RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17679
(303 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 = 261 bits (668), Expect = 3e-86
Identities = 112/284 (39%), Positives = 157/284 (55%), Gaps = 39/284 (13%)
Query: 45 KTIFLTGGTGFMGKTVVEKLLRSCPHLKHIYLLVRPKKGKDIQERLDAIFEDRLFWRLRA 104
K++ +TG TGF+GK ++EKLLRSCP + IYLL+R K G+ +ERL + +D+LF R R
Sbjct: 1 KSVLITGATGFLGKVLLEKLLRSCPDIGKIYLLIRGKSGQSAEERLRELLKDKLFDRGRN 60
Query: 105 EVPDFRSKVSAVAGDCSLPGLGLSETDRATLVKQVNIVFHGAATVRFDEHIKMAVKINVC 164
P F SK+ + GD S P LGLS+ D TL+++VNI+ H AATV FDE + A+ INV
Sbjct: 61 LNPLFESKIVPIEGDLSEPNLGLSDEDLQTLIEEVNIIIHCAATVTFDERLDEALSINVL 120
Query: 165 GVQAMLQLAREMKDLKAFVHVSTAFTHCPRERIDEEFYPVPLKYENLIQLISETGDEELS 224
G +L+LA+ K LKAFVHVSTA+ + R+ I+E+ YP P E LI ++ D EL
Sbjct: 121 GTLRLLELAKRCKKLKAFVHVSTAYVNGDRQLIEEKVYPPPADPEKLIDILELMDDLELE 180
Query: 225 EMTPNRVH---------------------------------ISGT------GWIDNVYGP 245
TP + + T GWIDN GP
Sbjct: 181 RATPKLLGGHPNTYTFTKALAERLVLKERGNLPLVIVRPSIVGATLKEPFPGWIDNFNGP 240
Query: 246 IGMLVGIATGVLHTHLINLNTVTDMVPVDLVVNSMISIAWSIGE 289
G+ + G+L T + N V D++PVD+V N++++ A G
Sbjct: 241 DGLFLAYGKGILRTMNADPNAVADIIPVDVVANALLAAAAYSGV 284
>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 = 214 bits (546), Expect = 7e-69
Identities = 96/260 (36%), Positives = 136/260 (52%), Gaps = 43/260 (16%)
Query: 49 LTGGTGFMGKTVVEKLLRSCPHLKHIYLLVRPKKGKDIQERL-DAIFEDRLFWRLRAEVP 107
LTG TGF+GK ++EKLLRS P +K IY LVR K G+ ERL + + LF RL+A
Sbjct: 1 LTGATGFLGKVLLEKLLRSTPEVK-IYCLVRAKDGESALERLRQELLKYGLFDRLKA--- 56
Query: 108 DFRSKVSAVAGDCSLPGLGLSETDRATLVKQVNIVFHGAATVRFDEHIKMAVKINVCGVQ 167
++ VAGD S P LGLS+ D L ++V+++ H AATV F E NV G +
Sbjct: 57 --LERIIPVAGDLSEPNLGLSDEDFQELAEEVDVIIHNAATVNFVEPYSDLRATNVLGTR 114
Query: 168 AMLQLAREMKDLKAFVHVSTAFTHCPRE-RIDEEFYPV-----------PLKY------- 208
+L+LA++MK F HVSTA+ + R ++E+ Y + P Y
Sbjct: 115 EVLRLAKQMK-KLPFHHVSTAYVNGERGGLLEEKPYKLDEDEPALLGGLPNGYTQSKWLA 173
Query: 209 ENLIQLISETGDEELSEMTPNRVH----ISG---TGWIDNVY-GPIGMLVGIATGVLHTH 260
E L++ E + P ++ I+G TGWI+ GP G+L G GVL
Sbjct: 174 EQLVR--------EAAGGLPVVIYRPSIITGESRTGWINGDDFGPRGLLGGAGLGVLPDI 225
Query: 261 LINLNTVTDMVPVDLVVNSM 280
L + + D+VPVD V N++
Sbjct: 226 LGDPDARLDLVPVDYVANAI 245
>gnl|CDD|215538 PLN02996, PLN02996, fatty acyl-CoA reductase.
Length = 491
Score = 112 bits (281), Expect = 7e-28
Identities = 60/157 (38%), Positives = 92/157 (58%), Gaps = 7/157 (4%)
Query: 40 EFYRDKTIFLTGGTGFMGKTVVEKLLRSCPHLKHIYLLVRPKKGKDIQERL-DAIFEDRL 98
+F +KTI +TG TGF+ K VEK+LR P++K +YLL+R K +RL D + L
Sbjct: 7 QFLENKTILVTGATGFLAKIFVEKILRVQPNVKKLYLLLRASDAKSATQRLHDEVIGKDL 66
Query: 99 FWRLRAEV-PDFRS----KVSAVAGDCSLPGLGLSETD-RATLVKQVNIVFHGAATVRFD 152
F LR ++ + S KV+ V GD S LG+ +++ R + K+++IV + AAT FD
Sbjct: 67 FKVLREKLGENLNSLISEKVTPVPGDISYDDLGVKDSNLREEMWKEIDIVVNLAATTNFD 126
Query: 153 EHIKMAVKINVCGVQAMLQLAREMKDLKAFVHVSTAF 189
E +A+ IN G +L A++ +K +HVSTA+
Sbjct: 127 ERYDVALGINTLGALNVLNFAKKCVKVKMLLHVSTAY 163
Score = 43.5 bits (103), Expect = 8e-05
Identities = 18/45 (40%), Positives = 28/45 (62%)
Query: 237 GWIDNVYGPIGMLVGIATGVLHTHLINLNTVTDMVPVDLVVNSMI 281
GWI+ + ++VG G L L + N+V D++P D+VVN+MI
Sbjct: 274 GWIEGLRTIDSVIVGYGKGKLTCFLADPNSVLDVIPADMVVNAMI 318
>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 = 102 bits (255), Expect = 2e-25
Identities = 66/250 (26%), Positives = 113/250 (45%), Gaps = 29/250 (11%)
Query: 47 IFLTGGTGFMGKTVVEKLLRSCPHLKHIYLLVRPKKGKDIQERLDAIFEDRLFWRLRAEV 106
+F+TGGTGF+G+ +V++LL + + +LVR + + ER++ E
Sbjct: 1 VFVTGGTGFLGRHLVKRLLEN---GFKVLVLVRSESLGEAHERIE-------------EA 44
Query: 107 PDFRSKVSAVAGDCSLPGLGLSETDRATLVKQVNIVFHGAATVRFDEHIKMAVKINVCGV 166
+V + GD + P LGLS L +V+ V H AA+ F + A + N+ G
Sbjct: 45 GLEADRVRVLEGDLTQPNLGLSAAASRELAGKVDHVIHCAASYDFQAPNEDAWRTNIDGT 104
Query: 167 QAMLQLAREMKDLKAFVHVSTAFTHCPRERIDEE--FYPVP--------LKYENLIQLIS 216
+ +L+LA D++ F +VSTA+ RE E P K E + +
Sbjct: 105 EHVLELAAR-LDIQRFHYVSTAYVAGNREGNIRETELNPGQNFKNPYEQSKAEAEQLVRA 163
Query: 217 ETGDEELSEMTPN-RVHISGTGWIDNVYGPIGMLVGIATGVLHTHLI-NLNTVTDMVPVD 274
L+ P+ V S TG I+ + G +L +A + N ++VPVD
Sbjct: 164 AATQIPLTVYRPSIVVGDSKTGRIEKIDGLYELLNLLAKLGRWLPMPGNKGARLNLVPVD 223
Query: 275 LVVNSMISIA 284
V ++++ ++
Sbjct: 224 YVADAIVYLS 233
>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 = 98.5 bits (246), Expect = 5e-24
Identities = 52/149 (34%), Positives = 75/149 (50%), Gaps = 13/149 (8%)
Query: 46 TIFLTGGTGFMGKTVVEKLLRSCPHLKHIYLLVRPKKGKDIQERL-DAIFEDRLFWRLRA 104
T+ LTG TGF+G ++ +LL+ ++ IY LVR K + ERL D + E L
Sbjct: 1 TVLLTGATGFLGAYLLRELLK-RKNVSKIYCLVRAKDEEAALERLIDNLKEYGLNLWDEL 59
Query: 105 EVPDFRSKVSAVAGDCSLPGLGLSETDRATLVKQVNIVFHGAATVRF---DEHIKMAVKI 161
S++ V GD S P LGLS+ D L ++V+++ H A V + E +K
Sbjct: 60 ----ELSRIKVVVGDLSKPNLGLSDDDYQELAEEVDVIIHNGANVNWVYPYEELK---PA 112
Query: 162 NVCGVQAMLQLAREMKDLKAFVHVSTAFT 190
NV G + +L+LA K LK VST
Sbjct: 113 NVLGTKELLKLAATGK-LKPLHFVSTLSV 140
>gnl|CDD|215279 PLN02503, PLN02503, fatty acyl-CoA reductase 2.
Length = 605
Score = 97.6 bits (243), Expect = 1e-22
Identities = 58/173 (33%), Positives = 94/173 (54%), Gaps = 7/173 (4%)
Query: 35 GTPMQEFYRDKTIFLTGGTGFMGKTVVEKLLRSCPHLKHIYLLVRPKKGKDIQERL-DAI 93
G + EF R K +TG TGF+ K ++EK+LR+ P + IYLL++ K + ERL + +
Sbjct: 110 GIGIAEFLRGKNFLITGATGFLAKVLIEKILRTNPDVGKIYLLIKAKDKEAAIERLKNEV 169
Query: 94 FEDRLFWRLR-AEVPDFRS----KVSAVAGDCSLPGLGLSETDRATLVKQVNIVFHGAAT 148
+ LF L+ ++S K+ V G+ LGL + K+V+++ + AA
Sbjct: 170 IDAELFKCLQETHGKSYQSFMLSKLVPVVGNVCESNLGLEPDLADEIAKEVDVIINSAAN 229
Query: 149 VRFDEHIKMAVKINVCGVQAMLQLAREMKDLKAFVHVSTAFTHCPRE-RIDEE 200
FDE +A+ IN G ++ A++ K LK F+ VSTA+ + R+ RI E+
Sbjct: 230 TTFDERYDVAIDINTRGPCHLMSFAKKCKKLKLFLQVSTAYVNGQRQGRIMEK 282
Score = 30.6 bits (69), Expect = 1.2
Identities = 19/58 (32%), Positives = 31/58 (53%), Gaps = 5/58 (8%)
Query: 237 GWIDN--VYGPIGMLVGIATGVLHTHLINLNTVTDMVPVDLVVN-SMISIAWSIGESG 291
GW++ + PI + G G L L + N V D+VP D+VVN ++ ++A G +
Sbjct: 388 GWMEGNRMMDPIVLYYG--KGQLTGFLADPNGVLDVVPADMVVNATLAAMAKHGGAAK 443
>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 = 89.8 bits (223), Expect = 2e-20
Identities = 44/143 (30%), Positives = 66/143 (46%), Gaps = 8/143 (5%)
Query: 45 KTIFLTGGTGFMGKTVVEKLLRSCPHLKHIYLLVRPKKGKDIQERLDAIFEDRLFWRLRA 104
+ + LTG TGF+G ++ +LL K + LVR + + RL+ F+ W +
Sbjct: 1 RNVLLTGATGFLGAYLLLELLDR-SDAK-VICLVRAQSDEAALARLEKTFDLYRHWDELS 58
Query: 105 EVPDFRSKVSAVAGDCSLPGLGLSETDRATLVKQVNIVFHGAATVRFDEHIKMAVKINVC 164
+V VAGD + P LGLSE L + V+++ H AA V NV
Sbjct: 59 A-----DRVEVVAGDLAEPDLGLSERTWQELAENVDLIIHNAALVNHVFPYSELRGANVL 113
Query: 165 GVQAMLQLAREMKDLKAFVHVST 187
G +L+LA K K +VS+
Sbjct: 114 GTAEVLRLAATGK-PKPLHYVSS 135
>gnl|CDD|233557 TIGR01746, Thioester-redct, thioester reductase domain. This model
includes the terminal domain from the fungal alpha
aminoadipate reductase enzyme (also known as
aminoadipate semialdehyde dehydrogenase) which is
involved in the biosynthesis of lysine , as well as the
reductase-containing component of the myxochelin
biosynthetic gene cluster, MxcG. The mechanism of
reduction involves activation of the substrate by
adenylation and transfer to a covalently-linked
pantetheine cofactor as a thioester. This thioester is
then reduced to give an aldehyde (thus releasing the
product) and a regenerated pantetheine thiol. (In
myxochelin biosynthesis this aldehyde is further reduced
to an alcohol or converted to an amine by an
aminotransferase.) This is a fundamentally different
reaction than beta-ketoreductase domains of polyketide
synthases which act at a carbonyl two carbons removed
from the thioester and forms an alcohol as a product.
