RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16546
(111 letters)
>gnl|CDD|187558 cd05247, UDP_G4E_1_SDR_e, UDP-glucose 4 epimerase, subgroup 1,
extended (e) SDRs. UDP-glucose 4 epimerase (aka
UDP-galactose-4-epimerase), is a homodimeric extended
SDR. It catalyzes the NAD-dependent conversion of
UDP-galactose to UDP-glucose, the final step in Leloir
galactose synthesis. This subgroup has the
characteristic active site tetrad and NAD-binding motif
of the extended SDRs. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately 100
amino acids. Extended SDRs are a diverse collection of
proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 323
Score = 168 bits (429), Expect = 3e-53
Identities = 55/110 (50%), Positives = 75/110 (68%), Gaps = 1/110 (0%)
Query: 2 ITVFGADYGTEDGTGIRDYIHVMDLAVGHVAALNKLQGEHLKIKFYNLGTGQGTSVLQLL 61
+ +FG DY T DGT +RDYIHV+DLA HV AL KL+ + YNLGTG+G SVL+++
Sbjct: 208 LAIFGDDYPTPDGTCVRDYIHVVDLADAHVLALEKLE-NGGGSEIYNLGTGRGYSVLEVV 266
Query: 62 RTFERVTGKPVPYIVEARREGDIVSMYANTDLAQRELGWSARCTVEKMCK 111
FE+V+GKP+PY + RR GD S+ A+ A+ ELGW + +E MC+
Sbjct: 267 EAFEKVSGKPIPYEIAPRRAGDPASLVADPSKAREELGWKPKRDLEDMCE 316
>gnl|CDD|177883 PLN02240, PLN02240, UDP-glucose 4-epimerase.
Length = 352
Score = 163 bits (415), Expect = 7e-51
Identities = 59/111 (53%), Positives = 84/111 (75%), Gaps = 1/111 (0%)
Query: 2 ITVFGADYGTEDGTGIRDYIHVMDLAVGHVAALNKLQGE-HLKIKFYNLGTGQGTSVLQL 60
+TVFG DY T+DGTG+RDYIHVMDLA GH+AAL KL + + + YNLGTG+GTSVL++
Sbjct: 222 LTVFGNDYPTKDGTGVRDYIHVMDLADGHIAALRKLFTDPDIGCEAYNLGTGKGTSVLEM 281
Query: 61 LRTFERVTGKPVPYIVEARREGDIVSMYANTDLAQRELGWSARCTVEKMCK 111
+ FE+ +GK +P + RR GD +YA+T+ A++ELGW A+ +++MC+
Sbjct: 282 VAAFEKASGKKIPLKLAPRRPGDAEEVYASTEKAEKELGWKAKYGIDEMCR 332
>gnl|CDD|224012 COG1087, GalE, UDP-glucose 4-epimerase [Cell envelope biogenesis,
outer membrane].
Length = 329
Score = 156 bits (398), Expect = 2e-48
Identities = 47/113 (41%), Positives = 69/113 (61%), Gaps = 6/113 (5%)
Query: 2 ITVFGADYGTEDGTGIRDYIHVMDLAVGHVAALNKLQ--GEHLKIKFYNLGTGQGTSVLQ 59
+ +FG DY T+DGT IRDYIHV DLA HV AL L+ G + +NLG+G G SVL+
Sbjct: 206 LFIFGDDYDTKDGTCIRDYIHVDDLADAHVLALKYLKEGGSNN---IFNLGSGNGFSVLE 262
Query: 60 LLRTFERVTGKPVPYIVEARREGDIVSMYANTDLAQRELGWSA-RCTVEKMCK 111
++ ++VTG+ +P + RR GD + A++ A++ LGW +E + K
Sbjct: 263 VIEAAKKVTGRDIPVEIAPRRAGDPAILVADSSKARQILGWQPTYDDLEDIIK 315
>gnl|CDD|213592 TIGR01179, galE, UDP-glucose-4-epimerase GalE. Alternate name:
UDPgalactose 4-epimerase This enzyme interconverts
UDP-glucose and UDP-galactose. A set of related
proteins, some of which are tentatively identified as
UDP-glucose-4-epimerase in Thermotoga maritima, Bacillus
halodurans, and several archaea, but deeply branched
from this set and lacking experimental evidence, are
excluded from This model and described by a separate
model [Energy metabolism, Sugars].
Length = 328
Score = 136 bits (345), Expect = 9e-41
Identities = 52/111 (46%), Positives = 69/111 (62%), Gaps = 2/111 (1%)
Query: 2 ITVFGADYGTEDGTGIRDYIHVMDLAVGHVAALNKLQGEHLKIKFYNLGTGQGTSVLQLL 61
+T+FG DY T DGT +RDYIHVMDLA H+AAL L YNLG GQG SVL+++
Sbjct: 210 LTIFGTDYPTPDGTCVRDYIHVMDLADAHLAALEYLLNGG-GSHVYNLGYGQGFSVLEVI 268
Query: 62 RTFERVTGKPVPYIVEARREGDIVSMYANTDLAQRELGWSA-RCTVEKMCK 111
F++V+GK P + RR GD S+ A+ +RELGW +E++ K
Sbjct: 269 EAFKKVSGKDFPVELAPRRPGDPASLVADASKIRRELGWQPKYTDLEEIIK 319
>gnl|CDD|182639 PRK10675, PRK10675, UDP-galactose-4-epimerase; Provisional.
