RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13684
(298 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 = 190 bits (484), Expect = 1e-58
Identities = 78/158 (49%), Positives = 104/158 (65%), Gaps = 1/158 (0%)
Query: 116 ILLTGGTGFLGKLVIVKLLRSFPGIRKIYMMVRDKKGASAEERLNALFRNVIFERLHLEV 175
+L+TG TGFLGK+++ KLLRS P I KIY+++R K G SAEERL L ++ +F+R
Sbjct: 3 VLITGATGFLGKVLLEKLLRSCPDIGKIYLLIRGKSGQSAEERLRELLKDKLFDRGRNLN 62
Query: 176 PDFKSKIHVLPCNLELRDLGLSPENKQMLISRVNIVLHGAATLRFDEDLQVAIQTNVRGT 235
P F+SKI + +L +LGLS E+ Q LI VNI++H AAT+ FDE L A+ NV GT
Sbjct: 63 PLFESKIVPIEGDLSEPNLGLSDEDLQTLIEEVNIIIHCAATVTFDERLDEALSINVLGT 122
Query: 236 REVLNLAKQCPNLKMLTYVSTAFSHA-RSQIGEVVYEP 272
+L LAK+C LK +VSTA+ + R I E VY P
Sbjct: 123 LRLLELAKRCKKLKAFVHVSTAYVNGDRQLIEEKVYPP 160
>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 = 163 bits (414), Expect = 4e-49
Identities = 64/144 (44%), Positives = 85/144 (59%), Gaps = 8/144 (5%)
Query: 118 LTGGTGFLGKLVIVKLLRSFPGIRKIYMMVRDKKGASAEERL-NALFRNVIFERLHLEVP 176
LTG TGFLGK+++ KLLRS P + KIY +VR K G SA ERL L + +F+RL
Sbjct: 1 LTGATGFLGKVLLEKLLRSTPEV-KIYCLVRAKDGESALERLRQELLKYGLFDRLKA--- 56
Query: 177 DFKSKIHVLPCNLELRDLGLSPENKQMLISRVNIVLHGAATLRFDEDLQVAIQTNVRGTR 236
+I + +L +LGLS E+ Q L V++++H AAT+ F E TNV GTR
Sbjct: 57 --LERIIPVAGDLSEPNLGLSDEDFQELAEEVDVIIHNAATVNFVEPYSDLRATNVLGTR 114
Query: 237 EVLNLAKQCPNLKMLTYVSTAFSH 260
EVL LAKQ +VSTA+ +
Sbjct: 115 EVLRLAKQMKK-LPFHHVSTAYVN 137
>gnl|CDD|215538 PLN02996, PLN02996, fatty acyl-CoA reductase.
Length = 491
Score = 108 bits (271), Expect = 1e-26
Identities = 59/161 (36%), Positives = 94/161 (58%), Gaps = 9/161 (5%)
Query: 106 SVEEFYRDGEILLTGGTGFLGKLVIVKLLRSFPGIRKIYMMVRDKKGASAEERLNA---- 161
S +F + IL+TG TGFL K+ + K+LR P ++K+Y+++R SA +RL+
Sbjct: 4 SCVQFLENKTILVTGATGFLAKIFVEKILRVQPNVKKLYLLLRASDAKSATQRLHDEVIG 63
Query: 162 --LFRNVIFERLHLEVPDFKS-KIHVLPCNLELRDLGLSPEN-KQMLISRVNIVLHGAAT 217
LF+ V+ E+L + S K+ +P ++ DLG+ N ++ + ++IV++ AAT
Sbjct: 64 KDLFK-VLREKLGENLNSLISEKVTPVPGDISYDDLGVKDSNLREEMWKEIDIVVNLAAT 122
Query: 218 LRFDEDLQVAIQTNVRGTREVLNLAKQCPNLKMLTYVSTAF 258
FDE VA+ N G VLN AK+C +KML +VSTA+
Sbjct: 123 TNFDERYDVALGINTLGALNVLNFAKKCVKVKMLLHVSTAY 163
>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 = 98.6 bits (246), Expect = 5e-24
Identities = 44/143 (30%), Positives = 74/143 (51%), Gaps = 17/143 (11%)
Query: 116 ILLTGGTGFLGKLVIVKLLRSFPGIRKIYMMVRDKKGASAEERLNALFRNVIFERLHLEV 175
+ +TGGTGFLG+ ++ +LL + K+ ++VR + A ER+ + +R+ +
Sbjct: 1 VFVTGGTGFLGRHLVKRLLEN---GFKVLVLVRSESLGEAHERIEEA--GLEADRVRVLE 55
Query: 176 PDFKSKIHVLPCNLELRDLGLSPENKQMLISRVNIVLHGAATLRFDEDLQVAIQTNVRGT 235
D L +LGLS + L +V+ V+H AA+ F + A +TN+ GT
Sbjct: 56 GD-----------LTQPNLGLSAAASRELAGKVDHVIHCAASYDFQAPNEDAWRTNIDGT 104
Query: 236 REVLNLAKQCPNLKMLTYVSTAF 258
VL LA + +++ YVSTA+
Sbjct: 105 EHVLELAARL-DIQRFHYVSTAY 126
>gnl|CDD|215279 PLN02503, PLN02503, fatty acyl-CoA reductase 2.
Length = 605
Score = 99.2 bits (247), Expect = 3e-23
Identities = 57/172 (33%), Positives = 97/172 (56%), Gaps = 7/172 (4%)
Query: 107 VEEFYRDGEILLTGGTGFLGKLVIVKLLRSFPGIRKIYMMVRDKKGASAEERL-NALFRN 165
+ EF R L+TG TGFL K++I K+LR+ P + KIY++++ K +A ERL N +
Sbjct: 113 IAEFLRGKNFLITGATGFLAKVLIEKILRTNPDVGKIYLLIKAKDKEAAIERLKNEVIDA 172
Query: 166 VIFERL-HLEVPDFKSKI--HVLPCNLELRD--LGLSPENKQMLISRVNIVLHGAATLRF 220
+F+ L ++S + ++P + + LGL P+ + V+++++ AA F
Sbjct: 173 ELFKCLQETHGKSYQSFMLSKLVPVVGNVCESNLGLEPDLADEIAKEVDVIINSAANTTF 232
Query: 221 DEDLQVAIQTNVRGTREVLNLAKQCPNLKMLTYVSTAFSHARSQIGEVVYEP 272
DE VAI N RG +++ AK+C LK+ VSTA+ + + Q G ++ +P
Sbjct: 233 DERYDVAIDINTRGPCHLMSFAKKCKKLKLFLQVSTAYVNGQRQ-GRIMEKP 283
Score = 31.4 bits (71), Expect = 0.56
Identities = 11/34 (32%), Positives = 21/34 (61%)
Query: 18 FDSANILHTWNQLGPTEKAKFPFNIADLDWDEYL 51
FD++N ++ EKA+F F++ +DW +Y+
Sbjct: 555 FDNSNTQRLMERMSEEEKAEFGFDVGSIDWRDYI 588
>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 = 91.6 bits (228), Expect = 2e-21
Identities = 55/166 (33%), Positives = 83/166 (50%), Gaps = 16/166 (9%)
Query: 116 ILLTGGTGFLGKLVIVKLLRSFPGIRKIYMMVRDKKGASAEERLNALFRNVIFERLHLEV 175
+LLTG TGFLG ++ +LL+ + KIY +VR K +A ERL N+ L+L
Sbjct: 2 VLLTGATGFLGAYLLRELLKR-KNVSKIYCLVRAKDEEAALERLI---DNLKEYGLNLWD 57
Query: 176 PDFKSKIHVLPCNLELRDLGLSPENKQMLISRVNIVLHGAATLRF---DEDLQVAIQTNV 232
S+I V+ +L +LGLS ++ Q L V++++H A + + E+L+ NV
Sbjct: 58 ELELSRIKVVVGDLSKPNLGLSDDDYQELAEEVDVIIHNGANVNWVYPYEELKP---ANV 114
Query: 233 RGTREVLNLAKQCPNLKMLTYVSTAFSHARSQIGEVVYEPKTHYKE 278
GT+E+L LA LK L +VST S Y +
Sbjct: 115 LGTKELLKLAATGK-LKPLHFVSTL-----SVFSAEEYNALDDEES 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 = 74.7 bits (184), Expect = 3e-15
Identities = 46/143 (32%), Positives = 65/143 (45%), Gaps = 12/143 (8%)
Query: 116 ILLTGGTGFLGKLVIVKLLRSFPGIRKIYMMVRDKKGASAEERLNALFRNVIFERLHLEV 175
+LLTG TGFLG ++++LL K+ +VR + +A RL F
Sbjct: 3 VLLTGATGFLGAYLLLELLDRSDA--KVICLVRAQSDEAALARLEKTFD-------LYRH 53
Query: 176 PD--FKSKIHVLPCNLELRDLGLSPENKQMLISRVNIVLHGAATLRFDEDLQVAIQTNVR 233
D ++ V+ +L DLGLS Q L V++++H AA + NV
Sbjct: 54 WDELSADRVEVVAGDLAEPDLGLSERTWQELAENVDLIIHNAALVNHVFPYSELRGANVL 113
Query: 234 GTREVLNLAKQCPNLKMLTYVST 256
GT EVL LA K L YVS+
Sbjct: 114 GTAEVLRLAAT-GKPKPLHYVSS 135
>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 = 74.8 bits (184), Expect = 3e-15
Identities = 50/142 (35%), Positives = 67/142 (47%), Gaps = 6/142 (4%)
Query: 116 ILLTGGTGFLGKLVIVKLLRSFPGIRKIYMMVRDKKGASAEERLNALFRNVIFERLHLEV 175
+LLTG TGFLG ++ +LLR K+ +VR A ERL R+ RL E
Sbjct: 2 VLLTGATGFLGAYLLEELLRRST-QAKVICLVRAASEEHAMERLREALRS---YRLWHED 57
Query: 176 PDFKSKIHVLPCNLELRDLGLSPENKQMLISRVNIVLHGAATLRFDEDLQVAIQTNVRGT 235
+ +I V+ +L LGLS + L V+ ++H A + + NV GT
Sbjct: 58 LA-RERIEVVAGDLSEPRLGLSDAEWERLAENVDTIVHNGALVNWVYPYSELRGANVLGT 116
Query: 236 REVLNLAKQCPNLKMLTYVSTA 257
REVL LA K L YVST
Sbjct: 117 REVLRLAASGR-AKPLHYVSTI 137
>gnl|CDD|176924 cd09071, FAR_C, C-terminal domain of fatty acyl CoA reductases.
