RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14522
(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 = 198 bits (506), Expect = 6e-62
Identities = 77/168 (45%), Positives = 103/168 (61%), Gaps = 15/168 (8%)
Query: 131 SVFVTGGTGFMGKTLTEKLLRACPHLERVYLLVRPKKGKTVSERLDELFEDRLFSRLKAE 190
SV +TG TGF+GK L EKLLR+CP + ++YLL+R K G++ ERL EL +D+LF R +
Sbjct: 2 SVLITGATGFLGKVLLEKLLRSCPDIGKIYLLIRGKSGQSAEERLRELLKDKLFDRGRNL 61
Query: 191 VPHFRSKISVVTGDVSLPGLGLSAADRAVLRRNVTVVFHGAATVRFDENIKVAIAINIFG 250
P F SKI + GD+S P LGLS D L V ++ H AATV FDE + A++IN+ G
Sbjct: 62 NPLFESKIVPIEGDLSEPNLGLSDEDLQTLIEEVNIIIHCAATVTFDERLDEALSINVLG 121
Query: 251 S---------------FVHVSTAYTHCPRQEIDEVFYPPPYDYKDFME 283
+ FVHVSTAY + RQ I+E YPPP D + ++
Sbjct: 122 TLRLLELAKRCKKLKAFVHVSTAYVNGDRQLIEEKVYPPPADPEKLID 169
>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 = 155 bits (393), Expect = 5e-46
Identities = 63/147 (42%), Positives = 77/147 (52%), Gaps = 21/147 (14%)
Query: 134 VTGGTGFMGKTLTEKLLRACPHLERVYLLVRPKKGKTVSERL-DELFEDRLFSRLKAEVP 192
+TG TGF+GK L EKLLR+ P + ++Y LVR K G++ ERL EL + LF RLKA
Sbjct: 1 LTGATGFLGKVLLEKLLRSTPEV-KIYCLVRAKDGESALERLRQELLKYGLFDRLKA--- 56
Query: 193 HFRSKISVVTGDVSLPGLGLSAADRAVLRRNVTVVFHGAATVRFDENIKVAIAINIFG-- 250
+I V GD+S P LGLS D L V V+ H AATV F E A N+ G
Sbjct: 57 --LERIIPVAGDLSEPNLGLSDEDFQELAEEVDVIIHNAATVNFVEPYSDLRATNVLGTR 114
Query: 251 ------------SFVHVSTAYTHCPRQ 265
F HVSTAY + R
Sbjct: 115 EVLRLAKQMKKLPFHHVSTAYVNGERG 141
Score = 68.0 bits (167), Expect = 2e-13
Identities = 23/52 (44%), Positives = 33/52 (63%), Gaps = 1/52 (1%)
Query: 76 VTGGTGFMGKTLTEKLLRACPHLERVYLLVRPKKGKTVSERLDELFEDREFY 127
+TG TGF+GK L EKLLR+ P + ++Y LVR K G++ ERL + +
Sbjct: 1 LTGATGFLGKVLLEKLLRSTPEV-KIYCLVRAKDGESALERLRQELLKYGLF 51
>gnl|CDD|215538 PLN02996, PLN02996, fatty acyl-CoA reductase.
Length = 491
Score = 96.7 bits (241), Expect = 1e-22
Identities = 53/163 (32%), Positives = 84/163 (51%), Gaps = 22/163 (13%)
Query: 119 ELFEDREFYRGASVFVTGGTGFMGKTLTEKLLRACPHLERVYLLVRPKKGKTVSERL-DE 177
E +F ++ VTG TGF+ K EK+LR P+++++YLL+R K+ ++RL DE
Sbjct: 1 EEGSCVQFLENKTILVTGATGFLAKIFVEKILRVQPNVKKLYLLLRASDAKSATQRLHDE 60
Query: 178 LFEDRLFSRLK----AEVPHFRS-KISVVTGDVSLPGLGLSAAD-RAVLRRNVTVVFHGA 231
+ LF L+ + S K++ V GD+S LG+ ++ R + + + +V + A
Sbjct: 61 VIGKDLFKVLREKLGENLNSLISEKVTPVPGDISYDDLGVKDSNLREEMWKEIDIVVNLA 120
Query: 232 ATVRFDENIKVAIAINIFGS---------------FVHVSTAY 259
AT FDE VA+ IN G+ +HVSTAY
Sbjct: 121 ATTNFDERYDVALGINTLGALNVLNFAKKCVKVKMLLHVSTAY 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 = 90.1 bits (224), Expect = 5e-21
Identities = 48/150 (32%), Positives = 67/150 (44%), Gaps = 30/150 (20%)
Query: 132 VFVTGGTGFMGKTLTEKLLRACPHLERVYLLVRPKKGKTVSERLDELFEDRLFSRLKAEV 191
VFVTGGTGF+G+ L ++LL +V +LVR + ER++E
Sbjct: 1 VFVTGGTGFLGRHLVKRLLEN---GFKVLVLVRSESLGEAHERIEEA------------- 44
Query: 192 PHFRSKISVVTGDVSLPGLGLSAADRAVLRRNVTVVFHGAATVRFDENIKVAIAINIFGS 251
++ V+ GD++ P LGLSAA L V V H AA+ F + A NI G+
Sbjct: 45 GLEADRVRVLEGDLTQPNLGLSAAASRELAGKVDHVIHCAASYDFQAPNEDAWRTNIDGT 104
Query: 252 --------------FVHVSTAYTHCPRQEI 267
F +VSTAY R+
Sbjct: 105 EHVLELAARLDIQRFHYVSTAYVAGNREGN 134
Score = 45.1 bits (107), Expect = 2e-05
Identities = 21/55 (38%), Positives = 32/55 (58%), Gaps = 3/55 (5%)
Query: 74 VFVTGGTGFMGKTLTEKLLRACPHLERVYLLVRPKKGKTVSERLDELFEDREFYR 128
VFVTGGTGF+G+ L ++LL +V +LVR + ER++E + + R
Sbjct: 1 VFVTGGTGFLGRHLVKRLLEN---GFKVLVLVRSESLGEAHERIEEAGLEADRVR 52
>gnl|CDD|215279 PLN02503, PLN02503, fatty acyl-CoA reductase 2.
Length = 605
Score = 92.2 bits (229), Expect = 7e-21
Identities = 57/162 (35%), Positives = 79/162 (48%), Gaps = 21/162 (12%)
Query: 125 EFYRGASVFVTGGTGFMGKTLTEKLLRACPHLERVYLLVRPKKGKTVSERL-DELFEDRL 183
EF RG + +TG TGF+ K L EK+LR P + ++YLL++ K + ERL +E+ + L
Sbjct: 115 EFLRGKNFLITGATGFLAKVLIEKILRTNPDVGKIYLLIKAKDKEAAIERLKNEVIDAEL 174
Query: 184 FSRL-----KAEVPHFRSKISVVTGDVSLPGLGLSAADRAVLRRNVTVVFHGAATVRFDE 238
F L K+ SK+ V G+V LGL + + V V+ + AA FDE
Sbjct: 175 FKCLQETHGKSYQSFMLSKLVPVVGNVCESNLGLEPDLADEIAKEVDVIINSAANTTFDE 234
Query: 239 NIKVAIAINIFGS---------------FVHVSTAYTHCPRQ 265
VAI IN G F+ VSTAY + RQ
Sbjct: 235 RYDVAIDINTRGPCHLMSFAKKCKKLKLFLQVSTAYVNGQRQ 276
>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 = 75.5 bits (186), Expect = 2e-15
Identities = 33/105 (31%), Positives = 49/105 (46%), Gaps = 7/105 (6%)
Query: 132 VFVTGGTGFMGKTLTEKLLRACPHLERVYLLVRPKKGKTVSERLDELFEDRLFSRLKAEV 191
V +TG TGF+G L +LL +V LVR + + RL++ F+ +
Sbjct: 3 VLLTGATGFLGAYLLLELLDRSD--AKVICLVRAQSDEAALARLEKTFDLYRHWDELSA- 59
Query: 192 PHFRSKISVVTGDVSLPGLGLSAADRAVLRRNVTVVFHGAATVRF 236
++ VV GD++ P LGLS L NV ++ H AA V
Sbjct: 60 ----DRVEVVAGDLAEPDLGLSERTWQELAENVDLIIHNAALVNH 100
>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 = 72.3 bits (178), Expect = 1e-14
Identities = 44/144 (30%), Positives = 63/144 (43%), Gaps = 18/144 (12%)
Query: 131 SVFVTGGTGFMGKTLTEKLLRACPHLERVYLLVRPKKGKTVSERLDELFEDRLFSRLKAE 190
+V +TG TGF+G L +LL+ ++ ++Y LVR K + ERL + ++ +
Sbjct: 1 TVLLTGATGFLGAYLLRELLK-RKNVSKIYCLVRAKDEEAALERLIDNLKEYGLNLWDEL 59
Query: 191 VPHFRSKISVVTGDVSLPGLGLSAADRAVLRRNVTVVFHGAATVRF---DENIKVA---- 243
S+I VV GD+S P LGLS D L V V+ H A V + E +K A
Sbjct: 60 ---ELSRIKVVVGDLSKPNLGLSDDDYQELAEEVDVIIHNGANVNWVYPYEELKPANVLG 116
Query: 244 -------IAINIFGSFVHVSTAYT 260
A VST
Sbjct: 117 TKELLKLAATGKLKPLHFVSTLSV 140
>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 = 72.8 bits (179), Expect = 1e-14
Identities = 39/106 (36%), Positives = 51/106 (48%), Gaps = 5/106 (4%)
Query: 131 SVFVTGGTGFMGKTLTEKLLRACPHLERVYLLVRPKKGKTVSERLDELFEDRLFSRLKAE 190
+V +TG TGF+G L E+LLR +V LVR + ERL E +
Sbjct: 1 TVLLTGATGFLGAYLLEELLRRSTQA-KVICLVRAASEEHAMERLREALRS-YRLWHEDL 58
Query: 191 VPHFRSKISVVTGDVSLPGLGLSAADRAVLRRNVTVVFHGAATVRF 236
R +I VV GD+S P LGLS A+ L NV + H A V +
Sbjct: 59 A---RERIEVVAGDLSEPRLGLSDAEWERLAENVDTIVHNGALVNW 101
Score = 37.4 bits (87), Expect = 0.007
Identities = 20/51 (39%), Positives = 26/51 (50%), Gaps = 1/51 (1%)
Query: 73 SVFVTGGTGFMGKTLTEKLLRACPHLERVYLLVRPKKGKTVSERLDELFED 123
+V +TG TGF+G L E+LLR +V LVR + ERL E
Sbjct: 1 TVLLTGATGFLGAYLLEELLRRSTQA-KVICLVRAASEEHAMERLREALRS 50
>gnl|CDD|235962 PRK07201, PRK07201, short chain dehydrogenase; Provisional.
Length = 657
Score = 61.5 bits (150), Expect = 1e-10
Identities = 36/100 (36%), Positives = 49/100 (49%), Gaps = 17/100 (17%)
Query: 133 FVTGGTGFMGKTLTEKLLRACPHLERVYLLVRPKKGKTVSERLDELFEDRLFSRLKAEVP 192
FVTGGTGF+G+ L +LL V++LVR + RL+ L R+
Sbjct: 4 FVTGGTGFIGRRLVSRLLDRRRE-ATVHVLVRRQS----LSRLEALAAYWGADRVVP--- 55
Query: 193 HFRSKISVVTGDVSLPGLGLSAADRAVLRRNVTVVFHGAA 232
+ GD++ PGLGLS AD A L ++ V H AA
Sbjct: 56 --------LVGDLTEPGLGLSEADIAEL-GDIDHVVHLAA 86
Score = 42.6 bits (101), Expect = 2e-04
Identities = 19/49 (38%), Positives = 26/49 (53%), Gaps = 5/49 (10%)
Query: 75 FVTGGTGFMGKTLTEKLLRACPHLERVYLLVRPKKGKTVSERLDELFED 123
FVTGGTGF+G+ L +LL V++LVR + RL+ L
Sbjct: 4 FVTGGTGFIGRRLVSRLLDRRRE-ATVHVLVRRQS----LSRLEALAAY 47
>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 = 51.6 bits (124), Expect = 2e-07
Identities = 39/131 (29%), Positives = 59/131 (45%), Gaps = 9/131 (6%)
Query: 108 KKGKTVSERLDELFEDREFYRGAS---VFVTGGTGFMGKTLTEKLL-RACPHLERVYLLV 163
K KT+ + L + + R+ ++ VF+TG TGF+G + LL R +V+ V
Sbjct: 947 KDAKTLVDSLPKSYPSRKELDASTPITVFLTGATGFLGSFILRDLLTRRSNSNFKVFAHV 1006
Query: 164 RPKKGKTVSERLDELFEDRLFSRLKAEVPHFRSKISVVTGDVSLPGLGLSAADRAVLRRN 223
R K + ERL + + + S+I VV GD+S GLS + L
Sbjct: 1007 RAKSEEAGLERLRKTGTTYGIWDEE-----WASRIEVVLGDLSKEKFGLSDEKWSDLTNE 1061
Query: 224 VTVVFHGAATV 234
V V+ H A V
Sbjct: 1062 VDVIIHNGALV 1072
Score = 34.3 bits (79), Expect = 0.087
Identities = 18/45 (40%), Positives = 24/45 (53%), Gaps = 1/45 (2%)
Query: 74 VFVTGGTGFMGKTLTEKLL-RACPHLERVYLLVRPKKGKTVSERL 117
VF+TG TGF+G + LL R +V+ VR K + ERL
Sbjct: 974 VFLTGATGFLGSFILRDLLTRRSNSNFKVFAHVRAKSEEAGLERL 1018
>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 = 50.4 bits (121), Expect = 4e-07
Identities = 37/161 (22%), Positives = 51/161 (31%), Gaps = 47/161 (29%)
Query: 132 VFVTGGTGFMGKTLTEKLLRACPHLERVYLLVRPKKGKTVSERLDELFEDRLFSRLKAEV 191
+ VTG TGF+G L LL RV LVR L
Sbjct: 1 ILVTGATGFLGSNLVRALLAQG---YRVRALVRSG------SDAVLLDGLP--------- 42
Query: 192 PHFRSKISVVTGDVSLPGLGLSAADRAVLRRNVTVVFHGAATVRF-DENIKVAIAINIFG 250
+ VV GD++ ++ A+ + VFH AA ++ K N+ G
Sbjct: 43 ------VEVVEGDLTDA----ASLAAAM--KGCDRVFHLAAFTSLWAKDRKELYRTNVEG 90
Query: 251 S--------------FVHVST--AYTHCPRQEIDEVFYPPP 275
+ VH S+ A P IDE
Sbjct: 91 TRNVLDAALEAGVRRVVHTSSIAALGGPPDGRIDETTPWNE 131
Score = 39.2 bits (92), Expect = 0.002
Identities = 15/35 (42%), Positives = 17/35 (48%), Gaps = 3/35 (8%)
Query: 74 VFVTGGTGFMGKTLTEKLLRACPHLERVYLLVRPK 108
+ VTG TGF+G L LL RV LVR
Sbjct: 1 ILVTGATGFLGSNLVRALLAQG---YRVRALVRSG 32
>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 = 41.8 bits (99), Expect = 2e-04
Identities = 35/126 (27%), Positives = 57/126 (45%), Gaps = 22/126 (17%)
Query: 129 GASVFVTGGTGFMGKTLTEKLLRACPHLERVYLLVRPKKGKTVSERLDELFEDRLFSRLK 188
G ++ VTGG G +G L ++L+ P +++ + R + L EL + L+
Sbjct: 2 GKTILVTGGAGSIGSELVRQILKFGP--KKLIVFDRDENK------LHELVRE-----LR 48
Query: 189 AEVPHFRSKISVVTGDVSLPGLGLSAADRAVLRRNVTVVFHGAAT--VRF-DENIKVAIA 245
+ PH K+ + GDV RA R +VFH AA V ++N + AI
Sbjct: 49 SRFPH--DKLRFIIGDVR----DKERLRRAFKERGPDIVFHAAALKHVPSMEDNPEEAIK 102
Query: 246 INIFGS 251
N+ G+
Sbjct: 103 TNVLGT 108
Score = 32.2 bits (74), Expect = 0.24
Identities = 10/26 (38%), Positives = 16/26 (61%)
Query: 71 GASVFVTGGTGFMGKTLTEKLLRACP 96
G ++ VTGG G +G L ++L+ P
Sbjct: 2 GKTILVTGGAGSIGSELVRQILKFGP 27
>gnl|CDD|187567 cd05257, Arna_like_SDR_e, Arna decarboxylase_like, extended (e)
SDRs. Decarboxylase domain of ArnA. ArnA, is an enzyme
involved in the modification of outer membrane protein
lipid A of gram-negative bacteria. It is a bifunctional
enzyme that catalyzes the NAD-dependent decarboxylation
of UDP-glucuronic acid and
N-10-formyltetrahydrofolate-dependent formylation of
UDP-4-amino-4-deoxy-l-arabinose; its NAD-dependent
decaboxylating activity is in the C-terminal 360
residues. This subgroup belongs to the extended SDR
family, however the NAD binding motif is not a perfect
match and the upstream Asn of the canonical active site
tetrad is not conserved. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately 100
amino acids. Extended SDRs are a diverse collection of
proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 316
Score = 40.4 bits (95), Expect = 7e-04
Identities = 37/158 (23%), Positives = 52/158 (32%), Gaps = 44/158 (27%)
Query: 131 SVFVTGGTGFMGKTLTEKLLRACPHLERVYLLVRPKKGKTVSERLDELFEDRLFSRLKAE 190
+V VTG GF+G LTE+LLR V L + D
Sbjct: 1 NVLVTGADGFIGSHLTERLLREGHE---VRALDI------YNSFNSWGLLD--------- 42
Query: 191 VPHFRSKISVVTGDVSLPGLGLSAADRAVLRRNVTVVFHGAATVRFDENIKVA---IAIN 247
+ ++GDV + V + VVFH AA + + + N
Sbjct: 43 -NAVHDRFHFISGDVRDASEV----EYLV--KKCDVVFHLAALIAIPYSYTAPLSYVETN 95
Query: 248 IFGS--------------FVHVSTA--YTHCPRQEIDE 269
+FG+ VH ST+ Y IDE
Sbjct: 96 VFGTLNVLEAACVLYRKRVVHTSTSEVYGTAQDVPIDE 133
Score = 33.0 bits (76), Expect = 0.13
Identities = 13/21 (61%), Positives = 16/21 (76%)