Length = 338
Score = 127 bits (321), Expect = 3e-37
Identities = 55/108 (50%), Positives = 72/108 (66%), Gaps = 1/108 (0%)
Query: 2 ITVFGADYGTEDGTGIRDYIHVMDLAVGHVAALNKLQGEHLKIKFYNLGTGQGTSVLQLL 61
+ +FG DY TEDGTG+RDYIHVMDLA GHVAA+ KL + + YNLG G G+SVL ++
Sbjct: 215 LAIFGNDYPTEDGTGVRDYIHVMDLADGHVAAMEKLANKP-GVHIYNLGAGVGSSVLDVV 273
Query: 62 RTFERVTGKPVPYIVEARREGDIVSMYANTDLAQRELGWSARCTVEKM 109
F + GKPV Y RREGD+ + +A+ A REL W T+++M
Sbjct: 274 NAFSKACGKPVNYHFAPRREGDLPAYWADASKADRELNWRVTRTLDEM 321
>gnl|CDD|206121 pfam13950, Epimerase_Csub, UDP-glucose 4-epimerase C-term subunit.
This domain is the very C-terminal subunit of
UDP-glucose 4-epimerase.
Length = 62
Score = 82.1 bits (204), Expect = 2e-22
Identities = 21/49 (42%), Positives = 31/49 (63%)
Query: 63 TFERVTGKPVPYIVEARREGDIVSMYANTDLAQRELGWSARCTVEKMCK 111
FE+ +GK +PY + RR GD+ YA+ A++ELGW A +E MC+
Sbjct: 1 AFEKASGKKIPYEIVPRRPGDVAECYADPSKAEKELGWKAERGLEDMCR 49
>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 = 65.3 bits (160), Expect = 5e-14
Identities = 31/106 (29%), Positives = 50/106 (47%), Gaps = 12/106 (11%)
Query: 3 TVFGADYGTEDGTGIRDYIHVMDLAVGHVAAL-NKLQGEHLKIKFYNLGTGQGTSVLQLL 61
T++G DG RD+ +V D+ ++ A GE YN+GTG+ TSV +L
Sbjct: 200 TIYG------DGEQTRDFTYVEDVVEANLLAATAGAGGE-----VYNIGTGKRTSVNELA 248
Query: 62 RTFERVTGKPVPYIVEARREGDIVSMYANTDLAQRELGWSARCTVE 107
+ GK + + R GD+ A+ A++ LGW + + E
Sbjct: 249 ELIREILGKELEPVYAPPRPGDVRHSLADISKAKKLLGWEPKVSFE 294
>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 = 64.3 bits (157), Expect = 1e-13
Identities = 36/112 (32%), Positives = 57/112 (50%), Gaps = 14/112 (12%)
Query: 2 ITVFGADYGTEDGTGIRDYIHVMDLAVGHVAALNKLQGEHLKIKFYNLGTGQGTSVLQLL 61
I ++G DG IRDYI++ DL +A L + +G + +N+G+G G S+ +L+
Sbjct: 195 IEIWG------DGESIRDYIYIDDLVEALMALL-RSKGLE---EVFNIGSGIGYSLAELI 244
Query: 62 RTFERVTGKPVPYIVEARREGDIVSMYANTDLAQRELGWS----ARCTVEKM 109
E+VTG+ V I R D+ + + A+ ELGWS +EK
Sbjct: 245 AEIEKVTGRSVQVIYTPARTTDVPKIVLDISRARAELGWSPKISLEDGLEKT 296
>gnl|CDD|223528 COG0451, WcaG, Nucleoside-diphosphate-sugar epimerases [Cell
envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 314
Score = 56.1 bits (135), Expect = 1e-10
Identities = 27/100 (27%), Positives = 45/100 (45%), Gaps = 9/100 (9%)
Query: 12 EDGTGIRDYIHVMDLAVGHVAALNKLQGEHLKIKFYNLGTGQG-TSVLQLLRTFERVTGK 70
DG+ RD+++V D+A + AL E+ +N+G+G +V +L G
Sbjct: 204 GDGSQTRDFVYVDDVADALLLAL-----ENPDGGVFNIGSGTAEITVRELAEAVAEAVGS 258
Query: 71 PVPYIV--EARREGDIV-SMYANTDLAQRELGWSARCTVE 107
P IV R GD+ + A+ LGW + ++E
Sbjct: 259 KAPLIVYIPLGRRGDLREGKLLDISKARAALGWEPKVSLE 298
>gnl|CDD|187563 cd05253, UDP_GE_SDE_e, UDP glucuronic acid epimerase, extended (e)