C-terminal domain of fatty acyl CoA reductases, a
family of SDR-like proteins. SDRs or short-chain
dehydrogenases/reductases are Rossmann-fold
NAD(P)H-binding proteins. Many proteins in this FAR_C
family may function as fatty acyl-CoA reductases
(FARs), acting on medium and long chain fatty acids,
and have been reported to be involved in diverse
processes such as the 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. The
function of this C-terminal domain is unclear.
Length = 92
Score = 66.0 bits (162), Expect = 6e-14
Identities = 20/61 (32%), Positives = 35/61 (57%)
Query: 1 MDKVIHLLRPFSTTDWIFDSANILHTWNQLGPTEKAKFPFNIADLDWDEYLDRYVRGTLV 60
+ K++ LL F+T +W FD+ N W +L ++ F F+I +DWD+Y + Y+ G
Sbjct: 30 IHKLLDLLEYFTTNEWRFDNDNTRALWERLSEEDRELFNFDIRSIDWDDYFENYIPGLRK 89
Query: 61 H 61
+
Sbjct: 90 Y 90
>gnl|CDD|111859 pfam03015, Sterile, 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 = 94
Score = 59.6 bits (145), Expect = 1e-11
Identities = 21/55 (38%), Positives = 32/55 (58%)
Query: 3 KVIHLLRPFSTTDWIFDSANILHTWNQLGPTEKAKFPFNIADLDWDEYLDRYVRG 57
K + +L+PFS +WIFD+ N ++ +K F F++ LDWDEY +RG
Sbjct: 32 KGLEVLQPFSLNEWIFDNKNTRELREKMSEEDKKLFNFDMESLDWDEYFRNAIRG 86
>gnl|CDD|235962 PRK07201, PRK07201, short chain dehydrogenase; Provisional.
Length = 657
Score = 61.5 bits (150), Expect = 1e-10
Identities = 39/130 (30%), Positives = 60/130 (46%), Gaps = 21/130 (16%)
Query: 117 LLTGGTGFLGKLVIVKLLRSFPGIRKIYMMVRDKKGASAEERLNALFRNVIFERLHLEVP 176
+TGGTGF+G+ ++ +LL ++++VR + RL AL +R+ V
Sbjct: 4 FVTGGTGFIGRRLVSRLLDRRREAT-VHVLVR----RQSLSRLEALAAYWGADRVVPLVG 58
Query: 177 DFKSKIHVLPCNLELRDLGLSPENKQMLISRVNIVLHGAAT--LRFDEDLQVAIQTNVRG 234
D LGLS + L ++ V+H AA L DE+ Q NV G
Sbjct: 59 DLTEP-----------GLGLSEADIAEL-GDIDHVVHLAAIYDLTADEEAQ--RAANVDG 104
Query: 235 TREVLNLAKQ 244
TR V+ LA++
Sbjct: 105 TRNVVELAER 114
>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 = 56.2 bits (136), Expect = 7e-09
Identities = 45/153 (29%), Positives = 66/153 (43%), Gaps = 29/153 (18%)
Query: 116 ILLTGGTGFLGKLVIVKLL-RSFPGIRKIYMMVRDKKGASAEERL--NALFRNVIFERLH 172
+ LTG TGFLG ++ LL R K++ VR K + ERL + E
Sbjct: 974 VFLTGATGFLGSFILRDLLTRRSNSNFKVFAHVRAKSEEAGLERLRKTGTTYGIWDEE-- 1031
Query: 173 LEVPDFKSKIHVLPCNLELRDLGLSPENKQMLISRVNIVLH-GA--------ATLRFDED 223
+ S+I V+ +L GLS E L + V++++H GA + LR
Sbjct: 1032 -----WASRIEVVLGDLSKEKFGLSDEKWSDLTNEVDVIIHNGALVHWVYPYSKLR---- 1082
Query: 224 LQVAIQTNVRGTREVLNLAKQCPNLKMLTYVST 256
NV GT VLNL + K ++VS+
Sbjct: 1083 -----DANVIGTINVLNLCAE-GKAKQFSFVSS 1109
>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 = 48.0 bits (115), Expect = 2e-06
Identities = 41/198 (20%), Positives = 71/198 (35%), Gaps = 52/198 (26%)
Query: 116 ILLTGGTGFLGKLVIVKLLRSFPGIRKIYMMVRDKKGASAEERLNALFRNVIFE-RLHL- 173
+L+TG TGF+ ++ +LL++ +R VR S +L AL + + RL
Sbjct: 2 VLVTGATGFIASHIVEQLLKAGYKVRGT---VRS---LSKSAKLKALLKAAGYNDRLEFV 55
Query: 174 EVPDFKSKIHVLPCNLELRDLGLSPENKQMLISRVNIVLHGAATLRF------DEDLQVA 227
V D +P + V+ V+H A+ F D+ + A
Sbjct: 56 IVDDL-----------------TAPNAWDEALKGVDYVIHVASPFPFTGPDAEDDVIDPA 98
Query: 228 IQTNVRGTREVLNLAKQCPNLK--MLTYVSTAFSHARSQIGEVVYEPKTHYKELL-ELS- 283
++ GT VL AK ++K +LT S + V ++ E
Sbjct: 99 VE----GTLNVLEAAKAAGSVKRVVLT----------SSVAAVGDPTAEDPGKVFTEEDW 144
Query: 284 ---MICPDDPRLPLMKAK 298
I + + +K
Sbjct: 145 NDLTISKSNGLDAYIASK 162
>gnl|CDD|187548 cd05237, UDP_invert_4-6DH_SDR_e, UDP-Glcnac (UDP-linked
N-acetylglucosamine) inverting 4,6-dehydratase, extended
(e) SDRs. UDP-Glcnac inverting 4,6-dehydratase was
identified in Helicobacter pylori as the hexameric flaA1
gene product (FlaA1). FlaA1 is hexameric, possesses
UDP-GlcNAc-inverting 4,6-dehydratase activity, and
catalyzes the first step in the creation of a
pseudaminic acid derivative in protein glycosylation.
