RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14739
(360 letters)
>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 = 493 bits (1271), Expect = e-177
Identities = 183/267 (68%), Positives = 209/267 (78%), Gaps = 23/267 (8%)
Query: 83 RRILITGGAGFVGSHLVDKLMLMGHEVTVVDNFFTGRKENVEHWFGHPNFEIIHQDIVTP 142
+RILITGGAGF+GSHL D+L+ GHEV VDNFFTGRK N+EH GHPNFE I D+ P
Sbjct: 1 KRILITGGAGFLGSHLCDRLLEDGHEVICVDNFFTGRKRNIEHLIGHPNFEFIRHDVTEP 60
Query: 143 LFVEVDEIYHLASPASPPHYMFNPVKTIKTNTIGTINMLGLAKRVGAKILFASTSEVYGD 202
L++EVD+IYHLA PASP HY +NP+KT+KTN +GT+NMLGLAKRVGA++L ASTSEVYGD
Sbjct: 61 LYLEVDQIYHLACPASPVHYQYNPIKTLKTNVLGTLNMLGLAKRVGARVLLASTSEVYGD 120
Query: 203 PEVHPQPETYWGHVNPIGPRACYDEAKRVAETLCYAYARHEDLSVRVARIFNTYGPRMHM 262
PEVHPQPE+YWG+VNPIGPR+CYDE KRVAETLC AY R + VR+ARIFNTYGPRMH
Sbjct: 121 PEVHPQPESYWGNVNPIGPRSCYDEGKRVAETLCMAYHRQHGVDVRIARIFNTYGPRMHP 180
Query: 263 NDGRVVSNFIIQALRNETITSDSSKSFTKFWDTLYIPHSFTQVYGLGNQTRSFQYVTDLV 322
NDGRVVSNFI+QALR E IT VYG G QTRSFQYV+DLV
Sbjct: 181 NDGRVVSNFIVQALRGEPIT----------------------VYGDGTQTRSFQYVSDLV 218
Query: 323 DGLIALMNSNY-TLPVNLGNPTEHSIL 348
+GLI LMNS+Y PVNLGNP E +IL
Sbjct: 219 EGLIRLMNSDYFGGPVNLGNPEEFTIL 245
>gnl|CDD|177856 PLN02206, PLN02206, UDP-glucuronate decarboxylase.
Length = 442
Score = 371 bits (953), Expect = e-127
Identities = 167/265 (63%), Positives = 196/265 (73%), Gaps = 22/265 (8%)
Query: 84 RILITGGAGFVGSHLVDKLMLMGHEVTVVDNFFTGRKENVEHWFGHPNFEIIHQDIVTPL 143
R+++TGGAGFVGSHLVD+LM G V VVDNFFTGRKENV H F +PNFE+I D+V P+
Sbjct: 121 RVVVTGGAGFVGSHLVDRLMARGDSVIVVDNFFTGRKENVMHHFSNPNFELIRHDVVEPI 180
Query: 144 FVEVDEIYHLASPASPPHYMFNPVKTIKTNTIGTINMLGLAKRVGAKILFASTSEVYGDP 203
+EVD+IYHLA PASP HY FNPVKTIKTN +GT+NMLGLAKRVGA+ L STSEVYGDP
Sbjct: 181 LLEVDQIYHLACPASPVHYKFNPVKTIKTNVVGTLNMLGLAKRVGARFLLTSTSEVYGDP 240
Query: 204 EVHPQPETYWGHVNPIGPRACYDEAKRVAETLCYAYARHEDLSVRVARIFNTYGPRMHMN 263
HPQ ETYWG+VNPIG R+CYDE KR AETL Y R ++ VR+ARIFNTYGPRM ++
Sbjct: 241 LQHPQVETYWGNVNPIGVRSCYDEGKRTAETLTMDYHRGANVEVRIARIFNTYGPRMCID 300
Query: 264 DGRVVSNFIIQALRNETITSDSSKSFTKFWDTLYIPHSFTQVYGLGNQTRSFQYVTDLVD 323
DGRVVSNF+ QALR E +T VYG G QTRSFQ+V+DLV+
Sbjct: 301 DGRVVSNFVAQALRKEPLT----------------------VYGDGKQTRSFQFVSDLVE 338
Query: 324 GLIALMNSNYTLPVNLGNPTEHSIL 348
GL+ LM + P NLGNP E ++L
Sbjct: 339 GLMRLMEGEHVGPFNLGNPGEFTML 363
>gnl|CDD|165812 PLN02166, PLN02166, dTDP-glucose 4,6-dehydratase.
Length = 436
Score = 362 bits (931), Expect = e-123
Identities = 166/265 (62%), Positives = 196/265 (73%), Gaps = 22/265 (8%)
Query: 84 RILITGGAGFVGSHLVDKLMLMGHEVTVVDNFFTGRKENVEHWFGHPNFEIIHQDIVTPL 143
RI++TGGAGFVGSHLVDKL+ G EV V+DNFFTGRKEN+ H FG+P FE+I D+V P+
Sbjct: 122 RIVVTGGAGFVGSHLVDKLIGRGDEVIVIDNFFTGRKENLVHLFGNPRFELIRHDVVEPI 181
Query: 144 FVEVDEIYHLASPASPPHYMFNPVKTIKTNTIGTINMLGLAKRVGAKILFASTSEVYGDP 203
+EVD+IYHLA PASP HY +NPVKTIKTN +GT+NMLGLAKRVGA+ L STSEVYGDP
Sbjct: 182 LLEVDQIYHLACPASPVHYKYNPVKTIKTNVMGTLNMLGLAKRVGARFLLTSTSEVYGDP 241
Query: 204 EVHPQPETYWGHVNPIGPRACYDEAKRVAETLCYAYARHEDLSVRVARIFNTYGPRMHMN 263
HPQ ETYWG+VNPIG R+CYDE KR AETL Y R + VR+ARIFNTYGPRM ++
Sbjct: 242 LEHPQKETYWGNVNPIGERSCYDEGKRTAETLAMDYHRGAGVEVRIARIFNTYGPRMCLD 301
Query: 264 DGRVVSNFIIQALRNETITSDSSKSFTKFWDTLYIPHSFTQVYGLGNQTRSFQYVTDLVD 323
DGRVVSNF+ Q +R + +T VYG G QTRSFQYV+DLVD
Sbjct: 302 DGRVVSNFVAQTIRKQPMT----------------------VYGDGKQTRSFQYVSDLVD 339
Query: 324 GLIALMNSNYTLPVNLGNPTEHSIL 348
GL+ALM + P NLGNP E ++L
Sbjct: 340 GLVALMEGEHVGPFNLGNPGEFTML 364
>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 = 197 bits (504), Expect = 4e-61
Identities = 101/274 (36%), Positives = 141/274 (51%), Gaps = 38/274 (13%)
Query: 84 RILITGGAGFVGSHLVDKLMLMGHEVTVVDNFFTGRKENVEHWFGHPNFEIIHQDI---- 139
R+L+TGGAGF+GSHLV++L+ GHEV V+DN TG+KEN+ PN + I DI
Sbjct: 1 RVLVTGGAGFIGSHLVERLLERGHEVIVLDNLSTGKKENLPE--VKPNVKFIEGDIRDDE 58
Query: 140 -VTPLFVEVDEIYHLASPASPPHYMFNPVKTIKTNTIGTINMLGLAKRVGAK-ILFASTS 197
V F VD ++H A+ AS P + +P+K + N +GT+N+L A++ G K ++AS+S
Sbjct: 59 LVEFAFEGVDYVFHQAAQASVPRSIEDPIKDHEVNVLGTLNLLEAARKAGVKRFVYASSS 118
Query: 198 EVYGDPEVHPQPETYWGHVNPIGPRACYDEAKRVAETLCYAYARHEDLSVRVARIFNTYG 257
VYGDP P+ E + NP+ P Y +K E C +AR L R FN YG
Sbjct: 119 SVYGDPPYLPKDEDHPP--NPLSP---YAVSKYAGELYCQVFARLYGLPTVSLRYFNVYG 173
Query: 258 PRMHMNDGR--VVSNFIIQALRNETITSDSSKSFTKFWDTLYIPHSFTQVYGLGNQTRSF 315
PR N G V+ FI +AL+ E T +YG G QTR F
Sbjct: 174 PRQDPNGGYAAVIPIFIERALKGEPPT----------------------IYGDGEQTRDF 211
Query: 316 QYVTDLVDGLIALMNSNYTLPV-NLGNPTEHSIL 348
YV D+V+ + + V N+G S+
Sbjct: 212 TYVEDVVEANLLAATAGAGGEVYNIGTGKRTSVN 245
>gnl|CDD|223528 COG0451, WcaG, Nucleoside-diphosphate-sugar epimerases [Cell
envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 314
Score = 190 bits (484), Expect = 5e-58
Identities = 90/267 (33%), Positives = 127/267 (47%), Gaps = 31/267 (11%)
Query: 84 RILITGGAGFVGSHLVDKLMLMGHEVTVVDNFFTGRKENVEHWFGHPNFEIIHQDIVTPL 143
RIL+TGGAGF+GSHLV++L+ GH+V +D G + ++ +D+V L
Sbjct: 2 RILVTGGAGFIGSHLVERLLAAGHDVRGLDRLRDGLDPLLSG-VEFVVLDLTDRDLVDEL 60
Query: 144 FVEVDE-IYHLASPASPPHYM-FNPVKTIKTNTIGTINMLGLAKRVG-AKILFAST-SEV 199
V + + HLA+ +S P +P + + N GT+N+L A+ G + +FAS+ S V
Sbjct: 61 AKGVPDAVIHLAAQSSVPDSNASDPAEFLDVNVDGTLNLLEAARAAGVKRFVFASSVSVV 120
Query: 200 YGDPEVHPQPETYWGHVNPIGPRACYDEAKRVAETLCYAYARHEDLSVRVARIFNTYGPR 259
YGDP P E P P Y +K AE L AYAR L V + R FN YGP
Sbjct: 121 YGDPPPLPIDEDL----GPPRPLNPYGVSKLAAEQLLRAYARLYGLPVVILRPFNVYGPG 176
Query: 260 MHMN-DGRVVSNFIIQALRNETITSDSSKSFTKFWDTLYIPHSFTQVYGLGNQTRSFQYV 318
+ VVS FI Q L+ E I + G G+QTR F YV
Sbjct: 177 DKPDLSSGVVSAFIRQLLKGEPI---------------------IVIGGDGSQTRDFVYV 215
Query: 319 TDLVDGLIALMNSNYTLPVNLGNPTEH 345
D+ D L+ + + N+G+ T
Sbjct: 216 DDVADALLLALENPDGGVFNIGSGTAE 242
>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 = 175 bits (445), Expect = 1e-53
Identities = 77/246 (31%), Positives = 113/246 (45%), Gaps = 60/246 (24%)
Query: 85 ILITGGAGFVGSHLVDKLMLMGHEVTVVDNFFTGRKENVEHWFGHPNFEIIHQDIVTPLF 144
IL+TGGAGF+GSHLV +L+ GHEV V+D
Sbjct: 1 ILVTGGAGFIGSHLVRRLLERGHEVVVIDRL----------------------------- 31
Query: 145 VEVDEIYHLASPASPPHYMFNPVKTIKTNTIGTINMLGLAKRVG-AKILFASTSEVYGDP 203
D + HLA+ P NP + +TN +GT+N+L A++ G + ++AS++ VYG P
Sbjct: 32 ---DVVVHLAALVGVPASWDNPDEDFETNVVGTLNLLEAARKAGVKRFVYASSASVYGSP 88
Query: 204 EVHPQPETYWGHVNPIGPRACYDEAKRVAETLCYAYARHEDLSVRVARIFNTYGPRMHMN 263
E P+ E P P + Y +K AE L +Y L V + R+ N YGP
Sbjct: 89 EGLPEEEET-----PPRPLSPYGVSKLAAEHLLRSYGESYGLPVVILRLANVYGPGQRPR 143
Query: 264 DGRVVSNFIIQALRNETITSDSSKSFTKFWDTLYIPHSFTQVYGLGNQTRSFQYVTDLVD 323
VV++FI +AL + +T V+G GNQTR F +V D+V
Sbjct: 144 LDGVVNDFIRRALEGKPLT----------------------VFGGGNQTRDFIHVDDVVR 181
Query: 324 GLIALM 329
++ +
Sbjct: 182 AILHAL 187
>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 = 172 bits (437), Expect = 4e-51
Identities = 93/268 (34%), Positives = 133/268 (49%), Gaps = 38/268 (14%)
Query: 84 RILITGGAGFVGSHLVDKLMLMGHEVTVVDNFFTGRKENVEHWFGHPNFEIIHQDIVTPL 143
RIL+TGGAGF+GSHLVD+L+ G+EV VVDN +GR+EN+E F + F + +D++
Sbjct: 1 RILVTGGAGFIGSHLVDRLLEEGNEVVVVDNLSSGRRENIEPEFENKAFRFVKRDLLDTA 60
Query: 144 ----FVEVDEIYHLASPASPPHYMFNPVKTIKTNTIGTINMLGLAKRVGAK-ILFASTSE 198
+ D ++HLA+ +P ++ N + T N+L + G K I+FAS+S
Sbjct: 61 DKVAKKDGDTVFHLAANPDVRLGATDPDIDLEENVLATYNVLEAMRANGVKRIVFASSST 120
Query: 199 VYGDPEVHPQPETYWGHVNPIGPRACYDEAKRVAETLCYAYARHEDLSVRVARIFNTYGP 258
VYG+ +V P PE Y P P + Y +K AE L AYA + R N GP
Sbjct: 121 VYGEAKVIPTPEDY-----PPLPISVYGASKLAAEALISAYAHLFGFQAWIFRFANIVGP 175
Query: 259 RMHMNDGRVVSNFIIQALRNETITSDSSKSFTKFWDTLYIPHSFTQVYGLGNQTRSFQYV 318
R V+ +FI + RN + L +V G G Q +S+ YV
Sbjct: 176 RST---HGVIYDFINKLKRNP--------------NEL-------EVLGDGRQRKSYLYV 211
Query: 319 TDLVDGLIALMNSNYTLPV---NLGNPT 343
+D VD ++ L T V NLGN
Sbjct: 212 SDCVDAML-LAWEKSTEGVNIFNLGNDD 238
>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 = 169 bits (429), Expect = 9e-50
Identities = 80/272 (29%), Positives = 124/272 (45%), Gaps = 33/272 (12%)
Query: 84 RILITGGAGFVGSHLVDKLMLMGHEVTVVDNFFTGRKENVEHWFGHPNFEIIHQDIVTPL 143
+L+TG GF+GSHL ++L+ GHEV +D + + + H F I D+
Sbjct: 1 NVLVTGADGFIGSHLTERLLREGHEVRALDIYNSFNSWGLLDNAVHDRFHFISGDVRDAS 60
Query: 144 FVE-----VDEIYHLASPASPPHYMFNPVKTIKTNTIGTINMLGLAKRVGAK-ILFASTS 197
VE D ++HLA+ + P+ P+ ++TN GT+N+L A + K ++ STS
Sbjct: 61 EVEYLVKKCDVVFHLAALIAIPYSYTAPLSYVETNVFGTLNVLEAACVLYRKRVVHTSTS 120
Query: 198 EVYGDPEVHPQPETYWGHVNPIGPRACYDEAKRVAETLCYAYARHEDLSVRVARIFNTYG 257
EVYG + P E + PR+ Y +K+ A+ L Y+Y R L V + R FNTYG
Sbjct: 121 EVYGTAQDVPIDEDHPLLYI-NKPRSPYSASKQGADRLAYSYGRSFGLPVTIIRPFNTYG 179
Query: 258 PRMHMNDGRVVSNFIIQALRNETITSDSSKSFTKFWDTLYIPHSFTQVYGLGNQTRSFQY 317
PR + V+ I Q + G G+ TR F +
Sbjct: 180 PR--QSARAVIPTIISQRAIGQ----------------------RLINLGDGSPTRDFNF 215
Query: 318 VTDLVDGLIALMNSNYTL--PVNLGNPTEHSI 347
V D G I ++++ + +N G+ E SI
Sbjct: 216 VKDTARGFIDILDAIEAVGEIINNGSGEEISI 247
>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 = 156 bits (396), Expect = 7e-46
Identities = 76/254 (29%), Positives = 108/254 (42%), Gaps = 42/254 (16%)
Query: 85 ILITGGAGFVGSHLVDKLMLMGHEVTVVDNFFTGRKENVEHWFGHPNFEIIHQDIVTPLF 144
IL+TGG GF+GSHLV +L+ G+EV R+ D+ P
Sbjct: 1 ILVTGGTGFIGSHLVRRLLQEGYEVI---VLGRRRRSES---LNTGRIRFHEGDLTDPDA 54
Query: 145 VE-------VDEIYHLASPASPPHYMFNPVKTIKTNTIGTINMLGLAKRVGA-KILFAST 196
+E D + HLA+ + +P I+ N +GT+ +L A+R G + +FAS+
Sbjct: 55 LERLLAEVQPDAVIHLAAQSGVGASFEDPADFIRANVLGTLRLLEAARRAGVKRFVFASS 114
Query: 197 SEVYGDPEVHPQPETYWGHVNPIGPRACYDEAKRVAETLCYAYARHEDLSVRVARIFNTY 256
SEVYGD P E P+GP + Y AK AE L AYAR L + R+FN Y
Sbjct: 115 SEVYGDVADPPITEDT-----PLGPLSPYAAAKLAAERLVEAYARAYGLRAVILRLFNVY 169
Query: 257 GPR-MHMNDGRVVSNFIIQALRNETITSDSSKSFTKFWDTLYIPHSFTQVYGLGNQTRSF 315
GP V+ I + L + I + G G Q R F
Sbjct: 170 GPGNPDPFVTHVIPALIRRILEGKPIL----------------------LLGDGTQRRDF 207
Query: 316 QYVTDLVDGLIALM 329
YV D+ ++ +
Sbjct: 208 LYVDDVARAILLAL 221
>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 = 148 bits (374), Expect = 1e-41
Identities = 81/271 (29%), Positives = 111/271 (40%), Gaps = 39/271 (14%)
Query: 84 RILITGGAGFVGSHLVDKLMLMGHEVTVVDNFFTGRKENVEHWFGHPNF--EIIHQDIVT 141
R L+TG GF+GSHL ++L GH V D P E D+
Sbjct: 2 RALVTGAGGFIGSHLAERLKAEGHYVRGADWKSPEHMT-------QPTDDDEFHLVDLRE 54
Query: 142 PLFVE-----VDEIYHLASPASPPHYMF-NPVKTIKTNTIGTINMLGLAKRVGAK-ILFA 194
VD ++HLA+ Y+ N + NT+ NML A+ G + LFA
Sbjct: 55 MENCLKATEGVDHVFHLAADMGGMGYIQSNHAVIMYNNTLINFNMLEAARINGVERFLFA 114
Query: 195 STSEVYGDPEVHPQPETYWG----HVNPIGPRACYDEAKRVAETLCYAYARHEDLSVRVA 250
S++ VY PE T P P+ Y K E LC Y + R+
Sbjct: 115 SSACVY--PEFKQLETTVVRLREEDAWPAEPQDAYGWEKLATERLCQHYNEDYGIETRIV 172
Query: 251 RIFNTYGPRMHMNDGRVVSNFIIQALRNETITSDSSKSFTKFWDTLYIPHSFTQVYGLGN 310
R N YGPR + GR A+ + T+ F +++G G
Sbjct: 173 RFHNIYGPRGTWDGGR---EKAPAAMCRKVATAKDGDRF--------------EIWGDGL 215
Query: 311 QTRSFQYVTDLVDGLIALMNSNYTLPVNLGN 341
QTRSF Y+ D V+GL LM S++ PVNLG+
Sbjct: 216 QTRSFTYIDDCVEGLRRLMESDFGEPVNLGS 246
>gnl|CDD|200431 TIGR04180, EDH_00030, NAD dependent epimerase/dehydratase,
LLPSF_EDH_00030 family. This clade within the NAD
dependent epimerase/dehydratase superfamily (pfam01370)
is characterized by inclusion of its members within a
cassette of seven distinctive enzymes. These include
four genes homologous to the elements of the neuraminic
(sialic) acid biosynthesis cluster (NeuABCD), an
aminotransferase and a nucleotidyltransferase in
addition to the epimerase/dehydratase. Together it is
very likely that these enzymes direct the biosynthesis
of a nine-carbon sugar analagous to CMP-neuraminic acid.
These seven genes form the core of the cassette,
although they are often accompanied by additional genes
that may further modify the product sugar. Although this
cassette is widely distributed in bacteria, the family
nomenclature arises from the instance in Leptospira
interrogans serovar Lai, str. 56601, where it appears as
the 30th gene in the 91-gene lipopolysaccharide
biosynthesis cluster.