SDRs. This subgroup contains UDP-D-glucuronic acid
4-epimerase, an extended SDR, which catalyzes the
conversion of UDP-alpha-D-glucuronic acid to
UDP-alpha-D-galacturonic acid. This group has the SDR's
canonical catalytic tetrad and the TGxxGxxG NAD-binding
motif of the extended SDRs. Extended SDRs are distinct
from classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately 100
amino acids. Extended SDRs are a diverse collection of
proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 332
Score = 53.9 bits (130), Expect = 9e-10
Identities = 27/120 (22%), Positives = 46/120 (38%), Gaps = 20/120 (16%)
Query: 2 ITVFGADYGTEDGTGIRDYIHVMDLAVGHVAALNKLQGE--------------HLKIKFY 47
I VF DG RD+ ++ D+ G V AL+ + Y
Sbjct: 206 IDVFN------DGNMSRDFTYIDDIVEGVVRALDTPAKPNPNWDAEAPDPSTSSAPYRVY 259
Query: 48 NLGTGQGTSVLQLLRTFERVTGKPVPYIVEARREGDIVSMYANTDLAQRELGWSARCTVE 107
N+G ++ + E+ GK ++GD+ YA+ QR LG+ + ++E
Sbjct: 260 NIGNNSPVKLMDFIEALEKALGKKAKKNYLPMQKGDVPETYADISKLQRLLGYKPKTSLE 319
>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 = 48.1 bits (115), Expect = 1e-07
Identities = 27/109 (24%), Positives = 49/109 (44%), Gaps = 9/109 (8%)
Query: 2 ITVFGADYGTEDGTGIRDYIHVMDLAVGHVAALNKLQGEHLKIKFYNLGTGQGTSV--LQ 59
+T+FG YG G +RD +H DL ++ K + +N+G G+ SV L+
Sbjct: 227 LTIFG--YG---GKQVRDVLHSADLVNLYLRQFQNPD--RRKGEVFNIGGGRENSVSLLE 279
Query: 60 LLRTFERVTGKPVPYIVEARREGDIVSMYANTDLAQRELGWSARCTVEK 108
L+ E +TG+ + + R GD + ++ + + GW +
Sbjct: 280 LIALCEEITGRKMESYKDENRPGDQIWYISDIRKIKEKPGWKPERDPRE 328
>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 = 46.0 bits (110), Expect = 5e-07
Identities = 33/102 (32%), Positives = 50/102 (49%), Gaps = 11/102 (10%)
Query: 9 YGTEDGTGIRDYIHVMDLAVGHVAALNKLQGEHLKIKFYNLGTGQGTSVLQLLRTFERVT 68
YG DG +RD+++V D A L K G +I YN+G G + L+L++ +
Sbjct: 207 YG--DGLNVRDWLYVEDHARAIELVLEK--GRVGEI--YNIGGGNELTNLELVKLILELL 260
Query: 69 GKPVPYI--VEARREGDIVSMYA-NTDLAQRELGWSARCTVE 107
GK I V+ R D YA ++ +RELGW + + E
Sbjct: 261 GKDESLITYVKDRPGHDR--RYAIDSSKIRRELGWRPKVSFE 300
>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 = 42.8 bits (101), Expect = 7e-06
Identities = 33/104 (31%), Positives = 50/104 (48%), Gaps = 15/104 (14%)
Query: 9 YGTEDGTGIRDYIHVMDLAVGHVAALNK--LQGEHLKIKFYNLGTGQGTSVLQLLRTFER 66
YG DG +RD+++V D H A+ +G + YN+G G + L+++ T
Sbjct: 207 YG--DGQQVRDWLYVED----HCRAIYLVLEKGRVGET--YNIGGGNERTNLEVVETILE 258
Query: 67 VTGKPVPYI--VEARREGDIVSMYA-NTDLAQRELGWSARCTVE 107
+ GK I VE R D YA + +RELGW+ + T E
Sbjct: 259 LLGKDEDLITHVEDRPGHDR--RYAIDASKIKRELGWAPKYTFE 300
>gnl|CDD|224013 COG1088, RfbB, dTDP-D-glucose 4,6-dehydratase [Cell envelope
biogenesis, outer membrane].
