RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17489
(177 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 = 177 bits (452), Expect = 1e-55
Identities = 66/136 (48%), Positives = 92/136 (67%)
Query: 39 ILVTGGTGFMGKLLIDKLLRSFPDIGAIYIMVRDKKGSSPEERVKNMLNSVIFDRLNKEV 98
+L+TG TGF+GK+L++KLLRS PDIG IY+++R K G S EER++ +L +FDR
Sbjct: 3 VLITGATGFLGKVLLEKLLRSCPDIGKIYLLIRGKSGQSAEERLRELLKDKLFDRGRNLN 62
Query: 99 PDFRSKIQVIPSNLESEHLGLSEDSEQLIKSKVNIIFHCAASLRFDEALQKAIRANLYAT 158
P F SKI I +L +LGLS++ Q + +VNII HCAA++ FDE L +A+ N+ T
Sbjct: 63 PLFESKIVPIEGDLSEPNLGLSDEDLQTLIEEVNIIIHCAATVTFDERLDEALSINVLGT 122
Query: 159 KQMLNLAKECVNLKRF 174
++L LAK C LK F
Sbjct: 123 LRLLELAKRCKKLKAF 138
>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 = 138 bits (350), Expect = 3e-41
Identities = 49/132 (37%), Positives = 78/132 (59%), Gaps = 7/132 (5%)
Query: 41 VTGGTGFMGKLLIDKLLRSFPDIGAIYIMVRDKKGSSPEERV-KNMLNSVIFDRLNKEVP 99
+TG TGF+GK+L++KLLRS P++ IY +VR K G S ER+ + +L +FDRL
Sbjct: 1 LTGATGFLGKVLLEKLLRSTPEV-KIYCLVRAKDGESALERLRQELLKYGLFDRLK---- 55
Query: 100 DFRSKIQVIPSNLESEHLGLSEDSEQLIKSKVNIIFHCAASLRFDEALQKAIRANLYATK 159
+I + +L +LGLS++ Q + +V++I H AA++ F E N+ T+
Sbjct: 56 -ALERIIPVAGDLSEPNLGLSDEDFQELAEEVDVIIHNAATVNFVEPYSDLRATNVLGTR 114
Query: 160 QMLNLAKECVNL 171
++L LAK+ L
Sbjct: 115 EVLRLAKQMKKL 126
>gnl|CDD|215279 PLN02503, PLN02503, fatty acyl-CoA reductase 2.
Length = 605
Score = 98.8 bits (246), Expect = 2e-24
Identities = 53/157 (33%), Positives = 87/157 (55%), Gaps = 6/157 (3%)
Query: 24 MQEEQKVDDFYRDGQILVTGGTGFMGKLLIDKLLRSFPDIGAIYIMVRDKKGSSPEERVK 83
M + + +F R L+TG TGF+ K+LI+K+LR+ PD+G IY++++ K + ER+K
Sbjct: 107 MADGIGIAEFLRGKNFLITGATGFLAKVLIEKILRTNPDVGKIYLLIKAKDKEAAIERLK 166
Query: 84 N-MLNSVIFDRLN----KEVPDFR-SKIQVIPSNLESEHLGLSEDSEQLIKSKVNIIFHC 137
N ++++ +F L K F SK+ + N+ +LGL D I +V++I +
Sbjct: 167 NEVIDAELFKCLQETHGKSYQSFMLSKLVPVVGNVCESNLGLEPDLADEIAKEVDVIINS 226
Query: 138 AASLRFDEALQKAIRANLYATKQMLNLAKECVNLKRF 174
AA+ FDE AI N +++ AK+C LK F
Sbjct: 227 AANTTFDERYDVAIDINTRGPCHLMSFAKKCKKLKLF 263
>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 = 82.8 bits (205), Expect = 2e-19
Identities = 39/137 (28%), Positives = 69/137 (50%), Gaps = 17/137 (12%)
Query: 39 ILVTGGTGFMGKLLIDKLLRSFPDIGAIYIMVRDKKGSSPEERVKNMLNSVIFDRLNKEV 98
+ VTGGTGF+G+ L+ +LL + + ++VR + ER++ E
Sbjct: 1 VFVTGGTGFLGRHLVKRLL---ENGFKVLVLVRSESLGEAHERIE-------------EA 44
Query: 99 PDFRSKIQVIPSNLESEHLGLSEDSEQLIKSKVNIIFHCAASLRFDEALQKAIRANLYAT 158
+++V+ +L +LGLS + + + KV+ + HCAAS F + A R N+ T
Sbjct: 45 GLEADRVRVLEGDLTQPNLGLSAAASRELAGKVDHVIHCAASYDFQAPNEDAWRTNIDGT 104
Query: 159 KQMLNLAKECVNLKRFC 175
+ +L LA +++RF
Sbjct: 105 EHVLELAARL-DIQRFH 120
>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 = 81.2 bits (201), Expect = 7e-19
Identities = 43/131 (32%), Positives = 72/131 (54%), Gaps = 10/131 (7%)
Query: 38 QILVTGGTGFMGKLLIDKLLRSFPDIGAIYIMVRDKKGSSPEERVKNMLNSVIFDRLNKE 97
+L+TG TGF+G L+ +LL+ ++ IY +VR K + ER+ + L L E
Sbjct: 1 TVLLTGATGFLGAYLLRELLKR-KNVSKIYCLVRAKDEEAALERLIDNLKEY-GLNLWDE 58
Query: 98 VPDFRSKIQVIPSNLESEHLGLSEDSEQLIKSKVNIIFHCAASLRF---DEALQKAIRAN 154
S+I+V+ +L +LGLS+D Q + +V++I H A++ + E L+ AN
Sbjct: 59 --LELSRIKVVVGDLSKPNLGLSDDDYQELAEEVDVIIHNGANVNWVYPYEELKP---AN 113
Query: 155 LYATKQMLNLA 165
+ TK++L LA
Sbjct: 114 VLGTKELLKLA 124
>gnl|CDD|215538 PLN02996, PLN02996, fatty acyl-CoA reductase.
Length = 491
Score = 77.1 bits (190), Expect = 6e-17
Identities = 43/154 (27%), Positives = 82/154 (53%), Gaps = 7/154 (4%)
Query: 26 EEQKVDDFYRDGQILVTGGTGFMGKLLIDKLLRSFPDIGAIYIMVRDKKGSSPEERVKN- 84
EE F + ILVTG TGF+ K+ ++K+LR P++ +Y+++R S +R+ +
Sbjct: 1 EEGSCVQFLENKTILVTGATGFLAKIFVEKILRVQPNVKKLYLLLRASDAKSATQRLHDE 60
Query: 85 MLNSVIFDRL-NKEVPDFRS----KIQVIPSNLESEHLGLSE-DSEQLIKSKVNIIFHCA 138
++ +F L K + S K+ +P ++ + LG+ + + + + +++I+ + A
Sbjct: 61 VIGKDLFKVLREKLGENLNSLISEKVTPVPGDISYDDLGVKDSNLREEMWKEIDIVVNLA 120
Query: 139 ASLRFDEALQKAIRANLYATKQMLNLAKECVNLK 172
A+ FDE A+ N +LN AK+CV +K
Sbjct: 121 ATTNFDERYDVALGINTLGALNVLNFAKKCVKVK 154
>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 = 58.6 bits (142), Expect = 1e-10
Identities = 35/127 (27%), Positives = 60/127 (47%), Gaps = 7/127 (5%)
Query: 39 ILVTGGTGFMGKLLIDKLLRSFPDIGAIYIMVRDKKGSSPEERVKNMLNSVIFDRLNKEV 98
+L+TG TGF+G L+ +LL + +VR S E + + + R E+
Sbjct: 3 VLLTGATGFLGAYLLLELLDRSD--AKVICLVR---AQSDEAALARLEKTFDLYRHWDEL 57
Query: 99 PDFRSKIQVIPSNLESEHLGLSEDSEQLIKSKVNIIFHCAASLRFDEALQKAIRANLYAT 158
+++V+ +L LGLSE + Q + V++I H AA + + AN+ T
Sbjct: 58 --SADRVEVVAGDLAEPDLGLSERTWQELAENVDLIIHNAALVNHVFPYSELRGANVLGT 115
Query: 159 KQMLNLA 165
++L LA
Sbjct: 116 AEVLRLA 122
>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 = 56.6 bits (137), Expect = 7e-10
Identities = 38/128 (29%), Positives = 63/128 (49%), Gaps = 5/128 (3%)
Query: 38 QILVTGGTGFMGKLLIDKLLRSFPDIGAIYIMVRDKKGSSPEERVKNMLNSVIFDRLNKE 97
+L+TG TGF+G L+++LLR + +VR ER++ L S RL E
Sbjct: 1 TVLLTGATGFLGAYLLEELLRRSTQAK-VICLVRAASEEHAMERLREALRSY---RLWHE 56
Query: 98 VPDFRSKIQVIPSNLESEHLGLSEDSEQLIKSKVNIIFHCAASLRFDEALQKAIRANLYA 157
R +I+V+ +L LGLS+ + + V+ I H A + + + AN+
Sbjct: 57 DLA-RERIEVVAGDLSEPRLGLSDAEWERLAENVDTIVHNGALVNWVYPYSELRGANVLG 115
Query: 158 TKQMLNLA 165
T+++L LA
Sbjct: 116 TREVLRLA 123
>gnl|CDD|235962 PRK07201, PRK07201, short chain dehydrogenase; Provisional.
