RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy18114
(359 letters)
>gnl|CDD|223528 COG0451, WcaG, Nucleoside-diphosphate-sugar epimerases [Cell
envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 314
Score = 92.3 bits (229), Expect = 3e-21
Identities = 60/253 (23%), Positives = 104/253 (41%), Gaps = 38/253 (15%)
Query: 8 VVILGGCGFVGRNLVEHLVENDL-LRVIDKVSPEIAWLNEKQKKIFKRPLVEFISGNLIH 66
+++ GG GF+G +LVE L+ +R +D++ + L VEF+ +L
Sbjct: 3 ILVTGGAGFIGSHLVERLLAAGHDVRGLDRLRDGLDPL---------LSGVEFVVLDLTD 53
Query: 67 PSTCELIFLNSADNSDLTWEYVINCAA--------ETRPGQAEEIYREGIYKLSINCATA 118
+ + + VI+ AA + P + ++ +G L A
Sbjct: 54 RDLVDELA-------KGVPDAVIHLAAQSSVPDSNASDPAEFLDVNVDGTLNL----LEA 102
Query: 119 AARYGILKYVEISSGEICTSHKHSCKESDEPQPWSTIAKY---KCQVEKALLE---IPGL 172
A G+ ++V SS + ++ P + Y K E+ L + GL
Sbjct: 103 ARAAGVKRFVFASSVSVVYGDPPPLPIDEDLGPPRPLNPYGVSKLAAEQLLRAYARLYGL 162
Query: 173 NYTIVRPGVVYGKSDRHNLAPRLVMCAIYQYL-GETLQLFGGKSLP-LNTVHVADLSRAI 230
I+RP VYG D+ +L+ +V I Q L GE + + GG + V+V D++ A+
Sbjct: 163 PVVILRPFNVYGPGDKPDLSSGVVSAFIRQLLKGEPIIVIGGDGSQTRDFVYVDDVADAL 222
Query: 231 WHLLSELPPAKVY 243
L E P V+
Sbjct: 223 LLAL-ENPDGGVF 234
>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 = 88.9 bits (221), Expect = 2e-20
Identities = 55/277 (19%), Positives = 94/277 (33%), Gaps = 53/277 (19%)
Query: 8 VVILGGCGFVGRNLVEHLVENDLLRVIDKVSPEIAWLNEKQKKIFKRPLVEFISGNLIHP 67
++I+GG F+G+ LVE L+ ++ N + K VE I G+
Sbjct: 3 ILIIGGTRFIGKALVEELLAAGH---------DVTVFNRGRTKPDLPEGVEHIVGDRNDR 53
Query: 68 STCELIFLNSADNSDLTWEYVINCAAETRPGQAEEIYREGIYKLSINCATAAARYGILKY 127
E + ++ V++ A T P Q E A A + + +Y
Sbjct: 54 DALEELL------GGEDFDVVVDTIAYT-PRQVER-------------ALDAFKGRVKQY 93
Query: 128 VEISSGEI----CTSHK----HSCKESDEPQPWSTIAKYKCQVEKALLEIPGLNYTIVRP 179
+ ISS + ++ + K E L+E YTIVRP
Sbjct: 94 IFISSASVYLKPGRVITESTPLREPDAVGLSDPWDYGRGKRAAEDVLIEAAAFPYTIVRP 153
Query: 180 GVVYGKSDRHNLAPRLVMCAIYQYL-----GETLQLFGGKSLPLNTVHVADLSRAIWHLL 234
+YG D RL + G + + G + +HV DL+RA+
Sbjct: 154 PYIYGPGDY---TGRL-----AYFFDRLARGRPILVPGDGHSLVQFIHVKDLARALLGAA 205
Query: 235 SELPPAKVYREIYHVVDMGNTCQEDLMSTLTDIFGVK 271
K I+++ ++L+ G +
Sbjct: 206 GN---PKAIGGIFNITGDEAVTWDELLEACAKALGKE 239
>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 = 79.6 bits (197), Expect = 3e-17
Identities = 53/241 (21%), Positives = 94/241 (39%), Gaps = 34/241 (14%)
Query: 8 VVILGGCGFVGRNLVEHLVENDLLRVIDKVSPEIAWLNEKQKKIFKRPLVEFISGNLIHP 67
+++ GG GF+G +LV L++ I ++ + + F G+L P
Sbjct: 1 ILVTGGTGFIGSHLVRRLLQEG--------YEVIVLGRRRRSESLNTGRIRFHEGDLTDP 52
Query: 68 STCELIFLNSADNSDLTWEYVINCAAETRPG----QAEEIYREGIYKLSINCATAAARYG 123
E + +++ + VI+ AA++ G + R + ++ AA R G
Sbjct: 53 DALERLL------AEVQPDAVIHLAAQSGVGASFEDPADFIRANV-LGTLRLLEAARRAG 105
Query: 124 ILKYVEISSGEICTSHKHS-CKESDEPQPWSTIAKYKCQVEKALLEI---PGLNYTIVRP 179
+ ++V SS E+ E P S A K E+ + GL I+R
Sbjct: 106 VKRFVFASSSEVYGDVADPPITEDTPLGPLSPYAAAKLAAERLVEAYARAYGLRAVILRL 165
Query: 180 GVVYGKSDRH----NLAPRLVMCAIYQYLGETLQLFG-GKSL-PLNTVHVADLSRAIWHL 233
VYG + ++ P L+ G+ + L G G ++V D++RAI
Sbjct: 166 FNVYGPGNPDPFVTHVIPALIRRI---LEGKPILLLGDGTQRRDF--LYVDDVARAILLA 220
Query: 234 L 234
L
Sbjct: 221 L 221
>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 = 77.3 bits (191), Expect = 9e-17
Identities = 57/253 (22%), Positives = 91/253 (35%), Gaps = 65/253 (25%)
Query: 8 VVILGGCGFVGRNLVEHLVENDL-LRVIDKVSPEIAWLNEKQKKIFKRPLVEFISGNLIH 66
+++ GG GF+G +LV L+E + VID
Sbjct: 1 ILVTGGAGFIGSHLVRRLLERGHEVVVID------------------------------- 29
Query: 67 PSTCELIFLNSADNSDLTWEYVINCAAETRPGQAEEIYREGI---YKLSINCATAAARYG 123
D V++ AA + + E ++N AA + G
Sbjct: 30 -------------RLD----VVVHLAALVGVPASWDNPDEDFETNVVGTLNLLEAARKAG 72
Query: 124 ILKYVEISSGEI-CTSHKHSCKESDEPQPWSTIAKYKCQVEKALL---EIPGLNYTIVRP 179
+ ++V SS + + +E P+P S K E L E GL I+R
Sbjct: 73 VKRFVYASSASVYGSPEGLPEEEETPPRPLSPYGVSKLAAEHLLRSYGESYGLPVVILRL 132
Query: 180 GVVYGKSDR---HNLAPRLVMCAIYQYLGETLQLFGGKSLPLNTVHVADLSRAIWHLLSE 236
VYG R + + A+ G+ L +FGG + + +HV D+ RAI H L E
Sbjct: 133 ANVYGPGQRPRLDGVVNDFIRRALE---GKPLTVFGGGNQTRDFIHVDDVVRAILHAL-E 188
Query: 237 LPPAKVYREIYHV 249
P +Y++
Sbjct: 189 NPLEG--GGVYNI 199
>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 = 73.5 bits (181), Expect = 1e-14
Identities = 67/288 (23%), Positives = 98/288 (34%), Gaps = 64/288 (22%)
Query: 8 VVILGGCGFVGRNLVEHLVEND-----LLRVIDKVSPEIAWLNEKQKKIFKRPLVEFISG 62
+++ G GF+G NLV L+ L+R + VE + G
Sbjct: 1 ILVTGATGFLGSNLVRALLAQGYRVRALVRSGSDAV------------LLDGLPVEVVEG 48
Query: 63 NLIHPSTCELIFLNSADNSDLTWEYVINCAAETRP--GQAEEIYR---EGIYKLSINCAT 117
+L ++ L +A + V + AA T +E+YR EG N
Sbjct: 49 DLTDAAS-----LAAAMKG---CDRVFHLAAFTSLWAKDRKELYRTNVEGTR----NVLD 96
Query: 118 AAARYGILKYVEISSGEICTSHKHSCKESDEPQPWSTIAK---Y---KCQVEKALLEI-- 169
AA G+ + V SS DE PW+ Y K E +LE
Sbjct: 97 AALEAGVRRVVHTSSIAALGGPPDG--RIDETTPWNERPFPNDYYRSKLLAELEVLEAAA 154
Query: 170 PGLNYTIVRPGVVYGKSDRHNLAPRLVMCAIYQ-----YLGETLQLFGGKSLPLNTVHVA 224
GL+ IV P V+G D + L + Y GG S V V
Sbjct: 155 EGLDVVIVNPSAVFGPGDEGPTSTGLDVLDYLNGKLPAYPP------GGTSF----VDVR 204
Query: 225 DLSRAIWHLLSELPPAKVYREIYHVVDMGNTCQEDLMSTLTDIFGVKH 272
D++ + + E Y + N + L TL +I GVK
Sbjct: 205 DVAEGHIAAMEKGRRG----ERYILGG-ENLSFKQLFETLAEITGVKP 247
>gnl|CDD|187552 cd05241, 3b-HSD-like_SDR_e, 3beta-hydroxysteroid dehydrogenases
(3b-HSD)-like, extended (e) SDRs. Extended SDR family
domains belonging to this subgroup have the
characteristic active site tetrad and a fairly
well-conserved NAD(P)-binding motif. 3b-HSD catalyzes
the NAD-dependent conversion of various steroids, such
as pregnenolone to progesterone, or androstenediol to
testosterone. This subgroup includes an unusual
bifunctional 3b-HSD/C-4 decarboxylase from Arabidopsis
thaliana, and Saccharomyces cerevisiae ERG26, a
3b-HSD/C-4 decarboxylase, involved in the synthesis of
ergosterol, the major sterol of yeast. It also includes
human 3 beta-HSD/HSD3B1 and C(27) 3beta-HSD/
[3beta-hydroxy-delta(5)-C(27)-steroid oxidoreductase;
HSD3B7]. C(27) 3beta-HSD/HSD3B7 is a membrane-bound
enzyme of the endoplasmic reticulum, that catalyzes the
isomerization and oxidation of 7alpha-hydroxylated
sterol intermediates, an early step in bile acid
biosynthesis. Mutations in the human NSDHL (NAD(P)H
steroid dehydrogenase-like protein) cause CHILD syndrome
(congenital hemidysplasia with ichthyosiform nevus and
limb defects), an X-linked dominant, male-lethal trait.