Length = 340
Score = 42.6 bits (101), Expect = 9e-06
Identities = 35/108 (32%), Positives = 54/108 (50%), Gaps = 19/108 (17%)
Query: 9 YGTEDGTGIRDYIHVMDLAVGHVAALNKL--QGEHLKIKFYNLGTGQGTSVLQLLRTFER 66
YG DG IRD+++V D H A++ + +G+ + YN+G G + L++++T
Sbjct: 209 YG--DGLQIRDWLYVED----HCRAIDLVLTKGKIGET--YNIGGGNERTNLEVVKTICE 260
Query: 67 VTGKPVP----YI--VEARREGDIVSMYA-NTDLAQRELGWSARCTVE 107
+ GK P I VE R D YA + +RELGW + T E
Sbjct: 261 LLGKDKPDYRDLITFVEDRPGHD--RRYAIDASKIKRELGWRPQETFE 306
>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 = 38.8 bits (91), Expect = 1e-04
Identities = 17/51 (33%), Positives = 24/51 (47%), Gaps = 12/51 (23%)
Query: 1 MITVFGADYGTEDGTGIRDYIHVMDLAVGHVAALNKLQ-GEHLKIKFYNLG 50
I + G DGT RD+++V D+A + AL GE YN+G
Sbjct: 194 PILLLG------DGTQRRDFLYVDDVARAILLALEHPDGGEI-----YNIG 233
>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 = 36.9 bits (86), Expect = 7e-04
Identities = 32/117 (27%), Positives = 46/117 (39%), Gaps = 34/117 (29%)
Query: 19 DYIHVMDLAVGHVAALNKLQ-GEHLKIKFYNLGTGQGTSVLQLLRTFERVTGKPVP---- 73
++ V D+A GH+AA+ K + GE Y LG G+ S QL T +TG P
Sbjct: 199 SFVDVRDVAEGHIAAMEKGRRGER-----YILG-GENLSFKQLFETLAEITGVKPPRRTI 252
Query: 74 -----YIV----------------EARREGDIVS--MYANTDLAQRELGWSARCTVE 107
V R ++ ++D A+RELG+S R E
Sbjct: 253 PPWLLKAVAALSELKARLTGKPPLLTPRTARVLRRNYLYSSDKARRELGYSPRPLEE 309
>gnl|CDD|187570 cd05260, GDP_MD_SDR_e, GDP-mannose 4,6 dehydratase, extended (e)
SDRs. GDP-mannose 4,6 dehydratase, a homodimeric SDR,
catalyzes the NADP(H)-dependent conversion of
GDP-(D)-mannose to GDP-4-keto, 6-deoxy-(D)-mannose in
the fucose biosynthesis pathway. These proteins have the
canonical active site triad and NAD-binding pattern,
however the active site Asn is often missing and may be
substituted with Asp. A Glu residue has been identified
as an important active site base. Extended SDRs are
distinct from classical SDRs. In addition to the
Rossmann fold (alpha/beta folding pattern with a central
beta-sheet) core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids. Extended SDRs are a
diverse collection of proteins, and include isomerases,
epimerases, oxidoreductases, and lyases; they typically
have a TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 316
Score = 36.4 bits (85), Expect = 0.001
Identities = 18/95 (18%), Positives = 35/95 (36%), Gaps = 9/95 (9%)
Query: 18 RDYIHVMDLAVGHVAALNKLQGEHLKIKFYNLGTGQGTSVLQLLRT-FERVTGKPVPYIV 76
RD+ D + L + + + Y + TG+ SV + + FE +
Sbjct: 216 RDWGDARDYVEAYWLLLQQGEPDD-----YVIATGETHSVREFVELAFEESGLTGDIEVE 270
Query: 77 ---EARREGDIVSMYANTDLAQRELGWSARCTVEK 108
R ++ + + A+ ELGW + E+
Sbjct: 271 IDPRYFRPTEVDLLLGDPSKAREELGWKPEVSFEE 305
>gnl|CDD|163279 TIGR03466, HpnA, hopanoid-associated sugar epimerase. The
sequences in this family are members of the pfam01370
superfamily of NAD-dependent epimerases and dehydratases
typically acting on nucleotide-sugar substrates. The
genes of the family modeled here are generally in the
same locus with genes involved in the biosynthesis and
elaboration of hopene, the cyclization product of the
polyisoprenoid squalene. This gene and its association
with hopene biosynthesis in Zymomonas mobilis has been
noted in the literature where the gene symbol hpnA was
assigned. Hopanoids are known to be components of the
plasma membrane and to have polar sugar head groups in
Z. mobilis and other species.
Length = 328
Score = 35.4 bits (82), Expect = 0.002
Identities = 32/111 (28%), Positives = 49/111 (44%), Gaps = 34/111 (30%)
Query: 21 IHVMDLAVGHVAALNKLQ-GEHLKIKFYNLGTGQGTSVLQLLRTFERVTGKPVP------ 73
+HV D+A GH+ AL + + GE Y LG G+ ++ Q+L +TG+P P
Sbjct: 205 VHVDDVAEGHLLALERGRIGER-----YILG-GENLTLKQILDKLAEITGRPAPRVKLPR 258
Query: 74 -------YIVEA-----RREG----DIVS-----MYANTDLAQRELGWSAR 103