This domain is invariably found at the C-terminus of the
proteins which contain it (presumably because it results
in the release of the product). The majority of hits to
this model are non-ribosomal peptide synthetases in
which this domain is similarly located proximal to a
thiolation domain (pfam00550). In some cases this domain
is found at the end of a polyketide synthetase enzyme,
but is unlike ketoreductase domains which are found
before the thiolase domains. Exceptions to this observed
relationship with the thiolase domain include three
proteins which consist of stand-alone reductase domains
(GP|466833 from M. leprae, GP|435954 from Anabaena and
OMNI|NTL02SC1199 from Strep. coelicolor) and one protein
(OMNI|NTL01NS2636 from Nostoc) which contains N-terminal
homology with a small group of hypothetical proteins but
no evidence of a thiolation domain next to the putative
reductase domain. Below the noise cutoff to this model
are proteins containing more distantly related
ketoreductase and dehydratase/epimerase domains. It has
been suggested that a NADP-binding motif can be found in
the N-terminal portion of this domain that may form a
Rossman-type fold.
Length = 367
Score = 87.9 bits (218), Expect = 1e-19
Identities = 57/192 (29%), Positives = 84/192 (43%), Gaps = 27/192 (14%)
Query: 46 TIFLTGGTGFMGKTVVEKLLRSCPHLKHIYLLVRPKKGKDIQERLDAIFEDRLFWRLRAE 105
T+ LTG TGF+G ++E+LLR K + LVR + ERL +RL E
Sbjct: 1 TVLLTGATGFLGAYLLEELLRRSTQAK-VICLVRAASEEHAMERLREALRS---YRLWHE 56
Query: 106 VPDFRSKVSAVAGDCSLPGLGLSETDRATLVKQVNIVFHGAATVRF---DEHIKMAVKIN 162
R ++ VAGD S P LGLS+ + L + V+ + H A V + ++ A N
Sbjct: 57 DLA-RERIEVVAGDLSEPRLGLSDAEWERLAENVDTIVHNGALVNWVYPYSELRGA---N 112
Query: 163 VCGVQAMLQLAREMKDLKAFVHVST----AFTHCPRERIDEEFYPVPL---------KY- 208
V G + +L+LA K +VST A D+ P K+
Sbjct: 113 VLGTREVLRLA-ASGRAKPLHYVSTISVGAAIDLSTVTEDDATVTPPPGLAGGYAQSKWV 171
Query: 209 -ENLIQLISETG 219
E L++ S+ G
Sbjct: 172 AELLVREASDRG 183
>gnl|CDD|235962 PRK07201, PRK07201, short chain dehydrogenase; Provisional.
Length = 657
Score = 78.8 bits (195), Expect = 2e-16
Identities = 75/271 (27%), Positives = 121/271 (44%), Gaps = 50/271 (18%)
Query: 46 TIFLTGGTGFMGKTVVEKLLRSCPHLKHIYLLVRPKKGKDIQERLDAIFEDRLFWRLRAE 105
F+TGGTGF+G+ +V +LL +++LVR + RL+A+ W
Sbjct: 2 RYFVTGGTGFIGRRLVSRLLDRRREAT-VHVLVRRQS----LSRLEALAAY---WGA--- 50
Query: 106 VPDFRSKVSAVAGDCSLPGLGLSETDRATLVKQVNIVFHGAAT--VRFDEHIKMAVKINV 163
+V + GD + PGLGLSE D A L ++ V H AA + DE + A NV
Sbjct: 51 -----DRVVPLVGDLTEPGLGLSEADIAELGD-IDHVVHLAAIYDLTADEEAQRAA--NV 102
Query: 164 CGVQAMLQLAREMKDLKAFVHVST---AFTHCPRERIDE----EFYPVPL---KYENLIQ 213
G + +++LA ++ F HVS+ A + R D+ + P P K+E +
Sbjct: 103 DGTRNVVELAERLQA-ATFHHVSSIAVAGDYEGVFREDDFDEGQGLPTPYHRTKFEAE-K 160
Query: 214 LISETGDEELSEMTPNRVHI-------SGTGWIDNVYGP---IGMLVGIATGVLHTHLIN 263
L+ E P RV+ S TG +D + GP +L +A ++
Sbjct: 161 LVREECG------LPWRVYRPAVVVGDSRTGEMDKIDGPYYFFKVLAKLAKLPSWLPMVG 214
Query: 264 LNT-VTDMVPVDLVVNSMISIAWSIGESGKV 293
+ T++VPVD V +++ + G G+
Sbjct: 215 PDGGRTNIVPVDYVADALDHLMHKDGRDGQT 245
>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 = 62.4 bits (152), Expect = 9e-11
Identities = 32/107 (29%), Positives = 48/107 (44%), Gaps = 6/107 (5%)
Query: 44 DKTIFLTGGTGFMGKTVVEKLL-RSCPHLKHIYLLVRPKKGKDIQERLDAIFEDRLFWRL 102
T+FLTG TGF+G ++ LL R ++ VR K + ERL W
Sbjct: 971 PITVFLTGATGFLGSFILRDLLTRRSNSNFKVFAHVRAKSEEAGLERLRKTGTTYGIWDE 1030
Query: 103 RAEVPDFRSKVSAVAGDCSLPGLGLSETDRATLVKQVNIVFHGAATV 149
+ S++ V GD S GLS+ + L +V+++ H A V
Sbjct: 1031 E-----WASRIEVVLGDLSKEKFGLSDEKWSDLTNEVDVIIHNGALV 1072
>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 = 56.1 bits (136), Expect = 5e-09
Identities = 38/160 (23%), Positives = 56/160 (35%), Gaps = 34/160 (21%)
Query: 47 IFLTGGTGFMGKTVVEKLLRSCPHLKHIYLLVRPKKGKDIQERLDAIFEDRLFWRLRAEV 106
I +TG TGF+G +V LL + LVR + + ++
Sbjct: 1 ILVTGATGFLGSNLVRALLAQG---YRVRALVRS------GSDAVLLDGLPVEVV-EGDL 50
Query: 107 PDFRSKVSAVAGDCSLPGLGLSETDRATLVKQVNIVFHGAATVRF-DEHIKMAVKINVCG 165
D S +A+ G + VFH AA + K + NV G
Sbjct: 51 TDAASLAAAMKG--------------------CDRVFHLAAFTSLWAKDRKELYRTNVEG 90
Query: 166 VQAMLQLAREMKDLKAFVHVST--AFTHCPRERIDEEFYP 203
+ +L A E ++ VH S+ A P RIDE
Sbjct: 91 TRNVLDAALE-AGVRRVVHTSSIAALGGPPDGRIDETTPW 129
>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 = 52.2 bits (126), Expect = 8e-08
Identities = 39/150 (26%), Positives = 62/150 (41%), Gaps = 29/150 (19%)
Query: 44 DKTIFLTGGTGFMGKTVVEKLLRSCPHLKHIYLLVRPKKGKDIQERLDAIFEDRLFWRLR 103
KTI +TGG G +G +V ++L+ P ++ D E + + E R R
Sbjct: 2 GKTILVTGGAGSIGSELVRQILKFGPKKLIVF---------DRDE--NKLHELVRELRSR 50
Query: 104 AEVPDFRSKVSAVAGDCSLPGLGLSETDRATLV---KQVNIVFHGAAT--VRFDEHIKM- 157
R + GD + + +R + +IVFH AA V E
Sbjct: 51 FPHDKLRF----IIGD-------VRDKERLRRAFKERGPDIVFHAAALKHVPSMEDNPEE 99
Query: 158 AVKINVCGVQAMLQLAREMKDLKAFVHVST 187
A+K NV G + ++ A E ++ FV +ST
Sbjct: 100 AIKTNVLGTKNVIDAAIENG-VEKFVCIST 128
>gnl|CDD|224011 COG1086, COG1086, Predicted nucleoside-diphosphate sugar epimerases
[Cell envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 588
Score = 48.8 bits (117), Expect = 2e-06
Identities = 39/159 (24%), Positives = 63/159 (39%), Gaps = 33/159 (20%)
Query: 37 PMQEFYRDKTIFLTGGTGFMGKTVVEKLLRSCPHLKHIYLLVRPKKGK-DIQERLDAIFE 95
+ KT+ +TGG G +G + ++L+ P K I L R + I L F
Sbjct: 243 LIGAMLTGKTVLVTGGGGSIGSELCRQILKFNP--KEIILFSRDEYKLYLIDMELREKFP 300
Query: 96 DRLFWRLRAEVPDFRSKVSAVAGDCSLPGLGLSETDRATLVKQVNIVFHGAATVRFDEHI 155
+ +V D A+ G +V+IVFH AA +H+
Sbjct: 301 ELKLRFYIGDVRDRDRVERAMEG------------------HKVDIVFHAAAL----KHV 338
Query: 156 KM-------AVKINVCGVQAMLQLAREMKDLKAFVHVST 187
+ A+K NV G + + + A + +K FV +ST
Sbjct: 339 PLVEYNPEEAIKTNVLGTENVAEAAIKNG-VKKFVLIST 376
>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 = 43.8 bits (104), Expect = 6e-05
Identities = 43/171 (25%), Positives = 60/171 (35%), Gaps = 46/171 (26%)
Query: 45 KTIFLTGGTGFMGKTVVEKLLRSCPHLKHIYLLVRPKKGKDIQERLDAIFEDRLFWR-LR 103
+ +TG TGF+G VV LL ++ +LVRP DR L
Sbjct: 1 MKVLVTGATGFVGSAVVRLLLEQGEEVR---VLVRPT-------------SDRRNLEGLD 44
Query: 104 AEVPDFRSKVSAVAGDCSLPGLGLSETDRATL---VKQVNIVFHGAATVRF---DEHIKM 157
E+ V GD D A+L V +FH AA R D
Sbjct: 45 VEI---------VEGDL---------RDPASLRKAVAGCRALFHVAADYRLWAPDPEEMY 86
Query: 158 AVKINVCGVQAMLQLAREMKDLKAFVHVST--AFTHCPRERIDEEFYPVPL 206
A NV G + +L+ A E ++ V+ S+ +E P L
Sbjct: 87 A--ANVEGTRNLLRAALE-AGVERVVYTSSVATLGVRGDGTPADETTPSSL 134
>gnl|CDD|223528 COG0451, WcaG, Nucleoside-diphosphate-sugar epimerases [Cell
envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 314
Score = 43.4 bits (102), Expect = 7e-05
Identities = 43/171 (25%), Positives = 59/171 (34%), Gaps = 46/171 (26%)
Query: 45 KTIFLTGGTGFMGKTVVEKLLRSCPHLKHIYLLVRPKKGKDIQERLDAIFEDRLFWRLRA 104
I +TGG GF+G +VE+LL G D+ R RLR
Sbjct: 1 MRILVTGGAGFIGSHLVERLL---------------AAGHDV----------RGLDRLRD 35
Query: 105 EVPDFRSKVSAVAGDCSLPGLGLSETDRATLVKQVN----IVFHGAATVRF----DEHIK 156
+ S V V D TDR + + V H AA
Sbjct: 36 GLDPLLSGVEFVVLD---------LTDRDLVDELAKGVPDAVIHLAAQSSVPDSNASDPA 86
Query: 157 MAVKINVCGVQAMLQLAREMKDLKAFVHVSTA---FTHCPRERIDEEFYPV 204
+ +NV G +L+ AR +K FV S+ + P IDE+ P
Sbjct: 87 EFLDVNVDGTLNLLEAARAAG-VKRFVFASSVSVVYGDPPPLPIDEDLGPP 136
>gnl|CDD|215720 pfam00106, adh_short, short chain dehydrogenase. This family
contains a wide variety of dehydrogenases.