Length = 297
Score = 130 bits (329), Expect = 2e-35
Identities = 89/278 (32%), Positives = 130/278 (46%), Gaps = 48/278 (17%)
Query: 85 ILITGGAGFVGSHLVDKLMLMGHEVT--VVDNFFT--GRKENVEHWFGHPNFEIIHQDIV 140
+L+TG GF+GSHLV+ L+ G+EV V+ N F G + E++ DI
Sbjct: 1 VLVTGADGFIGSHLVEALVRQGYEVRAFVLYNSFNSWGWLDTSPPEV-KDKIEVVTGDIR 59
Query: 141 TPLFVE-----VDEIYHLASPASPPHYMFNPVKTIKTNTIGTINMLGLAKRVG-AKILFA 194
P V D ++HLA+ + P+ P + TN GT+N+L A+ +G K++
Sbjct: 60 DPDSVRKAMKGCDVVFHLAALIAIPYSYIAPDSYVDTNVTGTLNVLQAARDLGVEKVVHT 119
Query: 195 STSEVYGDPEVHPQPETYWGHVNPIGPRACYDEAKRVAETLCYAYARHEDLSVRVARIFN 254
STSEVYG + P E + P+ ++ Y +K A+ L ++ R + V + R FN
Sbjct: 120 STSEVYGTAQYVPIDEKH-----PLQGQSPYSASKIGADQLALSFYRSFNTPVTIIRPFN 174
Query: 255 TYGPRMHMNDGR-VVSNFIIQALRNETITSDSSKSFTKFWDTLYIPHSFTQVYGLGN--Q 311
TYGPR R V+ I Q S K K LG+
Sbjct: 175 TYGPR---QSARAVIPTIITQIA--------SGKRRIK----------------LGSLSP 207
Query: 312 TRSFQYVTDLVDGLIALMNSNYTL--PVNLGNPTEHSI 347
TR F YVTD V G IA+ S+ T+ +N+G+ E SI
Sbjct: 208 TRDFNYVTDTVRGFIAIAESDKTVGEVINIGSNFEISI 245
>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 = 121 bits (307), Expect = 6e-32
Identities = 69/261 (26%), Positives = 115/261 (44%), Gaps = 43/261 (16%)
Query: 83 RRILITGGAGFVGSHLVDKLMLMGH---EVTVVDNF-FTGRKENVEHWFGHPNFEIIHQD 138
+IL+TGGAGF+GS+ V + +L + ++ +D + G EN+E P + + D
Sbjct: 1 MKILVTGGAGFIGSNFV-RYLLNKYPDYKIINLDKLTYAGNLENLEDVSSSPRYRFVKGD 59
Query: 139 IVTPLFV-------EVDEIYHLASPASPPHYMFNPVKTIKTNTIGTINMLGLAKRVGA-K 190
I V ++D + H A+ + + +P I+TN +GT +L A++ G +
Sbjct: 60 ICDAELVDRLFEEEKIDAVIHFAAESHVDRSISDPEPFIRTNVLGTYTLLEAARKYGVKR 119
Query: 191 ILFASTSEVYGD-PEVHPQPETYWGHVNPIGPRACYDEAKRVAETLCYAYARHEDLSVRV 249
+ ST EVYGD + ET +P+ P + Y +K A+ L AY R L V +
Sbjct: 120 FVHISTDEVYGDLLDDGEFTET-----SPLAPTSPYSASKAAADLLVRAYHRTYGLPVVI 174
Query: 250 ARIFNTYGPRMHMNDGRVVSNFIIQALRNETITSDSSKSFTKFWDTLYIPHSFTQVYGLG 309
R N YGP +++ FI+ AL + + +YG G
Sbjct: 175 TRCSNNYGPYQF--PEKLIPLFILNALDGKPLP----------------------IYGDG 210
Query: 310 NQTRSFQYVTDLVDGLIALMN 330
R + YV D + ++
Sbjct: 211 LNVRDWLYVEDHARAIELVLE 231
>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 = 117 bits (295), Expect = 2e-30
Identities = 76/258 (29%), Positives = 112/258 (43%), Gaps = 43/258 (16%)
Query: 84 RILITGGAGFVGSHLVDKLMLMGHEVTVVDNFF------TGRKENVEHWFGHPNFEIIHQ 137
R+LI GG GF+GSHLVD L+ G +V V D G + ++ + + +
Sbjct: 1 RVLIVGGNGFIGSHLVDALLEEGPQVRVFDRSIPPYELPLGGVDYIKGDYENRAD--LES 58
Query: 138 DIVTPLFVEVDEIYHLASPASPPHYMFNPVKTIKTNTIGTINMLGLAKRVG-AKILFAST 196
+ V +D + HLAS +P NP+ I+TN T+ +L G KI+FAS+
Sbjct: 59 AL-----VGIDTVIHLASTTNPATSNKNPILDIQTNVAPTVQLLEACAAAGIGKIIFASS 113
Query: 197 -SEVYGDPEVHPQPETYWGHVNPIGPRACYDEAKRVAETLCYAYARHEDLSVRVARIFNT 255
VYG PE P E+ +P P + Y +K E Y L V RI N
Sbjct: 114 GGTVYGVPEQLPISES-----DPTLPISSYGISKLAIEKYLRLYQYLYGLDYTVLRISNP 168
Query: 256 YGPRMHMNDGR-VVSNFIIQALRNETITSDSSKSFTKFWDTLYIPHSFTQVYGLGNQTRS 314
YGP + + V+ + + LR E I ++G G R
Sbjct: 169 YGPGQRPDGKQGVIPIALNKILRGEPIE----------------------IWGDGESIRD 206
Query: 315 FQYVTDLVDGLIALMNSN 332
+ Y+ DLV+ L+AL+ S
Sbjct: 207 YIYIDDLVEALMALLRSK 224
>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 = 111 bits (280), Expect = 4e-28
Identities = 77/304 (25%), Positives = 115/304 (37%), Gaps = 68/304 (22%)
Query: 83 RRILITGGAGFVGSHLVDKLMLMGHEVTVVDNFFTGRKENVEHWF----GHPNFEIIHQD 138
R+LITGGAGF+GS+L + G EV DN W +H D
Sbjct: 1 MRVLITGGAGFIGSNLARFFLKQGWEVIGFDNLMRRGSFGNLAWLKANREDGGVRFVHGD 60
Query: 139 I-----VTPLFVEVDEIYHLAS-PA-----SPPHYMFNPVKTIKTNTIGTINMLGLAKRV 187
I + LF ++D I H A+ P+ S P F TN +GT+N+L A++
Sbjct: 61 IRNRNDLEDLFEDIDLIIHTAAQPSVTTSASSPRLDFE------TNALGTLNVLEAARQH 114
Query: 188 G--AKILFASTSEVYGDPEVH---PQPETYWGHVNPIGPRAC-YDEA------------- 228
A +F ST++VYGD + + ET + + P G E+
Sbjct: 115 APNAPFIFTSTNKVYGDLPNYLPLEELETRY-ELAPEGWSPAGISESFPLDFSHSLYGAS 173
Query: 229 KRVAETLCYAYARHEDLSVRVARIFNTYGPRMHMN-DGRVVSNFIIQALRNETITSDSSK 287
K A+ Y R L V R GPR D V+ F+ A+ + +T
Sbjct: 174 KGAADQYVQEYGRIFGLKTVVFRCGCLTGPRQFGTEDQGWVAYFLKCAVTGKPLT----- 228
Query: 288 SFTKFWDTLYIPHSFTQVYGLG-NQTRSFQYVTDLVDGLIALMNSNYTLP---VNLGNPT 343
++G G Q R + DLV+ + + N+G
Sbjct: 229 -----------------IFGYGGKQVRDVLHSADLVNLYLRQFQNPDRRKGEVFNIGGGR 271
Query: 344 EHSI 347
E+S+
Sbjct: 272 ENSV 275
>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 = 108 bits (271), Expect = 6e-27
Identities = 70/259 (27%), Positives = 109/259 (42%), Gaps = 48/259 (18%)
Query: 84 RILITGGAGFVGSHLVDKLMLMGHEVTVVD----NFFTGRKENVEHWFGHPN-FEIIHQD 138
R LITG G GS+L + L+ G+EV + +F T R ++H + + + + + D
Sbjct: 1 RALITGITGQDGSYLAEFLLEKGYEVHGIVRRSSSFNTDR---IDHLYINKDRITLHYGD 57
Query: 139 I-----VTPLFVEV--DEIYHLASPASPPHYMFNPVKTIKTNTIGTINMLGLAK--RVGA 189
+ + +V DEIYHLA+ + +P T + N +GT+N+L + + A
Sbjct: 58 LTDSSSLRRAIEKVRPDEIYHLAAQSHVKVSFDDPEYTAEVNAVGTLNLLEAIRILGLDA 117
Query: 190 KILFASTSEVYGDPEVHPQPETYWGHVNPIGPRACYDEAKRVAETLCYAYARHEDLSVRV 249
+ AS+SE YG + PQ ET P PR+ Y +K A+ + Y L
Sbjct: 118 RFYQASSSEEYGKVQELPQSET-----TPFRPRSPYAVSKLYADWITRNYREAYGLFAVN 172
Query: 250 ARIFNTYGPRMHMNDGRVVSNFIIQALRNET-ITSDSSKSFTKFWDTLYIPHSFTQVYGL 308
R+FN GPR R ET +T ++ + I V L
Sbjct: 173 GRLFNHEGPR-----------------RGETFVTRKITRQVAR------IKAGLQPVLKL 209
Query: 309 GNQT--RSFQYVTDLVDGL 325
GN R + D V+
Sbjct: 210 GNLDAKRDWGDARDYVEAY 228
>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 = 107 bits (268), Expect = 2e-26
Identities = 68/267 (25%), Positives = 113/267 (42%), Gaps = 53/267 (19%)
Query: 84 RILITGGAGFVGSHLVDKLMLMGHEVTVVDNFFT--------GRKENVEHWFGHPNFEII 135
+IL+TG AGF+G H+ +L+ G EV +DN R E + F+ +
Sbjct: 2 KILVTGAAGFIGFHVAKRLLERGDEVVGIDNLNDYYDVRLKEARLELLGK---SGGFKFV 58
Query: 136 HQDI-----VTPLFVEV--DEIYHLASPASPPHYMFNPVKTIKTNTIGTINMLGLAKRVG 188
D+ + LF + D + HLA+ A + + NP + +N +G +N+L L + G
Sbjct: 59 KGDLEDREALRRLFKDHEFDAVIHLAAQAGVRYSLENPHAYVDSNIVGFLNLLELCRHFG 118
Query: 189 -AKILFASTSEVYGDPEVHPQPETYWGHVN-PIGPRACYDEAKRVAETLCYAYARHEDLS 246
+++AS+S VYG P E V+ PI Y K+ E + + Y+ +
Sbjct: 119 VKHLVYASSSSVYGLNTKMPFSED--DRVDHPISL---YAATKKANELMAHTYSHLYGIP 173
Query: 247 VRVARIFNTYGP--RMHMNDGRVVSNFIIQALRNETITSDSSKSFTKFWDTLYIPHSFTQ 304
R F YGP R M + F L + I
Sbjct: 174 TTGLRFFTVYGPWGRPDM----ALFLFTKAILEGKPI----------------------D 207
Query: 305 VYGLGNQTRSFQYVTDLVDGLIALMNS 331
V+ GN +R F Y+ D+V+G++ +++
Sbjct: 208 VFNDGNMSRDFTYIDDIVEGVVRALDT 234
>gnl|CDD|224012 COG1087, GalE, UDP-glucose 4-epimerase [Cell envelope biogenesis,
outer membrane].
Length = 329
Score = 104 bits (262), Expect = 1e-25
Identities = 79/292 (27%), Positives = 121/292 (41%), Gaps = 59/292 (20%)
Query: 84 RILITGGAGFVGSHLVDKLMLMGHEVTVVDNFFTGRKENVEHWFGHPNFEIIHQDI---- 139
++L+TGGAG++GSH V +L+ GHEV V+DN G K + + D+
Sbjct: 2 KVLVTGGAGYIGSHTVRQLLKTGHEVVVLDNLSNGHKIALLKLQF----KFYEGDLLDRA 57
Query: 140 -VTPLFVE--VDEIYHLASPASPPHYMFNPVKTIKTNTIGTINMLGLAKRVGAK-ILFAS 195
+T +F E +D + H A+ S + NP+K N +GT+N++ + G K +F+S
Sbjct: 58 LLTAVFEENKIDAVVHFAASISVGESVQNPLKYYDNNVVGTLNLIEAMLQTGVKKFIFSS 117
Query: 196 TSEVYGDPEVHPQPETYWGHVNPIGPRACYDEAKRVAETLCYAYARHEDLSVRVARIFNT 255
T+ VYG+P P ET + PI P Y +K ++E + A+ V + R FN
Sbjct: 118 TAAVYGEPTTSPISETS--PLAPINP---YGRSKLMSEEILRDAAKANPFKVVILRYFNV 172
Query: 256 YGPRMHMNDGRVVSNFIIQALRNETITSDSSKSFTKFWDTLYIPH---------SFTQVY 306
G DG + Q TL IP ++
Sbjct: 173 AGACP---DGT-----LGQRYPGA---------------TLLIPVAAEAALGKRDKLFIF 209
Query: 307 GLGNQT------RSFQYVTDLVDGLIA----LMNSNYTLPVNLGNPTEHSIL 348
G T R + +V DL D + L NLG+ S+L
Sbjct: 210 GDDYDTKDGTCIRDYIHVDDLADAHVLALKYLKEGGSNNIFNLGSGNGFSVL 261
>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 = 103 bits (260), Expect = 3e-25
Identities = 75/285 (26%), Positives = 123/285 (43%), Gaps = 42/285 (14%)
Query: 84 RILITGGAGFVGSHLVDKLMLMGHEVTVVDNFFTGRKENVEHWFGHPNFEIIHQDIVTPL 143
++L+TGGAG++GSH V +L+ G++V V+DN G +E + E DI
Sbjct: 1 KVLVTGGAGYIGSHTVVELLEAGYDVVVLDNLSNGHREALP-RIEKIRIEFYEGDIRDRA 59
Query: 144 FVE-------VDEIYHLASPASPPHYMFNPVKTIKTNTIGTINMLGLAKRVGAK-ILFAS 195
++ +D + H A+ + + P+K N +GT+N+L + G K +F+S
Sbjct: 60 ALDKVFAEHKIDAVIHFAALKAVGESVQKPLKYYDNNVVGTLNLLEAMRAHGVKNFVFSS 119
Query: 196 TSEVYGDPEVHPQPETYWGHVNPIGPRACYDEAKRVAETLCYAYARHEDLSVRVARIFNT 255
++ VYG+PE P E P+ P Y K + E + A+ L+ + R FN
Sbjct: 120 SAAVYGEPETVPITEEA-----PLNPTNPYGRTKLMVEQILRDLAKAPGLNYVILRYFNP 174
Query: 256 YGPRMHMN-----DGRVVSN---FIIQALRNETITSDSSKSFTKFWDTLYIPHSFTQVYG 307
G H + D ++ +N +++Q + F D Y T V
Sbjct: 175 AGA--HPSGLIGEDPQIPNNLIPYVLQVALGRR------EKLAIFGDD-YPTPDGTCV-- 223
Query: 308 LGNQTRSFQYVTDLVDG----LIALMNSNYTLPVNLGNPTEHSIL 348
R + +V DL D L L N + NLG +S+L
Sbjct: 224 -----RDYIHVVDLADAHVLALEKLENGGGSEIYNLGTGRGYSVL 263
>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 = 102 bits (256), Expect = 1e-24
Identities = 56/187 (29%), Positives = 93/187 (49%), Gaps = 14/187 (7%)
Query: 84 RILITGGAGFVGSHLVDKLMLMGHEVTVVDNFFTGRKENVEHWFGHPNFEIIHQDI---- 139
+IL+TGGAG++GSH V +L+ GHEV ++DN G +E + + D+
Sbjct: 1 KILVTGGAGYIGSHTVRQLLESGHEVVILDNLSNGSREALPRGERITPVTFVEGDLRDRE 60
Query: 140 -VTPLFVE--VDEIYHLASPASPPHYMFNPVKTIKTNTIGTINMLGLAKRVGAK-ILFAS 195
+ LF E +D + H A + + P+K + N +GT+N+L ++ G K +F+S
Sbjct: 61 LLDRLFEEHKIDAVIHFAGLIAVGESVQKPLKYYRNNVVGTLNLLEAMQQAGVKKFIFSS 120
Query: 196 TSEVYGDPEVHPQPETYWGHVNPIGPRACYDEAKRVAETLCYAYARHE-DLSVRVARIFN 254
++ VYG+P P E + PI P Y +K ++E + + + D S + R FN
Sbjct: 121 SAAVYGEPSSIPISEDS--PLGPINP---YGRSKLMSEQILRDLQKADPDWSYVILRYFN 175
Query: 255 TYGPRMH 261
G
Sbjct: 176 VAGAHPS 182
>gnl|CDD|178298 PLN02695, PLN02695, GDP-D-mannose-3',5'-epimerase.
Length = 370
Score = 99.1 bits (247), Expect = 2e-23
Identities = 79/283 (27%), Positives = 118/283 (41%), Gaps = 60/283 (21%)
Query: 80 QSKRRILITGGAGFVGSHLVDKLMLMGHEVTVVDNFFTGRKENVEHWFGHPNFEIIHQDI 139
K RI ITG GF+ SH+ +L GH + D K+N EH H+
Sbjct: 19 SEKLRICITGAGGFIASHIARRLKAEGHYIIASD-----WKKN-EHM---SEDMFCHEFH 69
Query: 140 VTPLFV---------EVDEIYHLASPASPPHY--------MFNPVKTIKTNTIGTINMLG 182
+ L V VD +++LA+ + M+N NT+ + NML
Sbjct: 70 LVDLRVMENCLKVTKGVDHVFNLAADMGGMGFIQSNHSVIMYN-------NTMISFNMLE 122
Query: 183 LAKRVGAKILF-ASTSEVYGDPEVHPQPETYWGHVN----PIGPRACYDEAKRVAETLCY 237
A+ G K F AS++ +Y PE Q ET P P+ Y K E LC
Sbjct: 123 AARINGVKRFFYASSACIY--PEFK-QLETNVSLKESDAWPAEPQDAYGLEKLATEELCK 179
Query: 238 AYARHEDLSVRVARIFNTYGPRMHMNDGRVVSNFIIQALRNETITSDSSKSFTKFWDTLY 297
Y + + R+ R N YGP GR + A + +TS +F
Sbjct: 180 HYTKDFGIECRIGRFHNIYGPFGTWKGGREKAP---AAFCRKALTST-----DEF----- 226
Query: 298 IPHSFTQVYGLGNQTRSFQYVTDLVDGLIALMNSNYTLPVNLG 340
+++G G QTRSF ++ + V+G++ L S++ PVN+G
Sbjct: 227 ------EMWGDGKQTRSFTFIDECVEGVLRLTKSDFREPVNIG 263
>gnl|CDD|224013 COG1088, RfbB, dTDP-D-glucose 4,6-dehydratase [Cell envelope
biogenesis, outer membrane].