+ EA +E D V M+ ++ A RELG+ R
Sbjct: 259 WLLLPVAWGAEALARLTGKEPRVTVDGVRMAKKKMFFSSAKAVRELGYRQR 309
>gnl|CDD|187562 cd05252, CDP_GD_SDR_e, CDP-D-glucose 4,6-dehydratase, extended (e)
SDRs. This subgroup contains CDP-D-glucose
4,6-dehydratase, an extended SDR, which catalyzes the
conversion of CDP-D-glucose to
CDP-4-keto-6-deoxy-D-glucose. This subgroup has the
characteristic active site tetrad and NAD-binding motif
of the extended SDRs. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately 100
amino acids. Extended SDRs are a diverse collection of
proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 336
Score = 34.6 bits (80), Expect = 0.004
Identities = 20/96 (20%), Positives = 38/96 (39%), Gaps = 4/96 (4%)
Query: 17 IRDYIHVMDLAVGHVAALNKL-QGEHLKIKFYNLG--TGQGTSVLQLLRTFERVTG-KPV 72
IR + HV++ G++ KL + + +N G +VL+L+ R G
Sbjct: 224 IRPWQHVLEPLSGYLLLAEKLYERGEEYAEAWNFGPDDEDAVTVLELVEAMARYWGEDAR 283
Query: 73 PYIVEARREGDIVSMYANTDLAQRELGWSARCTVEK 108
+ + + + A+ LGW R +E+
Sbjct: 284 WDLDGNSHPHEANLLKLDCSKAKTMLGWRPRWNLEE 319
>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 = 34.4 bits (79), Expect = 0.006
Identities = 22/95 (23%), Positives = 38/95 (40%), Gaps = 5/95 (5%)
Query: 13 DGTGIRDYIHVMDLAVGHVAALNKLQGEHLKIKFYNLGTGQGTSVLQLLRTFERVTGKPV 72
DG R + ++ D G + GE + NLG+ + S+ +L +GKP+
Sbjct: 213 DGLQTRSFTYIDDCVEGLRRLMESDFGEPV-----NLGSDEMVSMNELAEMVLSFSGKPL 267
Query: 73 PYIVEARREGDIVSMYANTDLAQRELGWSARCTVE 107
I + ++ L + ELGW +E
Sbjct: 268 EIIHHTPGPQGVRGRNSDNTLLKEELGWEPNTPLE 302
>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 = 33.8 bits (78), Expect = 0.010
Identities = 21/78 (26%), Positives = 36/78 (46%), Gaps = 10/78 (12%)
Query: 2 ITVFGADYGTEDGTGIRDYIHVMDLAVGHVAAL--NKLQGEHLKIKFYNLGTGQGTSVLQ 59
+ +F + G DG +RD+++V D+ ++ L + G +N+GTG+ S
Sbjct: 200 VKLFKSSDGYADGEQLRDFVYVKDVVKVNLFFLENPSVSG------IFNVGTGRARSFND 253
Query: 60 LLRTFERVTGKPVP--YI 75
L + GK V YI
Sbjct: 254 LASATFKALGKEVKIEYI 271
>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 = 33.4 bits (77), Expect = 0.013
Identities = 22/77 (28%), Positives = 36/77 (46%), Gaps = 12/77 (15%)
Query: 5 FGADYGTEDGTGIRDYIHVMDLAVGHVAALNKLQGEHLKIKFYNLGTGQGTS-------V 57
F + G +DG +RD+++V D V +N E+ +NLGTG+ S V
Sbjct: 201 FKSSEGFKDGEQLRDFVYVKD-----VVDVNLWLLENGVSGIFNLGTGRARSFNDLADAV 255
Query: 58 LQLLRTFERVTGKPVPY 74
+ L E++ P+P
Sbjct: 256 FKALGKDEKIEYIPMPE 272
>gnl|CDD|187550 cd05239, GDP_FS_SDR_e, GDP-fucose synthetase, extended (e) SDRs.
GDP-fucose synthetase (aka 3, 5-epimerase-4-reductase)
acts in the NADP-dependent synthesis of GDP-fucose from
GDP-mannose. Two activities have been proposed for the
same active site: epimerization and reduction. Proteins
in this subgroup are extended SDRs, which have a
characteristic active site tetrad and an NADP-binding
motif, [AT]GXXGXXG, that is a close match to the
archetypical form. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately 100
amino acids. Extended SDRs are a diverse collection of
proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 300
Score = 30.2 bits (69), Expect = 0.16
Identities = 18/69 (26%), Positives = 29/69 (42%), Gaps = 12/69 (17%)
Query: 2 ITVFGADYGTEDGTGIRDYIHVMDLAVGHVAALNKLQG-EHLKIKFYNLGTGQGTSVLQL 60
+TV+G GT R++++ DLA V L + N+G+G S+ +L
Sbjct: 195 VTVWG------SGTPRREFLYSDDLARAIVFLLENYDEPIIV-----NVGSGVEISIREL 243
Query: 61 LRTFERVTG 69
V G
Sbjct: 244 AEAIAEVVG 252
>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 = 29.6 bits (67), Expect = 0.20
Identities = 16/49 (32%), Positives = 21/49 (42%), Gaps = 9/49 (18%)
Query: 2 ITVFGADYGTEDGTGIRDYIHVMDLAVGHVAALNKLQGEHLKIKFYNLG 50
+TVFG G RD+IHV D+ + AL YN+G
Sbjct: 161 LTVFG------GGNQTRDFIHVDDVVRAILHALENPLEGG---GVYNIG 200
>gnl|CDD|215146 PLN02260, PLN02260, probable rhamnose biosynthetic enzyme.
