct: 9 LDGLRVLVTGGASGIGRAIAEAFAE----AGARVHVCDVSEAALAATAARLPGAKVTATV 64
Query: 66 ERLRKECPAQLSRL--HIIEG----DILQANLGI 93
+ PAQ+ R+ +E D+L N GI
Sbjct: 65 ADVAD--PAQVERVFDTAVERFGGLDVLVNNAGI 96
>gnl|CDD|177883 PLN02240, PLN02240, UDP-glucose 4-epimerase.
Length = 352
Score = 29.5 bits (67), Expect = 0.58
Identities = 9/15 (60%), Positives = 13/15 (86%)
Query: 9 AGRSVLVTGGTGFMG 23
GR++LVTGG G++G
Sbjct: 4 MGRTILVTGGAGYIG 18
>gnl|CDD|224015 COG1090, COG1090, Predicted nucleoside-diphosphate sugar
epimerase [General function prediction only].
Length = 297
Score = 29.5 bits (67), Expect = 0.60
Identities = 13/33 (39%), Positives = 19/33 (57%), Gaps = 3/33 (9%)
Query: 13 VLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCR 45
+L+TGGTG +G+ L +L + V IL R
Sbjct: 1 ILITGGTGLIGRALTARLRKGGHQ---VTILTR 30
>gnl|CDD|187572 cd05262, SDR_a7, atypical (a) SDRs, subgroup 7. This subgroup
contains atypical SDRs of unknown function. Members of
this subgroup have a glycine-rich NAD(P)-binding motif
consensus that matches the extended SDRs, TGXXGXXG, but
lacks the characteristic active site residues of the
SDRs. This subgroup has basic residues (HXXXR) in place
of the active site motif YXXXK, these may have a
catalytic role. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and
their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Atypical SDRs include biliverdin IX beta
reductase (BVR-B,aka flavin reductase), NMRa (a
negative transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane
reductase, isoflavone reductases, and others. SDRs are
a functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. In addition to the Rossmann fold
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids, and typically have a TGXXGXXG cofactor
binding motif. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 291
Score = 29.2 bits (66), Expect = 0.69
Identities = 9/19 (47%), Positives = 14/19 (73%)
Query: 13 VLVTGGTGFMGKVLLEKLL 31
V VTG TGF+G ++ +L+
Sbjct: 3 VFVTGATGFIGSAVVRELV 21
>gnl|CDD|181335 PRK08264, PRK08264, short chain dehydrogenase; Validated.
Length = 238
Score = 29.1 bits (66), Expect = 0.85
Identities = 15/44 (34%), Positives = 21/44 (47%), Gaps = 2/44 (4%)
Query: 9 AGRSVLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTP 52
G+ VLVTG +G+ +E+LL KVY R +T
Sbjct: 5 KGKVVLVTGANRGIGRAFVEQLLAR--GAAKVYAAARDPESVTD 46
>gnl|CDD|131715 TIGR02667, moaB_proteo, molybdenum cofactor biosynthesis protein B,
proteobacterial. This model represents the MoaB protein
molybdopterin biosynthesis regions in Proteobacteria.
This crystallized but incompletely characterized protein
is thought to be involved in, though not required for,
early steps in molybdopterin biosynthesis. It may bind a
molybdopterin precursor. A distinctive conserved motif
PCN near the C-terminus helps distinguish this clade
from other homologs, including sets of proteins
designated MogA [Biosynthesis of cofactors, prosthetic
groups, and carriers, Molybdopterin].
Length = 163
Score = 28.5 bits (64), Expect = 0.89
Identities = 24/67 (35%), Positives = 29/67 (43%), Gaps = 20/67 (29%)
Query: 4 VARWYAGRSV---LVTGGTGFMGK--------VLLEK-------LLR--SCPDIGKVYIL 43
V+ W A V L+TGGTGF G+ L +K L R S +IG I
Sbjct: 55 VSAWIADPDVQVILITGGTGFTGRDVTPEALEPLFDKTVEGFGELFRQLSYEEIGTSTIQ 114
Query: 44 CRAKRGL 50
RA GL
Sbjct: 115 SRALAGL 121
>gnl|CDD|215370 PLN02686, PLN02686, cinnamoyl-CoA reductase.
Length = 367
Score = 29.0 bits (65), Expect = 0.99
Identities = 11/22 (50%), Positives = 16/22 (72%)
Query: 11 RSVLVTGGTGFMGKVLLEKLLR 32
R V VTGG F+G ++++LLR
Sbjct: 54 RLVCVTGGVSFLGLAIVDRLLR 75
>gnl|CDD|187661 cd08958, FR_SDR_e, flavonoid reductase (FR), extended (e) SDRs.
This subgroup contains FRs of the extended SDR-type and
related proteins. These FRs act in the NADP-dependent
reduction of flavonoids, ketone-containing plant
secondary metabolites; they have the characteristic
active site triad of the SDRs (though not the upstream
active site Asn) and a NADP-binding motif that is very
similar to the typical extended SDR motif. Extended
SDRs are distinct from classical SDRs. In addition to
the Rossmann fold (alpha/beta folding pattern with a
central beta-sheet) core region typical of all SDRs,
extended SDRs have a less conserved C-terminal
extension of approximately 100 amino acids. Extended
SDRs are a diverse collection of proteins, and include
isomerases, epimerases, oxidoreductases, and lyases;
they typically have a TGXXGXXG cofactor binding motif.
SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving
as a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton
relay involving the conserved Tyr and Lys, a water
molecule stabilized by Asn, and nicotinamide. Atypical
SDRs generally lack the catalytic residues
characteristic of the SDRs, and their glycine-rich
NAD(P)-binding motif is often different from the forms
normally seen in classical or extended SDRs. Complex
(multidomain) SDRs such as ketoreductase domains of
fatty acid synthase have a GGXGXXG NAD(P)-binding motif
and an altered active site motif (YXXXN). Fungal type
ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding
motif.
Length = 293
Score = 28.7 bits (65), Expect = 1.1
Identities = 10/20 (50%), Positives = 16/20 (80%)
Query: 13 VLVTGGTGFMGKVLLEKLLR 32
V VTG +GF+G L+++LL+
Sbjct: 1 VCVTGASGFIGSWLVKRLLQ 20
>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 = 28.9 bits (65), Expect = 1.1
Identities = 15/45 (33%), Positives = 22/45 (48%), Gaps = 3/45 (6%)
Query: 13 VLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLA 57
VLVTG TG++G L+ +LL+ V L R+ L +
Sbjct: 1 VLVTGATGYVGGRLVPRLLQEGHQ---VRALVRSPEKLADRPWSE 42
>gnl|CDD|187550 cd05239, GDP_FS_SDR_e, GDP-fucose synthetase, extended (e) SDRs.