Length = 657
Score = 56.1 bits (136), Expect = 9e-10
Identities = 35/131 (26%), Positives = 59/131 (45%), Gaps = 23/131 (17%)
Query: 40 LVTGGTGFMGKLLIDKLLRSFPDIGAIYIMVRDKKGSSPEERVKNMLNSVIFDRLNKEVP 99
VTGGTGF+G+ L+ +LL + ++++VR R++ + DR
Sbjct: 4 FVTGGTGFIGRRLVSRLLDRRRE-ATVHVLVRR----QSLSRLEALAAYWGADR------ 52
Query: 100 DFRSKIQVIPSNLESEHLGLS-EDSEQLIKSKVNIIFHCAA--SLRFDEALQKAIRANLY 156
+ + +L LGLS D +L ++ + H AA L DE Q AN+
Sbjct: 53 -----VVPLVGDLTEPGLGLSEADIAEL--GDIDHVVHLAAIYDLTADEEAQ--RAANVD 103
Query: 157 ATKQMLNLAKE 167
T+ ++ LA+
Sbjct: 104 GTRNVVELAER 114
>gnl|CDD|223528 COG0451, WcaG, Nucleoside-diphosphate-sugar epimerases [Cell
envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 314
Score = 48.0 bits (114), Expect = 5e-07
Identities = 30/140 (21%), Positives = 54/140 (38%), Gaps = 35/140 (25%)
Query: 39 ILVTGGTGFMGKLLIDKLLRSFPDIGAIYIMVRDKKGSSPEERVKNMLNSVIFDRLNKEV 98
ILVTGG GF+G L+++LL + D+ DRL +
Sbjct: 3 ILVTGGAGFIGSHLVERLLAAGHDV-------------------------RGLDRLRDGL 37
Query: 99 PDFRSKIQVIPSNLESEHLGLSEDSEQLIKSKVNIIFHCAASLRFDEAL----QKAIRAN 154
S ++ + +L + ++L K + + H AA ++ + + N
Sbjct: 38 DPLLSGVEFVVLDLTD-----RDLVDELAKGVPDAVIHLAAQSSVPDSNASDPAEFLDVN 92
Query: 155 LYATKQMLNLAKECVNLKRF 174
+ T +L A+ +KRF
Sbjct: 93 VDGTLNLLEAARAA-GVKRF 111
>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 = 46.9 bits (112), Expect = 7e-07
Identities = 26/139 (18%), Positives = 42/139 (30%), Gaps = 66/139 (47%)
Query: 39 ILVTGGTGFMGKLLIDKLLRSFPDIGAIYIMVRDKKGSSPEERVKNMLNSVIFDRLNKEV 98
ILVTGG GF+G L+ +LL ++ V+ DRL
Sbjct: 1 ILVTGGAGFIGSHLVRRLLERGHEV-------------------------VVIDRL---- 31
Query: 99 PDFRSKIQVIPSNLESEHLGLSEDSEQLIKSKVNIIFHCAASLRFDEALQKA---IRANL 155
+++ H AA + + N+
Sbjct: 32 ---------------------------------DVVVHLAALVGVPASWDNPDEDFETNV 58
Query: 156 YATKQMLNLAKECVNLKRF 174
T +L A++ +KRF
Sbjct: 59 VGTLNLLEAARKA-GVKRF 76
>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 = 45.4 bits (108), Expect = 5e-06
Identities = 35/130 (26%), Positives = 64/130 (49%), Gaps = 6/130 (4%)
Query: 39 ILVTGGTGFMGKLLIDKLL-RSFPDIGAIYIMVRDKKGSSPEERVKNMLNSVIFDRLNKE 97
+ +TG TGF+G ++ LL R ++ VR K + ER++ + ++E
Sbjct: 974 VFLTGATGFLGSFILRDLLTRRSNSNFKVFAHVRAKSEEAGLERLRK--TGTTYGIWDEE 1031
Query: 98 VPDFRSKIQVIPSNLESEHLGLSEDSEQLIKSKVNIIFHCAASLRFDEALQKAIRANLYA 157
+ S+I+V+ +L E GLS++ + ++V++I H A + + K AN+
Sbjct: 1032 ---WASRIEVVLGDLSKEKFGLSDEKWSDLTNEVDVIIHNGALVHWVYPYSKLRDANVIG 1088
Query: 158 TKQMLNLAKE 167
T +LNL E
Sbjct: 1089 TINVLNLCAE 1098
>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 = 44.2 bits (105), Expect = 8e-06
Identities = 31/140 (22%), Positives = 54/140 (38%), Gaps = 35/140 (25%)
Query: 39 ILVTGGTGFMGKLLIDKLLRSFPDIGAIYIMVRDKKGSSPEERVKNMLNSVIFDRLNKEV 98
ILVTGGTGF+G L+ +LL+ ++ + + S+ R+
Sbjct: 1 ILVTGGTGFIGSHLVRRLLQEGYEVIVLGR--------------RRRSESLNTGRIRFHE 46
Query: 99 PDFRSKIQVIPSNLESEHLGLSEDSEQLIK-SKVNIIFHCAASLRFDEALQKA---IRAN 154
D + E+L+ + + + H AA + + IRAN
Sbjct: 47 GDLTDPDAL----------------ERLLAEVQPDAVIHLAAQSGVGASFEDPADFIRAN 90
Query: 155 LYATKQMLNLAKECVNLKRF 174
+ T ++L A+ +KRF
Sbjct: 91 VLGTLRLLEAARRA-GVKRF 109
>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 = 42.5 bits (101), Expect = 3e-05
Identities = 36/141 (25%), Positives = 56/141 (39%), Gaps = 28/141 (19%)
Query: 39 ILVTGGTGFMGKLLIDKLLRSFPDIGAIYIMVRDK--KGSSPEERVKNMLNSVIFDRLNK 96
ILVTGG GF+G + LL +PD I+ DK + E L V
Sbjct: 3 ILVTGGAGFIGSNFVRYLLNKYPD---YKIINLDKLTYAGNLEN-----LEDV------S 48
Query: 97 EVPDFRSKIQVIPSNLESEHLGLSEDSEQLIKSKVNIIFHCAASLRFDEALQKA---IRA 153
P +R + ++ L + K++ + H AA D ++ IR
Sbjct: 49 SSPRYR----FVKGDICDAELVDRL----FEEEKIDAVIHFAAESHVDRSISDPEPFIRT 100
Query: 154 NLYATKQMLNLAKECVNLKRF 174
N+ T +L A++ +KRF
Sbjct: 101 NVLGTYTLLEAARKY-GVKRF 120
>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 = 39.9 bits (94), Expect = 3e-04
Identities = 34/140 (24%), Positives = 66/140 (47%), Gaps = 25/140 (17%)
Query: 39 ILVTGGTGFMGKLLIDKLLRSFPDIGAIYIMVRDKKGSSPEERVKNMLNSVIFDRLNKEV 98
ILVTGG G +G L+ ++L+ + + RD+ E V+ + + D+L +
Sbjct: 5 ILVTGGAGSIGSELVRQILKF--GPKKLIVFDRDENKL--HELVRELRSRFPHDKLRFII 60
Query: 99 PDFRSKIQVIPSNLESEHLGLSEDSEQLIKSKVNIIFHCAASLRF----DEALQKAIRAN 154
D R K + L ++ +I+FH AA+L+ ++ ++AI+ N
Sbjct: 61 GDVRDKER------------LRRAFKER---GPDIVFH-AAALKHVPSMEDNPEEAIKTN 104
Query: 155 LYATKQMLNLAKECVNLKRF 174
+ TK +++ A E +++F
Sbjct: 105 VLGTKNVIDAAIEN-GVEKF 123
>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 = 38.8 bits (91), Expect = 6e-04
Identities = 33/132 (25%), Positives = 54/132 (40%), Gaps = 31/132 (23%)
Query: 39 ILVTGGTGFMGKLLIDKLLRSFPDIGAIYIMVRDKKGSSPEERVKNMLNSVIFDRLNKEV 98
I+VTGG GF+G L+++ + G I+V D + N+ + VI D ++K
Sbjct: 1 IIVTGGAGFIGS----NLVKALNERGITDILVVDNLRDG--HKFLNLADLVIADYIDK-- 52
Query: 99 PDFRSKIQVIPSNLESEHLGLSEDSEQLIKSKVNIIFH---CAASLRFDEALQKAIRANL 155
DF LE G K+ IFH C+ + D + + N
Sbjct: 53 EDF-------LDRLEKGAFG-----------KIEAIFHQGACSDTTETDG--EYMMENNY 92
Query: 156 YATKQMLNLAKE 167
+K++L+ E
Sbjct: 93 QYSKRLLDWCAE 104
>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 = 38.1 bits (89), Expect = 0.001
Identities = 35/142 (24%), Positives = 54/142 (38%), Gaps = 44/142 (30%)
Query: 39 ILVTGGTGFMGKLLIDKLLRSFPDIGA-IYIMVRDKKGSSPEERVKNMLNSVIFDRLNKE 97
+LVTG GF+G+ L+DKLL G + I VR +N SV+ E
Sbjct: 2 VLVTGANGFIGRALVDKLLSR----GEEVRIAVR---------NAENAEPSVVLA----E 44
Query: 98 VPDFRSKIQVIPSNLESEHLGLSEDSEQLIKSKVNIIFHCAA-----SLRFDEALQKAIR 152
+PD DS + V+ + H AA + + + L +
Sbjct: 45 LPDI--------------------DSFTDLFLGVDAVVHLAARVHVMNDQGADPLSDYRK 84
Query: 153 ANLYATKQMLNLAKECVNLKRF 174
N T+++ A +KRF
Sbjct: 85 VNTELTRRLARAAAR-QGVKRF 105
>gnl|CDD|187559 cd05248, ADP_GME_SDR_e, ADP-L-glycero-D-mannoheptose 6-epimerase
(GME), extended (e) SDRs. This subgroup contains
ADP-L-glycero-D-mannoheptose 6-epimerase, an extended
SDR, which catalyzes the NAD-dependent interconversion
of ADP-D-glycero-D-mannoheptose and
ADP-L-glycero-D-mannoheptose. This subgroup has the
canonical active site tetrad and NAD(P)-binding motif.
Extended SDRs are distinct from classical SDRs. In
addition to the Rossmann fold (alpha/beta folding
pattern with a central beta-sheet) core region typical
of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 317
Score = 36.9 bits (86), Expect = 0.003
Identities = 33/132 (25%), Positives = 56/132 (42%), Gaps = 30/132 (22%)
Query: 39 ILVTGGTGFMGKLLIDKLLRSFPDIGAIYIMVRDKKGSSPEERVKNMLNSVIFDRLNKEV 98
I+VTGG GF+G L+ L + G I+V D + E+ KN++ I D ++K+
Sbjct: 2 IIVTGGAGFIGSNLVKAL----NERGITDILVVDNLSN--GEKFKNLVGLKIADYIDKD- 54
Query: 99 PDFRSKIQVIPSNLESEHLGLSEDSEQLIKSKVNIIFH---CAASLRFDEALQKAIRANL 155
DF+ ++ + K+ IFH C+ + D + N
Sbjct: 55 -DFKDWVR-----------------KGDENFKIEAIFHQGACSDTTETDGKY--MMDNNY 94
Query: 156 YATKQMLNLAKE 167
TK++L+ E
Sbjct: 95 QYTKELLHYCLE 106
>gnl|CDD|224011 COG1086, COG1086, Predicted nucleoside-diphosphate sugar epimerases
[Cell envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 588
Score = 36.9 bits (86), Expect = 0.003
Identities = 29/151 (19%), Positives = 66/151 (43%), Gaps = 35/151 (23%)
Query: 33 FYRDGQILVTGGTGFMGKLLIDKLLRSFPDIGAIYIMVRDKKGSSPEERVKNMLNSVIFD 92
+LVTGG G +G L ++L+ + I + RD+ ++
Sbjct: 247 MLTGKTVLVTGGGGSIGSELCRQILKF--NPKEIILFSRDEYK--------------LYL 290
Query: 93 RLNKEVPDFRSKIQVIPSNLESEHLGLSEDSEQLIK----SKVNIIFHCAA-----SLRF 143
++ E+ + ++++ ++G D +++ + KV+I+FH AA + +
Sbjct: 291 -IDMELREKFPELKLRF------YIGDVRDRDRVERAMEGHKVDIVFHAAALKHVPLVEY 343
Query: 144 DEALQKAIRANLYATKQMLNLAKECVNLKRF 174
+ +AI+ N+ T+ + A + +K+F
Sbjct: 344 NPE--EAIKTNVLGTENVAEAAIKN-GVKKF 371
>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 = 36.1 bits (84), Expect = 0.005
Identities = 35/133 (26%), Positives = 56/133 (42%), Gaps = 33/133 (24%)
Query: 39 ILVTGGTGFMGKLLIDKLLRSFPDIGAIYIMVRDKKGSSPEERVKNMLNSVIFDRLNKEV 98
IL+TGG GF+G L D+LL G I V D + + +++++
Sbjct: 3 ILITGGAGFLGSHLCDRLLED----GHEVICV-DNFFTGRKRNIEHLIGH---------- 47
Query: 99 PDFRSKIQVIPSNLESEHLGLSEDSEQLIKSKVNIIFH--CAAS-LRFDEALQKAIRANL 155
P+F I H D + + +V+ I+H C AS + + K ++ N+
Sbjct: 48 PNFE----FI------RH-----DVTEPLYLEVDQIYHLACPASPVHYQYNPIKTLKTNV 92
Query: 156 YATKQMLNLAKEC 168
T ML LAK
Sbjct: 93 LGTLNMLGLAKRV 105
>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 = 35.0 bits (81), Expect = 0.012
Identities = 15/41 (36%), Positives = 22/41 (53%), Gaps = 1/41 (2%)
Query: 39 ILVTGGTGFMGKLLIDKLLRSFPDIGAIYIMVRDKKGSSPE 79
ILVTG G +G+LL +L S P + + + R + SP
Sbjct: 1 ILVTGAAGGLGRLLARRLAAS-PRVIGVDGLDRRRPPGSPP 40
>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 = 34.8 bits (81), Expect = 0.015
Identities = 28/141 (19%), Positives = 58/141 (41%), Gaps = 27/141 (19%)
Query: 39 ILVTGGTGFMGKLLIDKLLRSFPDIGAIYIMVRDKKGSSPEERVKNMLNSVIFDRLNKEV 98
+LVTGG G +G L ++L+ + I + RD+ E + + +L +
Sbjct: 1 VLVTGGGGSIGSELCRQILKF--NPKKIILFSRDEF--KLYEIRQELRQEYNDPKLRFFI 56
Query: 99 PDFRSKIQVIPSNLESEHLGLSEDSEQLIKSKVNIIFHCAA-----SLRFDEALQKAIRA 153
D R + ++ + + V+ +FH AA + ++ +AI+
Sbjct: 57 GDVRDRERL---------------ERAMEQHGVDTVFHAAALKHVPLVEYNPM--EAIKT 99
Query: 154 NLYATKQMLNLAKECVNLKRF 174
N+ T+ + A E +++F
Sbjct: 100 NVLGTENVAEAAIEN-GVEKF 119
>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 = 34.7 bits (80), Expect = 0.015
Identities = 26/101 (25%), Positives = 44/101 (43%), Gaps = 27/101 (26%)
Query: 39 ILVTGGTGFMGKLLIDKLLRSFPDIGAIYIMVRDKKGSSPEERVKNMLNSVIFDRLNKEV 98
+LVTGG+GF G+ L+ +LL + G Y+ D + P E + +
Sbjct: 2 VLVTGGSGFFGERLVKQLL----ERGGTYVRSFDI--APPGEALS-----------AWQH 44
Query: 99 PDFRSKIQVIPSNLESEHLGLSEDSEQLIKSKVNIIFHCAA 139
P+ I+ + ++ D EQ + S + +FH AA
Sbjct: 45 PN----IEFLKGDITD-----RNDVEQAL-SGADCVFHTAA 75
>gnl|CDD|177856 PLN02206, PLN02206, UDP-glucuronate decarboxylase.