Query: 73 SVFVTGGTGFMGKTLTEKLLR 93
+V VTG GF+G LTE+LLR
Sbjct: 1 NVLVTGADGFIGSHLTERLLR 21
>gnl|CDD|163279 TIGR03466, HpnA, hopanoid-associated sugar epimerase. The
sequences in this family are members of the pfam01370
superfamily of NAD-dependent epimerases and dehydratases
typically acting on nucleotide-sugar substrates. The
genes of the family modeled here are generally in the
same locus with genes involved in the biosynthesis and
elaboration of hopene, the cyclization product of the
polyisoprenoid squalene. This gene and its association
with hopene biosynthesis in Zymomonas mobilis has been
noted in the literature where the gene symbol hpnA was
assigned. Hopanoids are known to be components of the
plasma membrane and to have polar sugar head groups in
Z. mobilis and other species.
Length = 328
Score = 40.0 bits (94), Expect = 0.001
Identities = 33/107 (30%), Positives = 42/107 (39%), Gaps = 36/107 (33%)
Query: 132 VFVTGGTGFMGKTLTEKLLRACPHLERVYLLVRPKKGKTVSERLDELFEDRLFSRLKAEV 191
V VTG TGF+G + LL E V +LVRP S+R + L E
Sbjct: 3 VLVTGATGFVGSAVVRLLLEQG---EEVRVLVRPT-----SDRRN-------LEGLDVE- 46
Query: 192 PHFRSKISVVTGDVSLPGLGLSAADRAVLRRNVT---VVFHGAATVR 235
+V GD+ D A LR+ V +FH AA R
Sbjct: 47 --------IVEGDL---------RDPASLRKAVAGCRALFHVAADYR 76
Score = 34.6 bits (80), Expect = 0.055
Identities = 24/62 (38%), Positives = 29/62 (46%), Gaps = 8/62 (12%)
Query: 74 VFVTGGTGFMGKTLTEKLLRACPHLERVYLLVRPKKGKTVSERLD-ELFE----DREFYR 128
V VTG TGF+G + LL E V +LVRP + E LD E+ E D R
Sbjct: 3 VLVTGATGFVGSAVVRLLLEQG---EEVRVLVRPTSDRRNLEGLDVEIVEGDLRDPASLR 59
Query: 129 GA 130
A
Sbjct: 60 KA 61
>gnl|CDD|221970 pfam13191, AAA_16, AAA ATPase domain. This family of domains
contain a P-loop motif that is characteristic of the AAA
superfamily.
Length = 154
Score = 38.3 bits (89), Expect = 0.001
Identities = 29/117 (24%), Positives = 42/117 (35%), Gaps = 5/117 (4%)
Query: 115 ERLDELFEDREFYRGASVFVTGGTGFMGKT-LTEKLLRACPHLERVYLLVRPKKGKTVSE 173
ERL + SV +TG +G GKT L +LL S+
Sbjct: 10 ERLLDALRRARSGGPPSVLLTGPSG-TGKTSLLRELLEGLLVAAGKCDQAERNPPYAFSQ 68
Query: 174 RLDELFEDRLFSRLKAEVPHFRSKISVVTGDVSLPGL--GLSAADRAVLRRNVTVVF 228
L EL +L L AE+ R + G + GL + +R + R V+
Sbjct: 69 ALRELLR-QLLRELAAELLLLREALLAALGAELIEGLQDLVELLERLLARARPLVLV 124
>gnl|CDD|224011 COG1086, COG1086, Predicted nucleoside-diphosphate sugar epimerases
[Cell envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 588
Score = 39.2 bits (92), Expect = 0.002
Identities = 36/137 (26%), Positives = 52/137 (37%), Gaps = 36/137 (26%)
Query: 124 REFYRGASVFVTGGTGFMGKTLTEKLLRACPHLERVYLLVRPKKGKTVSERLDELFEDRL 183
G +V VTGG G +G L ++L+ P + + L R DE +
Sbjct: 245 GAMLTGKTVLVTGGGGSIGSELCRQILKFNP--KEIILFSR-----------DEYKLYLI 291
Query: 184 FSRLKAEVPHFRSKISVVTGDVSLPGLGLSAADRAVLRR-----NVTVVFHGAA-----T 233
L+ + P K+ GDV DR + R V +VFH AA
Sbjct: 292 DMELREKFPE--LKLRFYIGDV---------RDRDRVERAMEGHKVDIVFHAAALKHVPL 340
Query: 234 VRFDENIKVAIAINIFG 250
V + N + AI N+ G
Sbjct: 341 VEY--NPEEAIKTNVLG 355
Score = 36.9 bits (86), Expect = 0.011
Identities = 17/55 (30%), Positives = 24/55 (43%), Gaps = 8/55 (14%)
Query: 39 IDPFELLGENSFGKPRVVPPDEVGSPIQEFYRGASVFVTGGTGFMGKTLTEKLLR 93
I+ +LLG V D I G +V VTGG G +G L ++L+
Sbjct: 226 IEIEDLLGRPP------VALDT--ELIGAMLTGKTVLVTGGGGSIGSELCRQILK 272
>gnl|CDD|223528 COG0451, WcaG, Nucleoside-diphosphate-sugar epimerases [Cell
envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 314
Score = 38.8 bits (90), Expect = 0.002
Identities = 36/164 (21%), Positives = 52/164 (31%), Gaps = 51/164 (31%)
Query: 132 VFVTGGTGFMGKTLTEKLLRACPHLERVYLLVRPKKGKTVSERLDELFEDRLFSRLKAEV 191
+ VTGG GF+G L E+LL A G V R RL+ +
Sbjct: 3 ILVTGGAGFIGSHLVERLLAA---------------GHDV----------RGLDRLRDGL 37
Query: 192 PHFRSKISVVTGDVSLPGLGLSAADRAVLRRNVTVVFHGAATVRF----DENIKVAIAIN 247
S + V D++ + + V H AA + + +N
Sbjct: 38 DPLLSGVEFVVLDLTDR-----DLVDELAKGVPDAVIHLAAQSSVPDSNASDPAEFLDVN 92
Query: 248 IFGS--------------FVHVSTA---YTHCPRQEIDEVFYPP 274
+ G+ FV S+ Y P IDE PP
Sbjct: 93 VDGTLNLLEAARAAGVKRFVFASSVSVVYGDPPPLPIDEDLGPP 136
Score = 36.8 bits (85), Expect = 0.008
Identities = 20/56 (35%), Positives = 25/56 (44%), Gaps = 9/56 (16%)
Query: 74 VFVTGGTGFMGKTLTEKLLRACPHLERVYLLVRPKKGKTVSERLDELFEDREFYRG 129
+ VTGG GF+G L E+LL A V L R + + LD L EF
Sbjct: 3 ILVTGGAGFIGSHLVERLLAAG---HDVRGLDR------LRDGLDPLLSGVEFVVL 49
>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 = 38.2 bits (90), Expect = 0.003
Identities = 40/150 (26%), Positives = 54/150 (36%), Gaps = 50/150 (33%)
Query: 132 VFVTGGTGFMGKTLTEKLLRACPHLERVYLLVRPKKGKTVSERLDELFEDRLFSRLKAEV 191
V VTGG G +G L ++L+ P +++ L R DE + L+ E
Sbjct: 1 VLVTGGGGSIGSELCRQILKFNP--KKIILFSR-----------DEFKLYEIRQELRQEY 47
Query: 192 PHFRSKISVVTGDVSLPGLGLSAADRAVLRR-----NVTVVFHGAA-----TVRFDENIK 241
K+ GDV DR L R V VFH AA V + N
Sbjct: 48 ND--PKLRFFIGDV---------RDRERLERAMEQHGVDTVFHAAALKHVPLVEY--NPM 94
Query: 242 VAIAINIFGS--------------FVHVST 257
AI N+ G+ FV +ST
Sbjct: 95 EAIKTNVLGTENVAEAAIENGVEKFVLIST 124
Score = 27.4 bits (62), Expect = 9.3
Identities = 9/20 (45%), Positives = 13/20 (65%)
Query: 74 VFVTGGTGFMGKTLTEKLLR 93
V VTGG G +G L ++L+
Sbjct: 1 VLVTGGGGSIGSELCRQILK 20
>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 = 34/169 (20%), Positives = 53/169 (31%), Gaps = 51/169 (30%)
Query: 132 VFVTGGTGFMGKTLTEKLLRACPHLERVYLLVRPKKGKTVSERLDELFEDRLFSRLKAEV 191
+ VTGGTGF+G L +LL ++G V + R +
Sbjct: 1 ILVTGGTGFIGSHLVRRLL---------------QEGYEV----------IVLGRRRRSE 35
Query: 192 PHFRSKISVVTGDVSLPGLGLSAADRAVLRRNVTVVFHGAATVRFDENIK---------V 242
+I GD++ P A +R + V H AA + + V
Sbjct: 36 SLNTGRIRFHEGDLTDP----DALERLLAEVQPDAVIHLAAQSGVGASFEDPADFIRANV 91
Query: 243 AIAINIFGS--------FVHVSTA--YTHCPRQEIDE--VFYPP-PYDY 278
+ + + FV S++ Y I E P PY
Sbjct: 92 LGTLRLLEAARRAGVKRFVFASSSEVYGDVADPPITEDTPLGPLSPYAA 140
Score = 31.9 bits (73), Expect = 0.26
Identities = 11/21 (52%), Positives = 15/21 (71%)
Query: 74 VFVTGGTGFMGKTLTEKLLRA 94
+ VTGGTGF+G L +LL+
Sbjct: 1 ILVTGGTGFIGSHLVRRLLQE 21
>gnl|CDD|215720 pfam00106, adh_short, short chain dehydrogenase. This family
contains a wide variety of dehydrogenases.
Length = 167
Score = 36.4 bits (85), Expect = 0.007
Identities = 31/140 (22%), Positives = 46/140 (32%), Gaps = 41/140 (29%)
Query: 131 SVFVTGGTGFMGKTLTEKLLRACPHLERVYLLVRPKKGKTVSERLDELFEDRLFSRLKAE 190
+V +TGGTG +G L L + L+ R +E + EL L AE
Sbjct: 2 TVLITGGTGGLGLALARWLAAEGA--RHLVLVSRRGPAPGAAELVAEL------EALGAE 53
Query: 191 VPHFRSKISVVTGDVSLPGLGLSAADRAVLRR----------NVTVVFHGAATVR----- 235
V +V DV ADR L + V H A +
Sbjct: 54 V-------TVAACDV---------ADRDALAALLAALPAALGPLDGVVHNAGVLDDGPLE 97
Query: 236 --FDENIKVAIAINIFGSFV 253
E + +A + G++
Sbjct: 98 ELTPERFERVLAPKVTGAWN 117
>gnl|CDD|200431 TIGR04180, EDH_00030, NAD dependent epimerase/dehydratase,
LLPSF_EDH_00030 family. This clade within the NAD
dependent epimerase/dehydratase superfamily (pfam01370)
is characterized by inclusion of its members within a
cassette of seven distinctive enzymes. These include
four genes homologous to the elements of the neuraminic
(sialic) acid biosynthesis cluster (NeuABCD), an
aminotransferase and a nucleotidyltransferase in
addition to the epimerase/dehydratase. Together it is
very likely that these enzymes direct the biosynthesis
of a nine-carbon sugar analagous to CMP-neuraminic acid.
These seven genes form the core of the cassette,
although they are often accompanied by additional genes
that may further modify the product sugar. Although this
cassette is widely distributed in bacteria, the family
nomenclature arises from the instance in Leptospira
interrogans serovar Lai, str. 56601, where it appears as
the 30th gene in the 91-gene lipopolysaccharide
biosynthesis cluster.
Length = 297
Score = 36.5 bits (85), Expect = 0.012
Identities = 32/110 (29%), Positives = 38/110 (34%), Gaps = 40/110 (36%)
Query: 132 VFVTGGTGFMGKTLTEKLLRACPHLERVYLLVRPKKGKTVSERLDELFEDRLFSR----- 186
V VTG GF+G L E L+R +G V R F
Sbjct: 1 VLVTGADGFIGSHLVEALVR---------------QGYEV----------RAFVLYNSFN 35
Query: 187 ----LKAEVPHFRSKISVVTGDVSLPGLGLSAADRAVLRRNVTVVFHGAA 232
L P + KI VVTGD+ P A + VVFH AA
Sbjct: 36 SWGWLDTSPPEVKDKIEVVTGDIRDPDSVRKAM------KGCDVVFHLAA 79
Score = 31.5 bits (72), Expect = 0.52
Identities = 11/21 (52%), Positives = 13/21 (61%)
Query: 74 VFVTGGTGFMGKTLTEKLLRA 94
V VTG GF+G L E L+R
Sbjct: 1 VLVTGADGFIGSHLVEALVRQ 21
>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 = 35.1 bits (81), Expect = 0.021
Identities = 26/107 (24%), Positives = 39/107 (36%), Gaps = 30/107 (28%)
Query: 132 VFVTGGTGFMGKTLTEKLLRACPHLERVYLLVRPKKGKTVSERLDELFEDRLFSRLKAEV 191
+ + G TGF+G+ L +LL V LLVR K RL + ++
Sbjct: 1 ILILGATGFIGRALARELLEQG---HEVTLLVRNTK------RLSKEDQEP--------- 42
Query: 192 PHFRSKISVVTGDVSLPGLGLSAADRAVLRRNVTVVFHGAATVRFDE 238
++VV GD+ + + V VV H A R
Sbjct: 43 ------VAVVEGDL------RDLDSLSDAVQGVDVVIHLAGAPRDTR 77
Score = 31.2 bits (71), Expect = 0.40
Identities = 16/52 (30%), Positives = 24/52 (46%), Gaps = 5/52 (9%)
Query: 74 VFVTGGTGFMGKTLTEKLLRACPHLERVYLLVR--PKKGKTVSERLDELFED 123
+ + G TGF+G+ L +LL V LLVR + K E + + D
Sbjct: 1 ILILGATGFIGRALARELLEQG---HEVTLLVRNTKRLSKEDQEPVAVVEGD 49
>gnl|CDD|233895 TIGR02494, PFLE_PFLC, glycyl-radical enzyme activating protein
family. This subset of the radical-SAM family
(pfam04055) includes a number of probable activating
proteins acting on different enzymes all requiring an
amino-acid-centered radical. The closest relatives to
this family are the pyruvate-formate lyase activating
enzyme (PflA, 1.97.1.4, TIGR02493) and the anaerobic
ribonucleotide reductase activating enzyme (TIGR02491).