GDP-fucose synthetase (aka 3, 5-epimerase-4-reductase)
acts in the NADP-dependent synthesis of GDP-fucose from
GDP-mannose. Two activities have been proposed for the
same active site: epimerization and reduction. Proteins
in this subgroup are extended SDRs, which have a
characteristic active site tetrad and an NADP-binding
motif, [AT]GXXGXXG, that is a close match to the
archetypical form. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids. Extended SDRs are a diverse collection
of proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and
their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 300
Score = 28.7 bits (65), Expect = 1.1
Identities = 8/21 (38%), Positives = 12/21 (57%)
Query: 13 VLVTGGTGFMGKVLLEKLLRS 33
+LVTG G +G ++ L R
Sbjct: 2 ILVTGHRGLVGSAIVRVLARR 22
>gnl|CDD|224014 COG1089, Gmd, GDP-D-mannose dehydratase [Cell envelope biogenesis,
outer membrane].
Length = 345
Score = 28.5 bits (64), Expect = 1.2
Identities = 37/133 (27%), Positives = 55/133 (41%), Gaps = 25/133 (18%)
Query: 10 GRSVLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFSKLPVFERLR 69
G+ L+TG TG G L E LL K Y + KR R + F+ L
Sbjct: 2 GKVALITGITGQDGSYLAELLL------EKGYEVHGIKR------RSSSFN--TPRIHLY 47
Query: 70 KECPAQLSRLHIIEGDILQANLGIKDSDLLMLQEEV--SVVFNGAASLKLEAELK---EN 124
++ RLH+ GD+ + S+LL + EEV ++N AA + +
Sbjct: 48 EDPHLNDPRLHLHYGDLTDS------SNLLRILEEVQPDEIYNLAAQSHVGVSFEQPEYT 101
Query: 125 VAANTRGTQRLLD 137
+ GT RLL+
Sbjct: 102 ADVDAIGTLRLLE 114
>gnl|CDD|238562 cd01142, TroA_e, Periplasmic binding protein TroA_e. These
proteins are predicted to function as initial receptors
in the ABC metal ion uptake in eubacteria and archaea.
They belong to the TroA superfamily of helical backbone
metal receptor proteins that share a distinct fold and
ligand binding mechanism. A typical TroA protein is
comprised of two globular subdomains connected by a
single helix and can bind their ligands in the cleft
between these domains.
Length = 289
Score = 28.5 bits (64), Expect = 1.3
Identities = 15/51 (29%), Positives = 21/51 (41%), Gaps = 5/51 (9%)
Query: 10 GRSVLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRA--KRGLTPKARLAE 58
G +V G+V LE+LL+ PD V I+ A K + R
Sbjct: 195 GINVASEATKKGSGEVSLEQLLKWNPD---VIIVGNADTKAAILADPRWQN 242
>gnl|CDD|235738 PRK06199, PRK06199, ornithine cyclodeaminase; Validated.
Length = 379
Score = 28.5 bits (64), Expect = 1.3
Identities = 12/33 (36%), Positives = 17/33 (51%)
Query: 18 GTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGL 50
G G MGK +L + CP I + I R ++ L
Sbjct: 162 GPGVMGKTILAAFMAVCPGIDTIKIKGRGQKSL 194
>gnl|CDD|187549 cd05238, Gne_like_SDR_e, Escherichia coli Gne (a
nucleoside-diphosphate-sugar 4-epimerase)-like,
extended (e) SDRs. Nucleoside-diphosphate-sugar
4-epimerase has the characteristic active site tetrad
and NAD-binding motif of the extended SDR, and is
related to more specifically defined epimerases such as
UDP-glucose 4 epimerase (aka
UDP-galactose-4-epimerase), which catalyzes the
NAD-dependent conversion of UDP-galactose to
UDP-glucose, the final step in Leloir galactose
synthesis. This subgroup includes Escherichia coli
055:H7 Gne, a UDP-GlcNAc 4-epimerase, essential for O55
antigen 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 = 305
Score = 28.5 bits (64), Expect = 1.5
Identities = 12/26 (46%), Positives = 18/26 (69%)
Query: 12 SVLVTGGTGFMGKVLLEKLLRSCPDI 37
VL+TG +GF+G+ L E+LL P+
Sbjct: 2 KVLITGASGFVGQRLAERLLSDVPNE 27
>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 = 28.3 bits (64), Expect = 1.6
Identities = 13/34 (38%), Positives = 22/34 (64%), Gaps = 5/34 (14%)
Query: 13 VLVTGGTGFMGKVLLEKLLRSCPDIG-KVYILCR 45
+++TGGTGF+G+ L +L + G +V +L R
Sbjct: 2 IVITGGTGFIGRALTRRLTAA----GHEVVVLSR 31
>gnl|CDD|187660 cd08957, WbmH_like_SDR_e, Bordetella bronchiseptica enzymes WbmH
and WbmG-like, extended (e) SDRs. Bordetella
bronchiseptica enzymes WbmH and WbmG, and related
proteins. This subgroup exhibits the active site tetrad
and NAD-binding motif of the extended SDR family. It has
been proposed that the active site in Bordetella WbmG
and WbmH cannot function as an epimerase, and that it
plays a role in O-antigen synthesis pathway from
UDP-2,3-diacetamido-2,3-dideoxy-l-galacturonic acid.