Although this subgroup has the NADP-binding motif
characteristic of extended SDRs, its members tend to
have a Met substituted for the active site Tyr found in
most SDR families. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately 100
amino acids. Extended SDRs are a diverse collection of
proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 287
Score = 46.8 bits (112), Expect = 4e-06
Identities = 38/144 (26%), Positives = 62/144 (43%), Gaps = 23/144 (15%)
Query: 116 ILLTGGTGFLGKLVIVKLLRSFPGIRKIYMMVRDKKGASAEERLNALFRNVIFERLHLEV 175
IL+TGG G +G ++ ++L+ G +K+ + RD+ N L V R
Sbjct: 5 ILVTGGAGSIGSELVRQILKF--GPKKLIVFDRDE---------NKLHELVRELRSRFPH 53
Query: 176 PDFKSKIHVLPCNLELRDLGLSPENKQMLISRVNIVLHGAAT--LRFDEDLQV-AIQTNV 232
+ I ++RD + +IV H AA + ED AI+TNV
Sbjct: 54 DKLRFII------GDVRDKER--LRRAFKERGPDIVFHAAALKHVPSMEDNPEEAIKTNV 105
Query: 233 RGTREVLNLAKQCPNLKMLTYVST 256
GT+ V++ A + K + +ST
Sbjct: 106 LGTKNVIDAAIENGVEKFVC-IST 128
>gnl|CDD|224011 COG1086, COG1086, Predicted nucleoside-diphosphate sugar epimerases
[Cell envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 588
Score = 44.6 bits (106), Expect = 4e-05
Identities = 33/153 (21%), Positives = 53/153 (34%), Gaps = 36/153 (23%)
Query: 103 RLESVEEFYRDGEILLTGGTGFLGKLVIVKLLRSFPGIRKIYMMVRDKKGASA-EERLNA 161
E + +L+TGG G +G + ++L+ ++I + RD+ + L
Sbjct: 240 DTELIGAMLTGKTVLVTGGGGSIGSELCRQILKF--NPKEIILFSRDEYKLYLIDMELRE 297
Query: 162 LFRNVIFERLHLEVPDFKSKIHVLPCNLELRDLGLSPENKQMLISRVNIVLHGAATLRFD 221
F + +V D M +V+IV H AA L+
Sbjct: 298 KFPELKLRFYIGDVRDRDRVERA------------------MEGHKVDIVFHAAA-LK-- 336
Query: 222 EDLQV---------AIQTNVRGTREVLNLAKQC 245
V AI+TNV GT V A +
Sbjct: 337 ---HVPLVEYNPEEAIKTNVLGTENVAEAAIKN 366
>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 = 42.0 bits (99), Expect = 8e-05
Identities = 38/161 (23%), Positives = 66/161 (40%), Gaps = 35/161 (21%)
Query: 116 ILLTGGTGFLGKLVIVKLLRSFPGIRKIYMMVRDKKGASAEERLNALFRNVIFERLHLEV 175
IL+ G TGF+G+ + +LL ++ ++VR+ K S E++ E + +
Sbjct: 1 ILILGATGFIGRALARELLEQG---HEVTLLVRNTKRLSKEDQ----------EPVAVVE 47
Query: 176 PDFKSKIHVLPCNLELRDLGLSPENKQMLISRVNIVLHGAATLRFDEDLQVAIQTNVRGT 235
D LRD ++ + V++V+H A R D + +V GT
Sbjct: 48 GD-------------LRD----LDSLSDAVQGVDVVIHLAGAPRDTRDF---CEVDVEGT 87
Query: 236 REVLNLAKQCPNLKMLTYVSTAFSHARSQIGEVVYEPKTHY 276
R VL AK+ +K ++S+ E P + Y
Sbjct: 88 RNVLEAAKEAG-VKHFIFISSLG-AYGDLHEETEPSPSSPY 126
>gnl|CDD|187557 cd05246, dTDP_GD_SDR_e, dTDP-D-glucose 4,6-dehydratase, extended
(e) SDRs. This subgroup contains dTDP-D-glucose
4,6-dehydratase and related proteins, members of the
extended-SDR family, with the characteristic Rossmann
fold core region, active site tetrad and NAD(P)-binding
motif. dTDP-D-glucose 4,6-dehydratase is closely related
to other sugar epimerases of the SDR family.
dTDP-D-dlucose 4,6,-dehydratase catalyzes the second of
four steps in the dTDP-L-rhamnose pathway (the
dehydration of dTDP-D-glucose to
dTDP-4-keto-6-deoxy-D-glucose) in the synthesis of
L-rhamnose, a cell wall component of some pathogenic
bacteria. In many gram negative bacteria, L-rhamnose is
an important constituent of lipopoylsaccharide
O-antigen. The larger N-terminal portion of
dTDP-D-Glucose 4,6-dehydratase forms a Rossmann fold
NAD-binding domain, while the C-terminus binds the sugar
substrate. Extended SDRs are distinct from classical
SDRs. In addition to the Rossmann fold (alpha/beta
folding pattern with a central beta-sheet) core region
typical of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 315
Score = 41.8 bits (99), Expect = 3e-04
Identities = 40/145 (27%), Positives = 61/145 (42%), Gaps = 26/145 (17%)
Query: 116 ILLTGGTGFLGKLVIVKLLRSFPGIRKIYMMVRDKKG-ASAEERLNALFRNVIFERLHLE 174
IL+TGG GF+G + LL +P + I DK A E L + + R
Sbjct: 3 ILVTGGAGFIGSNFVRYLLNKYPDYKII---NLDKLTYAGNLENLEDVSSS---PRYRFV 56
Query: 175 VPDFKSKIHVLPCNLELRDLGLSPENKQMLISRVNIVLHGAATLRFD---EDLQVAIQTN 231
D C+ EL D E +++ V+H AA D D + I+TN
Sbjct: 57 KGDI--------CDAELVDRLFEEE-------KIDAVIHFAAESHVDRSISDPEPFIRTN 101
Query: 232 VRGTREVLNLAKQCPNLKMLTYVST 256
V GT +L A++ + + ++ST
Sbjct: 102 VLGTYTLLEAARKYGVKRFV-HIST 125
>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 = 39.5 bits (92), Expect = 0.001
Identities = 31/143 (21%), Positives = 51/143 (35%), Gaps = 23/143 (16%)
Query: 116 ILLTGGTGFLGKLVIVKLLRSFPGIRKIYMMVRDKKGASAEERLNALFRNVIFERLHLEV 175
+L+TG +GF+ V+ +LL +R VRD V L++
Sbjct: 1 VLVTGASGFVASHVVEQLLERGYKVRA---TVRDPS-------------KVKKVNHLLDL 44
Query: 176 PDFKSKIHVLPCNLELRDLGLSPENKQMLISRVNIVLHGAATLRF-DEDLQVAIQTNVRG 234
L + DL ++ +I V H A + F +D I+ + G
Sbjct: 45 DAKPG-----RLELAVADLTDE-QSFDEVIKGCAGVFHVATPVSFSSKDPNEVIKPAIGG 98
Query: 235 TREVLNLAKQCPNLKMLTYVSTA 257
T L A ++K S+A
Sbjct: 99 TLNALKAAAAAKSVKRFVLTSSA 121
>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 = 38.9 bits (91), Expect = 0.002
Identities = 28/142 (19%), Positives = 47/142 (33%), Gaps = 31/142 (21%)
Query: 116 ILLTGGTGFLGKLVIVKLLRSFPGIRKIYMMVRDKKGASAEERLNALFRNVIFERLHLEV 175
IL+TG G LG+L+ +L S I + R G+ + E + L++
Sbjct: 1 ILVTGAAGGLGRLLARRLAASPRVIGVDGLDRRRPPGSPPK-----------VEYVRLDI 49
Query: 176 PDFKSKIHVLPCNLELRDLGLSPENKQMLISRVNIVLHGAATLRFDEDLQVAIQTNVRGT 235
D + + V+H A L D + NV GT
Sbjct: 50 RDPAAADV-------------------FREREADAVVHLAFILDPPRDGAERHRINVDGT 90
Query: 236 REVLNLAKQCPNLKMLTYVSTA 257
+ VL+ + + S+
Sbjct: 91 QNVLDACAAAG-VPRVVVTSSV 111
>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 = 38.8 bits (91), Expect = 0.002
Identities = 33/142 (23%), Positives = 54/142 (38%), Gaps = 32/142 (22%)
Query: 116 ILLTGGTGFLGKLVIVKLLRSFPGIRKIYMMVRDKKGASAEERLNALFRNVIFERLHLEV 175
IL+TG TGFLG ++ LL G R + +VR L + +
Sbjct: 1 ILVTGATGFLGSNLVRALLAQ--GYR-VRALVRSG------SDAVLLDG----LPVEVVE 47
Query: 176 PDFKSKIHVLPCNLELRDLGLSPENKQMLISRVNIVLHGAATLRF-DEDLQVAIQTNVRG 234
D + L + + + V H AA +D + +TNV G
Sbjct: 48 GDL----------TDAASLAAAMKG-------CDRVFHLAAFTSLWAKDRKELYRTNVEG 90