Included within this subfamily are activators of
hydroxyphenyl acetate decarboxylase (HdpA, ),
benzylsuccinate synthase (BssD, ), gycerol dehydratase
(DhaB2,) as well as enzymes annotated in E. coli as
activators of different isozymes of pyruvate-formate
lyase (PFLC and PFLE) however, these appear to lack
characterization and may activate enzymes with
distinctive functions. Most of the sequence-level
variability between these forms is concentrated within
an N-terminal domain which follows a conserved group of
three cysteines and contains a variable pattern of 0 to
8 additional cysteines.
Length = 295
Score = 35.4 bits (82), Expect = 0.024
Identities = 15/45 (33%), Positives = 21/45 (46%), Gaps = 2/45 (4%)
Query: 111 KTVSERLDELFEDREFYR--GASVFVTGGTGFMGKTLTEKLLRAC 153
TV E + + D FYR G V ++GG + LL+AC
Sbjct: 106 MTVEEVMRVVLRDSIFYRNSGGGVTLSGGEPLLQPEFALALLQAC 150
>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 = 35.3 bits (82), Expect = 0.030
Identities = 16/48 (33%), Positives = 24/48 (50%), Gaps = 5/48 (10%)
Query: 74 VFVTGGTGFMGKTLTEKLLRACPHLERVYLLVR--PKKGKTVSERLDE 119
+ +TGGTGF+G+ LT++L + V +L R P T E
Sbjct: 1 ILITGGTGFIGRALTQRLTKRG---HEVTILTRSPPPGANTKWEGYKP 45
Score = 35.3 bits (82), Expect = 0.030
Identities = 16/48 (33%), Positives = 24/48 (50%), Gaps = 5/48 (10%)
Query: 132 VFVTGGTGFMGKTLTEKLLRACPHLERVYLLVR--PKKGKTVSERLDE 177
+ +TGGTGF+G+ LT++L + V +L R P T E
Sbjct: 1 ILITGGTGFIGRALTQRLTKRG---HEVTILTRSPPPGANTKWEGYKP 45
>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 = 34.6 bits (80), Expect = 0.033
Identities = 12/33 (36%), Positives = 17/33 (51%), Gaps = 3/33 (9%)
Query: 74 VFVTGGTGFMGKTLTEKLLRACPHLERVYLLVR 106
+ VTGG GF+G L +LL V ++ R
Sbjct: 1 ILVTGGAGFIGSHLVRRLLERG---HEVVVIDR 30
Score = 34.6 bits (80), Expect = 0.033
Identities = 12/33 (36%), Positives = 17/33 (51%), Gaps = 3/33 (9%)
Query: 132 VFVTGGTGFMGKTLTEKLLRACPHLERVYLLVR 164
+ VTGG GF+G L +LL V ++ R
Sbjct: 1 ILVTGGAGFIGSHLVRRLLERG---HEVVVIDR 30
Score = 27.6 bits (62), Expect = 6.5
Identities = 16/70 (22%), Positives = 24/70 (34%), Gaps = 17/70 (24%)
Query: 223 NVTVVFHGAATVRFDE---NIKVAIAINIFGS--------------FVHVSTAYTHCPRQ 265
+ VV H AA V N N+ G+ FV+ S+A + +
Sbjct: 30 RLDVVVHLAALVGVPASWDNPDEDFETNVVGTLNLLEAARKAGVKRFVYASSASVYGSPE 89
Query: 266 EIDEVFYPPP 275
+ E PP
Sbjct: 90 GLPEEEETPP 99
>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 = 34.6 bits (80), Expect = 0.046
Identities = 34/133 (25%), Positives = 44/133 (33%), Gaps = 36/133 (27%)
Query: 126 FYRGASVFVTGGTGFMGKTLTEKLLRACPHLERVYLLVRPKKGKTVSERLDELFEDRLFS 185
F++G V VTG TGF G L+ L V LF
Sbjct: 1 FWQGKRVLVTGHTGFKGSWLSLWLQELGAK---VIGYSLDPPTN------PNLF------ 45
Query: 186 RLKAEVPHFRSKISVVTGDVSLPGLGLSAADRAVLRRNVT-----VVFHGAAT--VRFDE 238
E+ + +KIS GD+ D LR + +VFH AA VR
Sbjct: 46 ----ELANLDNKISSTRGDIR---------DLNALREAIREYEPEIVFHLAAQPLVRLSY 92
Query: 239 NIKVA-IAINIFG 250
V N+ G
Sbjct: 93 KDPVETFETNVMG 105
Score = 33.1 bits (76), Expect = 0.14
Identities = 12/25 (48%), Positives = 15/25 (60%)
Query: 68 FYRGASVFVTGGTGFMGKTLTEKLL 92
F++G V VTG TGF G L+ L
Sbjct: 1 FWQGKRVLVTGHTGFKGSWLSLWLQ 25
>gnl|CDD|187538 cd05227, AR_SDR_e, aldehyde reductase, extended (e) SDRs. This
subgroup contains aldehyde reductase of the extended
SDR-type and related proteins. Aldehyde reductase I (aka
carbonyl reductase) is an NADP-binding SDR; it has an
NADP-binding motif consensus that is slightly different
from the canonical SDR form and lacks the Asn of the
extended SDR active site tetrad. Aldehyde reductase I
catalyzes the NADP-dependent reduction of ethyl
4-chloro-3-oxobutanoate to ethyl
(R)-4-chloro-3-hydroxybutanoate. Extended SDRs are
distinct from classical SDRs. In addition to the
Rossmann fold (alpha/beta folding pattern with a central
beta-sheet) core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids. Extended SDRs are a
diverse collection of proteins, and include isomerases,
epimerases, oxidoreductases, and lyases; they typically
have a TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 301
Score = 34.6 bits (80), Expect = 0.054
Identities = 35/127 (27%), Positives = 52/127 (40%), Gaps = 31/127 (24%)
Query: 132 VFVTGGTGFMGKTLTEKLLRACPHLERVYLLVRPKKGKTVSERLDELF-EDRLFSRLKAE 190
V VTG TGF+ + E+LL+A +V VR + S +L L RL
Sbjct: 2 VLVTGATGFIASHIVEQLLKAG---YKVRGTVR---SLSKSAKLKALLKAAGYNDRL--- 52
Query: 191 VPHFRSKISVVTGDVSLPGLGLSAADRAVLRRNVTVVFHGAATVRF------DENIKVAI 244
F V+ D++ P A D A+ + V V H A+ F D+ I A+
Sbjct: 53 --EF-----VIVDDLTAPN----AWDEAL--KGVDYVIHVASPFPFTGPDAEDDVIDPAV 99
Query: 245 --AINIF 249
+N+
Sbjct: 100 EGTLNVL 106
Score = 29.5 bits (67), Expect = 2.1
Identities = 11/21 (52%), Positives = 15/21 (71%)
Query: 74 VFVTGGTGFMGKTLTEKLLRA 94
V VTG TGF+ + E+LL+A
Sbjct: 2 VLVTGATGFIASHIVEQLLKA 22
>gnl|CDD|187560 cd05250, CC3_like_SDR_a, CC3(TIP30)-like, atypical (a) SDRs.
Atypical SDRs in this subgroup include CC3 (also known
as TIP30) which is implicated in tumor suppression.
Atypical SDRs are distinct from classical SDRs. Members
of this subgroup have a glycine rich NAD(P)-binding
motif that resembles the extended SDRs, and have an
active site triad of the SDRs (YXXXK and upstream Ser),
although the upstream Asn of the usual SDR active site
is substituted with Asp. For CC3, the Tyr of the triad
is displaced compared to the usual SDRs and the protein
is monomeric, both these observations suggest that the
usual SDR catalytic activity is not present. NADP
appears to serve an important role as a ligand, and may
be important in the interaction with other
macromolecules. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and their
glycine-rich NAD(P)-binding motif is often different
from the forms normally seen in classical or extended
SDRs. Atypical SDRs include biliverdin IX beta reductase
(BVR-B,aka flavin reductase), NMRa (a negative
transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. In addition to the
Rossmann fold core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 214
Score = 33.8 bits (78), Expect = 0.062
Identities = 21/69 (30%), Positives = 36/69 (52%), Gaps = 6/69 (8%)
Query: 131 SVFVTGGTGFMGKTLTEKLLRACPHLERVYLLVRPKKG--KTVSERLDELFEDRLFSRLK 188
+ V G TG +GK L +LL++ P+ +V +VR +K E+L ++ D F RL
Sbjct: 2 TALVLGATGLVGKHLLRELLKS-PYYSKVTAIVR-RKLTFPEAKEKLVQIVVD--FERLD 57
Query: 189 AEVPHFRSK 197
+ F++
Sbjct: 58 EYLEAFQNP 66
Score = 30.7 bits (70), Expect = 0.73
Identities = 13/34 (38%), Positives = 21/34 (61%), Gaps = 1/34 (2%)
Query: 73 SVFVTGGTGFMGKTLTEKLLRACPHLERVYLLVR 106
+ V G TG +GK L +LL++ P+ +V +VR
Sbjct: 2 TALVLGATGLVGKHLLRELLKS-PYYSKVTAIVR 34
>gnl|CDD|236372 PRK09072, PRK09072, short chain dehydrogenase; Provisional.
Length = 263
Score = 33.8 bits (78), Expect = 0.074
Identities = 34/132 (25%), Positives = 52/132 (39%), Gaps = 36/132 (27%)
Query: 129 GASVFVTGGTGFMGKTLTEKLLRACPHLERVYLLVRPKKGKTVSERLDELFEDRLFSRLK 188
V +TG +G +G+ L E L A L LLV G+ +E+L+ L
Sbjct: 5 DKRVLLTGASGGIGQALAEALAAAGARL----LLV----GRN-AEKLE---------ALA 46
Query: 189 AEVPHFRSKISVVTGDVSLPGLGLSAADRAVLRR-----NVTVVFHGAATVRF------- 236
A +P+ + V D L A AVL R + V+ + A F
Sbjct: 47 ARLPY-PGRHRWVVAD-----LTSEAGREAVLARAREMGGINVLINNAGVNHFALLEDQD 100
Query: 237 DENIKVAIAINI 248
E I+ +A+N+
Sbjct: 101 PEAIERLLALNL 112
>gnl|CDD|187566 cd05256, UDP_AE_SDR_e, UDP-N-acetylglucosamine 4-epimerase,
extended (e) SDRs. This subgroup contains
UDP-N-acetylglucosamine 4-epimerase of Pseudomonas
aeruginosa, WbpP, an extended SDR, that catalyzes the
NAD+ dependent conversion of UDP-GlcNAc and UDPGalNA to
UDP-Glc and UDP-Gal. This subgroup has the
characteristic active site tetrad and NAD-binding motif
of the extended SDRs. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately 100
amino acids. Extended SDRs are a diverse collection of
proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 304
Score = 33.3 bits (77), Expect = 0.11
Identities = 26/101 (25%), Positives = 35/101 (34%), Gaps = 27/101 (26%)
Query: 132 VFVTGGTGFMGKTLTEKLLRACPHLERVYLLVRPKKGKTVSERLDELFEDRLFSRLKAEV 191
V VTGG GF+G L E+LL V +L D L + K +
Sbjct: 2 VLVTGGAGFIGSHLVERLLERG---HEVIVL------------------DNLSTGKKENL 40
Query: 192 PHFRSKISVVTGDVSLPGLGLSAADRAVLRRNVTVVFHGAA 232
P + + + GD+ V VFH AA
Sbjct: 41 PEVKPNVKFIEGDIR------DDELVEFAFEGVDYVFHQAA 75
Score = 29.9 bits (68), Expect = 1.3
Identities = 12/20 (60%), Positives = 14/20 (70%)
Query: 74 VFVTGGTGFMGKTLTEKLLR 93
V VTGG GF+G L E+LL
Sbjct: 2 VLVTGGAGFIGSHLVERLLE 21
>gnl|CDD|233954 TIGR02622, CDP_4_6_dhtase, CDP-glucose 4,6-dehydratase. Members
of this protein family are CDP-glucose 4,6-dehydratase
from a variety of Gram-negative and Gram-positive
bacteria. Members typically are encoded next to a gene
that encodes a glucose-1-phosphate
cytidylyltransferase, which produces the substrate,
CDP-D-glucose, used by this enzyme to produce
CDP-4-keto-6-deoxyglucose [Cell envelope, Biosynthesis
and degradation of surface polysaccharides and
lipopolysaccharides].