Length = 340
Score = 93.8 bits (234), Expect = 1e-21
Identities = 71/253 (28%), Positives = 103/253 (40%), Gaps = 45/253 (17%)
Query: 83 RRILITGGAGFVGSHLVDKLMLMGH---EVTVVDNF-FTGRKENVEHWFGHPNFEIIHQD 138
+IL+TGGAGF+GS+ V + +L H V +D + G EN+ P + + D
Sbjct: 1 MKILVTGGAGFIGSNFV-RYILNKHPDDHVVNLDKLTYAGNLENLADVEDSPRYRFVQGD 59
Query: 139 IVTPLFVE-------VDEIYHLASPASPPHYMFNPVKTIKTNTIGTINMLGLAKRVGAKI 191
I V+ D + H A+ + + P I+TN +GT +L A++ K
Sbjct: 60 ICDRELVDRLFKEYQPDAVVHFAAESHVDRSIDGPAPFIQTNVVGTYTLLEAARKYWGKF 119
Query: 192 LF--ASTSEVYGD-PEVHPQ-PETYWGHVNPIGPRACYDEAKRVAETLCYAYARHEDLSV 247
F ST EVYGD ET P P + Y +K ++ L AY R L
Sbjct: 120 RFHHISTDEVYGDLGLDDDAFTET-----TPYNPSSPYSASKAASDLLVRAYVRTYGLPA 174
Query: 248 RVARIFNTYGPRMHMNDGRVVSNFIIQALRNETITSDSSKSFTKFWDTLYIPHSFTQVYG 307
+ R N YGP +++ II AL + + VYG
Sbjct: 175 TITRCSNNYGPYQFPE--KLIPLMIINALLGKPLP----------------------VYG 210
Query: 308 LGNQTRSFQYVTD 320
G Q R + YV D
Sbjct: 211 DGLQIRDWLYVED 223
>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 = 93.2 bits (232), Expect = 2e-21
Identities = 72/250 (28%), Positives = 107/250 (42%), Gaps = 42/250 (16%)
Query: 84 RILITGGAGFVGSHLVDKLMLMGH---EVTVVDNF-FTGRKENVEHWFGHPNFEIIHQDI 139
RIL+TGGAGF+GS+ V + +L H EV V+D + G EN+ +P + + DI
Sbjct: 1 RILVTGGAGFIGSNFV-RYILNEHPDAEVIVLDKLTYAGNLENLADLEDNPRYRFVKGDI 59
Query: 140 -----VTPLFVE--VDEIYHLASPASPPHYMFNPVKTIKTNTIGTINMLGLAKR--VGAK 190
V+ LF E D + H A+ + + P I+TN +GT +L ++ +
Sbjct: 60 GDRELVSRLFTEHQPDAVVHFAAESHVDRSISGPAAFIETNVVGTYTLLEAVRKYWHEFR 119
Query: 191 ILFASTSEVYGDPEVHPQPETYWGHVNPIGPRACYDEAKRVAETLCYAYARHEDLSVRVA 250
ST EVYGD E + P+ P + Y +K ++ L AY R L +
Sbjct: 120 FHHISTDEVYGDLE----KGDAFTETTPLAPSSPYSASKAASDHLVRAYHRTYGLPALIT 175
Query: 251 RIFNTYGPRMHMNDGRVVSNFIIQALRNETITSDSSKSFTKFWDTLYIPHSFTQVYGLGN 310
R N YGP +++ I AL + + VYG G
Sbjct: 176 RCSNNYGPYQFPE--KLIPLMITNALAGKPLP----------------------VYGDGQ 211
Query: 311 QTRSFQYVTD 320
Q R + YV D
Sbjct: 212 QVRDWLYVED 221
>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 = 88.3 bits (219), Expect = 9e-20
Identities = 55/185 (29%), Positives = 88/185 (47%), Gaps = 23/185 (12%)
Query: 84 RILITGGAGFVGSHLVDKLMLMGHEVTVVDNFFTGRKENVEHWFGHPNFEIIHQDIVTPL 143
++LITGGAG +GSHL++ L+ GH+V V+DNF TGR+E++ HPN ++ I
Sbjct: 2 KVLITGGAGQIGSHLIEHLLERGHQVVVIDNFATGRREHLPD---HPNLTVVEGSIADKA 58
Query: 144 FVEV-------DEIYHLASPASPPHYMFNPVKTIKTNTIGTINMLGLAKRVGAK-ILFAS 195
V+ D + H A+ P + + TN +G N++ AK+ G K +++
Sbjct: 59 LVDKLFGDFKPDAVVHTAAAYKDPD---DWYEDTLTNVVGGANVVQAAKKAGVKRLIYFQ 115
Query: 196 TSEVYG-DPEVHPQPETYWGHVNPIGPRACYDEAKRVAETLCYAYARHEDLSVRVARIFN 254
T+ YG P P + PRA + +++T Y + R+ N
Sbjct: 116 TALCYGLKPMQQPIRLDH--------PRAPPGSSYAISKTAGEYYLELSGVDFVTFRLAN 167
Query: 255 TYGPR 259
GPR
Sbjct: 168 VTGPR 172
>gnl|CDD|183375 PRK11908, PRK11908, NAD-dependent epimerase/dehydratase family
protein; Provisional.
Length = 347
Score = 84.8 bits (210), Expect = 2e-18
Identities = 77/296 (26%), Positives = 128/296 (43%), Gaps = 56/296 (18%)
Query: 83 RRILITGGAGFVGSHLVDK-LMLMGHEVTVVDNFFTGRKENVEHWFGHPNFEIIHQDI-V 140
+++LI G GF+G HL + L EV +D + + + HP DI +
Sbjct: 2 KKVLILGVNGFIGHHLSKRILETTDWEVYGMDM----QTDRLGDLVNHPRMHFFEGDITI 57
Query: 141 TPLFVE-----VDEIYHLASPASPPHYMFNPVKTIKTNTIGTINMLGLAKRVGAKILFAS 195
++E D I L + A+P Y+ P++ + + + ++ A + G ++F S
Sbjct: 58 NKEWIEYHVKKCDVILPLVAIATPATYVKQPLRVFELDFEANLPIVRSAVKYGKHLVFPS 117
Query: 196 TSEVYG---DPEVHPQ--PETYWGHVNPIG-PRACYDEAKRVAETLCYAYARHEDLSVRV 249
TSEVYG D E P+ P Y PI PR Y +K++ + + +AY E L+ +
Sbjct: 118 TSEVYGMCPDEEFDPEASPLVY----GPINKPRWIYACSKQLMDRVIWAYGMEEGLNFTL 173
Query: 250 ARIFNTYGPRM------HMNDGRVVSNFIIQALRNETITSDSSKSFTKFWDTLYIPHSFT 303
R FN GP + RVV+ F+ +R E I
Sbjct: 174 FRPFNWIGPGLDSIYTPKEGSSRVVTQFLGHIVRGEPI---------------------- 211
Query: 304 QVYGLGNQTRSFQYVTDLVDGLIALMNSNYTLPV----NLGNPT-EHSI--LACKL 352
+ G+Q R+F + D +D L+ ++ + + N+GNP HS+ LA K+
Sbjct: 212 SLVDGGSQKRAFTDIDDGIDALMKIIENKDGVASGKIYNIGNPKNNHSVRELANKM 267
>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 = 82.0 bits (203), Expect = 1e-17
Identities = 66/275 (24%), Positives = 109/275 (39%), Gaps = 51/275 (18%)
Query: 85 ILITGGAGFVGSHLVDKLMLMG-HEVTVVDNFFTGRK-ENVE-----HWFGHPNF--EII 135
I++TGGAGF+GS+LV L G ++ VVDN G K +N+ + +F +
Sbjct: 2 IIVTGGAGFIGSNLVKALNERGITDILVVDNLSNGEKFKNLVGLKIADYIDKDDFKDWVR 61
Query: 136 HQDIVTPLFVEVDEIYHLASPASPPHYMFNPVKTIKTNTIGTINMLGLAKRVGAKILFAS 195
D +++ I+H A + + N T +L + ++AS
Sbjct: 62 KGD----ENFKIEAIFHQG--ACSDTTETDGKYMMDNNYQYTKELLHYCLEKKIRFIYAS 115
Query: 196 TSEVYGDPEVHPQPETYWGHVNPIGPRA----CYDEAKRVAETLCYAYARHEDLSVRVA- 250
++ VYG+ + + ++ P+ +D +A +++ +V
Sbjct: 116 SAAVYGNGSLGFAEDIETPNLRPLNVYGYSKLLFD---------QWARRHGKEVLSQVVG 166
Query: 251 -RIFNTYGPRMHMNDGR---VVSNFIIQALRNETITSDSSKSFTKFWDTLYIPHSFTQVY 306
R FN YGPR + GR VV + Q E + K F + Y
Sbjct: 167 LRYFNVYGPR-EYHKGRMASVVFHLFNQIKAGEKV-----KLF-----------KSSDGY 209
Query: 307 GLGNQTRSFQYVTDLVD-GLIALMNSNYTLPVNLG 340
G Q R F YV D+V L L N + + N+G
Sbjct: 210 ADGEQLRDFVYVKDVVKVNLFFLENPSVSGIFNVG 244
>gnl|CDD|185103 PRK15181, PRK15181, Vi polysaccharide biosynthesis protein TviC;
Provisional.
Length = 348
Score = 80.5 bits (198), Expect = 6e-17
Identities = 71/245 (28%), Positives = 111/245 (45%), Gaps = 27/245 (11%)
Query: 71 YPSVKFQDYQSKRRILITGGAGFVGSHLVDKLMLMGHEVTVVDNFFTGRKENV------- 123
Y ++ + + +R LITG AGF+GS L+++L+ + V +DNF TG + N+
Sbjct: 4 YEELRTKLVLAPKRWLITGVAGFIGSGLLEELLFLNQTVIGLDNFSTGYQHNLDDVRTSV 63
Query: 124 --EHWFGHPNFEIIHQDI-----VTPLFVEVDEIYHLASPASPPHYMFNPVKTIKTNTIG 176
E W F I DI VD + H A+ S P + +P+ T N G
Sbjct: 64 SEEQW---SRFIFIQGDIRKFTDCQKACKNVDYVLHQAALGSVPRSLKDPIATNSANIDG 120
Query: 177 TINMLGLAKRVG-AKILFASTSEVYGDPEVHPQPETYWGHVNPIGPRACYDEAKRVAETL 235
+NML A+ + +A++S YGD P+ E G P+ P Y K V E
Sbjct: 121 FLNMLTAARDAHVSSFTYAASSSTYGDHPDLPKIEERIGR--PLSP---YAVTKYVNELY 175
Query: 236 CYAYARHEDLSVRVARIFNTYGPRMHMNDG--RVVSNFIIQALRNETITSDSSKSFTKFW 293
+AR + + R FN +G R + N V+ +I+ L++E I + S ++
Sbjct: 176 ADVFARSYEFNAIGLRYFNVFGRRQNPNGAYSAVIPRWILSLLKDEPIYINGDGSTSR-- 233
Query: 294 DTLYI 298
D YI
Sbjct: 234 DFCYI 238
>gnl|CDD|224014 COG1089, Gmd, GDP-D-mannose dehydratase [Cell envelope biogenesis,
outer membrane].
Length = 345
Score = 79.3 bits (196), Expect = 2e-16
Identities = 54/194 (27%), Positives = 79/194 (40%), Gaps = 22/194 (11%)
Query: 82 KRRILITGGAGFVGSHLVDKLMLMGHEV------TVVDNFFTGRKENVEHWFGHPNFEII 135
+ LITG G GS+L + L+ G+EV + N H P +
Sbjct: 2 GKVALITGITGQDGSYLAELLLEKGYEVHGIKRRSSSFNTPRIHLYEDPH-LNDPRLHLH 60
Query: 136 HQDIV--TPLF-----VEVDEIYHLASPASPPHYMFNPVKTIKTNTIGTINMLGLAKRVG 188
+ D+ + L V+ DEIY+LA+ + P T + IGT+ +L + +G
Sbjct: 61 YGDLTDSSNLLRILEEVQPDEIYNLAAQSHVGVSFEQPEYTADVDAIGTLRLLEAIRILG 120
Query: 189 ---AKILFASTSEVYGDPEVHPQPETYWGHVNPIGPRACYDEAKRVAETLCYAYARHEDL 245
+ ASTSE+YG + PQ ET P PR+ Y AK A + Y L
Sbjct: 121 EKKTRFYQASTSELYGLVQEIPQKET-----TPFYPRSPYAVAKLYAYWITVNYRESYGL 175
Query: 246 SVRVARIFNTYGPR 259
+FN P
Sbjct: 176 FACNGILFNHESPL 189
>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 = 75.3 bits (186), Expect = 2e-15
Identities = 73/277 (26%), Positives = 102/277 (36%), Gaps = 50/277 (18%)
Query: 84 RILITGGAGFVGSHLVDKLMLMG-HEVTVVDNFFTGRKENVEHWFGHPNFEIIHQDIVTP 142
+IL+TG G VGS +V L G V F KE ++ Q+ V
Sbjct: 1 KILVTGHRGLVGSAIVRVLARRGYENVV-----FRTSKE----------LDLTDQEAVRA 45
Query: 143 LFVEV--DEIYHLASPASPPHY-MFNPVKTIKTNTIGTINMLGLAKRVG-AKILFASTSE 198
F + D + HLA+ M P ++ N + N++ A R G K++F +S
Sbjct: 46 FFEKEKPDYVIHLAAKVGGIVANMTYPADFLRDNLLINDNVIHAAHRFGVKKLVFLGSSC 105
Query: 199 VYGDPEVHPQPETYWGHVNPIGP-RACYDEAKRVAETLCYAYARHEDLSVRVARIFNTYG 257
+Y D P E+ P P Y AKR LC AY + N YG
Sbjct: 106 IYPDLAPQPIDESDL-LTGPPEPTNEGYAIAKRAGLKLCEAYRKQYGCDYISVMPTNLYG 164
Query: 258 PR--MHMNDGRVVSNFI---IQALRNETITSDSSKSFTKFWDTLYIPHSFTQVYGLGNQT 312
P + V+ I +A K T V+G G
Sbjct: 165 PHDNFDPENSHVIPALIRKFHEAKLRG------GKEVT--------------VWGSGTPR 204
Query: 313 RSFQYVTDLVDGLIALMNSNYTLP--VNLGNPTEHSI 347
R F Y DL ++ L+ NY P VN+G+ E SI
Sbjct: 205 REFLYSDDLARAIVFLLE-NYDEPIIVNVGSGVEISI 240
>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 = 72.3 bits (178), Expect = 3e-14
Identities = 61/267 (22%), Positives = 101/267 (37%), Gaps = 37/267 (13%)
Query: 85 ILITGGAGFVGSHLVDKLMLMGH-EVTVVDNFFTG------RKENVEHWFGHPNFEIIHQ 137
I++TGGAGF+GS+LV L G ++ VVDN G + + +F
Sbjct: 1 IIVTGGAGFIGSNLVKALNERGITDILVVDNLRDGHKFLNLADLVIADYIDKEDFLD--- 57
Query: 138 DIVTPLFVEVDEIYHLASPASPPHYMFNPVKTIKTNTIGTINMLGLAKRVGAKILFASTS 197
+ F +++ I+H + + + ++ N + +L G ++AS++
Sbjct: 58 RLEKGAFGKIEAIFHQGACSDT--TETDGEYMMENNYQYSKRLLDWCAEKGIPFIYASSA 115
Query: 198 EVYGDPEVHPQPETYWGHVNPIGPRACYDEAKRVAETLCYAYARHEDLSVRVA--RIFNT 255
YGD + P Y +K + + E LS +V R FN
Sbjct: 116 ATYGD-----GEAGFREGRELERPLNVYGYSKFLFDQYVRRRVLPEALSAQVVGLRYFNV 170
Query: 256 YGPR-MHMND-GRVVSNFIIQALRNETITSDSSKSFTKFWDTLYIPHSFTQVYGLGNQTR 313
YGPR H V + Q + L+ + + G Q R
Sbjct: 171 YGPREYHKGKMASVAFHLFNQIKAGGNV-------------KLFKSS---EGFKDGEQLR 214
Query: 314 SFQYVTDLVDGLIALMNSNYTLPVNLG 340
F YV D+VD + L+ + + NLG
Sbjct: 215 DFVYVKDVVDVNLWLLENGVSGIFNLG 241
>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 = 69.8 bits (171), Expect = 2e-13
Identities = 51/187 (27%), Positives = 72/187 (38%), Gaps = 23/187 (12%)
Query: 84 RILITGGAGFVGSHLVDKLM-LMGHEVTVVDNFFTGRKENVEHW-FGHPNFEIIHQDIVT 141
+L+TGG+GF G LV +L+ G V D G + HPN E + DI
Sbjct: 1 SVLVTGGSGFFGERLVKQLLERGGTYVRSFDIAPPGEA----LSAWQHPNIEFLKGDITD 56
Query: 142 PLFVE-----VDEIYHLASPASPPHYMFNPVKTI-KTNTIGTINMLGLAKRVGAKIL-FA 194
VE D ++H A+ P + N GT N+L +R G + +
Sbjct: 57 RNDVEQALSGADCVFHTAAIVPL----AGPRDLYWEVNVGGTQNVLDACQRCGVQKFVYT 112
Query: 195 STSEVY--GDPEVHPQPETYWGHVNPIGPRACYDEAKRVAETLCYAYARHEDLSVRVARI 252
S+S V G +H ET P Y E K +AE + +DL R
Sbjct: 113 SSSSVIFGGQN-IHNGDETL---PYPPLDSDMYAETKAIAEIIVLEANGRDDLLTCALRP 168
Query: 253 FNTYGPR 259
+GP
Sbjct: 169 AGIFGPG 175
>gnl|CDD|182639 PRK10675, PRK10675, UDP-galactose-4-epimerase; Provisional.
Length = 338
Score = 69.8 bits (171), Expect = 2e-13
Identities = 73/288 (25%), Positives = 130/288 (45%), Gaps = 42/288 (14%)
Query: 84 RILITGGAGFVGSHLVDKLMLMGHEVTVVDNFFTGRK---ENVEHWFGH-PNF---EIIH 136
R+L+TGG+G++GSH +L+ GH+V ++DN ++ +E G P F +I +
Sbjct: 2 RVLVTGGSGYIGSHTCVQLLQNGHDVVILDNLCNSKRSVLPVIERLGGKHPTFVEGDIRN 61
Query: 137 QDIVTPLFVE--VDEIYHLASPASPPHYMFNPVKTIKTNTIGTINMLGLAKRVGAK-ILF 193
+ ++T + + +D + H A + + P++ N GT+ ++ + K ++F
Sbjct: 62 EALLTEILHDHAIDTVIHFAGLKAVGESVQKPLEYYDNNVNGTLRLISAMRAANVKNLIF 121
Query: 194 ASTSEVYGDPEVHPQPETYWGHVNPIG-PRACYDEAKRVAETLCYAYARHE-DLSVRVAR 251
+S++ VYGD P E++ P G P++ Y ++K + E + + + D S+ + R
Sbjct: 122 SSSATVYGDQPKIPYVESF-----PTGTPQSPYGKSKLMVEQILTDLQKAQPDWSIALLR 176
Query: 252 IFNTYG--PRMHM-NDGRVVSN----FIIQALRNETITSDSSKSFTKFWDTLYIPHSFTQ 304
FN G P M D + + N +I Q + S F + +
Sbjct: 177 YFNPVGAHPSGDMGEDPQGIPNNLMPYIAQ------VAVGRRDSLAIF------GNDYPT 224
Query: 305 VYGLGNQTRSFQYVTDLVDGLIALMNSNYTLP----VNLGNPTEHSIL 348
G G R + +V DL DG +A M P NLG S+L
Sbjct: 225 EDGTG--VRDYIHVMDLADGHVAAMEKLANKPGVHIYNLGAGVGSSVL 270
>gnl|CDD|178047 PLN02427, PLN02427, UDP-apiose/xylose synthase.
Length = 386
Score = 69.1 bits (169), Expect = 5e-13
Identities = 82/297 (27%), Positives = 116/297 (39%), Gaps = 61/297 (20%)
Query: 84 RILITGGAGFVGSHLVDKLML-MGHEVTVVDNFFTGRKENVE----HWFGHPNF---EII 135
I + G GF+GSHL +KLM H+V +D + K +E W G F I
Sbjct: 16 TICMIGAGGFIGSHLCEKLMTETPHKVLALDVYNDKIKHLLEPDTVPWSGRIQFHRINIK 75
Query: 136 HQDIVTPLFVEVDEIYHLASPASPPHYMFNPVKTIKTNTIGTINMLGLAKRVGAKILFAS 195
H + L D +LA+ +P Y P+ TI +N I + ++ +++ S
Sbjct: 76 HDSRLEGLIKMADLTINLAAICTPADYNTRPLDTIYSNFIDALPVVKYCSENNKRLIHFS 135
Query: 196 TSEVYGD------PEVHP---QPETYW--GHVNP--IGP----RACYDEAKRVAETLCYA 238
T EVYG P+ HP P Y +P G R Y AK++ E L YA
Sbjct: 136 TCEVYGKTIGSFLPKDHPLRQDPAFYVLKEDESPCIFGSIEKQRWSYACAKQLIERLIYA 195
Query: 239 YARHEDLSVRVARIFNTYGPRMHMNDG---------RVVSNFIIQALRNETITSDSSKSF 289
L + R FN GPRM G RV++ F LR E +
Sbjct: 196 EGAENGLEFTIVRPFNWIGPRMDFIPGIDGPSEGVPRVLACFSNNLLRREPL-------- 247
Query: 290 TKFWDTLYIPHSFTQVYGLGNQTRSFQYVTDLVDGLIALMNSNYTLP----VNLGNP 342
K D G R+F Y+ D ++ ++ LM N N+GNP
Sbjct: 248 -KLVDG-------------GQSQRTFVYIKDAIEAVL-LMIENPARANGHIFNVGNP 289
>gnl|CDD|177883 PLN02240, PLN02240, UDP-glucose 4-epimerase.
Length = 352
Score = 68.8 bits (169), Expect = 6e-13
Identities = 57/196 (29%), Positives = 89/196 (45%), Gaps = 33/196 (16%)
Query: 83 RRILITGGAGFVGSHLVDKLMLMGHEVTVVDNFFTGRKENVEH---WFGHP-------NF 132
R IL+TGGAG++GSH V +L+L G++V V+DN +E + G
Sbjct: 6 RTILVTGGAGYIGSHTVLQLLLAGYKVVVIDNLDNSSEEALRRVKELAGDLGDNLVFHKV 65
Query: 133 EIIHQDIVTPLFVE--VDEIYHLA-------SPASPPHYMFNPVKTIKTNTIGTINMLG- 182
++ ++ + +F D + H A S A P Y N N +GTIN+L
Sbjct: 66 DLRDKEALEKVFASTRFDAVIHFAGLKAVGESVAKPLLYYDN-------NLVGTINLLEV 118
Query: 183 LAKRVGAKILFASTSEVYGDPEVHPQPETYWGHVNPIGPRACYDEAKRVAETLCYAYARH 242
+AK K++F+S++ VYG PE P E + P+ Y K E +C
Sbjct: 119 MAKHGCKKLVFSSSATVYGQPEEVPCTEEF-----PLSATNPYGRTKLFIEEICRDIHAS 173
Query: 243 E-DLSVRVARIFNTYG 257
+ + + + R FN G
Sbjct: 174 DPEWKIILLRYFNPVG 189
>gnl|CDD|215146 PLN02260, PLN02260, probable rhamnose biosynthetic enzyme.