Query: 235 TREVLNLAKQCPNLKMLTYVST 256
TR VL+ A + ++ + + S+
Sbjct: 91 TRNVLDAALEA-GVRRVVHTSS 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 = 38.1 bits (89), Expect = 0.002
Identities = 28/145 (19%), Positives = 45/145 (31%), Gaps = 66/145 (45%)
Query: 116 ILLTGGTGFLGKLVIVKLLRSFPGIRKIYMMVRDKKGASAEERLNALFRNVIFERLHLEV 175
IL+TGG GF+G ++ RL V+
Sbjct: 1 ILVTGGAGFIGSHLV--------------------------RRLLERGHEVV-------- 26
Query: 176 PDFKSKIHVLPCNLELRDLGLSPENKQMLISRVNIVLHGAATLRFDEDLQ---VAIQTNV 232
+I R+++V+H AA + +TNV
Sbjct: 27 ----------------------------VIDRLDVVVHLAALVGVPASWDNPDEDFETNV 58
Query: 233 RGTREVLNLAKQCPNLKMLTYVSTA 257
GT +L A++ +K Y S+A
Sbjct: 59 VGTLNLLEAARKA-GVKRFVYASSA 82
>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 = 38.4 bits (90), Expect = 0.003
Identities = 35/153 (22%), Positives = 62/153 (40%), Gaps = 32/153 (20%)
Query: 110 FYRDGEILLTGGTGFLGKLVIVKLLRSFPGIRKIYMMVRDKKGASAEERLNALFRNVIFE 169
F++ ++L+TG TGF G + + LL + + G S L+ +FE
Sbjct: 1 FWQGKKVLVTGHTGFKGSWLSLWLL----------ELGAEVYGYS----LDPPTSPNLFE 46
Query: 170 RLHLEVPDFKSKIHVLPCNLELRDLGLSPENKQMLISRVN--IVLHGAA----TLRFDED 223
L+L K ++RD + I+ IV H AA + +
Sbjct: 47 LLNLA----KKIEDHFG---DIRD----AAKLRKAIAEFKPEIVFHLAAQPLVRKSYADP 95
Query: 224 LQVAIQTNVRGTREVLNLAKQCPNLKMLTYVST 256
L+ +TNV GT +L + ++K + V++
Sbjct: 96 LE-TFETNVMGTVNLLEAIRAIGSVKAVVNVTS 127
>gnl|CDD|223528 COG0451, WcaG, Nucleoside-diphosphate-sugar epimerases [Cell
envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 314
Score = 38.0 bits (88), Expect = 0.004
Identities = 29/146 (19%), Positives = 51/146 (34%), Gaps = 35/146 (23%)
Query: 116 ILLTGGTGFLGKLVIVKLLRSFPGIRKIYMMVRDKKGASAEERLNALFRNVIFERLHLEV 175
IL+TGG GF+G ++ +LL + +R + + + L + V+ + ++
Sbjct: 3 ILVTGGAGFIGSHLVERLLAAGHDVRGL------DRLRDGLDPLLSGVEFVVLDLTDRDL 56
Query: 176 PDFKSKIHVLPCNLELRDLGLSPENKQMLISRVNIVLHGAA----TLRFDEDLQVAIQTN 231
D +K D V+H AA D + N
Sbjct: 57 VDELAKGV--------PD----------------AVIHLAAQSSVPDSNASDPAEFLDVN 92
Query: 232 VRGTREVLNLAKQCPNLKMLTYVSTA 257
V GT +L A+ K + S+
Sbjct: 93 VDGTLNLLEAARAAGV-KRFVFASSV 117
>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 = 37.8 bits (89), Expect = 0.004
Identities = 33/150 (22%), Positives = 58/150 (38%), Gaps = 35/150 (23%)
Query: 116 ILLTGGTGFLGKLVIVKLLRSFPGIRKIYMMVRDKKGASAEERLNALFRNVIFERLHLEV 175
+L+TGG G +G + ++L+ +KI + RD+ + L + +L +
Sbjct: 1 VLVTGGGGSIGSELCRQILKF--NPKKIILFSRDEFKLYEIRQ--ELRQEYNDPKLRFFI 56
Query: 176 PDFKSKIHVLPCNLELRDLGLSPENKQMLISRVNIVLHGAATLRFDEDLQV--------- 226
D + + + + M V+ V H AA L+ V
Sbjct: 57 GDVRDRERLE---------------RAMEQHGVDTVFHAAA-LK-----HVPLVEYNPME 95
Query: 227 AIQTNVRGTREVLNLAKQCPNLKMLTYVST 256
AI+TNV GT V A + ++ +ST
Sbjct: 96 AIKTNVLGTENVAEAAIEN-GVEKFVLIST 124
>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 = 37.3 bits (87), Expect = 0.005
Identities = 36/145 (24%), Positives = 58/145 (40%), Gaps = 33/145 (22%)
Query: 116 ILLTGGTGFLGKLVIVKLLRSFPGIRKIYMMVRDKKGASAEERLNALFRNVIFERLHLEV 175
IL+TGGTGF+G ++ +LL+ G I + R + + R+ F L
Sbjct: 1 ILVTGGTGFIGSHLVRRLLQE--GYEVIVLGRRRRSESLNTGRIR-------FHEGDLTD 51
Query: 176 PDFKSKIHVLPCNLELRDLGLSPENKQMLISRVNIVLHGAA---TLRFDEDLQVAIQTNV 232
PD L L + + + V+H AA ED I+ NV
Sbjct: 52 PD------------ALERL--------LAEVQPDAVIHLAAQSGVGASFEDPADFIRANV 91
Query: 233 RGTREVLNLAKQCPNLKMLTYVSTA 257
GT +L A++ +K + S++
Sbjct: 92 LGTLRLLEAARRA-GVKRFVFASSS 115
>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 = 36.6 bits (85), Expect = 0.010
Identities = 31/142 (21%), Positives = 57/142 (40%), Gaps = 28/142 (19%)
Query: 116 ILLTGGTGFLGKLVIVKLLRSFPGIRKIYMMVRDKKGASAEERLNALFRNVIFERLHLEV 175
+L+TGG+GF G+ ++ +LL Y+ D A E L+A I
Sbjct: 2 VLVTGGSGFFGERLVKQLLE----RGGTYVRSFDI--APPGEALSAWQHPNI-------- 47
Query: 176 PDFKSKIHVLPCNLELRDLGLSPENKQMLISRVNIVLHGAATLRFDEDLQVAIQTNVRGT 235
+ D+ + + +S + V H AA + + + NV GT
Sbjct: 48 -----EFLK-------GDI-TDRNDVEQALSGADCVFHTAAIVPLAGPRDLYWEVNVGGT 94
Query: 236 REVLNLAKQCPNLKMLTYVSTA 257
+ VL+ ++C ++ Y S++
Sbjct: 95 QNVLDACQRC-GVQKFVYTSSS 115
>gnl|CDD|215720 pfam00106, adh_short, short chain dehydrogenase. This family
contains a wide variety of dehydrogenases.
Length = 167
Score = 35.2 bits (82), Expect = 0.016
Identities = 33/146 (22%), Positives = 49/146 (33%), Gaps = 30/146 (20%)
Query: 114 GEILLTGGTGFLGKLVIVKLLRSFPGIRKIYMMVRDKKGASAEE---RLNALFRNVIFER 170
G +L+TGGTG LG + L G R + ++ R A E L AL V
Sbjct: 1 GTVLITGGTGGLGLALARWLAAE--GARHLVLVSRRGPAPGAAELVAELEALGAEVTVAA 58
Query: 171 LHLEVPDFKSKIHVLPCNLELRDLGLSPENKQMLISRVNIVLHGAATLR-------FDED 223
+ D L L L+ + ++ V+H A L E
Sbjct: 59 CDVADRD------------ALAAL-LAALPAALG--PLDGVVHNAGVLDDGPLEELTPER 103
Query: 224 LQVAIQTNVRGTREVLNLAKQCPNLK 249
+ + V G NL + +L
Sbjct: 104 FERVLAPKVTGAW---NLHELTRDLD 126
>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 = 35.2 bits (81), Expect = 0.029
Identities = 37/142 (26%), Positives = 61/142 (42%), Gaps = 24/142 (16%)
Query: 117 LLTGGTGFLGKLVIVKLLRSFPGIRKIYMMVRDKKGASAEERLNALFRNVIFERLHLEVP 176
L+TGG GFLG+ +I LL +++I ++ DK A +I
Sbjct: 3 LVTGGGGFLGQHIIRLLLERKEELKEIRVL--DK----------AFGPELIEHF-----E 45
Query: 177 DFKSKIHVLPCNLELRDLGLSPENKQMLISRVNIVLHGAATLRFD--EDLQVAIQTNVRG 234
+ K +V +++DL V++V+H AA + + + + NV G
Sbjct: 46 KSQGKTYVTDIEGDIKDL----SFLFRACQGVSVVIHTAAIVDVFGPPNYEELEEVNVNG 101
Query: 235 TREVLNLAKQCPNLKMLTYVST 256
T+ VL Q N+K L Y S+
Sbjct: 102 TQAVLEACVQN-NVKRLVYTSS 122
>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 = 34.5 bits (80), Expect = 0.039
Identities = 14/46 (30%), Positives = 23/46 (50%), Gaps = 3/46 (6%)
Query: 116 ILLTGGTGFLGKLVIVKLLRSFPGIRKIYMMVRDKKGASAEERLNA 161
+L+ G TG +G+ V+ +LL ++ +VRD A E A
Sbjct: 2 VLVVGATGKVGRHVVRELLDRG---YQVRALVRDPSQAEKLEAAGA 44
>gnl|CDD|187585 cd05324, carb_red_PTCR-like_SDR_c, Porcine testicular carbonyl
reductase (PTCR)-like, classical (c) SDRs. PTCR is a
classical SDR which catalyzes the NADPH-dependent
reduction of ketones on steroids and prostaglandins.