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 = 307
Score = 28.2 bits (63), Expect = 1.8
Identities = 32/136 (23%), Positives = 54/136 (39%), Gaps = 28/136 (20%)
Query: 13 VLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFSKLPVFERLRKEC 72
VL+TGG G +G L+E LL +V ++ G R+E
Sbjct: 3 VLITGGAGQIGSHLIEHLL---ERGHQVVVIDNFATG-------------------RREH 40
Query: 73 PAQLSRLHIIEGDILQANLGIKDSDLLMLQEEVSVVFNGAASLKLEAELKENVAANTRGT 132
L ++EG I A+ + D + + V + AA+ K + E+ N G
Sbjct: 41 LPDHPNLTVVEGSI--ADKALVDKLFGDFKPD--AVVHTAAAYKDPDDWYEDTLTNVVGG 96
Query: 133 QRLLDIALK--MKKLV 146
++ A K +K+L+
Sbjct: 97 ANVVQAAKKAGVKRLI 112
>gnl|CDD|200381 TIGR04130, FnlA, UDP-N-acetylglucosamine
4,6-dehydratase/5-epimerase. The FnlA enzyme is the
first step in the biosynthesis of UDP-FucNAc from
UDP-GlcNAc in E. coli (along with FnlB and FnlC). The
proteins identified by this model include FnlA homologs
in the O-antigen clusters of O4, O25, O26, O29
(Shigella D11), O118, O145 and O172 serotype strains,
all of which produce O-antigens containing FucNAc (or
the further modified FucNAm). A homolog from
Pseudomonas aerugiosa serotype O11, WbjB, also involved
in the biosynthesis of UDP-FucNAc has been
characterized and is now believed to carry out both the
initial 4,6-dehydratase reaction and the subsequent
epimerization of the resulting methyl group at C-5. A
phylogenetic tree of related sequences shows a distinct
clade of enzymes involved in the biosynthesis of
UDP-QuiNAc (Qui=qinovosamine). This clade appears to be
descendant from the common ancestor of the Pseudomonas
and E. coli fucose-biosynthesis enzymes. It has been
hypothesized that the first step in the biosynthesis of
these two compounds may be the same, and thus that
these enzymes all have the same function. At present,
lacking sufficient confirmation of this, the current
model trusted cutoff only covers the tree segment
surrounding the E. coli genes. The clades containing
the Pseudomonas and QuiNAc biosynthesis enzymes score
above the noise cutoff. Immediately below the noise
cutoff are enzymes involved in the biosynthesis of
UDP-RhaNAc (Rha=rhamnose), which again may or may not
produce the same product.
Length = 337
Score = 28.0 bits (62), Expect = 1.8
Identities = 13/41 (31%), Positives = 24/41 (58%), Gaps = 2/41 (4%)
Query: 8 YAGRSVLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKR 48
+ + +L+TGGTG G +L + L + DI ++ I R ++
Sbjct: 2 FKDKILLITGGTGSFGNAVLRRFLDT--DIKEIRIFSRDEK 40
>gnl|CDD|187536 cd05193, AR_like_SDR_e, aldehyde reductase, flavonoid reductase,
and related proteins, extended (e) SDRs. This subgroup
contains aldehyde reductase and flavonoid reductase of
the extended SDR-type and related proteins. Proteins in
this subgroup have a complete SDR-type active site
tetrad and a close match to the canonical extended SDR
NADP-binding motif. Aldehyde reductase I (aka carbonyl
reductase) is an NADP-binding SDR; it 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 = 295
Score = 28.0 bits (62), Expect = 1.9
Identities = 10/19 (52%), Positives = 15/19 (78%)
Query: 13 VLVTGGTGFMGKVLLEKLL 31
VLVTG +GF+ ++E+LL
Sbjct: 1 VLVTGASGFVASHVVEQLL 19
>gnl|CDD|224328 COG1410, MetH, Methionine synthase I, cobalamin-binding domain
[Amino acid transport and metabolism].
Length = 842
Score = 28.1 bits (63), Expect = 1.9
Identities = 16/52 (30%), Positives = 23/52 (44%), Gaps = 15/52 (28%)
Query: 53 KARLAEFSKLPVFERLR---------------KECPAQLSRLHIIEGDILQA 89
+AR AE+ LPV ERL+ +E Q L +IEG ++
Sbjct: 312 EARDAEWRSLPVEERLKHAIVDGIREGLEEDLEEARQQKPPLEVIEGPLMDG 363
>gnl|CDD|237218 PRK12825, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 249
Score = 27.5 bits (62), Expect = 2.3
Identities = 9/23 (39%), Positives = 13/23 (56%)
Query: 10 GRSVLVTGGTGFMGKVLLEKLLR 32
GR LVTG +G+ + +L R
Sbjct: 6 GRVALVTGAARGLGRAIALRLAR 28
>gnl|CDD|217556 pfam03435, Saccharop_dh, Saccharopine dehydrogenase. This family
comprised of three structural domains that can not be
separated in the linear sequence. In some organisms
this enzyme is found as a bifunctional polypeptide with
lysine ketoglutarate reductase. The saccharopine
dehydrogenase can also function as a saccharopine
reductase.
Length = 380
Score = 28.0 bits (63), Expect = 2.3
Identities = 16/77 (20%), Positives = 29/77 (37%), Gaps = 9/77 (11%)
Query: 13 VLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFSKLPVFE--RLRK 70
VL+ G G +G+ + L R ++ + R+ LA F +
Sbjct: 1 VLIIGA-GGVGQGVAPLLARHGD--LEITVADRSLEKA---QALAAPKLGLRFIAIAVDA 54
Query: 71 ECPAQLSRLHIIEGDIL 87
+ L L + EGD++
Sbjct: 55 DNYEALVAL-LKEGDLV 70
>gnl|CDD|177856 PLN02206, PLN02206, UDP-glucuronate decarboxylase.
Length = 442
Score = 28.0 bits (62), Expect = 2.3
Identities = 11/23 (47%), Positives = 17/23 (73%)
Query: 10 GRSVLVTGGTGFMGKVLLEKLLR 32
G V+VTGG GF+G L+++L+
Sbjct: 119 GLRVVVTGGAGFVGSHLVDRLMA 141
>gnl|CDD|187581 cd05273, GME-like_SDR_e, Arabidopsis thaliana
GDP-mannose-3',5'-epimerase (GME)-like, extended (e)
SDRs. This subgroup of NDP-sugar
epimerase/dehydratases are extended SDRs; they have the
characteristic active site tetrad, and an NAD-binding
motif: TGXXGXX[AG], which is a close match to the
canonical NAD-binding motif. Members include
Arabidopsis thaliana GDP-mannose-3',5'-epimerase (GME)
which catalyzes the epimerization of two positions of
GDP-alpha-D-mannose to form GDP-beta-L-galactose.
Extended SDRs are distinct from classical SDRs. In
addition to the Rossmann fold (alpha/beta folding
pattern with a central beta-sheet) core region typical
of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving
as a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton
relay involving the conserved Tyr and Lys, a water
molecule stabilized by Asn, and nicotinamide. Atypical
SDRs generally lack the catalytic residues
characteristic of the SDRs, and their glycine-rich
NAD(P)-binding motif is often different from the forms
normally seen in classical or extended SDRs. Complex
(multidomain) SDRs such as ketoreductase domains of
fatty acid synthase have a GGXGXXG NAD(P)-binding motif
and an altered active site motif (YXXXN). Fungal type
ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding
motif.
Length = 328
Score = 27.8 bits (62), Expect = 2.3
Identities = 10/20 (50%), Positives = 12/20 (60%)
Query: 13 VLVTGGTGFMGKVLLEKLLR 32
LVTG GF+G L E+L
Sbjct: 3 ALVTGAGGFIGSHLAERLKA 22
>gnl|CDD|183775 PRK12826, PRK12826, 3-ketoacyl-(acyl-carrier-protein) reductase;
Reviewed.