Length = 442
Score = 35.0 bits (80), Expect = 0.016
Identities = 37/132 (28%), Positives = 59/132 (44%), Gaps = 33/132 (25%)
Query: 38 QILVTGGTGFMGKLLIDKLLRSFPDIGAIYIMVRDKKGSSPEERVKNMLNSVIFDRLNKE 97
+++VTGG GF+G L+D+L+ G I+V D + +E V + ++ F+ + +
Sbjct: 121 RVVVTGGAGFVGSHLVDRLMAR----GDSVIVV-DNFFTGRKENVMHHFSNPNFELIRHD 175
Query: 98 VPDFRSKIQVIPSNLESEHLGLSEDSEQLIKSKVNIIFH--CAAS-LRFDEALQKAIRAN 154
V V P LE V+ I+H C AS + + K I+ N
Sbjct: 176 V--------VEPILLE-----------------VDQIYHLACPASPVHYKFNPVKTIKTN 210
Query: 155 LYATKQMLNLAK 166
+ T ML LAK
Sbjct: 211 VVGTLNMLGLAK 222
>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 = 34.6 bits (80), Expect = 0.018
Identities = 31/147 (21%), Positives = 53/147 (36%), Gaps = 41/147 (27%)
Query: 39 ILVTGGTGFMGKLLIDKLLRSFPDIGAIYIM---VRDKKGSSPEERVKNMLNSVIFDRLN 95
+LVTG TGF+ ++++LL+ A Y + VR S ++K +L
Sbjct: 2 VLVTGATGFIASHIVEQLLK------AGYKVRGTVRSL---SKSAKLKALL--------- 43
Query: 96 KEVPDFRSKIQVIPSNLESEHLGLSEDSEQLIK--SKVNIIFHCAASLRF------DEAL 147
K LE + + V+ + H A+ F D+ +
Sbjct: 44 --------KAAGYNDRLEFVIVDDLTAPNAWDEALKGVDYVIHVASPFPFTGPDAEDDVI 95
Query: 148 QKAIRANLYATKQMLNLAKECVNLKRF 174
A+ T +L AK ++KR
Sbjct: 96 DPAVE----GTLNVLEAAKAAGSVKRV 118
>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 = 34.4 bits (79), Expect = 0.021
Identities = 27/140 (19%), Positives = 52/140 (37%), Gaps = 30/140 (21%)
Query: 40 LVTGGTGFMGKLLIDKLLRSFPDIGAIYIMVRDKKGSSPEERVKNMLNSVIFDRLNKEVP 99
LVTGG GF+G+ +I LL ++ I ++ K PE + E
Sbjct: 3 LVTGGGGFLGQHIIRLLLERKEELKEIRVL---DKAFGPE------------LIEHFEKS 47
Query: 100 DFRSKIQVIPSNLESEHLGLSEDSEQLIKSKVN---IIFHCAASLR-FDEALQKAI-RAN 154
++ + I +++ + ++ H AA + F + + N
Sbjct: 48 QGKTYVTDIEGDIKDLS---------FLFRACQGVSVVIHTAAIVDVFGPPNYEELEEVN 98
Query: 155 LYATKQMLNLAKECVNLKRF 174
+ T+ +L + N+KR
Sbjct: 99 VNGTQAVLEACVQN-NVKRL 117
>gnl|CDD|223774 COG0702, COG0702, Predicted nucleoside-diphosphate-sugar
epimerases [Cell envelope biogenesis, outer membrane /
Carbohydrate transport and metabolism].
Length = 275
Score = 34.1 bits (78), Expect = 0.026
Identities = 13/36 (36%), Positives = 21/36 (58%), Gaps = 3/36 (8%)
Query: 39 ILVTGGTGFMGKLLIDKLLRSFPDIGAIYIMVRDKK 74
ILVTG TGF+G ++ +LL + + VR+ +
Sbjct: 3 ILVTGATGFVGGAVVRELLARGHE---VRAAVRNPE 35
>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 = 33.8 bits (78), Expect = 0.028
Identities = 13/20 (65%), Positives = 16/20 (80%)
Query: 39 ILVTGGTGFMGKLLIDKLLR 58
ILVTGG GF+G L+D+LL
Sbjct: 2 ILVTGGAGFIGSHLVDRLLE 21
>gnl|CDD|165812 PLN02166, PLN02166, dTDP-glucose 4,6-dehydratase.
Length = 436
Score = 33.8 bits (77), Expect = 0.030
Identities = 36/132 (27%), Positives = 59/132 (44%), Gaps = 33/132 (25%)
Query: 38 QILVTGGTGFMGKLLIDKLLRSFPDIGAIYIMVRDKKGSSPEERVKNMLNSVIFDRLNKE 97
+I+VTGG GF+G L+DKL+ + ++V D + +E + ++ + F+ + +
Sbjct: 122 RIVVTGGAGFVGSHLVDKLIGRGDE-----VIVIDNFFTGRKENLVHLFGNPRFELIRHD 176
Query: 98 VPDFRSKIQVIPSNLESEHLGLSEDSEQLIKSKVNIIFH--CAAS-LRFDEALQKAIRAN 154
V V P LE V+ I+H C AS + + K I+ N
Sbjct: 177 V--------VEPILLE-----------------VDQIYHLACPASPVHYKYNPVKTIKTN 211
Query: 155 LYATKQMLNLAK 166
+ T ML LAK
Sbjct: 212 VMGTLNMLGLAK 223
>gnl|CDD|224015 COG1090, COG1090, Predicted nucleoside-diphosphate sugar
epimerase [General function prediction only].
Length = 297
Score = 33.8 bits (78), Expect = 0.031
Identities = 13/39 (33%), Positives = 21/39 (53%), Gaps = 3/39 (7%)
Query: 39 ILVTGGTGFMGKLLIDKLLRSFPDIGAIYIMVRDKKGSS 77
IL+TGGTG +G+ L +L + + I+ R +S
Sbjct: 1 ILITGGTGLIGRALTARLRKGGHQ---VTILTRRPPKAS 36
>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 = 0.035
Identities = 25/132 (18%), Positives = 48/132 (36%), Gaps = 33/132 (25%)
Query: 40 LVTGGTGFMGKLLIDKLL-RSFPDIGAIYIMVRDKKGSSPEERVKNMLNSVIFDRLNKEV 98
LV GG+GF+G+ L+++LL R P + I + S RV+
Sbjct: 3 LVVGGSGFLGRHLVEQLLRRGNPTVHVFDIRPTFELDPSSSGRVQFHTG----------- 51
Query: 99 PDFRSKIQVIPSNLESEHLGLSEDSEQLIKSKVNIIFHCAASLRFDEALQKAI--RANLY 156
D + + + N++FH A+ D + + N+
Sbjct: 52 -DLTDPQDLEKA---------------FNEKGPNVVFHTASP---DHGSNDDLYYKVNVQ 92
Query: 157 ATKQMLNLAKEC 168
T+ ++ ++C
Sbjct: 93 GTRNVIEACRKC 104
>gnl|CDD|233570 TIGR01777, yfcH, TIGR01777 family protein. This model represents
a clade of proteins of unknown function including the
E. coli yfcH protein [Hypothetical proteins,
Conserved].
Length = 291
Score = 33.4 bits (77), Expect = 0.042
Identities = 13/35 (37%), Positives = 21/35 (60%), Gaps = 3/35 (8%)
Query: 39 ILVTGGTGFMGKLLIDKLLRSFPDIGAIYIMVRDK 73
IL+TGGTGF+G+ L +L + + + I+ R
Sbjct: 1 ILITGGTGFIGRALTQRLTKRGHE---VTILTRSP 32
>gnl|CDD|187578 cd05269, TMR_SDR_a, triphenylmethane reductase (TMR)-like
proteins, NMRa-like, atypical (a) SDRs. TMR is an
atypical NADP-binding protein of the SDR family. It
lacks the active site residues of the SDRs but has a
glycine rich NAD(P)-binding motif that matches the
extended SDRs. Proteins in this subgroup however, are
more similar in length to the classical SDRs. TMR was
identified as a reducer of triphenylmethane dyes,
important environmental pollutants. This subgroup also
includes Escherichia coli NADPH-dependent quinine
oxidoreductase (QOR2), which catalyzes two-electron
reduction of quinone; but is unlikely to play a major
role in protecting against quinone cytotoxicity.
Atypical SDRs are distinct from classical SDRs.
Atypical SDRs include biliverdin IX beta reductase
(BVR-B,aka flavin reductase), NMRa (a negative
transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane
reductase, isoflavone reductases, and others. SDRs are
a functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. In addition to the Rossmann fold
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids, and typically have a TGXXGXXG cofactor
binding motif. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 272
Score = 33.4 bits (77), Expect = 0.042
Identities = 13/34 (38%), Positives = 20/34 (58%), Gaps = 3/34 (8%)
Query: 39 ILVTGGTGFMGKLLIDKLLRSFPDIGAIYIMVRD 72
ILVTG TG +G +++ LL + A+ VR+
Sbjct: 1 ILVTGATGKLGTAVVELLLAKVASVVAL---VRN 31
>gnl|CDD|215146 PLN02260, PLN02260, probable rhamnose biosynthetic enzyme.
Length = 668
Score = 33.6 bits (77), Expect = 0.045
Identities = 39/145 (26%), Positives = 62/145 (42%), Gaps = 25/145 (17%)
Query: 34 YRDGQILVTGGTGFMGKLLIDKLLRSFPDIGAIY-IMVRDKKGSSPEERVKNMLNSVIFD 92
Y IL+TG GF+ + ++L+R++PD Y I+V DK +KN+ S
Sbjct: 4 YEPKNILITGAAGFIASHVANRLIRNYPD----YKIVVLDKLDYC--SNLKNLNPS---- 53
Query: 93 RLNKEVPDFRSKIQVIPSNLESEHLGLSEDSEQLIKSKVNIIFHCAASLRFDEALQKAI- 151
K P+F+ I S +L LI ++ I H AA D + +
Sbjct: 54 ---KSSPNFKFVKGDIASADLVNYL--------LITEGIDTIMHFAAQTHVDNSFGNSFE 102
Query: 152 --RANLYATKQMLNLAKECVNLKRF 174
+ N+Y T +L K ++RF
Sbjct: 103 FTKNNIYGTHVLLEACKVTGQIRRF 127
>gnl|CDD|178263 PLN02657, PLN02657, 3,8-divinyl protochlorophyllide a 8-vinyl
reductase.