Length = 349
Score = 33.4 bits (77), Expect = 0.12
Identities = 11/21 (52%), Positives = 14/21 (66%)
Query: 68 FYRGASVFVTGGTGFMGKTLT 88
F++G V VTG TGF G L+
Sbjct: 1 FWQGKKVLVTGHTGFKGSWLS 21
Score = 33.4 bits (77), Expect = 0.12
Identities = 11/21 (52%), Positives = 14/21 (66%)
Query: 126 FYRGASVFVTGGTGFMGKTLT 146
F++G V VTG TGF G L+
Sbjct: 1 FWQGKKVLVTGHTGFKGSWLS 21
>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 = 33.2 bits (76), Expect = 0.14
Identities = 29/104 (27%), Positives = 43/104 (41%), Gaps = 21/104 (20%)
Query: 131 SVFVTGGTGFMGKTLTEKLLRACPHLERVYLLVRPKKGKTVSERLDELFEDRLFSRLKAE 190
VTGG GF+G+ + LL L+ + +L K L E FE
Sbjct: 1 VCLVTGGGGFLGQHIIRLLLERKEELKEIRVL-----DKAFGPELIEHFEKSQ------- 48
Query: 191 VPHFRSKISVVTGDVSLPGLGLSAADRAVLRRNVTVVFHGAATV 234
++ ++ + GD+ LS RA + V+VV H AA V
Sbjct: 49 ---GKTYVTDIEGDI----KDLSFLFRAC--QGVSVVIHTAAIV 83
>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 = 32.5 bits (75), Expect = 0.15
Identities = 32/114 (28%), Positives = 38/114 (33%), Gaps = 27/114 (23%)
Query: 130 ASVFVTGGTGFMGKTLTEKLL-RACPHLERVYLLVRPKKGKTVSERLDELFEDRLFSRLK 188
+ VTGG G +G L L R HL V L L EL
Sbjct: 1 GTYLVTGGLGGLGLELARWLAERGARHL--VLLSRSGAPDPEAEALLAEL------EARG 52
Query: 189 AEVPHFRSKISVVTGDVSLPGLGLSAADRAVLRR------NVTVVFHGAATVRF 236
AEV +VV DVS A RA+L + V H A +R
Sbjct: 53 AEV-------TVVACDVSDR-----DAVRALLAEIRADGPPLRGVIHAAGVLRD 94
>gnl|CDD|187575 cd05265, SDR_a1, atypical (a) SDRs, subgroup 1. Atypical SDRs in
this subgroup are poorly defined and have been
identified putatively as isoflavones reductase, sugar
dehydratase, mRNA binding protein etc. Atypical SDRs are
distinct from classical SDRs. Members of this subgroup
retain the canonical active site triad (though not the
upstream Asn found in most SDRs) but have an unusual
putative glycine-rich NAD(P)-binding motif, GGXXXXG, in
the usual location. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and their
glycine-rich NAD(P)-binding motif is often different
from the forms normally seen in classical or extended
SDRs. Atypical SDRs include biliverdin IX beta reductase
(BVR-B,aka flavin reductase), NMRa (a negative
transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. In addition to the
Rossmann fold core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 250
Score = 32.6 bits (75), Expect = 0.17
Identities = 17/53 (32%), Positives = 27/53 (50%), Gaps = 3/53 (5%)
Query: 73 SVFVTGGTGFMGKTLTEKLLRACPHLERVYLLVRPKKGKTVSERLDELFEDRE 125
+ + GGT F+GK L E+LL A H V + R + + E ++ + DR
Sbjct: 2 KILIIGGTRFIGKALVEELL-AAGH--DVTVFNRGRTKPDLPEGVEHIVGDRN 51
Score = 31.9 bits (73), Expect = 0.31
Identities = 17/52 (32%), Positives = 27/52 (51%), Gaps = 3/52 (5%)
Query: 131 SVFVTGGTGFMGKTLTEKLLRACPHLERVYLLVRPKKGKTVSERLDELFEDR 182
+ + GGT F+GK L E+LL A H V + R + + E ++ + DR
Sbjct: 2 KILIIGGTRFIGKALVEELL-AAGH--DVTVFNRGRTKPDLPEGVEHIVGDR 50
>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 = 32.8 bits (75), Expect = 0.19
Identities = 12/36 (33%), Positives = 17/36 (47%), Gaps = 1/36 (2%)
Query: 68 FYRGASVFVTGGTGFMGKTLTEKLL-RACPHLERVY 102
+ S+ +TGGTG GK +LL P +Y
Sbjct: 1 MFNNKSILITGGTGSFGKAFISRLLENYNPKKIIIY 36
Score = 32.8 bits (75), Expect = 0.19
Identities = 12/36 (33%), Positives = 17/36 (47%), Gaps = 1/36 (2%)
Query: 126 FYRGASVFVTGGTGFMGKTLTEKLL-RACPHLERVY 160
+ S+ +TGGTG GK +LL P +Y
Sbjct: 1 MFNNKSILITGGTGSFGKAFISRLLENYNPKKIIIY 36
>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 = 32.3 bits (74), Expect = 0.22
Identities = 11/21 (52%), Positives = 15/21 (71%)
Query: 74 VFVTGGTGFMGKTLTEKLLRA 94
VFVTG TGF+G + +L+ A
Sbjct: 3 VFVTGATGFIGSAVVRELVAA 23
Score = 32.3 bits (74), Expect = 0.22
Identities = 11/21 (52%), Positives = 15/21 (71%)
Query: 132 VFVTGGTGFMGKTLTEKLLRA 152
VFVTG TGF+G + +L+ A
Sbjct: 3 VFVTGATGFIGSAVVRELVAA 23
>gnl|CDD|224015 COG1090, COG1090, Predicted nucleoside-diphosphate sugar epimerase
[General function prediction only].
Length = 297
Score = 32.6 bits (75), Expect = 0.23
Identities = 12/33 (36%), Positives = 20/33 (60%), Gaps = 3/33 (9%)
Query: 74 VFVTGGTGFMGKTLTEKLLRACPHLERVYLLVR 106
+ +TGGTG +G+ LT +L + +V +L R
Sbjct: 1 ILITGGTGLIGRALTARLRK---GGHQVTILTR 30
Score = 32.6 bits (75), Expect = 0.23
Identities = 12/33 (36%), Positives = 20/33 (60%), Gaps = 3/33 (9%)
Query: 132 VFVTGGTGFMGKTLTEKLLRACPHLERVYLLVR 164
+ +TGGTG +G+ LT +L + +V +L R
Sbjct: 1 ILITGGTGLIGRALTARLRK---GGHQVTILTR 30
>gnl|CDD|214833 smart00822, PKS_KR, This enzymatic domain is part of bacterial
polyketide synthases. It catalyses 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 = 180
Score = 31.7 bits (73), Expect = 0.26
Identities = 28/113 (24%), Positives = 38/113 (33%), Gaps = 27/113 (23%)
Query: 130 ASVFVTGGTGFMGKTLTEKLLRACPHLERVYLLVR-PKKGKTVSERLDELFEDRLFSRLK 188
+ +TGG G +G+ L L R+ LL R + L EL
Sbjct: 1 GTYLITGGLGGLGRALARWLAERGA--RRLVLLSRSGPDAPGAAALLAEL------EAAG 52
Query: 189 AEVPHFRSKISVVTGDVSLPGLGLSAADRAVLRR------NVTVVFHGAATVR 235
A V +VV DV+ A AVL +T V H A +
Sbjct: 53 ARV-------TVVACDVADR-----DALAAVLAAIPAVEGPLTGVIHAAGVLD 93
>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 = 31.8 bits (73), Expect = 0.27
Identities = 19/83 (22%), Positives = 26/83 (31%), Gaps = 14/83 (16%)
Query: 73 SVFVTGGTGFMGKTLTEKLLRACPHLERVYLLVRPKKGKTVSER---------LDELFED 123
V V G TG +G+ + +LL +V LVR E L +
Sbjct: 1 KVLVVGATGKVGRHVVRELLD---RGYQVRALVRDPSQAEKLEAAGAEVVVGDLTDAESL 57
Query: 124 REFYRG--ASVFVTGGTGFMGKT 144
G A + G G G
Sbjct: 58 AAALEGIDAVISAAGSGGKGGPR 80
Score = 31.1 bits (71), Expect = 0.52
Identities = 19/78 (24%), Positives = 29/78 (37%), Gaps = 24/78 (30%)
Query: 131 SVFVTGGTGFMGKTLTEKLLRACPHLERVYLLVRPKKGKTVSERLDELFEDRLFSRLKAE 190
V V G TG +G+ + +LL +V LVR + ++L AE
Sbjct: 1 KVLVVGATGKVGRHVVRELLD---RGYQVRALVRDP------SQAEKLEA------AGAE 45
Query: 191 VPHFRSKISVVTGDVSLP 208
VV GD++
Sbjct: 46 ---------VVVGDLTDA 54
>gnl|CDD|187552 cd05241, 3b-HSD-like_SDR_e, 3beta-hydroxysteroid dehydrogenases
(3b-HSD)-like, extended (e) SDRs. Extended SDR family
domains belonging to this subgroup have the
characteristic active site tetrad and a fairly
well-conserved NAD(P)-binding motif. 3b-HSD catalyzes
the NAD-dependent conversion of various steroids, such
as pregnenolone to progesterone, or androstenediol to
testosterone. This subgroup includes an unusual
bifunctional 3b-HSD/C-4 decarboxylase from Arabidopsis
thaliana, and Saccharomyces cerevisiae ERG26, a
3b-HSD/C-4 decarboxylase, involved in the synthesis of
ergosterol, the major sterol of yeast. It also includes
human 3 beta-HSD/HSD3B1 and C(27) 3beta-HSD/
[3beta-hydroxy-delta(5)-C(27)-steroid oxidoreductase;
HSD3B7]. C(27) 3beta-HSD/HSD3B7 is a membrane-bound
enzyme of the endoplasmic reticulum, that catalyzes the
isomerization and oxidation of 7alpha-hydroxylated
sterol intermediates, an early step in bile acid
biosynthesis. Mutations in the human NSDHL (NAD(P)H
steroid dehydrogenase-like protein) cause CHILD syndrome
(congenital hemidysplasia with ichthyosiform nevus and
limb defects), an X-linked dominant, male-lethal trait.
Mutations in the human gene encoding C(27) 3beta-HSD
underlie a rare autosomal recessive form of neonatal
cholestasis. Extended SDRs are distinct from classical
SDRs. In addition to the Rossmann fold (alpha/beta
folding pattern with a central beta-sheet) core region
typical of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid sythase have
a GGXGXXG NAD(P)-binding motif and an altered active
site motif (YXXXN). Fungal type ketoacyl reductases have
a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 331
Score = 32.4 bits (74), Expect = 0.28
Identities = 25/107 (23%), Positives = 35/107 (32%), Gaps = 33/107 (30%)
Query: 131 SVFVTGGTGFMGKTLTEKLLRACPHLERVYLLVRPKKGKTVSERLDELFEDRLFSRLKAE 190
SV VTGG+GF G+ L ++LL R + D
Sbjct: 1 SVLVTGGSGFFGERLVKQLLERGGTYVRSF--------------------DIAPPGEALS 40
Query: 191 VPHFRSKISVVTGDVSLPGLGLSAADRAVLRRN---VTVVFHGAATV 234
I + GD++ DR + + VFH AA V
Sbjct: 41 AWQ-HPNIEFLKGDIT---------DRNDVEQALSGADCVFHTAAIV 77
Score = 29.7 bits (67), Expect = 1.7
Identities = 12/21 (57%), Positives = 16/21 (76%)
Query: 73 SVFVTGGTGFMGKTLTEKLLR 93
SV VTGG+GF G+ L ++LL
Sbjct: 1 SVLVTGGSGFFGERLVKQLLE 21
>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 = 32.4 bits (74), Expect = 0.29
Identities = 39/164 (23%), Positives = 55/164 (33%), Gaps = 58/164 (35%)
Query: 131 SVFVTGGTGFMGKTLTEKLLRACPHLERVYLLVRPKKGKTVSERLDELFEDRLFSRLKAE 190
+ VTGG GF+G +L P E + L T + L+ L +
Sbjct: 1 RILVTGGAGFIGSNFVRYILNEHPDAEVIVL-----DKLTYAGNLENL-------ADLED 48
Query: 191 VPHFRSKISVVTGDVSLPGLGLSAADRAVLRRNVT-----VVFHGAATVRFDENIKVA-- 243
P +R V GD+ DR ++ R T V H AA D +I
Sbjct: 49 NPRYR----FVKGDI---------GDRELVSRLFTEHQPDAVVHFAAESHVDRSISGPAA 95
Query: 244 -IAINIFGS---------------FVHVSTAYTHCPRQEIDEVF 271
I N+ G+ F H+ST DEV+
Sbjct: 96 FIETNVVGTYTLLEAVRKYWHEFRFHHIST----------DEVY 129
Score = 29.3 bits (66), Expect = 2.4
Identities = 11/31 (35%), Positives = 15/31 (48%)
Query: 73 SVFVTGGTGFMGKTLTEKLLRACPHLERVYL 103
+ VTGG GF+G +L P E + L
Sbjct: 1 RILVTGGAGFIGSNFVRYILNEHPDAEVIVL 31
>gnl|CDD|212491 cd05233, SDR_c, classical (c) SDRs. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold
(alpha/beta folding pattern with a central beta-sheet),
an NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRs are approximately
350 residues. Sequence identity between different SDR
enzymes are typically in the 15-30% range, but the
enzymes share the Rossmann fold NAD-binding motif and
characteristic NAD-binding and catalytic sequence
patterns. These enzymes catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human prostaglandin dehydrogenase
(PGDH) numbering). In addition to the Tyr and Lys, there
is often an upstream Ser (Ser-138, PGDH numbering)
and/or an Asn (Asn-107, PGDH numbering) contributing to
the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 234
Score = 31.5 bits (72), Expect = 0.45
Identities = 27/136 (19%), Positives = 47/136 (34%), Gaps = 30/136 (22%)
Query: 132 VFVTGGTGFMGKTLTEKLLRA-CPHLERVYLLVRPKKGKTVSERLDELFEDRLFSRLKAE 190
VTG + +G+ + +L R +V L R E L EL A
Sbjct: 1 ALVTGASSGIGRAIARRLAREGA----KVVLADR------NEEALAEL----------AA 40
Query: 191 VPHFRSKISVVTGDVSLPGLGLSAADRAVLRR-NVTVVFHGAATVRF-------DENIKV 242
+ V DVS + + A+ + ++ + A R DE+
Sbjct: 41 IEALGGNAVAVQADVSDEEDVEALVEEALEEFGRLDILVNNAGIARPGPLEELTDEDWDR 100
Query: 243 AIAINIFGSFVHVSTA 258
+ +N+ G F ++ A
Sbjct: 101 VLDVNLTGVF-LLTRA 115
>gnl|CDD|188518 TIGR04003, rSAM_BssD, [benzylsuccinate synthase]-activating enzyme.
Members of this radical SAM protein family are
[benzylsuccinate synthase]-activating enzyme, a glycyl
radical active site-creating enzyme related to [pyruvate
formate-lyase]-activating enzyme and additional
uncharacterized homologs activating additional glycyl
radical-containing enzymes [Protein fate, Protein
modification and repair].
Length = 314
Score = 31.4 bits (71), Expect = 0.48
Identities = 23/88 (26%), Positives = 34/88 (38%), Gaps = 9/88 (10%)
Query: 112 TVSERLDELFEDREFYR--GASVFVTGGTGFMGKTLTEKLLRACPHLERVYLLVR----P 165
+V E L E D FYR G V ++GG M T +L R H V++ + P
Sbjct: 109 SVDEILREALSDSPFYRNSGGGVTISGGDPLMYPEFTLELARRL-HDRGVHVAIETSCFP 167
Query: 166 KKGKTVSERLDELFEDRLFSRLKAEVPH 193
K + + ++ D LK
Sbjct: 168 KHWEVMEPLVE--HVDLFIVDLKCLNAK 193
>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 = 0.53
Identities = 26/112 (23%), Positives = 35/112 (31%), Gaps = 25/112 (22%)
Query: 130 ASVFVTGGTGFMGKTLTEKLLRACPHLERVYLLVRPKKGKTVSERLDELFEDRLFSRLKA 189
+ +TGG G +G + L + LL R L A
Sbjct: 151 GTYLITGGLGGLGLLVARWLAAR--GARHLVLLSRR------GPAPRAAARAALLRAGGA 202
Query: 190 EVPHFRSKISVVTGDVSLPGLGLSAADRAVLRR-----NVTVVFHGAATVRF 236
V SVV DV+ P AA A+L + V H A +R
Sbjct: 203 RV-------SVVRCDVTDP-----AALAALLAELAAGGPLAGVIHAAGVLRD 242
>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 = 31.0 bits (71), Expect = 0.72
Identities = 43/171 (25%), Positives = 58/171 (33%), Gaps = 52/171 (30%)
Query: 132 VFVTGGTGFMGKTLTEKLLRACPHLERVYL--LVRPKKGKTVSERLDELFEDRLFSRLKA 189
+ VTGG GF+G LL P + + L L T + L+ L + R +
Sbjct: 3 ILVTGGAGFIGSNFVRYLLNKYPDYKIINLDKL-------TYAGNLENLEDVSSSPRYR- 54
Query: 190 EVPHFRSKISVVTGDVSLPGLGLSAADRAVLRRNVTVVFHGAATVRFDENIK---VAIAI 246
V GD+ L DR + V H AA D +I I
Sbjct: 55 ----------FVKGDICDAEL----VDRLFEEEKIDAVIHFAAESHVDRSISDPEPFIRT 100
Query: 247 NIFGS--------------FVHVSTAYTHCPRQEIDEVFYPPPYDYKDFME 283
N+ G+ FVH+ST DEV Y D +F E
Sbjct: 101 NVLGTYTLLEAARKYGVKRFVHIST----------DEV-YGDLLDDGEFTE 140
>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 = 31.1 bits (71), Expect = 0.77
Identities = 34/114 (29%), Positives = 43/114 (37%), Gaps = 35/114 (30%)
Query: 132 VFVTGGTGFMGKTLTEKLLRACPHLERVYLLV--RPKKGKTVSERLDELFEDRLFSRLKA 189
V +TGGTG +G L L+ H R LLV R +E + EL + L A
Sbjct: 196 VLITGGTGTLGALLARHLVTE--HGVRHLLLVSRRGPDAPGAAELVAEL------AALGA 247
Query: 190 EVPHFRSKISVVTGDVSLPGLGLSAADRAVLR---------RNVTVVFHGAATV 234
EV +V DV ADRA L +T V H A +
Sbjct: 248 EV-------TVAACDV---------ADRAALAALLAAVPADHPLTAVVHAAGVL 285
>gnl|CDD|187568 cd05258, CDP_TE_SDR_e, CDP-tyvelose 2-epimerase, extended (e) SDRs.