Mutations in the human gene encoding C(27) 3beta-HSD
underlie a rare autosomal recessive form of neonatal
cholestasis. Extended SDRs are distinct from classical
SDRs. In addition to the Rossmann fold (alpha/beta
folding pattern with a central beta-sheet) core region
typical of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid sythase have
a GGXGXXG NAD(P)-binding motif and an altered active
site motif (YXXXN). Fungal type ketoacyl reductases have
a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 331
Score = 72.8 bits (179), Expect = 2e-14
Identities = 59/257 (22%), Positives = 100/257 (38%), Gaps = 34/257 (13%)
Query: 8 VVILGGCGFVGRNLVEHLVENDLLRVI--DKVSPEIAWLNEKQKKIFKRPLVEFISGNLI 65
V++ GG GF G LV+ L+E V D P A ++ P +EF+ G++
Sbjct: 2 VLVTGGSGFFGERLVKQLLERGGTYVRSFDIAPPGEA------LSAWQHPNIEFLKGDIT 55
Query: 66 HPSTCELIFLNSADNSDLTWEYVINCAAETRPGQAEEIYREGIYKLSINCATAAARYGIL 125
+ E + +D V + AA ++Y E + N A R G+
Sbjct: 56 DRNDVE----QALSGADC----VFHTAAIVPLAGPRDLYWEVNVGGTQNVLDACQRCGVQ 107
Query: 126 KYVEISSGEICTSHKHSCKESDEPQPWSTIAKYKCQVEKALLEI--------PGLNYTIV 177
K+V SS + + DE P+ + KA+ EI L +
Sbjct: 108 KFVYTSSSSV-IFGGQNIHNGDETLPYPPLDSDMYAETKAIAEIIVLEANGRDDLLTCAL 166
Query: 178 RPGVVYGKSDRHNLAPRLVMCAIYQYLGETLQLFGGKSLPLNTVHVADLSRAIWHLLSE- 236
RP ++G D+ L P L A G +FG + ++ +V +L+ A H+L+
Sbjct: 167 RPAGIFGPGDQ-GLVPILFEWAE---KGLVKFVFGRGNNLVDFTYVHNLAHA--HILAAA 220
Query: 237 --LPPAKVYREIYHVVD 251
+ + + Y + D
Sbjct: 221 ALVKGKTISGQTYFITD 237
>gnl|CDD|187543 cd05232, UDP_G4E_4_SDR_e, UDP-glucose 4 epimerase, subgroup 4,
extended (e) SDRs. UDP-glucose 4 epimerase (aka
UDP-galactose-4-epimerase), is a homodimeric extended
SDR. It catalyzes the NAD-dependent conversion of
UDP-galactose to UDP-glucose, the final step in Leloir
galactose synthesis. This subgroup is comprised of
bacterial proteins, and includes the Staphylococcus
aureus capsular polysaccharide Cap5N, which may have a
role in the synthesis of UDP-N-acetyl-d-fucosamine. This
subgroup has the characteristic active site tetrad and
NAD-binding motif of the extended SDRs. Extended SDRs
are distinct from classical SDRs. In addition to the
Rossmann fold (alpha/beta folding pattern with a central
beta-sheet) core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids. Extended SDRs are a
diverse collection of proteins, and include isomerases,
epimerases, oxidoreductases, and lyases; they typically
have a TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 303
Score = 68.9 bits (169), Expect = 4e-13
Identities = 69/257 (26%), Positives = 106/257 (41%), Gaps = 45/257 (17%)
Query: 8 VVILGGCGFVGRNLVEHLVENDLLRVIDKVSPEIAWLNEKQKKIFKRPLVEFISGNLIHP 67
V++ G GF+GR LV+ L+ E+ + + S L
Sbjct: 2 VLVTGANGFIGRALVDKLLSR----------------GEEVRIAVRNAENAEPSVVLA-- 43
Query: 68 STCELIFLNSADNSDLTWEYVINCAA-----ETRPGQAEEIYREGIYKLSINCATAAARY 122
EL ++S + L + V++ AA + YR+ +L+ A AAAR
Sbjct: 44 ---ELPDIDSFTDLFLGVDAVVHLAARVHVMNDQGADPLSDYRKVNTELTRRLARAAARQ 100
Query: 123 GILKYVEISS----GEICTSHKHSCKESDEPQPWSTIAKYKCQVEKALLEI---PGLNYT 175
G+ ++V +SS GE T E+D P P + K + E+ALLE+ G+
Sbjct: 101 GVKRFVFLSSVKVNGE-GTVGAPFD-ETDPPAPQDAYGRSKLEAERALLELGASDGMEVV 158
Query: 176 IVRPGVVYGKSDRHNLAPRLVMCAIYQYLGETLQLFGGK-SLPLNTVHVADLSRAIWHLL 234
I+RP +VYG R N A RL M I + L + SL V + +L AI+ +
Sbjct: 159 ILRPPMVYGPGVRGNFA-RL-MRLIDRGLPLPPGAVKNRRSL----VSLDNLVDAIYLCI 212
Query: 235 SELPPAKVYREIYHVVD 251
S K + V D
Sbjct: 213 SL---PKAANGTFLVSD 226
>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 = 66.5 bits (163), Expect = 2e-12
Identities = 66/287 (22%), Positives = 98/287 (34%), Gaps = 56/287 (19%)
Query: 8 VVILGGCGFVGRNLVEHLVENDLLRVIDKVSPEIAWLNEKQKKIFKRPLVEFISGNLIHP 67
++I G G +GR LV L E I R +L P
Sbjct: 2 ILITGATGMLGRALVRLLKERGY--------EVIGTG---------RSRASLFKLDLTDP 44
Query: 68 ST-CELIFLNSADNSDLTWEYVINCAAETRPGQAEEIYREGIYKL----SINCATAAARY 122
E I D +INCAA TR + E E Y++ N A AA
Sbjct: 45 DAVEEAIRDYKPD-------VIINCAAYTRVDKCES-DPELAYRVNVLAPENLARAAKEV 96
Query: 123 GILKYVEISSGEICTSHKHSCKESDEPQPWSTIAKYKCQVEKALLEIPGLNYTIVRPGVV 182
G + + IS+ + K KE D P P + K K E A+L Y I+R +
Sbjct: 97 GA-RLIHISTDYVFDGKKGPYKEEDAPNPLNVYGKSKLLGEVAVLNANP-RYLILRTSWL 154
Query: 183 YGKSDRHNLAPRLVMCAIYQYLGETLQLFGGKSLPLNTVH--------VADLSRAIWHLL 234
YG+ ++ + +N VH ADL+ AI L+
Sbjct: 155 YGELKNGENFVEWMLRLA------------AERKEVNVVHDQIGSPTYAADLADAILELI 202
Query: 235 SELPPAKVYREIYHVVDMGNTCQEDLMSTLTDIFGVKHDYVGSVTAS 281
IYH+ + G + + + D G+ + +T+S
Sbjct: 203 ERNS----LTGIYHLSNSGPISKYEFAKLIADALGLPDVEIKPITSS 245
>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 = 66.2 bits (162), Expect = 2e-12
Identities = 61/278 (21%), Positives = 116/278 (41%), Gaps = 29/278 (10%)
Query: 8 VVILGGCGFVGRNLVEHLVENDL-LRVIDKVSPEIAWLNEKQKKIFKRPLVEFISGNLIH 66
V + GG GF+GR+LV+ L+EN + V+ + ++ + V + G+L
Sbjct: 1 VFVTGGTGFLGRHLVKRLLENGFKVLVLVRSESLGEAHERIEEAGLEADRVRVLEGDLTQ 60
Query: 67 PSTCELIFLNSADNSDLTWEY--VINCAAETRPGQAEEIYREGIYKLSINCATA----AA 120
P + L++A + +L + VI+CAA + E ++ +I+ AA
Sbjct: 61 P----NLGLSAAASRELAGKVDHVIHCAASYDF----QAPNEDAWRTNIDGTEHVLELAA 112
Query: 121 RYGILKYVEISSGEICTSHKHSCKESDEPQPWSTIAKY---KCQVEKALLEIPGL-NYTI 176
R I ++ +S+ + + + + +E++ + Y K + E+ + T+
Sbjct: 113 RLDIQRFHYVSTAYVAGNREGNIRETELNPGQNFKNPYEQSKAEAEQLVRAAATQIPLTV 172
Query: 177 VRPGVVYGKSD---RHNLAPRLVMCAIYQYLGETLQLFGGKSLPLNTVHVADLSRAIWHL 233
RP +V G S + + + LG L + G K LN V V ++ AI +L
Sbjct: 173 YRPSIVVGDSKTGRIEKIDGLYELLNLLAKLGRWLPMPGNKGARLNLVPVDYVADAIVYL 232
Query: 234 LSELPPAKVYREIYHVVDMGNTCQEDLMSTLTDIFGVK 271
+ +I+H+ D T Q + D+F
Sbjct: 233 SKKPEAN---GQIFHLTD--PTPQTLRE--IADLFKSA 263
>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 = 65.3 bits (160), Expect = 4e-12
Identities = 58/250 (23%), Positives = 101/250 (40%), Gaps = 47/250 (18%)
Query: 8 VVILGGCGFVGRNLVEHLVENDLLRVIDKVSPEIAWLNEKQKKIFKR----PLVEFISGN 63
V + G GF+GR +V L + +VI + + E + V F+ +
Sbjct: 3 VTVFGATGFIGRYVVNRLAKRGS-QVI------VPYRCEAYARRLLVMGDLGQVLFVEFD 55
Query: 64 LIHPSTCELIFLNSADNSDLTWEYVINCAA---ETRPGQAEEIYREGIYKLSINCATAAA 120
L + + SD+ VIN ET+ E+++ EG +L A AA
Sbjct: 56 LRDDESIRKAL----EGSDV----VINLVGRLYETKNFSFEDVHVEGPERL----AKAAK 103
Query: 121 RYGILKYVEISSGEICTSHKHSCKESDEPQPWSTIAKYKCQVEKALLEIPGLNYTIVRPG 180
G+ + + IS +++ P + +K + E+A+ E TIVRP
Sbjct: 104 EAGVERLIHIS---------ALGADANSPSKYLR-SKAE--GEEAVREAFP-EATIVRPS 150
Query: 181 VVYGKSDRHNLAPRLVMCAIYQYLGETLQLFGGKSLPLNTVHVADLSRAIWHLLSELPPA 240
VV+G+ DR R + +L + GG++ V+V D++ AI L +
Sbjct: 151 VVFGREDR--FLNRFAK--LLAFLPFPPLIGGGQTK-FQPVYVGDVAEAIARALKD---P 202
Query: 241 KVYREIYHVV 250
+ + Y +V
Sbjct: 203 ETEGKTYELV 212
>gnl|CDD|218026 pfam04321, RmlD_sub_bind, RmlD substrate binding domain.
L-rhamnose is a saccharide required for the virulence of
some bacteria. Its precursor, dTDP-L-rhamnose, is
synthesised by four different enzymes the final one of
which is RmlD. The RmlD substrate binding domain is
responsible for binding a sugar nucleotide.
Length = 284
Score = 61.1 bits (149), Expect = 1e-10
Identities = 54/265 (20%), Positives = 87/265 (32%), Gaps = 66/265 (24%)
Query: 8 VVILGGCGFVGRNLVEHLVENDLLRVIDKVSPEIAWLNEKQKKIFKRPLVEFISGNLIHP 67
+++ G G +GR L L E + E+ L+ + +L P
Sbjct: 1 ILVTGANGQLGRELTRLLAERGV---------EVVALDRPE-------------LDLTDP 38
Query: 68 STCELIFLNSADNSDLTWEYVINCAAETRPGQAEEIYREGIYKL----SINCATAAARYG 123
+ + + V+N AA T +AE E Y + N A A A G
Sbjct: 39 EAVAALV------REARPDVVVNAAAYTAVDKAES-EPELAYAVNALGPGNLAEACAARG 91
Query: 124 ILKYVEISS-----GEICTSHKHSCKESDEPQPWSTIAKYKCQVEKALLEIPGLNYTIVR 178
+ IS+ G +E D P + + K E+A+L + I+R
Sbjct: 92 AP-LIHISTDYVFDGA----KGGPYREDDPTGPLNVYGRTKLAGEQAVLAA-NPRHLILR 145
Query: 179 PGVVYGKSDRHNLAPRLVMCAIYQYLGETLQLFGGKSLPLNTV--------HVADLSRAI 230
VYG+ +N M L+L + L V DL+ A+
Sbjct: 146 TAWVYGEYG-NNFV--KTM----------LRL-AAERDELRVVDDQLGSPTSARDLADAL 191
Query: 231 WHLLSELPPAKVYREIYHVVDMGNT 255
L+ + YH+ G T
Sbjct: 192 LALIRKRLRGPALAGTYHLAGSGET 216
>gnl|CDD|187574 cd05264, UDP_G4E_5_SDR_e, UDP-glucose 4-epimerase (G4E), subgroup
5, extended (e) SDRs. This subgroup partially conserves
the characteristic active site tetrad and NAD-binding
motif of the extended SDRs, and has been identified as
possible UDP-glucose 4-epimerase (aka UDP-galactose
4-epimerase), a homodimeric member of the extended SDR
family. UDP-glucose 4-epimerase catalyzes the
NAD-dependent conversion of UDP-galactose to
UDP-glucose, the final step in Leloir galactose
synthesis. Extended SDRs are distinct from classical
SDRs. In addition to the Rossmann fold (alpha/beta
folding pattern with a central beta-sheet) core region
typical of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 300
Score = 61.2 bits (149), Expect = 2e-10
Identities = 59/235 (25%), Positives = 101/235 (42%), Gaps = 31/235 (13%)
Query: 8 VVILGGCGFVGRNLVEHLVENDL-LRVID-KVSPEI--AWLNEKQKKIFKRP--LVEFIS 61
V+I+GG GF+G +LV+ L+E +RV D + P + K ++ L +
Sbjct: 2 VLIVGGNGFIGSHLVDALLEEGPQVRVFDRSIPPYELPLGGVDYIKGDYENRADLESALV 61
Query: 62 G--NLIHPSTCELIFLNSADNSDLTWEYVINCAAETRPGQAEEIYREGIYKLSINCATAA 119
G +IH ++ S N L + N A + E GI K+ I ++
Sbjct: 62 GIDTVIHLASTTNP-ATSNKNPIL--DIQTNVAPTVQ--LLEACAAAGIGKI-IFASSGG 115
Query: 120 ARYGILKYVEISSGEICTSHKHSCKESDEPQPWSTIAKYKCQVEKALLEIP---GLNYTI 176
YG+ + + IS ESD P S+ K +EK L GL+YT+
Sbjct: 116 TVYGVPEQLPIS-------------ESDPTLPISSYGISKLAIEKYLRLYQYLYGLDYTV 162
Query: 177 VRPGVVYGKSDRHNLAPRLVMCAIYQYL-GETLQLFGGKSLPLNTVHVADLSRAI 230
+R YG R + ++ A+ + L GE ++++G + +++ DL A+
Sbjct: 163 LRISNPYGPGQRPDGKQGVIPIALNKILRGEPIEIWGDGESIRDYIYIDDLVEAL 217
>gnl|CDD|187551 cd05240, UDP_G4E_3_SDR_e, UDP-glucose 4 epimerase (G4E), subgroup
3, extended (e) SDRs. Members of this bacterial
subgroup are identified as possible sugar epimerases,
such as UDP-glucose 4 epimerase. However, while the
NAD(P)-binding motif is fairly well conserved, not all
members retain the canonical active site tetrad of the
extended SDRs. UDP-glucose 4 epimerase (aka
UDP-galactose-4-epimerase), is a homodimeric extended
SDR. It catalyzes the NAD-dependent conversion of
UDP-galactose to UDP-glucose, the final step in Leloir
galactose synthesis. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately 100
amino acids. Extended SDRs are a diverse collection of
proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 306
Score = 60.5 bits (147), Expect = 2e-10
Identities = 47/232 (20%), Positives = 85/232 (36%), Gaps = 32/232 (13%)
Query: 8 VVILGGCGFVGRNLVEHLVENDLLRVIDKVSPEIAWLNEKQKKIFKRPLVEFISGNLIHP 67
+++ G G +GR L L + + +D + P VE++ ++ P
Sbjct: 1 ILVTGAAGGLGRLLARRLAASPRVIGVDGLDRRRPPG--------SPPKVEYVRLDIRDP 52
Query: 68 STCELIFLNSADNSDLTWEYVINCAAETRPGQAEEIYREGIYKLSINCATAAARYGILKY 127
+ ++ AD V++ A P + + N A A G+ +
Sbjct: 53 AAADVFREREAD-------AVVHLAFILDPPRDGAERHRINVDGTQNVLDACAAAGVPRV 105
Query: 128 VEISSGEICTSHKHS---CKESDEPQPW--STIAKYKCQVEKALLEI----PGLNYTIVR 178
V SS + +H + E + ++ K +VE+ L E P LN T++R
Sbjct: 106 VVTSSVAVYGAHPDNPAPLTEDAPLRGSPEFAYSRDKAEVEQLLAEFRRRHPELNVTVLR 165
Query: 179 PGVVYGKSDRHNLAPRLVMCAIYQYLGETLQLFGGKSLPLNTVHVADLSRAI 230
P + G R+ L L + GG P +H D++RA+
Sbjct: 166 PATILGPGTRNTTRDFL--------SPRRLPVPGGFDPPFQFLHEDDVARAL 209
>gnl|CDD|224016 COG1091, RfbD, dTDP-4-dehydrorhamnose reductase [Cell envelope
biogenesis, outer membrane].