Length = 668
Score = 69.0 bits (169), Expect = 1e-12
Identities = 66/255 (25%), Positives = 106/255 (41%), Gaps = 48/255 (18%)
Query: 83 RRILITGGAGFVGSHLVDKLM--LMGHEVTVVDNF-FTGRKENVEHWFGHPNFEIIHQDI 139
+ ILITG AGF+ SH+ ++L+ +++ V+D + +N+ PNF+ + DI
Sbjct: 7 KNILITGAAGFIASHVANRLIRNYPDYKIVVLDKLDYCSNLKNLNPSKSSPNFKFVKGDI 66
Query: 140 -----VTPLFV--EVDEIYHLASPASPPHYMFNPVKTIKTNTIGTINMLGLAKRVGA--K 190
V L + +D I H A+ + N + K N GT +L K G +
Sbjct: 67 ASADLVNYLLITEGIDTIMHFAAQTHVDNSFGNSFEFTKNNIYGTHVLLEACKVTGQIRR 126
Query: 191 ILFASTSEVYGDPEVHPQPETYWGHVN-----PIGPRACYDEAKRVAETLCYAYARHEDL 245
+ ST EVYG+ + + G+ P P Y K AE L AY R L
Sbjct: 127 FIHVSTDEVYGETDE----DADVGNHEASQLLPTNP---YSATKAGAEMLVMAYGRSYGL 179
Query: 246 SVRVARIFNTYGPRMHMNDGRVVSNFIIQALRNETITSDSSKSFTKFWDTLYIPHSFTQV 305
V R N YGP + +++ FI+ A++ + + +
Sbjct: 180 PVITTRGNNVYGP--NQFPEKLIPKFILLAMQGKPLP----------------------I 215
Query: 306 YGLGNQTRSFQYVTD 320
+G G+ RS+ Y D
Sbjct: 216 HGDGSNVRSYLYCED 230
>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 = 66.5 bits (163), Expect = 2e-12
Identities = 42/173 (24%), Positives = 65/173 (37%), Gaps = 24/173 (13%)
Query: 85 ILITGGAGFVGSHLVDKLMLMGHEVTVVDNFFTGRKENVEHWFGHPNFEIIHQDI----- 139
IL+TG GF+GS+LV L+ G+ V + E++ D+
Sbjct: 1 ILVTGATGFLGSNLVRALLAQGYRVRA----LVRSGSDAVL-LDGLPVEVVEGDLTDAAS 55
Query: 140 VTPLFVEVDEIYHLASPASP----PHYMFNPVKTIKTNTIGTINMLGLAKRVGAK-ILFA 194
+ D ++HLA+ S ++ +TN GT N+L A G + ++
Sbjct: 56 LAAAMKGCDRVFHLAAFTSLWAKDRKELY------RTNVEGTRNVLDAALEAGVRRVVHT 109
Query: 195 STSEVYGDPEVHPQPETYWGHVNPIGPRACYDEAKRVAETLCYAYARHEDLSV 247
S+ G P ET N Y +K +AE A E L V
Sbjct: 110 SSIAALGGPPDGRIDET--TPWNERPFPNDYYRSKLLAELEVLEAAA-EGLDV 159
>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 = 66.2 bits (162), Expect = 3e-12
Identities = 51/198 (25%), Positives = 77/198 (38%), Gaps = 43/198 (21%)
Query: 84 RILITGGAGFVGSHLVDKLMLMGHEVTVVDNFFTGRKENVEHWFGHPNFEIIHQ----DI 139
++L+TG GF+G LVDKL+ G EV + V + ++ + D
Sbjct: 1 KVLVTGANGFIGRALVDKLLSRGEEVRI----------AVRNAENAEPSVVLAELPDIDS 50
Query: 140 VTPLFVEVDEIYHLASPASPPHYMFNPVKT-----IKTNTIGTINMLGLAKRVGAK-ILF 193
T LF+ VD + HLA+ H M + K NT T + A R G K +F
Sbjct: 51 FTDLFLGVDAVVHLAARV---HVMNDQGADPLSDYRKVNTELTRRLARAAARQGVKRFVF 107
Query: 194 ASTSEVYGDPEVH--------PQPETYWGHVNPIGPRACYDEAKRVAETLCYAYARHEDL 245
S+ +V G+ V P P+ +G +K AE + +
Sbjct: 108 LSSVKVNGEGTVGAPFDETDPPAPQDAYG------------RSKLEAERALLELGASDGM 155
Query: 246 SVRVARIFNTYGPRMHMN 263
V + R YGP + N
Sbjct: 156 EVVILRPPMVYGPGVRGN 173
>gnl|CDD|182313 PRK10217, PRK10217, dTDP-glucose 4,6-dehydratase; Provisional.
Length = 355
Score = 64.7 bits (157), Expect = 1e-11
Identities = 70/257 (27%), Positives = 106/257 (41%), Gaps = 46/257 (17%)
Query: 83 RRILITGGAGFVGSHLVDKLM-LMGHEVTVVDNF-FTGRKENVEHWFGHPNFEIIHQDI- 139
R+ILITGGAGF+GS LV ++ V VVD + G ++ F DI
Sbjct: 2 RKILITGGAGFIGSALVRYIINETSDAVVVVDKLTYAGNLMSLAPVAQSERFAFEKVDIC 61
Query: 140 ----VTPLFVEV--DEIYHLASPASPPHYMFNPVKTIKTNTIGTINMLGLA--------- 184
+ +F E D + HLA+ + + P I+TN +GT +L A
Sbjct: 62 DRAELARVFTEHQPDCVMHLAAESHVDRSIDGPAAFIETNIVGTYTLLEAARAYWNALTE 121
Query: 185 -KRVGAKILFASTSEVYGDPEVHPQPETYWGHVNPIGPRACYDEAKRVAETLCYAYARHE 243
K+ + ST EVYGD +H + ++ P P + Y +K ++ L A+ R
Sbjct: 122 DKKSAFRFHHISTDEVYGD--LH-STDDFFTETTPYAPSSPYSASKASSDHLVRAWLRTY 178
Query: 244 DLSVRVARIFNTYGPRMHMNDGRVVSNFIIQALRNETITSDSSKSFTKFWDTLYIPHSFT 303
L + N YGP H + +++ I+ AL + +
Sbjct: 179 GLPTLITNCSNNYGP-YHFPE-KLIPLMILNALAGKPLP--------------------- 215
Query: 304 QVYGLGNQTRSFQYVTD 320
VYG G Q R + YV D
Sbjct: 216 -VYGNGQQIRDWLYVED 231
>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 = 63.4 bits (155), Expect = 1e-11
Identities = 44/203 (21%), Positives = 73/203 (35%), Gaps = 51/203 (25%)
Query: 87 ITGGAGFVGSHLVDKLMLMGHEVTVV-----DNFFTGRKENVEHWFGHPNFEIIHQ---- 137
+TG GF+G L++KL+ EV + + + + + + F+ +
Sbjct: 1 LTGATGFLGKVLLEKLLRSTPEVKIYCLVRAKDGESALERLRQELLKYGLFDRLKALERI 60
Query: 138 -----DIVTPLFV-----------EVDEIYHLASPASPPHYMFN-PVKTIK-TNTIGTIN 179
D+ P EVD I H A+ + F P ++ TN +GT
Sbjct: 61 IPVAGDLSEPNLGLSDEDFQELAEEVDVIIHNAATVN-----FVEPYSDLRATNVLGTRE 115
Query: 180 MLGLAKRVGAKIL-FASTSEVYGDPEVHPQ----------PETYWGHVNPIGPRACYDEA 228
+L LAK++ ST+ V G+ + P G N Y ++
Sbjct: 116 VLRLAKQMKKLPFHHVSTAYVNGERGGLLEEKPYKLDEDEPALLGGLPNG------YTQS 169
Query: 229 KRVAETLCYAYARHEDLSVRVAR 251
K +AE L L V + R
Sbjct: 170 KWLAEQLVREA--AGGLPVVIYR 190
>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 = 60.8 bits (148), Expect = 2e-10
Identities = 47/179 (26%), Positives = 78/179 (43%), Gaps = 28/179 (15%)
Query: 79 YQSKRRILITGGAGFVGSHLVDKLMLMGHEVT-------VVDNFF-TGRKENV-EHWFGH 129
+Q KR +L+TG GF GS L L +G +V N F +N G
Sbjct: 2 WQGKR-VLVTGHTGFKGSWLSLWLQELGAKVIGYSLDPPTNPNLFELANLDNKISSTRGD 60
Query: 130 PNFEIIHQDIVTPLFVEVDEIYHLASPASP---PHYMFNPVKTIKTNTIGTINMLGLAKR 186
++ + E + ++HLA A P Y +PV+T +TN +GT+N+L +
Sbjct: 61 IRDLNALREAIR--EYEPEIVFHLA--AQPLVRLSYK-DPVETFETNVMGTVNLLEAIRE 115
Query: 187 VG-AK-ILFASTSEVYGDPEVHPQPETYWGHV--NPIGPRACYDEAKRVAETLCYAYAR 241
G K ++ ++ + Y + E WG+ +P+G Y +K AE + +Y
Sbjct: 116 TGSVKAVVNVTSDKCYEN------KEWGWGYRENDPLGGHDPYSSSKGCAELIISSYRN 168
>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 = 59.3 bits (144), Expect = 5e-10
Identities = 35/135 (25%), Positives = 57/135 (42%), Gaps = 18/135 (13%)
Query: 85 ILITGGAGFVGSHLVDKLMLMGHEVTVVD---NFFTGRKENVEHWFGHPNFEIIHQDIVT 141
+ +TGG GF+G HLV +L+ G +V V+ + + E ++ D+
Sbjct: 1 VFVTGGTGFLGRHLVKRLLENGFKVLVLVRSESLGEAHERIEEAGLEADRVRVLEGDLTQ 60
Query: 142 PLF-----------VEVDEIYHLASPASPPHYMFNPVKTIKTNTIGTINMLGLAKRVGAK 190
P +VD + H A AS + +TN GT ++L LA R+ +
Sbjct: 61 PNLGLSAAASRELAGKVDHVIHCA--AS-YDFQAPNEDAWRTNIDGTEHVLELAARLDIQ 117
Query: 191 ILFA-STSEVYGDPE 204
ST+ V G+ E
Sbjct: 118 RFHYVSTAYVAGNRE 132
>gnl|CDD|178326 PLN02725, PLN02725,
GDP-4-keto-6-deoxymannose-3,5-epimerase-4-reductase.
Length = 306
Score = 58.9 bits (143), Expect = 8e-10
Identities = 67/271 (24%), Positives = 95/271 (35%), Gaps = 42/271 (15%)
Query: 86 LITGGAGFVGSHLVDKLMLMGHEVTVVDNFFTG---RKENVEHWFGHPNFEIIHQDIVTP 142
+ G G VGS +V KL +G V+ R+ +VE +F P
Sbjct: 1 FVAGHRGLVGSAIVRKLEALGFTNLVLRTHKELDLTRQADVEAFF----------AKEKP 50
Query: 143 LFVEVDEIYHLASPASPPHY-MFNPVKTIKTNTIGTINMLGLAKRVG-AKILFASTSEVY 200
+V A+ H M P I+ N N++ A R G K+LF +S +Y
Sbjct: 51 TYV-----ILAAAKVGGIHANMTYPADFIRENLQIQTNVIDAAYRHGVKKLLFLGSSCIY 105
Query: 201 GDPEVHPQPETYWGHVNPIGP-RACYDEAKRVAETLCYAYARHEDLSVRVARIFNTYGPR 259
P PET P P Y AK +C AY N YGP
Sbjct: 106 PKFAPQPIPETAL-LTGPPEPTNEWYAIAKIAGIKMCQAYRIQYGWDAISGMPTNLYGPH 164
Query: 260 --MHMNDGRVVSNFIIQALRNETITSDSSKSFTKFWDTLYIPHSFTQVYGLGNQTRSFQY 317
H + V+ I +F + V+G G+ R F +
Sbjct: 165 DNFHPENSHVIPALI-----------------RRFHEAKANGAPEVVVWGSGSPLREFLH 207
Query: 318 VTDLVDGLIALMNSNYTL-PVNLGNPTEHSI 347
V DL D ++ LM VN+G+ E +I
Sbjct: 208 VDDLADAVVFLMRRYSGAEHVNVGSGDEVTI 238
>gnl|CDD|236156 PRK08125, PRK08125, bifunctional UDP-glucuronic acid
decarboxylase/UDP-4-amino-4-deoxy-L-arabinose
formyltransferase; Validated.
Length = 660
Score = 59.2 bits (144), Expect = 1e-09
Identities = 81/284 (28%), Positives = 129/284 (45%), Gaps = 46/284 (16%)
Query: 84 RILITGGAGFVGSHLVDKLMLMGH-EVTVVDNFFTGRKENVEHWFGHPNFEIIHQDI-VT 141
R+LI G GF+G+HL ++L+ + EV +D G + + + GHP F + DI +
Sbjct: 317 RVLILGVNGFIGNHLTERLLRDDNYEVYGLD---IG-SDAISRFLGHPRFHFVEGDISIH 372
Query: 142 PLFVE-----VDEIYHLASPASPPHYMFNPVKTIKTNTIGTINMLGLAKRVGAKILFAST 196
++E D + L + A+P Y NP++ + + + ++ + +I+F ST
Sbjct: 373 SEWIEYHIKKCDVVLPLVAIATPIEYTRNPLRVFELDFEENLKIIRYCVKYNKRIIFPST 432
Query: 197 SEVYG---DPEVHPQPETYWGHVNPIG-PRACYDEAKRVAETLCYAYARHEDLSVRVARI 252
SEVYG D +T V PI R Y +K++ + + +AY E L + R
Sbjct: 433 SEVYGMCTDKYF--DEDTSNLIVGPINKQRWIYSVSKQLLDRVIWAYGEKEGLRFTLFRP 490
Query: 253 FNTYGPRM-HMNDGRVVSNFIIQALRNETITSDSSKSFTKFWDTLYIPHSFTQVYGLGNQ 311
FN GPR+ ++N R+ SS++ T+ L V G G Q
Sbjct: 491 FNWMGPRLDNLNAARI----------------GSSRAITQLILNLVEGSPIKLVDG-GKQ 533
Query: 312 TRSFQYVTDLVDGLIALM----NSNYTLP---VNLGNPT-EHSI 347
R F TD+ DG+ AL N + +N+GNP E SI
Sbjct: 534 KRCF---TDIRDGIEALFRIIENKDNRCDGQIINIGNPDNEASI 574
>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 = 56.9 bits (138), Expect = 4e-09
Identities = 64/234 (27%), Positives = 92/234 (39%), Gaps = 48/234 (20%)
Query: 81 SKRRILITGGAGFVGSHLVDKLMLMG-HEVTVVDNFFTGRKEN--------VEHWFGHPN 131
+ IL+TGGAG +GS LV +++ G ++ V D R EN + F H
Sbjct: 1 KGKTILVTGGAGSIGSELVRQILKFGPKKLIVFD-----RDENKLHELVRELRSRFPHDK 55
Query: 132 FEIIHQDIVTPLFV-------EVDEIYHLASPASPPHYMFNPVKTIKTNTIGTINMLGLA 184
I D+ + D ++H A+ P NP + IKTN +GT N++ A
Sbjct: 56 LRFIIGDVRDKERLRRAFKERGPDIVFHAAALKHVPSMEDNPEEAIKTNVLGTKNVIDAA 115
Query: 185 KRVG-AKILFASTSEVYGDPEVHPQPETYWGHVNPIGPRACYDEAKRVAETLCYAYA-RH 242
G K + ST D V+P VN +G KRVAE L A
Sbjct: 116 IENGVEKFVCIST-----DKAVNP--------VNVMG------ATKRVAEKLLLAKNEYS 156
Query: 243 EDLSVRVARIFNTYGPRMHMNDGRVVSNFIIQALRNETITSDSSKSFTKFWDTL 296
R N G R G V+ F Q + +T + T+F+ T+
Sbjct: 157 SSTKFSTVRFGNVLGSR-----GSVLPLFKKQIKKGGPLTV-TDPDMTRFFMTI 204
>gnl|CDD|236649 PRK10084, PRK10084, dTDP-glucose 4,6 dehydratase; Provisional.
Length = 352
Score = 56.7 bits (137), Expect = 5e-09
Identities = 68/261 (26%), Positives = 106/261 (40%), Gaps = 48/261 (18%)
Query: 84 RILITGGAGFVGSHLVDKLMLMGHEVTV-VDNF-FTGRKENVEHWFGHPNFEIIHQDI-- 139
+IL+TGGAGF+GS +V ++ + V VD + G E++ + H DI
Sbjct: 2 KILVTGGAGFIGSAVVRHIINNTQDSVVNVDKLTYAGNLESLADVSDSERYVFEHADICD 61
Query: 140 ---VTPLFVEV--DEIYHLASPASPPHYMFNPVKTIKTNTIGTINMLGLAKR------VG 188
+ +F + D + HLA+ + + P I+TN +GT +L A+
Sbjct: 62 RAELDRIFAQHQPDAVMHLAAESHVDRSITGPAAFIETNIVGTYVLLEAARNYWSALDED 121
Query: 189 AKILF----ASTSEVYGD----PEVHPQPE-TYWGHVNPIGPRACYDEAKRVAETLCYAY 239
K F ST EVYGD EV E + P + Y +K ++ L A+
Sbjct: 122 KKNAFRFHHISTDEVYGDLPHPDEVENSEELPLFTETTAYAPSSPYSASKASSDHLVRAW 181
Query: 240 ARHEDLSVRVARIFNTYGPRMHMNDGRVVSNFIIQALRNETITSDSSKSFTKFWDTLYIP 299
R L V N YGP H + +++ I+ AL + +
Sbjct: 182 LRTYGLPTIVTNCSNNYGP-YHFPE-KLIPLVILNALEGKPLP----------------- 222
Query: 300 HSFTQVYGLGNQTRSFQYVTD 320
+YG G+Q R + YV D
Sbjct: 223 -----IYGKGDQIRDWLYVED 238
>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 = 56.2 bits (136), Expect = 5e-09
Identities = 51/184 (27%), Positives = 68/184 (36%), Gaps = 22/184 (11%)
Query: 85 ILITGGAGFVGSHLVDKLMLMGHEVTVVDNFFTGRKENVEHWFGHPNFEIIHQDIVTP-- 142
IL+TG AG +G L +L V VD R P E + DI P
Sbjct: 1 ILVTGAAGGLGRLLARRL-AASPRVIGVDGLDRRRPPG-----SPPKVEYVRLDIRDPAA 54
Query: 143 ----LFVEVDEIYHLASPASPPHYMFNPVKTIKTNTIGTINMLGLAKRVGAK-ILFASTS 197
E D + HLA PP + + + N GT N+L G ++ S+
Sbjct: 55 ADVFREREADAVVHLAFILDPPR---DGAERHRINVDGTQNVLDACAAAGVPRVVVTSSV 111
Query: 198 EVYGDPEVHPQPETYW--GHVNPIGPRACYDEAKRVAETLCYAY-ARHEDLSVRVARIFN 254
VYG +P P T + P Y K E L + RH +L+V V R
Sbjct: 112 AVYGAHPDNPAPLTEDAPLRGS---PEFAYSRDKAEVEQLLAEFRRRHPELNVTVLRPAT 168
Query: 255 TYGP 258
GP
Sbjct: 169 ILGP 172
>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 = 53.9 bits (130), Expect = 1e-08
Identities = 35/125 (28%), Positives = 52/125 (41%), Gaps = 17/125 (13%)
Query: 85 ILITGGAGFVGSHLVDKLMLMGHEVTVVDNFFTGRKENVEHWFGHPNFEIIHQDI----- 139
ILI G GF+G L +L+ GHEVT++ R ++ D+
Sbjct: 1 ILILGATGFIGRALARELLEQGHEVTLLV-----RNTKRLSKEDQEPVAVVEGDLRDLDS 55
Query: 140 VTPLFVEVDEIYHLASPASPPHYMFNPVKTIKTNTIGTINMLGLAKRVGAK-ILFASTSE 198
++ VD + HL A P + + + GT N+L AK G K +F S+
Sbjct: 56 LSDAVQGVDVVIHL---AGAPRDTRDF---CEVDVEGTRNVLEAAKEAGVKHFIFISSLG 109
Query: 199 VYGDP 203
YGD
Sbjct: 110 AYGDL 114
>gnl|CDD|187565 cd05255, SQD1_like_SDR_e, UDP_sulfoquinovose_synthase (Arabidopsis
thaliana SQD1 and related proteins), extended (e) SDRs.