Length = 390
Score = 33.2 bits (76), Expect = 0.050
Identities = 25/90 (27%), Positives = 44/90 (48%), Gaps = 14/90 (15%)
Query: 36 DGQILVTGGTGFMGKLLIDKLLRSFPDIGAIYIMVRDKKG----SSPEERVKNMLNS-VI 90
D +LV G TG++GK ++ +L+R ++ A+ R+K G + E+ K + + V+
Sbjct: 60 DVTVLVVGATGYIGKFVVRELVRRGYNVVAV---AREKSGIRGKNGKEDTKKELPGAEVV 116
Query: 91 F------DRLNKEVPDFRSKIQVIPSNLES 114
F D L K + + V+ S L S
Sbjct: 117 FGDVTDADSLRKVLFSEGDPVDVVVSCLAS 146
>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 = 33.0 bits (76), Expect = 0.060
Identities = 33/145 (22%), Positives = 58/145 (40%), Gaps = 30/145 (20%)
Query: 33 FYRDGQILVTGGTGFMGKLLIDKLLRSFPDIGAIYIMVRDKKG-SSPEERVKNMLNSVIF 91
F++ ++LVTG TGF G L LL ++GA + G S N+ +
Sbjct: 1 FWQGKKVLVTGHTGFKGSWLSLWLL----ELGA------EVYGYSLDPPTSPNLFELL-- 48
Query: 92 DRLNKEVPDFRSKIQVIPSNLESEHLGLSEDSEQLIKSKVNIIFHCAA----SLRFDEAL 147
L K++ D I+ + L + + + K I+FH AA + + L
Sbjct: 49 -NLAKKIEDHFGDIRD-AAKLR----------KAIAEFKPEIVFHLAAQPLVRKSYADPL 96
Query: 148 QKAIRANLYATKQMLNLAKECVNLK 172
+ N+ T +L + ++K
Sbjct: 97 -ETFETNVMGTVNLLEAIRAIGSVK 120
>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 = 32.9 bits (76), Expect = 0.064
Identities = 32/141 (22%), Positives = 57/141 (40%), Gaps = 34/141 (24%)
Query: 41 VTGGTGFMGKLLIDKLLRSFPDIG-AIYIMVRDKKGSSPEERVKNMLNSVIFDRLNKEVP 99
VTG +GF+G L+ +LL+ G + VRD P + K L E+
Sbjct: 3 VTGASGFIGSWLVKRLLQR----GYTVRATVRD-----PGDEKKV-------AHL-LELE 45
Query: 100 DFRSKIQVIPSNLESEHLGLSEDSEQLIKSKVN---IIFHCAASLRFDEALQKAIRANLY 156
+ ++++ ++L L S + ++ +FH A+ + FD +
Sbjct: 46 GAKERLKLFKADL------LDYGS---FDAAIDGCDGVFHVASPVDFDSEDPEEEMIEP- 95
Query: 157 ATKQMLNLAKECVN---LKRF 174
A K LN+ + C +KR
Sbjct: 96 AVKGTLNVLEACAKAKSVKRV 116
>gnl|CDD|187564 cd05254, dTDP_HR_like_SDR_e, dTDP-6-deoxy-L-lyxo-4-hexulose
reductase and related proteins, extended (e) SDRs.
dTDP-6-deoxy-L-lyxo-4-hexulose reductase, an extended
SDR, synthesizes dTDP-L-rhamnose from
alpha-D-glucose-1-phosphate, providing the precursor of
L-rhamnose, an essential cell wall component of many
pathogenic bacteria. This subgroup has the
characteristic active site tetrad and NADP-binding
motif. This subgroup also contains human MAT2B, the
regulatory subunit of methionine adenosyltransferase
(MAT); MAT catalyzes S-adenosylmethionine synthesis. The
human gene encoding MAT2B encodes two major splicing
variants which are induced in human cell liver cancer
and regulate HuR, an mRNA-binding protein which
stabilizes the mRNA of several cyclins, to affect cell
proliferation. Both MAT2B variants include this extended
SDR domain. Extended SDRs are distinct from classical
SDRs. In addition to the Rossmann fold (alpha/beta
folding pattern with a central beta-sheet) core region
typical of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 280
Score = 32.6 bits (75), Expect = 0.075
Identities = 25/133 (18%), Positives = 43/133 (32%), Gaps = 44/133 (33%)
Query: 39 ILVTGGTGFMGKLLIDKLLRSFPDIGAIYIMVRDKKGSSPEERVKNMLNSVIFDRLNKEV 98
IL+TG TG +G+ L+ L ++ ++ + D +
Sbjct: 2 ILITGATGMLGRALVRLLKERGYEVIGT---------------GRSRASLFKLDLTD--- 43
Query: 99 PDFRSKIQVIPSNLESEHLGLSEDSEQLIKSKVNIIFHCAASLRFDEA---LQKAIRANL 155
E + K ++I +CAA R D+ + A R N+
Sbjct: 44 --------------------PDAVEEAIRDYKPDVIINCAAYTRVDKCESDPELAYRVNV 83
Query: 156 YATKQMLNLAKEC 168
A NLA+
Sbjct: 84 LAP---ENLARAA 93
>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 = 32.6 bits (75), Expect = 0.086
Identities = 11/20 (55%), Positives = 16/20 (80%)
Query: 39 ILVTGGTGFMGKLLIDKLLR 58
+LVTGG GF+G L+++LL
Sbjct: 2 VLVTGGAGFIGSHLVERLLE 21
>gnl|CDD|224013 COG1088, RfbB, dTDP-D-glucose 4,6-dehydratase [Cell envelope
biogenesis, outer membrane].
Length = 340
Score = 32.6 bits (75), Expect = 0.089
Identities = 33/143 (23%), Positives = 54/143 (37%), Gaps = 29/143 (20%)
Query: 38 QILVTGGTGFMGKLLIDKLLRSFPDIGAIYIMVRDK--KGSSPEERVKNMLNSVIFDRLN 95
+ILVTGG GF+G + +L PD ++ DK + E L V
Sbjct: 2 KILVTGGAGFIGSNFVRYILNKHPDDH---VVNLDKLTYAGNLEN-----LADVEDS--- 50
Query: 96 KEVPDFRSKIQVIPSNLESEHLGLSEDSEQLIK-SKVNIIFHCAASLRFDEALQKA---I 151
P +R + E ++L K + + + H AA D ++ I
Sbjct: 51 ---PRYR---------FVQGDICDRELVDRLFKEYQPDAVVHFAAESHVDRSIDGPAPFI 98
Query: 152 RANLYATKQMLNLAKECVNLKRF 174
+ N+ T +L A++ RF
Sbjct: 99 QTNVVGTYTLLEAARKYWGKFRF 121
>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 = 32.2 bits (74), Expect = 0.094
Identities = 16/61 (26%), Positives = 28/61 (45%), Gaps = 7/61 (11%)
Query: 39 ILVTGGTGFMGKLLIDKLL-RSFPDIGAIYIMVRDKKGSSPEERVKNMLNSVIFDRLNKE 97
+LV G TG +G+ ++ +LL R + + +VRD + E V+ D + E
Sbjct: 2 VLVVGATGKVGRHVVRELLDRGYQ----VRALVRDPSQAEKLEAAG--AEVVVGDLTDAE 55
Query: 98 V 98
Sbjct: 56 S 56
>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 = 32.3 bits (74), Expect = 0.099
Identities = 23/145 (15%), Positives = 54/145 (37%), Gaps = 42/145 (28%)
Query: 39 ILVTGGTGFMGKLLIDKLLRSFPDIGA-IYIMVRDKKGSSPEERVKNMLNSVIFDRLNKE 97
LVTG + +G+ + +L R GA + + R+++ + ++ + + +
Sbjct: 1 ALVTGASSGIGRAIARRLARE----GAKVVLADRNEEALAELAAIEALGGNAVA------ 50
Query: 98 VPDFRSKIQVIPSNLESEHLGLSEDSEQLIKS------KVNIIFHCAASLRF-------D 144
+ +++ E ED E L++ +++I+ + A R D
Sbjct: 51 ----------VQADVSDE-----EDVEALVEEALEEFGRLDILVNNAGIARPGPLEELTD 95
Query: 145 EALQKAIRANLYATKQMLNLAKECV 169
E + + NL L + +
Sbjct: 96 EDWDRVLDVNLTGV---FLLTRAAL 117
>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 = 32.3 bits (74), Expect = 0.11
Identities = 30/140 (21%), Positives = 49/140 (35%), Gaps = 38/140 (27%)
Query: 39 ILVTGGTGFMGKLLIDKLLRSFPDIG-AIYIMVRDKKGSSPEERVKNMLNSVIFDRLNKE 97
ILVTG TGF+G L+ LL G + +VR +
Sbjct: 1 ILVTGATGFLGSNLVRALLAQ----GYRVRALVRSG---------------------SDA 35
Query: 98 VPDFRSKIQVIPSNLESEHLGLSEDSEQLIKSKVNIIFHCAASLRF---DEALQKAIRAN 154
V ++V+ +L L+ + + +FH AA D N
Sbjct: 36 VLLDGLPVEVVEGDLTDAAS-LAAAMKG-----CDRVFHLAAFTSLWAKDRKELYRT--N 87
Query: 155 LYATKQMLNLAKECVNLKRF 174
+ T+ +L+ A E ++R
Sbjct: 88 VEGTRNVLDAALEA-GVRRV 106
>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 = 31.6 bits (72), Expect = 0.14
Identities = 15/43 (34%), Positives = 26/43 (60%), Gaps = 3/43 (6%)
Query: 39 ILVTGGTGFMGKLLIDKLLRSFPDIGAIYIMVRDKKGSSPEER 81
IL+ G TGF+G+ L +LL + + ++VR+ K S E++
Sbjct: 1 ILILGATGFIGRALARELLEQGHE---VTLLVRNTKRLSKEDQ 40
>gnl|CDD|187643 cd08939, KDSR-like_SDR_c, 3-ketodihydrosphingosine reductase (KDSR)
and related proteins, classical (c) SDR. These proteins
include members identified as KDSR, ribitol type
dehydrogenase, and others. The group shows strong
conservation of the active site tetrad and glycine rich
NAD-binding motif of the classical SDRs. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold (alpha/beta folding pattern with a central
beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRs are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes catalyze a
wide range of activities including the metabolism of
steroids, cofactors, carbohydrates, lipids, aromatic
compounds, and amino acids, and act in redox sensing.