Length = 251
Score = 27.6 bits (62), Expect = 2.6
Identities = 22/93 (23%), Positives = 29/93 (31%), Gaps = 14/93 (15%)
Query: 10 GRSVLVTGGTGFMGKVLLEKLLRS---------CPDIGKVYILCRAKRGLTPKARLAEFS 60
GR LVTG +G+ + +L C D G +AR +
Sbjct: 6 GRVALVTGAARGIGRAIAVRLAADGAEVIVVDICGDDAAATAELVEAAGGKARARQVDVR 65
Query: 61 KLPVFERLRKECPAQLSRLHIIEGDILQANLGI 93
+ RL DIL AN GI
Sbjct: 66 DRAALKAAVAAGVEDFGRL-----DILVANAGI 93
>gnl|CDD|234708 PRK00274, ksgA, 16S ribosomal RNA methyltransferase KsgA/Dim1
family protein; Reviewed.
Length = 272
Score = 27.4 bits (62), Expect = 2.8
Identities = 9/26 (34%), Positives = 12/26 (46%), Gaps = 2/26 (7%)
Query: 66 ERLRKECPAQLSRLHIIEGDILQANL 91
L + L IIEGD L+ +L
Sbjct: 78 PILAE--TFAEDNLTIIEGDALKVDL 101
>gnl|CDD|187646 cd08942, RhlG_SDR_c, RhlG and related beta-ketoacyl reductases,
classical (c) SDRs. Pseudomonas aeruginosa RhlG is an
SDR-family beta-ketoacyl reductase involved in
Rhamnolipid biosynthesis. RhlG is similar to but
distinct from the FabG family of beta-ketoacyl-acyl
carrier protein (ACP) of type II fatty acid synthesis.
RhlG and related proteins are classical SDRs, with a
canonical active site tetrad and glycine-rich
NAD(P)-binding motif. SDRs are a functionally diverse
family of oxidoreductases that have a single domain
with a structurally conserved Rossmann fold (alpha/beta
folding pattern with a central beta-sheet), an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRs are
approximately 350 residues. Sequence identity between
different SDR enzymes are typically in the 15-30%
range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes catalyze a
wide range of activities including the metabolism of
steroids, cofactors, carbohydrates, lipids, aromatic
compounds, and amino acids, and act in redox sensing.
Classical SDRs have an TGXXX[AG]XG cofactor binding
motif and a YXXXK active site motif, with the Tyr
residue of the active site motif serving as a critical
catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 250
Score = 27.1 bits (60), Expect = 3.5
Identities = 23/80 (28%), Positives = 35/80 (43%), Gaps = 17/80 (21%)
Query: 9 AGRSVLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCR-AKRGLTPKARLAEFSKLPVFER 67
AG+ VLVTGG+ +G+++ + L + +V I R A+ L+ +
Sbjct: 5 AGKIVLVTGGSRGIGRMIAQGFLEAG---ARVIISARKAEACADAAEELSAYG------- 54
Query: 68 LRKEC---PAQLSRLHIIEG 84
EC PA LS IE
Sbjct: 55 ---ECIAIPADLSSEEGIEA 71
>gnl|CDD|181609 PRK09009, PRK09009, C factor cell-cell signaling protein;
Provisional.
Length = 235
Score = 26.9 bits (60), Expect = 3.6
Identities = 10/25 (40%), Positives = 18/25 (72%)
Query: 13 VLVTGGTGFMGKVLLEKLLRSCPDI 37
+L+ GG+G +GK ++++LL PD
Sbjct: 3 ILIVGGSGGIGKAMVKQLLERYPDA 27
>gnl|CDD|187656 cd08953, KR_2_SDR_x, ketoreductase (KR), subgroup 2, complex (x)
SDRs. Ketoreductase, a module of the multidomain
polyketide synthase (PKS), has 2 subdomains, each
corresponding to a SDR family monomer. The C-terminal
subdomain catalyzes the NADPH-dependent reduction of the
beta-carbonyl of a polyketide to a hydroxyl group, a
step in the biosynthesis of polyketides, such as
erythromycin. The N-terminal subdomain, an interdomain
linker, is a truncated Rossmann fold which acts to
stabilizes the catalytic subdomain. Unlike typical SDRs,
the isolated domain does not oligomerize but is composed
of 2 subdomains, each resembling an SDR monomer. The
active site resembles that of typical SDRs, except that
the usual positions of the catalytic Asn and Tyr are
swapped, so that the canonical YXXXK motif changes to
YXXXN. Modular PKSs are multifunctional structures in
which the makeup recapitulates that found in (and may
have evolved from) FAS. Polyketide synthesis also
proceeds via the addition of 2-carbon units as in fatty
acid synthesis. The complex SDR NADP-binding motif,
GGXGXXG, is often present, but is not strictly conserved
in each instance of the module. This subfamily includes
both KR domains of the Bacillus subtilis Pks J,-L, and
PksM, and all three KR domains of PksN, components of
the megacomplex bacillaene synthase, which synthesizes
the antibiotic bacillaene. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold
(alpha/beta folding pattern with a central beta-sheet),
an NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRs are approximately
350 residues. Sequence identity between different SDR
enzymes are typically in the 15-30% range, but the
enzymes share the Rossmann fold NAD-binding motif and
characteristic NAD-binding and catalytic sequence
patterns. These enzymes catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human prostaglandin dehydrogenase
(PGDH) numbering). In addition to the Tyr and Lys, there
is often an upstream Ser (Ser-138, PGDH numbering)
and/or an Asn (Asn-107, PGDH numbering) contributing to
the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type KRs have a TGXXXGX(1-2)G
NAD(P)-binding motif. Some atypical SDRs have lost
catalytic activity and/or have an unusual NAD(P)-binding
motif and missing or unusual active site residues.
Reactions catalyzed within the SDR family include
isomerization, decarboxylation, epimerization, C=N bond
reduction, dehydratase activity, dehalogenation,
Enoyl-CoA reduction, and carbonyl-alcohol
oxidoreduction.