Arabidopsis thaliana UDP-sulfoquinovose-synthase (
SQD1), an extended SDR, catalyzes the transfer of
SO(3)(-) to UDP-glucose in the biosynthesis of plant
sulfolipids. Members of this subgroup share the
conserved SDR catalytic residues, and a partial match to
the characteristic extended-SDR 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 = 382
Score = 55.5 bits (134), Expect = 2e-08
Identities = 68/302 (22%), Positives = 97/302 (32%), Gaps = 78/302 (25%)
Query: 84 RILITGGAGFVGSHLVDKLMLMGHEVTVVDNFFTGR----------------KENVEHWF 127
++LI GG G+ G L GHEV +VDN R E + W
Sbjct: 2 KVLILGGDGYCGWPTALHLSKRGHEVCIVDNLVRRRIDVELGLESLTPIASIHERLRAWK 61
Query: 128 GHPNFEIIHQ--DIVTPLFV-------EVDEIYHLASPASPPHYMFN---PVKTIKTNTI 175
I D F+ E D + H A S P+ M + T N I
Sbjct: 62 ELTGKTIEFYVGDACDYEFLAELLASHEPDAVVHFAEQRSAPYSMIDREHANYTQHNNVI 121
Query: 176 GTINMLGLAKRVG--AKILFASTSEVYGDPEVHPQPETYWGHVN---------PIGPRAC 224
GT+N+L K ++ T YG P + PE Y + P +
Sbjct: 122 GTLNLLFAIKEFDPDCHLVKLGTMGEYGTPNI-DIPEGYITIEHNGRRDTLPYPKQAGSW 180
Query: 225 YDEAKRVAETLCYAYARHEDLS---VRVARIFNTYGPRMHMND------------GRVVS 269
Y +K + + + ++ T ++ G V++
Sbjct: 181 YHLSKVHDSHNIMFACKAWGIRITDLNQGVVYGTKTEETEADERLINRFDYDGVFGTVLN 240
Query: 270 NFIIQALRNETITSDSSKSFTKFWDTLYIPHSFTQVYGLGNQTRSFQYVTDLVDGL-IAL 328
F +QA I H T VYG G QTR F + D V L +AL
Sbjct: 241 RFCVQAA---------------------IGHPLT-VYGKGGQTRGFISIRDTVQCLELAL 278
Query: 329 MN 330
N
Sbjct: 279 EN 280
>gnl|CDD|233427 TIGR01472, gmd, GDP-mannose 4,6-dehydratase. Alternate name:
GDP-D-mannose dehydratase. This enzyme converts
GDP-mannose to GDP-4-dehydro-6-deoxy-D-mannose, the
first of three steps for the conversion of GDP-mannose
to GDP-fucose in animals, plants, and bacteria. In
bacteria, GDP-L-fucose acts as a precursor of surface
antigens such as the extracellular polysaccharide
colanic acid of E. coli. Excluded from this model are
members of the clade that score poorly because of highly
dervied (phylogenetically long-branch) sequences, e.g.
Aneurinibacillus thermoaerophilus Gmd, described as a
bifunctional GDP-mannose
4,6-dehydratase/GDP-6-deoxy-D-lyxo-4-hexulose reductase
(PUBMED:11096116) [Cell envelope, Biosynthesis and
degradation of surface polysaccharides and
lipopolysaccharides].
Length = 343
Score = 54.8 bits (132), Expect = 2e-08
Identities = 54/177 (30%), Positives = 78/177 (44%), Gaps = 39/177 (22%)
Query: 86 LITGGAGFVGSHLVDKLMLMGHEVTVV----DNFFTGRKENVEHWFGHP------NFEII 135
LITG G GS+L + L+ G+EV + +F T R +EH + P ++
Sbjct: 4 LITGITGQDGSYLAEFLLEKGYEVHGLIRRSSSFNTQR---IEHIYEDPHNVNKARMKLH 60
Query: 136 HQDIVTPL-------FVEVDEIYHLASPASPPHYMFNPVKTIKTNTIGTINML------G 182
+ D+ ++ EIY+LA+ + P T + IGT+ +L G
Sbjct: 61 YGDLTDSSNLRRIIDEIKPTEIYNLAAQSHVKVSFEIPEYTADVDGIGTLRLLEAVRTLG 120
Query: 183 LAKRVGAKILFASTSEVYGDPEVHPQPETYWGHVNPIGPRACYDEAKRVAETLCYAY 239
L K V K ASTSE+YG + PQ ET P PR+ Y AK YA+
Sbjct: 121 LIKSV--KFYQASTSELYGKVQEIPQNET-----TPFYPRSPYAAAK------LYAH 164
>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 = 53.9 bits (130), Expect = 3e-08
Identities = 43/164 (26%), Positives = 67/164 (40%), Gaps = 22/164 (13%)
Query: 86 LITGGAGFVGSHLVDKLMLMGH--EVTVVDNFFTGRKENVEHWFGHPNFEII--HQ-DIV 140
L+TGG GF+G H+V L+ G EV V D + + E ++I + D+
Sbjct: 1 LVTGGGGFLGRHIVRLLLREGELQEVRVFD-----LRFSPELLEDFSKLQVITYIEGDVT 55
Query: 141 TPLFVE-----VDEIYHLASPASPPHYMFNPVKTIKTNTIGTINMLGLAKRVGAKIL-FA 194
+ D + H A+ +K N GT N+L + G ++L +
Sbjct: 56 DKQDLRRALQGSDVVIHTAA-IIDVFGKAYRDTIMKVNVKGTQNVLDACVKAGVRVLVYT 114
Query: 195 STSEVYGDPEVHPQPETYWGHVN---PIGPRACYDEAKRVAETL 235
S+ EV G P + QP G + Y E+K +AE L
Sbjct: 115 SSMEVVG-PNSYGQP-IVNGDETTPYESTHQDPYPESKALAEKL 156
>gnl|CDD|187538 cd05227, AR_SDR_e, aldehyde reductase, extended (e) SDRs. This
subgroup contains aldehyde reductase of the extended
SDR-type and related proteins. Aldehyde reductase I (aka
carbonyl reductase) is an NADP-binding SDR; it has an
NADP-binding motif consensus that is slightly different
from the canonical SDR form and lacks the Asn of the
extended SDR active site tetrad. Aldehyde reductase I
catalyzes the NADP-dependent reduction of ethyl
4-chloro-3-oxobutanoate to ethyl
(R)-4-chloro-3-hydroxybutanoate. Extended SDRs are
distinct from classical SDRs. In addition to the
Rossmann fold (alpha/beta folding pattern with a central
beta-sheet) core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids. Extended SDRs are a
diverse collection of proteins, and include isomerases,
epimerases, oxidoreductases, and lyases; they typically
have a TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 301
Score = 53.0 bits (128), Expect = 6e-08
Identities = 39/187 (20%), Positives = 71/187 (37%), Gaps = 32/187 (17%)
Query: 84 RILITGGAGFVGSHLVDKLMLMGHEVTVVDNFFTGR----KENVEHWFGH----PNFEII 135
+L+TG GF+ SH+V++L+ G++V T R ++ E +
Sbjct: 1 LVLVTGATGFIASHIVEQLLKAGYKVR-----GTVRSLSKSAKLKALLKAAGYNDRLEFV 55
Query: 136 HQDIVT------PLFVEVDEIYHLASPASPPHYMFNPVKT--IKTNTIGTINMLGLAKRV 187
D +T VD + H+ASP + + I GT+N+L AK
Sbjct: 56 IVDDLTAPNAWDEALKGVDYVIHVASPF---PFTGPDAEDDVIDPAVEGTLNVLEAAKAA 112
Query: 188 GA--KILFASTSEVYGDPEVHPQPETY----WGHVN--PIGPRACYDEAKRVAETLCYAY 239
G+ +++ S+ GDP + + W + Y +K +AE + +
Sbjct: 113 GSVKRVVLTSSVAAVGDPTAEDPGKVFTEEDWNDLTISKSNGLDAYIASKTLAEKAAWEF 172
Query: 240 ARHEDLS 246
+
Sbjct: 173 VKENKPK 179
>gnl|CDD|224011 COG1086, COG1086, Predicted nucleoside-diphosphate sugar epimerases
[Cell envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 588
Score = 53.8 bits (130), Expect = 7e-08
Identities = 59/232 (25%), Positives = 89/232 (38%), Gaps = 46/232 (19%)
Query: 83 RRILITGGAGFVGSHLVDKLMLMG-HEVTVVD----NFFTGRKENVEHWFGHPNFEIIHQ 137
+ +L+TGG G +GS L +++ E+ + + E E F
Sbjct: 251 KTVLVTGGGGSIGSELCRQILKFNPKEIILFSRDEYKLYLIDMELREK-FPELKLRFYIG 309
Query: 138 DI-----VTPLF--VEVDEIYHLASPASPPHYMFNPVKTIKTNTIGTINMLGLAKRVG-A 189
D+ V +VD ++H A+ P +NP + IKTN +GT N+ A + G
Sbjct: 310 DVRDRDRVERAMEGHKVDIVFHAAALKHVPLVEYNPEEAIKTNVLGTENVAEAAIKNGVK 369
Query: 190 KILFASTSEVYGDPEVHPQPETYWGHVNPIGPRACYDEAKRVAETLCYAYARH---EDLS 246
K + ST D V+P N +G KR+AE L A R+
Sbjct: 370 KFVLIST-----DKAVNP--------TNVMG------ATKRLAEKLFQAANRNVSGTGTR 410
Query: 247 VRVARIFNTYGPRMHMNDGRVVSNFIIQALRNE--TITSDSSKSFTKFWDTL 296
V R N G R G V+ F Q T+T T+F+ T+
Sbjct: 411 FCVVRFGNVLGSR-----GSVIPLFKKQIAEGGPLTVT---DPDMTRFFMTI 454
>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 = 52.4 bits (126), Expect = 9e-08
Identities = 59/258 (22%), Positives = 85/258 (32%), Gaps = 69/258 (26%)
Query: 84 RILITGGAGFVGSHLVDKLMLMGHEVTVVDNFFTGRKENVEHWFGHPNFEIIHQDIVTPL 143
+ILITG GF+G +L+ +L E D FF R+ +
Sbjct: 2 KILITGAKGFIGKNLIARL----KEQKDDDIFFYDRESDESE---------------LDD 42
Query: 144 FV-EVDEIYHLASPASPPHYMFNPVKTIKTNTIGTINMLGLAKRVGAK--ILFASTSEVY 200
F+ D I+HLA P + N T +L R G K IL +S+ +
Sbjct: 43 FLQGADFIFHLAGVNRPKD----EAEFESGNVGLTERLLDALTRNGKKPPILLSSSIQAA 98
Query: 201 GDPEVHPQPETYWGHVNPIGPRACYDEAKRVAETLCYAYARHEDLSVRVARIFNTYGPRM 260
D NP Y ++K AE L YAR V + R+ N +G
Sbjct: 99 LD--------------NP------YGKSKLAAEELLQEYARETGAPVYIYRLPNVFGKWC 138
Query: 261 HMNDGRVVSNFIIQALRNETITSDSSKSFTKFWDTLYIPHSFTQVYGLGNQTRSFQYVTD 320
N V+ F R+ I + + Y+ D
Sbjct: 139 RPNYNSAVATFCYNIARDLPIQINDP-----------------------AAELTLVYIDD 175
Query: 321 LVDGLIALMNSNYTLPVN 338
+VD LI L+ T
Sbjct: 176 VVDELIQLLEGAPTYSGG 193
>gnl|CDD|187546 cd05235, SDR_e1, extended (e) SDRs, subgroup 1. This family
consists of an SDR module of multidomain proteins
identified as putative polyketide sythases fatty acid
synthases (FAS), and nonribosomal peptide synthases,
among others. However, unlike the usual ketoreductase
modules of FAS and polyketide synthase, these domains
are related to the extended SDRs, and have canonical
NAD(P)-binding motifs and an active site tetrad.
Extended SDRs are distinct from classical SDRs. In
addition to the Rossmann fold (alpha/beta folding
pattern with a central beta-sheet) core region typical
of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 290
Score = 51.5 bits (124), Expect = 2e-07
Identities = 38/188 (20%), Positives = 67/188 (35%), Gaps = 34/188 (18%)
Query: 84 RILITGGAGFVGSHLVDKLMLMGHEVTVV----------------DNFFTGRKENVEHWF 127
+L+TG GF+G++L+ +L+ + + DN +
Sbjct: 1 TVLLTGATGFLGAYLLRELLKRKNVSKIYCLVRAKDEEAALERLIDNLKEYGLNLWDELE 60
Query: 128 GHPNFEIIHQDIVTPLFV-----------EVDEIYHLASPASPPHYMFNPVKTIKTNTIG 176
+++ D+ P EVD I H + ++++ + N +G
Sbjct: 61 L-SRIKVVVGDLSKPNLGLSDDDYQELAEEVDVIIHNGANV---NWVYPYEELKPANVLG 116
Query: 177 TINMLGLAKRVGAKIL-FASTSEVYGDPEVHPQPETYWGH--VNPIGPRACYDEAKRVAE 233
T +L LA K L F ST V+ E + + + G Y ++K VAE
Sbjct: 117 TKELLKLAATGKLKPLHFVSTLSVFSAEEYNALDDEESDDMLESQNGLPNGYIQSKWVAE 176
Query: 234 TLCYAYAR 241
L A
Sbjct: 177 KLLREAAN 184
>gnl|CDD|233954 TIGR02622, CDP_4_6_dhtase, CDP-glucose 4,6-dehydratase. Members of
this protein family are CDP-glucose 4,6-dehydratase from
a variety of Gram-negative and Gram-positive bacteria.
Members typically are encoded next to a gene that
encodes a glucose-1-phosphate cytidylyltransferase,
which produces the substrate, CDP-D-glucose, used by
this enzyme to produce CDP-4-keto-6-deoxyglucose [Cell
envelope, Biosynthesis and degradation of surface
polysaccharides and lipopolysaccharides].
Length = 349
Score = 51.1 bits (123), Expect = 3e-07
Identities = 44/172 (25%), Positives = 78/172 (45%), Gaps = 23/172 (13%)
Query: 82 KRRILITGGAGFVGSHLVDKLMLMGHEV--------TVVDNF-FTGRKENVEHWFGHPNF 132
+++L+TG GF GS L L+ +G EV T + F + +E FG
Sbjct: 4 GKKVLVTGHTGFKGSWLSLWLLELGAEVYGYSLDPPTSPNLFELLNLAKKIEDHFG---- 59
Query: 133 EIIHQDIVTPLFVEV--DEIYHLASPASPPHYMFNPVKTIKTNTIGTINMLGLAKRVG-A 189
+I + E + ++HLA+ +P++T +TN +GT+N+L + +G
Sbjct: 60 DIRDAAKLRKAIAEFKPEIVFHLAAQPLVRKSYADPLETFETNVMGTVNLLEAIRAIGSV 119
Query: 190 KILFASTSEVYGDPEVHPQPETYWGHV--NPIGPRACYDEAKRVAETLCYAY 239
K + TS+ + + E WG+ +P+G Y +K AE + +Y
Sbjct: 120 KAVVNVTSD-----KCYRNDEWVWGYRETDPLGGHDPYSSSKACAELVIASY 166
>gnl|CDD|224016 COG1091, RfbD, dTDP-4-dehydrorhamnose reductase [Cell envelope
biogenesis, outer membrane].
Length = 281
Score = 50.4 bits (121), Expect = 5e-07
Identities = 44/182 (24%), Positives = 65/182 (35%), Gaps = 36/182 (19%)
Query: 84 RILITGGAGFVGSHLVDKLMLMGHEVTVVDNFFTGRKENVEHWFGHPNFEIIHQDIVTPL 143
+ILITG G +G+ L + + EV D +I D V +
Sbjct: 2 KILITGANGQLGTELR-RALPGEFEVIATD---------------RAELDITDPDAVLEV 45
Query: 144 FVEV--DEIYHLA-----SPASPPHYMFNPVKTIKTNTIGTINMLGLAKRVGAKILFAST 196
E D + + A A P N G N+ A VGA+++ ST
Sbjct: 46 IRETRPDVVINAAAYTAVDKAES-----EPELAFAVNATGAENLARAAAEVGARLVHIST 100
Query: 197 SEVYGDPEVHPQPETYWGHVNPIGPRACYDEAKRVAETLCYAYA-RHEDLSVRVARIFNT 255
V+ + P ET NP+ Y +K E A RH L +R + ++
Sbjct: 101 DYVFDGEKGGPYKET--DTPNPLN---VYGRSKLAGEEAVRAAGPRH--LILRTSWVYGE 153
Query: 256 YG 257
YG
Sbjct: 154 YG 155
>gnl|CDD|178259 PLN02653, PLN02653, GDP-mannose 4,6-dehydratase.
Length = 340
Score = 50.2 bits (120), Expect = 7e-07
Identities = 55/200 (27%), Positives = 75/200 (37%), Gaps = 39/200 (19%)
Query: 86 LITGGAGFVGSHLVDKLMLMGHEVTVV----DNFFTGRKENVEHWFGHPNFEIIHQ---- 137
LITG G GS+L + L+ G+EV + NF T R +++ HPN +
Sbjct: 10 LITGITGQDGSYLTEFLLSKGYEVHGIIRRSSNFNTQRLDHIYI-DPHPNKARMKLHYGD 68
Query: 138 -----------DIVTPLFVEVDEIYHLASPASPPHYMFNPVKTIKTNTIGTINML----- 181
D + P DE+Y+LA+ + P T G + +L
Sbjct: 69 LSDASSLRRWLDDIKP-----DEVYNLAAQSHVAVSFEMPDYTADVVATGALRLLEAVRL 123
Query: 182 -GLAKRVGAKILFASTSEVYGD-PEVHPQPETYWGHVNPIGPRACYDEAKRVAETLCYAY 239
G K A +SE+YG P PQ ET P PR+ Y AK A Y
Sbjct: 124 HGQETGRQIKYYQAGSSEMYGSTPP--PQSET-----TPFHPRSPYAVAKVAAHWYTVNY 176
Query: 240 ARHEDLSVRVARIFNTYGPR 259
L +FN PR
Sbjct: 177 REAYGLFACNGILFNHESPR 196
>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 = 49.6 bits (119), Expect = 9e-07
Identities = 46/176 (26%), Positives = 75/176 (42%), Gaps = 26/176 (14%)
Query: 84 RILITGGAGFVGSHLVDKLMLMGHEVTVVDNFFTGRKENVEHWFGHPNFEIIHQDIVTPL 143
++L+TG GFVGS +V L+ G EV V+ T + N+E + EI+ D+ P
Sbjct: 2 KVLVTGATGFVGSAVVRLLLEQGEEVRVLVR-PTSDRRNLEGL----DVEIVEGDLRDPA 56
Query: 144 FVE-----VDEIYHLASPASPPHYMF---NPVKTIKTNTIGTINMLGLAKRVGAK-ILFA 194
+ ++H+A+ Y +P + N GT N+L A G + +++
Sbjct: 57 SLRKAVAGCRALFHVAA-----DYRLWAPDPEEMYAANVEGTRNLLRAALEAGVERVVYT 111
Query: 195 STSEVYGDPEVHPQP--ETYWGHV-NPIGPRACYDEAKRVAETLCYAYARHEDLSV 247
S+ G P ET + + IG Y +K +AE A + L V
Sbjct: 112 SSVATLGVRG-DGTPADETTPSSLDDMIGH---YKRSKFLAEQAALEMAAEKGLPV 163
>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 = 47.4 bits (113), Expect = 6e-06
Identities = 48/213 (22%), Positives = 81/213 (38%), Gaps = 40/213 (18%)
Query: 85 ILITGGAGFVGSHLVDKLMLMGHEVTVV----------------DNF-------FTGRKE 121
+L+TG GF+G++L+++L+ + V+ + +E
Sbjct: 2 VLLTGATGFLGAYLLEELLRRSTQAKVICLVRAASEEHAMERLREALRSYRLWHEDLARE 61
Query: 122 NVEHWFGH---PNFEIIHQDIVTPLFVEVDEIYHLASPAS---PPHYMFNPVKTIKTNTI 175
+E G P + + L VD I H + + P + N +
Sbjct: 62 RIEVVAGDLSEPRLGLSDAEWER-LAENVDTIVHNGALVNWVYPYSELR------GANVL 114
Query: 176 GTINMLGLAKRVGAKIL-FASTSEVYGDPEVHPQPETYWGHVNPIGPRACYDEAKRVAET 234
GT +L LA AK L + ST V ++ E P G Y ++K VAE
Sbjct: 115 GTREVLRLAASGRAKPLHYVSTISVGAAIDLSTVTEDDATVTPPPGLAGGYAQSKWVAEL 174
Query: 235 LCY-AYARHEDLSV-RVARI-FNTYGPRMHMND 264
L A R +++ R RI N+Y ++ +D
Sbjct: 175 LVREASDRGLPVTIVRPGRILGNSYTGAINSSD 207
>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 = 47.0 bits (112), Expect = 7e-06
Identities = 56/207 (27%), Positives = 85/207 (41%), Gaps = 29/207 (14%)
Query: 84 RILITGGAGFVGSHLVDKLM-LMGHEVTVVDNFFTGRKENVEHWFGHPNFEII----HQD 138
L+ GG+GF+G HLV++L+ V V D T E G F QD
Sbjct: 1 SCLVVGGSGFLGRHLVEQLLRRGNPTVHVFDIRPT--FELDPSSSGRVQFHTGDLTDPQD 58
Query: 139 IVTPL-FVEVDEIYHLASPASPPHYMFNPVKTIKTNTIGTINMLGLAKRVGAKILF--AS 195
+ + ++H ASP H N K N GT N++ ++ G K L +S
Sbjct: 59 LEKAFNEKGPNVVFHT---ASPDHGS-NDDLYYKVNVQGTRNVIEACRKCGVKKLVYTSS 114
Query: 196 TSEVYGDPEVHPQPETYWGHVNPIGPRACYDEAKRVAETLCY-AYARHEDL---SVRVAR 251
S V+ ++ E+ P + Y+E K +AE L A L ++R A
Sbjct: 115 ASVVFNGQDIINGDESL---PYPDKHQDAYNETKALAEKLVLKANDPESGLLTCALRPAG 171
Query: 252 IFNTYGPRMHMNDGRVVSNFIIQALRN 278
IF GP D ++V ++A +N
Sbjct: 172 IF---GPG----DRQLVPGL-LKAAKN 190
>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 = 46.8 bits (112), Expect = 7e-06
Identities = 23/74 (31%), Positives = 34/74 (45%), Gaps = 12/74 (16%)
Query: 84 RILITGGAGFVGSHLVDKLMLMGHEVTVVDNFFTGRKENVEHWFGHPNFEIIHQDIVTPL 143
+I+ITGG GF+G L +L GHEV V+ R+ E+I D ++
Sbjct: 1 KIVITGGTGFIGRALTRRLTAAGHEVVVL-----SRRPGKAEG----LAEVITWDGLSLG 51
Query: 144 FVE---VDEIYHLA 154
E D + +LA
Sbjct: 52 PWELPGADAVINLA 65
>gnl|CDD|223774 COG0702, COG0702, Predicted nucleoside-diphosphate-sugar epimerases
[Cell envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 275
Score = 46.4 bits (110), Expect = 8e-06
Identities = 16/52 (30%), Positives = 22/52 (42%), Gaps = 4/52 (7%)
Query: 83 RRILITGGAGFVGSHLVDKLMLMGHEVTVVDNFFTGRKENVEHWFGHPNFEI 134
+IL+TG GFVG +V +L+ GHEV E G +
Sbjct: 1 MKILVTGATGFVGGAVVRELLARGHEVRAA----VRNPEAAAALAGGVEVVL 48
>gnl|CDD|187661 cd08958, FR_SDR_e, flavonoid reductase (FR), extended (e) SDRs.