Length = 167
Score = 41.8 bits (99), Expect = 1e-04
Identities = 34/156 (21%), Positives = 55/156 (35%), Gaps = 36/156 (23%)
Query: 45 KTIFLTGGTGFMGKTVVEKLLRSCPHLKHIYLLVRPKKGKDIQERLDAIFEDRLFWRLRA 104
T+ +TGGTG +G + L +H+ L+ R E L A
Sbjct: 1 GTVLITGGTGGLGLALARWLAAEGA--RHLVLVSRRGPAPGAAE-------------LVA 45
Query: 105 EVPDFRSKVSAVAGDCSLPGLGLSETDRATLVKQVN-------IVFHGAATVR------- 150
E+ ++V+ A D + A L+ + V H A +
Sbjct: 46 ELEALGAEVTVAACDVA------DRDALAALLAALPAALGPLDGVVHNAGVLDDGPLEEL 99
Query: 151 FDEHIKMAVKINVCGVQAMLQLAREMKDLKAFVHVS 186
E + + V G + +L R++ DL AFV S
Sbjct: 100 TPERFERVLAPKVTGAWNLHELTRDL-DLGAFVLFS 134
>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 = 42.2 bits (99), Expect = 1e-04
Identities = 35/144 (24%), Positives = 51/144 (35%), Gaps = 29/144 (20%)
Query: 49 LTGGTGFMGKTVVEKLLRSCPHLKHIYLLVRPKKGKDI---QERLDAIFEDRLFWRLRAE 105
+TG +GF+ VVE+LL + VR LDA A+
Sbjct: 3 VTGASGFVASHVVEQLLE---RGYKVRATVRDPSKVKKVNHLLDLDAKPGRLELA--VAD 57
Query: 106 VPDFRSKVSAVAGDCSLPGLGLSETDRATLVKQVNIVFHGAATVRF-DEHIKMAVKINVC 164
+ D +S + G C+ VFH A V F + +K +
Sbjct: 58 LTDEQSFDEVIKG-CAG-------------------VFHVATPVSFSSKDPNEVIKPAIG 97
Query: 165 GVQAMLQLAREMKDLKAFVHVSTA 188
G L+ A K +K FV S+A
Sbjct: 98 GTLNALKAAAAAKSVKRFVLTSSA 121
>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 = 40.9 bits (97), Expect = 4e-04
Identities = 40/154 (25%), Positives = 65/154 (42%), Gaps = 43/154 (27%)
Query: 47 IFLTGGTGFMGKTVVEKLLRSCPHLKHIYLLVR-PKKGKDIQERLDAIFEDRLFWRLRAE 105
+ +TGG G +G + ++L+ P K I L R K +I++ L + D +LR
Sbjct: 1 VLVTGGGGSIGSELCRQILKFNP--KKIILFSRDEFKLYEIRQELRQEYND---PKLRFF 55
Query: 106 VPDFRSKVSAVAGDCSLPGLGLSETDRATLVK-----QVNIVFHGAATVRFDEHIKM--- 157
+ D R DR L + V+ VFH AA +H+ +
Sbjct: 56 IGDVR--------------------DRERLERAMEQHGVDTVFHAAAL----KHVPLVEY 91
Query: 158 ----AVKINVCGVQAMLQLAREMKDLKAFVHVST 187
A+K NV G + + + A E ++ FV +ST
Sbjct: 92 NPMEAIKTNVLGTENVAEAAIENG-VEKFVLIST 124
>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 = 41.0 bits (96), Expect = 5e-04
Identities = 38/141 (26%), Positives = 62/141 (43%), Gaps = 24/141 (17%)
Query: 49 LTGGTGFMGKTVVEKLLRSCPHLKHIYLLVRPKKGKDIQERLDAIFEDRLFWRLRAEVPD 108
+TGG GF+G+ ++ LL LK I + LD F L E
Sbjct: 4 VTGGGGFLGQHIIRLLLERKEELKEIRV-------------LDKAFGPELIEHF--EKSQ 48
Query: 109 FRSKVSAVAGDCSLPGLGLSETDRATLVKQVNIVFHGAATVRFD--EHIKMAVKINVCGV 166
++ V+ + GD LS RA + V++V H AA V + + ++NV G
Sbjct: 49 GKTYVTDIEGDI----KDLSFLFRA--CQGVSVVIHTAAIVDVFGPPNYEELEEVNVNGT 102
Query: 167 QAMLQLAREMKDLKAFVHVST 187
QA+L+ + ++K V+ S+
Sbjct: 103 QAVLEACVQ-NNVKRLVYTSS 122
>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 = 40.0 bits (94), Expect = 6e-04
Identities = 37/165 (22%), Positives = 58/165 (35%), Gaps = 35/165 (21%)
Query: 47 IFLTGGTGFMGKTVVEKLLRSCPHLKHIYLLVRPKKGKDIQERLDAIFEDRLFWRLRAEV 106
I +TGGTGF+G +V +LL+ + +L R ++ E R+R
Sbjct: 1 ILVTGGTGFIGSHLVRRLLQ---EGYEVIVLGRRRR-----------SESLNTGRIRFHE 46
Query: 107 PDFRSKVSAVAGDCSLPGLGLSETDRATLVKQVNIVFHGAATVRFDEHIKMAV---KINV 163
D +R Q + V H AA + + NV
Sbjct: 47 GDLTDP---------------DALERLLAEVQPDAVIHLAAQSGVGASFEDPADFIRANV 91
Query: 164 CGVQAMLQLAREMKDLKAFVHVSTA--FTHCPRERIDEEFYPVPL 206
G +L+ AR +K FV S++ + I E+ PL
Sbjct: 92 LGTLRLLEAARRA-GVKRFVFASSSEVYGDVADPPITEDTPLGPL 135
>gnl|CDD|200381 TIGR04130, FnlA, UDP-N-acetylglucosamine
4,6-dehydratase/5-epimerase. The FnlA enzyme is the
first step in the biosynthesis of UDP-FucNAc from
UDP-GlcNAc in E. coli (along with FnlB and FnlC). The
proteins identified by this model include FnlA homologs
in the O-antigen clusters of O4, O25, O26, O29 (Shigella
D11), O118, O145 and O172 serotype strains, all of which
produce O-antigens containing FucNAc (or the further
modified FucNAm). A homolog from Pseudomonas aerugiosa
serotype O11, WbjB, also involved in the biosynthesis of
UDP-FucNAc has been characterized and is now believed to
carry out both the initial 4,6-dehydratase reaction and
the subsequent epimerization of the resulting methyl
group at C-5. A phylogenetic tree of related sequences
shows a distinct clade of enzymes involved in the
biosynthesis of UDP-QuiNAc (Qui=qinovosamine). This
clade appears to be descendant from the common ancestor
of the Pseudomonas and E. coli fucose-biosynthesis
enzymes. It has been hypothesized that the first step in
the biosynthesis of these two compounds may be the same,
and thus that these enzymes all have the same function.
At present, lacking sufficient confirmation of this, the
current model trusted cutoff only covers the tree
segment surrounding the E. coli genes. The clades
containing the Pseudomonas and QuiNAc biosynthesis
enzymes score above the noise cutoff. Immediately below
the noise cutoff are enzymes involved in the
biosynthesis of UDP-RhaNAc (Rha=rhamnose), which again
may or may not produce the same product.
Length = 337
Score = 40.0 bits (93), Expect = 0.001
Identities = 36/136 (26%), Positives = 64/136 (47%), Gaps = 30/136 (22%)
Query: 42 YRDKTIFLTGGTGFMGKTVVEKLLRSCPHLKHIYLLVR-PKKGKDIQERLDAIFEDRLFW 100
++DK + +TGGTG G V+ + L + +K I + R KK D++++ + +L +
Sbjct: 2 FKDKILLITGGTGSFGNAVLRRFLDT--DIKEIRIFSRDEKKQDDMRKKYN---NSKLKF 56
Query: 101 RLRAEVPDFRSKVSAVAGDCSLPGLGLSETDRATLVKQVNIVFHGAATVRFDE---HIKM 157
+ +V D+RS ++A G V+ ++H AA + H
Sbjct: 57 YI-GDVRDYRSILNATRG--------------------VDFIYHAAALKQVPSCEFHPME 95
Query: 158 AVKINVCGVQAMLQLA 173
AVK NV G + +L+ A
Sbjct: 96 AVKTNVLGTENVLEAA 111
>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 = 39.6 bits (93), Expect = 0.001
Identities = 40/170 (23%), Positives = 62/170 (36%), Gaps = 34/170 (20%)
Query: 46 TIFLTGGTGFMGKTVVEKLLRSCPHLKHIYLLVRPKKGKDIQERLDAIFEDRLFWRLRAE 105
+ +TG GF+G + E+LLR ++ + I+ W L
Sbjct: 1 NVLVTGADGFIGSHLTERLLREGHEVRAL-----------------DIYNSFNSWGL--L 41
Query: 106 VPDFRSKVSAVAGDCSLPGLGLSETDRATLVKQVNIVFHGAATVRFDEHIKMA---VKIN 162
+ ++GD LVK+ ++VFH AA + V+ N
Sbjct: 42 DNAVHDRFHFISGDVRDASEVEY------LVKKCDVVFHLAALIAIPYSYTAPLSYVETN 95
Query: 163 VCGVQAMLQLAREMKDLKAFVHVSTA--FTHCPRERIDEEFYPVPLKYEN 210
V G +L+ A K VH ST+ + IDE+ PL Y N
Sbjct: 96 VFGTLNVLEAACV-LYRKRVVHTSTSEVYGTAQDVPIDEDH---PLLYIN 141
>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 = 38.2 bits (89), Expect = 0.002
Identities = 34/144 (23%), Positives = 58/144 (40%), Gaps = 36/144 (25%)
Query: 47 IFLTGGTGFMGKTVVEKLLRSCPHLKH-IYLLVRPKKGKDIQERLDAIFEDRLFWRLRAE 105
I + G TGF+G+ + +LL H + LLVR K RL ++
Sbjct: 1 ILILGATGFIGRALARELLE----QGHEVTLLVRNTK------RLSKEDQEP-------- 42
Query: 106 VPDFRSKVSAVAGDCSLPGLGLSETDRATLVKQVNIVFHGAATVRFDEHIKMAVKINVCG 165
V+ V GD + V+ V++V H A R +++V G
Sbjct: 43 -------VAVVEGDL------RDLDSLSDAVQGVDVVIHLAGAPRDTRDF---CEVDVEG 86
Query: 166 VQAMLQLAREMKDLKAFVHVSTAF 189
+ +L+ A+E +K F+ +S+
Sbjct: 87 TRNVLEAAKEAG-VKHFIFISSLG 109
>gnl|CDD|224013 COG1088, RfbB, dTDP-D-glucose 4,6-dehydratase [Cell envelope
biogenesis, outer membrane].
Length = 340
Score = 38.7 bits (91), Expect = 0.002
Identities = 35/154 (22%), Positives = 51/154 (33%), Gaps = 39/154 (25%)
Query: 45 KTIFLTGGTGFMGKTVVEKLLRSCPHLKHIYLLVRPKKGKDIQERLDAIFEDRLFWRLRA 104
I +TGG GF+G V +L P + L D+L
Sbjct: 1 MKILVTGGAGFIGSNFVRYILNKHPDDHVVNL-------------------DKL------ 35
Query: 105 EVPDFRSKVSAVAGDCSLPGLGLSETDRAT------LVK--QVNIVFHGAATVRFDEHIK 156
+ + +A P + D L K Q + V H AA D I
Sbjct: 36 ---TYAGNLENLADVEDSPRYRFVQGDICDRELVDRLFKEYQPDAVVHFAAESHVDRSID 92
Query: 157 MA---VKINVCGVQAMLQLAREMKDLKAFVHVST 187
++ NV G +L+ AR+ F H+ST
Sbjct: 93 GPAPFIQTNVVGTYTLLEAARKYWGKFRFHHIST 126
>gnl|CDD|236372 PRK09072, PRK09072, short chain dehydrogenase; Provisional.