Unlike most SDRs, PTCR functions as a monomer. This
subgroup also includes human carbonyl reductase 1 (CBR1)
and CBR3. CBR1 is an NADPH-dependent SDR with broad
substrate specificity and may be responsible for the in
vivo reduction of quinones, prostaglandins, and other
carbonyl-containing compounds. In addition it includes
poppy NADPH-dependent salutaridine reductase which
catalyzes the stereospecific reduction of salutaridine
to 7(S)-salutaridinol in the biosynthesis of morphine,
and Arabidopsis SDR1,a menthone reductase, which
catalyzes the reduction of menthone to neomenthol, a
compound with antimicrobial activity; SDR1 can also
carry out neomenthol oxidation. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold
(alpha/beta folding pattern with a central beta-sheet),
an NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRs are approximately
350 residues. Sequence identity between different SDR
enzymes are typically in the 15-30% range, but the
enzymes share the Rossmann fold NAD-binding motif and
characteristic NAD-binding and catalytic sequence
patterns. These enzymes catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, 15-hydroxyprostaglandin dehydrogenase
(15-PGDH) numbering). In addition to the Tyr and Lys,
there is often an upstream Ser (Ser-138, 15-PGDH
numbering) and/or an Asn (Asn-107, 15-PGDH numbering)
contributing to the active site; while substrate binding
is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. Extended SDRs have additional
elements in the C-terminal region, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Some atypical SDRs have lost catalytic activity and/or
have an unusual NAD(P)-binding motif and missing or
unusual active site residues. Reactions catalyzed within
the SDR family include isomerization, decarboxylation,
epimerization, C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 225
Score = 33.7 bits (78), Expect = 0.072
Identities = 33/124 (26%), Positives = 58/124 (46%), Gaps = 12/124 (9%)
Query: 117 LLTGGTGFLGKLVIVKLLRSFPGIRKIYMMVRD-KKGASAEERLNALFRNVIFERLHLEV 175
L+TG +G ++ +L +S PG + + RD ++G +A E+L A +V F +L +V
Sbjct: 4 LVTGANRGIGFEIVRQLAKSGPG--TVILTARDVERGQAAVEKLRAEGLSVRFHQL--DV 59
Query: 176 PDFKSKIHVLPCNLELRDLGLSPENKQMLISRVNIVL-HGAATLRFDEDLQVAIQTNVRG 234
D S I +E + GL +L++ I + E + ++TN G
Sbjct: 60 TDDAS-IEAAADFVEEKYGGLD-----ILVNNAGIAFKGFDDSTPTREQARETMKTNFFG 113
Query: 235 TREV 238
T +V
Sbjct: 114 TVDV 117
>gnl|CDD|219957 pfam08659, KR, KR domain. This enzymatic domain is part of
bacterial polyketide synthases and catalyzes the first
step in the reductive modification of the beta-carbonyl
centres in the growing polyketide chain. It uses NADPH
to reduce the keto group to a hydroxy group.
Length = 181
Score = 32.9 bits (76), Expect = 0.12
Identities = 34/149 (22%), Positives = 50/149 (33%), Gaps = 43/149 (28%)
Query: 117 LLTGGTGFLGKLVIVKLLRSFPGIRKIYMMVRDK-KGASAEERLNALFRNVIFERLHLEV 175
L+TGG G LG + L G R + ++ R AE L L E EV
Sbjct: 4 LVTGGLGGLGLELARWLAER--GARHLVLLSRSGAPDPEAEALLAEL------EARGAEV 55
Query: 176 PDFKSKIHVLPCNLELRDLGLSPENKQM--LISRVNI-------VLHGAATLRF------ 220
V+ C++ RD + L++ + V+H A LR
Sbjct: 56 -------TVVACDVSDRD--------AVRALLAEIRADGPPLRGVIHAAGVLRDALLANM 100
Query: 221 -DEDLQVAIQTNVRGTREVLNLAKQCPNL 248
ED + V G NL + +
Sbjct: 101 TAEDFARVLAPKVTGAW---NLHEATRDR 126
>gnl|CDD|224013 COG1088, RfbB, dTDP-D-glucose 4,6-dehydratase [Cell envelope
biogenesis, outer membrane].
Length = 340
Score = 33.4 bits (77), Expect = 0.13
Identities = 33/145 (22%), Positives = 55/145 (37%), Gaps = 25/145 (17%)
Query: 116 ILLTGGTGFLGKLVIVKLLRSFPGIRKIYMMVRDKKG-ASAEERLNALFRNVIFERLHLE 174
IL+TGG GF+G + +L P + DK A E L + + + + +
Sbjct: 3 ILVTGGAGFIGSNFVRYILNKHPDDHVV---NLDKLTYAGNLENLADVEDSPRYRFVQGD 59
Query: 175 VPDFKSKIHVLPCNLELRDLGLSPENKQMLISRVNIVLHGAATLRFD---EDLQVAIQTN 231
+ D + + L + + V+H AA D + IQTN
Sbjct: 60 ICDRE----------LVDRL--------FKEYQPDAVVHFAAESHVDRSIDGPAPFIQTN 101
Query: 232 VRGTREVLNLAKQCPNLKMLTYVST 256
V GT +L A++ ++ST
Sbjct: 102 VVGTYTLLEAARKYWGKFRFHHIST 126
>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 = 33.1 bits (76), Expect = 0.15
Identities = 39/145 (26%), Positives = 56/145 (38%), Gaps = 25/145 (17%)
Query: 116 ILLTGGTGFLGKLVIVKLLRSFPGIRKIYMMVRDKKG-ASAEERLNALFRNVIFERLHLE 174
IL+TGG GF+G + +L P I V DK A E L L N R
Sbjct: 2 ILVTGGAGFIGSNFVRYILNEHPDAEVI---VLDKLTYAGNLENLADLEDN---PRYRFV 55
Query: 175 VPDFKSKIHVLPCNLELRDLGLSPENKQMLISRVNIVLHGAATLRFDEDL---QVAIQTN 231
D + EL L E+ + + V+H AA D + I+TN
Sbjct: 56 KGDI--------GDRELVS-RLFTEH------QPDAVVHFAAESHVDRSISGPAAFIETN 100
Query: 232 VRGTREVLNLAKQCPNLKMLTYVST 256
V GT +L ++ + ++ST
Sbjct: 101 VVGTYTLLEAVRKYWHEFRFHHIST 125
>gnl|CDD|187651 cd08947, NmrA_TMR_like_SDR_a, NmrA (a transcriptional regulator),
HSCARG (an NADPH sensor), and triphenylmethane reductase
(TMR) like proteins, atypical (a) SDRs. Atypical SDRs
belonging to this subgroup include NmrA, HSCARG, and
TMR, these proteins bind NAD(P) but they lack the usual
catalytic residues of the SDRs. Atypical SDRs are
distinct from classical SDRs. NmrA is a negative
transcriptional regulator of various fungi, involved in
the post-translational modulation of the GATA-type
transcription factor AreA. NmrA lacks the canonical
GXXGXXG NAD-binding motif and has altered residues at
the catalytic triad, including a Met instead of the
critical Tyr residue. NmrA may bind nucleotides but
appears to lack any dehydrogenase activity. HSCARG has
been identified as a putative NADP-sensing molecule, and
redistributes and restructures in response to NADPH/NADP
ratios. Like NmrA, it lacks most of the active site
residues of the SDR family, but has an NAD(P)-binding
motif similar to the extended SDR family, GXXGXXG. TMR,
an NADP-binding protein, lacks the active site residues
of the SDRs but has a glycine rich NAD(P)-binding motif
that matches the extended SDRs. Atypical SDRs include
biliverdin IX beta reductase (BVR-B,aka flavin
reductase), NMRa (a negative transcriptional regulator
of various fungi), progesterone 5-beta-reductase like
proteins, phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. In addition to the
Rossmann fold core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 224
Score = 31.7 bits (72), Expect = 0.32
Identities = 14/40 (35%), Positives = 21/40 (52%), Gaps = 2/40 (5%)
Query: 116 ILLTGGTGFLGKLVIVKLLRSFPGIRKIYMMVRDKKGASA 155
I +TG TG G VI LL G ++ +VR+ + A+
Sbjct: 1 IAVTGATGQQGGSVIRHLLAK--GASQVRAVVRNVEKAAT 38
>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 = 31.9 bits (73), Expect = 0.39
Identities = 37/143 (25%), Positives = 57/143 (39%), Gaps = 32/143 (22%)
Query: 117 LLTGGTGFLGKLVIVKLL-RSFPGIRKIYMMVRDKKGASAEERLNALFRNVIFERLHLEV 175
L+ GG+GFLG+ ++ +LL R P + V D E + V F H
Sbjct: 3 LVVGGSGFLGRHLVEQLLRRGNPTVH-----VFDI--RPTFELDPSSSGRVQF---HT-- 50
Query: 176 PDFKSKIHVLPCNLELRDLGLSPENKQMLISRVNIVLHGAA-TLRFDEDLQVAIQTNVRG 234
D + E N+V H A+ ++DL + NV+G
Sbjct: 51 GDLTDPQDLEKAFNE---------------KGPNVVFHTASPDHGSNDDLYYKV--NVQG 93
Query: 235 TREVLNLAKQCPNLKMLTYVSTA 257
TR V+ ++C +K L Y S+A
Sbjct: 94 TRNVIEACRKC-GVKKLVYTSSA 115
>gnl|CDD|223774 COG0702, COG0702, Predicted nucleoside-diphosphate-sugar epimerases
[Cell envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 275
Score = 31.4 bits (71), Expect = 0.48
Identities = 16/40 (40%), Positives = 24/40 (60%), Gaps = 3/40 (7%)
Query: 116 ILLTGGTGFLGKLVIVKLLRSFPGIRKIYMMVRDKKGASA 155
IL+TG TGF+G V+ +LL G + VR+ + A+A
Sbjct: 3 ILVTGATGFVGGAVVRELLAR--GHE-VRAAVRNPEAAAA 39
>gnl|CDD|187582 cd05274, KR_FAS_SDR_x, ketoreductase (KR) and fatty acid synthase
(FAS), complex (x) SDRs. Ketoreductase, a module of the
multidomain polyketide synthase (PKS), has 2 subdomains,
each corresponding to a SDR family monomer. The
C-terminal subdomain catalyzes the NADPH-dependent
reduction of the beta-carbonyl of a polyketide to a
hydroxyl group, a step in the biosynthesis of
polyketides, such as erythromycin. The N-terminal
subdomain, an interdomain linker, is a truncated
Rossmann fold which acts to stabilizes the catalytic
subdomain. Unlike typical SDRs, the isolated domain does
not oligomerize but is composed of 2 subdomains, each
resembling an SDR monomer. The active site resembles
that of typical SDRs, except that the usual positions of
the catalytic Asn and Tyr are swapped, so that the
canonical YXXXK motif changes to YXXXN. Modular PKSs are
multifunctional structures in which the makeup
recapitulates that found in (and may have evolved from)
FAS. In some instances, such as porcine FAS, an enoyl
reductase (ER) module is inserted between the
sub-domains. Fatty acid synthesis occurs via the
stepwise elongation of a chain (which is attached to
acyl carrier protein, ACP) with 2-carbon units.