Classical SDRs have an TGXXX[AG]XG cofactor binding
motif and a YXXXK active site motif, with the Tyr
residue of the active site motif serving as a critical
catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 239
Score = 31.5 bits (72), Expect = 0.17
Identities = 27/145 (18%), Positives = 56/145 (38%), Gaps = 37/145 (25%)
Query: 39 ILVTGGTGFMGKLLIDKLLRSFPDIGA-IYIMVRDKKGSSPEERVKNMLNSVIFDRLNKE 97
+L+TGG+ +GK L +L++ GA + I+ R E +++ + + E
Sbjct: 4 VLITGGSSGIGKALAKELVKE----GANVIIVARS------ESKLEEAVE-----EIEAE 48
Query: 98 VPDFRSKIQVIPSNLESEHLGLSEDSEQLIK------SKVNIIFHCAASLRF-------D 144
K+ I ++L E+ EQ +++ +CA
Sbjct: 49 ANASGQKVSYISADLSDY-----EEVEQAFAQAVEKGGPPDLVVNCAGISIPGLFEDLTA 103
Query: 145 EALQKAIRANLYATKQMLNLAKECV 169
E ++ + N + + LN+A +
Sbjct: 104 EEFERGMDVNYFGS---LNVAHAVL 125
>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 = 31.5 bits (71), Expect = 0.18
Identities = 16/41 (39%), Positives = 25/41 (60%), Gaps = 2/41 (4%)
Query: 34 YRDGQILVTGGTGFMGKLLIDKLLRSFPDIGAIYIMVRDKK 74
++D +L+TGGTG G ++ + L + DI I I RD+K
Sbjct: 2 FKDKILLITGGTGSFGNAVLRRFLDT--DIKEIRIFSRDEK 40
>gnl|CDD|182998 PRK11150, rfaD, ADP-L-glycero-D-mannoheptose-6-epimerase;
Provisional.
Length = 308
Score = 31.2 bits (71), Expect = 0.20
Identities = 23/69 (33%), Positives = 38/69 (55%), Gaps = 12/69 (17%)
Query: 39 ILVTGGTGFMGKLLIDKLLRSFPDIGAIYIMVRD--KKGSSPEERVKNMLNSVIFDRLNK 96
I+VTGG GF+G ++ ++ D G I+V D K G + N+++ I D ++K
Sbjct: 2 IIVTGGAGFIGSNIV----KALNDKGITDILVVDNLKDG----TKFVNLVDLDIADYMDK 53
Query: 97 EVPDFRSKI 105
E DF ++I
Sbjct: 54 E--DFLAQI 60
>gnl|CDD|187575 cd05265, SDR_a1, atypical (a) SDRs, subgroup 1. Atypical SDRs in
this subgroup are poorly defined and have been
identified putatively as isoflavones reductase, sugar
dehydratase, mRNA binding protein etc. Atypical SDRs
are distinct from classical SDRs. Members of this
subgroup retain the canonical active site triad (though
not the upstream Asn found in most SDRs) but have an
unusual putative glycine-rich NAD(P)-binding motif,
GGXXXXG, in the usual location. Atypical SDRs generally
lack the catalytic residues characteristic of the SDRs,
and their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Atypical SDRs include biliverdin IX beta
reductase (BVR-B,aka flavin reductase), NMRa (a
negative transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane
reductase, isoflavone reductases, and others. SDRs are
a functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. In addition to the Rossmann fold
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids, and typically have a TGXXGXXG cofactor
binding motif. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 250
Score = 31.1 bits (71), Expect = 0.20
Identities = 11/20 (55%), Positives = 17/20 (85%)
Query: 38 QILVTGGTGFMGKLLIDKLL 57
+IL+ GGT F+GK L+++LL
Sbjct: 2 KILIIGGTRFIGKALVEELL 21
>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 = 31.2 bits (71), Expect = 0.20
Identities = 33/134 (24%), Positives = 53/134 (39%), Gaps = 33/134 (24%)
Query: 40 LVTGGTGFMGKLLIDKLLRSFPDIGAIYIMVRDKKGSSPEERVKNMLNSVIFD-RLNKEV 98
LVTGG GF+G+ ++ LLR +G E RV FD R + E+
Sbjct: 1 LVTGGGGFLGRHIVRLLLR---------------EGELQEVRV--------FDLRFSPEL 37
Query: 99 PDFRSKIQVIPSNLESEHLGLSEDSEQLIK----SKVNIIFHCAASLRFDEALQKAIRAN 154
+ SK+QVI + G D + L + S V I + ++ N
Sbjct: 38 LEDFSKLQVI-----TYIEGDVTDKQDLRRALQGSDVVIHTAAIIDVFGKAYRDTIMKVN 92
Query: 155 LYATKQMLNLAKEC 168
+ T+ +L+ +
Sbjct: 93 VKGTQNVLDACVKA 106
>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 = 31.2 bits (71), Expect = 0.23
Identities = 16/34 (47%), Positives = 21/34 (61%), Gaps = 1/34 (2%)
Query: 39 ILVTGGTGFMGKLLIDKLLRSFPDIGAIYIMVRD 72
IL+TGGTG GK I +LL ++ + I I RD
Sbjct: 7 ILITGGTGSFGKAFISRLLENY-NPKKIIIYSRD 39
>gnl|CDD|181609 PRK09009, PRK09009, C factor cell-cell signaling protein;
Provisional.
Length = 235
Score = 30.8 bits (70), Expect = 0.26
Identities = 11/25 (44%), Positives = 18/25 (72%)
Query: 39 ILVTGGTGFMGKLLIDKLLRSFPDI 63
IL+ 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 = 30.8 bits (70), Expect = 0.31
Identities = 35/165 (21%), Positives = 57/165 (34%), Gaps = 25/165 (15%)
Query: 18 LPESPIMQEEQKVDDFYRDGQILVTGGTGFMGKLLIDKLLRSFPDIGAIYIMVRDKKGSS 77
LP K Y LVTGG G +G+ L L R + GA +++ G S
Sbjct: 192 LPAGAAASAPLKPGGVY-----LVTGGAGGIGRALARALARRY---GARLVLL----GRS 239
Query: 78 PEERVKNMLNSVIFDRLNKEVPDFRSKIQVIPSNLESEHLGLSEDSEQLIKS--KVNIIF 135
P + + L I ++ + + E++ + ++ +
Sbjct: 240 PLPPEE-EWKAQTLAALEALGARVLY-ISADVTDAAA----VRRLLEKVRERYGAIDGVI 293
Query: 136 HCAASLRFDEALQKAIR--ANLYATKQ--MLNLAKECVNLK-RFC 175
H A LR QK + A K +LNLA+ + F
Sbjct: 294 HAAGVLRDALLAQKTAEDFEAVLAPKVDGLLNLAQALADEPLDFF 338
>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 = 30.8 bits (70), Expect = 0.33
Identities = 32/142 (22%), Positives = 55/142 (38%), Gaps = 29/142 (20%)
Query: 39 ILVTGGTGFMGKLLIDKLLRSFPDIGAIYIMVRDK--KGSSPEERVKNMLNSVIFDRLNK 96
ILVTGG GF+G + +L PD ++V DK + E L + +
Sbjct: 2 ILVTGGAGFIGSNFVRYILNEHPD---AEVIVLDKLTYAGNLEN-----LADL------E 47
Query: 97 EVPDFRSKIQVIPSNLESEHLGLSEDSEQLI-KSKVNIIFHCAASLRFDEALQKA---IR 152
+ P +R +G E +L + + + + H AA D ++ I
Sbjct: 48 DNPRYR---------FVKGDIGDRELVSRLFTEHQPDAVVHFAAESHVDRSISGPAAFIE 98
Query: 153 ANLYATKQMLNLAKECVNLKRF 174
N+ T +L ++ + RF
Sbjct: 99 TNVVGTYTLLEAVRKYWHEFRF 120
>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 = 30.6 bits (70), Expect = 0.34
Identities = 9/21 (42%), Positives = 12/21 (57%)
Query: 39 ILVTGGTGFMGKLLIDKLLRS 59
ILVTG G +G ++ L R
Sbjct: 2 ILVTGHRGLVGSAIVRVLARR 22
>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 = 30.7 bits (70), Expect = 0.36
Identities = 24/101 (23%), Positives = 41/101 (40%), Gaps = 25/101 (24%)
Query: 39 ILVTGGTGFMGKLLIDKLLRSFPDIGAIYIMVRDKKGSSPEERVKNMLNSVIFDRLNKEV 98
+LVTG GF+G L ++LLR ++ A+ ++ NS F+
Sbjct: 2 VLVTGADGFIGSHLTERLLREGHEVRAL-----------------DIYNS--FNSWGLLD 42
Query: 99 PDFRSKIQVIPSNLESEHLGLSEDSEQLIKSKVNIIFHCAA 139
+ I ++ E L+K K +++FH AA
Sbjct: 43 NAVHDRFHFISGDVRDASEV-----EYLVK-KCDVVFHLAA 77
>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 = 30.3 bits (69), Expect = 0.40
Identities = 23/69 (33%), Positives = 39/69 (56%), Gaps = 2/69 (2%)
Query: 40 LVTGGTGFMGKLLIDKLLRSFPDIGAIYIMVRDKKGSSPEERVKNMLNSVIFDRLNKEVP 99
LV G TG +GK L+ +LL+S P + +VR +K + PE + K + V F+RL++ +
Sbjct: 4 LVLGATGLVGKHLLRELLKS-PYYSKVTAIVR-RKLTFPEAKEKLVQIVVDFERLDEYLE 61
Query: 100 DFRSKIQVI 108
F++
Sbjct: 62 AFQNPDVGF 70
>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 = 30.3 bits (69), Expect = 0.43
Identities = 7/21 (33%), Positives = 15/21 (71%)
Query: 39 ILVTGGTGFMGKLLIDKLLRS 59
+ V G TGF+G+ ++++L +
Sbjct: 3 VTVFGATGFIGRYVVNRLAKR 23
>gnl|CDD|238789 cd01531, Acr2p, Eukaryotic arsenate resistance proteins are members
of the Rhodanese Homology Domain superfamily. Included
in this CD is the Saccharomyces cerevisiae arsenate
reductase protein, Acr2p, and other yeast and plant
homologs.
Length = 113
Score = 28.9 bits (65), Expect = 0.65
Identities = 14/75 (18%), Positives = 23/75 (30%), Gaps = 25/75 (33%)
Query: 102 RSKIQVIP---SNLESEHLG---------LSEDSEQLIK-----SKVNIIFHCAAS---- 140
R QV+ + H+ QL++ K ++FHCA S
Sbjct: 17 RPPFQVVDVRDEDYAGGHIKGSWHYPSTRFKAQLNQLVQLLSGSKKDTVVFHCALSQVRG 76
Query: 141 ----LRFDEALQKAI 151
+F L +
Sbjct: 77 PSAARKFLRYLDEED 91
>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 = 29.9 bits (68), Expect = 0.68
Identities = 30/141 (21%), Positives = 46/141 (32%), Gaps = 34/141 (24%)
Query: 40 LVTGGTGFMGKLLIDKLLRSFPDIGAIYIMVRDKKGSSPEERVKNMLNSVIFDRLNKEVP 99
LV G TG G L++ LL +Y + R + + R+ + D L+
Sbjct: 3 LVVGATGISGWALVEHLLSDPGTWWKVYGLSRRPLPTEDDPRLVEHIG---IDLLDPADT 59
Query: 100 DFRSKIQVIPSNLESEHLGLSEDSEQLIKSKVNIIFHCAASLRFDEALQKAIRANLYATK 159
R+K+ + V +F+ A R DEA + + N
Sbjct: 60 VLRAKLPGL--------------------EDVTHVFYAAYIERPDEA--ELVEVNG---- 93
Query: 160 QMLN-----LAKECVNLKRFC 175
ML L NLK
Sbjct: 94 AMLRNFLDALEPASPNLKHVV 114
>gnl|CDD|187659 cd08956, KR_3_FAS_SDR_x, beta-ketoacyl reductase (KR) domain of
fatty acid synthase (FAS), subgroup 3, complex (x).