Length = 668
Score = 29.3 bits (66), Expect = 0.35
Identities = 27/99 (27%), Positives = 45/99 (45%), Gaps = 11/99 (11%)
Query: 13 DGTGIRDYIHVMDLAVGHVAALNKLQGEHLKIKFYNLGTGQGTSVLQ----LLRTFERVT 68
DG+ +R Y++ D+A L+K + H+ YN+GT + V+ + + F
Sbjct: 218 DGSNVRSYLYCEDVAEAFEVVLHKGEVGHV----YNIGTKKERRVIDVAKDICKLFGLDP 273
Query: 69 GKPVPYIVEARREGDIVSMYANTDLAQRELGWSARCTVE 107
K + + VE R D Y D ++LGW R + E
Sbjct: 274 EKSIKF-VENRPFND--QRYFLDDQKLKKLGWQERTSWE 309
>gnl|CDD|224014 COG1089, Gmd, GDP-D-mannose dehydratase [Cell envelope biogenesis,
outer membrane].
Length = 345
Score = 28.9 bits (65), Expect = 0.54
Identities = 17/86 (19%), Positives = 32/86 (37%), Gaps = 21/86 (24%)
Query: 47 YNLGTGQGTSVLQLLR-TFERV------TGKPVPYIVEARREGDIV-------------- 85
Y + TG+ SV + + FE V G V + G I+
Sbjct: 247 YVIATGETHSVREFVELAFEMVGIDLEWEGTGVDEKGVDAKTGKIIVEIDPRYFRPAEVD 306
Query: 86 SMYANTDLAQRELGWSARCTVEKMCK 111
+ + A+ +LGW ++E++ +
Sbjct: 307 LLLGDPTKAKEKLGWRPEVSLEELVR 332
>gnl|CDD|178326 PLN02725, PLN02725,
GDP-4-keto-6-deoxymannose-3,5-epimerase-4-reductase.
Length = 306
Score = 28.5 bits (64), Expect = 0.61
Identities = 17/57 (29%), Positives = 31/57 (54%), Gaps = 6/57 (10%)
Query: 14 GTGIRDYIHVMDLAVGHVAALNKLQG-EHLKIKFYNLGTGQGTSVLQLLRTFERVTG 69
G+ +R+++HV DLA V + + G EH+ N+G+G ++ +L + V G
Sbjct: 199 GSPLREFLHVDDLADAVVFLMRRYSGAEHV-----NVGSGDEVTIKELAELVKEVVG 250
>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 = 27.6 bits (62), Expect = 1.2
Identities = 14/61 (22%), Positives = 23/61 (37%), Gaps = 3/61 (4%)
Query: 12 EDGTGIRDYIHVMDLAVGHVAALNKLQGEHLKIKFYNLGTGQGTSVLQLLRTFERVTGKP 71
DG + +IHV DLA + A +N+ + + +LL + GK
Sbjct: 183 GDGHSLVQFIHVKDLARALLGAAGN---PKAIGGIFNITGDEAVTWDELLEACAKALGKE 239
Query: 72 V 72
Sbjct: 240 A 240
>gnl|CDD|177808 PLN00415, PLN00415, 3-ketoacyl-CoA synthase.
Length = 466
Score = 27.3 bits (60), Expect = 1.6
Identities = 13/39 (33%), Positives = 21/39 (53%), Gaps = 6/39 (15%)
Query: 67 VTGKPVPYIVEARREGDIV------SMYANTDLAQRELG 99
+T P P + EAR E ++V S++ T + RE+G
Sbjct: 119 LTSPPTPSMYEARHESELVIFGALNSLFKKTGIEPREVG 157
>gnl|CDD|200106 TIGR01456, CECR5, HAD-superfamily class IIA hydrolase, TIGR01456,
CECR5. This hypothetical equivalog is a member of the
Class IIA subfamily of the haloacid dehalogenase
superfamily of aspartate-nucleophile hydrolases. The
sequences modelled by this equivalog are all eukaryotes.
One sequence (GP|13344995) is called "Cat Eye Syndrome
critical region protein 5" (CECR5). This gene has been
cloned from a pericentromere region of human chromosome
22 believed to be the location of the gene or genes
responsible for Cat Eye Syndrome. This is one of a
number of candidate genes. The Schizosaccharomyces pombe
sequence (EGAD|138276) is annotated as "phosphatidyl
synthase," however this is due entirely to a C-terminal
region of the protein (outside the region of similarity
of This model) which is highly homologous to a family of
CDP-alcohol phosphatidyltransferases. (Thus, the
annotation of GP|4226073 from C. elegans as similar to
phosphatidyl synthase, is a mistake as this gene does
not contain the C-terminal portion). The physical
connection of the phosphatidyl synthase and the
HAD-superfamily hydrolase domain in S. pombe may,
however, be an important clue to the substrate for the
hydrolases in this equivalog.
Length = 321
Score = 26.8 bits (59), Expect = 2.8
Identities = 10/23 (43%), Positives = 13/23 (56%)
Query: 52 GQGTSVLQLLRTFERVTGKPVPY 74
GQG L L R + + GKP+ Y
Sbjct: 206 GQGAFRLLLERIYLELNGKPLQY 228
>gnl|CDD|218462 pfam05140, ResB, ResB-like family. This family includes both ResB
and cytochrome c biogenesis proteins. Mutations in ResB
indicate that they are essential for growth. ResB is
predicted to be a transmembrane protein.