Eukaryotic systems consist of large, multifunctional
synthases (type I) while bacterial, type II systems, use
single function proteins. Fungal fatty acid synthase
uses a dodecamer of 6 alpha and 6 beta subunits. In
mammalian type FAS cycles, ketoacyl synthase forms
acetoacetyl-ACP which is reduced by the NADP-dependent
beta-KR, forming beta-hydroxyacyl-ACP, which is in turn
dehydrated by dehydratase to a beta-enoyl intermediate,
which is reduced by NADP-dependent beta-ER. Polyketide
synthesis also proceeds via the addition of 2-carbon
units as in fatty acid synthesis. The complex SDR
NADP-binding motif, GGXGXXG, is often present, but is
not strictly conserved in each instance of the module.
SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold (alpha/beta folding
pattern with a central beta-sheet), an NAD(P)(H)-binding
region, and a structurally diverse C-terminal region.
Classical SDRs are typically about 250 residues long,
while extended SDRs are approximately 350 residues.
Sequence identity between different SDR enzymes are
typically in the 15-30% range, but the enzymes share the
Rossmann fold NAD-binding motif and characteristic
NAD-binding and catalytic sequence patterns. These
enzymes catalyze a wide range of activities including
the metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
prostaglandin dehydrogenase (PGDH) numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser (Ser-138, PGDH numbering) and/or an Asn (Asn-107,
PGDH numbering) contributing to the active site; while
substrate binding is in the C-terminal region, which
determines specificity. The standard reaction mechanism
is a 4-pro-S hydride transfer and proton relay involving
the conserved Tyr and Lys, a water molecule stabilized
by Asn, and nicotinamide. Extended SDRs have additional
elements in the C-terminal region, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type KRs have
a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 375
Score = 31.6 bits (72), Expect = 0.50
Identities = 33/156 (21%), Positives = 50/156 (32%), Gaps = 35/156 (22%)
Query: 117 LLTGGTGFLGKLVIVKLLRSFPGIRKIYMMVRDKKGASAEERLNALFRNVIFERLHLEVP 176
L+TGG G LG LV L G R + ++ R +G + A R + V
Sbjct: 154 LITGGLGGLGLLVARWLAAR--GARHLVLLSR--RGPAPR----AAARAALLRAGGARV- 204
Query: 177 DFKSKIHVLPCNLELRDLGLSPENKQMLISRVN------IVLHGAATLRF-------DED 223
V+ C D+ P L++ + V+H A LR
Sbjct: 205 ------SVVRC-----DVT-DPAALAALLAELAAGGPLAGVIHAAGVLRDALLAELTPAA 252
Query: 224 LQVAIQTNVRGTREVLNLAKQCPNLKMLTYVSTAFS 259
+ V G + L P L S+ +
Sbjct: 253 FAAVLAAKVAGALNLHELTPDLP-LDFFVLFSSVAA 287
>gnl|CDD|224015 COG1090, COG1090, Predicted nucleoside-diphosphate sugar epimerase
[General function prediction only].
Length = 297
Score = 30.7 bits (70), Expect = 0.84
Identities = 16/60 (26%), Positives = 29/60 (48%), Gaps = 3/60 (5%)
Query: 116 ILLTGGTGFLGKLVIVKLLRSFPGIRKIYMMVRDKKGASAEERLNALFRNVIFERLHLEV 175
IL+TGGTG +G+ + +L + G ++ ++ R AS N + + L L +
Sbjct: 1 ILITGGTGLIGRALTARLRK---GGHQVTILTRRPPKASQNLHPNVTLWEGLADALTLGI 57
>gnl|CDD|178263 PLN02657, PLN02657, 3,8-divinyl protochlorophyllide a 8-vinyl
reductase.
Length = 390
Score = 30.5 bits (69), Expect = 1.1
Identities = 21/92 (22%), Positives = 38/92 (41%), Gaps = 16/92 (17%)
Query: 113 DGEILLTGGTGFLGKLVIVKLL-RSFPGIRKIYMMVRDKKG----ASAEERLNALF-RNV 166
D +L+ G TG++GK V+ +L+ R + + + R+K G E+ L V
Sbjct: 60 DVTVLVVGATGYIGKFVVRELVRRGY----NVVAVAREKSGIRGKNGKEDTKKELPGAEV 115
Query: 167 IF------ERLHLEVPDFKSKIHVLPCNLELR 192
+F + L + + V+ L R
Sbjct: 116 VFGDVTDADSLRKVLFSEGDPVDVVVSCLASR 147
>gnl|CDD|233570 TIGR01777, yfcH, TIGR01777 family protein. This model represents a
clade of proteins of unknown function including the E.
coli yfcH protein [Hypothetical proteins, Conserved].
Length = 291
Score = 29.9 bits (68), Expect = 1.3
Identities = 11/41 (26%), Positives = 22/41 (53%), Gaps = 3/41 (7%)
Query: 116 ILLTGGTGFLGKLVIVKLLRSFPGIRKIYMMVRDKKGASAE 156
IL+TGGTGF+G+ + +L + ++ ++ R +
Sbjct: 1 ILITGGTGFIGRALTQRLTKRG---HEVTILTRSPPPGANT 38
>gnl|CDD|218047 pfam04367, DUF502, Protein of unknown function (DUF502). Predicted
to be an integral membrane protein.
Length = 108
Score = 28.6 bits (65), Expect = 1.5
Identities = 12/39 (30%), Positives = 19/39 (48%), Gaps = 5/39 (12%)
Query: 116 ILLTG--GTGFLGKLVIV---KLLRSFPGIRKIYMMVRD 149
I L G F+G+ ++ +LL P +R IY V+
Sbjct: 8 IFLVGLLARNFIGRWLLSLGERLLNRIPLVRSIYSSVKQ 46
>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 = 29.5 bits (67), Expect = 1.8
Identities = 16/55 (29%), Positives = 24/55 (43%), Gaps = 3/55 (5%)
Query: 116 ILLTGGTGFLGKLVIVKLLRSFPGIRKIYMMVRDKKGASAEERLNALFRNVIFER 170
IL+TG TG LG V+ LL + +VR+ + A A R ++
Sbjct: 1 ILVTGATGKLGTAVVELLLAKVASVV---ALVRNPEKAKAFAADGVEVRQGDYDD 52
>gnl|CDD|215146 PLN02260, PLN02260, probable rhamnose biosynthetic enzyme.