CDP-tyvelose 2-epimerase is a tetrameric SDR that
catalyzes the conversion of CDP-D-paratose to
CDP-D-tyvelose, the last step in tyvelose biosynthesis.
This subgroup is a member of the extended SDR subfamily,
with a characteristic active site tetrad and NAD-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 = 337
Score = 30.7 bits (70), Expect = 0.81
Identities = 23/105 (21%), Positives = 36/105 (34%), Gaps = 21/105 (20%)
Query: 130 ASVFVTGGTGFMGKTLTEKLLRACPHLERVYLLVRPKKGKTVSERLDELFEDRLFSRLKA 189
V +TGG GF+G L L+ + L+R L + LKA
Sbjct: 1 MRVLITGGAGFIGSNLARFFLKQGWEVIGFDNLMRRG------------SFGNL-AWLKA 47
Query: 190 EVPHFRSKISVVTGDVSLPGLGLSAADRAVLRRNVTVVFHGAATV 234
+ V GD+ + D L ++ ++ H AA
Sbjct: 48 NREDGG--VRFVHGDIR------NRNDLEDLFEDIDLIIHTAAQP 84
>gnl|CDD|212492 cd05327, retinol-DH_like_SDR_c_like, retinol dehydrogenase
(retinol-DH), Light dependent Protochlorophyllide
(Pchlide) OxidoReductase (LPOR) and related proteins,
classical (c) SDRs. Classical SDR subgroup containing
retinol-DHs, LPORs, and related proteins. Retinol is
processed by a medium chain alcohol dehydrogenase
followed by retinol-DHs. Pchlide reductases act in
chlorophyll biosynthesis. There are distinct enzymes
that catalyze Pchlide reduction in light or dark
conditions. Light-dependent reduction is via an
NADP-dependent SDR, LPOR. Proteins in this subfamily
share the glycine-rich NAD-binding motif of the
classical SDRs, have a partial match to the canonical
active site tetrad, but lack the typical active site
Ser. This subgroup includes the human proteins: retinol
dehydrogenase -12, -13 ,and -14, dehydrogenase/reductase
SDR family member (DHRS)-12 , -13 and -X (a DHRS on
chromosome X), and WWOX (WW domain-containing
oxidoreductase), as well as a Neurospora crassa SDR
encoded by the blue light inducible bli-4 gene. SDRs are
a functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold (alpha/beta folding pattern with a central
beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRs are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes catalyze a
wide range of activities including the metabolism of
steroids, cofactors, carbohydrates, lipids, aromatic
compounds, and amino acids, and act in redox sensing.
Classical SDRs have an TGXXX[AG]XG cofactor binding
motif and a YXXXK active site motif, with the Tyr
residue of the active site motif serving as a critical
catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 269
Score = 30.7 bits (70), Expect = 0.82
Identities = 14/65 (21%), Positives = 25/65 (38%), Gaps = 10/65 (15%)
Query: 71 GASVFVTGGTGFMGKTLTEKLLRACPHLERVYLLVR-PKKGKTVSERLDELFEDREFYRG 129
G V +TG +GK +L + V + R +KG+ + + ++
Sbjct: 1 GKVVVITGANSGIGKETARELAK---RGAHVIIACRNEEKGEEAAAEI------KKETGN 51
Query: 130 ASVFV 134
A V V
Sbjct: 52 AKVEV 56
Score = 29.5 bits (67), Expect = 1.8
Identities = 17/79 (21%), Positives = 31/79 (39%), Gaps = 18/79 (22%)
Query: 129 GASVFVTGGTGFMGKTLTEKLLRACPHLERVYLLVR-PKKGKTVSERLDELFEDRLFSRL 187
G V +TG +GK +L + V + R +KG+ + +
Sbjct: 1 GKVVVITGANSGIGKETARELAK---RGAHVIIACRNEEKGEEAAA------------EI 45
Query: 188 KAEVPHFRSKISVVTGDVS 206
K E + +K+ V+ D+S
Sbjct: 46 KKETGN--AKVEVIQLDLS 62
>gnl|CDD|237568 PRK13943, PRK13943, protein-L-isoaspartate O-methyltransferase;
Provisional.
Length = 322
Score = 30.6 bits (69), Expect = 0.90
Identities = 15/52 (28%), Positives = 26/52 (50%), Gaps = 4/52 (7%)
Query: 246 INIFGSFVHVSTAYTHCPRQEIDEVFYPPPYDYKDFMELVMSRSDDNLEEFS 297
+ +G H++ A+ PR+E YP Y Y+D + + D+ EE+S
Sbjct: 14 LKKYGISDHIAKAFLEVPREEFLTKSYPLSYVYEDIVLVSY----DDGEEYS 61
>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 = 30.7 bits (69), Expect = 0.92
Identities = 34/119 (28%), Positives = 48/119 (40%), Gaps = 29/119 (24%)
Query: 132 VFVTGGTGFMGKTLTEKLLRACPHLERVYLLVR-PKKGKTVSERLDELFEDRLFSRLKAE 190
V VTG +GF+ + E+LL +V VR P K K V+ LD L A+
Sbjct: 1 VLVTGASGFVASHVVEQLLE---RGYKVRATVRDPSKVKKVNHLLD----------LDAK 47
Query: 191 VPHFRSKISVVTGDVSLPGLGLSAADRAVLRRNVTVVFHGAATVRF-----DENIKVAI 244
++ +T + S D + + VFH A V F +E IK AI
Sbjct: 48 PGRLELAVADLTDEQSF--------DEVI--KGCAGVFHVATPVSFSSKDPNEVIKPAI 96
Score = 27.6 bits (61), Expect = 7.8
Identities = 18/46 (39%), Positives = 24/46 (52%), Gaps = 4/46 (8%)
Query: 74 VFVTGGTGFMGKTLTEKLLRACPHLERVYLLVR-PKKGKTVSERLD 118
V VTG +GF+ + E+LL +V VR P K K V+ LD
Sbjct: 1 VLVTGASGFVASHVVEQLLE---RGYKVRATVRDPSKVKKVNHLLD 43
>gnl|CDD|201603 pfam01118, Semialdhyde_dh, Semialdehyde dehydrogenase, NAD binding
domain. This Pfam entry contains the following members:
N-acetyl-glutamine semialdehyde dehydrogenase (AgrC)
Aspartate-semialdehyde dehydrogenase.
Length = 121
Score = 29.4 bits (67), Expect = 0.93
Identities = 17/53 (32%), Positives = 27/53 (50%), Gaps = 2/53 (3%)
Query: 74 VFVTGGTGFMGKTLTEKLLRACPHLERVYLLVRPKK-GKTVSERLDELFEDRE 125
V + G TG++G+ L +LL P LE V L+ + GK V+ L ++
Sbjct: 2 VAIVGATGYVGQELL-RLLAEHPPLELVALVASSRSAGKKVAFAYPILEGGKD 53
Score = 29.0 bits (66), Expect = 1.1
Identities = 16/44 (36%), Positives = 24/44 (54%), Gaps = 2/44 (4%)
Query: 132 VFVTGGTGFMGKTLTEKLLRACPHLERVYLLVRPKK-GKTVSER 174
V + G TG++G+ L +LL P LE V L+ + GK V+
Sbjct: 2 VAIVGATGYVGQELL-RLLAEHPPLELVALVASSRSAGKKVAFA 44
>gnl|CDD|187657 cd08954, KR_1_FAS_SDR_x, beta-ketoacyl reductase (KR) domain of
fatty acid synthase (FAS), subgroup 1, complex (x) SDRs.
NADP-dependent KR domain of the multidomain type I FAS,
a complex SDR family. This subfamily also includes
proteins identified as polyketide synthase (PKS), a
protein with related modular protein architecture and
similar function. It includes the KR domains of
mammalian and chicken FAS, and Dictyostelium discoideum
putative polyketide synthases (PKSs). These KR domains
contain two subdomains, each of which is related to SDR
Rossmann fold domains. However, while the C-terminal
subdomain has an active site similar to the other SDRs
and a NADP-binding capability, the N-terminal SDR-like
subdomain is truncated and lacks these functions,
serving a supportive structural role. In some instances,
such as porcine FAS, an enoyl reductase (a Rossman fold
NAD-binding domain of the medium-chain
dehydrogenase/reductase, MDR family) 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-ketoacyl reductase (KR), forming
beta-hydroxyacyl-ACP, which is in turn dehydrated by
dehydratase to a beta-enoyl intermediate, which is
reduced by NADP-dependent beta-enoyl reductase (ER);
this KR and ER are members of the SDR family. This KR
subfamily has an active site tetrad with a similar 3D
orientation compared to archetypical SDRs, but the
active site Lys and Asn residue positions are swapped.
The characteristic NADP-binding is typical of the
multidomain complex SDRs, with a GGXGXXG NADP binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold (alpha/beta folding
pattern with a central beta-sheet), an NAD(P)(H)-binding
region, and a structurally diverse C-terminal region.
Classical SDRs are typically about 250 residues long,
while extended SDRs are approximately 350 residues.
Sequence identity between different SDR enzymes are
typically in the 15-30% range, but the enzymes share the
Rossmann fold NAD-binding motif and characteristic
NAD-binding and catalytic sequence patterns. These
enzymes catalyze a wide range of activities including
the metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
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 = 452
Score = 30.9 bits (70), Expect = 0.94
Identities = 29/113 (25%), Positives = 43/113 (38%), Gaps = 21/113 (18%)
Query: 129 GASVFVTGGTGFMGKTLTEKLLRACPHLERVYLLVRPKKG-KTVSERLDELFEDRLFSRL 187
G S +TGG+G +G + K L +E + +L R G K E L
Sbjct: 218 GKSYLITGGSGGLGLEIL-KWLVKRGAVENIIILSR--SGMKWELE--------LLIREW 266
Query: 188 KAEVPHFRSKISVVTGDVSLPGLGLSAADRAVLRR----NVTVVFHGAATVRF 236
K++ F +SV DVS L A +L + +FH A +
Sbjct: 267 KSQNIKF-HFVSVDVSDVS----SLEKAINLILNAPKIGPIGGIFHLAFVLID 314
>gnl|CDD|187541 cd05230, UGD_SDR_e, UDP-glucuronate decarboxylase (UGD) and
related proteins, extended (e) SDRs. UGD catalyzes the
formation of UDP-xylose from UDP-glucuronate; it is an
extended-SDR, and has the characteristic glycine-rich
NAD-binding pattern, TGXXGXXG, and active site tetrad.
Extended SDRs are distinct from classical SDRs. In
addition to the Rossmann fold (alpha/beta folding
pattern with a central beta-sheet) core region typical
of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving
as a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton
relay involving the conserved Tyr and Lys, a water
molecule stabilized by Asn, and nicotinamide. Atypical
SDRs generally lack the catalytic residues
characteristic of the SDRs, and their glycine-rich
NAD(P)-binding motif is often different from the forms
normally seen in classical or extended SDRs. Complex
(multidomain) SDRs such as ketoreductase domains of
fatty acid synthase have a GGXGXXG NAD(P)-binding motif
and an altered active site motif (YXXXN). Fungal type
ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding
motif.
Length = 305
Score = 30.3 bits (69), Expect = 0.97
Identities = 9/21 (42%), Positives = 14/21 (66%)
Query: 74 VFVTGGTGFMGKTLTEKLLRA 94
+ +TGG GF+G L ++LL
Sbjct: 3 ILITGGAGFLGSHLCDRLLED 23
Score = 30.3 bits (69), Expect = 0.97
Identities = 9/21 (42%), Positives = 14/21 (66%)
Query: 132 VFVTGGTGFMGKTLTEKLLRA 152
+ +TGG GF+G L ++LL
Sbjct: 3 ILITGGAGFLGSHLCDRLLED 23
>gnl|CDD|213195 cd03228, ABCC_MRP_Like, ATP-binding cassette domain of multidrug
resistance protein-like transporters. The MRP
(Multidrug Resistance Protein)-like transporters are
involved in drug, peptide, and lipid export. They belong
to the subfamily C of the ATP-binding cassette (ABC)
superfamily of transport proteins. The ABCC subfamily
contains transporters with a diverse functional spectrum
that includes ion transport, cell surface receptor, and
toxin secretion activities. The MRP-like family, similar
to all ABC proteins, have a common four-domain core
structure constituted by two membrane-spanning domains,
each composed of six transmembrane (TM) helices, and two
nucleotide-binding domains (NBD). ABC transporters are a
subset of nucleotide hydrolases that contain a signature
motif, Q-loop, and H-loop/switch region, in addition to,
the Walker A motif/P-loop and Walker B motif commonly
found in a number of ATP- and GTP-binding and
hydrolyzing proteins.
Length = 171
Score = 29.7 bits (68), Expect = 1.1
Identities = 18/56 (32%), Positives = 27/56 (48%), Gaps = 17/56 (30%)
Query: 203 GDVSLPGLGLSAADRAVLRRNVTVV------FHGAATVRFDENI-------KVAIA 245
G++ + G+ L D LR+N+ V F G T+R ENI ++AIA
Sbjct: 57 GEILIDGVDLRDLDLESLRKNIAYVPQDPFLFSG--TIR--ENILSGGQRQRIAIA 108
>gnl|CDD|237903 PRK15078, PRK15078, polysaccharide export protein Wza; Provisional.
Length = 379
Score = 30.4 bits (69), Expect = 1.2
Identities = 16/50 (32%), Positives = 25/50 (50%), Gaps = 10/50 (20%)
Query: 167 KGKTVSE-------RLDELFEDRLFSRLKAEVPHFRSKISVVTGDVSLPG 209
GKTV+E RL + E ++ + FRS+ + VTG+V+ G
Sbjct: 137 AGKTVTEIRSDITGRLAKYIES---PQVDVNIAAFRSQKAYVTGEVNKSG 183
>gnl|CDD|236461 PRK09302, PRK09302, circadian clock protein KaiC; Reviewed.
Length = 509
Score = 30.2 bits (69), Expect = 1.3
Identities = 19/51 (37%), Positives = 26/51 (50%), Gaps = 4/51 (7%)
Query: 114 SERLDELFEDREFYRGASVFVTGGTGFMGKTL--TEKLLRACPHLERVYLL 162
LDE+ F+RG+ + V+G TG GKTL ++ AC ER L
Sbjct: 259 VPDLDEML-GGGFFRGSIILVSGATG-TGKTLLASKFAEAACRRGERCLLF 307
Score = 29.1 bits (66), Expect = 3.2
Identities = 16/39 (41%), Positives = 22/39 (56%), Gaps = 3/39 (7%)
Query: 68 FYRGASVFVTGGTGFMGKTL--TEKLLRACPHLERVYLL 104
F+RG+ + V+G TG GKTL ++ AC ER L
Sbjct: 270 FFRGSIILVSGATG-TGKTLLASKFAEAACRRGERCLLF 307
>gnl|CDD|215072 PLN00141, PLN00141, Tic62-NAD(P)-related group II protein;
Provisional.
Length = 251
Score = 29.8 bits (67), Expect = 1.3
Identities = 13/33 (39%), Positives = 17/33 (51%)
Query: 60 EVGSPIQEFYRGASVFVTGGTGFMGKTLTEKLL 92
E E + +VFV G TG GK + E+LL
Sbjct: 6 EASEEDAENVKTKTVFVAGATGRTGKRIVEQLL 38
Score = 29.1 bits (65), Expect = 2.7
Identities = 14/29 (48%), Positives = 18/29 (62%)
Query: 122 EDREFYRGASVFVTGGTGFMGKTLTEKLL 150
ED E + +VFV G TG GK + E+LL
Sbjct: 10 EDAENVKTKTVFVAGATGRTGKRIVEQLL 38
>gnl|CDD|219158 pfam06745, KaiC, KaiC. This family represents a conserved region
within bacterial and archaeal proteins, most of which
are hypothetical. More than one copy is sometimes found
in each protein. This family includes KaiC, which is one
of the Kai proteins among which direct protein-protein
association may be a critical process in the generation
of circadian rhythms in cyanobacteria.