Length = 436
Score = 27.3 bits (61), Expect = 4.1
Identities = 30/151 (19%), Positives = 47/151 (31%), Gaps = 38/151 (25%)
Query: 4 VARWYAGRSVLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFSKLP 63
A G LVTGG G +G+ L L R ++ +L R L P+ K
Sbjct: 199 SAPLKPGGVYLVTGGAGGIGRALARALARRYG--ARLVLLGR--SPLPPEEE----WKAQ 250
Query: 64 VFERLRKECPAQLSRLHIIEGDILQANLGIKDSDLLMLQEEVS----------VVFNGAA 113
L A +R+ I D+ +D ++ + V + A
Sbjct: 251 TLAALE----ALGARVLYISADV---------TDAAAVRRLLEKVRERYGAIDGVIHAAG 297
Query: 114 SL-------KLEAELKENVAANTRGTQRLLD 137
L K + + +A G L
Sbjct: 298 VLRDALLAQKTAEDFEAVLAPKVDGLLNLAQ 328
>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 = 26.9 bits (60), Expect = 4.1
Identities = 25/93 (26%), Positives = 35/93 (37%), Gaps = 21/93 (22%)
Query: 13 VLVTGGTGFMGKVLLEKLLRSCPDIG-KVYILCRAKRGLTPKARLAEFSKLPVF------ 65
LVTG + +G+ + +L R G KV + R + L A + V
Sbjct: 1 ALVTGASSGIGRAIARRLARE----GAKVVLADRNEEALAELAAIEALGGNAVAVQADVS 56
Query: 66 -----ERLRKECPAQLSRLHIIEGDILQANLGI 93
E L +E + RL DIL N GI
Sbjct: 57 DEEDVEALVEEALEEFGRL-----DILVNNAGI 84
>gnl|CDD|187543 cd05232, UDP_G4E_4_SDR_e, UDP-glucose 4 epimerase, subgroup 4,
extended (e) SDRs. UDP-glucose 4 epimerase (aka
UDP-galactose-4-epimerase), is a homodimeric extended
SDR. It catalyzes the NAD-dependent conversion of
UDP-galactose to UDP-glucose, the final step in Leloir
galactose synthesis. This subgroup is comprised of
bacterial proteins, and includes the Staphylococcus
aureus capsular polysaccharide Cap5N, which may have a
role in the synthesis of UDP-N-acetyl-d-fucosamine.
This subgroup has the characteristic active site tetrad
and NAD-binding motif of the extended SDRs. Extended
SDRs are distinct from classical SDRs. In addition to
the Rossmann fold (alpha/beta folding pattern with a
central beta-sheet) core region typical of all SDRs,
extended SDRs have a less conserved C-terminal
extension of approximately 100 amino acids. Extended
SDRs are a diverse collection of proteins, and include
isomerases, epimerases, oxidoreductases, and lyases;
they typically have a TGXXGXXG cofactor binding motif.
SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving
as a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton
relay involving the conserved Tyr and Lys, a water
molecule stabilized by Asn, and nicotinamide. Atypical
SDRs generally lack the catalytic residues
characteristic of the SDRs, and their glycine-rich
NAD(P)-binding motif is often different from the forms
normally seen in classical or extended SDRs. Complex
(multidomain) SDRs such as ketoreductase domains of
fatty acid synthase have a GGXGXXG NAD(P)-binding motif
and an altered active site motif (YXXXN). Fungal type
ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding
motif.
Length = 303
Score = 26.9 bits (60), Expect = 4.4
Identities = 12/20 (60%), Positives = 16/20 (80%)
Query: 12 SVLVTGGTGFMGKVLLEKLL 31
VLVTG GF+G+ L++KLL
Sbjct: 1 KVLVTGANGFIGRALVDKLL 20
>gnl|CDD|165812 PLN02166, PLN02166, dTDP-glucose 4,6-dehydratase.
Length = 436
Score = 26.9 bits (59), Expect = 4.8
Identities = 10/19 (52%), Positives = 16/19 (84%)
Query: 13 VLVTGGTGFMGKVLLEKLL 31
++VTGG GF+G L++KL+
Sbjct: 123 IVVTGGAGFVGSHLVDKLI 141
>gnl|CDD|187558 cd05247, UDP_G4E_1_SDR_e, UDP-glucose 4 epimerase, subgroup 1,
extended (e) SDRs. UDP-glucose 4 epimerase (aka
UDP-galactose-4-epimerase), is a homodimeric extended
SDR. It catalyzes the NAD-dependent conversion of
UDP-galactose to UDP-glucose, the final step in Leloir
galactose synthesis. This subgroup has the
characteristic active site tetrad and NAD-binding motif
of the extended SDRs. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately 100
amino acids. Extended SDRs are a diverse collection of
proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 323
Score = 26.7 bits (60), Expect = 4.8
Identities = 36/147 (24%), Positives = 55/147 (37%), Gaps = 41/147 (27%)
Query: 13 VLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFSKLPVFERLRKEC 72
VLVTGG G++G + +LL + D+ + L R P R+ +
Sbjct: 2 VLVTGGAGYIGSHTVVELLEAGYDVVVLDNLSNGHREALP--RIEKI------------- 46
Query: 73 PAQLSRLHIIEGDILQANLGIKDSDLL--MLQEE-VSVVFNGAA------SLKLEAELKE 123
R+ EGDI D L + E + V + AA S++ + +
Sbjct: 47 -----RIEFYEGDIR-------DRAALDKVFAEHKIDAVIHFAALKAVGESVQKPLKYYD 94
Query: 124 NVAANTRGTQRLLDIALK--MKKLVVS 148
N N GT LL+ +K V S
Sbjct: 95 N---NVVGTLNLLEAMRAHGVKNFVFS 118
>gnl|CDD|213592 TIGR01179, galE, UDP-glucose-4-epimerase GalE. Alternate name:
UDPgalactose 4-epimerase This enzyme interconverts
UDP-glucose and UDP-galactose. A set of related
proteins, some of which are tentatively identified as
UDP-glucose-4-epimerase in Thermotoga maritima, Bacillus
halodurans, and several archaea, but deeply branched
from this set and lacking experimental evidence, are
excluded from This model and described by a separate
model [Energy metabolism, Sugars].
Length = 328
Score = 26.9 bits (60), Expect = 5.0
Identities = 34/144 (23%), Positives = 57/144 (39%), Gaps = 34/144 (23%)
Query: 13 VLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFSKLPVFERLRKEC 72
+LVTGG G++G + +LL S ++ + L R LP ER+
Sbjct: 2 ILVTGGAGYIGSHTVRQLLESGHEVVILDNLSNGSR-----------EALPRGERITP-- 48
Query: 73 PAQLSRLHIIEGDILQANLGIKDSDLLMLQEEVSVVFNGAA------SLKLEAELKENVA 126
+ +EGD+ L D L + ++ V + A S++ + N
Sbjct: 49 ------VTFVEGDLRDREL----LDRLFEEHKIDAVIHFAGLIAVGESVQKPLKYYRN-- 96
Query: 127 ANTRGTQRLLDIALK--MKKLVVS 148
N GT LL+ + +KK + S
Sbjct: 97 -NVVGTLNLLEAMQQAGVKKFIFS 119
>gnl|CDD|221514 pfam12297, EVC2_like, Ellis van Creveld protein 2 like protein.