Length = 281
Score = 56.1 bits (136), Expect = 6e-09
Identities = 58/248 (23%), Positives = 88/248 (35%), Gaps = 47/248 (18%)
Query: 8 VVILGGCGFVGRNLVEHLVENDLLRVIDKVSPEIAWLNEKQKKIFKRPLVEFISGNLIHP 67
++I G G +G L L VI E+ ++ P
Sbjct: 3 ILITGANGQLGTELRRAL--PGEFEVIATDRAEL---------------------DITDP 39
Query: 68 STCELIFLNSADNSDLTWEYVINCAAETRPGQAEEIYREGIYK----LSINCATAAARYG 123
+ D+ VIN AA T +AE E + + N A AAA G
Sbjct: 40 DAVLEVI--RETRPDV----VINAAAYTAVDKAES-EPELAFAVNATGAENLARAAAEVG 92
Query: 124 ILKYVEISSGEICTSHKHSC-KESDEPQPWSTIAKYKCQVEKALLEIPGLNYTIVRPGVV 182
+ V IS+ + K KE+D P P + + K E+A+ G + I+R V
Sbjct: 93 A-RLVHISTDYVFDGEKGGPYKETDTPNPLNVYGRSKLAGEEAVRAA-GPRHLILRTSWV 150
Query: 183 YGKSDRHNLAPRLVMCAIYQYLGETLQLFGGKSLPLNTVHVADLSRAIWHLLSELPPAKV 242
YG+ +N M + E +L + + DL+ AI LL + V
Sbjct: 151 YGEY-GNNFV--KTM---LRLAKEGKELKVVDDQYGSPTYTEDLADAILELLEKEKEGGV 204
Query: 243 YREIYHVV 250
YH+V
Sbjct: 205 ----YHLV 208
>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 = 55.8 bits (135), Expect = 9e-09
Identities = 52/200 (26%), Positives = 82/200 (41%), Gaps = 27/200 (13%)
Query: 8 VVILGGCGFVGRNLVEHLVE--NDLLRVIDKVSPEIAWLNEKQKKIFKRPLVEFISGNLI 65
+++GG GF+GR+LVE L+ N + V D I E R V+F +G+L
Sbjct: 2 CLVVGGSGFLGRHLVEQLLRRGNPTVHVFD-----IRPTFELDPSSSGR--VQFHTGDLT 54
Query: 66 HPSTCELIFLNSADNSDLTWEYVINCAAETRPGQAEEIYREGIYKLSINCATAAARYGIL 125
P E F N V + A+ G +++Y + + + N A + G+
Sbjct: 55 DPQDLEKAFNEKGPNV------VFHTASPD-HGSNDDLYYKVNVQGTRNVIEACRKCGVK 107
Query: 126 KYVEISSGEICTSHKHSCKESDEPQPW-----STIAKYKCQVEKALLE----IPGLNYTI 176
K V SS + + DE P+ + K EK +L+ GL
Sbjct: 108 KLVYTSSASV-VFNGQDIINGDESLPYPDKHQDAYNETKALAEKLVLKANDPESGLLTCA 166
Query: 177 VRPGVVYGKSDRHNLAPRLV 196
+RP ++G DR L P L+
Sbjct: 167 LRPAGIFGPGDRQ-LVPGLL 185
>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 = 53.8 bits (130), Expect = 1e-08
Identities = 50/236 (21%), Positives = 82/236 (34%), Gaps = 67/236 (28%)
Query: 8 VVILGGCGFVGRNLVEHLVEND-----LLRVIDKVSPEIAWLNEKQKKIFKRPLVEFISG 62
V+++G G VGR++V L++ L+R + Q + + E + G
Sbjct: 2 VLVVGATGKVGRHVVRELLDRGYQVRALVR------------DPSQAEKLEAAGAEVVVG 49
Query: 63 NLIHPSTCELIFLNSADNSDLTWEYVINCAAETRPGQ--AEEIYREGIYKLSINCATAAA 120
+L + L D VI+ A G E + +G IN AA
Sbjct: 50 DLTDAES-LAAALEGID-------AVISAAGSGGKGGPRTEAVDYDGN----INLIDAAK 97
Query: 121 RYGILKYVEISSGEICTSHKHSCKESDEPQPWS----TIAKYKCQVEKALLEIPGLNYTI 176
+ G+ ++V +SS I D+P K + E L GL+YTI
Sbjct: 98 KAGVKRFVLVSS--IGA---------DKPSHPLEALGPYLDAKRKAEDYLRAS-GLDYTI 145
Query: 177 VRPGVVYGKSDRHNLAPRLVMCAIYQYLGET--LQLFGGKSLPLNTVHVADLSRAI 230
VRPG + T + L G + + AD++ +
Sbjct: 146 VRPG------------------GLTDDPAGTGRVVLGGDGTRLDGPISRADVAEVL 183
>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 = 49.7 bits (119), Expect = 2e-07
Identities = 48/182 (26%), Positives = 65/182 (35%), Gaps = 33/182 (18%)
Query: 8 VVILGGCGFVGRNLVEHLVEND----LLRVIDKVSPEIAWLNEKQKKIFKRPLVEFISGN 63
++ILG GF+GR L L+E LL K + + R L + +S
Sbjct: 1 ILILGATGFIGRALARELLEQGHEVTLLVRNTKRLSKEDQEPVAVVEGDLRDL-DSLSDA 59
Query: 64 LIHPSTCELIFLNSADNSDLTWEYVINCAAETRPGQA-EEIYREGIYKLSINCATAAARY 122
+ VI+ A R + E+ EG N AA
Sbjct: 60 VQGVDV------------------VIHLAGAPRDTRDFCEVDVEGTR----NVLEAAKEA 97
Query: 123 GILKYVEISSGEICTSHKHSCKESDEPQPWSTIAKYKCQVEKALLEIPGLNYTIVRPGVV 182
G+ ++ ISS H E P K + E L E L YTIVRPGV+
Sbjct: 98 GVKHFIFISSLGA-YGDLHEETEPSPSSP---YLAVKAKTEAVLRE-ASLPYTIVRPGVI 152
Query: 183 YG 184
YG
Sbjct: 153 YG 154
>gnl|CDD|200085 TIGR01214, rmlD, dTDP-4-dehydrorhamnose reductase. This enzyme
catalyzes the last of 4 steps in making dTDP-rhamnose, a
precursor of LPS core antigen, O-antigen, etc [Cell
envelope, Biosynthesis and degradation of surface
polysaccharides and lipopolysaccharides].
Length = 287
Score = 50.5 bits (121), Expect = 4e-07
Identities = 48/181 (26%), Positives = 66/181 (36%), Gaps = 32/181 (17%)
Query: 88 VINCAAETRPGQAEEIYREGIYKL----SINCATAAARYGILKYVEISSGEICTSHKHS- 142
V+N AA T AE E + + N A AAAR+G V IS+ +
Sbjct: 54 VVNTAAYTDVDGAE-SDPEKAFAVNALAPQNLARAAARHGAR-LVHISTDYVFDGEGKRP 111
Query: 143 CKESDEPQPWSTIAKYKCQVEKALLEIPGLNYTIVRPGVVYGKSDRHNLAPRLVMCAIYQ 202
+E D P + + K E+A+ G N IVR +YG N
Sbjct: 112 YREDDATNPLNVYGQSKLAGEQAVRAA-GPNALIVRTSWLYGGGGGRNF----------- 159
Query: 203 YLGETLQLFGGKSLPLNTVH--------VADLSRAIWHLLSELPPAKVYREIYHVVDMGN 254
T+ G+ L V DL+R I LL L A R +YH+ + G
Sbjct: 160 --VRTMLRLAGRGEELRVVDDQIGSPTYAKDLARVIAALLQRLARA---RGVYHLANSGQ 214
Query: 255 T 255
Sbjct: 215 C 215
>gnl|CDD|216283 pfam01073, 3Beta_HSD, 3-beta hydroxysteroid dehydrogenase/isomerase
family. The enzyme 3 beta-hydroxysteroid
dehydrogenase/5-ene-4-ene isomerase (3 beta-HSD)
catalyzes the oxidation and isomerisation of 5-ene-3
beta-hydroxypregnene and 5-ene-hydroxyandrostene steroid
precursors into the corresponding 4-ene-ketosteroids
necessary for the formation of all classes of steroid
hormones.
Length = 280
Score = 50.4 bits (121), Expect = 5e-07
Identities = 60/248 (24%), Positives = 103/248 (41%), Gaps = 43/248 (17%)
Query: 9 VILGGCGFVGRNLVEHLVENDLL---RVIDKVSPEIAWLNEKQKKIFKRPLVEFISGNLI 65
++ GG GF+GR++V L+ L RV D + + E + K ++ +I G++
Sbjct: 1 LVTGGGGFLGRHIVRLLLREGELQEVRVFD-----LRFSPELLEDFSKLQVITYIEGDVT 55
Query: 66 HPSTCELIFLNSADNSDLTWEYVINCAAETRPGQAEEIYREGIYKLSI----NCATAAAR 121
+ SD+ VI+ AA + YR+ I K+++ N A +
Sbjct: 56 DKQDLR----RALQGSDV----VIHTAAII--DVFGKAYRDTIMKVNVKGTQNVLDACVK 105
Query: 122 YGILKYVEISSGEIC--TSHKHSCKESDEPQPWSTI-----AKYKCQVEKALLE------ 168
G+ V SS E+ S+ DE P+ + + K EK +L+
Sbjct: 106 AGVRVLVYTSSMEVVGPNSYGQPIVNGDETTPYESTHQDPYPESKALAEKLVLKANGSTL 165
Query: 169 -IPGLNYTI-VRPGVVYGKSDRHNLAPRLVMCAIYQYLGETLQLFGGKSLPLNTVHVADL 226
G YT +RP ++G+ D L P LV G G K++ + V+V ++
Sbjct: 166 KNGGRLYTCALRPAGIFGEGDPF-LFPFLVRLLK---NGLAKFRTGDKNVLSDRVYVGNV 221
Query: 227 SRAIWHLL 234
+ A H+L
Sbjct: 222 AWA--HIL 227
>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 = 49.9 bits (120), Expect = 7e-07
Identities = 62/272 (22%), Positives = 107/272 (39%), Gaps = 63/272 (23%)
Query: 8 VVILGGCGFVGRNLVEHLVE---NDLLRVIDKV----SPEIAWLNEKQKKIFKRPLVEFI 60
+++ GG GF+G N V +L+ + + +DK+ + E N + R F+
Sbjct: 3 ILVTGGAGFIGSNFVRYLLNKYPDYKIINLDKLTYAGNLE----NLEDVSSSPR--YRFV 56
Query: 61 SGNLIHPSTCELIFLNSADNSDLTWEYVINCAAET---RP-GQAEEIYREGIYKLSINCA 116
G++ + +F + D VI+ AAE+ R E R +
Sbjct: 57 KGDICDAELVDRLF--EEEKID----AVIHFAAESHVDRSISDPEPFIRTNVL------G 104
Query: 117 T-----AAARYGILKYVEISS----GEICTSHKHSCKESDEPQPWSTIAKYKCQVE---K 164
T AA +YG+ ++V IS+ G++ E+ P S + K + +
Sbjct: 105 TYTLLEAARKYGVKRFVHISTDEVYGDLL--DDGEFTETSPLAPTSPYSASKAAADLLVR 162
Query: 165 ALLEIPGLNYTIVRPGVVYGKSDRHN---LAPRLVMCAIYQYLGETLQLFG-GKSLPLNT 220
A GL I R YG L P ++ A+ G+ L ++G G N
Sbjct: 163 AYHRTYGLPVVITRCSNNYGP--YQFPEKLIPLFILNAL---DGKPLPIYGDGL----NV 213
Query: 221 ---VHVADLSRAIWHLLSELPPAKVYREIYHV 249
++V D +RAI +L + EIY++
Sbjct: 214 RDWLYVEDHARAIELVLEKGRV----GEIYNI 241
>gnl|CDD|187576 cd05266, SDR_a4, atypical (a) SDRs, subgroup 4. Atypical SDRs in
this subgroup are poorly defined, one member is
identified 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 related to,
but is different from, the archetypical SDRs, GXGXXG.