Length = 231
Score = 29.9 bits (68), Expect = 1.4
Identities = 14/35 (40%), Positives = 18/35 (51%), Gaps = 2/35 (5%)
Query: 111 KTVSERLDELFEDREFYRGASVFVTGGTGFMGKTL 145
T LDE+ + RG V +TGG G GKT+
Sbjct: 2 PTGIPGLDEILKGG-IPRGRVVLITGGPG-TGKTI 34
>gnl|CDD|187656 cd08953, KR_2_SDR_x, ketoreductase (KR), subgroup 2, complex (x)
SDRs. Ketoreductase, a module of the multidomain
polyketide synthase (PKS), has 2 subdomains, each
corresponding to a SDR family monomer. The C-terminal
subdomain catalyzes the NADPH-dependent reduction of the
beta-carbonyl of a polyketide to a hydroxyl group, a
step in the biosynthesis of polyketides, such as
erythromycin. The N-terminal subdomain, an interdomain
linker, is a truncated Rossmann fold which acts to
stabilizes the catalytic subdomain. Unlike typical SDRs,
the isolated domain does not oligomerize but is composed
of 2 subdomains, each resembling an SDR monomer. The
active site resembles that of typical SDRs, except that
the usual positions of the catalytic Asn and Tyr are
swapped, so that the canonical YXXXK motif changes to
YXXXN. Modular PKSs are multifunctional structures in
which the makeup recapitulates that found in (and may
have evolved from) FAS. Polyketide synthesis also
proceeds via the addition of 2-carbon units as in fatty
acid synthesis. The complex SDR NADP-binding motif,
GGXGXXG, is often present, but is not strictly conserved
in each instance of the module. This subfamily includes
both KR domains of the Bacillus subtilis Pks J,-L, and
PksM, and all three KR domains of PksN, components of
the megacomplex bacillaene synthase, which synthesizes
the antibiotic bacillaene. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold
(alpha/beta folding pattern with a central beta-sheet),
an NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRs are approximately
350 residues. Sequence identity between different SDR
enzymes are typically in the 15-30% range, but the
enzymes share the Rossmann fold NAD-binding motif and
characteristic NAD-binding and catalytic sequence
patterns. These enzymes catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human prostaglandin dehydrogenase
(PGDH) numbering). In addition to the Tyr and Lys, there
is often an upstream Ser (Ser-138, PGDH numbering)
and/or an Asn (Asn-107, PGDH numbering) contributing to
the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type KRs have a TGXXXGX(1-2)G
NAD(P)-binding motif. Some atypical SDRs have lost
catalytic activity and/or have an unusual NAD(P)-binding
motif and missing or unusual active site residues.
Reactions catalyzed within the SDR family include
isomerization, decarboxylation, epimerization, C=N bond
reduction, dehydratase activity, dehalogenation,
Enoyl-CoA reduction, and carbonyl-alcohol
oxidoreduction.
Length = 436
Score = 30.0 bits (68), Expect = 1.5
Identities = 27/107 (25%), Positives = 42/107 (39%), Gaps = 21/107 (19%)
Query: 134 VTGGTGFMGKTLTEKLLRACPHLERVYLLVR---PKKGKTVSERLDELFEDRLFSRLKAE 190
VTGG G +G+ L L R + R+ LL R P + + ++ L L L A
Sbjct: 210 VTGGAGGIGRALARALARR--YGARLVLLGRSPLPPEEEWKAQTLAAL------EALGAR 261
Query: 191 VPHFRSKISVVTGDVSLPGLGLSAADRAVLRR--NVTVVFHGAATVR 235
V + ++ DV+ + V R + V H A +R
Sbjct: 262 VLY-------ISADVTDA-AAVRRLLEKVRERYGAIDGVIHAAGVLR 300
>gnl|CDD|133446 cd01078, NAD_bind_H4MPT_DH, NADP binding domain of methylene
tetrahydromethanopterin dehydrogenase. Methylene
Tetrahydromethanopterin Dehydrogenase (H4MPT DH) NADP
binding domain. NADP-dependent H4MPT DH catalyzes the
dehydrogenation of methylene- H4MPT and
methylene-tetrahydrofolate (H4F) with NADP+ as cofactor.
H4F and H4MPT are both cofactors that carry the
one-carbon units between the formyl and methyl oxidation
level. H4F and H4MPT are structurally analogous to each
other with respect to the pterin moiety, but each has
distinct side chain. H4MPT is present only in anaerobic
methanogenic archaea and aerobic methylotrophic
proteobacteria. H4MPT seems to have evolved
independently from H4F and functions as a distinct
carrier in C1 metabolism. Amino acid DH-like
NAD(P)-binding domains are members of the Rossmann fold
superfamily and include glutamate, leucine, and
phenylalanine DHs, methylene tetrahydrofolate DH,
methylene-tetrahydromethanopterin DH,
methylene-tetrahydropholate DH/cyclohydrolase, Shikimate
DH-like proteins, malate oxidoreductases, and glutamyl
tRNA reductase. Amino acid DHs catalyze the deamination
of amino acids to keto acids with NAD(P)+ as a cofactor.
The NAD(P)-binding Rossmann fold superfamily includes a
wide variety of protein families including NAD(P)-
binding domains of alcohol DHs, tyrosine-dependent
oxidoreductases, glyceraldehyde-3-phosphate DH,
lactate/malate DHs, formate/glycerate DHs, siroheme
synthases, 6-phosphogluconate DH, amino acid DHs,
repressor rex, NAD-binding potassium channel domain,
CoA-binding, and ornithine cyclodeaminase-like domains.
These domains have an alpha-beta-alpha configuration.
NAD binding involves numerous hydrogen and van der Waals
contacts.
Length = 194
Score = 29.3 bits (66), Expect = 1.8
Identities = 28/109 (25%), Positives = 35/109 (32%), Gaps = 17/109 (15%)
Query: 70 RGASVFVTGGTGFMGKTLTEKLLRACPH-------LERV-----YLLVRPKKGKT-VSER 116
+G + V GGTG +G+ L R LER L R +G V
Sbjct: 27 KGKTAVVLGGTGPVGQRAAVLLAREGARVVLVGRDLERAQKAADSLRARFGEGVGAVETS 86
Query: 117 LDELFEDREFYRGASVFVTGGTGFMGKTLTEKLLRACPHLERVYLLVRP 165
D +GA V G G L EKL A L +
Sbjct: 87 DDA--ARAAAIKGADVVFA--AGAAGVELLEKLAWAPKPLAVAADVNAV 131
>gnl|CDD|187553 cd05242, SDR_a8, atypical (a) SDRs, subgroup 8. This subgroup
contains atypical SDRs of unknown function. Proteins in
this subgroup have a glycine-rich NAD(P)-binding motif
consensus that resembles that of the extended SDRs,
(GXXGXXG or GGXGXXG), but lacks the characteristic
active site residues of the SDRs. A Cys often replaces
the usual Lys of the YXXXK active site motif, while the
upstream Ser is generally present and Arg replaces the
usual Asn. Atypical SDRs generally lack the catalytic
residues characteristic of the SDRs, and their
glycine-rich NAD(P)-binding motif is often different
from the forms normally seen in classical or extended
SDRs. Atypical SDRs include biliverdin IX beta reductase
(BVR-B,aka flavin reductase), NMRa (a negative
transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. In addition to the
Rossmann fold core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 296
Score = 29.5 bits (67), Expect = 1.8
Identities = 19/64 (29%), Positives = 26/64 (40%), Gaps = 6/64 (9%)
Query: 74 VFVTGGTGFMGKTLTEKLLRACPHLERVYLLVR--PKKGKTVSE-RLDELFEDREFYRGA 130
+ +TGGTGF+G+ LT +L A V +L R K D L GA
Sbjct: 2 IVITGGTGFIGRALTRRLTAAGHE---VVVLSRRPGKAEGLAEVITWDGLSLGPWELPGA 58
Query: 131 SVFV 134
+
Sbjct: 59 DAVI 62
Score = 29.5 bits (67), Expect = 1.9
Identities = 14/33 (42%), Positives = 20/33 (60%), Gaps = 3/33 (9%)
Query: 132 VFVTGGTGFMGKTLTEKLLRACPHLERVYLLVR 164
+ +TGGTGF+G+ LT +L A V +L R
Sbjct: 2 IVITGGTGFIGRALTRRLTAAGHE---VVVLSR 31
>gnl|CDD|181335 PRK08264, PRK08264, short chain dehydrogenase; Validated.
Length = 238
Score = 29.5 bits (67), Expect = 2.0
Identities = 24/111 (21%), Positives = 37/111 (33%), Gaps = 35/111 (31%)
Query: 129 GASVFVTGGTGFMGKTLTEKLLRACPHLER----VYLLVRPKKGKTVSERLDELFEDRLF 184
G V VTG +G+ E+L L R VY R
Sbjct: 6 GKVVLVTGANRGIGRAFVEQL------LARGAAKVYAAARD------------------- 40
Query: 185 SRLKAEVPHFRSKISVVTGDVSLPGLGLSAADRAVLRRNVTVVFHGAATVR 235
V ++ + DV+ P +AA+ A +VT++ + A R
Sbjct: 41 ---PESVTDLGPRVVPLQLDVTDPASVAAAAEAA---SDVTILVNNAGIFR 85
Score = 27.5 bits (62), Expect = 7.0
Identities = 13/40 (32%), Positives = 16/40 (40%), Gaps = 10/40 (25%)
Query: 71 GASVFVTGGTGFMGKTLTEKLLRACPHLER----VYLLVR 106
G V VTG +G+ E+L L R VY R
Sbjct: 6 GKVVLVTGANRGIGRAFVEQL------LARGAAKVYAAAR 39
>gnl|CDD|113251 pfam04475, DUF555, Protein of unknown function (DUF555). Family of
uncharacterized, hypothetical archaeal proteins.
Length = 102
Score = 28.1 bits (63), Expect = 2.0
Identities = 19/60 (31%), Positives = 28/60 (46%), Gaps = 11/60 (18%)
Query: 223 NVTVVFHGAATVR----FDENIKVAIA-----INIFGSFVHVSTAYTHCPR--QEIDEVF 271
+ VV A VR D+ I VAI+ +N FV + T CP+ +E++ VF
Sbjct: 2 DYLVVLEAAWIVRDVESVDDAIGVAISEAGKRLNPKLDFVEIEVGSTACPKCGEELESVF 61
>gnl|CDD|187550 cd05239, GDP_FS_SDR_e, GDP-fucose synthetase, extended (e) SDRs.
GDP-fucose synthetase (aka 3, 5-epimerase-4-reductase)
acts in the NADP-dependent synthesis of GDP-fucose from
GDP-mannose. Two activities have been proposed for the
same active site: epimerization and reduction. Proteins
in this subgroup are extended SDRs, which have a
characteristic active site tetrad and an NADP-binding
motif, [AT]GXXGXXG, that is a close match to the
archetypical form. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids. Extended SDRs are a diverse collection
of proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and
their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 300
Score = 29.5 bits (67), Expect = 2.1
Identities = 7/20 (35%), Positives = 10/20 (50%)
Query: 74 VFVTGGTGFMGKTLTEKLLR 93
+ VTG G +G + L R
Sbjct: 2 ILVTGHRGLVGSAIVRVLAR 21
Score = 29.5 bits (67), Expect = 2.1
Identities = 7/20 (35%), Positives = 10/20 (50%)
Query: 132 VFVTGGTGFMGKTLTEKLLR 151
+ VTG G +G + L R
Sbjct: 2 ILVTGHRGLVGSAIVRVLAR 21
>gnl|CDD|187673 cd09813, 3b-HSD-NSDHL-like_SDR_e, human NSDHL (NAD(P)H steroid
dehydrogenase-like protein)-like, extended (e) SDRs.
This subgroup includes human NSDHL and related
proteins. These proteins have the characteristic active
site tetrad of extended SDRs, and also have a close
match to their NAD(P)-binding motif. Human NSDHL is a
3beta-hydroxysteroid dehydrogenase (3 beta-HSD) which
functions in the cholesterol biosynthetic pathway. 3
beta-HSD catalyzes the oxidative conversion of delta
5-3 beta-hydroxysteroids to the delta 4-3-keto
configuration; this activity is essential for the
biosynthesis of all classes of hormonal steroids.
Mutations in the gene encoding NSDHL cause CHILD
syndrome (congenital hemidysplasia with ichthyosiform
nevus and limb defects), an X-linked dominant,
male-lethal trait. This subgroup also includes an
unusual bifunctional [3beta-hydroxysteroid
dehydrogenase (3b-HSD)/C-4 decarboxylase from
Arabidopsis thaliana, and Saccharomyces cerevisiae
ERG26, a 3b-HSD/C-4 decarboxylase, involved in the
synthesis of ergosterol, the major sterol of yeast.
Extended SDRs are distinct from classical SDRs. In
addition to the Rossmann fold (alpha/beta folding
pattern with a central beta-sheet) core region typical
of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving
as a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton
relay involving the conserved Tyr and Lys, a water
molecule stabilized by Asn, and nicotinamide. Atypical
SDRs generally lack the catalytic residues
characteristic of the SDRs, and their glycine-rich
NAD(P)-binding motif is often different from the forms
normally seen in classical or extended SDRs. Complex
(multidomain) SDRs such as ketoreductase domains of
fatty acid sythase have a GGXGXXG NAD(P)-binding motif
and an altered active site motif (YXXXN). Fungal type
ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding
motif.
Length = 335
Score = 29.6 bits (67), Expect = 2.1
Identities = 12/21 (57%), Positives = 16/21 (76%)
Query: 73 SVFVTGGTGFMGKTLTEKLLR 93
S V GG+GF+G+ L E+LLR
Sbjct: 1 SCLVVGGSGFLGRHLVEQLLR 21
Score = 29.6 bits (67), Expect = 2.1
Identities = 12/21 (57%), Positives = 16/21 (76%)
Query: 131 SVFVTGGTGFMGKTLTEKLLR 151
S V GG+GF+G+ L E+LLR
Sbjct: 1 SCLVVGGSGFLGRHLVEQLLR 21
>gnl|CDD|187545 cd05234, UDP_G4E_2_SDR_e, UDP-glucose 4 epimerase, subgroup 2,
extended (e) SDRs. UDP-glucose 4 epimerase (aka
UDP-galactose-4-epimerase), is a homodimeric extended
SDR. It catalyzes the NAD-dependent conversion of
UDP-galactose to UDP-glucose, the final step in Leloir
galactose synthesis. This subgroup is comprised of
archaeal and bacterial proteins, and has the
characteristic active site tetrad and NAD-binding motif
of the extended SDRs. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids. Extended SDRs are a diverse collection
of proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and
their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 305
Score = 29.2 bits (66), Expect = 2.4
Identities = 10/20 (50%), Positives = 14/20 (70%)
Query: 74 VFVTGGTGFMGKTLTEKLLR 93
+ VTGG GF+G L ++LL
Sbjct: 2 ILVTGGAGFIGSHLVDRLLE 21
Score = 29.2 bits (66), Expect = 2.4
Identities = 10/20 (50%), Positives = 14/20 (70%)
Query: 132 VFVTGGTGFMGKTLTEKLLR 151
+ VTGG GF+G L ++LL
Sbjct: 2 ILVTGGAGFIGSHLVDRLLE 21
>gnl|CDD|223774 COG0702, COG0702, Predicted nucleoside-diphosphate-sugar epimerases
[Cell envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 275
Score = 29.1 bits (65), Expect = 2.6
Identities = 29/127 (22%), Positives = 41/127 (32%), Gaps = 16/127 (12%)
Query: 132 VFVTGGTGFMGKTLTEKLLRACPHLERVYLLVRPKKGKTVSERLDELFEDRLFSRLKAEV 191
+ VTG TGF+G + +LL H V VR + E+ L V
Sbjct: 3 ILVTGATGFVGGAVVRELLAR-GH--EVRAAVRNPEAAAALAGGVEVVLGDLRDPKSL-V 58
Query: 192 PHFRSKISVVTGDVSLPGLGLSAADRAVLRRNVTVVFHGAATVRFDENIKVAIAINIFGS 251
+ V+ + L S A RAV V VR E + + S
Sbjct: 59 AGAKGVDGVL---LISGLLDGSDAFRAVQVTAV---------VRAAEAAGAGVKHGVSLS 106
Query: 252 FVHVSTA 258
+ A
Sbjct: 107 VLGADAA 113
Score = 29.1 bits (65), Expect = 2.8
Identities = 18/67 (26%), Positives = 24/67 (35%), Gaps = 5/67 (7%)
Query: 74 VFVTGGTGFMGKTLTEKLLRACPHLERVYLLVRPKKGKTVSERLDELFEDREFYRGASVF 133
+ VTG TGF+G + +LL H V VR + E+ R
Sbjct: 3 ILVTGATGFVGGAVVRELLAR-GH--EVRAAVRNPEAAAALAGGVEVVLGD--LRDPKSL 57
Query: 134 VTGGTGF 140
V G G
Sbjct: 58 VAGAKGV 64
>gnl|CDD|223959 COG1028, FabG, Dehydrogenases with different specificities (related
to short-chain alcohol dehydrogenases) [Secondary
metabolites biosynthesis, transport, and catabolism /
General function prediction only].