This family of proteins is found in eukaryotes. Proteins
in this family are typically between 571 and 1310 amino
acids in length. There are two conserved sequence
motifs: LPA and ELH. EVC2 is implicated in Ellis van
Creveld chondrodysplastic dwarfism in humans. Mutations
in this protein can give rise to this congenital
condition. LIMBIN is a protein which shares around 80%
sequence homology with EVC2 and it is implicated in a
similar condition in bovine chondrodysplastic dwarfism.
Length = 429
Score = 26.7 bits (59), Expect = 5.1
Identities = 24/101 (23%), Positives = 37/101 (36%), Gaps = 18/101 (17%)
Query: 66 ERLRKECPAQLSRLHIIEGDILQANLGIK---DSDLLMLQEEV-------SVVFNGAASL 115
ER EC + L LH +E + LQ +L ++ D Q V S+ F S
Sbjct: 257 EREAVECSSLLDTLHGLEQEHLQRSLLLQQEEDFAKAHRQLAVFQRVELHSIFFTQLKSA 316
Query: 116 KLEAELKENVAA--------NTRGTQRLLDIALKMKKLVVS 148
+ ELK A + L+D ++ +S
Sbjct: 317 TFKGELKPEEAKSLLQEYSKIQETIEELMDFFQASQRYHLS 357
>gnl|CDD|236230 PRK08304, PRK08304, stage V sporulation protein AD; Validated.
Length = 337
Score = 26.7 bits (60), Expect = 5.1
Identities = 13/33 (39%), Positives = 21/33 (63%), Gaps = 1/33 (3%)
Query: 13 VLVTGGTGFMGKVLLEKLLRSCP-DIGKVYILC 44
++VTG G +G+ +L++LL+ DIG Y C
Sbjct: 230 LIVTGDLGRVGREILKELLKEEGYDIGDNYNDC 262
>gnl|CDD|187574 cd05264, UDP_G4E_5_SDR_e, UDP-glucose 4-epimerase (G4E), subgroup
5, extended (e) SDRs. This subgroup partially
conserves the characteristic active site tetrad and
NAD-binding motif of the extended SDRs, and has been
identified as possible UDP-glucose 4-epimerase (aka
UDP-galactose 4-epimerase), a homodimeric member of the
extended SDR family. UDP-glucose 4-epimerase catalyzes
the NAD-dependent conversion of UDP-galactose to
UDP-glucose, the final step in Leloir galactose
synthesis. Extended SDRs are distinct from classical
SDRs. In addition to the Rossmann fold (alpha/beta
folding pattern with a central beta-sheet) core region
typical of all SDRs, extended SDRs have a less
conserved C-terminal extension of approximately 100
amino acids. Extended SDRs are a diverse collection of
proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and
their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 300
Score = 26.9 bits (60), Expect = 5.1
Identities = 10/20 (50%), Positives = 14/20 (70%)
Query: 12 SVLVTGGTGFMGKVLLEKLL 31
VL+ GG GF+G L++ LL
Sbjct: 1 RVLIVGGNGFIGSHLVDALL 20
>gnl|CDD|173846 cd01157, MCAD, Medium chain acyl-CoA dehydrogenase. MCADs are
mitochondrial beta-oxidation enzymes, which catalyze the
alpha,beta dehydrogenation of the corresponding medium
chain acyl-CoA by FAD, which becomes reduced. The
reduced form of MCAD is reoxidized in the oxidative
half-reaction by electron-transferring flavoprotein
(ETF), from which the electrons are transferred to the
mitochondrial respiratory chain coupled with ATP
synthesis. MCAD is a homotetramer.
Length = 378
Score = 26.8 bits (59), Expect = 5.2
Identities = 12/31 (38%), Positives = 18/31 (58%)
Query: 2 GDVARWYAGRSVLVTGGTGFMGKVLLEKLLR 32
D+A A +V + GG GF + +EKL+R
Sbjct: 322 ADIANQLATDAVQIFGGNGFNSEYPVEKLMR 352
>gnl|CDD|187635 cd08930, SDR_c8, classical (c) SDR, subgroup 8. This subgroup
has a fairly well conserved active site tetrad and
domain size of the classical SDRs, but has an atypical
NAD-binding motif ([ST]G[GA]XGXXG). SDRs are a
functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold (alpha/beta folding pattern with a
central beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRs are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes catalyze a
wide range of activities including the metabolism of
steroids, cofactors, carbohydrates, lipids, aromatic
compounds, and amino acids, and act in redox sensing.
Classical SDRs have an TGXXX[AG]XG cofactor binding
motif and a YXXXK active site motif, with the Tyr
residue of the active site motif serving as a critical
catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 250
Score = 26.5 bits (59), Expect = 5.3
Identities = 8/22 (36%), Positives = 13/22 (59%)
Query: 10 GRSVLVTGGTGFMGKVLLEKLL 31
+ +L+TG G +GK + LL
Sbjct: 2 DKIILITGAAGLIGKAFCKALL 23
>gnl|CDD|223959 COG1028, FabG, Dehydrogenases with different specificities (related
to short-chain alcohol dehydrogenases) [Secondary
metabolites biosynthesis, transport, and catabolism /
General function prediction only].
Length = 251
Score = 26.7 bits (59), Expect = 5.5
Identities = 24/146 (16%), Positives = 46/146 (31%), Gaps = 25/146 (17%)
Query: 9 AGRSVLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFSKLPVFERL 68
+G+ LVTG + +G+ + L R + +V + R +A A +
Sbjct: 4 SGKVALVTGASSGIGRAIARALAR---EGARVVVAARRSEEEAAEALAAAIKE------- 53
Query: 69 RKECPAQLSRLHIIEGDILQANLGIKD--SDLLMLQEEVSVVFNGAASLKL--------E 118
A R + D+ ++ + + ++ N A E
Sbjct: 54 -----AGGGRAAAVAADVSDDEESVEALVAAAEEEFGRIDILVNNAGIAGPDAPLEELTE 108
Query: 119 AELKENVAANTRGTQRLLDIALKMKK 144
+ + N G L AL + K
Sbjct: 109 EDWDRVIDVNLLGAFLLTRAALPLMK 134
>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 = 26.4 bits (59), Expect = 5.6
Identities = 9/22 (40%), Positives = 14/22 (63%)
Query: 12 SVLVTGGTGFMGKVLLEKLLRS 33
VLV G TG +G+ ++ +LL
Sbjct: 1 KVLVVGATGKVGRHVVRELLDR 22
>gnl|CDD|233775 TIGR02197, heptose_epim,
ADP-L-glycero-D-manno-heptose-6-epimerase. This family
consists of examples of
ADP-L-glycero-D-mannoheptose-6-epimerase, an enzyme
involved in biosynthesis of the inner core of
lipopolysaccharide (LPS) for Gram-negative bacteria.