This subgroup also lacks most of the characteristic
active site residues of the SDRs; however, the upstream
Ser is present at the usual place, and some potential
catalytic residues are present in place of the usual
YXXXK active site 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. 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 = 251
Score = 47.3 bits (113), Expect = 3e-06
Identities = 56/247 (22%), Positives = 86/247 (34%), Gaps = 44/247 (17%)
Query: 8 VVILGGCGFVGRNLVEHLVENDLLRVIDKVSPEIAWLNEKQKKIFKRPLVEFISGNLIHP 67
V+ILG CG++G+ L L+ SPE K RP + P
Sbjct: 1 VLILG-CGYLGQRLARQLLAQGWQVTGTTRSPE--------KLAADRPA-------GVTP 44
Query: 68 STCELIFLNSADNSDLTWEYVINCAAETRPGQAE--EIYREGIYKLSINCATAAARYGIL 125
+L + D VI+ + R + L+ A + I
Sbjct: 45 LAADLTQPGLLADVDH---LVISLPPPAGSYRGGYDPGLRALLDALA---QLPAVQRVIY 98
Query: 126 KYVEISSGEICTSHKHSCKESDEP-QPWSTIAKYKCQVEKALLEIPGLNYTIVRPGVVYG 184
+SS + + + P P + + + E+ALL + TI+R +YG
Sbjct: 99 ----LSSTGVYGDQQGEWVDETSPPNPSTESGRALLEAEQALLALGSKPTTILRLAGIYG 154
Query: 185 KSDRHNLAPRLVMCAIYQYLGETLQLFGGKSLPLNTVHVADLSRAIWHLLSELPPAKVYR 244
RH RL T + G + P N +HV DL A+ L P
Sbjct: 155 P-GRH-PLRRLA--------QGTGRPPAGNA-PTNRIHVDDLVGALAFALQRPAP----G 199
Query: 245 EIYHVVD 251
+Y+VVD
Sbjct: 200 PVYNVVD 206
>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 = 45.3 bits (108), Expect = 1e-05
Identities = 51/253 (20%), Positives = 89/253 (35%), Gaps = 44/253 (17%)
Query: 12 GGCGFVGRNLVEHLVEND-------LLRVIDKVSPEIAWLNE-KQKKIFKR----PLVEF 59
G GF+G+ L+E L+ + L+R D S E + +F R +
Sbjct: 3 GATGFLGKVLLEKLLRSTPEVKIYCLVRAKDGESALERLRQELLKYGLFDRLKALERIIP 62
Query: 60 ISGNLIHPSTCELIFLNSADNSDLTWE--YVINCAAETRPGQAEEIYR----EGIYKLSI 113
++G+L P + L+ D +L E +I+ AA + R G +
Sbjct: 63 VAGDLSEP----NLGLSDEDFQELAEEVDVIIHNAATVNFVEPYSDLRATNVLG----TR 114
Query: 114 NCATAAARYGILKYVEISSGEICTSHKHSCKESDEPQPWSTIAKY----------KCQVE 163
A + L + +S+ + +E A K E
Sbjct: 115 EVLRLAKQMKKLPFHHVSTAYVNGERGGLLEEKPYKLDEDEPALLGGLPNGYTQSKWLAE 174
Query: 164 KALLEI-PGLNYTIVRPGVVYGKS-----DRHNLAPRLVMCAIYQYLGETLQLFGGKSLP 217
+ + E GL I RP ++ G+S + + PR ++ LG + G
Sbjct: 175 QLVREAAGGLPVVIYRPSIITGESRTGWINGDDFGPRGLL--GGAGLGVLPDILGDPDAR 232
Query: 218 LNTVHVADLSRAI 230
L+ V V ++ AI
Sbjct: 233 LDLVPVDYVANAI 245
>gnl|CDD|187560 cd05250, CC3_like_SDR_a, CC3(TIP30)-like, atypical (a) SDRs.
Atypical SDRs in this subgroup include CC3 (also known
as TIP30) which is implicated in tumor suppression.
Atypical SDRs are distinct from classical SDRs. Members
of this subgroup have a glycine rich NAD(P)-binding
motif that resembles the extended SDRs, and have an
active site triad of the SDRs (YXXXK and upstream Ser),
although the upstream Asn of the usual SDR active site
is substituted with Asp. For CC3, the Tyr of the triad
is displaced compared to the usual SDRs and the protein
is monomeric, both these observations suggest that the
usual SDR catalytic activity is not present. NADP
appears to serve an important role as a ligand, and may
be important in the interaction with other
macromolecules. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and their
glycine-rich NAD(P)-binding motif is often different
from the forms normally seen in classical or extended
SDRs. Atypical SDRs include biliverdin IX beta reductase
(BVR-B,aka flavin reductase), NMRa (a negative
transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. In addition to the
Rossmann fold core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 214
Score = 42.7 bits (101), Expect = 1e-04
Identities = 47/245 (19%), Positives = 88/245 (35%), Gaps = 38/245 (15%)
Query: 6 PAVVILGGCGFVGRNLVEHLVENDLLRVIDKVSPEIAWLNEKQKKIFKRPLVEFISGNLI 65
++LG G VG++L+ L+++ KV I +R L + +
Sbjct: 1 KTALVLGATGLVGKHLLRELLKSPY---YSKV-----------TAIVRRKLTFPEAKEKL 46
Query: 66 HPSTCELIFLNSADNSDLTWEYVINCAAETRPGQA--EEIYREGIYKLSINCATAAARYG 123
+ L+ + + C TR +A +E +R+ + + A A G
Sbjct: 47 VQIVVDFERLDEYLEAFQNPDVGFCCLGTTR-KKAGSQENFRKVDHDYVLKLAKLAKAAG 105
Query: 124 ILKYVEISSGEICTSHKHSCKESDEPQPWSTIAKYKCQVEKALLEIPGLNYTIVRPGVVY 183
+ ++ +SS + +S K K +VE+ L ++ TI RPG++
Sbjct: 106 VQHFLLVSS-------LGADPKSSFLYL-----KVKGEVERDLQKLGFERLTIFRPGLLL 153
Query: 184 GKSDRHNLAPRLVMCAIYQYLGETLQLFGGKSLPLNTVHVADLSRAIWHLLSELPPAKVY 243
G +R P + Q L L G + +++A+ + KV
Sbjct: 154 G--ERQESRPGERLA---QKLLRILSPLGFPK--YKPIPAETVAKAMVKAALKESSNKV- 205
Query: 244 REIYH 248
EI
Sbjct: 206 -EILE 209
>gnl|CDD|224013 COG1088, RfbB, dTDP-D-glucose 4,6-dehydratase [Cell envelope
biogenesis, outer membrane].
Length = 340
Score = 41.4 bits (98), Expect = 4e-04
Identities = 59/263 (22%), Positives = 110/263 (41%), Gaps = 43/263 (16%)
Query: 8 VVILGGCGFVGRNLVEHLVEN---DLLRVIDKVSPEIAWLNEKQKKIFKRPLVEFISGNL 64
+++ GG GF+G N V +++ D + +DK++ A E + P F+ G++
Sbjct: 3 ILVTGGAGFIGSNFVRYILNKHPDDHVVNLDKLT--YAGNLENLADVEDSPRYRFVQGDI 60
Query: 65 IHPSTCELIFLNSADNSDLTWEYVINCAAET---RPGQAEEIYRE----GIYKLSINCAT 117
+ +F + V++ AAE+ R + + G Y L
Sbjct: 61 CDRELVDRLFKEY------QPDAVVHFAAESHVDRSIDGPAPFIQTNVVGTYTL----LE 110
Query: 118 AAARY-GILKYVEISS----GEICTSHKHSCKESDEPQPWSTIAKYKCQVE---KALLEI 169
AA +Y G ++ IS+ G++ + E+ P S + K + +A +
Sbjct: 111 AARKYWGKFRFHHISTDEVYGDLGLDDD-AFTETTPYNPSSPYSASKAASDLLVRAYVRT 169
Query: 170 PGLNYTIVRPGVVYGKSDRH---NLAPRLVMCAIYQYLGETLQLFGGKSLPLNTVHVADL 226
GL TI R YG L P +++ A+ LG+ L ++G + ++V D
Sbjct: 170 YGLPATITRCSNNYGP--YQFPEKLIPLMIINAL---LGKPLPVYGDGLQIRDWLYVEDH 224
Query: 227 SRAIWHLLSELPPAKVYREIYHV 249
RAI +L++ K+ E Y++
Sbjct: 225 CRAIDLVLTK---GKI-GETYNI 243
>gnl|CDD|222146 pfam13460, NAD_binding_10, NADH(P)-binding.
Length = 182
Score = 39.6 bits (93), Expect = 7e-04
Identities = 41/228 (17%), Positives = 77/228 (33%), Gaps = 49/228 (21%)
Query: 8 VVILGGCGFVGRNLVEHLVENDL-LRVIDKVSPEIAWLNEKQKKIFKRPLVEFISGNLIH 66
+ ++G G GR LV+ L+ + + + + P V + +L
Sbjct: 1 IAVIGATGKTGRRLVKELLARGHQVTALSRNPSKAP-----------APGVTPVQKDLFD 49
Query: 67 PSTCELIFLNSADNSDLTWEYVINCAAETRPGQAEEIYREGIYKLSINCATAAARYGILK 126
+ L D V++ R + AAAR G+ +
Sbjct: 50 LADLA-EALAGVD-------AVVDAFGA----------RPDDSDGVKHLLDAAARAGVRR 91
Query: 127 YVEISSGEICTSHKHSCKESDEPQPWSTIAKYKCQVEKALLEIPGLNYTIVRPGVVYGKS 186
V +S+ + + + D P A+ K E+ L GL++TIVRPG ++ +
Sbjct: 92 IVVVSAAGLYRDEPGTFRLDDAPLF-PPYARAKAAAEELLRA-SGLDWTIVRPGALFDEE 149
Query: 187 DRHNLAPRLVMCAIYQYLGETLQLFGGKSLPLNTVHVADLSRAIWHLL 234
Y+ E +++ AD++ A+ L
Sbjct: 150 GET-----------YEIGTEGDP------AGESSISRADVAAALLDEL 180
>gnl|CDD|187660 cd08957, WbmH_like_SDR_e, Bordetella bronchiseptica enzymes WbmH
and WbmG-like, extended (e) SDRs. Bordetella
bronchiseptica enzymes WbmH and WbmG, and related
proteins. This subgroup exhibits the active site tetrad
and NAD-binding motif of the extended SDR family. It has
been proposed that the active site in Bordetella WbmG
and WbmH cannot function as an epimerase, and that it
plays a role in O-antigen synthesis pathway from
UDP-2,3-diacetamido-2,3-dideoxy-l-galacturonic acid.