Length = 251
Score = 29.0 bits (65), Expect = 2.8
Identities = 29/149 (19%), Positives = 52/149 (34%), Gaps = 29/149 (19%)
Query: 129 GASVFVTGGTGFMGKTLTEKLLR--ACPHLERVYLLVRPKKGKTVSERLDELFEDRLFSR 186
G VTG + +G+ + L R A RV + R R +E + L +
Sbjct: 5 GKVALVTGASSGIGRAIARALAREGA-----RVVVAAR---------RSEEEAAEALAAA 50
Query: 187 LKAEVPHFRSKISVVTGDVSLPGLGLSAADRAVLRR--NVTVVFHGAATVRF-------- 236
+K + + V DVS + A A + ++ + A
Sbjct: 51 IKEA---GGGRAAAVAADVSDDEESVEALVAAAEEEFGRIDILVNNAGIAGPDAPLEELT 107
Query: 237 DENIKVAIAINIFGSFVHVSTAYTHCPRQ 265
+E+ I +N+ G+F+ A +Q
Sbjct: 108 EEDWDRVIDVNLLGAFLLTRAALPLMKKQ 136
>gnl|CDD|240648 cd12171, 2-Hacid_dh_10, Putative D-isomer specific 2-hydroxyacid
dehydrogenases. 2-Hydroxyacid dehydrogenases catalyze
the conversion of a wide variety of D-2-hydroxy acids
to their corresponding keto acids. The general
mechanism is (R)-lactate + acceptor to pyruvate +
reduced acceptor. Formate/glycerate and related
dehydrogenases of the D-specific 2-hydroxyacid
dehydrogenase superfamily include groups such as
formate dehydrogenase, glycerate dehydrogenase,
L-alanine dehydrogenase, and S-adenosylhomocysteine
hydrolase. Despite often low sequence identity, these
proteins typically have a characteristic arrangement of
2 similar subdomains of the alpha/beta Rossmann fold
NAD+ binding form. The NAD+ binding domain is inserted
within the linear sequence of the mostly N-terminal
catalytic domain, which has a similar domain structure
to the internal NAD binding domain. Structurally, these
domains are connected by extended alpha helices and
create a cleft in which NAD is bound, primarily to the
C-terminal portion of the 2nd (internal) domain. Some
related proteins have similar structural subdomain but
with a tandem arrangement of the catalytic and
NAD-binding subdomains in the linear sequence. While
many members of this family are dimeric, alanine DH is
hexameric and phosphoglycerate DH is tetrameric.
Length = 310
Score = 29.0 bits (66), Expect = 3.0
Identities = 22/77 (28%), Positives = 33/77 (42%), Gaps = 16/77 (20%)
Query: 29 MSEIVTA--QYPIDPFELLGEN-----SFGKPRVVPPDEVGSPIQEFYRGASVFVTGGTG 81
M E+ TA +P +PFE L E G V P +E + E + A + +T
Sbjct: 1 MKELETAPIDWPDEPFEDLQEVILVVEKSGPEAVEPEEE----LLEALKDADILITHFAP 56
Query: 82 FMGKTLTEKLLRACPHL 98
T+K++ A P L
Sbjct: 57 V-----TKKVIEAAPKL 68
>gnl|CDD|216304 pfam01113, DapB_N, Dihydrodipicolinate reductase, N-terminus.
Dihydrodipicolinate reductase (DapB) reduces the
alpha,beta-unsaturated cyclic imine,
dihydro-dipicolinate. This reaction is the second
committed step in the biosynthesis of L-lysine and its
precursor meso-diaminopimelate, which are critical for
both protein and cell wall biosynthesis. The N-terminal
domain of DapB binds the dinucleotide NADPH.
Length = 122
Score = 28.0 bits (63), Expect = 3.2
Identities = 13/40 (32%), Positives = 18/40 (45%), Gaps = 1/40 (2%)
Query: 76 VTGGTGFMGKTLTEKLLRACPHLERVYLLVRPKKGKTVSE 115
V G +G MG+ L K + P E V + RP S+
Sbjct: 5 VVGASGRMGRELI-KAILEAPDFELVAAVDRPGSSLLGSD 43
Score = 28.0 bits (63), Expect = 3.2
Identities = 13/40 (32%), Positives = 18/40 (45%), Gaps = 1/40 (2%)
Query: 134 VTGGTGFMGKTLTEKLLRACPHLERVYLLVRPKKGKTVSE 173
V G +G MG+ L K + P E V + RP S+
Sbjct: 5 VVGASGRMGRELI-KAILEAPDFELVAAVDRPGSSLLGSD 43
>gnl|CDD|187542 cd05231, NmrA_TMR_like_1_SDR_a, NmrA (a transcriptional regulator)
and triphenylmethane reductase (TMR) like proteins,
subgroup 1, atypical (a) SDRs. Atypical SDRs related to
NMRa, TMR, and HSCARG (an NADPH sensor). This subgroup
resembles the SDRs and has a partially conserved
characteristic [ST]GXXGXXG NAD-binding motif, but lacks
the conserved active site residues. NmrA is a negative
transcriptional regulator of various fungi, involved in
the post-translational modulation of the GATA-type
transcription factor AreA. NmrA lacks the canonical
GXXGXXG NAD-binding motif and has altered residues at
the catalytic triad, including a Met instead of the
critical Tyr residue. NmrA may bind nucleotides but
appears to lack any dehydrogenase activity. HSCARG has
been identified as a putative NADP-sensing molecule, and
redistributes and restructures in response to NADPH/NADP
ratios. Like NmrA, it lacks most of the active site
residues of the SDR family, but has an NAD(P)-binding
motif similar to the extended SDR family, GXXGXXG. SDRs
are a functionally diverse family of oxidoreductases
that have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Atypical SDRs
are distinct from classical SDRs. Classical SDRs have an
TGXXX[AG]XG cofactor binding motif and a YXXXK active
site motif, with the Tyr residue of the active site
motif serving as a critical catalytic residue (Tyr-151,
human 15-hydroxyprostaglandin dehydrogenase numbering).
In addition to the Tyr and Lys, there is often an
upstream Ser and/or an Asn, contributing to the active
site; while substrate binding is in the C-terminal
region, which determines specificity. The standard
reaction mechanism is a 4-pro-S hydride transfer and
proton relay involving the conserved Tyr and Lys, a
water molecule stabilized by Asn, and nicotinamide. In
addition to the Rossmann fold core region typical of all
SDRs, extended SDRs have a less conserved C-terminal
extension of approximately 100 amino acids, and
typically have a TGXXGXXG cofactor binding motif.
Complex (multidomain) SDRs such as ketoreductase domains
of fatty acid synthase have a GGXGXXG NAD(P)-binding
motif and an altered active site motif (YXXXN). Fungal
type ketoacyl reductases have a TGXXXGX(1-2)G
NAD(P)-binding motif.
Length = 259
Score = 28.4 bits (64), Expect = 3.7
Identities = 27/91 (29%), Positives = 33/91 (36%), Gaps = 22/91 (24%)
Query: 76 VTGGTGFMGKTLTEKLLRACPHLERVYLLVRPKKGKTVSERLDELFEDREFYRGASVFVT 135
VTG TG +G + LL A V LVR ER L RGA V V
Sbjct: 3 VTGATGRIGSKVATTLLEAG---RPVRALVRS------DERAAALAA-----RGAEVVV- 47
Query: 136 GGTGFMGKTLTEKLLRACPH-LERVYLLVRP 165
G +L A ++ V+ L P
Sbjct: 48 ------GDLDDPAVLAAALAGVDAVFFLAPP 72
>gnl|CDD|218921 pfam06167, MtfA, Phosphoenolpyruvate:glucose-phosphotransferase
regulator. MtfA (earlier known as YeeI) is a
transcription factor A that binds Mlc (make large
colonies), itself a repressor of glucose and hence a
protein important in regulation of the
phosphoenolpyruvate:glucose-phosphotransferase (ptsG)
system, the major glucose transporter in E.coli. Mlc is
a repressor of ptsG, and MtfA is found to bind and
inactivate Mlc with high affinity. The membrane-bound
protein EIICBGlc encoded by the ptsG gene is the major
glucose transporter in Escherichia coli.
Length = 248
Score = 28.3 bits (64), Expect = 4.0
Identities = 12/40 (30%), Positives = 18/40 (45%), Gaps = 5/40 (12%)
Query: 211 GLSAADRAVLRRNVTVV-----FHGAATVRFDENIKVAIA 245
LSA +R LR + F GA + + ++V IA
Sbjct: 35 RLSAEERQRLRELAQLFLAEKEFTGAGGLEVTDEMRVTIA 74
>gnl|CDD|178263 PLN02657, PLN02657, 3,8-divinyl protochlorophyllide a 8-vinyl
reductase.
Length = 390
Score = 28.6 bits (64), Expect = 4.1
Identities = 16/56 (28%), Positives = 26/56 (46%), Gaps = 6/56 (10%)
Query: 73 SVFVTGGTGFMGKTLTEKLLRACPHLERVYLLVRPK---KGKTVSERLDELFEDRE 125
+V V G TG++GK + +L+R + V + R K +GK E + E
Sbjct: 62 TVLVVGATGYIGKFVVRELVRRGYN---VVAVAREKSGIRGKNGKEDTKKELPGAE 114
Score = 28.6 bits (64), Expect = 4.6
Identities = 15/54 (27%), Positives = 25/54 (46%), Gaps = 6/54 (11%)
Query: 131 SVFVTGGTGFMGKTLTEKLLRACPHLERVYLLVRPK---KGKTVSERLDELFED 181
+V V G TG++GK + +L+R + V + R K +GK E +
Sbjct: 62 TVLVVGATGYIGKFVVRELVRRGYN---VVAVAREKSGIRGKNGKEDTKKELPG 112
>gnl|CDD|187549 cd05238, Gne_like_SDR_e, Escherichia coli Gne (a
nucleoside-diphosphate-sugar 4-epimerase)-like, extended
(e) SDRs. Nucleoside-diphosphate-sugar 4-epimerase has
the characteristic active site tetrad and NAD-binding
motif of the extended SDR, and is related to more
specifically defined epimerases such as UDP-glucose 4
epimerase (aka UDP-galactose-4-epimerase), which
catalyzes the NAD-dependent conversion of UDP-galactose
to UDP-glucose, the final step in Leloir galactose
synthesis. This subgroup includes Escherichia coli
055:H7 Gne, a UDP-GlcNAc 4-epimerase, essential for O55
antigen synthesis. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately 100
amino acids. Extended SDRs are a diverse collection of
proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 305
Score = 28.5 bits (64), Expect = 4.3
Identities = 29/106 (27%), Positives = 45/106 (42%), Gaps = 32/106 (30%)
Query: 131 SVFVTGGTGFMGKTLTEKLLRACPHLERVYLL--VRPKKGKTVSERLDELFEDRLFSRLK 188
V +TG +GF+G+ L E+LL + ER+ L+ V PK
Sbjct: 2 KVLITGASGFVGQRLAERLL-SDVPNERLILIDVVSPK---------------------- 38
Query: 189 AEVPHFRSKISVVTGDVSLPGLGLSAADRAVLRRNVTVVFHGAATV 234
P +++ + GD+++P A A+ VVFH AA V
Sbjct: 39 --APSGAPRVTQIAGDLAVP-----ALIEALANGRPDVVFHLAAIV 77
>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 = 28.4 bits (64), Expect = 4.4
Identities = 16/42 (38%), Positives = 21/42 (50%), Gaps = 4/42 (9%)
Query: 76 VTGGTGFMGKTLTEKLLRACPHLERVYLLVR-PKKGKTVSER 116
VTG TG +G + E LL + V LVR P+K K +
Sbjct: 3 VTGATGKLGTAVVELLLA---KVASVVALVRNPEKAKAFAAD 41
Score = 28.4 bits (64), Expect = 4.4
Identities = 16/42 (38%), Positives = 21/42 (50%), Gaps = 4/42 (9%)
Query: 134 VTGGTGFMGKTLTEKLLRACPHLERVYLLVR-PKKGKTVSER 174
VTG TG +G + E LL + V LVR P+K K +
Sbjct: 3 VTGATGKLGTAVVELLLA---KVASVVALVRNPEKAKAFAAD 41
>gnl|CDD|222146 pfam13460, NAD_binding_10, NADH(P)-binding.
Length = 182
Score = 28.0 bits (63), Expect = 5.0
Identities = 22/85 (25%), Positives = 30/85 (35%), Gaps = 10/85 (11%)
Query: 76 VTGGTGFMGKTLTEKLLRACPHLERVYLLVR------PKKGKTVSERLDELFEDREFYRG 129
V G TG G+ L ++LL H +V L R V + L +L + E G
Sbjct: 3 VIGATGKTGRRLVKELLAR-GH--QVTALSRNPSKAPAPGVTPVQKDLFDLADLAEALAG 59
Query: 130 AS-VFVTGGTGFMGKTLTEKLLRAC 153
V G + LL A
Sbjct: 60 VDAVVDAFGARPDDSDGVKHLLDAA 84
>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 = 28.0 bits (63), Expect = 5.3
Identities = 8/21 (38%), Positives = 13/21 (61%)
Query: 74 VFVTGGTGFMGKTLTEKLLRA 94
V V G TGF+G+ + +L +
Sbjct: 3 VTVFGATGFIGRYVVNRLAKR 23
Score = 28.0 bits (63), Expect = 5.3
Identities = 8/21 (38%), Positives = 13/21 (61%)
Query: 132 VFVTGGTGFMGKTLTEKLLRA 152
V V G TGF+G+ + +L +
Sbjct: 3 VTVFGATGFIGRYVVNRLAKR 23
>gnl|CDD|187602 cd05344, BKR_like_SDR_like, putative beta-ketoacyl acyl carrier
protein [ACP] reductase (BKR)-like, SDR. This subgroup
resembles the SDR family, but does not have a perfect
match to the NAD-binding motif or the catalytic tetrad
characteristic of the SDRs. It includes the SDRs, Q9HYA2
from Pseudomonas aeruginosa PAO1 and APE0912 from
Aeropyrum pernix K1. BKR catalyzes the NADPH-dependent
reduction of ACP in the first reductive step of de novo
fatty acid synthesis (FAS). FAS consists of four
elongation steps, which are repeated to extend the fatty
acid chain through the addition of two-carbo units from
malonyl acyl-carrier protein (ACP): condensation,
reduction, dehydration, and a final reduction. Type II
FAS, typical of plants and many bacteria, maintains
these activities on discrete polypeptides, while type I
FAS utilizes one or two multifunctional polypeptides.