Length = 263
Score = 38.0 bits (89), Expect = 0.004
Identities = 34/145 (23%), Positives = 58/145 (40%), Gaps = 39/145 (26%)
Query: 44 DKTIFLTGGTGFMGKTVVEKLLRSCPHLKHIYLLVRPKKGKDIQERLDAIFEDRLFWRLR 103
DK + LTG +G +G+ + E L + L LLV G++ E+L+ L
Sbjct: 5 DKRVLLTGASGGIGQALAEALAAAGARL----LLV----GRN-AEKLE---------ALA 46
Query: 104 AEVPDFRSKVSAVAGDCSLPGLGLSE-----TDRATLVKQVNIVFHGAATVRF------- 151
A +P + + V D L RA + +N++ + A F
Sbjct: 47 ARLP-YPGRHRWVVAD-----LTSEAGREAVLARAREMGGINVLINNAGVNHFALLEDQD 100
Query: 152 DEHIKMAVKINVCGVQAMLQLAREM 176
E I+ + +N + A +QL R +
Sbjct: 101 PEAIERLLALN---LTAPMQLTRAL 122
>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 = 38.1 bits (89), Expect = 0.004
Identities = 32/165 (19%), Positives = 57/165 (34%), Gaps = 44/165 (26%)
Query: 42 YRDKTIFL-TGGTGFMGKTVVEKLLRSCPHLKHIYLLVRPKKGKDIQERLDAIFEDRLFW 100
+ ++L TGG G +G+ + L R + + LL R + + + +
Sbjct: 202 LKPGGVYLVTGGAGGIGRALARALARR--YGARLVLLGRSPLPPEEEWKAQTLAA----- 254
Query: 101 RLRAEVPDFRSKVSAVAGDCSLPGLGLSETDRA---TLVKQV-------NIVFHGAATVR 150
L A V ++ D TD A L+++V + V H A +R
Sbjct: 255 -LEALGAR----VLYISAD---------VTDAAAVRRLLEKVRERYGAIDGVIHAAGVLR 300
Query: 151 FDEHIKM---------AVKINVCGVQAMLQLAREMKDLKAFVHVS 186
+ A K++ G+ + Q + L FV S
Sbjct: 301 DALLAQKTAEDFEAVLAPKVD--GLLNLAQALADE-PLDFFVLFS 342
>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 = 37.3 bits (87), Expect = 0.006
Identities = 37/145 (25%), Positives = 63/145 (43%), Gaps = 28/145 (19%)
Query: 47 IFLTGGTGFMGKTVVEKLLRSCPHLKHIYLLVRPKKGKDIQERLDAIFEDRLFWR-LRAE 105
+ +TG GF+G +VE L+R +G ++ R ++ W L
Sbjct: 1 VLVTGADGFIGSHLVEALVR---------------QGYEV--RAFVLYNSFNSWGWLDTS 43
Query: 106 VPDFRSKVSAVAGDCSLPGLGLSETDRATLVKQVNIVFHGAATVR--FDEHIKMA-VKIN 162
P+ + K+ V GD P + + +K ++VFH AA + + + V N
Sbjct: 44 PPEVKDKIEVVTGDIRDPD-SVRKA-----MKGCDVVFHLAALIAIPYSYIAPDSYVDTN 97
Query: 163 VCGVQAMLQLAREMKDLKAFVHVST 187
V G +LQ AR++ ++ VH ST
Sbjct: 98 VTGTLNVLQAARDL-GVEKVVHTST 121
>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 = 37.1 bits (87), Expect = 0.008
Identities = 42/153 (27%), Positives = 58/153 (37%), Gaps = 38/153 (24%)
Query: 45 KTIFLTGGTGFMGKTVVEKLLRSCPHLKHIYLLVRPKKGKDIQERLDAIFEDRL-----F 99
I +TGG GF+G V LL P K I L D+L
Sbjct: 1 MKILVTGGAGFIGSNFVRYLLNKYPDYKIINL-------------------DKLTYAGNL 41
Query: 100 WRLR--AEVPDFRSKVSAVAGDCSLPGLGLSETDRATLVKQVNIVFHGAATVRFDEHIKM 157
L + P +R V GD L DR ++++ V H AA D I
Sbjct: 42 ENLEDVSSSPRYR----FVKGDICDAEL----VDRLFEEEKIDAVIHFAAESHVDRSISD 93
Query: 158 A---VKINVCGVQAMLQLAREMKDLKAFVHVST 187
++ NV G +L+ AR+ + FVH+ST
Sbjct: 94 PEPFIRTNVLGTYTLLEAARKYGVKR-FVHIST 125
>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 = 36.5 bits (85), Expect = 0.012
Identities = 38/155 (24%), Positives = 57/155 (36%), Gaps = 43/155 (27%)
Query: 46 TIFLTGGTGFMGKTVVEKLLRSCPHLKHIYLL---VR-PKKGKDIQERLDAIF-EDRL-F 99
+ +TG TGF+ +VE+L LK Y + VR K ++ L A DRL F
Sbjct: 1 LVLVTGATGFIASHIVEQL------LKAGYKVRGTVRSLSKSAKLKALLKAAGYNDRLEF 54
Query: 100 WRLRAEVPDFRSKVSAVAGDCSLPGLGLSETDRATLVKQVNIVFHGAATVRF------DE 153
V D + +K V+ V H A+ F D+
Sbjct: 55 ----VIVDDL-----------------TAPNAWDEALKGVDYVIHVASPFPFTGPDAEDD 93
Query: 154 HIKMAVKINVCGVQAMLQLAREMKDLKAFVHVSTA 188
I AV+ G +L+ A+ +K V S+
Sbjct: 94 VIDPAVE----GTLNVLEAAKAAGSVKRVVLTSSV 124
>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 = 35.4 bits (82), Expect = 0.028
Identities = 36/149 (24%), Positives = 52/149 (34%), Gaps = 31/149 (20%)
Query: 46 TIFLTGGTGFMGKTVVEKLLRSCPHLKHIYLLVRPKKGKDIQERLDAIFEDRLFWRLR-- 103
I +TGG GF+G V +L P + I L D+L +
Sbjct: 1 RILVTGGAGFIGSNFVRYILNEHPDAEVIVL-------------------DKLTYAGNLE 41
Query: 104 --AEVPDFRSKVSAVAGDCSLPGLGLSETDRATLVKQVNIVFHGAATVRFDEHIKMA--- 158
A++ D + V GD R Q + V H AA D I
Sbjct: 42 NLADLED-NPRYRFVKGDIG----DRELVSRLFTEHQPDAVVHFAAESHVDRSISGPAAF 96
Query: 159 VKINVCGVQAMLQLAREMKDLKAFVHVST 187
++ NV G +L+ R+ F H+ST
Sbjct: 97 IETNVVGTYTLLEAVRKYWHEFRFHHIST 125
>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 = 35.1 bits (81), Expect = 0.041
Identities = 34/157 (21%), Positives = 47/157 (29%), Gaps = 39/157 (24%)
Query: 42 YRDKTIFLTGGTGFMGKTVVEKLLRSCPHLKHIYLLVRPKKGKDIQERLDAIFEDRLFWR 101
D T +TGG G +G V L +H+ LL R A L
Sbjct: 148 GLDGTYLITGGLGGLGLLVARWLAAR--GARHLVLLSRR------GPAPRAAARAALLRA 199
Query: 102 LRAEVPDFRSKVSAVAGDCSLPGLGLSETDRATLVKQVN------IVFHGAATVRF---- 151
A VS V D + A L+ ++ V H A +R
Sbjct: 200 GGAR-------VSVVRCDVT------DPAALAALLAELAAGGPLAGVIHAAGVLRDALLA 246
Query: 152 ---DEHIK--MAVKINVCGVQAMLQLAREMKDLKAFV 183
+A K V G + +L + L FV
Sbjct: 247 ELTPAAFAAVLAAK--VAGALNLHELTPD-LPLDFFV 280
>gnl|CDD|215072 PLN00141, PLN00141, Tic62-NAD(P)-related group II protein;
Provisional.
Length = 251
Score = 34.5 bits (79), Expect = 0.042
Identities = 14/33 (42%), Positives = 19/33 (57%)
Query: 33 EIGTPMQEFYRDKTIFLTGGTGFMGKTVVEKLL 65
E E + KT+F+ G TG GK +VE+LL
Sbjct: 6 EASEEDAENVKTKTVFVAGATGRTGKRIVEQLL 38
>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 = 34.6 bits (80), Expect = 0.043
Identities = 10/19 (52%), Positives = 15/19 (78%)
Query: 47 IFLTGGTGFMGKTVVEKLL 65
+F+TG TGF+G VV +L+
Sbjct: 3 VFVTGATGFIGSAVVRELV 21
>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 = 34.2 bits (79), Expect = 0.044
Identities = 33/162 (20%), Positives = 49/162 (30%), Gaps = 66/162 (40%)
Query: 47 IFLTGGTGFMGKTVVEKLLRSCPHLKHIYLLVRPKKGKDIQERLDAIFEDRLFWRLRAEV 106
I +TGG GF+G +V +LL + I +RLD +
Sbjct: 1 ILVTGGAGFIGSHLVRRLLERGHEVVVI-------------DRLDVV------------- 34
Query: 107 PDFRSKVSAVAGDCSLPGLGLSETDRATLVKQVNIVFHGAATVRFDEHIKMAV---KINV 163
H AA V + NV
Sbjct: 35 ------------------------------------VHLAALVGVPASWDNPDEDFETNV 58
Query: 164 CGVQAMLQLAREMKDLKAFVHVSTAFTHCPRERIDEEFYPVP 205
G +L+ AR+ +K FV+ S+A + E + EE P
Sbjct: 59 VGTLNLLEAARKA-GVKRFVYASSASVYGSPEGLPEEEETPP 99
>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 = 34.0 bits (79), Expect = 0.044
Identities = 34/162 (20%), Positives = 52/162 (32%), Gaps = 47/162 (29%)
Query: 45 KTIFLTGGTGFMGKTVVEKLLRSCPHLKHIYLLVRPKKGKDIQERLDAIFEDRLFWRLRA 104
T +TGG G +G+ + L + + LL R G D L A
Sbjct: 1 GTYLITGGLGGLGRALARWLAERGA--RRLVLLSR--SGPD----------APGAAALLA 46
Query: 105 EVPDFRSKVSAVAGDCSLPGLGLSETDRATLVKQVNI----------VFHGAATVRFDEH 154
E+ ++V+ VA D DR L + V H A + D
Sbjct: 47 ELEAAGARVTVVACD---------VADRDALAAVLAAIPAVEGPLTGVIHAAGVLD-DGV 96
Query: 155 IK----------MAVKINVCGVQAMLQLAREMKDLKAFVHVS 186
+ +A K G + +L ++ L FV S
Sbjct: 97 LASLTPERFAAVLAPK--AAGAWNLHELTADL-PLDFFVLFS 135
>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 = 34.4 bits (79), Expect = 0.047
Identities = 25/159 (15%), Positives = 53/159 (33%), Gaps = 35/159 (22%)
Query: 44 DKTIFLTGGTGFMGKTVVEKLLRSCPHLKHIYLLVRPKKGKDIQERLDAIFEDRLFWRLR 103
K +TG + +G+ + L R + + R + + + AI E
Sbjct: 5 GKVALVTGASSGIGRAIARALAR---EGARVVVAARRSEEEAAEALAAAIKE-------- 53
Query: 104 AEVPDFRSKVSAVAGDCSLPGLGLSETDRATLVKQ-------VNIVFHGAATVRF----- 151
+ +AVA D + E LV ++I+ + A
Sbjct: 54 ----AGGGRAAAVAAD-----VSDDEESVEALVAAAEEEFGRIDILVNNAGIAGPDAPLE 104
Query: 152 ---DEHIKMAVKINVCGVQAMLQLAREMKDLKAFVHVST 187
+E + +N+ G + + A + + V++S+
Sbjct: 105 ELTEEDWDRVIDVNLLGAFLLTRAALPLMKKQRIVNISS 143
>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 = 33.6 bits (78), Expect = 0.063
Identities = 33/160 (20%), Positives = 55/160 (34%), Gaps = 41/160 (25%)
Query: 46 TIFLTGGTGFMGKTVVEKLLRSCPHLKHIYLLVR-PKKGKDIQERLDAIFEDRLFWRLRA 104
T +TGG G +G + L +H+ LL R + + L + E R
Sbjct: 2 TYLVTGGLGGLGLELARWLAERGA--RHLVLLSRSGAPDPEAEALLAEL-EARG------ 52
Query: 105 EVPDFRSKVSAVAGDCSLPGLGLSETDRATLVKQVNI-------VFHGAATVRF------ 151
++V+ VA D S L+ ++ V H A +R
Sbjct: 53 ------AEVTVVACDVS------DRDAVRALLAEIRADGPPLRGVIHAAGVLRDALLANM 100
Query: 152 -DEHIK--MAVKINVCGVQAMLQLAREMKDLKAFVHVSTA 188
E +A K+ G + + R+ + L FV S+
Sbjct: 101 TAEDFARVLAPKVT--GAWNLHEATRD-RPLDFFVLFSSI 137
>gnl|CDD|187673 cd09813, 3b-HSD-NSDHL-like_SDR_e, human NSDHL (NAD(P)H steroid
dehydrogenase-like protein)-like, extended (e) SDRs.