Length = 668
Score = 29.7 bits (67), Expect = 2.3
Identities = 14/40 (35%), Positives = 23/40 (57%), Gaps = 3/40 (7%)
Query: 111 YRDGEILLTGGTGFLGKLVIVKLLRSFPGIRKIYMMVRDK 150
Y IL+TG GF+ V +L+R++P + ++V DK
Sbjct: 4 YEPKNILITGAAGFIASHVANRLIRNYPDYK---IVVLDK 40
>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 = 29.2 bits (65), Expect = 2.6
Identities = 15/41 (36%), Positives = 26/41 (63%), Gaps = 2/41 (4%)
Query: 111 YRDGEILLTGGTGFLGKLVIVKLLRSFPGIRKIYMMVRDKK 151
++D +L+TGGTG G V+ + L + I++I + RD+K
Sbjct: 2 FKDKILLITGGTGSFGNAVLRRFLDT--DIKEIRIFSRDEK 40
>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 = 2.6
Identities = 32/151 (21%), Positives = 61/151 (40%), Gaps = 28/151 (18%)
Query: 110 FYRDGEILLTGGTGFLGKLVIVKLLRSFPGIRKIYMMVRDKKGASAEERLNALFRNVIFE 169
F++ +L+TG TGF G + + L + G S L+ +FE
Sbjct: 1 FWQGKRVLVTGHTGFKGSWLSLWLQE----------LGAKVIGYS----LDPPTNPNLFE 46
Query: 170 RLHLEVPDFKSKIHVLPCNLELRDLGLSPENKQMLISRVNIVLHGAAT----LRFDEDLQ 225
+L+ ++RD L+ + + IV H AA L + + ++
Sbjct: 47 LANLD----NKISSTRG---DIRD--LNALREAIREYEPEIVFHLAAQPLVRLSYKDPVE 97
Query: 226 VAIQTNVRGTREVLNLAKQCPNLKMLTYVST 256
+TNV GT +L ++ ++K + V++
Sbjct: 98 -TFETNVMGTVNLLEAIRETGSVKAVVNVTS 127
>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 = 29.2 bits (66), Expect = 2.7
Identities = 39/152 (25%), Positives = 64/152 (42%), Gaps = 46/152 (30%)
Query: 117 LLTGGTGFLGKLVIVKLLRSFPGIRKIYMMVRDKKGASAEERLNALFRNVIFERLHLEVP 176
L+TGG GFLG+ ++ LLR E L + V R E+
Sbjct: 1 LVTGGGGFLGRHIVRLLLR--------------------EGELQEV--RVFDLRFSPELL 38
Query: 177 DFKSKIHVLPCNLE--LRDLGLSPENKQML---ISRVNIVLHGAA------TLRFDEDLQ 225
+ SK+ V+ +E + D KQ L + ++V+H AA D ++
Sbjct: 39 EDFSKLQVITY-IEGDVTD-------KQDLRRALQGSDVVIHTAAIIDVFGKAYRDTIMK 90
Query: 226 VAIQTNVRGTREVLNLAKQCPNLKMLTYVSTA 257
V NV+GT+ VL+ + +++L Y S+
Sbjct: 91 V----NVKGTQNVLDACVKA-GVRVLVYTSSM 117
>gnl|CDD|181609 PRK09009, PRK09009, C factor cell-cell signaling protein;
Provisional.
Length = 235
Score = 28.9 bits (65), Expect = 3.0
Identities = 10/27 (37%), Positives = 17/27 (62%)
Query: 115 EILLTGGTGFLGKLVIVKLLRSFPGIR 141
IL+ GG+G +GK ++ +LL +P
Sbjct: 2 NILIVGGSGGIGKAMVKQLLERYPDAT 28
>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 = 28.9 bits (65), Expect = 3.0
Identities = 16/34 (47%), Positives = 22/34 (64%), Gaps = 1/34 (2%)
Query: 116 ILLTGGTGFLGKLVIVKLLRSFPGIRKIYMMVRD 149
IL+TGGTG GK I +LL ++ +KI + RD
Sbjct: 7 ILITGGTGSFGKAFISRLLENY-NPKKIIIYSRD 39
>gnl|CDD|187535 cd02266, SDR, Short-chain dehydrogenases/reductases (SDR). SDRs
are a functionally diverse family of oxidoreductases
that have a single domain with a structurally conserved
Rossmann fold (alpha/beta folding pattern with a central
beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRs are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes catalyze a
wide range of activities including the metabolism of
steroids, cofactors, carbohydrates, lipids, aromatic
compounds, and amino acids, and act in redox sensing.
Classical SDRs have an TGXXX[AG]XG cofactor binding
motif and a YXXXK active site motif, with the Tyr
residue of the active site motif serving as a critical
catalytic residue (Tyr-151, human prostaglandin
dehydrogenase (PGDH) numbering). In addition to the Tyr
and Lys, there is often an upstream Ser (Ser-138, PGDH
numbering) and/or an Asn (Asn-107, PGDH numbering)
contributing to the active site; while substrate binding
is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. Extended SDRs have additional
elements in the C-terminal region, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase (KR) domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type KRs have
a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 186
Score = 28.3 bits (63), Expect = 3.8
Identities = 23/91 (25%), Positives = 38/91 (41%), Gaps = 9/91 (9%)
Query: 191 LRDLGLSPENKQMLISRVNIVLHGAATLR-------FDEDLQVAIQTNVRGTREVLNLAK 243
R L K +++SR ++V+H AA L ++ AI+ NV GTR +L A+
Sbjct: 15 ARWLASRGSPKVLVVSRRDVVVHNAAILDDGRLIDLTGSRIERAIRANVVGTRRLLEAAR 74
Query: 244 QCPNLKMLTYV--STAFSHARSQIGEVVYEP 272
+ K L ++ + G Y
Sbjct: 75 ELMKAKRLGRFILISSVAGLFGAPGLGGYAA 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 = 28.4 bits (64), Expect = 4.0
Identities = 30/145 (20%), Positives = 57/145 (39%), Gaps = 32/145 (22%)
Query: 116 ILLTGGTGFLGKLVIVKLLRSFPGIRKIYMMVRDKKGASAEERLNALFRNVIFERLHLEV 175
I++TGG GF+G ++ L GI I V D + F+N++ L++
Sbjct: 2 IIVTGGAGFIGSNLVKALNER--GITDIL--VVDNLSNGEK------FKNLVG----LKI 47
Query: 176 PDFKSKIHVLPCNLELRDLGLSPENKQMLISRVNIVLHGAA---TLRFDEDLQVAIQTNV 232
D+ K + +D + ++ + H A T D + N
Sbjct: 48 ADYIDKD-------DFKDWVRKGDENF----KIEAIFHQGACSDTTETDGKY--MMDNNY 94
Query: 233 RGTREVLNLAKQCPNLKMLTYVSTA 257
+ T+E+L+ ++ + Y S+A
Sbjct: 95 QYTKELLHYC-LEKKIRFI-YASSA 117
>gnl|CDD|112407 pfam03588, Leu_Phe_trans, Leucyl/phenylalanyl-tRNA protein
transferase.
Length = 173
Score = 28.1 bits (63), Expect = 4.0
Identities = 21/86 (24%), Positives = 32/86 (37%), Gaps = 22/86 (25%)
Query: 62 HLQDSMETTVRKKAME-RANRS------GCTSKP----------NFQQLYRNFHAMGKRL 104
H+ S++ T+R+ + + GC +K FQ+ Y H MG
Sbjct: 40 HISKSLKKTLRQSPFRVTIDYAFEAVIEGCAAKRRNQDGTWITEEFQEAYYKLHTMGY-A 98
Query: 105 ESVEEFYRD----GEILLTGGTGFLG 126
SVE + D G + G F G
Sbjct: 99 HSVEVWRGDELVGGIYGVALGRVFFG 124
>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 = 28.8 bits (65), Expect = 4.3
Identities = 11/17 (64%), Positives = 14/17 (82%)
Query: 113 DGEILLTGGTGFLGKLV 129
DG +L+TGGTG LG L+
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 = 28.4 bits (64), Expect = 4.7
Identities = 34/131 (25%), Positives = 53/131 (40%), Gaps = 30/131 (22%)
Query: 116 ILLTGGTGFLGKLVIVKLLRSFPGIRKIYMMVRDKKGASAEERLNALFRNVIFERLHLEV 175
IL+TGG G +G + KLLR G + K A + FE L +V
Sbjct: 2 ILITGGLGQIGS-ELAKLLRKRYGKDNVIASDIRKPPAHV-------VLSGPFEYL--DV 51
Query: 176 PDFKSKIHVLPCNLELRDLGLSPENKQMLISRVNIVLHGAATL--RFDEDLQVAIQTNVR 233
DFKS ++ N ++ ++H AA L +++ +A N+
Sbjct: 52 LDFKSLEEIV-------------VNH-----KITWIIHLAALLSAVGEKNPPLAWDVNMN 93
Query: 234 GTREVLNLAKQ 244
G VL LA++
Sbjct: 94 GLHNVLELARE 104
>gnl|CDD|178567 PLN02986, PLN02986, cinnamyl-alcohol dehydrogenase family protein.