This enzyme is homologous to UDP-glucose 4-epimerase
(TIGR01179) and belongs to the NAD dependent
epimerase/dehydratase family (pfam01370) [Cell
envelope, Biosynthesis and degradation of surface
polysaccharides and lipopolysaccharides].
Length = 314
Score = 26.5 bits (59), Expect = 6.0
Identities = 9/18 (50%), Positives = 14/18 (77%)
Query: 13 VLVTGGTGFMGKVLLEKL 30
++VTGG GF+G L++ L
Sbjct: 1 IIVTGGAGFIGSNLVKAL 18
>gnl|CDD|178484 PLN02896, PLN02896, cinnamyl-alcohol dehydrogenase.
Length = 353
Score = 26.7 bits (59), Expect = 6.0
Identities = 42/160 (26%), Positives = 59/160 (36%), Gaps = 55/160 (34%)
Query: 9 AGRSVLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFSKLPVFERL 68
A + VTG TG++G L++ LL+ RG T A L + +K
Sbjct: 9 ATGTYCVTGATGYIGSWLVKLLLQ---------------RGYTVHATLRDPAKSLHLLSK 53
Query: 69 RKECPAQLSRLHIIEGDILQANLGIKDSDLLMLQEEVSV---------VFNGAASLKL-- 117
KE RL + D LQEE S VF+ AAS++
Sbjct: 54 WKEG----DRLRLFRAD---------------LQEEGSFDEAVKGCDGVFHVAASMEFDV 94
Query: 118 ---EAELKENVAAN-----TRGTQRLLDIALKMK--KLVV 147
++E V + +GT +L LK K K VV
Sbjct: 95 SSDHNNIEEYVQSKVIDPAIKGTLNVLKSCLKSKTVKRVV 134
>gnl|CDD|222146 pfam13460, NAD_binding_10, NADH(P)-binding.
Length = 182
Score = 26.1 bits (58), Expect = 6.2
Identities = 23/128 (17%), Positives = 45/128 (35%), Gaps = 35/128 (27%)
Query: 13 VLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFSKLPVFERLRKEC 72
+ V G TG G+ L+++LL RG A S R
Sbjct: 1 IAVIGATGKTGRRLVKELLA---------------RGHQVTA----LS--------RNPS 33
Query: 73 PAQLSRLHIIEGDILQANLGIKDSDLLMLQEEVSVVFNGAASLKLEAELKENV--AANTR 130
A + ++ D+ +L L V V + + +++ +++ AA
Sbjct: 34 KAPAPGVTPVQKDLF--DLADLAEAL----AGVDAVVDAFGARPDDSDGVKHLLDAAARA 87
Query: 131 GTQRLLDI 138
G +R++ +
Sbjct: 88 GVRRIVVV 95
>gnl|CDD|187612 cd05354, SDR_c7, classical (c) SDR, subgroup 7. These proteins
are members of the classical SDR family, with a
canonical active site triad (and also an active site
Asn) and a typical Gly-rich NAD-binding motif. SDRs are
a functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold (alpha/beta folding pattern with a
central beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRS are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes have a
3-glycine N-terminal NAD(P)(H)-binding pattern
(typically, TGxxxGxG in classical SDRs and TGxxGxxG in
extended SDRs), while substrate binding is in the
C-terminal region. A critical catalytic Tyr residue
(Tyr-151, human 15-hydroxyprostaglandin dehydrogenase
(15-PGDH) numbering), is often found in a conserved
YXXXK pattern. In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) or
additional Ser, contributing to the active site.
Substrates for these enzymes include sugars, steroids,
alcohols, and aromatic compounds. The standard reaction
mechanism is a proton relay involving the conserved Tyr
and Lys, as well as Asn (or Ser). Some SDR family
members, including 17 beta-hydroxysteroid dehydrogenase
contain an additional helix-turn-helix motif that is
not generally found among SDRs.
Length = 235
Score = 26.2 bits (58), Expect = 6.4
Identities = 14/36 (38%), Positives = 18/36 (50%), Gaps = 2/36 (5%)
Query: 10 GRSVLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCR 45
++VLVTG +GK +E LL KVY R
Sbjct: 3 DKTVLVTGANRGIGKAFVESLLAH--GAKKVYAAVR 36
>gnl|CDD|178263 PLN02657, PLN02657, 3,8-divinyl protochlorophyllide a 8-vinyl
reductase.
Length = 390
Score = 26.6 bits (59), Expect = 6.4
Identities = 10/21 (47%), Positives = 17/21 (80%)
Query: 12 SVLVTGGTGFMGKVLLEKLLR 32
+VLV G TG++GK ++ +L+R
Sbjct: 62 TVLVVGATGYIGKFVVRELVR 82
>gnl|CDD|236649 PRK10084, PRK10084, dTDP-glucose 4,6 dehydratase; Provisional.
Length = 352
Score = 26.3 bits (58), Expect = 6.7
Identities = 9/24 (37%), Positives = 16/24 (66%)
Query: 13 VLVTGGTGFMGKVLLEKLLRSCPD 36
+LVTGG GF+G ++ ++ + D
Sbjct: 3 ILVTGGAGFIGSAVVRHIINNTQD 26
>gnl|CDD|187535 cd02266, SDR, Short-chain dehydrogenases/reductases (SDR). SDRs
are a functionally diverse family of oxidoreductases
that have a single domain with a structurally conserved
Rossmann fold (alpha/beta folding pattern with a
central beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRs are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes catalyze a
wide range of activities including the metabolism of
steroids, cofactors, carbohydrates, lipids, aromatic
compounds, and amino acids, and act in redox sensing.
Classical SDRs have an TGXXX[AG]XG cofactor binding
motif and a YXXXK active site motif, with the Tyr
residue of the active site motif serving as a critical
catalytic residue (Tyr-151, human prostaglandin
dehydrogenase (PGDH) numbering). In addition to the Tyr
and Lys, there is often an upstream Ser (Ser-138, PGDH
numbering) and/or an Asn (Asn-107, PGDH numbering)
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. Extended SDRs have additional
elements in the C-terminal region, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase (KR) domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type KRs have
a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical
SDRs have lost catalytic activity and/or have an
unusual NAD(P)-binding motif and missing or unusual
active site residues. Reactions catalyzed within the
SDR family include isomerization, decarboxylation,
epimerization, C=N bond reduction, dehydratase
activity, dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 186
Score = 26.3 bits (58), Expect = 6.9
Identities = 9/20 (45%), Positives = 12/20 (60%)
Query: 13 VLVTGGTGFMGKVLLEKLLR 32
VLVTGG+G +G + L
Sbjct: 1 VLVTGGSGGIGGAIARWLAS 20
>gnl|CDD|217337 pfam03050, DDE_Tnp_IS66, Transposase IS66 family. Transposase
proteins are necessary for efficient DNA transposition.