This subgroup includes human NSDHL and related proteins.
These proteins have the characteristic active site
tetrad of extended SDRs, and also have a close match to
their NAD(P)-binding motif. Human NSDHL is a
3beta-hydroxysteroid dehydrogenase (3 beta-HSD) which
functions in the cholesterol biosynthetic pathway. 3
beta-HSD catalyzes the oxidative conversion of delta 5-3
beta-hydroxysteroids to the delta 4-3-keto
configuration; this activity is essential for the
biosynthesis of all classes of hormonal steroids.
Mutations in the gene encoding NSDHL cause CHILD
syndrome (congenital hemidysplasia with ichthyosiform
nevus and limb defects), an X-linked dominant,
male-lethal trait. This subgroup also includes an
unusual bifunctional [3beta-hydroxysteroid dehydrogenase
(3b-HSD)/C-4 decarboxylase from Arabidopsis thaliana,
and Saccharomyces cerevisiae ERG26, a 3b-HSD/C-4
decarboxylase, involved in the synthesis of ergosterol,
the major sterol of yeast. Extended SDRs are distinct
from classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately 100
amino acids. Extended SDRs are a diverse collection of
proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid sythase have
a GGXGXXG NAD(P)-binding motif and an altered active
site motif (YXXXN). Fungal type ketoacyl reductases have
a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 335
Score = 33.9 bits (78), Expect = 0.075
Identities = 42/165 (25%), Positives = 69/165 (41%), Gaps = 32/165 (19%)
Query: 46 TIFLTGGTGFMGKTVVEKLLRSCPHLKHIYLLVRPKKGKDIQERLDAIFEDRLFWRLRAE 105
+ + GG+GF+G+ +VE+LLR H++ DI+ FE
Sbjct: 1 SCLVVGGSGFLGRHLVEQLLRRGNPTVHVF---------DIRPT----FELD-------- 39
Query: 106 VPDFRSKVSAVAGDCSLPGLGLSETDRATLVKQVNIVFHGAATVRFDEHIKMAVKINVCG 165
P +V GD + P + ++A K N+VFH A+ + + K+NV G
Sbjct: 40 -PSSSGRVQFHTGDLTDP----QDLEKAFNEKGPNVVFHTASPDH-GSNDDLYYKVNVQG 93
Query: 166 VQAMLQLAREMKDLKAFVHVSTA---FTHCPRERIDEEFYPVPLK 207
+ +++ R+ K V+ S+A F DE P P K
Sbjct: 94 TRNVIEACRKCGV-KKLVYTSSASVVFNGQDIINGDESL-PYPDK 136
>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 = 33.5 bits (77), Expect = 0.097
Identities = 11/25 (44%), Positives = 17/25 (68%)
Query: 41 FYRDKTIFLTGGTGFMGKTVVEKLL 65
+ +K+I +TGGTG GK + +LL
Sbjct: 1 MFNNKSILITGGTGSFGKAFISRLL 25
>gnl|CDD|215370 PLN02686, PLN02686, cinnamoyl-CoA reductase.
Length = 367
Score = 33.2 bits (76), Expect = 0.13
Identities = 18/79 (22%), Positives = 35/79 (44%), Gaps = 7/79 (8%)
Query: 44 DKTIFLTGGTGFMGKTVVEKLLRSCPHLKHIYLLVRPKKGKDIQERLDAIFEDRLF---- 99
+ + +TGG F+G +V++LLR H + + V ++ K+ ++ E
Sbjct: 53 ARLVCVTGGVSFLGLAIVDRLLR---HGYSVRIAVDTQEDKEKLREMEMFGEMGRSNDGI 109
Query: 100 WRLRAEVPDFRSKVSAVAG 118
W + A + + S A G
Sbjct: 110 WTVMANLTEPESLHEAFDG 128
>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 = 33.1 bits (76), Expect = 0.17
Identities = 33/151 (21%), Positives = 56/151 (37%), Gaps = 28/151 (18%)
Query: 41 FYRDKTIFLTGGTGFMGKTVVEKLLRSCPHLKHIYLLVRPKKGKDIQERLDAIFEDRLFW 100
F++ K + +TG TGF G + L + L LD
Sbjct: 1 FWQGKRVLVTGHTGFKGSWLSLWLQELGAKVIGYSLDPPTNPNLFELANLDNKISS---- 56
Query: 101 RLRAEVPDFRSKVSAVAGDCSLPGLGLSETDRATLVKQVNIVFHGAAT--VR--FDEHIK 156
R ++ D + + + E + IVFH AA VR + + ++
Sbjct: 57 -TRGDIRDL-NALREAIREY--------EPE---------IVFHLAAQPLVRLSYKDPVE 97
Query: 157 MAVKINVCGVQAMLQLAREMKDLKAFVHVST 187
+ NV G +L+ RE +KA V+V++
Sbjct: 98 -TFETNVMGTVNLLEAIRETGSVKAVVNVTS 127
>gnl|CDD|215146 PLN02260, PLN02260, probable rhamnose biosynthetic enzyme.
Length = 668
Score = 33.2 bits (76), Expect = 0.18
Identities = 36/157 (22%), Positives = 59/157 (37%), Gaps = 39/157 (24%)
Query: 42 YRDKTIFLTGGTGFMGKTVVEKLLRSCPHLKHIYLLVRPKKGKDIQERLDAIFEDRLFWR 101
Y K I +TG GF+ V +L+R+ P K + L D+L
Sbjct: 4 YEPKNILITGAAGFIASHVANRLIRNYPDYKIVVL-------------------DKL--- 41
Query: 102 LRAEVPDFRSKVSAVAGDCSLPGLGLSETD--RATLV------KQVNIVFHGAATVRFDE 153
D+ S + + S P + D A LV + ++ + H AA D
Sbjct: 42 ------DYCSNLKNLNPSKSSPNFKFVKGDIASADLVNYLLITEGIDTIMHFAAQTHVDN 95
Query: 154 HIKMA---VKINVCGVQAMLQLAREMKDLKAFVHVST 187
+ K N+ G +L+ + ++ F+HVST
Sbjct: 96 SFGNSFEFTKNNIYGTHVLLEACKVTGQIRRFIHVST 132
>gnl|CDD|187575 cd05265, SDR_a1, atypical (a) SDRs, subgroup 1. Atypical SDRs in
this subgroup are poorly defined and have been
identified putatively as isoflavones reductase, sugar
dehydratase, mRNA binding protein etc. Atypical SDRs
are distinct from classical SDRs. Members of this
subgroup retain the canonical active site triad (though
not the upstream Asn found in most SDRs) but have an
unusual putative glycine-rich NAD(P)-binding motif,
GGXXXXG, in the usual location. Atypical SDRs generally
lack the catalytic residues characteristic of the SDRs,
and their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Atypical SDRs include biliverdin IX beta
reductase (BVR-B,aka flavin reductase), NMRa (a
negative transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane
reductase, isoflavone reductases, and others. SDRs are
a functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. In addition to the Rossmann fold
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids, and typically have a TGXXGXXG cofactor
binding motif. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 250
Score = 32.3 bits (74), Expect = 0.21
Identities = 18/53 (33%), Positives = 29/53 (54%), Gaps = 3/53 (5%)
Query: 45 KTIFLTGGTGFMGKTVVEKLLRSCPHLKHIYLLVRPKKGKDIQERLDAIFEDR 97
I + GGT F+GK +VE+LL + H + + R + D+ E ++ I DR
Sbjct: 1 MKILIIGGTRFIGKALVEELL-AAGH--DVTVFNRGRTKPDLPEGVEHIVGDR 50
>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 = 11/33 (33%), Positives = 19/33 (57%), Gaps = 3/33 (9%)
Query: 47 IFLTGGTGFMGKTVVEKLLRSCPHLKHIYLLVR 79
I +TGGTG +G+ + +L + H + +L R
Sbjct: 1 ILITGGTGLIGRALTARLRKG-GH--QVTILTR 30
>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 = 32.2 bits (74), Expect = 0.27
Identities = 14/47 (29%), Positives = 23/47 (48%), Gaps = 5/47 (10%)
Query: 47 IFLTGGTGFMGKTVVEKLLRSCPHLKHIYLLVR--PKKGKDIQERLD 91
I +TGGTGF+G+ + ++L + H + +L R P E
Sbjct: 1 ILITGGTGFIGRALTQRLTKR-GH--EVTILTRSPPPGANTKWEGYK 44
>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 = 31.9 bits (73), Expect = 0.38
Identities = 8/17 (47%), Positives = 12/17 (70%)
Query: 41 FYRDKTIFLTGGTGFMG 57
F++ K + +TG TGF G
Sbjct: 1 FWQGKKVLVTGHTGFKG 17
>gnl|CDD|178263 PLN02657, PLN02657, 3,8-divinyl protochlorophyllide a 8-vinyl
reductase.
Length = 390
Score = 31.7 bits (72), Expect = 0.42
Identities = 14/40 (35%), Positives = 23/40 (57%), Gaps = 3/40 (7%)
Query: 44 DKTIFLTGGTGFMGKTVVEKLLRSCPHLKHIYLLVRPKKG 83
D T+ + G TG++GK VV +L+R ++ + R K G
Sbjct: 60 DVTVLVVGATGYIGKFVVRELVRRG---YNVVAVAREKSG 96
>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 = 31.5 bits (72), Expect = 0.43
Identities = 23/70 (32%), Positives = 29/70 (41%), Gaps = 20/70 (28%)
Query: 47 IFLTGGTGFMGKTVVEKLLRSCPHLKHIYLLVR-PKKGKDIQER--------------LD 91
I +TG TG +G VVE LL + + LVR P+K K L+
Sbjct: 1 ILVTGATGKLGTAVVELLLA---KVASVVALVRNPEKAKAFAADGVEVRQGDYDDPETLE 57
Query: 92 AIFE--DRLF 99
FE DRL
Sbjct: 58 RAFEGVDRLL 67
>gnl|CDD|187541 cd05230, UGD_SDR_e, UDP-glucuronate decarboxylase (UGD) and related
proteins, extended (e) SDRs. UGD catalyzes the
formation of UDP-xylose from UDP-glucuronate; it is an
extended-SDR, and has the characteristic glycine-rich
NAD-binding pattern, TGXXGXXG, and active site tetrad.