Ketoreductase, a module of the multidomain polyketide
synthase (PKS), has 2 subdomains, each corresponding to
a SDR family monomer. The C-terminal subdomain catalyzes
the NADPH-dependent reduction of the beta-carbonyl of a
polyketide to a hydroxyl group, a step in the
biosynthesis of polyketides, such as erythromycin. The
N-terminal subdomain, an interdomain linker, is a
truncated Rossmann fold which acts to stabilizes the
catalytic subdomain. Unlike typical SDRs, the isolated
domain does not oligomerize but is composed of 2
subdomains, each resembling an SDR monomer. The active
site resembles that of typical SDRs, except that the
usual positions of the catalytic Asn and Tyr are
swapped, so that the canonical YXXXK motif changes to
YXXXN. Modular PKSs are multifunctional structures in
which the makeup recapitulates that found in (and may
have evolved from) FAS. In some instances, such as
porcine FAS, an enoyl reductase (ER) module is inserted
between the sub-domains. Fatty acid synthesis occurs via
the stepwise elongation of a chain (which is attached to
acyl carrier protein, ACP) with 2-carbon units.
Eukaryotic systems consists of large, multifunctional
synthases (type I) while bacterial, type II systems, use
single function proteins. Fungal fatty acid synthesis
uses a dodecamer of 6 alpha and 6 beta subunits. In
mammalian type FAS cycles, ketoacyl synthase forms
acetoacetyl-ACP which is reduced by the NADP-dependent
beta-KR, forming beta-hydroxyacyl-ACP, which is in turn
dehydrated by dehydratase to a beta-enoyl intermediate,
which is reduced by NADP-dependent beta- ER. Polyketide
synthesis also proceeds via the addition of 2-carbon
units as in fatty acid synthesis. The complex SDR
NADP-binding motif, GGXGXXG, is often present, but is
not strictly conserved in each instance of the module.
This subfamily includes KR domains found in many
multidomain PKSs, including six of seven Sorangium
cellulosum PKSs (encoded by spiDEFGHIJ) which
participate in the synthesis of the polyketide scaffold
of the cytotoxic spiroketal polyketide spirangien. These
seven PKSs have either a single PKS module (SpiF), two
PKR modules (SpiD,-E,-I,-J), or three PKS modules
(SpiG,-H). This subfamily includes the second KR domains
of SpiE,-G, I, and -J, both KR domains of SpiD, and the
third KR domain of SpiH. The single KR domain of SpiF,
the first and second KR domains of SpiH, the first KR
domains of SpiE,-G,- I, and -J, and the third KR domain
of SpiG, belong to a different KR_FAS_SDR subfamily.
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 = 448
Score = 29.9 bits (68), Expect = 0.69
Identities = 11/17 (64%), Positives = 14/17 (82%)
Query: 36 DGQILVTGGTGFMGKLL 52
DG +L+TGGTG +G LL
Sbjct: 193 DGTVLITGGTGTLGALL 209
>gnl|CDD|187580 cd05272, TDH_SDR_e, L-threonine dehydrogenase, extended (e) SDRs.
This subgroup contains members identified as L-threonine
dehydrogenase (TDH). TDH catalyzes the zinc-dependent
formation of 2-amino-3-ketobutyrate from L-threonine via
NAD(H)-dependent oxidation. This group is distinct from
TDHs that are members of the medium chain
dehydrogenase/reductase family. This group has the
NAD-binding motif and active site tetrad 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 = 308
Score = 29.6 bits (67), Expect = 0.79
Identities = 34/144 (23%), Positives = 55/144 (38%), Gaps = 43/144 (29%)
Query: 39 ILVTGGTGFMGKLLIDKLLRSFPDIGAIYIMVRDKKG------SSPEERVKNMLNSVIFD 92
IL+TGG G +G L L R + G S + +++ S F+
Sbjct: 2 ILITGGLGQIGSELAKLL--------------RKRYGKDNVIASDIRKPPAHVVLSGPFE 47
Query: 93 RLNKEVPDFRSKIQVIPSNLESEHLGLSEDSEQLIKSKVNIIFHCAA--SLRFDEALQKA 150
L+ V DF+S +++ + K+ I H AA S ++ A
Sbjct: 48 YLD--VLDFKSLEEIV------------------VNHKITWIIHLAALLSAVGEKNPPLA 87
Query: 151 IRANLYATKQMLNLAKECVNLKRF 174
N+ +L LA+E NL+ F
Sbjct: 88 WDVNMNGLHNVLELARE-HNLRIF 110
>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 = 29.2 bits (66), Expect = 0.95
Identities = 26/108 (24%), Positives = 44/108 (40%), Gaps = 23/108 (21%)
Query: 33 FYRDGQILVTGGTGFMGKLLIDKLLRSFPDIGAIYIMVRDKKGSSPEERVKNMLNSVIFD 92
F++ ++LVTG TGF G L L ++GA I ++P N
Sbjct: 1 FWQGKRVLVTGHTGFKGSWLSLWLQ----ELGAKVIGYSLDPPTNP--------NLFELA 48
Query: 93 RLNKEVPDFRSKIQVIPSNLESEHLGLSEDSEQLIKSKVNIIFHCAAS 140
L+ ++ R I+ + + L E + + + I+FH AA
Sbjct: 49 NLDNKISSTRGDIRDL-NALR----------EAIREYEPEIVFHLAAQ 85
>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 = 29.2 bits (66), Expect = 1.0
Identities = 14/44 (31%), Positives = 22/44 (50%)
Query: 39 ILVTGGTGFMGKLLIDKLLRSFPDIGAIYIMVRDKKGSSPEERV 82
+LVTG TG++G L+ +LL+ + A+ ERV
Sbjct: 1 VLVTGATGYVGGRLVPRLLQEGHQVRALVRSPEKLADRPWSERV 44
>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 = 28.9 bits (65), Expect = 1.2
Identities = 29/127 (22%), Positives = 53/127 (41%), Gaps = 30/127 (23%)
Query: 39 ILVTGGTGFMGKLLIDKLLRSFPDIGAIYIMVRDKKGSSPEERVKNMLNSVIFDRLNKEV 98
+L+TG +GF+G+ L ++LL P+ ER+ + D ++ +
Sbjct: 3 VLITGASGFVGQRLAERLLSDVPN-----------------ERLILI------DVVSPKA 39
Query: 99 PDFRSKIQVIPSNLESEHLGLSEDSEQLIKSKVNIIFHCAASL-RFDEA-LQKAIRANLY 156
P ++ I +L L E L + +++FH AA + EA R N+
Sbjct: 40 PSGAPRVTQIAGDLAVPAL-----IEALANGRPDVVFHLAAIVSGGAEADFDLGYRVNVD 94
Query: 157 ATKQMLN 163
T+ +L
Sbjct: 95 GTRNLLE 101
>gnl|CDD|214888 smart00891, ERCC4, ERCC4 domain. This entry represents a
structural motif found in several DNA repair nucleases,
such as Rad1/Mus81/XPF endonucleases, and in
ATP-dependent helicases. The XPF/Rad1/Mus81-dependent
nuclease family specifically cleaves branched structures
generated during DNA repair, replication, and
recombination, and is essential for maintaining genome
stability. The nuclease domain architecture exhibits
remarkable similarity to those of restriction
endonucleases.
Length = 98
Score = 27.7 bits (62), Expect = 1.3
Identities = 9/63 (14%), Positives = 21/63 (33%)
Query: 101 FRSKIQVIPSNLESEHLGLSEDSEQLIKSKVNIIFHCAASLRFDEALQKAIRANLYATKQ 160
++ ++V LE+ L +Q + VN + + + L+ +
Sbjct: 23 WKRGVKVEYDRLEAGDFVLVARDKQSLLPHVNSLNELVERKSLTDLVASIPDGRLFEQVR 82
Query: 161 MLN 163
L
Sbjct: 83 RLQ 85
>gnl|CDD|187574 cd05264, UDP_G4E_5_SDR_e, UDP-glucose 4-epimerase (G4E), subgroup
5, extended (e) SDRs. This subgroup partially
conserves the characteristic active site tetrad and
NAD-binding motif of the extended SDRs, and has been
identified as possible UDP-glucose 4-epimerase (aka
UDP-galactose 4-epimerase), a homodimeric member of the
extended SDR family. UDP-glucose 4-epimerase catalyzes
the NAD-dependent conversion of UDP-galactose to
UDP-glucose, the final step in Leloir galactose
synthesis. Extended SDRs are distinct from classical
SDRs. In addition to the Rossmann fold (alpha/beta
folding pattern with a central beta-sheet) core region
typical of all SDRs, extended SDRs have a less
conserved C-terminal extension of approximately 100
amino acids. Extended SDRs are a diverse collection of
proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and
their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 300
Score = 28.8 bits (65), Expect = 1.5
Identities = 11/25 (44%), Positives = 16/25 (64%)
Query: 39 ILVTGGTGFMGKLLIDKLLRSFPDI 63
+L+ GG GF+G L+D LL P +
Sbjct: 2 VLIVGGNGFIGSHLVDALLEEGPQV 26
>gnl|CDD|234595 PRK00048, PRK00048, dihydrodipicolinate reductase; Provisional.
Length = 257
Score = 28.6 bits (65), Expect = 1.6
Identities = 17/66 (25%), Positives = 28/66 (42%), Gaps = 11/66 (16%)
Query: 39 ILVTGGTGFMGKLLIDKLLRSFPDI---GAIYIMVRDKKGSSPEERVKNMLNSVIFDRLN 95
+ V G +G MG+ LI + + + D+ A+ D+ GS + L I D L
Sbjct: 4 VAVAGASGRMGRELI-EAVEAAEDLELVAAV-----DRPGS--PLVGQGALGVAITDDLE 55
Query: 96 KEVPDF 101
+ D
Sbjct: 56 AVLADA 61
>gnl|CDD|222146 pfam13460, NAD_binding_10, NADH(P)-binding.
Length = 182
Score = 28.4 bits (64), Expect = 1.6
Identities = 9/20 (45%), Positives = 12/20 (60%)
Query: 39 ILVTGGTGFMGKLLIDKLLR 58
I V G TG G+ L+ +LL
Sbjct: 1 IAVIGATGKTGRRLVKELLA 20
>gnl|CDD|129694 TIGR00606, rad50, rad50. All proteins in this family for which
functions are known are involvedin recombination,
recombinational repair, and/or non-homologous end
joining.They are components of an exonuclease complex
with MRE11 homologs. This family is distantly related to
the SbcC family of bacterial proteins.This family is
based on the phylogenomic analysis of JA Eisen (1999,
Ph.D. Thesis, Stanford University).
Length = 1311
Score = 28.9 bits (64), Expect = 1.7
Identities = 16/75 (21%), Positives = 31/75 (41%), Gaps = 1/75 (1%)
Query: 53 IDKLLRSFPD-IGAIYIMVRDKKGSSPEERVKNMLNSVIFDRLNKEVPDFRSKIQVIPSN 111
+ LR PD + + ++ K+ E I D KE+P+ R+K+Q + +
Sbjct: 700 LQSKLRLAPDKLKSTESELKKKEKRRDEMLGLAPGRQSIIDLKEKEIPELRNKLQKVNRD 759
Query: 112 LESEHLGLSEDSEQL 126
++ + E L
Sbjct: 760 IQRLKNDIEEQETLL 774
>gnl|CDD|236461 PRK09302, PRK09302, circadian clock protein KaiC; Reviewed.
Length = 509
Score = 28.7 bits (65), Expect = 1.8
Identities = 11/21 (52%), Positives = 14/21 (66%), Gaps = 1/21 (4%)
Query: 33 FYRDGQILVTGGTGFMGKLLI 53
F+R ILV+G TG GK L+
Sbjct: 270 FFRGSIILVSGATG-TGKTLL 289
>gnl|CDD|191263 pfam05368, NmrA, NmrA-like family. NmrA is a negative
transcriptional regulator involved in the
post-translational modification of the transcription
factor AreA. NmrA is part of a system controlling
nitrogen metabolite repression in fungi. This family
only contains a few sequences as iteration results in
significant matches to other Rossmann fold families.