Extended SDRs are distinct from classical SDRs. In
addition to the Rossmann fold (alpha/beta folding
pattern with a central beta-sheet) core region typical
of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 307
Score = 40.6 bits (95), Expect = 8e-04
Identities = 61/269 (22%), Positives = 101/269 (37%), Gaps = 57/269 (21%)
Query: 8 VVILGGCGFVGRNLVEHLVEN-DLLRVID-------KVSPEIAWLNEKQKKIFKRPLVEF 59
V+I GG G +G +L+EHL+E + VID + P+ L + I + LV+
Sbjct: 3 VLITGGAGQIGSHLIEHLLERGHQVVVIDNFATGRREHLPDHPNLTVVEGSIADKALVD- 61
Query: 60 ISGNLIHPSTCELIFLNSADNSDLTWEYVINCAAETR-PGQAEEIYREGIYKLSINCATA 118
+L D + V++ AA + P E + N A
Sbjct: 62 -----------KLF-------GDFKPDAVVHTAAAYKDPDDWYEDTLTNVVG-GANVVQA 102
Query: 119 AARYGILKYVEISSGEICTSHKHSCK--ESDEP--QPWSTIAKYKCQVEKALLEIPGLNY 174
A + G+ + + + +C K + D P P S+ A K E LE+ G+++
Sbjct: 103 AKKAGVKRLIYFQTA-LCYGLKPMQQPIRLDHPRAPPGSSYAISKTAGE-YYLELSGVDF 160
Query: 175 TIVRPGVVYGKSDRHNLAPRLVMCAI---YQYLGETLQLFGGKSLPLNTVHVADLSRAIW 231
R V G PR V+ + YQ L + F + + V V DL+R +
Sbjct: 161 VTFRLANVTG--------PRNVIGPLPTFYQRLKAGKKCFVTDTRR-DFVFVKDLARVVD 211
Query: 232 HLLSELPPAKVY----------REIYHVV 250
L + Y +E++ V
Sbjct: 212 KALDGIRGHGAYHFSSGEDVSIKELFDAV 240
>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 = 0.002
Identities = 42/189 (22%), Positives = 69/189 (36%), Gaps = 23/189 (12%)
Query: 8 VVILGGCGFVGRNLVEHLVENDL-LRVIDKVSPEIAWLNEKQKKIFKRPLVEFISGNLIH 66
V++ G GF+G +L E L+ +R +D + +W FISG++
Sbjct: 2 VLVTGADGFIGSHLTERLLREGHEVRALDIYNSFNSWGLLDNA---VHDRFHFISGDVRD 58
Query: 67 PSTCELIFLNSADNSDLTWEYVINCAAETRPGQ---AEEIYREGIYKLSINCATAAARYG 123
S E D+ V + AA A Y E ++N AA
Sbjct: 59 ASEVE----YLVKKCDV----VFHLAALIAIPYSYTAPLSYVETNVFGTLNVLEAACVLY 110
Query: 124 ILKYVEISSGEI---CTS----HKHSCKESDEPQ-PWSTIAKYKCQVEKALLEIPGLNYT 175
+ V S+ E+ H ++P+ P+S + ++ + GL T
Sbjct: 111 RKRVVHTSTSEVYGTAQDVPIDEDHPLLYINKPRSPYSASKQGADRLAYSYGRSFGLPVT 170
Query: 176 IVRPGVVYG 184
I+RP YG
Sbjct: 171 IIRPFNTYG 179
>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 = 38.9 bits (91), Expect = 0.003
Identities = 61/272 (22%), Positives = 101/272 (37%), Gaps = 39/272 (14%)
Query: 7 AVVILGGCGFVGRNLVEHLVE-NDLLRVIDKV---SPEIAWLNEKQKKIFK--------- 53
V++ G GF+G L+E L+ + +VI V S E A E+ ++ +
Sbjct: 1 TVLLTGATGFLGAYLLEELLRRSTQAKVICLVRAASEEHAM--ERLREALRSYRLWHEDL 58
Query: 54 -RPLVEFISGNLIHPSTC--ELIFLNSADNSDLTWEYVINCAAETRPGQAEEIYR----E 106
R +E ++G+L P + + A+N D +++ A R
Sbjct: 59 ARERIEVVAGDLSEPRLGLSDAEWERLAENVD----TIVHNGALVNWVYPYSELRGANVL 114
Query: 107 GIYKLSINCATAAARYGILKYVEISSGEICT-SHKHSCKESDEPQ--PWSTIAKY---KC 160
G ++ A+ A+ L YV S+ + + E D P Y K
Sbjct: 115 GTREVLRLAASGRAK--PLHYV--STISVGAAIDLSTVTEDDATVTPPPGLAGGYAQSKW 170
Query: 161 QVEKALLEIP--GLNYTIVRPGVVYGKSDRHNLAPRLVMCAIYQYLGETLQLFGGKSLPL 218
E + E GL TIVRPG + G S + ++ + + L
Sbjct: 171 VAELLVREASDRGLPVTIVRPGRILGNSYTGAINSSDILWRMVKGCLALGAYPQSPELTE 230
Query: 219 NTVHVADLSRAIWHLLSELPPAKVYREIYHVV 250
+ V ++RAI L S P A ++HVV
Sbjct: 231 DLTPVDFVARAIVVLSSR-PAASAGGPVFHVV 261
>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 = 37.1 bits (86), Expect = 0.011
Identities = 45/203 (22%), Positives = 75/203 (36%), Gaps = 35/203 (17%)
Query: 9 VILGGCGFVGRNLVEHLVEND----LLRVIDKV-SPEIAWLNEKQKKIFKRPLVEFISGN 63
++ GG GF+G++++ L+E +RV+DK PE+ EK + + V I G+
Sbjct: 3 LVTGGGGFLGQHIIRLLLERKEELKEIRVLDKAFGPELIEHFEKSQ---GKTYVTDIEGD 59
Query: 64 LIHPSTCELIFLNSADNSDLTWEYVINCAAETR---PGQAEEIYREGIYKLSINCATAAA 120
+ +L FL A VI+ AA P EE+ + + A
Sbjct: 60 IK-----DLSFLFRACQGV---SVVIHTAAIVDVFGPPNYEELEEVNV-NGTQAVLEACV 110
Query: 121 RYGILKYVEISSGEIC--TSHKHSCKESDEPQPWSTIAKY-----KCQVEKALLEIPGLN 173
+ + + V SS E+ E P+ + K E +L G
Sbjct: 111 QNNVKRLVYTSSIEVAGPNFKGRPIFNGVEDTPYEDTSTPPYASSKLLAENIVLNANGAP 170
Query: 174 -------YT-IVRPGVVYGKSDR 188
T +RP +YG+
Sbjct: 171 LKQGGYLVTCALRPMYIYGEGSH 193
>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 = 36.9 bits (86), Expect = 0.011
Identities = 22/94 (23%), Positives = 40/94 (42%), Gaps = 18/94 (19%)
Query: 8 VVILGGCGFVGRNLVEHLVENDL-LRVIDKVSP-----EIAWLNEKQKKIFKRPLVEFIS 61
V+I GG GF+G NL ++ + D + +AWL K + V F+
Sbjct: 3 VLITGGAGFIGSNLARFFLKQGWEVIGFDNLMRRGSFGNLAWL----KANREDGGVRFVH 58
Query: 62 GNLIHPSTCELIFLNSADNSDLTWEYVINCAAET 95
G++ + + E +F + +I+ AA+
Sbjct: 59 GDIRNRNDLEDLFEDID--------LIIHTAAQP 84
Score = 28.0 bits (63), Expect = 8.6
Identities = 20/85 (23%), Positives = 35/85 (41%), Gaps = 12/85 (14%)
Query: 171 GLNYTIVRPGVVYG-----KSDRHNLAPRLVMCAIYQYLGETLQLFG-GKSLPLNTVHVA 224
GL + R G + G D+ +A + CA+ G+ L +FG G + +H A
Sbjct: 189 GLKTVVFRCGCLTGPRQFGTEDQGWVA-YFLKCAVT---GKPLTIFGYGGKQVRDVLHSA 244
Query: 225 DLSRAIWHLLSELPPAKVYREIYHV 249
DL P + E++++
Sbjct: 245 DLVNLYLRQFQN--PDRRKGEVFNI 267
>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 = 36.4 bits (85), Expect = 0.013
Identities = 31/131 (23%), Positives = 55/131 (41%), Gaps = 13/131 (9%)
Query: 8 VVILGGCGFVGRNLVEHLVEND--LLRVIDKVSPEIAWLNEKQKKIFKRPLVEFISGNLI 65
+++ GG G +G LV +++ L V D+ ++ L + + F + FI G++
Sbjct: 5 ILVTGGAGSIGSELVRQILKFGPKKLIVFDRDENKLHELVRELRSRFPHDKLRFIIGDV- 63
Query: 66 HPSTCELIFLNSADNSDLTWEYVINCAAETRPGQAEEIYREGIYKL----SINCATAAAR 121
+ L A + + V + AA E+ E I K + N AA
Sbjct: 64 ----RDKERLRRAFK-ERGPDIVFHAAALKHVPSMEDNPEEAI-KTNVLGTKNVIDAAIE 117
Query: 122 YGILKYVEISS 132
G+ K+V IS+
Sbjct: 118 NGVEKFVCIST 128
>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 = 36.5 bits (85), Expect = 0.014
Identities = 12/32 (37%), Positives = 22/32 (68%), Gaps = 1/32 (3%)
Query: 8 VVILGGCGFVGRNLVEHLVEND-LLRVIDKVS 38
+++ GG GF+G +LV+ L+E + V+D +S
Sbjct: 2 ILVTGGAGFIGSHLVDRLLEEGNEVVVVDNLS 33
>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 = 35.7 bits (83), Expect = 0.024
Identities = 60/232 (25%), Positives = 91/232 (39%), Gaps = 55/232 (23%)
Query: 8 VVILGGCGFVGRNLVEHLVENDL-LRVIDKVSPEIAW-LNEKQKKIFKRPLVEFISGNLI 65
V++ GG GF+G +LVE L+E + V+D +S L E +P V+FI G++
Sbjct: 2 VLVTGGAGFIGSHLVERLLERGHEVIVLDNLSTGKKENLPE------VKPNVKFIEGDIR 55
Query: 66 HPSTCELIFLNSADNSDLTWEYVINCAAET-------RPGQAEEIYREGIYKLSINCATA 118
E F +YV + AA+ P + E+ G ++N A
Sbjct: 56 DDELVEFAFEGV--------DYVFHQAAQASVPRSIEDPIKDHEVNVLG----TLNLLEA 103
Query: 119 AARYGILKYVEISSGEICTSHKHSC---------KESDEPQPWS--TIAKYK----CQVE 163
A + G+ ++V SS S E P P S ++KY CQV
Sbjct: 104 ARKAGVKRFVYASSS--------SVYGDPPYLPKDEDHPPNPLSPYAVSKYAGELYCQV- 154
Query: 164 KALLEIPGLNYTIVRPGVVYGKSDRHNLAPRLVMCA-IYQYL-GETLQLFGG 213
+ GL +R VYG N V+ I + L GE ++G
Sbjct: 155 --FARLYGLPTVSLRYFNVYGPRQDPNGGYAAVIPIFIERALKGEPPTIYGD 204
>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 = 35.8 bits (83), Expect = 0.026
Identities = 63/293 (21%), Positives = 117/293 (39%), Gaps = 44/293 (15%)
Query: 8 VVILGGCGFVGRNLVEHLVE---NDLLRVIDKVSPEIAWLNEKQKKIFKRPLVEFISGNL 64
+++ GG GF+G N V +++ + + V+DK++ A E + P F+ G++
Sbjct: 2 ILVTGGAGFIGSNFVRYILNEHPDAEVIVLDKLT--YAGNLENLADLEDNPRYRFVKGDI 59
Query: 65 IHPSTCELIFLNSADNSDLTWEY----VINCAAET---RPGQAEEIYRE----GIYKLSI 113
EL+ S L E+ V++ AAE+ R + E G Y L
Sbjct: 60 ---GDRELV-------SRLFTEHQPDAVVHFAAESHVDRSISGPAAFIETNVVGTYTL-- 107
Query: 114 NCATAAARYGI-LKYVEISSGEICTSHK--HSCKESDEPQPWSTIAKYKC---QVEKALL 167
A +Y ++ IS+ E+ + + E+ P S + K + +A
Sbjct: 108 --LEAVRKYWHEFRFHHISTDEVYGDLEKGDAFTETTPLAPSSPYSASKAASDHLVRAYH 165
Query: 168 EIPGLNYTIVRPGVVYGKSDR-HNLAPRLVMCAIYQYLGETLQLFGGKSLPLNTVHVADL 226
GL I R YG L P ++ A+ G+ L ++G + ++V D
Sbjct: 166 RTYGLPALITRCSNNYGPYQFPEKLIPLMITNAL---AGKPLPVYGDGQQVRDWLYVEDH 222
Query: 227 SRAIWHLLSELPPAKVYREIYHVVDMGNTCQEDLMSTLTDIFGVKHDYVGSVT 279
RAI+ +L + E Y++ +++ T+ ++ G D + V
Sbjct: 223 CRAIYLVLEK----GRVGETYNIGGGNERTNLEVVETILELLGKDEDLITHVE 271
>gnl|CDD|178263 PLN02657, PLN02657, 3,8-divinyl protochlorophyllide a 8-vinyl
reductase.