Extended SDRs are distinct from classical SDRs. In
addition to the Rossmann fold (alpha/beta folding
pattern with a central beta-sheet) core region typical
of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 305
Score = 31.5 bits (72), Expect = 0.45
Identities = 32/152 (21%), Positives = 53/152 (34%), Gaps = 47/152 (30%)
Query: 45 KTIFLTGGTGFMGKTVVEKLLRSCPHLKHIYLLVRPKKGKDIQERLDAIFEDRLFWRLRA 104
K I +TGG GF+G + ++LL G ++ I D F +
Sbjct: 1 KRILITGGAGFLGSHLCDRLLE---------------DGHEV------ICVDNFFTGRKR 39
Query: 105 EV------PDFRSKVSAVAGDCSLPGLGLSETDRATLVKQVNIVFHGAATVRFDEHIKMA 158
+ P+F + D + P L +V+ ++H A +
Sbjct: 40 NIEHLIGHPNFE----FIRHDVTEP-----------LYLEVDQIYHLACPASPVHYQYNP 84
Query: 159 VKI---NVCGVQAMLQLAREMKDLKAFVHVST 187
+K NV G ML LA+ + + ST
Sbjct: 85 IKTLKTNVLGTLNMLGLAKRVG--ARVLLAST 114
>gnl|CDD|212497 cd11731, Lin1944_like_SDR_c, Lin1944 and related proteins,
classical (c) SDRs. Lin1944 protein from Listeria
Innocua is a classical SDR, it contains a glycine-rich
motif similar to the canonical motif of the SDR
NAD(P)-binding site. However, the typical SDR active
site residues are absent in this subgroup of proteins of
undetermined function. SDRs are a functionally diverse
family of oxidoreductases that have a single domain with
a structurally conserved Rossmann fold (alpha/beta
folding pattern with a central beta-sheet), an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRs are approximately
350 residues. Sequence identity between different SDR
enzymes are typically in the 15-30% range, but the
enzymes share the Rossmann fold NAD-binding motif and
characteristic NAD-binding and catalytic sequence
patterns. These enzymes catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 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 = 198
Score = 30.6 bits (70), Expect = 0.59
Identities = 28/115 (24%), Positives = 41/115 (35%), Gaps = 25/115 (21%)
Query: 47 IFLTGGTGFMGKTVVEKLLRSCPHLKHIYLLVRPKKGK---DI--QERLDAIFEDRLFWR 101
I + G TG +G V + L H + G DI + + A+FE
Sbjct: 1 IIVIGATGTIGLAVAQLLSAH----GHEVITAGRSSGDYQVDITDEASIKALFE------ 50
Query: 102 LRAEVPDFRSKVSAVAGDCSLPGLGLSETDRAT------LVKQVNIVFHGAATVR 150
+V F + VS AGD L L+ Q+N+V HG +
Sbjct: 51 ---KVGHFDAIVST-AGDAEFAPLAELTDADFQRGLNSKLLGQINLVRHGLPYLN 101
>gnl|CDD|187535 cd02266, SDR, Short-chain dehydrogenases/reductases (SDR). SDRs
are a functionally diverse family of oxidoreductases
that have a single domain with a structurally conserved
Rossmann fold (alpha/beta folding pattern with a central
beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRs are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes catalyze a
wide range of activities including the metabolism of
steroids, cofactors, carbohydrates, lipids, aromatic
compounds, and amino acids, and act in redox sensing.
Classical SDRs have an TGXXX[AG]XG cofactor binding
motif and a YXXXK active site motif, with the Tyr
residue of the active site motif serving as a critical
catalytic residue (Tyr-151, human prostaglandin
dehydrogenase (PGDH) numbering). In addition to the Tyr
and Lys, there is often an upstream Ser (Ser-138, PGDH
numbering) and/or an Asn (Asn-107, PGDH numbering)
contributing to the active site; while substrate binding
is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. Extended SDRs have additional
elements in the C-terminal region, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase (KR) domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type KRs have
a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 186
Score = 30.6 bits (69), Expect = 0.61
Identities = 18/74 (24%), Positives = 35/74 (47%), Gaps = 10/74 (13%)
Query: 124 GLGLSETDRATLVKQVNIVFHGAATVRFDEHIKM-------AVKINVCGVQAMLQLAREM 176
L + + +V + ++V H AA + I + A++ NV G + +L+ ARE+
Sbjct: 17 WLASRGSPKVLVVSRRDVVVHNAAILDDGRLIDLTGSRIERAIRANVVGTRRLLEAAREL 76
Query: 177 KDLK---AFVHVST 187
K F+ +S+
Sbjct: 77 MKAKRLGRFILISS 90
>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 = 31.1 bits (71), Expect = 0.62
Identities = 12/37 (32%), Positives = 17/37 (45%), Gaps = 2/37 (5%)
Query: 46 TIFLTGGTGFMGKTVVEKLLRSCPHLKHIYLLVRPKK 82
I + G TG +G +V LL S + +L RP
Sbjct: 1 KIAIAGATGTLGGPIVSALLASPGF--TVTVLTRPSS 35
>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 = 31.1 bits (71), Expect = 0.62
Identities = 29/146 (19%), Positives = 50/146 (34%), Gaps = 40/146 (27%)
Query: 47 IFLTGGTGFMGKTVVEKLLRSCPHLKHIYLLVRPKKGKDIQERLDAIFEDRLFWRLRAEV 106
+TG + +G+ + +L R + L R +E L + A +
Sbjct: 1 ALVTGASSGIGRAIARRLAR---EGAKVVLADRN------EEALAEL----------AAI 41
Query: 107 PDFRSKVSAVAGDCSLPGLGLSETDRATLVKQ-------VNIVFHGAATVRF-------D 152
AV D S E D LV++ ++I+ + A R D
Sbjct: 42 EALGGNAVAVQADVS------DEEDVEALVEEALEEFGRLDILVNNAGIARPGPLEELTD 95
Query: 153 EHIKMAVKINVCGVQAMLQLA-REMK 177
E + +N+ GV + + A MK
Sbjct: 96 EDWDRVLDVNLTGVFLLTRAALPHMK 121
>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 = 31.0 bits (71), Expect = 0.64
Identities = 43/165 (26%), Positives = 70/165 (42%), Gaps = 39/165 (23%)
Query: 50 TGGTGFMGKTVVEKLLRSCPHLKHIYLLVRPKKGKDIQERLDAIFEDRLFWRLRAEVPDF 109
TGG GF+G +VE+LL ++G ++ I D L + +P+
Sbjct: 5 TGGAGFIGSHLVERLL---------------ERGHEV------IVLDNLSTGKKENLPEV 43
Query: 110 RSKVSAVAGDCSLPGLGLSETDRATL---VKQVNIVFHGAATVRFDEHIKMAVK---INV 163
+ V + GD D + + V+ VFH AA I+ +K +NV
Sbjct: 44 KPNVKFIEGDI---------RDDELVEFAFEGVDYVFHQAAQASVPRSIEDPIKDHEVNV 94
Query: 164 CGVQAMLQLAREMKDLKAFVHVSTAFTHC--PRERIDEEFYPVPL 206
G +L+ AR+ +K FV+ S++ + P DE+ P PL
Sbjct: 95 LGTLNLLEAARKAG-VKRFVYASSSSVYGDPPYLPKDEDHPPNPL 138
>gnl|CDD|187635 cd08930, SDR_c8, classical (c) SDR, subgroup 8. This subgroup
has a fairly well conserved active site tetrad and
domain size of the classical SDRs, but has an atypical
NAD-binding motif ([ST]G[GA]XGXXG). SDRs are a
functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold (alpha/beta folding pattern with a
central beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRs are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes catalyze a
wide range of activities including the metabolism of
steroids, cofactors, carbohydrates, lipids, aromatic
compounds, and amino acids, and act in redox sensing.
Classical SDRs have an TGXXX[AG]XG cofactor binding
motif and a YXXXK active site motif, with the Tyr
residue of the active site motif serving as a critical
catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 250
Score = 30.8 bits (70), Expect = 0.70
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 44 DKTIFLTGGTGFMGKTVVEKLL 65
DK I +TG G +GK + LL
Sbjct: 2 DKIILITGAAGLIGKAFCKALL 23
>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 = 30.3 bits (69), Expect = 0.84
Identities = 13/47 (27%), Positives = 20/47 (42%), Gaps = 3/47 (6%)
Query: 46 TIFLTGGTGFMGKTVVEKLLRSCPHLKHIYLLVRPKKGKDIQERLDA 92
+ + G TG +G+ VV +LL + LVR + E A
Sbjct: 1 KVLVVGATGKVGRHVVRELLD---RGYQVRALVRDPSQAEKLEAAGA 44
>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 = 30.3 bits (69), Expect = 1.0
Identities = 10/50 (20%), Positives = 21/50 (42%), Gaps = 4/50 (8%)
Query: 44 DKTIFLTGGTGFMGKTVVEKLLRSCPHLKHIYLLVR-PKKGKDIQERLDA 92
K + +TG +GK +L + H+ + R +KG++ +
Sbjct: 1 GKVVVITGANSGIGKETARELAK---RGAHVIIACRNEEKGEEAAAEIKK 47
>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 = 30.3 bits (69), Expect = 1.3
Identities = 31/146 (21%), Positives = 50/146 (34%), Gaps = 24/146 (16%)
Query: 45 KTIFLTGGTGFMGKTVVEKLLRSCPHLKHIYLLVRPKKGKDIQERLDAIFEDRLFWRLRA 104
+ +TGG GF+G + L+ + L+R L W L+A
Sbjct: 1 MRVLITGGAGFIGSNLARFFLKQGWEVIGFDNLMRRG------------SFGNLAW-LKA 47
Query: 105 EVPDFRSKVSAVAGDCSLPGLGLSETDRATLVKQVNIVFHGAATVRFDEHIK---MAVKI 161
D V V GD D L + ++++ H AA + +
Sbjct: 48 NREDGG--VRFVHGDIRNRN------DLEDLFEDIDLIIHTAAQPSVTTSASSPRLDFET 99
Query: 162 NVCGVQAMLQLAREMKDLKAFVHVST 187
N G +L+ AR+ F+ ST
Sbjct: 100 NALGTLNVLEAARQHAPNAPFIFTST 125
>gnl|CDD|237568 PRK13943, PRK13943, protein-L-isoaspartate O-methyltransferase;
Provisional.
Length = 322
Score = 30.2 bits (68), Expect = 1.3
Identities = 12/38 (31%), Positives = 22/38 (57%)
Query: 184 HVSTAFTHCPRERIDEEFYPVPLKYENLIQLISETGDE 221
H++ AF PRE + YP+ YE+++ + + G+E
Sbjct: 22 HIAKAFLEVPREEFLTKSYPLSYVYEDIVLVSYDDGEE 59
>gnl|CDD|187585 cd05324, carb_red_PTCR-like_SDR_c, Porcine testicular carbonyl
reductase (PTCR)-like, classical (c) SDRs. PTCR is a
classical SDR which catalyzes the NADPH-dependent
reduction of ketones on steroids and prostaglandins.