Length = 437
Score = 26.5 bits (59), Expect = 2.9
Identities = 13/63 (20%), Positives = 24/63 (38%), Gaps = 5/63 (7%)
Query: 2 ITVFGADYGTEDGTGIRDYIHVMDLAVGHVAALNKLQGEHLKIKFYNLGTGQGTSVLQLL 61
+T++ A +G G + D ++ V L +L G +LG + L+
Sbjct: 248 VTIYQASWGYAPGETVTDTSGLVVFDTETVPFLPQLPGN-----LLSLGGEKVGYQLEFW 302
Query: 62 RTF 64
F
Sbjct: 303 GFF 305
>gnl|CDD|191263 pfam05368, NmrA, NmrA-like family. NmrA is a negative
transcriptional regulator involved in the
post-translational modification of the transcription
factor AreA. NmrA is part of a system controlling
nitrogen metabolite repression in fungi. This family
only contains a few sequences as iteration results in
significant matches to other Rossmann fold families.
Length = 232
Score = 26.5 bits (59), Expect = 3.5
Identities = 5/19 (26%), Positives = 9/19 (47%)
Query: 56 SVLQLLRTFERVTGKPVPY 74
S ++ + + GK V Y
Sbjct: 212 SGNEIAELWSKKIGKTVKY 230
>gnl|CDD|235681 PRK06039, ileS, isoleucyl-tRNA synthetase; Reviewed.
Length = 975
Score = 25.9 bits (58), Expect = 5.2
Identities = 10/16 (62%), Positives = 11/16 (68%), Gaps = 1/16 (6%)
Query: 3 TVFGADY-GTEDGTGI 17
V AD+ TEDGTGI
Sbjct: 302 RVVLADFVTTEDGTGI 317
>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 = 25.8 bits (57), Expect = 5.7
Identities = 21/89 (23%), Positives = 30/89 (33%), Gaps = 14/89 (15%)
Query: 21 IHVMDLAVGHVAAL-NKLQGEHLKIKFYNLGTGQGTSVLQLLRTFERVTGKPV---PYIV 76
+H D A + AL G Y+ +G V + R G PV P
Sbjct: 197 VHRDDAARLYRLALEKGKAGSV-----YHAVAEEGIPVKDIAEAIGRRLGVPVVSIPAEE 251
Query: 77 EARREGDIVSMYA-----NTDLAQRELGW 100
A G + A ++ +R LGW
Sbjct: 252 AAAHFGWLAMFVALDQPVSSQKTRRRLGW 280
>gnl|CDD|225787 COG3248, Tsx, Nucleoside-binding outer membrane protein [Cell
envelope biogenesis, outer membrane].
Length = 284
Score = 25.6 bits (56), Expect = 6.0
Identities = 13/50 (26%), Positives = 20/50 (40%)
Query: 4 VFGADYGTEDGTGIRDYIHVMDLAVGHVAALNKLQGEHLKIKFYNLGTGQ 53
+G+D G + G I +A H+ ALN + + Y GQ
Sbjct: 207 DWGSDLGDDSGRAINGTRTNNSIASSHILALNYDHWHYSVVARYWHDGGQ 256
>gnl|CDD|182227 PRK10079, PRK10079, phosphonate metabolism transcriptional
regulator PhnF; Provisional.
Length = 241
Score = 25.5 bits (56), Expect = 6.5
Identities = 11/27 (40%), Positives = 15/27 (55%), Gaps = 1/27 (3%)
Query: 49 LGTGQGTSVLQLLRTFERVTGKPVPYI 75
LG +G +V+ L RT RV G + I
Sbjct: 121 LGITEGENVIHL-RTLRRVNGVALCLI 146
>gnl|CDD|173878 cd08513, PBP2_thermophilic_Hb8_like, The substrate-binding
component of ABC-type thermophilic oligopeptide-binding
protein Hb8-like import systems, contains the type 2
periplasmic binding fold. This family includes the
substrate-binding domain of an ABC-type
oligopeptide-binding protein Hb8 from Thermus
thermophilius and its closest homologs from other
bacteria. The structural topology of this
substrate-binding domain is similar to those of DppA
from Escherichia coli and OppA from Salmonella
typhimurium, and thus belongs to the type 2 periplasmic
binding fold protein (PBP2) superfamily. The DppA binds
dipeptides and some tripeptides and is involved in
chemotaxis toward dipeptides, whereas the OppA binds
peptides of a wide range of lengths (2-35 amino acid
residues) and plays a role in recycling of cell wall
peptides, which precludes any involvement in chemotaxis.
The type 2 periplasmic binding proteins are soluble
ligand-binding components of ABC or tripartite
ATP-independent transporters and chemotaxis systems.
Members of the PBP2 superfamily function in uptake of a
variety of metabolites in bacteria such as amino acids,
carbohydrate, ions, and polyamines. Ligands are then
transported across the cytoplasmic membrane energized by
ATP hydrolysis or electrochemical ion gradient. Besides
transport proteins, the PBP2 superfamily includes the
ligand-binding domains from ionotropic glutamate
receptors, LysR-type transcriptional regulators, and
unorthodox sensor proteins involved in signal
transduction.