Length = 390
Score = 35.9 bits (83), Expect = 0.026
Identities = 36/180 (20%), Positives = 71/180 (39%), Gaps = 33/180 (18%)
Query: 8 VVILGGCGFVGRNLVEHLVENDLLRVIDKVSPEIAWLNEKQKKIFKRP-----LVEFISG 62
V+++G G++G+ +V LV R + V+ + ++ I + E
Sbjct: 63 VLVVGATGYIGKFVVRELV----RRGYNVVA-----VAREKSGIRGKNGKEDTKKELPGA 113
Query: 63 NLIHPSTCELIFLNSADNSD-LTWEYVINCAAETRPGQAEEIYREGI-YKLSINCATAAA 120
++ + L S+ + V++C A +R G ++ ++ I Y+ + N A
Sbjct: 114 EVVFGDVTDADSLRKVLFSEGDPVDVVVSCLA-SRTGGVKDSWK--IDYQATKNSLDAGR 170
Query: 121 RYGILKYVEISSGEICTSHKHSCKESDEPQPWSTIAKYKCQVEKALLEI-PGLNYTIVRP 179
G +V +S+ IC +P + K + E L + Y+IVRP
Sbjct: 171 EVGAKHFVLLSA--ICVQ-----------KPLLEFQRAKLKFEAELQALDSDFTYSIVRP 217
>gnl|CDD|187643 cd08939, KDSR-like_SDR_c, 3-ketodihydrosphingosine reductase (KDSR)
and related proteins, classical (c) SDR. These proteins
include members identified as KDSR, ribitol type
dehydrogenase, and others. The group shows strong
conservation of the active site tetrad and glycine rich
NAD-binding motif of the classical SDRs. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold (alpha/beta folding pattern with a central
beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRs are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes catalyze a
wide range of activities including the metabolism of
steroids, cofactors, carbohydrates, lipids, aromatic
compounds, and amino acids, and act in redox sensing.
Classical SDRs have an TGXXX[AG]XG cofactor binding
motif and a YXXXK active site motif, with the Tyr
residue of the active site motif serving as a critical
catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 239
Score = 35.3 bits (82), Expect = 0.028
Identities = 33/134 (24%), Positives = 52/134 (38%), Gaps = 29/134 (21%)
Query: 8 VVILGGCGFVGRNLVEHLV------------ENDLLRVIDKVSPEIAWLNEKQKKIFKRP 55
V+I GG +G+ L + LV E+ L ++++ E QK
Sbjct: 4 VLITGGSSGIGKALAKELVKEGANVIIVARSESKLEEAVEEI--EAEANASGQK------ 55
Query: 56 LVEFISGNLIHPSTCELIFLNSADNSDLTWEYVINCAAETRPGQAEEI----YREGI--- 108
V +IS +L E F A + V+NCA + PG E++ + G+
Sbjct: 56 -VSYISADLSDYEEVEQAF-AQAVEKGGPPDLVVNCAGISIPGLFEDLTAEEFERGMDVN 113
Query: 109 YKLSINCATAAARY 122
Y S+N A A
Sbjct: 114 YFGSLNVAHAVLPL 127
>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 = 35.7 bits (83), Expect = 0.028
Identities = 58/257 (22%), Positives = 77/257 (29%), Gaps = 78/257 (30%)
Query: 8 VVILGGCGFVGRNLVEHLVEN-DLLRVIDKVSPEIAWLNEKQKKIFKRPLVEFISGNLIH 66
+VI GG GF+GR L L + V+ + + L E I
Sbjct: 2 IVITGGTGFIGRALTRRLTAAGHEVVVLSRRPGKAEGLAEV-----------------IT 44
Query: 67 PSTCELIF--LNSADNSDLTWEYVINCA----AETR--PGQAEEIYR----------EGI 108
L L AD VIN A A R +EI E I
Sbjct: 45 WDGLSLGPWELPGAD-------AVINLAGEPIACRRWTEANKKEILSSRIESTRVLVEAI 97
Query: 109 YKLSIN-----CATAAARYGILKYVEISSGEICTSHKHSCKESDEPQPWSTIAKYKCQVE 163
A+A YG SG+ E+ +A+ E
Sbjct: 98 ANAPAPPKVLISASAVGYYG-------HSGD------EVLTENSPS-GKDFLAEVCKAWE 143
Query: 164 KALL--EIPGLNYTIVRPGVVYGKS----DRHNLAPRLVMCAIYQYLGETLQLFGGKSLP 217
KA G I+R GVV G + L RL LG L G
Sbjct: 144 KAAQPASELGTRVVILRTGVVLGPDGGALPKMLLPFRL-------GLGGPL---GSGRQW 193
Query: 218 LNTVHVADLSRAIWHLL 234
++ +H+ DL R I +
Sbjct: 194 MSWIHIDDLVRLIEFAI 210
>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 = 35.8 bits (83), Expect = 0.028
Identities = 33/121 (27%), Positives = 51/121 (42%), Gaps = 20/121 (16%)
Query: 137 TSHKHSCKESDEPQPWSTIAKYKCQVEKALLEI--PGLNYTIVR-PGVVYGKSDRHNLAP 193
++ + P T A + E A LE+ G+ ++VR P VV+G+ D H P
Sbjct: 115 GPTGGQEEDEEAPDDPPTPA-ARAVSEAAALELAERGVRASVVRLPPVVHGRGD-HGFVP 172
Query: 194 RLVMCA----IYQYLGETLQLFGGKSLPLNTVHVADLSRAIWHLLSELPPAKVYREIYHV 249
L+ A + Y+G+ GK+ VH D +R + L E A +YH
Sbjct: 173 MLIAIAREKGVSAYVGD------GKNR-WPAVHRDDAARL-YRLALEKGKA---GSVYHA 221
Query: 250 V 250
V
Sbjct: 222 V 222
>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 = 34.3 bits (79), Expect = 0.079
Identities = 18/38 (47%), Positives = 23/38 (60%), Gaps = 3/38 (7%)
Query: 6 PAVVILGGCGFVGRNLVEHL---VENDLLRVIDKVSPE 40
V+I G GFVG+ L E L V N+ L +ID VSP+
Sbjct: 1 MKVLITGASGFVGQRLAERLLSDVPNERLILIDVVSPK 38
>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 = 34.2 bits (79), Expect = 0.090
Identities = 29/105 (27%), Positives = 45/105 (42%), Gaps = 17/105 (16%)
Query: 8 VVILGGCGFVGRNLVEHLVEND--------LLRVIDKVSPEIAWLNE-KQKKIFKRPLVE 58
V+I G GF+G+ L+E L+ + L+R S E L E + K+F R
Sbjct: 3 VLITGATGFLGKVLLEKLLRSCPDIGKIYLLIRGKSGQSAE-ERLRELLKDKLFDRGRNL 61
Query: 59 F-ISGNLIHPSTCEL----IFLNSADNSDLTWE--YVINCAAETR 96
+ + I P +L + L+ D L E +I+CAA
Sbjct: 62 NPLFESKIVPIEGDLSEPNLGLSDEDLQTLIEEVNIIIHCAATVT 106
>gnl|CDD|233570 TIGR01777, yfcH, TIGR01777 family protein. This model represents
a clade of proteins of unknown function including the
E. coli yfcH protein [Hypothetical proteins,
Conserved].
Length = 291
Score = 33.8 bits (78), Expect = 0.11
Identities = 9/22 (40%), Positives = 14/22 (63%)
Query: 8 VVILGGCGFVGRNLVEHLVEND 29
++I GG GF+GR L + L +
Sbjct: 1 ILITGGTGFIGRALTQRLTKRG 22
>gnl|CDD|187559 cd05248, ADP_GME_SDR_e, ADP-L-glycero-D-mannoheptose 6-epimerase
(GME), extended (e) SDRs. This subgroup contains
ADP-L-glycero-D-mannoheptose 6-epimerase, an extended
SDR, which catalyzes the NAD-dependent interconversion
of ADP-D-glycero-D-mannoheptose and
ADP-L-glycero-D-mannoheptose. This subgroup has the
canonical active site tetrad and NAD(P)-binding motif.
Extended SDRs are distinct from classical SDRs. In
addition to the Rossmann fold (alpha/beta folding
pattern with a central beta-sheet) core region typical
of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving
as a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton
relay involving the conserved Tyr and Lys, a water
molecule stabilized by Asn, and nicotinamide. Atypical
SDRs generally lack the catalytic residues
characteristic of the SDRs, and their glycine-rich
NAD(P)-binding motif is often different from the forms
normally seen in classical or extended SDRs. Complex
(multidomain) SDRs such as ketoreductase domains of
fatty acid synthase have a GGXGXXG NAD(P)-binding motif
and an altered active site motif (YXXXN). Fungal type
ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding
motif.
Length = 317
Score = 33.4 bits (77), Expect = 0.14
Identities = 18/47 (38%), Positives = 27/47 (57%), Gaps = 4/47 (8%)
Query: 8 VVILGGCGFVGRNLVEHLVEN---DLLRVIDKVSPEIAWLNEKQKKI 51
+++ GG GF+G NLV+ L E D+L V+D +S + N KI
Sbjct: 2 IIVTGGAGFIGSNLVKALNERGITDIL-VVDNLSNGEKFKNLVGLKI 47
>gnl|CDD|187561 cd05251, NmrA_like_SDR_a, NmrA (a transcriptional regulator) and
HSCARG (an NADPH sensor) like proteins, atypical (a)
SDRs. NmrA and HSCARG like proteins. NmrA is a negative
transcriptional regulator of various fungi, involved in
the post-translational modulation of the GATA-type
transcription factor AreA. NmrA lacks the canonical
GXXGXXG NAD-binding motif and has altered residues at
the catalytic triad, including a Met instead of the
critical Tyr residue. NmrA may bind nucleotides but
appears to lack any dehydrogenase activity. HSCARG has
been identified as a putative NADP-sensing molecule, and
redistributes and restructures in response to NADPH/NADP
ratios. Like NmrA, it lacks most of the active site
residues of the SDR family, but has an NAD(P)-binding
motif similar to the extended SDR family, GXXGXXG. SDRs
are a functionally diverse family of oxidoreductases
that have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Atypical SDRs
are distinct from classical SDRs. Classical SDRs have an
TGXXX[AG]XG cofactor binding motif and a YXXXK active
site motif, with the Tyr residue of the active site
motif serving as a critical catalytic residue (Tyr-151,
human 15-hydroxyprostaglandin dehydrogenase numbering).
In addition to the Tyr and Lys, there is often an
upstream Ser and/or an Asn, contributing to the active
site; while substrate binding is in the C-terminal
region, which determines specificity. The standard
reaction mechanism is a 4-pro-S hydride transfer and
proton relay involving the conserved Tyr and Lys, a
water molecule stabilized by Asn, and nicotinamide. In
addition to the Rossmann fold core region typical of all
SDRs, extended SDRs have a less conserved C-terminal
extension of approximately 100 amino acids, and
typically have a TGXXGXXG cofactor binding motif.
Complex (multidomain) SDRs such as ketoreductase domains
of fatty acid synthase have a GGXGXXG NAD(P)-binding
motif and an altered active site motif (YXXXN). Fungal
type ketoacyl reductases have a TGXXXGX(1-2)G
NAD(P)-binding motif.
Length = 242
Score = 33.0 bits (76), Expect = 0.16
Identities = 39/175 (22%), Positives = 60/175 (34%), Gaps = 23/175 (13%)
Query: 102 EIYREGIYKLSINCATAAARYGILKYVEISSGEICTSHKHSCKESDEPQPWSTIAKYKCQ 161
E E N AA R G+ +V SS + D +K +
Sbjct: 77 EAGGEDEIAQGKNVVDAAKRAGVQHFV-FSSVPDVEKLTLAVPHFD--------SKAE-- 125
Query: 162 VEKALLEIPGLNYTIVRPGVVYGKSDRHN-LAPRLVMCAIYQYLGETLQLFGGKSLPLNT 220
VE+ + GL TI+RP N L P L L L LP+
Sbjct: 126 VEEYIRAS-GLPATILRPAFFM-----ENFLTPPAPQKMEDGTLTLVLPLDPDTKLPM-- 177
Query: 221 VHVADLSRAIWHLLSELPPAKVYREIYHVVDMGNTCQEDLMSTLTDIFGVKHDYV 275
+ VAD+ A+ + + PAK + + E++ + + + G YV
Sbjct: 178 IDVADIGPAVAAIFKD--PAKFNGKTIELAG-DELTPEEIAAAFSKVLGKPVTYV 229
>gnl|CDD|223774 COG0702, COG0702, Predicted nucleoside-diphosphate-sugar epimerases
[Cell envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 275
Score = 32.6 bits (74), Expect = 0.24
Identities = 44/239 (18%), Positives = 72/239 (30%), Gaps = 43/239 (17%)
Query: 6 PAVVILGGCGFVGRNLVEHLVENDLLRVIDKVSPEIAWLNEKQKKIFKRPLVEFISGNLI 65
+++ G GFVG +V L+ +PE A VE + G+L
Sbjct: 1 MKILVTGATGFVGGAVVRELLARGHEVRAAVRNPEAAAALAGG--------VEVVLGDLR 52
Query: 66 HPSTCELIFLNSADNSDLTWEYVINCAAETRPGQAEEIYREGIYKLSINCATAAARYGIL 125
P + A D V+ + A + + A AA G+
Sbjct: 53 DP----KSLVAGAKGVD----GVLLISGLLDGSDAFRA-VQVTA---VVRAAEAAGAGVK 100
Query: 126 KYVEISSGEICTSHKHSCKESDEPQPWSTIAKYKCQVEKALLEIPGLNYTIVRPGVVYGK 185
V +S + S +A+ K VE AL G+ YT +R Y
Sbjct: 101 HGVSLSVLG------------ADAASPSALARAKAAVEAALRS-SGIPYTTLRRAAFYL- 146
Query: 186 SDRHNLAPRLVMCAIYQYLGETLQLFGGKSLPLNTVHVADLSRAIWHLL-SELPPAKVY 243
+ G+ P + V D++ A+ L + + Y
Sbjct: 147 -GAGAAFIEAAE----AAGLPVIPRGIGRLSP---IAVDDVAEALAAALDAPATAGRTY 197
>gnl|CDD|233775 TIGR02197, heptose_epim,
ADP-L-glycero-D-manno-heptose-6-epimerase. This family
consists of examples of
ADP-L-glycero-D-mannoheptose-6-epimerase, an enzyme
involved in biosynthesis of the inner core of
lipopolysaccharide (LPS) for Gram-negative bacteria.