Length = 232
Score = 28.4 bits (64), Expect = 1.9
Identities = 13/38 (34%), Positives = 20/38 (52%), Gaps = 5/38 (13%)
Query: 39 ILVTGGTGFMGKLLIDKLLRS-FPDIGAIYIMVRDKKG 75
ILV G TG+ G ++ L++ P + +VRD K
Sbjct: 1 ILVFGATGYQGGSVVRASLKAGHP----VRALVRDPKS 34
>gnl|CDD|100016 cd02187, beta_tubulin, The tubulin superfamily includes five
distinct families, the alpha-, beta-, gamma-, delta-,
and epsilon-tubulins and a sixth family (zeta-tubulin)
which is present only in kinetoplastid protozoa. The
alpha- and beta-tubulins are the major components of
microtubules, while gamma-tubulin plays a major role in
the nucleation of microtubule assembly. The delta- and
epsilon-tubulins are widespread but unlike the alpha,
beta, and gamma-tubulins they are not ubiquitous among
eukaryotes. The alpha/beta-tubulin heterodimer is the
structural subunit of microtubules. The alpha- and
beta-tubulins share 40% amino-acid sequence identity,
exist in several isotype forms, and undergo a variety of
posttranslational modifications. The structures of
alpha- and beta-tubulin are basically identical: each
monomer is formed by a core of two beta-sheets
surrounded by alpha-helices. The monomer structure is
very compact, but can be divided into three regions
based on function: the amino-terminal nucleotide-binding
region, an intermediate taxol-binding region and the
carboxy-terminal region which probably constitutes the
binding surface for motor proteins.
Length = 425
Score = 28.4 bits (64), Expect = 1.9
Identities = 12/21 (57%), Positives = 14/21 (66%), Gaps = 1/21 (4%)
Query: 43 GGTGF-MGKLLIDKLLRSFPD 62
GGTG MG LLI K+ +PD
Sbjct: 140 GGTGSGMGTLLISKIREEYPD 160
>gnl|CDD|178484 PLN02896, PLN02896, cinnamyl-alcohol dehydrogenase.
Length = 353
Score = 28.2 bits (63), Expect = 2.3
Identities = 14/46 (30%), Positives = 25/46 (54%), Gaps = 7/46 (15%)
Query: 134 IFHCAASLRFD-----EALQKAIRANLY--ATKQMLNLAKECVNLK 172
+FH AAS+ FD +++ +++ + A K LN+ K C+ K
Sbjct: 83 VFHVAASMEFDVSSDHNNIEEYVQSKVIDPAIKGTLNVLKSCLKSK 128
>gnl|CDD|182313 PRK10217, PRK10217, dTDP-glucose 4,6-dehydratase; Provisional.
Length = 355
Score = 28.1 bits (62), Expect = 2.4
Identities = 10/25 (40%), Positives = 16/25 (64%)
Query: 38 QILVTGGTGFMGKLLIDKLLRSFPD 62
+IL+TGG GF+G L+ ++ D
Sbjct: 3 KILITGGAGFIGSALVRYIINETSD 27
>gnl|CDD|187570 cd05260, GDP_MD_SDR_e, GDP-mannose 4,6 dehydratase, extended (e)
SDRs. GDP-mannose 4,6 dehydratase, a homodimeric SDR,
catalyzes the NADP(H)-dependent conversion of
GDP-(D)-mannose to GDP-4-keto, 6-deoxy-(D)-mannose in
the fucose biosynthesis pathway. These proteins have the
canonical active site triad and NAD-binding pattern,
however the active site Asn is often missing and may be
substituted with Asp. A Glu residue has been identified
as an important active site base. Extended SDRs are
distinct from classical SDRs. In addition to the
Rossmann fold (alpha/beta folding pattern with a central
beta-sheet) core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids. Extended SDRs are a
diverse collection of proteins, and include isomerases,
epimerases, oxidoreductases, and lyases; they typically
have a TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 316
Score = 27.9 bits (63), Expect = 2.4
Identities = 22/102 (21%), Positives = 36/102 (35%), Gaps = 23/102 (22%)
Query: 39 ILVTGGTGFMGKLLIDKLLRSFPDIGA-IYIMVRDKKGSSPEERVKNMLNSVIFDRLNKE 97
L+TG TG G L + LL + G ++ +VR SS + + DR+
Sbjct: 2 ALITGITGQDGSYLAEFLL----EKGYEVHGIVR---RSSSFNTDRIDHLYINKDRITLH 54
Query: 98 VPDFRSKIQVIPSNLESEHLGLSEDSEQLIKSKVNIIFHCAA 139
D + + K + + I+H AA
Sbjct: 55 YGDLTDSSSLR---------------RAIEKVRPDEIYHLAA 81
>gnl|CDD|224012 COG1087, GalE, UDP-glucose 4-epimerase [Cell envelope biogenesis,
outer membrane].
Length = 329
Score = 28.3 bits (64), Expect = 2.5
Identities = 29/139 (20%), Positives = 51/139 (36%), Gaps = 41/139 (29%)
Query: 39 ILVTGGTGFMGKLLIDKLLRSFPDIGAIYIMVRDKKGSSPEERVKNMLNSVIFDRLNKEV 98
+LVTGG G++G + +LL K G V+ D L+
Sbjct: 3 VLVTGGAGYIGSHTVRQLL---------------KTGHEV----------VVLDNLSN-- 35
Query: 99 PDFRSKIQVIPSNLESEHLGLSEDSEQL----IKSKVNIIFHCAASLRFDEALQKAI--- 151
+ + + L D L ++K++ + H AAS+ E++Q +
Sbjct: 36 -GHKIALLKLQFKFYEGDLL---DRALLTAVFEENKIDAVVHFAASISVGESVQNPLKYY 91
Query: 152 RANLYATKQMLNLAKECVN 170
N+ T LNL + +
Sbjct: 92 DNNVVGT---LNLIEAMLQ 107
>gnl|CDD|215370 PLN02686, PLN02686, cinnamoyl-CoA reductase.
Length = 367
Score = 28.2 bits (63), Expect = 2.6
Identities = 10/18 (55%), Positives = 14/18 (77%)
Query: 41 VTGGTGFMGKLLIDKLLR 58
VTGG F+G ++D+LLR
Sbjct: 58 VTGGVSFLGLAIVDRLLR 75
>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 = 2.9
Identities = 8/19 (42%), Positives = 15/19 (78%)
Query: 39 ILVTGGTGFMGKLLIDKLL 57
+LVTG +GF+ ++++LL
Sbjct: 1 VLVTGASGFVASHVVEQLL 19
>gnl|CDD|218047 pfam04367, DUF502, Protein of unknown function (DUF502).
Predicted to be an integral membrane protein.
Length = 108
Score = 26.7 bits (60), Expect = 3.1
Identities = 11/39 (28%), Positives = 20/39 (51%), Gaps = 5/39 (12%)
Query: 39 ILVTG--GTGFMGKLLI---DKLLRSFPDIGAIYIMVRD 72
I + G F+G+ L+ ++LL P + +IY V+
Sbjct: 8 IFLVGLLARNFIGRWLLSLGERLLNRIPLVRSIYSSVKQ 46
>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 = 27.6 bits (62), Expect = 3.3
Identities = 10/20 (50%), Positives = 15/20 (75%)
Query: 39 ILVTGGTGFMGKLLIDKLLR 58
I++TGGTGF+G+ L +L
Sbjct: 2 IVITGGTGFIGRALTRRLTA 21
>gnl|CDD|216304 pfam01113, DapB_N, Dihydrodipicolinate reductase, N-terminus.
Dihydrodipicolinate reductase (DapB) reduces the
alpha,beta-unsaturated cyclic imine,
dihydro-dipicolinate. This reaction is the second
committed step in the biosynthesis of L-lysine and its
precursor meso-diaminopimelate, which are critical for
both protein and cell wall biosynthesis. The N-terminal
domain of DapB binds the dinucleotide NADPH.
Length = 122
Score = 26.8 bits (60), Expect = 3.3
Identities = 10/24 (41%), Positives = 14/24 (58%), Gaps = 1/24 (4%)
Query: 39 ILVTGGTGFMGKLLIDKLLRSFPD 62
+ V G +G MG+ LI K + PD
Sbjct: 3 VAVVGASGRMGRELI-KAILEAPD 25
>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 = 27.7 bits (62), Expect = 3.4
Identities = 10/20 (50%), Positives = 15/20 (75%)
Query: 39 ILVTGGTGFMGKLLIDKLLR 58
+LVTG GF+G L++ L+R
Sbjct: 1 VLVTGADGFIGSHLVEALVR 20
>gnl|CDD|224016 COG1091, RfbD, dTDP-4-dehydrorhamnose reductase [Cell envelope
biogenesis, outer membrane].
Length = 281
Score = 27.6 bits (62), Expect = 3.7
Identities = 10/30 (33%), Positives = 15/30 (50%), Gaps = 1/30 (3%)
Query: 38 QILVTGGTGFMGKLLIDKLLRSFPDIGAIY 67
+IL+TG G +G L L F ++ A
Sbjct: 2 KILITGANGQLGTELRRALPGEF-EVIATD 30
>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 = 27.0 bits (60), Expect = 3.9
Identities = 19/50 (38%), Positives = 23/50 (46%), Gaps = 17/50 (34%)
Query: 39 ILVTGGTGFMGK--------LLIDK-------LLR--SFPDIGAIYIMVR 71
IL+TGGTGF G+ L DK L R S+ +IG I R
Sbjct: 67 ILITGGTGFTGRDVTPEALEPLFDKTVEGFGELFRQLSYEEIGTSTIQSR 116
>gnl|CDD|177773 PLN00178, PLN00178, sulfite reductase.
Length = 623
Score = 27.8 bits (62), Expect = 3.9
Identities = 16/53 (30%), Positives = 23/53 (43%), Gaps = 17/53 (32%)
Query: 95 NKEVPDFRSKIQVIPSN-----------LESEHLGLSEDSEQLIKSKVNIIFH 136
P RSK+++I N L +E ++ED+ QLIK FH
Sbjct: 46 PTTEPPKRSKVEIIKENSNFLRHPLNEELATEAPNINEDAVQLIK------FH 92
>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 = 27.5 bits (61), Expect = 4.0
Identities = 10/20 (50%), Positives = 15/20 (75%)
Query: 38 QILVTGGTGFMGKLLIDKLL 57
++L+TGG G +G LI+ LL
Sbjct: 2 KVLITGGAGQIGSHLIEHLL 21
>gnl|CDD|235947 PRK07152, nadD, putative nicotinate-nucleotide adenylyltransferase;
Validated.
Length = 342
Score = 27.6 bits (62), Expect = 4.2
Identities = 13/35 (37%), Positives = 18/35 (51%), Gaps = 1/35 (2%)
Query: 72 DKKGSSPEERVKNMLNSVIFDRLNKEVPDFRSKIQ 106
+K S+ E R+ NML + + EV DF K Q
Sbjct: 46 KQKASNGEHRL-NMLKLALKNLPKMEVSDFEIKRQ 79
>gnl|CDD|240228 PTZ00010, PTZ00010, tubulin beta chain; Provisional.