This family includes IS66 from Agrobacterium
tumefaciens.
Length = 277
Score = 26.4 bits (59), Expect = 7.1
Identities = 18/47 (38%), Positives = 27/47 (57%), Gaps = 4/47 (8%)
Query: 36 DIGKVYILCRAKRGLTPKARLA---EFSKLPVFERLRKECPAQLSRL 79
IG++Y + R RGL P+ RLA E+S+ P+ + L AQL +
Sbjct: 171 RIGELYAIEREARGLPPEERLALRQEYSR-PLLDALEAWLEAQLPGV 216
>gnl|CDD|178268 PLN02662, PLN02662, cinnamyl-alcohol dehydrogenase family
protein.
Length = 322
Score = 26.2 bits (58), Expect = 7.2
Identities = 21/80 (26%), Positives = 37/80 (46%), Gaps = 16/80 (20%)
Query: 9 AGRSVLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFSKLPVFERL 68
G+ V VTG +G++ L++ LL+ RG T KA + + + E L
Sbjct: 3 EGKVVCVTGASGYIASWLVKLLLQ---------------RGYTVKATVRDPNDPKKTEHL 47
Query: 69 RKECPAQLSRLHIIEGDILQ 88
A+ RLH+ + ++L+
Sbjct: 48 LALDGAK-ERLHLFKANLLE 66
>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 = 26.0 bits (58), Expect = 8.0
Identities = 6/25 (24%), Positives = 11/25 (44%)
Query: 8 YAGRSVLVTGGTGFMGKVLLEKLLR 32
G+ +TGG +GK + +
Sbjct: 1 LKGKVAFITGGGTGIGKAIAKAFAE 25
>gnl|CDD|179571 PRK03369, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
synthetase; Provisional.
Length = 488
Score = 26.2 bits (58), Expect = 8.6
Identities = 11/31 (35%), Positives = 14/31 (45%), Gaps = 1/31 (3%)
Query: 2 GDVARWYAGRSVLVTGGTGFMGKVLLEKLLR 32
G + G VLV G G G+ +L L R
Sbjct: 4 GMLDPLLPGAPVLVAGA-GVTGRAVLAALTR 33
>gnl|CDD|223109 COG0030, KsgA, Dimethyladenosine transferase (rRNA methylation)
[Translation, ribosomal structure and biogenesis].
Length = 259
Score = 26.0 bits (58), Expect = 8.8
Identities = 8/27 (29%), Positives = 13/27 (48%), Gaps = 1/27 (3%)
Query: 66 ERLRKECPAQLSRLHIIEGDILQANLG 92
E L++ A L +I GD L+ +
Sbjct: 66 EVLKER-FAPYDNLTVINGDALKFDFP 91
>gnl|CDD|178256 PLN02650, PLN02650, dihydroflavonol-4-reductase.
Length = 351
Score = 25.9 bits (57), Expect = 8.8
Identities = 10/20 (50%), Positives = 15/20 (75%)
Query: 12 SVLVTGGTGFMGKVLLEKLL 31
+V VTG +GF+G L+ +LL
Sbjct: 7 TVCVTGASGFIGSWLVMRLL 26
>gnl|CDD|215720 pfam00106, adh_short, short chain dehydrogenase. This family
contains a wide variety of dehydrogenases.
Length = 167
Score = 25.6 bits (57), Expect = 9.0
Identities = 19/76 (25%), Positives = 31/76 (40%), Gaps = 15/76 (19%)
Query: 11 RSVLVTGGTGFMGKVLLEKLLRSCPDIGKVYILCRAKRGLTPKARLAEFSKLPVFERLRK 70
+VL+TGGTG +G L L + + +L ++RG P A L
Sbjct: 1 GTVLITGGTGGLGLALARWLAA---EGARHLVLV-SRRGPAPGA-----------AELVA 45
Query: 71 ECPAQLSRLHIIEGDI 86
E A + + + D+
Sbjct: 46 ELEALGAEVTVAACDV 61
>gnl|CDD|187590 cd05329, TR_SDR_c, tropinone reductase-I and II (TR-1, and
TR-II)-like, classical (c) SDRs. This subgroup
includes TR-I and TR-II; these proteins are members of
the SDR family. TRs catalyze the NADPH-dependent
reductions of the 3-carbonyl group of tropinone, to a
beta-hydroxyl group. TR-I and TR-II produce different
stereoisomers from tropinone, TR-I produces tropine
(3alpha-hydroxytropane), and TR-II, produces
pseudotropine (sigma-tropine, 3beta-hydroxytropane).
SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold (alpha/beta
folding pattern with a central beta-sheet), an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRs are
approximately 350 residues. Sequence identity between
different SDR enzymes are typically in the 15-30%
range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes catalyze a
wide range of activities including the metabolism of
steroids, cofactors, carbohydrates, lipids, aromatic
compounds, and amino acids, and act in redox sensing.
Classical SDRs have an TGXXX[AG]XG cofactor binding
motif and a YXXXK active site motif, with the Tyr
residue of the active site motif serving as a critical
catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 251
Score = 25.9 bits (57), Expect = 9.5
Identities = 12/27 (44%), Positives = 18/27 (66%), Gaps = 1/27 (3%)
Query: 6 RW-YAGRSVLVTGGTGFMGKVLLEKLL 31
RW G++ LVTGGT +G ++E+L
Sbjct: 1 RWNLEGKTALVTGGTKGIGYAIVEELA 27
>gnl|CDD|128898 smart00650, rADc, Ribosomal RNA adenine dimethylases.
Length = 169
Score = 25.5 bits (57), Expect = 9.9
Identities = 10/27 (37%), Positives = 15/27 (55%), Gaps = 1/27 (3%)
Query: 66 ERLRKECPAQLSRLHIIEGDILQANLG 92
RLR++ A L +I GD L+ +L
Sbjct: 49 PRLREK-FAAADNLTVIHGDALKFDLP 74
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
0.322 0.139 0.391
Gapped
Lambda K H
0.267 0.0845 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,800,827
Number of extensions: 725583
Number of successful extensions: 1037
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1014
Number of HSP's successfully gapped: 149
Length of query: 152
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 64
Effective length of database: 7,034,450
Effective search space: 450204800
Effective search space used: 450204800
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 55 (24.8 bits)