This enzyme is homologous to UDP-glucose 4-epimerase
(TIGR01179) and belongs to the NAD dependent
epimerase/dehydratase family (pfam01370) [Cell
envelope, Biosynthesis and degradation of surface
polysaccharides and lipopolysaccharides].
Length = 314
Score = 32.6 bits (75), Expect = 0.26
Identities = 14/46 (30%), Positives = 24/46 (52%), Gaps = 2/46 (4%)
Query: 8 VVILGGCGFVGRNLVEHLVENDLLRVI--DKVSPEIAWLNEKQKKI 51
+++ GG GF+G NLV+ L E + ++ D + +LN I
Sbjct: 1 IIVTGGAGFIGSNLVKALNERGITDILVVDNLRDGHKFLNLADLVI 46
>gnl|CDD|178748 PLN03209, PLN03209, translocon at the inner envelope of chloroplast
subunit 62; Provisional.
Length = 576
Score = 31.8 bits (72), Expect = 0.63
Identities = 26/73 (35%), Positives = 37/73 (50%), Gaps = 19/73 (26%)
Query: 158 YKCQVEKALLEIPGLNYTIVRPGVVYGKSD----RHNLAPRLVMCAIYQYLGETLQLFGG 213
+K + E+AL+ GL YTIVRPG + +D HNL L E LFGG
Sbjct: 230 WKRKAEEALIA-SGLPYTIVRPGGMERPTDAYKETHNLT-----------LSEEDTLFGG 277
Query: 214 KSLPLNTVHVADL 226
+ ++ + VA+L
Sbjct: 278 Q---VSNLQVAEL 287
>gnl|CDD|165812 PLN02166, PLN02166, dTDP-glucose 4,6-dehydratase.
Length = 436
Score = 31.5 bits (71), Expect = 0.63
Identities = 21/66 (31%), Positives = 32/66 (48%), Gaps = 4/66 (6%)
Query: 8 VVILGGCGFVGRNLVEHLV-ENDLLRVIDKVSPEIAWLNEKQKKIFKRPLVEFISGNLIH 66
+V+ GG GFVG +LV+ L+ D + VID E +F P E I +++
Sbjct: 123 IVVTGGAGFVGSHLVDKLIGRGDEVIVIDNF---FTGRKENLVHLFGNPRFELIRHDVVE 179
Query: 67 PSTCEL 72
P E+
Sbjct: 180 PILLEV 185
>gnl|CDD|216996 pfam02364, Glucan_synthase, 1,3-beta-glucan synthase component.
This family consists of various 1,3-beta-glucan synthase
components including Gls1, Gls2 and Gls3 from yeast.
1,3-beta-glucan synthase EC:2.4.1.34 also known as
callose synthase catalyzes the formation of a
beta-1,3-glucan polymer that is a major component of the
fungal cell wall. The reaction catalyzed is:-
UDP-glucose + {(1,3)-beta-D-glucosyl}(N) <=> UDP +
{(1,3)-beta-D-glucosyl}(N+1).
Length = 818
Score = 31.6 bits (72), Expect = 0.64
Identities = 19/70 (27%), Positives = 29/70 (41%), Gaps = 12/70 (17%)
Query: 144 KESDEPQPWSTIAKYKCQVEKALLEIPGLNYTIVRPGVVY---GKSDRHNLAPRLVMCAI 200
E EP +S + C++++ +P + I G GKSD N A+
Sbjct: 234 AEGGEPDYYSALIDGHCELDENGRRVP--KFRIKLSGNPILGDGKSDNQNH-------AL 284
Query: 201 YQYLGETLQL 210
Y GE +QL
Sbjct: 285 IFYRGEYIQL 294
>gnl|CDD|177856 PLN02206, PLN02206, UDP-glucuronate decarboxylase.
Length = 442
Score = 31.1 bits (70), Expect = 0.92
Identities = 21/66 (31%), Positives = 31/66 (46%), Gaps = 4/66 (6%)
Query: 8 VVILGGCGFVGRNLVEHLV-ENDLLRVIDKVSPEIAWLNEKQKKIFKRPLVEFISGNLIH 66
VV+ GG GFVG +LV+ L+ D + V+D E F P E I +++
Sbjct: 122 VVVTGGAGFVGSHLVDRLMARGDSVIVVDNF---FTGRKENVMHHFSNPNFELIRHDVVE 178
Query: 67 PSTCEL 72
P E+
Sbjct: 179 PILLEV 184
>gnl|CDD|173004 PRK14538, PRK14538, putative bifunctional signaling protein/50S
ribosomal protein L9; Provisional.
Length = 838
Score = 30.2 bits (68), Expect = 1.9
Identities = 11/25 (44%), Positives = 13/25 (52%)
Query: 33 VIDKVSPEIAWLNEKQKKIFKRPLV 57
+ID S EI WLN I K P +
Sbjct: 117 LIDISSKEIQWLNPYANFILKNPEI 141
>gnl|CDD|187555 cd05244, BVR-B_like_SDR_a, biliverdin IX beta reductase (BVR-B, aka
flavin reductase)-like proteins; atypical (a) SDRs.
Human BVR-B catalyzes pyridine nucleotide-dependent
production of bilirubin-IX beta during fetal
development; in the adult BVR-B has flavin and ferric
reductase activities. Human BVR-B catalyzes the
reduction of FMN, FAD, and riboflavin. Recognition of
flavin occurs mostly by hydrophobic interactions,
accounting for the broad substrate specificity. Atypical
SDRs are distinct from classical SDRs. BVR-B does not
share the key catalytic triad, or conserved tyrosine
typical of SDRs. The glycine-rich NADP-binding motif of
BVR-B is GXXGXXG, which is similar but not identical to
the pattern seen in extended SDRs. 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 = 207
Score = 29.5 bits (67), Expect = 2.2
Identities = 19/98 (19%), Positives = 35/98 (35%), Gaps = 8/98 (8%)
Query: 86 EYVINCAAETRPGQAEEIYREGIYKLSINCATAAARYGILKYVEIS---SGEICTSHKHS 142
+ VI+ ++ EG N +A G+ + + + S +
Sbjct: 64 DAVISALGTRNDLSPTTLHSEGT----RNIVSAMKAAGVKRLIVVGGAGSLDDRPKVTLV 119
Query: 143 CKESDEPQPWSTIAKYKCQVEKALLEIPGLNYTIVRPG 180
P +A+ ++ K L E GL++T VRP
Sbjct: 120 LDTLLFPPALRRVAEDHARMLKVLRE-SGLDWTAVRPP 156
>gnl|CDD|212673 cd10231, YegD_like, Escherichia coli YegD, a putative chaperone
protein, and related proteins. This bacterial subfamily
includes the uncharacterized Escherichia coli YegD. It
belongs to the heat shock protein 70 (HSP70) family of
chaperones that assist in protein folding and assembly
and can direct incompetent "client" proteins towards
degradation. Typically, HSP70s have a nucleotide-binding
domain (NBD) and a substrate-binding domain (SBD). The
nucleotide sits in a deep cleft formed between the two
lobes of the NBD. The two subdomains of each lobe change
conformation between ATP-bound, ADP-bound, and
nucleotide-free states. ATP binding opens up the
substrate-binding site; substrate-binding increases the
rate of ATP hydrolysis. YegD lacks the SBD. HSP70
chaperone activity is regulated by various
co-chaperones: J-domain proteins and nucleotide exchange
factors (NEFs). Some family members are not chaperones
but instead, function as NEFs for their Hsp70 partners,
other family members function as both chaperones and
NEFs.
Length = 415
Score = 29.4 bits (67), Expect = 2.8
Identities = 19/59 (32%), Positives = 27/59 (45%), Gaps = 10/59 (16%)
Query: 188 RHNLAPRLVMCAIYQYLGETLQLFGGKSLPLNTVHVADLSRAIWHLLSELPPAKVYREI 246
H + P L G T + GGK LP+ + ADL+ WH ++ L K RE+
Sbjct: 227 LHAVMPLLGK-------GSTYRS-GGKGLPVPNSYFADLAT--WHKINFLYTPKTLREL 275
>gnl|CDD|224015 COG1090, COG1090, Predicted nucleoside-diphosphate sugar
epimerase [General function prediction only].
Length = 297
Score = 29.2 bits (66), Expect = 2.9
Identities = 8/22 (36%), Positives = 12/22 (54%)
Query: 8 VVILGGCGFVGRNLVEHLVEND 29
++I GG G +GR L L +
Sbjct: 1 ILITGGTGLIGRALTARLRKGG 22
>gnl|CDD|187571 cd05261, CAPF_like_SDR_e, capsular polysaccharide assembling
protein (CAPF) like, extended (e) SDRs. This subgroup
of extended SDRs, includes some members which have been
identified as capsular polysaccharide assembling
proteins, such as Staphylococcus aureus Cap5F which is
involved in the biosynthesis of N-acetyl-l-fucosamine,
a constituent of surface polysaccharide structures of
S. aureus. This subgroup has the characteristic active
site tetrad and NAD-binding motif of 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 = 248
Score = 28.9 bits (65), Expect = 3.3
Identities = 21/67 (31%), Positives = 29/67 (43%), Gaps = 11/67 (16%)
Query: 8 VVILGGCGFVGRNLVEHLVENDLLRVI--DKVSPEIAWLNEKQKKIF-------KRPL-- 56
++I G GF+G+NL+ L E + D+ S E + Q F RP
Sbjct: 3 ILITGAKGFIGKNLIARLKEQKDDDIFFYDRESDESELDDFLQGADFIFHLAGVNRPKDE 62
Query: 57 VEFISGN 63
EF SGN
Sbjct: 63 AEFESGN 69
>gnl|CDD|215377 PLN02700, PLN02700, homoserine dehydrogenase family protein.
Length = 377
Score = 29.4 bits (66), Expect = 3.4
Identities = 11/18 (61%), Positives = 15/18 (83%)
Query: 9 VILGGCGFVGRNLVEHLV 26
V+L GCG VGR+L+ H+V
Sbjct: 6 VLLLGCGGVGRHLLRHIV 23
>gnl|CDD|237108 PRK12467, PRK12467, peptide synthase; Provisional.
Length = 3956
Score = 29.7 bits (67), Expect = 3.5
Identities = 26/84 (30%), Positives = 31/84 (36%), Gaps = 26/84 (30%)
Query: 147 DEPQPWSTIAKYKCQVEKALLEIPGLNYTIVRPGVVYGKSDRHNLAPRLVMCAIY----- 201
D Q +A Q LL P L T+VR G DRH+L IY
Sbjct: 2734 DLEQALDALAAADRQQGFDLLSAPLLRLTLVRTG-----EDRHHL--------IYTNHHI 2780
Query: 202 --------QYLGETLQLFGGKSLP 217
Q LGE LQ + G+ P
Sbjct: 2781 LMDGWSGSQLLGEVLQRYFGQPPP 2804
>gnl|CDD|212585 cd11716, THUMP_ThiI, THUMP domain of thiamine biosynthesis protein
ThiI. ThiI is an enzyme responsible for the formation
of the modified base S(4)U (4-thiouridine) found at
position 8 in some prokaryotic tRNAs. This modification
acts as a signal for UV exposure, triggering a response
that provides protection against its damaging effects.
ThiI consists of an N-terminal THUMP domain, followed by
an NFLD domain, and a C-terminal PP-loop pyrophosphatase
domain. The N-terminal THUMP domain has been implicated
in the recognition of the acceptor-stem region. The
THUMP domain is named after thiouridine synthases,
methylases and PSUSs. The domain consists of about 110
amino acid residues. It is predicted to be an
RNA-binding domain and probably functions by delivering
a variety of RNA modification enzymes to their targets.
Length = 166
Score = 28.6 bits (65), Expect = 3.8
Identities = 16/50 (32%), Positives = 25/50 (50%), Gaps = 5/50 (10%)
Query: 226 LSRAIWHLLSELPPAKVYRE---IYHVVDMGNTCQEDLMSTLTDIFGVKH 272
L + I L +LP KV RE IY V++ E+++ L +FG+
Sbjct: 23 LVKNIRRALKDLPDVKVEREWGRIY--VELNGEDLEEVIERLKKVFGIVS 70
>gnl|CDD|178256 PLN02650, PLN02650, dihydroflavonol-4-reductase.