Unlike most SDRs, PTCR functions as a monomer. This
subgroup also includes human carbonyl reductase 1 (CBR1)
and CBR3. CBR1 is an NADPH-dependent SDR with broad
substrate specificity and may be responsible for the in
vivo reduction of quinones, prostaglandins, and other
carbonyl-containing compounds. In addition it includes
poppy NADPH-dependent salutaridine reductase which
catalyzes the stereospecific reduction of salutaridine
to 7(S)-salutaridinol in the biosynthesis of morphine,
and Arabidopsis SDR1,a menthone reductase, which
catalyzes the reduction of menthone to neomenthol, a
compound with antimicrobial activity; SDR1 can also
carry out neomenthol oxidation. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold
(alpha/beta folding pattern with a central beta-sheet),
an NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRs are approximately
350 residues. Sequence identity between different SDR
enzymes are typically in the 15-30% range, but the
enzymes share the Rossmann fold NAD-binding motif and
characteristic NAD-binding and catalytic sequence
patterns. These enzymes catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, 15-hydroxyprostaglandin dehydrogenase
(15-PGDH) numbering). In addition to the Tyr and Lys,
there is often an upstream Ser (Ser-138, 15-PGDH
numbering) and/or an Asn (Asn-107, 15-PGDH numbering)
contributing to the active site; while substrate binding
is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. Extended SDRs have additional
elements in the C-terminal region, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Some atypical SDRs have lost catalytic activity and/or
have an unusual NAD(P)-binding motif and missing or
unusual active site residues. Reactions catalyzed within
the SDR family include isomerization, decarboxylation,
epimerization, C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 225
Score = 29.5 bits (67), Expect = 1.6
Identities = 36/156 (23%), Positives = 56/156 (35%), Gaps = 33/156 (21%)
Query: 45 KTIFLTGGTGFMGKTVVEKLLRSCPHLKHIYLLVR-PKKGKDIQERLDAIFEDRLFWRLR 103
K +TG +G +V +L +S P + L R ++G+ E+L A F +L
Sbjct: 1 KVALVTGANRGIGFEIVRQLAKSGPG--TVILTARDVERGQAAVEKLRAEGLSVRFHQL- 57
Query: 104 AEVPD------FRSKVSAVAG--DCSLPGLGLSETDRATLVKQVNIVF-HGAATVRFDEH 154
+V D V G D LV I F + E
Sbjct: 58 -DVTDDASIEAAADFVEEKYGGLDI--------------LVNNAGIAFKGFDDSTPTREQ 102
Query: 155 IKMAVKINVCGV----QAMLQLAREMKDLKAFVHVS 186
+ +K N G QA+L L ++ + V+VS
Sbjct: 103 ARETMKTNFFGTVDVTQALLPLLKKSPAGR-IVNVS 137
>gnl|CDD|187564 cd05254, dTDP_HR_like_SDR_e, dTDP-6-deoxy-L-lyxo-4-hexulose
reductase and related proteins, extended (e) SDRs.
dTDP-6-deoxy-L-lyxo-4-hexulose reductase, an extended
SDR, synthesizes dTDP-L-rhamnose from
alpha-D-glucose-1-phosphate, providing the precursor of
L-rhamnose, an essential cell wall component of many
pathogenic bacteria. This subgroup has the
characteristic active site tetrad and NADP-binding
motif. This subgroup also contains human MAT2B, the
regulatory subunit of methionine adenosyltransferase
(MAT); MAT catalyzes S-adenosylmethionine synthesis. The
human gene encoding MAT2B encodes two major splicing
variants which are induced in human cell liver cancer
and regulate HuR, an mRNA-binding protein which
stabilizes the mRNA of several cyclins, to affect cell
proliferation. Both MAT2B variants include this extended
SDR domain. Extended SDRs are distinct from classical
SDRs. In addition to the Rossmann fold (alpha/beta
folding pattern with a central beta-sheet) core region
typical of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 280
Score = 29.5 bits (67), Expect = 2.1
Identities = 12/51 (23%), Positives = 28/51 (54%), Gaps = 5/51 (9%)
Query: 140 NIVFHGAATVRFDE---HIKMAVKINVCGVQAMLQLAREMKDLKAFVHVST 187
+++ + AA R D+ ++A ++NV + + + A+E+ +H+ST
Sbjct: 57 DVIINCAAYTRVDKCESDPELAYRVNVLAPENLARAAKEVGAR--LIHIST 105
>gnl|CDD|187579 cd05271, NDUFA9_like_SDR_a, NADH dehydrogenase (ubiquinone) 1
alpha subcomplex, subunit 9, 39 kDa, (NDUFA9) -like,
atypical (a) SDRs. This subgroup of extended SDR-like
proteins are atypical SDRs. They have a glycine-rich
NAD(P)-binding motif similar to the typical SDRs,
GXXGXXG, and have the YXXXK active site motif (though
not the other residues of the SDR tetrad). Members
identified include NDUFA9 (mitochondrial) and putative
nucleoside-diphosphate-sugar epimerase. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif
is often different from the forms normally seen in
classical or extended SDRs. Atypical SDRs include
biliverdin IX beta reductase (BVR-B,aka flavin
reductase), NMRa (a negative transcriptional regulator
of various fungi), progesterone 5-beta-reductase like
proteins, phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane
reductase, isoflavone reductases, and others. SDRs are
a functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. In addition to the Rossmann fold
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids, and typically have a TGXXGXXG cofactor
binding motif. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 273
Score = 29.5 bits (67), Expect = 2.1
Identities = 8/23 (34%), Positives = 14/23 (60%)
Query: 45 KTIFLTGGTGFMGKTVVEKLLRS 67
+ + G TGF+G+ VV +L +
Sbjct: 1 MVVTVFGATGFIGRYVVNRLAKR 23
>gnl|CDD|187860 cd09729, Cse1_I-E, CRISPR/Cas system-associated protein Cse1.
CRISPR (Clustered Regularly Interspaced Short
Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
Large proteins, some contain Zn-finger domain; subunit
of the Cascade complex; signature gene for I-E subtype;
also known as Cse1/CasA/YgcL family.
Length = 465
Score = 29.6 bits (67), Expect = 2.4
Identities = 18/74 (24%), Positives = 25/74 (33%), Gaps = 12/74 (16%)
Query: 79 RPKKGKDIQERLDAIFEDRLFWRLRAEVPDFRSKVSAVAGDCSLPGLGLSETDRATLVKQ 138
GKD + AI E+ FW+ R E FR+ ++ + D D
Sbjct: 404 FALGGKDAKGDASAIDEESRFWQ-RLE-SAFRALLADLEED----------DDADEARAA 451
Query: 139 VNIVFHGAATVRFD 152
AA FD
Sbjct: 452 WRKTLRRAALRAFD 465
>gnl|CDD|236399 PRK09186, PRK09186, flagellin modification protein A;
Provisional.
Length = 256
Score = 29.2 bits (66), Expect = 2.6
Identities = 9/22 (40%), Positives = 14/22 (63%)
Query: 44 DKTIFLTGGTGFMGKTVVEKLL 65
KTI +TG G +G +V+ +L
Sbjct: 4 GKTILITGAGGLIGSALVKAIL 25
>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 = 29.1 bits (66), Expect = 2.8
Identities = 8/22 (36%), Positives = 11/22 (50%)
Query: 46 TIFLTGGTGFMGKTVVEKLLRS 67
I +TG G +G +V L R
Sbjct: 1 KILVTGHRGLVGSAIVRVLARR 22
>gnl|CDD|191263 pfam05368, NmrA, NmrA-like family. NmrA is a negative
transcriptional regulator involved in the
post-translational modification of the transcription
factor AreA. NmrA is part of a system controlling
nitrogen metabolite repression in fungi. This family
only contains a few sequences as iteration results in
significant matches to other Rossmann fold families.
Length = 232
Score = 28.8 bits (65), Expect = 3.2
Identities = 13/42 (30%), Positives = 21/42 (50%), Gaps = 3/42 (7%)
Query: 47 IFLTGGTGFMGKTVVEKLLRSCPHLKHIYLLVRPKKGKDIQE 88
I + G TG+ G +VV L++ H + LVR K + +
Sbjct: 1 ILVFGATGYQGGSVVRASLKA-GH--PVRALVRDPKSELAKS 39
>gnl|CDD|187549 cd05238, Gne_like_SDR_e, Escherichia coli Gne (a
nucleoside-diphosphate-sugar 4-epimerase)-like, extended
(e) SDRs. Nucleoside-diphosphate-sugar 4-epimerase has
the characteristic active site tetrad and NAD-binding
motif of the extended SDR, and is related to more
specifically defined epimerases such as UDP-glucose 4
epimerase (aka UDP-galactose-4-epimerase), which
catalyzes the NAD-dependent conversion of UDP-galactose
to UDP-glucose, the final step in Leloir galactose
synthesis. This subgroup includes Escherichia coli
055:H7 Gne, a UDP-GlcNAc 4-epimerase, essential for O55
antigen synthesis. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately 100
amino acids. Extended SDRs are a diverse collection of
proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 305
Score = 28.9 bits (65), Expect = 3.2
Identities = 35/149 (23%), Positives = 62/149 (41%), Gaps = 40/149 (26%)
Query: 46 TIFLTGGTGFMGKTVVEKLLRSCPHLKHIYLLVRPKKGKDIQERLDAIFEDRLFWRLRAE 105
+ +TG +GF+G+ + E+LL S + + L+ D+ +
Sbjct: 2 KVLITGASGFVGQRLAERLL-SDVPNERLILI-------DVVS---------------PK 38
Query: 106 VPDFRSKVSAVAGDCSLPGLGLSETDRATLVKQV-NIVFHGAATVR------FDEHIKMA 158
P +V+ +AGD ++P L L ++VFH AA V FD +
Sbjct: 39 APSGAPRVTQIAGDLAVPAL------IEALANGRPDVVFHLAAIVSGGAEADFD----LG 88
Query: 159 VKINVCGVQAMLQLAREMKDLKAFVHVST 187
++NV G + +L+ R+ FV S+
Sbjct: 89 YRVNVDGTRNLLEALRKNGPKPRFVFTSS 117
>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 = 28.8 bits (65), Expect = 3.4
Identities = 10/20 (50%), Positives = 15/20 (75%)
Query: 47 IFLTGGTGFMGKTVVEKLLR 66
I +TGG GF+G +V++LL
Sbjct: 2 ILVTGGAGFIGSHLVDRLLE 21
>gnl|CDD|212493 cd08932, HetN_like_SDR_c, HetN oxidoreductase-like, classical (c)
SDR. This subgroup includes Anabaena sp. strain PCC
7120 HetN, a putative oxidoreductase involved in
heterocyst differentiation, and related proteins. SDRs
are a functionally diverse family of oxidoreductases
that have a single domain with a structurally conserved
Rossmann fold (alpha/beta folding pattern with a
central beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRs are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes catalyze a
wide range of activities including the metabolism of
steroids, cofactors, carbohydrates, lipids, aromatic
compounds, and amino acids, and act in redox sensing.
Classical SDRs have an TGXXX[AG]XG cofactor binding
motif and a YXXXK active site motif, with the Tyr
residue of the active site motif serving as a critical
catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 223
Score = 28.5 bits (64), Expect = 3.4
Identities = 8/36 (22%), Positives = 14/36 (38%), Gaps = 3/36 (8%)
Query: 45 KTIFLTGGTGFMGKTVVEKLLRSCPHLKHIYLLVRP 80
K +TG + +G + L R + L +R
Sbjct: 1 KVALVTGASRGIGIEIARALAR---DGYRVSLGLRN 33
>gnl|CDD|234587 PRK00039, ruvC, Holliday junction resolvase; Reviewed.
Length = 164
Score = 28.2 bits (64), Expect = 3.8
Identities = 12/46 (26%), Positives = 20/46 (43%), Gaps = 4/46 (8%)
Query: 52 GTGFMGKTVVEKLLRSCPHLKHI-YLLVRPKKGKDIQERLDAIFED 96
G G V+E R L ++ ++R D+ ERL I++
Sbjct: 10 GLRRTGYGVIEVEGR---RLSYVASGVIRTPSDLDLPERLKQIYDG 52
>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 = 28.1 bits (63), Expect = 4.2
Identities = 32/119 (26%), Positives = 43/119 (36%), Gaps = 26/119 (21%)
Query: 43 RDKTIFLTGGTGFMGKTVVEKLLRSCPHLKHIYLLVRPKKGKDIQERLDAIFEDRLFWRL 102
+ KT + GGTG +G+ L R + L+ R ER D L R
Sbjct: 27 KGKTAVVLGGTGPVGQRAAVLLAREGARVV---LVGRDL------ERAQK-AADSLRAR- 75
Query: 103 RAEVPDFRSKVSAVAGDCSLPGLGLSETDRATLVKQVNIVF-HGAATVRFDEHIKMAVK 160
F V AV + RA +K ++VF GAA V E + A K
Sbjct: 76 ------FGEGVGAVETS--------DDAARAAAIKGADVVFAAGAAGVELLEKLAWAPK 120
>gnl|CDD|224016 COG1091, RfbD, dTDP-4-dehydrorhamnose reductase [Cell envelope
biogenesis, outer membrane].