Length = 482
Score = 25.3 bits (56), Expect = 7.9
Identities = 8/26 (30%), Positives = 12/26 (46%), Gaps = 3/26 (11%)
Query: 67 VTGKPVPYIVEARREGDIVSMYANTD 92
TG PY +E GD + + N +
Sbjct: 160 GTG---PYKLEEFVPGDSIELVRNPN 182
>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 = 25.3 bits (56), Expect = 8.0
Identities = 14/54 (25%), Positives = 20/54 (37%), Gaps = 3/54 (5%)
Query: 21 IHVMDLAVGHVAALNKLQGEHLKIKFYNLGTGQGTSVLQLLRTFERVTGKPVPY 74
I V D +G A K L + + ++ F +V GKPV Y
Sbjct: 178 IDVAD--IGPAVAAIFKDPAKFNGKTIELAGDE-LTPEEIAAAFSKVLGKPVTY 228
>gnl|CDD|203489 pfam06644, ATP11, ATP11 protein. This family consists of several
eukaryotic ATP11 proteins. In Saccharomyces cerevisiae,
expression of functional F1-ATPase requires two proteins
encoded by the ATP11 and ATP12 genes. Atp11p is a
molecular chaperone of the mitochondrial matrix that
participates in the biogenesis pathway to form F1, the
catalytic unit of the ATP synthase.
Length = 250
Score = 25.0 bits (55), Expect = 8.6
Identities = 10/33 (30%), Positives = 14/33 (42%), Gaps = 6/33 (18%)
Query: 34 LNKLQGEHLKIKFYNLGTGQGTSVLQLLRTFER 66
+LQ +FY T L+LL TF +
Sbjct: 210 ALQLQ------RFYGEETQLAKERLKLLETFTK 236
>gnl|CDD|187536 cd05193, AR_like_SDR_e, aldehyde reductase, flavonoid reductase,
and related proteins, extended (e) SDRs. This subgroup
contains aldehyde reductase and flavonoid reductase of
the extended SDR-type and related proteins. Proteins in
this subgroup have a complete SDR-type active site
tetrad and a close match to the canonical extended SDR
NADP-binding motif. Aldehyde reductase I (aka carbonyl
reductase) is an NADP-binding SDR; it catalyzes the
NADP-dependent reduction of ethyl
4-chloro-3-oxobutanoate to ethyl
(R)-4-chloro-3-hydroxybutanoate. The related flavonoid
reductases act in the NADP-dependent reduction of
flavonoids, ketone-containing plant secondary
metabolites. Extended SDRs are distinct from classical
SDRs. In addition to the Rossmann fold (alpha/beta
folding pattern with a central beta-sheet) core region
typical of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 295
Score = 25.3 bits (55), Expect = 9.5
Identities = 12/56 (21%), Positives = 20/56 (35%), Gaps = 6/56 (10%)
Query: 20 YIHVMDLAVGHVAALNKLQGEHLKIKFYNLGTGQGTSVLQLLRTF-ERVTGKPVPY 74
Y+HV+D+ + H+ L I T LL+T ++ P
Sbjct: 225 YVHVVDICLAHIGCLELPIARGRYI-----CTAGNFDWNTLLKTLRKKYPSYTFPT 275
>gnl|CDD|193586 cd09972, LOTUS_TDRD_OSKAR, The first LOTUS domain in Oskar and
Tudor-containing proteins 5 and 7. The first LOTUS
domain in Oskar and Tudor-containing proteins 5 and 7:
The LOTUS containing proteins are germline-specific and
are found in the nuage/polar granules of germ cells.
Tudor-containing protein 5 and 7 belong to the
evolutionary conserved Tudor domain-containing protein
(TDRD) family involved in germ cell development. In
mice, TDRD5 and TDRD7 are components of the
intermitochondrial cements (IMCs) and the chromatoid
bodies (CBs), which are cytoplasmic ribonucleoprotein
granules involved in RNA processing for
spermatogenesis. Oskar protein is a critical component
of the pole plasm in the Drosophila oocyte, which is
required for germ cell formation.The exact molecular
function of LOTUS domain remains to be identified. Its
occurrence in proteins associated with RNA metabolism
suggests that it might be involved in RNA binding
function. The presence of several basic residues and
RNA fold recognition motifs support this hypothesis.
The RNA binding function might be the first step of
regulating mRNA translation or localization.
Length = 87
Score = 24.4 bits (54), Expect = 9.7
Identities = 7/21 (33%), Positives = 14/21 (66%)
Query: 54 GTSVLQLLRTFERVTGKPVPY 74
G ++ +L R + + G+P+PY
Sbjct: 18 GLTLSELERDYRELEGEPIPY 38
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.321 0.138 0.410
Gapped
Lambda K H
0.267 0.0869 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,773,009
Number of extensions: 498055
Number of successful extensions: 465
Number of sequences better than 10.0: 1
Number of HSP's gapped: 440
Number of HSP's successfully gapped: 50
Length of query: 111
Length of database: 10,937,602
Length adjustment: 75
Effective length of query: 36
Effective length of database: 7,611,052
Effective search space: 273997872
Effective search space used: 273997872
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 53 (23.9 bits)