Length = 351
Score = 28.6 bits (64), Expect = 5.0
Identities = 9/20 (45%), Positives = 12/20 (60%)
Query: 326 NLKPVHLDNAKLRDTGFEFQ 345
+LK V + KL D GF F+
Sbjct: 286 DLKSVEFSSKKLTDLGFTFK 305
>gnl|CDD|224659 COG1745, COG1745, Predicted metal-binding protein [General function
prediction only].
Length = 94
Score = 27.0 bits (60), Expect = 5.4
Identities = 11/31 (35%), Positives = 16/31 (51%), Gaps = 3/31 (9%)
Query: 307 RKHNIDNTPLTPYIVPDMLNLKPVHLDNAKL 337
++ IDN Y D LN+ PVH+ +K
Sbjct: 22 NEYGIDNEEFKEY---DELNISPVHIHRSKA 49
>gnl|CDD|215072 PLN00141, PLN00141, Tic62-NAD(P)-related group II protein;
Provisional.
Length = 251
Score = 28.3 bits (63), Expect = 5.4
Identities = 13/22 (59%), Positives = 16/22 (72%), Gaps = 1/22 (4%)
Query: 159 KCQVEKALLEIPGLNYTIVRPG 180
K Q EK + + G+NYTIVRPG
Sbjct: 161 KLQAEKYIRK-SGINYTIVRPG 181
>gnl|CDD|187581 cd05273, GME-like_SDR_e, Arabidopsis thaliana
GDP-mannose-3',5'-epimerase (GME)-like, extended (e)
SDRs. This subgroup of NDP-sugar
epimerase/dehydratases are extended SDRs; they have the
characteristic active site tetrad, and an NAD-binding
motif: TGXXGXX[AG], which is a close match to the
canonical NAD-binding motif. Members include
Arabidopsis thaliana GDP-mannose-3',5'-epimerase (GME)
which catalyzes the epimerization of two positions of
GDP-alpha-D-mannose to form GDP-beta-L-galactose.
Extended SDRs are distinct from classical SDRs. In
addition to the Rossmann fold (alpha/beta folding
pattern with a central beta-sheet) core region typical
of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving
as a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton
relay involving the conserved Tyr and Lys, a water
molecule stabilized by Asn, and nicotinamide. Atypical
SDRs generally lack the catalytic residues
characteristic of the SDRs, and their glycine-rich
NAD(P)-binding motif is often different from the forms
normally seen in classical or extended SDRs. Complex
(multidomain) SDRs such as ketoreductase domains of
fatty acid synthase have a GGXGXXG NAD(P)-binding motif
and an altered active site motif (YXXXN). Fungal type
ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding
motif.
Length = 328
Score = 28.6 bits (64), Expect = 5.4
Identities = 17/65 (26%), Positives = 23/65 (35%), Gaps = 9/65 (13%)
Query: 8 VVILGGCGFVGRNLVEHLV-ENDLLRVIDKVSPEIAWLNEKQKKIFKRPLVEFISGNLIH 66
++ G GF+G +L E L E +R D SPE EF +L
Sbjct: 3 ALVTGAGGFIGSHLAERLKAEGHYVRGADWKSPEHMTQPTDD--------DEFHLVDLRE 54
Query: 67 PSTCE 71
C
Sbjct: 55 MENCL 59
>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 = 28.5 bits (64), Expect = 5.5
Identities = 9/55 (16%), Positives = 22/55 (40%), Gaps = 2/55 (3%)
Query: 7 AVVILGGCGFVGRNLVEHLVENDLLRVIDKVSPEIAWLNEKQKKIFKRPLVEFIS 61
++I G G +G+ + L+ R+I L + ++++ I+
Sbjct: 4 IILITGAAGLIGKAFCKALLSAG-ARLI-LADINAPALEQLKEELTNLYKNRVIA 56
>gnl|CDD|216949 pfam02254, TrkA_N, TrkA-N domain. This domain is found in a wide
variety of proteins. These protein include potassium
channels, phosphoesterases, and various other
transporters. This domain binds to NAD.
Length = 116
Score = 27.5 bits (62), Expect = 5.5
Identities = 19/72 (26%), Positives = 31/72 (43%), Gaps = 9/72 (12%)
Query: 9 VILGGCGFVGRNLVEHLVE-NDLLRVIDKVSPEIAWLNEKQKKIFKRPLVEFISGNLIHP 67
+I+ G G VGR+L E L E + VIDK + ++ + + V + G+
Sbjct: 1 IIIIGYGRVGRSLAEELREGGPDVVVIDK--------DPERVEELREEGVPVVVGDATDE 52
Query: 68 STCELIFLNSAD 79
E + AD
Sbjct: 53 EVLEEAGIEEAD 64
>gnl|CDD|192965 pfam12243, CTK3, CTD kinase subunit gamma CTK3. The C-terminal
domain kinase (CTDK-1), is a three-subunit complex
comprised of Ctk1, Ctk2, and Ctk3, that plays a key role
in regulation of transcription and translation and in
coordinating these two processes. Both Ctk2 and Ctk3 are
regulated at the level of protein turnover, and are
unstable proteins processed through a
ubiquitin-proteasome pathway. Their physical interaction
is required to protect both subunits from degradation,
and both Ctk2 and Ctk3 are required for Ctk1 CTD kinase
activation. The mammalian P-TEFb is mirrored by the
combined complexes in yeast of the CTDK1 and the Bur1/2.
Length = 139
Score = 27.7 bits (62), Expect = 6.0
Identities = 6/20 (30%), Positives = 12/20 (60%)
Query: 24 HLVENDLLRVIDKVSPEIAW 43
+++ D+ R++D V PE
Sbjct: 83 RMLQRDIPRLVDSVVPEENS 102
>gnl|CDD|233071 TIGR00649, MG423, conserved hypothetical protein. Contains an
ATP-binding domain at the N-terminal end of the
protein. Possibly part of a superfamily of
beta-lactmases [Hypothetical proteins, Conserved].
Length = 422
Score = 28.5 bits (64), Expect = 6.7
Identities = 17/59 (28%), Positives = 28/59 (47%), Gaps = 15/59 (25%)
Query: 7 AVVILGGCGFVGRNL--VE------------HLVENDLLRVIDKVSPEIAWLNEKQKKI 51
+ LGG G +G+N+ VE E+++L V D V P+ +L E + K+
Sbjct: 2 KIFALGGLGEIGKNMYVVEIDDEIVIFDAGILFPEDEMLGV-DGVIPDFTYLQENEDKV 59
>gnl|CDD|182313 PRK10217, PRK10217, dTDP-glucose 4,6-dehydratase; Provisional.
Length = 355
Score = 28.5 bits (63), Expect = 6.8
Identities = 12/33 (36%), Positives = 22/33 (66%), Gaps = 2/33 (6%)
Query: 8 VVILGGCGFVGRNLVEHLVEN--DLLRVIDKVS 38
++I GG GF+G LV +++ D + V+DK++
Sbjct: 4 ILITGGAGFIGSALVRYIINETSDAVVVVDKLT 36
>gnl|CDD|224012 COG1087, GalE, UDP-glucose 4-epimerase [Cell envelope biogenesis,
outer membrane].
Length = 329
Score = 28.3 bits (64), Expect = 6.9
Identities = 54/261 (20%), Positives = 102/261 (39%), Gaps = 55/261 (21%)
Query: 6 PAVVILGGCGFVGRNLVEHLVENDLLRVI-DKVSPEIAWLNEKQKKIFKRPLVEFISGNL 64
V++ GG G++G + V L++ V+ D +S N + + + +F G+L
Sbjct: 1 MKVLVTGGAGYIGSHTVRQLLKTGHEVVVLDNLS------NGHKIAL-LKLQFKFYEGDL 53
Query: 65 IHPSTCELIFLNSADNSDLTWEYVINCAAETRPGQAEEI----YREGIYKLSINCATAAA 120
+ + +F +N + V++ AA G++ + Y + ++N A
Sbjct: 54 LDRALLTAVF---EENK---IDAVVHFAASISVGESVQNPLKYYDNNVVG-TLNLIEAML 106
Query: 121 RYGILKYVEISS----GEICTSHKHSCKESDEPQPWSTIAKYKCQVEKALLEI---PGLN 173
+ G+ K++ S+ GE TS E+ P + + K E+ L +
Sbjct: 107 QTGVKKFIFSSTAAVYGEPTTS---PISETSPLAPINPYGRSKLMSEEILRDAAKANPFK 163
Query: 174 YTIVRPGVVYGKSD------RH----NLAPRLVMCAIYQYLGETLQLFGGKSLPLNT--- 220
I+R V G R+ L P A+ + + L +FG +T
Sbjct: 164 VVILRYFNVAGACPDGTLGQRYPGATLLIPVAAEAALGKR--DKLFIFGDD---YDTKDG 218
Query: 221 ------VHVADLSRAIWHLLS 235
+HV DL+ A H+L+
Sbjct: 219 TCIRDYIHVDDLADA--HVLA 237
>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 = 28.0 bits (63), Expect = 7.7
Identities = 9/20 (45%), Positives = 15/20 (75%)
Query: 8 VVILGGCGFVGRNLVEHLVE 27
++I GG GF+G +L + L+E
Sbjct: 3 ILITGGAGFLGSHLCDRLLE 22
>gnl|CDD|239431 cd03315, MLE_like, Muconate lactonizing enzyme (MLE) like subgroup
of the enolase superfamily. Enzymes of this subgroup
share three conserved carboxylate ligands for the
essential divalent metal ion (usually Mg2+), two
aspartates and a glutamate, and residues that can
function as general acid/base catalysts, a Lys-X-Lys
motif and another conserved lysine. Despite these
conserved residues, the members of the MLE subgroup,
like muconate lactonizing enzyme, o-succinylbenzoate
synthase (OSBS) and N-acylamino acid racemase (NAAAR),
catalyze different reactions.
Length = 265
Score = 27.7 bits (62), Expect = 8.5
Identities = 17/70 (24%), Positives = 27/70 (38%), Gaps = 14/70 (20%)
Query: 192 APR-LVMCAIY----QYLGETLQLFGGKSLPLNTVHVADLSRAIWHLLSELPPAKVYREI 246
A + V A++ + LG + L G + V VA H+L PA+V E
Sbjct: 43 ATKAAVDMALWDLWGKRLGVPVYLLLGG--YRDRVRVA-------HMLGLGEPAEVAEEA 93
Query: 247 YHVVDMGNTC 256
++ G
Sbjct: 94 RRALEAGFRT 103
>gnl|CDD|215100 PLN00198, PLN00198, anthocyanidin reductase; Provisional.
Length = 338
Score = 27.9 bits (62), Expect = 8.5
Identities = 23/79 (29%), Positives = 36/79 (45%), Gaps = 12/79 (15%)
Query: 5 KPAVVILGGCGFVGRNLVEHLVE-----NDLLRVID---KVSPEIAWLNEKQKKIFKRPL 56
K A VI GG GF+ L++ L++ N +R + K++ A KIF L
Sbjct: 10 KTACVI-GGTGFLASLLIKLLLQKGYAVNTTVRDPENQKKIAHLRALQELGDLKIFGADL 68
Query: 57 VEFISGNLIHP-STCELIF 74
+ S P + C+L+F
Sbjct: 69 TDEESFE--APIAGCDLVF 85
>gnl|CDD|133444 cd01075, NAD_bind_Leu_Phe_Val_DH, NAD(P) binding domain of
leucine dehydrogenase, phenylalanine dehydrogenase, and
valine dehydrogenase. Amino acid dehydrogenase (DH) is
a widely distributed family of enzymes that catalyzes
the oxidative deamination of an amino acid to its keto
acid and ammonia with concomitant reduction of NADP+.
For example, leucine DH catalyzes the reversible
oxidative deamination of L-leucine and several other
straight or branched chain amino acids to the
corresponding 2-oxoacid derivative. 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 = 200
Score = 27.6 bits (62), Expect = 8.6
Identities = 10/20 (50%), Positives = 12/20 (60%)
Query: 9 VILGGCGFVGRNLVEHLVEN 28
V + G G VG L EHL+E
Sbjct: 31 VAVQGLGKVGYKLAEHLLEE 50
>gnl|CDD|215803 pfam00225, Kinesin, Kinesin motor domain.
Length = 326
Score = 27.9 bits (63), Expect = 8.8
Identities = 11/45 (24%), Positives = 16/45 (35%), Gaps = 7/45 (15%)
Query: 67 PSTCELIFLNSADNSDLTWEYVINCAAETRPGQAEEIYREGIYKL 111
P E +F + + W + + EIY E IY L
Sbjct: 104 PRALEDLFERIEERKERKWSFSVRV-------SYLEIYNEKIYDL 141
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
0.319 0.137 0.416
Gapped
Lambda K H
0.267 0.0728 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 18,397,361
Number of extensions: 1759316
Number of successful extensions: 1621
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1576
Number of HSP's successfully gapped: 82
Length of query: 359
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 261
Effective length of database: 6,590,910
Effective search space: 1720227510
Effective search space used: 1720227510
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 (21.7 bits)
S2: 60 (26.9 bits)