Length = 281
Score = 28.4 bits (64), Expect = 4.5
Identities = 15/66 (22%), Positives = 29/66 (43%), Gaps = 10/66 (15%)
Query: 130 TDRATLVKQVN-----IVFHGAATVRFD---EHIKMAVKINVCGVQAMLQLAREMKDLKA 181
TD +++ + +V + AA D ++A +N G + + + A E+
Sbjct: 37 TDPDAVLEVIRETRPDVVINAAAYTAVDKAESEPELAFAVNATGAENLARAAAEVGAR-- 94
Query: 182 FVHVST 187
VH+ST
Sbjct: 95 LVHIST 100
>gnl|CDD|181162 PRK07904, PRK07904, short chain dehydrogenase; Provisional.
Length = 253
Score = 28.1 bits (63), Expect = 4.7
Identities = 12/36 (33%), Positives = 19/36 (52%), Gaps = 2/36 (5%)
Query: 45 KTIFLTGGTGFMGKTVVEKLLRSCPHLKHIYLLVRP 80
+TI L GGT +G + E+ L++ P + L P
Sbjct: 9 QTILLLGGTSEIGLAICERYLKNAP--ARVVLAALP 42
>gnl|CDD|182313 PRK10217, PRK10217, dTDP-glucose 4,6-dehydratase; Provisional.
Length = 355
Score = 28.5 bits (63), Expect = 5.0
Identities = 40/162 (24%), Positives = 60/162 (37%), Gaps = 48/162 (29%)
Query: 45 KTIFLTGGTGFMGKTVVEKLLRSCPHLKHIYLLVRPKKGKDIQERLDA-IFEDRLFW--R 101
+ I +TGG GF+G +V ++I I E DA + D+L +
Sbjct: 2 RKILITGGAGFIGSALV----------RYI-----------INETSDAVVVVDKLTYAGN 40
Query: 102 LRAEVPDFRSKVSAVAGDCSLPGLGLSETDRATLVK-----QVNIVFHGAATVRFDEHIK 156
L + P VA + DRA L + Q + V H AA D I
Sbjct: 41 LMSLAP--------VAQSERFAFEKVDICDRAELARVFTEHQPDCVMHLAAESHVDRSID 92
Query: 157 ---MAVKINVCGVQAMLQLAR--------EMKDLKAFVHVST 187
++ N+ G +L+ AR + K F H+ST
Sbjct: 93 GPAAFIETNIVGTYTLLEAARAYWNALTEDKKSAFRFHHIST 134
>gnl|CDD|223457 COG0380, OtsA, Trehalose-6-phosphate synthase [Carbohydrate
transport and metabolism].
Length = 486
Score = 28.1 bits (63), Expect = 6.0
Identities = 18/55 (32%), Positives = 24/55 (43%), Gaps = 7/55 (12%)
Query: 61 VEKLLRSCPHLKHIYLLV-RPKKGKDIQERLDAIFEDRLFWRLRAEVPDFRSKVS 114
V +L K + + V R K I +RL A F RL E P++R KV
Sbjct: 271 VLELKAELGRNKKLIVGVDRLDYSKGIPQRLLA------FERLLEEYPEWRGKVV 319
>gnl|CDD|187612 cd05354, SDR_c7, classical (c) SDR, subgroup 7. These proteins are
members of the classical SDR family, with a canonical
active site triad (and also an active site Asn) and a
typical Gly-rich NAD-binding motif. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold (alpha/beta folding pattern with a central
beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRS are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes have a
3-glycine N-terminal NAD(P)(H)-binding pattern
(typically, TGxxxGxG in classical SDRs and TGxxGxxG in
extended SDRs), while substrate binding is in the
C-terminal region. A critical catalytic Tyr residue
(Tyr-151, human 15-hydroxyprostaglandin dehydrogenase
(15-PGDH) numbering), is often found in a conserved
YXXXK pattern. In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) or additional
Ser, contributing to the active site. Substrates for
these enzymes include sugars, steroids, alcohols, and
aromatic compounds. The standard reaction mechanism is a
proton relay involving the conserved Tyr and Lys, as
well as Asn (or Ser). Some SDR family members, including
17 beta-hydroxysteroid dehydrogenase contain an
additional helix-turn-helix motif that is not generally
found among SDRs.
Length = 235
Score = 27.8 bits (62), Expect = 6.5
Identities = 32/130 (24%), Positives = 51/130 (39%), Gaps = 17/130 (13%)
Query: 43 RDKTIFLTGGTGFMGKTVVEKLLRSCPHLKHIYLLVRPKKGKDIQERLDAIFEDRLFWRL 102
+DKT+ +TG +GK VE LL K +Y VR L A + D++ L
Sbjct: 2 KDKTVLVTGANRGIGKAFVESLLAH--GAKKVYAAVRDPGSAA---HLVAKYGDKVV-PL 55
Query: 103 RAEVPDFRSKVSAVAGDCSLPGLGLSETDRATLVKQVNIV-FHGAATVRFDEHIKMAVKI 161
R +V D S + A A D ++ ++ E +K + +
Sbjct: 56 RLDVTDPES-IKAAAAQAK---------DVDVVINNAGVLKPATLLEEGALEALKQEMDV 105
Query: 162 NVCGVQAMLQ 171
NV G+ + Q
Sbjct: 106 NVFGLLRLAQ 115
>gnl|CDD|181417 PRK08416, PRK08416, 7-alpha-hydroxysteroid dehydrogenase;
Provisional.
Length = 260
Score = 27.8 bits (62), Expect = 6.6
Identities = 9/26 (34%), Positives = 16/26 (61%)
Query: 38 MQEFYRDKTIFLTGGTGFMGKTVVEK 63
M + KT+ ++GGT +GK +V +
Sbjct: 2 MSNEMKGKTLVISGGTRGIGKAIVYE 27
>gnl|CDD|187553 cd05242, SDR_a8, atypical (a) SDRs, subgroup 8. This subgroup
contains atypical SDRs of unknown function. Proteins in
this subgroup have a glycine-rich NAD(P)-binding motif
consensus that resembles that of the extended SDRs,
(GXXGXXG or GGXGXXG), but lacks the characteristic
active site residues of the SDRs. A Cys often replaces
the usual Lys of the YXXXK active site motif, while the
upstream Ser is generally present and Arg replaces the
usual Asn. Atypical SDRs generally lack the catalytic
residues characteristic of the SDRs, and their
glycine-rich NAD(P)-binding motif is often different
from the forms normally seen in classical or extended
SDRs. Atypical SDRs include biliverdin IX beta
reductase (BVR-B,aka flavin reductase), NMRa (a
negative transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane
reductase, isoflavone reductases, and others. SDRs are
a functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. In addition to the Rossmann fold
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids, and typically have a TGXXGXXG cofactor
binding motif. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 296
Score = 27.6 bits (62), Expect = 7.7
Identities = 14/43 (32%), Positives = 23/43 (53%), Gaps = 4/43 (9%)
Query: 46 TIFLTGGTGFMGKTVVEKLLRSCPHLKHIYLLVRPKKGKDIQE 88
I +TGGTGF+G+ + + L + H + +L R + GK
Sbjct: 1 KIVITGGTGFIGRALT-RRLTAAGH--EVVVLSR-RPGKAEGL 39
>gnl|CDD|223774 COG0702, COG0702, Predicted nucleoside-diphosphate-sugar
epimerases [Cell envelope biogenesis, outer membrane /
Carbohydrate transport and metabolism].
Length = 275
Score = 27.6 bits (61), Expect = 7.8
Identities = 14/35 (40%), Positives = 18/35 (51%), Gaps = 3/35 (8%)
Query: 45 KTIFLTGGTGFMGKTVVEKLLRSCPHLKHIYLLVR 79
I +TG TGF+G VV +LL H + VR
Sbjct: 1 MKILVTGATGFVGGAVVRELLAR-GH--EVRAAVR 32
>gnl|CDD|193493 cd02690, M28, M28 Zn-peptidases include aminopeptidases and
carboxypeptidases. Peptidase M28 family (also called
aminopeptidase Y family) contains aminopeptidases as
well as carboxypeptidases. They have co-catalytic zinc
ions; each zinc ion is tetrahedrally co-ordinated, with
three amino acid ligands plus activated water; one
aspartate residue binds both metal ions. The
aminopeptidases in this family are also called bacterial
leucyl aminopeptidases, but are able to release a
variety of N-terminal amino acids. IAP aminopeptidase
and aminopeptidase Y preferentially release basic amino
acids while glutamate carboxypeptidase II preferentially
releases C-terminal glutamates. Plasma glutamate
carboxypeptidase (PGCP) and glutamate carboxypeptidase
II (NAALADase) hydrolyze dipeptides. Several members of
the M28 peptidase family have PA domain inserts which
may participate in substrate binding and/or in promoting
conformational changes, which influence the stability
and accessibility of the site to substrate. These
include prostate-specific membrane antigen (PSMA), yeast
aminopeptidase S (SGAP), human transferrin receptors
(TfR1 and TfR2), plasma glutamate carboxypeptidase
(PGCP) and several predicted aminopeptidases where
relatively little is known about them. Also included in
the M28 family are the glutaminyl cyclases (QC) which
are involved in N-terminal glutamine cyclization of many
endocrine peptides. Nicastrin and nicalin belong to this
family but lack the amino-acid conservation required for
catalytically active aminopeptidases.
Length = 252
Score = 27.8 bits (62), Expect = 7.8
Identities = 8/19 (42%), Positives = 11/19 (57%)
Query: 162 NVCGVQAMLQLAREMKDLK 180
N GV +L+LAR + L
Sbjct: 91 NASGVAVLLELARVLSKLP 109
>gnl|CDD|235738 PRK06199, PRK06199, ornithine cyclodeaminase; Validated.
Length = 379
Score = 27.8 bits (62), Expect = 8.8
Identities = 12/34 (35%), Positives = 18/34 (52%)
Query: 52 GTGFMGKTVVEKLLRSCPHLKHIYLLVRPKKGKD 85
G G MGKT++ + CP + I + R +K D
Sbjct: 162 GPGVMGKTILAAFMAVCPGIDTIKIKGRGQKSLD 195
>gnl|CDD|177883 PLN02240, PLN02240, UDP-glucose 4-epimerase.
Length = 352
Score = 27.6 bits (62), Expect = 9.6
Identities = 11/23 (47%), Positives = 17/23 (73%), Gaps = 1/23 (4%)
Query: 44 DKTIFLTGGTGFMGK-TVVEKLL 65
+TI +TGG G++G TV++ LL
Sbjct: 5 GRTILVTGGAGYIGSHTVLQLLL 27
>gnl|CDD|187563 cd05253, UDP_GE_SDE_e, UDP glucuronic acid epimerase, extended
(e) SDRs. This subgroup contains UDP-D-glucuronic acid
4-epimerase, an extended SDR, which catalyzes the
conversion of UDP-alpha-D-glucuronic acid to
UDP-alpha-D-galacturonic acid. This group has the SDR's
canonical catalytic tetrad and the TGxxGxxG 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 = 332
Score = 27.3 bits (61), Expect = 9.7
Identities = 9/22 (40%), Positives = 13/22 (59%)
Query: 45 KTIFLTGGTGFMGKTVVEKLLR 66
I +TG GF+G V ++LL
Sbjct: 1 MKILVTGAAGFIGFHVAKRLLE 22
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.320 0.138 0.413
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: 16,024,503
Number of extensions: 1583848
Number of successful extensions: 1740
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1713
Number of HSP's successfully gapped: 108
Length of query: 303
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 207
Effective length of database: 6,679,618
Effective search space: 1382680926
Effective search space used: 1382680926
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)