Length = 445
Score = 27.4 bits (61), Expect = 4.3
Identities = 13/21 (61%), Positives = 14/21 (66%), Gaps = 1/21 (4%)
Query: 43 GGTGF-MGKLLIDKLLRSFPD 62
GGTG MG LLI KL +PD
Sbjct: 141 GGTGSGMGTLLISKLREEYPD 161
>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 = 27.3 bits (61), Expect = 4.8
Identities = 8/19 (42%), Positives = 14/19 (73%)
Query: 39 ILVTGGTGFMGKLLIDKLL 57
+ VTG TGF+G ++ +L+
Sbjct: 3 VFVTGATGFIGSAVVRELV 21
>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 = 27.1 bits (61), Expect = 5.0
Identities = 11/38 (28%), Positives = 17/38 (44%), Gaps = 13/38 (34%)
Query: 39 ILVTGGTGFMG-----KLL--------IDKLLRSFPDI 63
+LVTGG G++G +LL +D L +
Sbjct: 2 VLVTGGAGYIGSHTVVELLEAGYDVVVLDNLSNGHREA 39
>gnl|CDD|131703 TIGR02655, circ_KaiC, circadian clock protein KaiC. Members of
this family are the circadian clock protein KaiC, part
of the kaiABC operon that controls circadian rhythm. It
may be universal in Cyanobacteria. Each member has two
copies of the KaiC domain (pfam06745), which is also
found in other proteins. KaiC performs
autophosphorylation and acts as its own transcriptional
repressor [Cellular processes, Other].
Length = 484
Score = 27.2 bits (60), Expect = 5.0
Identities = 12/25 (48%), Positives = 15/25 (60%)
Query: 33 FYRDGQILVTGGTGFMGKLLIDKLL 57
F++D IL TG TG LL+ K L
Sbjct: 260 FFKDSIILATGATGTGKTLLVSKFL 284
>gnl|CDD|187569 cd05259, PCBER_SDR_a, phenylcoumaran benzylic ether reductase
(PCBER) like, atypical (a) SDRs. PCBER and
pinoresinol-lariciresinol reductases are
NADPH-dependent aromatic alcohol reductases, and are
atypical members of the SDR family. Other proteins in
this subgroup are identified as eugenol synthase. These
proteins contain an N-terminus characteristic of
NAD(P)-binding proteins and a small C-terminal domain
presumed to be involved in substrate binding, but they
do not have the conserved active site Tyr residue
typically found in SDRs. Numerous other members have
unknown functions. The glycine rich NADP-binding motif
in this subgroup is of 2 forms: GXGXXG and G[GA]XGXXG;
it tends to be atypical compared with the forms
generally seen in classical or extended SDRs. The usual
SDR active site tetrad is not present, but a critical
active site Lys at the usual SDR position has been
identified in various members, though other charged and
polar residues are found at this position in this
subgroup. Atypical SDR-related proteins retain the
Rossmann fold of the SDRs, but have limited sequence
identity and generally lack the catalytic properties of
the archetypical members. Atypical SDRs include
biliverdin IX beta reductase (BVR-B,aka flavin
reductase), NMRa (a negative transcriptional regulator
of various fungi), progesterone 5-beta-reductase like
proteins, phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane
reductase, isoflavone reductases, and others. SDRs are
a functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. In addition to the Rossmann fold
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids, and typically have a TGXXGXXG cofactor
binding motif. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 282
Score = 27.3 bits (61), Expect = 5.1
Identities = 13/43 (30%), Positives = 20/43 (46%), Gaps = 6/43 (13%)
Query: 39 ILVTGGTGFMGKLLIDKLLRS--FPDIGAIYIMVRDKKGSSPE 79
I + G TG +G ++ LL S F + ++ R SS E
Sbjct: 2 IAIAGATGTLGGPIVSALLASPGFT----VTVLTRPSSTSSNE 40
>gnl|CDD|236649 PRK10084, PRK10084, dTDP-glucose 4,6 dehydratase; Provisional.
Length = 352
Score = 27.1 bits (60), Expect = 5.5
Identities = 10/25 (40%), Positives = 17/25 (68%)
Query: 38 QILVTGGTGFMGKLLIDKLLRSFPD 62
+ILVTGG GF+G ++ ++ + D
Sbjct: 2 KILVTGGAGFIGSAVVRHIINNTQD 26
>gnl|CDD|181075 PRK07670, PRK07670, RNA polymerase sigma factor SigD; Validated.
Length = 251
Score = 26.9 bits (60), Expect = 5.9
Identities = 22/87 (25%), Positives = 43/87 (49%), Gaps = 6/87 (6%)
Query: 65 AIYIMVRDKKGSSPEERVKNMLNSVIFDRLNKEVPDFRSKIQVIPSNLESEHLGLSEDSE 124
+ + +RD K +PEE+ +L + + L +++ K Q++ S E L L+E +
Sbjct: 169 NVSVTIRDDKTPTPEEK---LLKEELIEELAEKIKQLSEKEQLVISLFYKEELTLTEIGQ 225
Query: 125 --QLIKSKVNIIFHCAASLRFDEALQK 149
L S+++ I H A + + L+K
Sbjct: 226 VLNLSTSRISQI-HSKALFKLKKLLEK 251
>gnl|CDD|143406 cd07087, ALDH_F3-13-14_CALDH-like, ALDH subfamily: Coniferyl
aldehyde dehydrogenase, ALDH families 3, 13, and 14, and
other related proteins. ALDH subfamily which includes
NAD(P)+-dependent, aldehyde dehydrogenase, family 3
member A1 and B1 (ALDH3A1, ALDH3B1, EC=1.2.1.5) and
fatty aldehyde dehydrogenase, family 3 member A2
(ALDH3A2, EC=1.2.1.3), and also plant ALDH family
members ALDH3F1, ALDH3H1, and ALDH3I1, fungal ALDH14
(YMR110C) and the protozoan family 13 member (ALDH13),
as well as coniferyl aldehyde dehydrogenases (CALDH,
EC=1.2.1.68), and other similar sequences, such as the
Pseudomonas putida benzaldehyde dehydrogenase I that is
involved in the metabolism of mandelate.
Length = 426
Score = 26.7 bits (60), Expect = 6.6
Identities = 9/15 (60%), Positives = 12/15 (80%)
Query: 13 LLDTALPESPIMQEE 27
+LD P+SP+MQEE
Sbjct: 316 ILDDVSPDSPLMQEE 330
>gnl|CDD|215107 PLN00220, PLN00220, tubulin beta chain; Provisional.
Length = 447
Score = 27.1 bits (60), Expect = 6.6
Identities = 12/21 (57%), Positives = 14/21 (66%), Gaps = 1/21 (4%)
Query: 43 GGTGF-MGKLLIDKLLRSFPD 62
GGTG MG LLI K+ +PD
Sbjct: 141 GGTGSGMGTLLISKIREEYPD 161
>gnl|CDD|178256 PLN02650, PLN02650, dihydroflavonol-4-reductase.
Length = 351
Score = 26.7 bits (59), Expect = 8.1
Identities = 9/21 (42%), Positives = 14/21 (66%)
Query: 37 GQILVTGGTGFMGKLLIDKLL 57
+ VTG +GF+G L+ +LL
Sbjct: 6 ETVCVTGASGFIGSWLVMRLL 26
>gnl|CDD|180439 PRK06171, PRK06171, sorbitol-6-phosphate 2-dehydrogenase;
Provisional.
Length = 266
Score = 26.5 bits (59), Expect = 8.2
Identities = 15/66 (22%), Positives = 27/66 (40%), Gaps = 19/66 (28%)
Query: 39 ILVTGGTGFMGKLLIDKLLRSFPDIGAIYIMVRDKKGSSPE--------------ERVKN 84
I+VTGG+ +G ++ +LL + GA + D G + E V +
Sbjct: 12 IIVTGGSSGIGLAIVKELLAN----GANVVNA-DIHGGDGQHENYQFVPTDVSSAEEVNH 66
Query: 85 MLNSVI 90
+ +I
Sbjct: 67 TVAEII 72
>gnl|CDD|236372 PRK09072, PRK09072, short chain dehydrogenase; Provisional.
Length = 263
Score = 26.4 bits (59), Expect = 8.4
Identities = 27/140 (19%), Positives = 52/140 (37%), Gaps = 40/140 (28%)
Query: 36 DGQILVTGGTGFMGKLLIDKLLRSFPDIGAIYIMVRDKKGSSPEERVKNMLNSVIFDRLN 95
D ++L+TG +G +G+ L + L + GA ++V G + E+ + L
Sbjct: 5 DKRVLLTGASGGIGQALAEALAAA----GARLLLV----GRNAEK----------LEALA 46
Query: 96 KEVPDFRSKIQVIPSNLESEH--LGLSEDSEQLIK-----SKVNIIFHCAASLRF----- 143
+P P L E ++ +N++ + A F
Sbjct: 47 ARLPY--------PGRHRWVVADLTSEAGREAVLARAREMGGINVLINNAGVNHFALLED 98
Query: 144 --DEALQKAIRANLYATKQM 161
EA+++ + NL A Q+
Sbjct: 99 QDPEAIERLLALNLTAPMQL 118
>gnl|CDD|187581 cd05273, GME-like_SDR_e, Arabidopsis thaliana
GDP-mannose-3',5'-epimerase (GME)-like, extended (e)
SDRs. This subgroup of NDP-sugar
epimerase/dehydratases are extended SDRs; they have the
characteristic active site tetrad, and an NAD-binding
motif: TGXXGXX[AG], which is a close match to the
canonical NAD-binding motif. Members include
Arabidopsis thaliana GDP-mannose-3',5'-epimerase (GME)
which catalyzes the epimerization of two positions of
GDP-alpha-D-mannose to form GDP-beta-L-galactose.
Extended SDRs are distinct from classical SDRs. In
addition to the Rossmann fold (alpha/beta folding
pattern with a central beta-sheet) core region typical
of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving
as a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton
relay involving the conserved Tyr and Lys, a water
molecule stabilized by Asn, and nicotinamide. Atypical
SDRs generally lack the catalytic residues
characteristic of the SDRs, and their glycine-rich
NAD(P)-binding motif is often different from the forms
normally seen in classical or extended SDRs. Complex
(multidomain) SDRs such as ketoreductase domains of
fatty acid synthase have a GGXGXXG NAD(P)-binding motif
and an altered active site motif (YXXXN). Fungal type
ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding
motif.
Length = 328
Score = 26.7 bits (59), Expect = 8.5
Identities = 9/20 (45%), Positives = 12/20 (60%)
Query: 39 ILVTGGTGFMGKLLIDKLLR 58
LVTG GF+G L ++L
Sbjct: 3 ALVTGAGGFIGSHLAERLKA 22
>gnl|CDD|214474 smart00022, PLAc, Cytoplasmic phospholipase A2, catalytic subunit.
Cytosolic phospholipases A2 hydrolyse arachidonyl
phospholipids. Family includes phospholipases B
isoforms.
Length = 549
Score = 26.6 bits (59), Expect = 8.8
Identities = 13/44 (29%), Positives = 20/44 (45%), Gaps = 12/44 (27%)
Query: 11 GGLLDTALPESPIMQEEQKVD------------DFYRDGQILVT 42
GG +P SP++Q E+ VD +F+ +G LV
Sbjct: 374 GGEDGENIPLSPLLQPERSVDVIFAVDASADTDEFWPNGSSLVK 417
>gnl|CDD|181080 PRK07680, PRK07680, late competence protein ComER; Validated.
Length = 273
Score = 26.1 bits (58), Expect = 9.6
Identities = 9/16 (56%), Positives = 11/16 (68%)
Query: 44 GTGFMGKLLIDKLLRS 59
GTG MG +LI+ L S
Sbjct: 7 GTGNMGTILIEAFLES 22
>gnl|CDD|177883 PLN02240, PLN02240, UDP-glucose 4-epimerase.
Length = 352
Score = 26.5 bits (59), Expect = 9.8
Identities = 8/11 (72%), Positives = 10/11 (90%)
Query: 39 ILVTGGTGFMG 49
ILVTGG G++G
Sbjct: 8 ILVTGGAGYIG 18
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
0.320 0.138 0.390
Gapped
Lambda K H
0.267 0.0710 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,120,002
Number of extensions: 851317
Number of successful extensions: 1109
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1091
Number of HSP's successfully gapped: 136
Length of query: 177
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 86
Effective length of database: 6,901,388
Effective search space: 593519368
Effective search space used: 593519368
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 56 (25.4 bits)