Length = 322
Score = 28.4 bits (63), Expect = 4.8
Identities = 37/144 (25%), Positives = 63/144 (43%), Gaps = 26/144 (18%)
Query: 116 ILLTGGTGFLGKLVI-VKLLRSFPGIRKIYMMVRDKKGASAEERLNALFRNVIFERLHLE 174
+ +TG +G++ ++ + LLR + + VRD E L AL + ERL L
Sbjct: 8 VCVTGASGYIASWIVKLLLLRGY----TVKATVRDLTDRKKTEHLLAL--DGAKERLKL- 60
Query: 175 VPDFKSKIHVLPCNLELRDLGLSPENKQMLISRVNIVLHGAATLRFD-EDLQVA-IQTNV 232
FK+ + L + + I + V H A+ + F +D Q I +
Sbjct: 61 ---FKADL-------------LEESSFEQAIEGCDAVFHTASPVFFTVKDPQTELIDPAL 104
Query: 233 RGTREVLNLAKQCPNLKMLTYVST 256
+GT VLN K+ P++K + S+
Sbjct: 105 KGTINVLNTCKETPSVKRVILTSS 128
>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 = 28.4 bits (64), Expect = 4.9
Identities = 7/21 (33%), Positives = 14/21 (66%)
Query: 116 ILLTGGTGFLGKLVIVKLLRS 136
+ + G TGF+G+ V+ +L +
Sbjct: 3 VTVFGATGFIGRYVVNRLAKR 23
>gnl|CDD|187660 cd08957, WbmH_like_SDR_e, Bordetella bronchiseptica enzymes WbmH
and WbmG-like, extended (e) SDRs. Bordetella
bronchiseptica enzymes WbmH and WbmG, and related
proteins. This subgroup exhibits the active site tetrad
and NAD-binding motif of the extended SDR family. It has
been proposed that the active site in Bordetella WbmG
and WbmH cannot function as an epimerase, and that it
plays a role in O-antigen synthesis pathway from
UDP-2,3-diacetamido-2,3-dideoxy-l-galacturonic acid.
Extended SDRs are distinct from classical SDRs. In
addition to the Rossmann fold (alpha/beta folding
pattern with a central beta-sheet) core region typical
of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 307
Score = 28.2 bits (63), Expect = 5.1
Identities = 17/52 (32%), Positives = 24/52 (46%), Gaps = 1/52 (1%)
Query: 211 VLHGAATLRFDEDLQVAIQTNVRGTREVLNLAKQCPNLKMLTYVSTAFSHAR 262
V+H AA + +D TNV G V+ AK+ +K L Y TA +
Sbjct: 72 VVHTAAAYKDPDDWYEDTLTNVVGGANVVQAAKKA-GVKRLIYFQTALCYGL 122
>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 = 28.1 bits (63), Expect = 5.2
Identities = 8/20 (40%), Positives = 15/20 (75%)
Query: 115 EILLTGGTGFLGKLVIVKLL 134
++ +TG TGF+G V+ +L+
Sbjct: 2 KVFVTGATGFIGSAVVRELV 21
>gnl|CDD|222146 pfam13460, NAD_binding_10, NADH(P)-binding.
Length = 182
Score = 27.7 bits (62), Expect = 5.2
Identities = 7/20 (35%), Positives = 12/20 (60%)
Query: 116 ILLTGGTGFLGKLVIVKLLR 135
I + G TG G+ ++ +LL
Sbjct: 1 IAVIGATGKTGRRLVKELLA 20
>gnl|CDD|236372 PRK09072, PRK09072, short chain dehydrogenase; Provisional.
Length = 263
Score = 28.0 bits (63), Expect = 5.3
Identities = 31/158 (19%), Positives = 62/158 (39%), Gaps = 42/158 (26%)
Query: 116 ILLTGGTGFLGKLVIVKLLRSFPGIRKIYMMVRDKKGASAEERLNALFRNVIFERLHLEV 175
+LLTG +G +G+ + L + G R + ++ R+ E+L AL L
Sbjct: 8 VLLTGASGGIGQALAEALAAA--GARLL-LVGRN------AEKLEALAA-------RLPY 51
Query: 176 PDFKSKIHVLPCNLELRDLGLSPENKQMLIS------RVNIVLHGAATLRF-------DE 222
P + DL S ++ +++ +N++++ A F E
Sbjct: 52 PG--------RHRWVVADLT-SEAGREAVLARAREMGGINVLINNAGVNHFALLEDQDPE 102
Query: 223 DLQVAIQTNVRG----TREVLNLAKQCPNLKMLTYVST 256
++ + N+ TR +L L + P+ ++ ST
Sbjct: 103 AIERLLALNLTAPMQLTRALLPLLRAQPSAMVVNVGST 140
>gnl|CDD|235657 PRK05967, PRK05967, cystathionine beta-lyase; Provisional.
Length = 395
Score = 28.2 bits (63), Expect = 5.5
Identities = 34/116 (29%), Positives = 42/116 (36%), Gaps = 19/116 (16%)
Query: 84 CTSKPNFQQLYRNFHAMGKRLESVEEFYRDGEILLTGGTGFLGKLVIVKLLRSFPG--IR 141
C + Q+ R MG RLE + + L G V+ L SFPG I
Sbjct: 243 CAGPDDTYQILRGLRTMGIRLEHHRKSALEIARWLEGRPDV--ARVLHPALPSFPGHEIW 300
Query: 142 KIYMMVRDKKGASAEERLNALFRNVIFERLHLEVPDFKSKIHVLPCNLELRDLGLS 197
K RD GAS +F V L K+K H LE+ LG S
Sbjct: 301 K-----RDFSGAS------GIFSFV----LAAGPEKGKAKAHAFLDALEIFGLGYS 341
>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 = 28.0 bits (63), Expect = 5.8
Identities = 30/145 (20%), Positives = 52/145 (35%), Gaps = 33/145 (22%)
Query: 116 ILLTGGTGFLGKLVIVKLLRSFPGIRKIYMMVRDKKGASAEERLNALFRNVIFERLHLEV 175
I++TGG GF+G ++ L GI I V D + LN + L +
Sbjct: 1 IIVTGGAGFIGSNLVKALNER--GITDIL--VVDNLR-DGHKFLN--LAD-------LVI 46
Query: 176 PDFKSKIHVLPCNLELRDLGLSPENKQMLISRVNIVLHGAA---TLRFDEDLQVAIQTNV 232
D+ K LE G ++ + H A T D + + + N
Sbjct: 47 ADYIDK-EDFLDRLEKGAFG-----------KIEAIFHQGACSDTTETDGEYMM--ENNY 92
Query: 233 RGTREVLNLAKQCPNLKMLTYVSTA 257
+ ++ +L+ + Y S+A
Sbjct: 93 QYSKRLLDWCAE--KGIPFIYASSA 115
>gnl|CDD|188267 TIGR03001, Sig-70_gmx1, RNA polymerase sigma-70 factor,
Myxococcales family 1. This group of sigma factors are
members of the sigma-70 family (TIGR02937) and are found
in multiple copies in the order Myxococcales. This model
supercedes TIGR02233, which has now been retired.
Length = 244
Score = 27.7 bits (62), Expect = 6.1
Identities = 16/45 (35%), Positives = 23/45 (51%), Gaps = 3/45 (6%)
Query: 153 ASAEERLNALFRNVIFERLHLEVPDFKSKIHVLPCNLELRDLGLS 197
A A ERL R + ERL L P+ +S + ++ L D+ LS
Sbjct: 199 AQARERLLERTRRRLAERLKLSSPELESLLGLVRSRL---DVSLS 240
>gnl|CDD|213592 TIGR01179, galE, UDP-glucose-4-epimerase GalE. Alternate name:
UDPgalactose 4-epimerase This enzyme interconverts
UDP-glucose and UDP-galactose. A set of related
proteins, some of which are tentatively identified as
UDP-glucose-4-epimerase in Thermotoga maritima, Bacillus
halodurans, and several archaea, but deeply branched
from this set and lacking experimental evidence, are
excluded from This model and described by a separate
model [Energy metabolism, Sugars].
Length = 328
Score = 27.7 bits (62), Expect = 7.3
Identities = 10/21 (47%), Positives = 15/21 (71%)
Query: 116 ILLTGGTGFLGKLVIVKLLRS 136
IL+TGG G++G + +LL S
Sbjct: 2 ILVTGGAGYIGSHTVRQLLES 22
>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 = 27.6 bits (62), Expect = 7.5
Identities = 14/43 (32%), Positives = 22/43 (51%), Gaps = 5/43 (11%)
Query: 116 ILLTGGTGFLGKLVIVKLLRS-FPGIRKIYMMVRDKKGASAEE 157
IL+ G TG+ G V+ L++ P + +VRD K A+
Sbjct: 1 ILVFGATGYQGGSVVRASLKAGHP----VRALVRDPKSELAKS 39
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.322 0.138 0.409
Gapped
Lambda K H
0.267 0.0735 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,367,668
Number of extensions: 1477653
Number of successful extensions: 1549
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1522
Number of HSP's successfully gapped: 83
Length of query: 298
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 202
Effective length of database: 6,679,618
Effective search space: 1349282836
Effective search space used: 1349282836
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 59 (26.5 bits)