This subgroup contains FRs of the extended SDR-type and
related proteins. These FRs act in the NADP-dependent
reduction of flavonoids, ketone-containing plant
secondary metabolites; they have the characteristic
active site triad of the SDRs (though not the upstream
active site Asn) and a NADP-binding motif that is very
similar to the typical extended SDR motif. Extended SDRs
are distinct from classical SDRs. In addition to the
Rossmann fold (alpha/beta folding pattern with a central
beta-sheet) core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids. Extended SDRs are a
diverse collection of proteins, and include isomerases,
epimerases, oxidoreductases, and lyases; they typically
have a TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 293
Score = 45.6 bits (109), Expect = 1e-05
Identities = 44/185 (23%), Positives = 74/185 (40%), Gaps = 36/185 (19%)
Query: 88 TGGAGFVGSHLVDKLMLMGHEV-TVVDNFFTGRKENVEHWFGHPNF----EIIHQDIVTP 142
TG +GF+GS LV +L+ G+ V V + G ++ V H ++ D++
Sbjct: 4 TGASGFIGSWLVKRLLQRGYTVRATVRD--PGDEKKVAHLLELEGAKERLKLFKADLLDY 61
Query: 143 L-FVEV----DEIYHLASP-----ASPPHYMFNPVKTIKTNTIGTINML------GLAKR 186
F D ++H+ASP P M P +K GT+N+L KR
Sbjct: 62 GSFDAAIDGCDGVFHVASPVDFDSEDPEEEMIEP--AVK----GTLNVLEACAKAKSVKR 115
Query: 187 VGAKILFASTSEVYGDPEVHPQP---ETYWGHVNPIGPRAC-YDEAKRVAETLCYAYARH 242
V + +S + V +P E+ W ++ Y +K +AE + +A
Sbjct: 116 V---VFTSSVAAVVWNPNRGEGKVVDESCWSDLDFCKKTKLWYALSKTLAEKAAWEFAEE 172
Query: 243 EDLSV 247
L +
Sbjct: 173 NGLDL 177
>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 = 45.4 bits (108), Expect = 2e-05
Identities = 21/48 (43%), Positives = 28/48 (58%), Gaps = 8/48 (16%)
Query: 83 RRILITGGAGFVGSHLVDKLMLMGHEVTVVDNFFTGRKEN-----VEH 125
+ILI GG F+G LV++L+ GH+VTV F GR + VEH
Sbjct: 1 MKILIIGGTRFIGKALVEELLAAGHDVTV---FNRGRTKPDLPEGVEH 45
>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 = 45.5 bits (108), Expect = 2e-05
Identities = 44/197 (22%), Positives = 69/197 (35%), Gaps = 35/197 (17%)
Query: 84 RILITGGAGFVGSHLVDKLMLMGHEVTVVDNFFTGRKENVEHWFGHPNFEIIHQDIVTPL 143
RILITG G +G LV +L G V + ++ + + L
Sbjct: 1 RILITGANGQLGRELVQQLSPEGRVVVALT---------------RSQLDLTDPEALERL 45
Query: 144 FVEV--DEIYHLASPASPPHYMFNPVKTIKTNTIGTINMLGLAKRVGAKILFASTSEVYG 201
+ D + + A+ +P K N + N+ A R GA+++ ST V+
Sbjct: 46 LRAIRPDAVVNTAAYTDVDGAESDPEKAFAVNALAPQNLARAAARHGARLVHISTDYVFD 105
Query: 202 DPEVHPQPETYWGHVNPIGPRACYDEAKRVAETLCYAYA-RHEDLSVRVARIFNTYGPRM 260
P E NP+ Y ++K E A L VR + ++ G R
Sbjct: 106 GEGKRPYRED--DATNPLN---VYGQSKLAGEQAVRAAGPNA--LIVRTSWLYGGGGGR- 157
Query: 261 HMNDGRVVSNFIIQALR 277
NF+ LR
Sbjct: 158 ---------NFVRTMLR 165
>gnl|CDD|224015 COG1090, COG1090, Predicted nucleoside-diphosphate sugar epimerase
[General function prediction only].
Length = 297
Score = 44.9 bits (107), Expect = 3e-05
Identities = 14/28 (50%), Positives = 19/28 (67%)
Query: 85 ILITGGAGFVGSHLVDKLMLMGHEVTVV 112
ILITGG G +G L +L GH+VT++
Sbjct: 1 ILITGGTGLIGRALTARLRKGGHQVTIL 28
>gnl|CDD|225857 COG3320, COG3320, Putative dehydrogenase domain of multifunctional
non-ribosomal peptide synthetases and related enzymes
[Secondary metabolites biosynthesis, transport, and
catabolism].
Length = 382
Score = 44.7 bits (106), Expect = 4e-05
Identities = 47/221 (21%), Positives = 74/221 (33%), Gaps = 48/221 (21%)
Query: 83 RRILITGGAGFVGSHLVDKLMLMGHEVTVV-----DNFFTGRK----------------- 120
R +L+TG GF+G++L+ +L L + V+ +
Sbjct: 1 RNVLLTGATGFLGAYLLLEL-LDRSDAKVICLVRAQSDEAALARLEKTFDLYRHWDELSA 59
Query: 121 ENVEHWFGH---PNFEIIHQDIVTPLFVEVDEIYHLASPASPPHYMFNPVKTIKTNTIGT 177
+ VE G P+ + + L VD I H A+ +++F + N +GT
Sbjct: 60 DRVEVVAGDLAEPDLGLSERTWQE-LAENVDLIIH---NAALVNHVFPYSELRGANVLGT 115
Query: 178 INMLGLAKRVGAKIL-FASTSEVYGDPEVH-------PQPETYWGHVNPIGPRACYDEAK 229
+L LA K L + S+ V T G Y +K
Sbjct: 116 AEVLRLAATGKPKPLHYVSSISVGETEYYSNFTVDFDEISPTRNVGQGLAGG---YGRSK 172
Query: 230 RVAETLC-YAYARHEDLSVRVARIFNTYGP----RMHMNDG 265
VAE L A R L V + R G ++ D
Sbjct: 173 WVAEKLVREAGDRG--LPVTIFRPGYITGDSRTGALNTRDF 211
>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 = 44.2 bits (105), Expect = 5e-05
Identities = 32/119 (26%), Positives = 48/119 (40%), Gaps = 12/119 (10%)
Query: 84 RILITGGAGFVGSHLVDKLMLMGHEVTVVDNFFTGRKENVEHWFGHPNFEIIHQDIVTPL 143
+ILITG G +G LV L G+EV TGR ++ D V
Sbjct: 1 KILITGATGMLGRALVRLLKERGYEV-----IGTGRSR-----ASLFKLDLTDPDAVEEA 50
Query: 144 FVEV--DEIYHLASPASPPHYMFNPVKTIKTNTIGTINMLGLAKRVGAKILFASTSEVY 200
+ D I + A+ +P + N + N+ AK VGA+++ ST V+
Sbjct: 51 IRDYKPDVIINCAAYTRVDKCESDPELAYRVNVLAPENLARAAKEVGARLIHISTDYVF 109
>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 = 43.5 bits (103), Expect = 8e-05
Identities = 42/185 (22%), Positives = 68/185 (36%), Gaps = 56/185 (30%)
Query: 84 RILITGGAGFVGSHLVDKLMLMGHEVTVVDNFFTGRKENVEHWFGHPNFEIIHQDIVTP- 142
++LITG +GFVG L ++L+ PN +I D+V+P
Sbjct: 2 KVLITGASGFVGQRLAERLLSDV-----------------------PNERLILIDVVSPK 38
Query: 143 -----------------------LFVEV-DEIYHLASPASPPHYMFNPVKTIKTNTIGTI 178
L D ++HLA+ S + + N GT
Sbjct: 39 APSGAPRVTQIAGDLAVPALIEALANGRPDVVFHLAAIVSG-GAEADFDLGYRVNVDGTR 97
Query: 179 NMLGLAKRVGA--KILFASTSEVYGDPEVHPQPETYWGHVNPIGPRACYDEAKRVAETLC 236
N+L ++ G + +F S+ VYG P +P + + P + Y K + E L
Sbjct: 98 NLLEALRKNGPKPRFVFTSSLAVYGLPLPNPVTDHT-----ALDPASSYGAQKAMCELLL 152
Query: 237 YAYAR 241
Y+R
Sbjct: 153 NDYSR 157
>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 = 43.0 bits (102), Expect = 1e-04
Identities = 21/70 (30%), Positives = 29/70 (41%), Gaps = 6/70 (8%)
Query: 85 ILITGGAGFVGSHLVDKLMLMGHEVTVVDNFFTGRKENVEHWFGHPNFEIIHQDIVTPLF 144
ILITGG GF+G L +L GHEVT+ T + +D +
Sbjct: 1 ILITGGTGFIGRALTQRLTKRGHEVTI----LTRSPPPGANTKWEGYKPWAGEDADSLE- 55
Query: 145 VEVDEIYHLA 154
D + +LA
Sbjct: 56 -GADAVINLA 64
>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 = 42.2 bits (100), Expect = 2e-04
Identities = 9/29 (31%), Positives = 17/29 (58%)
Query: 84 RILITGGAGFVGSHLVDKLMLMGHEVTVV 112
+ + G GF+G ++V++L G +V V
Sbjct: 2 VVTVFGATGFIGRYVVNRLAKRGSQVIVP 30
>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 = 41.5 bits (98), Expect = 3e-04
Identities = 33/139 (23%), Positives = 54/139 (38%), Gaps = 41/139 (29%)
Query: 83 RRILITGGAGFVGSHLVDKLMLMGHEV----------------------TVVDNFFTGRK 120
+ +LITG GF+G L++KL+ ++ F GR
Sbjct: 1 KSVLITGATGFLGKVLLEKLLRSCPDIGKIYLLIRGKSGQSAEERLRELLKDKLFDRGRN 60
Query: 121 ENVEHWFGH----------PNFEIIHQDIVTPLFVEVDEIYHLASPASPPHYMFNP--VK 168
N + PN + +D+ T L EV+ I H A+ + F+ +
Sbjct: 61 LN-PLFESKIVPIEGDLSEPNLGLSDEDLQT-LIEEVNIIIHCAATVT-----FDERLDE 113
Query: 169 TIKTNTIGTINMLGLAKRV 187
+ N +GT+ +L LAKR
Sbjct: 114 ALSINVLGTLRLLELAKRC 132
>gnl|CDD|138873 PRK12320, PRK12320, hypothetical protein; Provisional.
Length = 699
Score = 41.5 bits (97), Expect = 5e-04
Identities = 35/137 (25%), Positives = 56/137 (40%), Gaps = 34/137 (24%)
Query: 85 ILITGGAGFVGSHLVDKLMLMGHEVTVVDNFFTGRKENVEHWFGHPNFEIIHQDIVTPLF 144
IL+T G VG + +L+ GH V+ + H P + + + P+
Sbjct: 3 ILVTDATGAVGRSVTRQLIAAGHTVSGI--------AQHPHDALDPRVDYVCASLRNPVL 54
Query: 145 VEV----DEIYHLASPASPPHYMFNPVKTIKTNTIGTINMLGLAK------RVGAKILFA 194
E+ D + HLA + T+ G + + GLA R GA++LF
Sbjct: 55 QELAGEADAVIHLAP--------------VDTSAPGGVGITGLAHVANAAARAGARLLF- 99
Query: 195 STSEVYGDPEVHPQPET 211
S+ G PE++ Q ET
Sbjct: 100 -VSQAAGRPELYRQAET 115
>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 = 40.8 bits (96), Expect = 5e-04
Identities = 12/27 (44%), Positives = 19/27 (70%)
Query: 84 RILITGGAGFVGSHLVDKLMLMGHEVT 110
++ +TG GF+GS +V +L+ GHEV
Sbjct: 2 KVFVTGATGFIGSAVVRELVAAGHEVV 28
>gnl|CDD|217199 pfam02719, Polysacc_synt_2, Polysaccharide biosynthesis protein.
This is a family of diverse bacterial polysaccharide
biosynthesis proteins including the CapD protein, WalL
protein mannosyl-transferase and several putative
epimerases (e.g. WbiI).
Length = 280
Score = 40.9 bits (97), Expect = 5e-04
Identities = 42/171 (24%), Positives = 70/171 (40%), Gaps = 33/171 (19%)
Query: 85 ILITGGAGFVGSHLVDKLMLMG-HEVTVVD----NFFTGRKENVEHWFGHPNFEIIHQDI 139
+L+TGG G +GS L +++ ++ + + R+E + + P D+
Sbjct: 1 VLVTGGGGSIGSELCRQILKFNPKKIILFSRDEFKLYEIRQE-LRQEYNDPKLRFFIGDV 59
Query: 140 -----VTPLF--VEVDEIYHLASPASPPHYMFNPVKTIKTNTIGTINMLGLAKRVGAK-I 191
+ VD ++H A+ P +NP++ IKTN +GT N+ A G +
Sbjct: 60 RDRERLERAMEQHGVDTVFHAAALKHVPLVEYNPMEAIKTNVLGTENVAEAAIENGVEKF 119
Query: 192 LFASTSEVYGDPEVHPQPETYWGHVNPIGPRACYDEAKRVAETLCYAYARH 242
+ ST D V+P N +G KR+AE L A R
Sbjct: 120 VLIST-----DKAVNP--------TNVMG------ATKRLAEKLFQAANRE 151
>gnl|CDD|182998 PRK11150, rfaD, ADP-L-glycero-D-mannoheptose-6-epimerase;
Provisional.
Length = 308
Score = 40.8 bits (96), Expect = 7e-04
Identities = 18/37 (48%), Positives = 25/37 (67%), Gaps = 1/37 (2%)
Query: 85 ILITGGAGFVGSHLVDKLMLMGH-EVTVVDNFFTGRK 120
I++TGGAGF+GS++V L G ++ VVDN G K
Sbjct: 2 IIVTGGAGFIGSNIVKALNDKGITDILVVDNLKDGTK 38
>gnl|CDD|178567 PLN02986, PLN02986, cinnamyl-alcohol dehydrogenase family protein.
Length = 322
Score = 40.4 bits (94), Expect = 0.001
Identities = 50/204 (24%), Positives = 83/204 (40%), Gaps = 39/204 (19%)
Query: 85 ILITGGAGFVGSHLVDKLMLMGHEVTVVDNFFTGRKENVEHWF----GHPNFEIIHQDIV 140
+ +TG +G++ S +V L+L G+ V T RK+ EH ++ D++
Sbjct: 8 VCVTGASGYIASWIVKLLLLRGYTVKATVRDLTDRKKT-EHLLALDGAKERLKLFKADLL 66
Query: 141 TPLFVE-----VDEIYHLASPASPPHYMFNPVKTIKTNTI-----GTINMLGLAKRVGA- 189
E D ++H ASP +F VK +T I GTIN+L K +
Sbjct: 67 EESSFEQAIEGCDAVFHTASP------VFFTVKDPQTELIDPALKGTINVLNTCKETPSV 120
Query: 190 --KILFASTSEV-YGDPEVHPQ---PETYWGHVNPIGPRAC------YDEAKRVAETLCY 237
IL +ST+ V + P + ET++ P C Y +K +AE +
Sbjct: 121 KRVILTSSTAAVLFRQPPIEANDVVDETFFSD-----PSLCRETKNWYPLSKILAENAAW 175
Query: 238 AYARHEDLSVRVARIFNTYGPRMH 261
+A+ + + V GP +
Sbjct: 176 EFAKDNGIDMVVLNPGFICGPLLQ 199
>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 = 39.6 bits (93), Expect = 0.001
Identities = 26/120 (21%), Positives = 45/120 (37%), Gaps = 15/120 (12%)
Query: 85 ILITGGAGFVGSHLVDKLMLMGHEVTVVDNFFTGRKENVEHWFGHPNFEIIHQDIVTPLF 144
+LI G G++G L +L+ G +VT T E + + D+ P
Sbjct: 1 VLILG-CGYLGQRLARQLLAQGWQVTGT----TRSPEKLAADRPAGVTPLA-ADLTQPGL 54
Query: 145 VEVDEI--YHLASPASPPHYMFNPVKTIKTNTIGTINMLGLAKRVGAKILFASTSEVYGD 202
+ + L PA ++P + + L +RV + S++ VYGD
Sbjct: 55 LADVDHLVISLPPPAGSYRGGYDPG---LRALLDALAQLPAVQRVI----YLSSTGVYGD 107
>gnl|CDD|187580 cd05272, TDH_SDR_e, L-threonine dehydrogenase, extended (e) SDRs.
This subgroup contains members identified as L-threonine
dehydrogenase (TDH). TDH catalyzes the zinc-dependent
formation of 2-amino-3-ketobutyrate from L-threonine via
NAD(H)-dependent oxidation. This group is distinct from
TDHs that are members of the medium chain
dehydrogenase/reductase family. This group has the
NAD-binding motif and active site tetrad of the extended
SDRs. Extended SDRs are distinct from classical SDRs. In
addition to the Rossmann fold (alpha/beta folding
pattern with a central beta-sheet) core region typical
of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 308
Score = 39.2 bits (92), Expect = 0.002
Identities = 45/168 (26%), Positives = 64/168 (38%), Gaps = 20/168 (11%)
Query: 84 RILITGGAGFVGSHLVDKLMLM-GHEVTVVDNFFTGRKENVEHWFGHPNFEIIH------ 136
RILITGG G +GS L L G + + + ++ H FE +
Sbjct: 1 RILITGGLGQIGSELAKLLRKRYGKDNVIA----SDIRKPPAHVVLSGPFEYLDVLDFKS 56
Query: 137 -QDIVTPLFVEVDEIYHLASPASPPHYMFNPVKTIKTNTIGTINMLGLAKRVGAKILFAS 195
++IV ++ I HLA+ S NP N G N+L LA+ +I S
Sbjct: 57 LEEIVVNH--KITWIIHLAALLSAVGEK-NPPLAWDVNMNGLHNVLELAREHNLRIFVPS 113
Query: 196 TSEVYGDPEVHPQPETYWGHVNPIGPRACYDEAKRVAETLC-YAYARH 242
T +G P P PR Y +K AE L Y + +
Sbjct: 114 TIGAFG-PT---TPRNNTPDDTIQRPRTIYGVSKVAAELLGEYYHHKF 157
>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 = 38.4 bits (90), Expect = 0.002
Identities = 10/29 (34%), Positives = 19/29 (65%)
Query: 84 RILITGGAGFVGSHLVDKLMLMGHEVTVV 112
++L+ G G VG H+V +L+ G++V +
Sbjct: 1 KVLVVGATGKVGRHVVRELLDRGYQVRAL 29
>gnl|CDD|200381 TIGR04130, FnlA, UDP-N-acetylglucosamine
4,6-dehydratase/5-epimerase. The FnlA enzyme is the
first step in the biosynthesis of UDP-FucNAc from
UDP-GlcNAc in E. coli (along with FnlB and FnlC). The
proteins identified by this model include FnlA homologs
in the O-antigen clusters of O4, O25, O26, O29 (Shigella
D11), O118, O145 and O172 serotype strains, all of which
produce O-antigens containing FucNAc (or the further
modified FucNAm). A homolog from Pseudomonas aerugiosa
serotype O11, WbjB, also involved in the biosynthesis of
UDP-FucNAc has been characterized and is now believed to
carry out both the initial 4,6-dehydratase reaction and
the subsequent epimerization of the resulting methyl
group at C-5. A phylogenetic tree of related sequences
shows a distinct clade of enzymes involved in the
biosynthesis of UDP-QuiNAc (Qui=qinovosamine). This
clade appears to be descendant from the common ancestor
of the Pseudomonas and E. coli fucose-biosynthesis
enzymes. It has been hypothesized that the first step in
the biosynthesis of these two compounds may be the same,
and thus that these enzymes all have the same function.