BKR resembles enoyl reductase, which catalyzes the
second reduction step in FAS. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold
(alpha/beta folding pattern with a central beta-sheet),
an NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRS are approximately
350 residues. Sequence identity between different SDR
enzymes are typically in the 15-30% range, but the
enzymes share the Rossmann fold NAD-binding motif and
characteristic NAD-binding and catalytic sequence
patterns. These enzymes have a 3-glycine N-terminal
NAD(P)(H)-binding pattern (typically, TGxxxGxG in
classical SDRs and TGxxGxxG in extended SDRs), while
substrate binding is in the C-terminal region. A
critical catalytic Tyr residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering), is often found in a conserved YXXXK pattern.
In addition to the Tyr and Lys, there is often an
upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn
(Asn-107, 15-PGDH numbering) or additional Ser,
contributing to the active site. Substrates for these
enzymes include sugars, steroids, alcohols, and aromatic
compounds. The standard reaction mechanism is a proton
relay involving the conserved Tyr and Lys, as well as
Asn (or Ser). Some SDR family members, including 17
beta-hydroxysteroid dehydrogenase contain an additional
helix-turn-helix motif that is not generally found among
SDRs.
Length = 253
Score = 28.0 bits (63), Expect = 5.3
Identities = 39/169 (23%), Positives = 61/169 (36%), Gaps = 31/169 (18%)
Query: 71 GASVFVTGGTGFMGKTLTEKLLRA-CPHLERVYLLVRPKKGKTVSERLDELFEDREFYRG 129
G VT + +G + L R RV + R + E L+ + G
Sbjct: 1 GKVALVTAASSGIGLAIARALAREGA----RVAICARNR------ENLERAASELRAG-G 49
Query: 130 ASVFVTGGTGFMGKTLTEKLLRACPHLERVYLLV----RPKKGKTVSERLDELFED---- 181
A V + + + +A RV +LV P G +E DE + +
Sbjct: 50 AGVLAVVADLTDPEDIDRLVEKAGDAFGRVDILVNNAGGPPPG-PFAELTDEDWLEAFDL 108
Query: 182 RLFS--RL-KAEVPHFRSK-------ISVVTGDVSLPGLGLSAADRAVL 220
+L S R+ +A +P + + IS +T P L LS RA L
Sbjct: 109 KLLSVIRIVRAVLPGMKERGWGRIVNISSLTVKEPEPNLVLSNVARAGL 157
>gnl|CDD|237218 PRK12825, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 249
Score = 27.9 bits (63), Expect = 5.4
Identities = 8/24 (33%), Positives = 12/24 (50%)
Query: 71 GASVFVTGGTGFMGKTLTEKLLRA 94
G VTG +G+ + +L RA
Sbjct: 6 GRVALVTGAARGLGRAIALRLARA 29
Score = 27.9 bits (63), Expect = 5.4
Identities = 8/24 (33%), Positives = 12/24 (50%)
Query: 129 GASVFVTGGTGFMGKTLTEKLLRA 152
G VTG +G+ + +L RA
Sbjct: 6 GRVALVTGAARGLGRAIALRLARA 29
>gnl|CDD|184381 PRK13900, PRK13900, type IV secretion system ATPase VirB11;
Provisional.
Length = 332
Score = 28.2 bits (63), Expect = 5.7
Identities = 14/42 (33%), Positives = 21/42 (50%), Gaps = 5/42 (11%)
Query: 65 IQEFYRGA-----SVFVTGGTGFMGKTLTEKLLRACPHLERV 101
I+EF A ++ ++GGT T T LR P +ER+
Sbjct: 149 IKEFLEHAVISKKNIIISGGTSTGKTTFTNAALREIPAIERL 190
>gnl|CDD|183778 PRK12829, PRK12829, short chain dehydrogenase; Provisional.
Length = 264
Score = 28.1 bits (63), Expect = 6.1
Identities = 9/26 (34%), Positives = 12/26 (46%)
Query: 69 YRGASVFVTGGTGFMGKTLTEKLLRA 94
G V VTGG +G+ + E A
Sbjct: 9 LDGLRVLVTGGASGIGRAIAEAFAEA 34
Score = 28.1 bits (63), Expect = 6.1
Identities = 9/26 (34%), Positives = 12/26 (46%)
Query: 127 YRGASVFVTGGTGFMGKTLTEKLLRA 152
G V VTGG +G+ + E A
Sbjct: 9 LDGLRVLVTGGASGIGRAIAEAFAEA 34
>gnl|CDD|187556 cd05245, SDR_a2, atypical (a) SDRs, subgroup 2. This subgroup
contains atypical SDRs, one member is identified as
Escherichia coli protein ybjT, function unknown.
Atypical SDRs are distinct from classical SDRs. Members
of this subgroup have a glycine-rich NAD(P)-binding
motif consensus that generally matches the extended
SDRs, TGXXGXXG, but lacks the characteristic active site
residues of the SDRs. This subgroup has basic residues
(HXXXR) in place of the active site motif YXXXK, these
may have a catalytic role. Atypical SDRs generally lack
the catalytic residues characteristic of the SDRs, and
their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Atypical SDRs include biliverdin IX beta
reductase (BVR-B,aka flavin reductase), NMRa (a negative
transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. In addition to the
Rossmann fold core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 293
Score = 28.1 bits (63), Expect = 6.5
Identities = 17/48 (35%), Positives = 24/48 (50%), Gaps = 6/48 (12%)
Query: 74 VFVTGGTGFMGKTLTEKLLRACPHLERVYLLVRPKKGKT---VSERLD 118
V VTG TG++G L +LL+ +V LVR + SER+
Sbjct: 1 VLVTGATGYVGGRLVPRLLQ---EGHQVRALVRSPEKLADRPWSERVT 45
Score = 28.1 bits (63), Expect = 6.5
Identities = 17/48 (35%), Positives = 24/48 (50%), Gaps = 6/48 (12%)
Query: 132 VFVTGGTGFMGKTLTEKLLRACPHLERVYLLVRPKKGKT---VSERLD 176
V VTG TG++G L +LL+ +V LVR + SER+
Sbjct: 1 VLVTGATGYVGGRLVPRLLQ---EGHQVRALVRSPEKLADRPWSERVT 45
>gnl|CDD|212493 cd08932, HetN_like_SDR_c, HetN oxidoreductase-like, classical (c)
SDR. This subgroup includes Anabaena sp. strain PCC
7120 HetN, a putative oxidoreductase involved in
heterocyst differentiation, and related proteins. SDRs
are a functionally diverse family of oxidoreductases
that have a single domain with a structurally conserved
Rossmann fold (alpha/beta folding pattern with a central
beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRs are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes catalyze a
wide range of activities including the metabolism of
steroids, cofactors, carbohydrates, lipids, aromatic
compounds, and amino acids, and act in redox sensing.
Classical SDRs have an TGXXX[AG]XG cofactor binding
motif and a YXXXK active site motif, with the Tyr
residue of the active site motif serving as a critical
catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 223
Score = 27.7 bits (62), Expect = 7.1
Identities = 10/34 (29%), Positives = 14/34 (41%), Gaps = 3/34 (8%)
Query: 74 VFVTGGTGFMGKTLTEKLLRACPHLERVYLLVRP 107
VTG + +G + L R RV L +R
Sbjct: 3 ALVTGASRGIGIEIARALAR---DGYRVSLGLRN 33
Score = 27.7 bits (62), Expect = 7.1
Identities = 10/34 (29%), Positives = 14/34 (41%), Gaps = 3/34 (8%)
Query: 132 VFVTGGTGFMGKTLTEKLLRACPHLERVYLLVRP 165
VTG + +G + L R RV L +R
Sbjct: 3 ALVTGASRGIGIEIARALAR---DGYRVSLGLRN 33
>gnl|CDD|187661 cd08958, FR_SDR_e, flavonoid reductase (FR), extended (e) SDRs.
This subgroup contains FRs of the extended SDR-type and
related proteins. These FRs act in the NADP-dependent
reduction of flavonoids, ketone-containing plant
secondary metabolites; they have the characteristic
active site triad of the SDRs (though not the upstream
active site Asn) and a NADP-binding motif that is very
similar to the typical extended SDR motif. Extended SDRs
are distinct from classical SDRs. In addition to the
Rossmann fold (alpha/beta folding pattern with a central
beta-sheet) core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids. Extended SDRs are a
diverse collection of proteins, and include isomerases,
epimerases, oxidoreductases, and lyases; they typically
have a TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 293
Score = 27.9 bits (63), Expect = 7.2
Identities = 30/125 (24%), Positives = 55/125 (44%), Gaps = 30/125 (24%)
Query: 132 VFVTGGTGFMGKTLTEKLLRACPHLERVYLLVRPKKGKTVSERLDELFEDRLFSRLKAEV 191
V VTG +GF+G L ++LL+ +G TV + + +++ + L E+
Sbjct: 1 VCVTGASGFIGSWLVKRLLQ---------------RGYTVRATVRDPGDEKKVAHLL-EL 44
Query: 192 PHFRSKISVVTGDVSLPGLGLSAADRAVLRRNVTVVFHGAATVRFD------ENIKVAI- 244
+ ++ + D+ G + D A+ VFH A+ V FD E I+ A+
Sbjct: 45 EGAKERLKLFKADLLDYG----SFDAAI--DGCDGVFHVASPVDFDSEDPEEEMIEPAVK 98
Query: 245 -AINI 248
+N+
Sbjct: 99 GTLNV 103
>gnl|CDD|184048 PRK13428, PRK13428, F0F1 ATP synthase subunit delta; Provisional.
Length = 445
Score = 27.8 bits (62), Expect = 7.2
Identities = 28/87 (32%), Positives = 43/87 (49%), Gaps = 17/87 (19%)
Query: 149 LLRACPHLERVYLLVRPKKGKTVSERLDELFEDRLFSR-LKAEVPHFRSKISVVTGDVSL 207
L+ A H+ R+ LL R ++ V E D+LF FSR L A+ +++++ D ++
Sbjct: 267 LIDALEHVARLALLERAERAGQVDEVEDQLFR---FSRILDAQ-----PRLAILLSDYTV 318
Query: 208 PGLGLSAADRAVLRRNVTVVFHGAATV 234
P A R L R V GA+TV
Sbjct: 319 P-----ADGRVALLRK---VLGGASTV 337
>gnl|CDD|187569 cd05259, PCBER_SDR_a, phenylcoumaran benzylic ether reductase
(PCBER) like, atypical (a) SDRs. PCBER and
pinoresinol-lariciresinol reductases are NADPH-dependent
aromatic alcohol reductases, and are atypical members of
the SDR family. Other proteins in this subgroup are
identified as eugenol synthase. These proteins contain
an N-terminus characteristic of NAD(P)-binding proteins
and a small C-terminal domain presumed to be involved in
substrate binding, but they do not have the conserved
active site Tyr residue typically found in SDRs.
Numerous other members have unknown functions. The
glycine rich NADP-binding motif in this subgroup is of 2
forms: GXGXXG and G[GA]XGXXG; it tends to be atypical
compared with the forms generally seen in classical or
extended SDRs. The usual SDR active site tetrad is not
present, but a critical active site Lys at the usual SDR
position has been identified in various members, though
other charged and polar residues are found at this
position in this subgroup. Atypical SDR-related proteins
retain the Rossmann fold of the SDRs, but have limited
sequence identity and generally lack the catalytic
properties of the archetypical members. Atypical SDRs
include biliverdin IX beta reductase (BVR-B,aka flavin
reductase), NMRa (a negative transcriptional regulator
of various fungi), progesterone 5-beta-reductase like
proteins, phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. In addition to the
Rossmann fold core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 282
Score = 27.7 bits (62), Expect = 7.4
Identities = 10/37 (27%), Positives = 16/37 (43%), Gaps = 2/37 (5%)
Query: 73 SVFVTGGTGFMGKTLTEKLLRACPHLERVYLLVRPKK 109
+ + G TG +G + LL + V +L RP
Sbjct: 1 KIAIAGATGTLGGPIVSALLASPGF--TVTVLTRPSS 35
Score = 27.7 bits (62), Expect = 7.4
Identities = 10/37 (27%), Positives = 16/37 (43%), Gaps = 2/37 (5%)
Query: 131 SVFVTGGTGFMGKTLTEKLLRACPHLERVYLLVRPKK 167
+ + G TG +G + LL + V +L RP
Sbjct: 1 KIAIAGATGTLGGPIVSALLASPGF--TVTVLTRPSS 35
>gnl|CDD|99785 cd06188, NADH_quinone_reductase, Na+-translocating NADH:quinone
oxidoreductase (Na+-NQR) FAD/NADH binding domain.
(Na+-NQR) provides a means of storing redox reaction
energy via the transmembrane translocation of Na2+ ions.
The C-terminal domain resembles ferredoxin:NADP+
oxidoreductase, and has NADH and FAD binding sites.
(Na+-NQR) is distinct from H+-translocating NADH:quinone
oxidoreductases and noncoupled NADH:quinone
oxidoreductases. The NAD(P) binding domain of ferredoxin
reductase-like proteins catalyze electron transfer
between an NAD(P)-binding domain of the alpha/beta class
and a discrete (usually N-terminal) domain which vary in
orientation with respect to the NAD(P) binding domain.
The N-terminal domain of this group typically contains
an iron-sulfur cluster binding domain.
Length = 283
Score = 27.7 bits (62), Expect = 7.6
Identities = 22/69 (31%), Positives = 30/69 (43%), Gaps = 16/69 (23%)
Query: 132 VFVTGGTGFMGKTLTEKLLRACPHLERVYLLVRPKKGKTVS-----ERLDELFEDRLFSR 186
VF+ GG G M LR+ H+ LL K + +S L ELF F
Sbjct: 154 VFIGGGAG-MAP------LRS--HIFH--LLKTLKSKRKISFWYGARSLKELFYQEEFEA 202
Query: 187 LKAEVPHFR 195
L+ E P+F+
Sbjct: 203 LEKEFPNFK 211
>gnl|CDD|235738 PRK06199, PRK06199, ornithine cyclodeaminase; Validated.
Length = 379
Score = 27.8 bits (62), Expect = 7.7
Identities = 10/32 (31%), Positives = 17/32 (53%)
Query: 79 GTGFMGKTLTEKLLRACPHLERVYLLVRPKKG 110
G G MGKT+ + CP ++ + + R +K
Sbjct: 162 GPGVMGKTILAAFMAVCPGIDTIKIKGRGQKS 193
Score = 27.8 bits (62), Expect = 7.7
Identities = 10/32 (31%), Positives = 17/32 (53%)
Query: 137 GTGFMGKTLTEKLLRACPHLERVYLLVRPKKG 168
G G MGKT+ + CP ++ + + R +K
Sbjct: 162 GPGVMGKTILAAFMAVCPGIDTIKIKGRGQKS 193
>gnl|CDD|222580 pfam14180, DOCK_C2, GTP-GDP exchange factor. Dock proteins are
atypical GTP-GDP exchange factors for the small GTPases
Pac and Cdc42, and are implicated in biological roles
related to cell-migration and phagocytosis.
Length = 178
Score = 26.9 bits (60), Expect = 9.0
Identities = 7/40 (17%), Positives = 18/40 (45%), Gaps = 6/40 (15%)
Query: 224 VTVVFHGAATVRFDENIKVAIAINIFG------SFVHVST 257
+ V + +F++ K+ + +++ +F HVS
Sbjct: 61 FSSVSYHNKNPQFNDEFKLQLPLDLTPGHHLLFTFYHVSV 100
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
0.321 0.139 0.405
Gapped
Lambda K H
0.267 0.0845 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,959,765
Number of extensions: 1604243
Number of successful extensions: 2230
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2191
Number of HSP's successfully gapped: 202
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 (21.8 bits)
S2: 59 (26.3 bits)