At present, lacking sufficient confirmation of this, the
current model trusted cutoff only covers the tree
segment surrounding the E. coli genes. The clades
containing the Pseudomonas and QuiNAc biosynthesis
enzymes score above the noise cutoff. Immediately below
the noise cutoff are enzymes involved in the
biosynthesis of UDP-RhaNAc (Rha=rhamnose), which again
may or may not produce the same product.
Length = 337
Score = 38.8 bits (90), Expect = 0.003
Identities = 50/154 (32%), Positives = 74/154 (48%), Gaps = 29/154 (18%)
Query: 147 VDEIYHLASPASPPHYMFNPVKTIKTNTIGTINMLGLAKRVGAK-ILFASTSEVYGDPEV 205
VD IYH A+ P F+P++ +KTN +GT N+L A G K ++ ST D V
Sbjct: 74 VDFIYHAAALKQVPSCEFHPMEAVKTNVLGTENVLEAAIANGVKRVVCLST-----DKAV 128
Query: 206 HPQPETYWGHVNPIGPRACYDEAKRVAETLCYAYARHEDLSVRVARIFNT-YGPRMHMND 264
+P +N +G +K + E + A +R+ D S V I T YG M +
Sbjct: 129 YP--------INAMGI------SKAMMEKVMVAKSRNVDSSKTV--ICGTRYGNVM-ASR 171
Query: 265 GRVVSNFI--IQALRNETITSDSSKSFTKFWDTL 296
G V+ F+ I+A + TIT + T+F TL
Sbjct: 172 GSVIPLFVDLIKAGKPLTIT---DPNMTRFMMTL 202
>gnl|CDD|222146 pfam13460, NAD_binding_10, NADH(P)-binding.
Length = 182
Score = 37.3 bits (87), Expect = 0.004
Identities = 36/157 (22%), Positives = 56/157 (35%), Gaps = 34/157 (21%)
Query: 85 ILITGGAGFVGSHLVDKLMLMGHEVTVVDNFFTGRKENVEHWFGHPNFEIIHQDIVTPLF 144
I + G G G LV +L+ GH+VT + R + P + +D+
Sbjct: 1 IAVIGATGKTGRRLVKELLARGHQVTAL-----SRNPSKA---PAPGVTPVQKDLFDLAD 52
Query: 145 VE-----VDEIYHLASPASPPHYMFNPVKTIKTNTIGTINMLGLAKRVGAK-ILFASTSE 198
+ VD + A A P G ++L A R G + I+ S +
Sbjct: 53 LAEALAGVDAVV-DAFGARPDDSD------------GVKHLLDAAARAGVRRIVVVSAAG 99
Query: 199 VYGDPEVHPQPETYWGHVNPIGPRACYDEAKRVAETL 235
+Y D + + P+ P Y AK AE L
Sbjct: 100 LYRDEPGTFRLDD-----APLFPP--YARAKAAAEEL 129
>gnl|CDD|187540 cd05229, SDR_a3, atypical (a) SDRs, subgroup 3. These atypical SDR
family members of unknown function have a glycine-rich
NAD(P)-binding motif consensus that is very similar to
the extended SDRs, GXXGXXG. Generally, this group has
poor conservation of the active site tetrad, However,
individual sequences do contain matches to the YXXXK
active site motif, and generally Tyr or Asn in place of
the upstream Ser found in most 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 = 302
Score = 38.1 bits (89), Expect = 0.005
Identities = 31/132 (23%), Positives = 48/132 (36%), Gaps = 20/132 (15%)
Query: 85 ILITGGAGFVGSHLVDKLMLMGHEVTVVDNFFTGRKENVEHWFGHPNFEIIHQDIVTPLF 144
+ G +G +G + +L G +V +V R + W P EI+ D +
Sbjct: 2 AHVLGASGPIGREVARELRRRGWDVRLV-----SRSGSKLAW--LPGVEIVAADAMDASS 54
Query: 145 VE-----VDEIYHLASPASPPHYMFNPVKTIKTNTIGTINMLGLAKRVGAKILFASTSEV 199
V D IYH A+PA P + N + A+ GAK++ +
Sbjct: 55 VIAAARGADVIYHCANPAYTRWEELFP--PLMENVVAA------AEANGAKLVLPGNVYM 106
Query: 200 YGDPEVHPQPET 211
YG P E
Sbjct: 107 YGPQAGSPITED 118
>gnl|CDD|187535 cd02266, SDR, Short-chain dehydrogenases/reductases (SDR). SDRs
are a functionally diverse family of oxidoreductases
that have a single domain with a structurally conserved
Rossmann fold (alpha/beta folding pattern with a central
beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRs are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes catalyze a
wide range of activities including the metabolism of
steroids, cofactors, carbohydrates, lipids, aromatic
compounds, and amino acids, and act in redox sensing.
Classical SDRs have an TGXXX[AG]XG cofactor binding
motif and a YXXXK active site motif, with the Tyr
residue of the active site motif serving as a critical
catalytic residue (Tyr-151, human prostaglandin
dehydrogenase (PGDH) numbering). In addition to the Tyr
and Lys, there is often an upstream Ser (Ser-138, PGDH
numbering) and/or an Asn (Asn-107, PGDH numbering)
contributing to the active site; while substrate binding
is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. Extended SDRs have additional
elements in the C-terminal region, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase (KR) domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type KRs have
a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 186
Score = 37.1 bits (86), Expect = 0.006
Identities = 33/185 (17%), Positives = 52/185 (28%), Gaps = 53/185 (28%)
Query: 85 ILITGGAGFVGSHLVDKLMLMGHEVTVVDNFFTGRKENVEHWFGHPNFEIIHQDIVTPLF 144
+L+TGG+G +G + L G +V R++ V H + L
Sbjct: 1 VLVTGGSGGIGGAIARWLASRGSPKVLV----VSRRDVVVHNAAILD--------DGRLI 48
Query: 145 VEVDEIYHLASPASPPHYMFNPVKTIKTNTIGTINMLGLA------KRVGAKILFASTSE 198
+ I+ N +GT +L A KR+G IL +S
Sbjct: 49 DLTGS---------------RIERAIRANVVGTRRLLEAARELMKAKRLGRFILISS--- 90
Query: 199 VYGDPEVHPQPETYWGHVNPIGPRACYDEAKRVAETLCYAYAR---HEDLSVRVARIFNT 255
+G Y +K + L +A L
Sbjct: 91 ----------VAGLFGA----PGLGGYAASKAALDGLAQQWASEGWGNGLPATAVACGTW 136
Query: 256 YGPRM 260
G M
Sbjct: 137 AGSGM 141
>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 = 37.2 bits (87), Expect = 0.008
Identities = 44/185 (23%), Positives = 62/185 (33%), Gaps = 43/185 (23%)
Query: 85 ILITGGAGFVGSHLVDKLMLMGHEVTVVDNFFTGRKENVEHWFGHPNFEIIHQDIVTPLF 144
IL+TG G +G L L G EV +D P ++ + V L
Sbjct: 1 ILVTGANGQLGRELTRLLAERGVEVVALD---------------RPELDLTDPEAVAALV 45
Query: 145 VEV--DEIYHLA---------SPASPPHYMFNPVKTIKTNTIGTINMLGLAKRVGAKILF 193
E D + + A S P N +G N+ GA ++
Sbjct: 46 REARPDVVVNAAAYTAVDKAES---------EPELAYAVNALGPGNLAEACAARGAPLIH 96
Query: 194 ASTSEVYGDPEVHPQPETYWGHVNPIGPRACYDEAKRVAETLCYAY-ARHEDLSVRVARI 252
ST V+ + P E +P GP Y K E A RH L +R A +
Sbjct: 97 ISTDYVFDGAKGGPYRED-----DPTGPLNVYGRTKLAGEQAVLAANPRH--LILRTAWV 149
Query: 253 FNTYG 257
+ YG
Sbjct: 150 YGEYG 154
>gnl|CDD|235962 PRK07201, PRK07201, short chain dehydrogenase; Provisional.
Length = 657
Score = 37.6 bits (88), Expect = 0.010
Identities = 30/127 (23%), Positives = 51/127 (40%), Gaps = 26/127 (20%)
Query: 84 RILITGGAGFVGSHLVDKLMLMGHEVTVVDNFFTGRKEN-------VEHWFGHPNFEIIH 136
R +TGG GF+G LV +L+ E TV R+++ +W G +
Sbjct: 2 RYFVTGGTGFIGRRLVSRLLDRRREATV---HVLVRRQSLSRLEALAAYW-GADRVVPLV 57
Query: 137 QDIVTPLF----------VEVDEIYHLASPASPPHYMFNPVKT-IKTNTIGTINMLGLAK 185
D+ P ++D + HLA+ + + + N GT N++ LA+
Sbjct: 58 GDLTEPGLGLSEADIAELGDIDHVVHLAAI----YDLTADEEAQRAANVDGTRNVVELAE 113
Query: 186 RVGAKIL 192
R+ A
Sbjct: 114 RLQAATF 120
>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 = 0.010
Identities = 45/172 (26%), Positives = 73/172 (42%), Gaps = 34/172 (19%)
Query: 86 LITGGAGFVGSHLVDKLMLMGH----EVTVVDNFFTGRKENVEH---WFGHPNFEIIHQD 138
L+TGG GF+G H++ +L+L E+ V+D F E +EH G I D
Sbjct: 3 LVTGGGGFLGQHII-RLLLERKEELKEIRVLDKAFG--PELIEHFEKSQGKTYVTDIEGD 59
Query: 139 I--VTPLFVE---VDEIYHLASPAS---PPHYMFNPVKTI-KTNTIGTINMLGLAKRVGA 189
I ++ LF V + H A+ PP+Y + + + N GT +L +
Sbjct: 60 IKDLSFLFRACQGVSVVIHTAAIVDVFGPPNY-----EELEEVNVNGTQAVLEACVQNNV 114
Query: 190 KIL-FASTSEV-----YGDPEVHPQPETYWGHVNPIGPRACYDEAKRVAETL 235
K L + S+ EV G P + +T + + Y +K +AE +
Sbjct: 115 KRLVYTSSIEVAGPNFKGRPIFNGVEDTPYEDTSTPP----YASSKLLAENI 162
>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 = 36.4 bits (84), Expect = 0.015
Identities = 35/133 (26%), Positives = 61/133 (45%), Gaps = 18/133 (13%)
Query: 85 ILITGGAGFVGSHLVDKLMLMGHEV-TVVDNFFTGRKENVE-HWFGHPN-FEIIHQDIVT 141
+L+TG +GFV SH+V++L+ G++V V + +K N P E+ D+
Sbjct: 1 VLVTGASGFVASHVVEQLLERGYKVRATVRDPSKVKKVNHLLDLDAKPGRLELAVADLTD 60
Query: 142 PL-FVEV----DEIYHLASPASPPHYMF---NPVKTIKTNTIGTINMLGLAKRVGA--KI 191
F EV ++H+A+P F +P + IK GT+N L A + +
Sbjct: 61 EQSFDEVIKGCAGVFHVATP-----VSFSSKDPNEVIKPAIGGTLNALKAAAAAKSVKRF 115
Query: 192 LFASTSEVYGDPE 204
+ S++ P+
Sbjct: 116 VLTSSAGSVLIPK 128
>gnl|CDD|215310 PLN02572, PLN02572, UDP-sulfoquinovose synthase.
Length = 442
Score = 36.7 bits (85), Expect = 0.016
Identities = 36/153 (23%), Positives = 55/153 (35%), Gaps = 30/153 (19%)
Query: 81 SKRRILITGGAGFVGSHLVDKLMLMGHEVTVVDNF----------------FTGRKENVE 124
K+++++ GG G+ G L G+EV +VDN E V
Sbjct: 46 KKKKVMVIGGDGYCGWATALHLSKRGYEVAIVDNLCRRLFDHQLGLDSLTPIASIHERVR 105
Query: 125 HW-------FGHPNFEIIHQDIVTPLF--VEVDEIYHLASPASPPHYMFN---PVKTIKT 172
W +I + ++ F E D + H S P+ M + V T
Sbjct: 106 RWKEVSGKEIELYVGDICDFEFLSEAFKSFEPDAVVHFGEQRSAPYSMIDRSRAVFTQHN 165
Query: 173 NTIGTINMLGLAK--RVGAKILFASTSEVYGDP 203
N IGT+N+L K ++ T YG P
Sbjct: 166 NVIGTLNVLFAIKEFAPDCHLVKLGTMGEYGTP 198
>gnl|CDD|132628 TIGR03589, PseB, UDP-N-acetylglucosamine 4,6-dehydratase. This
enzyme catalyzes the first step in the biosynthesis of
pseudaminic acid, the conversion of
UDP-N-acetylglucosamine to
UDP-4-keto-6-deoxy-N-acetylglucosamine. These sequences
are members of the broader pfam01073 (3-beta
hydroxysteroid dehydrogenase/isomerase family) family.
Length = 324
Score = 36.2 bits (84), Expect = 0.017
Identities = 58/233 (24%), Positives = 86/233 (36%), Gaps = 48/233 (20%)
Query: 81 SKRRILITGGAGFVGSHLVDKLMLMGHEVTVVDNFFTGRKENVEHW-----FGHPNFEII 135
+ + ILITGG G G + +L L + + + R E ++ W F P
Sbjct: 3 NNKSILITGGTGSFGKAFISRL-LENYNPKKIIIY--SRDE-LKQWEMQQKFPAPCLRFF 58
Query: 136 HQDI-----VTPLFVEVDEIYHLASPASPPHYMFNPVKTIKTNTIGTINMLGLAKRVGAK 190
D+ +T VD + H A+ P +NP + I+TN G N++ A G K
Sbjct: 59 IGDVRDKERLTRALRGVDYVVHAAALKQVPAAEYNPFECIRTNINGAQNVIDAAIDNGVK 118
Query: 191 ILFA-STSEVYGDPEVHPQPETYWGHVNPIGPRACYDEAKRVAETLCYA---YARHEDLS 246
+ A ST D +P +N Y K ++ L A + +
Sbjct: 119 RVVALST-----DKAANP--------IN------LYGATKLASDKLFVAANNISGSKGTR 159
Query: 247 VRVARIFNTYGPRMHMNDGRVVSNF---IIQALRNETITSDSSKSFTKFWDTL 296
V R N G R G VV F + + IT T+FW TL
Sbjct: 160 FSVVRYGNVVGSR-----GSVVPFFKSLKEEGVTELPITDP---RMTRFWITL 204
>gnl|CDD|234212 TIGR03443, alpha_am_amid, L-aminoadipate-semialdehyde
dehydrogenase. Members of this protein family are
L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31),
product of the LYS2 gene. It is also called
alpha-aminoadipate reductase. In fungi, lysine is
synthesized via aminoadipate. Currently, all members of
this family are fungal.
Length = 1389
Score = 37.0 bits (86), Expect = 0.018
Identities = 16/46 (34%), Positives = 26/46 (56%)
Query: 58 EKLKSLDVRIPKKYPSVKFQDYQSKRRILITGGAGFVGSHLVDKLM 103
+ K+L +PK YPS K D + + +TG GF+GS ++ L+
Sbjct: 947 KDAKTLVDSLPKSYPSRKELDASTPITVFLTGATGFLGSFILRDLL 992
>gnl|CDD|212497 cd11731, Lin1944_like_SDR_c, Lin1944 and related proteins,
classical (c) SDRs. Lin1944 protein from Listeria
Innocua is a classical SDR, it contains a glycine-rich
motif similar to the canonical motif of the SDR
NAD(P)-binding site. However, the typical SDR active
site residues are absent in this subgroup of proteins of
undetermined function. SDRs are a functionally diverse
family of oxidoreductases that have a single domain with
a structurally conserved Rossmann fold (alpha/beta
folding pattern with a central beta-sheet), an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRs are approximately
350 residues. Sequence identity between different SDR
enzymes are typically in the 15-30% range, but the
enzymes share the Rossmann fold NAD-binding motif and
characteristic NAD-binding and catalytic sequence
patterns. These enzymes catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human prostaglandin dehydrogenase
(PGDH) numbering). In addition to the Tyr and Lys, there
is often an upstream Ser (Ser-138, PGDH numbering)
and/or an Asn (Asn-107, PGDH numbering) contributing to
the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 198
Score = 35.3 bits (82), Expect = 0.027
Identities = 25/115 (21%), Positives = 37/115 (32%), Gaps = 22/115 (19%)
Query: 85 ILITGGAGFVGSHLVDKLMLMGHEVTVVDNFFTGRKENVEHWFGHPNFEIIHQDIVTPLF 144
I++ G G +G + L GHEV GR G +I + + LF
Sbjct: 1 IIVIGATGTIGLAVAQLLSAHGHEVITA-----GRSS------GDYQVDITDEASIKALF 49
Query: 145 VEVDEIYHLASPASPPHYMFNPVKTIKTNTI-------GTINMLGLAKRVGAKIL 192
+V + S A + T G IN++ R G L
Sbjct: 50 EKVGHFDAIVSTAGDAEFAPLAELTDADFQRGLNSKLLGQINLV----RHGLPYL 100
>gnl|CDD|187556 cd05245, SDR_a2, atypical (a) SDRs, subgroup 2. This subgroup
contains atypical SDRs, one member is identified as
Escherichia coli protein ybjT, function unknown.
Atypical SDRs are distinct from classical SDRs. Members
of this subgroup have a glycine-rich NAD(P)-binding
motif consensus that generally matches the extended
SDRs, TGXXGXXG, but lacks the characteristic active site
residues of the SDRs. This subgroup has basic residues
(HXXXR) in place of the active site motif YXXXK, these
may have a catalytic role. Atypical SDRs generally lack
the catalytic residues characteristic of the SDRs, and
their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Atypical SDRs include biliverdin IX beta
reductase (BVR-B,aka flavin reductase), NMRa (a negative
transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. In addition to the
Rossmann fold core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 293
Score = 35.8 bits (83), Expect = 0.027
Identities = 16/74 (21%), Positives = 29/74 (39%), Gaps = 9/74 (12%)
Query: 85 ILITGGAGFVGSHLVDKLMLMGHEVTVVDNFFTGRKENVEHWFGHPNFEII-----HQDI 139
+L+TG G+VG LV +L+ GH+V E + ++ +
Sbjct: 1 VLVTGATGYVGGRLVPRLLQEGHQVRA----LVRSPEKLADRPWSERVTVVRGDLEDPES 56
Query: 140 VTPLFVEVDEIYHL 153
+ +D Y+L
Sbjct: 57 LRAALEGIDTAYYL 70
>gnl|CDD|237219 PRK12827, PRK12827, short chain dehydrogenase; Provisional.
Length = 249
Score = 34.7 bits (80), Expect = 0.050
Identities = 17/43 (39%), Positives = 24/43 (55%), Gaps = 1/43 (2%)
Query: 83 RRILITGGAGFVGSHLVDKLMLMGHEVTVVDNF-FTGRKENVE 124
RR+LITGG+G +G + +L G +V V+D GR E
Sbjct: 7 RRVLITGGSGGLGRAIAVRLAADGADVIVLDIHPMRGRAEADA 49
>gnl|CDD|236541 PRK09496, trkA, potassium transporter peripheral membrane
component; Reviewed.
Length = 453
Score = 35.1 bits (82), Expect = 0.057
Identities = 13/31 (41%), Positives = 19/31 (61%), Gaps = 1/31 (3%)
Query: 84 RILITGGAGFVGSHLVDKLMLMGHEVTVVDN 114
+I+I G AG VG L + L ++VTV+D
Sbjct: 2 KIIIVG-AGQVGYTLAENLSGENNDVTVIDT 31
>gnl|CDD|234026 TIGR02823, oxido_YhdH, putative quinone oxidoreductase, YhdH/YhfP
family. This model represents a subfamily of pfam00107
as defined by Pfam, a superfamily in which some members
are zinc-binding medium-chain alcohol dehydrogenases
while others are quinone oxidoreductases with no bound
zinc. This subfamily includes proteins studied
crystallographically for insight into function: YhdH
from Escherichia coli and YhfP from Bacillus subtilis.
Members bind NADPH or NAD, but not zinc [Unknown
function, Enzymes of unknown specificity].
Length = 323
Score = 34.5 bits (80), Expect = 0.061
Identities = 15/41 (36%), Positives = 22/41 (53%), Gaps = 4/41 (9%)
Query: 85 ILITGGAGFVGSHLVDKLMLMGHEVTVVDNFFTGRKENVEH 125
+L+TG G VGS V L +G+EV TG+ E ++
Sbjct: 149 VLVTGATGGVGSLAVAILSKLGYEVVAS----TGKAEEEDY 185
>gnl|CDD|178569 PLN02989, PLN02989, cinnamyl-alcohol dehydrogenase family protein.
Length = 325
Score = 34.2 bits (78), Expect = 0.096
Identities = 40/196 (20%), Positives = 80/196 (40%), Gaps = 22/196 (11%)
Query: 85 ILITGGAGFVGSHLVDKLMLMGHEVTVVDNFFTGRKENVEHWF----GHPNFEIIHQDIV 140
+ +TG +G++ S +V L+ G+ + RK+ +H ++ D++
Sbjct: 8 VCVTGASGYIASWIVKLLLFRGYTINATVRDPKDRKKT-DHLLALDGAKERLKLFKADLL 66
Query: 141 TPLFVEV-----DEIYHLASPASPPHYMFNPVKTIKTNTIGTINMLGLAKRVGA--KILF 193
E+ + ++H ASP + V+ I GTIN+L +V + +++
Sbjct: 67 DEGSFELAIDGCETVFHTASPVAITVKTDPQVELINPAVNGTINVLRTCTKVSSVKRVIL 126
Query: 194 ASTSEVYGDPEVHPQP-----ETYWGHVNPI---GPRACYDEAKRVAETLCYAYARHEDL 245
S+ PE P ET++ NP + Y +K +AE + +A+ ++
Sbjct: 127 TSSMAAVLAPETKLGPNDVVDETFF--TNPSFAEERKQWYVLSKTLAEDAAWRFAKDNEI 184
Query: 246 SVRVARIFNTYGPRMH 261
+ V GP +
Sbjct: 185 DLIVLNPGLVTGPILQ 200
>gnl|CDD|223643 COG0569, TrkA, K+ transport systems, NAD-binding component
[Inorganic ion transport and metabolism].
Length = 225
Score = 33.4 bits (77), Expect = 0.12
Identities = 12/32 (37%), Positives = 18/32 (56%), Gaps = 1/32 (3%)
Query: 83 RRILITGGAGFVGSHLVDKLMLMGHEVTVVDN 114
+I+I GAG VG + +L GH V ++D
Sbjct: 1 MKIII-IGAGRVGRSVARELSEEGHNVVLIDR 31
>gnl|CDD|176248 cd08288, MDR_yhdh, Yhdh putative quinone oxidoreductases. Yhdh
putative quinone oxidoreductases (QOR). QOR catalyzes
the conversion of a quinone + NAD(P)H to a hydroquinone
+ NAD(P)+. Quinones are cyclic diones derived from
aromatic compounds. Membrane bound QOR actin the
respiratory chains of bacteria and mitochondria, while
soluble QOR acts to protect from toxic quinones (e.g.
DT-diaphorase) or as a soluble eye-lens protein in some
vertebrates (e.g. zeta-crystalin). QOR reduces quinones
through a semi-quinone intermediate via a
NAD(P)H-dependent single electron transfer. QOR is a
member of the medium chain dehydrogenase/reductase
family, but lacks the zinc-binding sites of the
prototypical alcohol dehydrogenases of this group.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which has a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES. These
proteins typically form dimers (typically higher plants,
mammals) or tetramers (yeast, bacteria), and have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site and a structural zinc in a lobe of
the catalytic domain. NAD(H) binding occurs in the
cleft between the catalytic and coenzyme-binding
domains at the active site, and coenzyme binding induces
a conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
In human ADH catalysis, the zinc ion helps coordinate
the alcohol, followed by deprotonation of a histidine,
the ribose of NAD, a serine, then the alcohol, which
allows the transfer of a hydride to NAD+, creating NADH
and a zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 324
Score = 33.3 bits (77), Expect = 0.17
Identities = 17/38 (44%), Positives = 21/38 (55%), Gaps = 4/38 (10%)
Query: 85 ILITGGAGFVGSHLVDKLMLMGHEVTVVDNFFTGRKEN 122
+L+TG AG VGS V L +G+EV TGR E
Sbjct: 150 VLVTGAAGGVGSVAVALLARLGYEVVAS----TGRPEE 183
>gnl|CDD|176228 cd08267, MDR1, Medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family.
This group is a member of the medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, but lacks the zinc-binding
sites of the zinc-dependent alcohol dehydrogenases. The
medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P)-binding Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 319
Score = 33.3 bits (77), Expect = 0.18
Identities = 12/33 (36%), Positives = 18/33 (54%)
Query: 80 QSKRRILITGGAGFVGSHLVDKLMLMGHEVTVV 112
+ +R+LI G +G VG+ V +G VT V
Sbjct: 142 KPGQRVLINGASGGVGTFAVQIAKALGAHVTGV 174
>gnl|CDD|176232 cd08271, MDR5, Medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family.
This group is a member of the medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, but lacks the zinc-binding
sites of the zinc-dependent alcohol dehydrogenases. The
medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P)-binding Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 325
Score = 32.6 bits (75), Expect = 0.25
Identities = 19/45 (42%), Positives = 21/45 (46%), Gaps = 5/45 (11%)
Query: 80 QSKRRILITGGAGFVGSHLVDKLMLMGHEVTVVDNFFTGRKENVE 124
++ R ILITGGAG VGS V G V T K N E
Sbjct: 140 EAGRTILITGGAGGVGSFAVQLAKRAGLRVIT-----TCSKRNFE 179
>gnl|CDD|223677 COG0604, Qor, NADPH:quinone reductase and related Zn-dependent
oxidoreductases [Energy production and conversion /
General function prediction only].
Length = 326
Score = 32.7 bits (75), Expect = 0.28
Identities = 16/64 (25%), Positives = 23/64 (35%), Gaps = 6/64 (9%)
Query: 84 RILITGGAGFVGSHLVDKLMLMGHEVTVVDNFFTGRKENVEHWFGHPNFEIIHQDIVTPL 143
+L+ G AG VGS + +G V V E +E +I+
Sbjct: 145 TVLVHGAAGGVGSAAIQLAKALGATVVAV----VSSSEKLELLKELGADHVINYR--EED 198
Query: 144 FVEV 147
FVE
Sbjct: 199 FVEQ 202
>gnl|CDD|235876 PRK06849, PRK06849, hypothetical protein; Provisional.
Length = 389
Score = 32.3 bits (74), Expect = 0.40
Identities = 10/33 (30%), Positives = 14/33 (42%)
Query: 82 KRRILITGGAGFVGSHLVDKLMLMGHEVTVVDN 114
K+ +LITG L GH V + D+
Sbjct: 4 KKTVLITGARAPAALELARLFHNAGHTVILADS 36
>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 = 31.4 bits (72), Expect = 0.42
Identities = 35/182 (19%), Positives = 54/182 (29%), Gaps = 33/182 (18%)
Query: 84 RILITGGAGFVGSHLVDKLMLMGHEVTVVDNFFTGRKENVEHWFGHPNFEIIHQDI---- 139
+I I G G GS +V + + GHEVT + H +++ D+
Sbjct: 1 KIAIIGATGRTGSAIVREALARGHEVTA----LVRDPAKLPA--EHEKLKVVQGDVLDLE 54
Query: 140 -VTPLFVEVD---EIYHLASPASPPHYMFNPVKTIKTNTIGTINMLGLAKRVGAKILFAS 195
V D + SP + GT N++ K G K L
Sbjct: 55 DVKEALEGQDAVISALGTRNDLSPTTLH----------SEGTRNIVSAMKAAGVKRLIVV 104
Query: 196 TSEVYGDPEVHPQPETYWGHVNPIGPRACYDEAKRVAETLCYAYARHEDLS---VRVARI 252
D P R ++ R+ + L R L VR +
Sbjct: 105 GGAGSLDDRPKVTLVLDTLLFPPALRRV-AEDHARMLKVL-----RESGLDWTAVRPPAL 158
Query: 253 FN 254
F+
Sbjct: 159 FD 160
>gnl|CDD|187542 cd05231, NmrA_TMR_like_1_SDR_a, NmrA (a transcriptional regulator)
and triphenylmethane reductase (TMR) like proteins,
subgroup 1, atypical (a) SDRs. Atypical SDRs related to
NMRa, TMR, and HSCARG (an NADPH sensor). This subgroup
resembles the SDRs and has a partially conserved
characteristic [ST]GXXGXXG NAD-binding motif, but lacks
the conserved active site residues. NmrA is a negative
transcriptional regulator of various fungi, involved in
the post-translational modulation of the GATA-type
transcription factor AreA. NmrA lacks the canonical
GXXGXXG NAD-binding motif and has altered residues at
the catalytic triad, including a Met instead of the
critical Tyr residue. NmrA may bind nucleotides but
appears to lack any dehydrogenase activity. HSCARG has
been identified as a putative NADP-sensing molecule, and
redistributes and restructures in response to NADPH/NADP
ratios. Like NmrA, it lacks most of the active site
residues of the SDR family, but has an NAD(P)-binding
motif similar to the extended SDR family, GXXGXXG. SDRs
are a functionally diverse family of oxidoreductases
that have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Atypical SDRs
are distinct from classical SDRs. Classical SDRs have an
TGXXX[AG]XG cofactor binding motif and a YXXXK active
site motif, with the Tyr residue of the active site
motif serving as a critical catalytic residue (Tyr-151,
human 15-hydroxyprostaglandin dehydrogenase numbering).
In addition to the Tyr and Lys, there is often an
upstream Ser and/or an Asn, contributing to the active
site; while substrate binding is in the C-terminal
region, which determines specificity. The standard
reaction mechanism is a 4-pro-S hydride transfer and
proton relay involving the conserved Tyr and Lys, a
water molecule stabilized by Asn, and nicotinamide. In
addition to the Rossmann fold core region typical of all
SDRs, extended SDRs have a less conserved C-terminal
extension of approximately 100 amino acids, and
typically have a TGXXGXXG cofactor binding motif.
Complex (multidomain) SDRs such as ketoreductase domains
of fatty acid synthase have a GGXGXXG NAD(P)-binding
motif and an altered active site motif (YXXXN). Fungal
type ketoacyl reductases have a TGXXXGX(1-2)G
NAD(P)-binding motif.
Length = 259
Score = 31.9 bits (73), Expect = 0.44
Identities = 10/28 (35%), Positives = 15/28 (53%)
Query: 85 ILITGGAGFVGSHLVDKLMLMGHEVTVV 112
IL+TG G +GS + L+ G V +
Sbjct: 1 ILVTGATGRIGSKVATTLLEAGRPVRAL 28
>gnl|CDD|176183 cd05280, MDR_yhdh_yhfp, Yhdh and yhfp-like putative quinone
oxidoreductases. Yhdh and yhfp-like putative quinone
oxidoreductases (QOR). QOR catalyzes the conversion of a
quinone + NAD(P)H to a hydroquinone + NAD(P)+. Quinones
are cyclic diones derived from aromatic compounds.
Membrane bound QOR actin the respiratory chains of
bacteria and mitochondria, while soluble QOR acts to
protect from toxic quinones (e.g. DT-diaphorase) or as a
soluble eye-lens protein in some vertebrates (e.g.
zeta-crystalin). QOR reduces quinones through a
semi-quinone intermediate via a NAD(P)H-dependent single
electron transfer. QOR is a member of the medium chain
dehydrogenase/reductase family, but lacks the
zinc-binding sites of the prototypical alcohol
dehydrogenases of this group. NAD(P)(H)-dependent
oxidoreductases are the major enzymes in the
interconversion of alcohols and aldehydes, or ketones.
Alcohol dehydrogenase in the liver converts ethanol and
NAD+ to acetaldehyde and NADH, while in yeast and some
other microorganisms ADH catalyzes the conversion
acetaldehyde to ethanol in alcoholic fermentation. ADH
is a member of the medium chain alcohol dehydrogenase
family (MDR), which has a NAD(P)(H)-binding domain in a
Rossmann fold of a beta-alpha form. The NAD(H)-binding
region is comprised of 2 structurally similar halves,
each of which contacts a mononucleotide. A GxGxxG motif
after the first mononucleotide contact half allows the
close contact of the coenzyme with the ADH backbone.
The N-terminal catalytic domain has a distant homology
to GroES. These proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and have 2 tightly bound zinc atoms per
subunit, a catalytic zinc at the active site and a
structural zinc in a lobe of the catalytic domain.
NAD(H) binding occurs in the cleft between the catalytic
and coenzyme-binding domains at the active site, and
coenzyme binding induces a conformational closing of
this cleft. Coenzyme binding typically precedes and
contributes to substrate binding. In human ADH
catalysis, the zinc ion helps coordinate the alcohol,
followed by deprotonation of a histidine, the ribose of
NAD, a serine, then the alcohol, which allows the
transfer of a hydride to NAD+, creating NADH and a
zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 325
Score = 31.7 bits (73), Expect = 0.46
Identities = 15/54 (27%), Positives = 28/54 (51%), Gaps = 4/54 (7%)
Query: 85 ILITGGAGFVGSHLVDKLMLMGHEVTVVDNFFTGRKENVEHWFGHPNFEIIHQD 138
+L+TG G VGS V L +G+ V + TG++E ++ E++ ++
Sbjct: 150 VLVTGATGGVGSIAVAILAKLGYTVVAL----TGKEEQADYLKSLGASEVLDRE 199
>gnl|CDD|176210 cd08248, RTN4I1, Human Reticulon 4 Interacting Protein 1. Human
Reticulon 4 Interacting Protein 1 is a member of the
medium chain dehydrogenase/ reductase (MDR) family.
Riticulons are endoplasmic reticulum associated proteins
involved in membrane trafficking and neuroendocrine
secretion. The MDR/zinc-dependent alcohol
dehydrogenase-like family, which contains the
zinc-dependent alcohol dehydrogenase (ADH-Zn) and
related proteins, is a diverse group of proteins related
to the first identified member, class I mammalian ADH.
MDRs display a broad range of activities and are
distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES.
Length = 350
Score = 31.4 bits (72), Expect = 0.60
Identities = 12/32 (37%), Positives = 18/32 (56%)
Query: 81 SKRRILITGGAGFVGSHLVDKLMLMGHEVTVV 112
+ +R+LI GG+G VG+ + L G VT
Sbjct: 162 AGKRVLILGGSGGVGTFAIQLLKAWGAHVTTT 193
>gnl|CDD|225462 COG2910, COG2910, Putative NADH-flavin reductase [General function
prediction only].
Length = 211
Score = 31.2 bits (71), Expect = 0.63
Identities = 11/29 (37%), Positives = 18/29 (62%)
Query: 84 RILITGGAGFVGSHLVDKLMLMGHEVTVV 112
+I I G +G GS ++ + + GHEVT +
Sbjct: 2 KIAIIGASGKAGSRILKEALKRGHEVTAI 30
>gnl|CDD|181608 PRK09004, PRK09004, FMN-binding protein MioC; Provisional.
Length = 146
Score = 30.2 bits (69), Expect = 0.81
Identities = 11/30 (36%), Positives = 14/30 (46%), Gaps = 4/30 (13%)
Query: 86 LITG----GAGFVGSHLVDKLMLMGHEVTV 111
LI+G GA +V HL +KL G
Sbjct: 6 LISGSTLGGAEYVADHLAEKLEEAGFSTET 35
>gnl|CDD|215720 pfam00106, adh_short, short chain dehydrogenase. This family
contains a wide variety of dehydrogenases.
Length = 167
Score = 30.2 bits (69), Expect = 0.92
Identities = 12/41 (29%), Positives = 16/41 (39%), Gaps = 4/41 (9%)
Query: 85 ILITGGAGFVGSHLVDKLMLMGHEVTVVDNFFTGRKENVEH 125
+LITGG G +G L L G V+ R+
Sbjct: 3 VLITGGTGGLGLALARWLAAEGARHLVL----VSRRGPAPG 39
>gnl|CDD|180439 PRK06171, PRK06171, sorbitol-6-phosphate 2-dehydrogenase;
Provisional.
Length = 266
Score = 30.7 bits (70), Expect = 1.1
Identities = 15/75 (20%), Positives = 31/75 (41%), Gaps = 13/75 (17%)
Query: 83 RRILITGGAGFVGSHLVDKLMLMGHEVTVVDNFFTGRKENVEHWFGHPNFEIIHQDIVTP 142
+ I++TGG+ +G +V +L+ G V D H N++ + D+ +
Sbjct: 10 KIIIVTGGSSGIGLAIVKELLANGANVVNAD-----IHGGDGQ---HENYQFVPTDVSSA 61
Query: 143 LFVEVDEIYHLASPA 157
+E+ H +
Sbjct: 62 -----EEVNHTVAEI 71
>gnl|CDD|235967 PRK07208, PRK07208, hypothetical protein; Provisional.
Length = 479
Score = 31.0 bits (71), Expect = 1.1
Identities = 19/67 (28%), Positives = 24/67 (35%), Gaps = 14/67 (20%)
Query: 65 VRIPKKYPSVKFQDYQSKRRILITGGAGFVGSHLV-----------DKLMLMGHEVTVVD 113
VR+PK YP V Y+ I+ F HLV D ML + V+
Sbjct: 399 VRVPKAYP-VYDGTYERNVEIIRDLLDHFPNLHLVGRNGMHRYNNQDHSMLTA--MLAVE 455
Query: 114 NFFTGRK 120
N G
Sbjct: 456 NIIAGET 462
>gnl|CDD|176220 cd08259, Zn_ADH5, Alcohol dehydrogenases of the MDR family.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. This group contains proteins that
share the characteristic catalytic and structural
zinc-binding sites of the zinc-dependent alcohol
dehydrogenase family. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which have a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES. These
proteins typically form dimers (typically higher plants,
mammals) or tetramers (yeast, bacteria), and have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site and a structural zinc in a lobe of
the catalytic domain. NAD(H)-binding occurs in the cleft
between the catalytic and coenzyme-binding domains at
the active site, and coenzyme binding induces a
conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
In human ADH catalysis, the zinc ion helps coordinate
the alcohol, followed by deprotonation of a histidine
(His-51), the ribose of NAD, a serine (Ser-48), then the
alcohol, which allows the transfer of a hydride to NAD+,
creating NADH and a zinc-bound aldehyde or ketone. In
yeast and some bacteria, the active site zinc binds an
aldehyde, polarizing it, and leading to the reverse
reaction.
Length = 332
Score = 30.4 bits (69), Expect = 1.3
Identities = 10/33 (30%), Positives = 15/33 (45%)
Query: 80 QSKRRILITGGAGFVGSHLVDKLMLMGHEVTVV 112
+ +L+TG G VG H + +G V V
Sbjct: 161 KKGDTVLVTGAGGGVGIHAIQLAKALGARVIAV 193
>gnl|CDD|178256 PLN02650, PLN02650, dihydroflavonol-4-reductase.
Length = 351
Score = 30.6 bits (69), Expect = 1.4
Identities = 15/34 (44%), Positives = 22/34 (64%), Gaps = 2/34 (5%)
Query: 82 KRRILITGGAGFVGSHLVDKLMLMGHEV--TVVD 113
K + +TG +GF+GS LV +L+ G+ V TV D
Sbjct: 5 KETVCVTGASGFIGSWLVMRLLERGYTVRATVRD 38
>gnl|CDD|187569 cd05259, PCBER_SDR_a, phenylcoumaran benzylic ether reductase
(PCBER) like, atypical (a) SDRs. PCBER and
pinoresinol-lariciresinol reductases are NADPH-dependent
aromatic alcohol reductases, and are atypical members of
the SDR family. Other proteins in this subgroup are
identified as eugenol synthase. These proteins contain
an N-terminus characteristic of NAD(P)-binding proteins
and a small C-terminal domain presumed to be involved in
substrate binding, but they do not have the conserved
active site Tyr residue typically found in SDRs.
Numerous other members have unknown functions. The
glycine rich NADP-binding motif in this subgroup is of 2
forms: GXGXXG and G[GA]XGXXG; it tends to be atypical
compared with the forms generally seen in classical or
extended SDRs. The usual SDR active site tetrad is not
present, but a critical active site Lys at the usual SDR
position has been identified in various members, though
other charged and polar residues are found at this
position in this subgroup. Atypical SDR-related proteins
retain the Rossmann fold of the SDRs, but have limited
sequence identity and generally lack the catalytic
properties of the archetypical members. Atypical SDRs
include biliverdin IX beta reductase (BVR-B,aka flavin
reductase), NMRa (a negative transcriptional regulator
of various fungi), progesterone 5-beta-reductase like
proteins, phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. In addition to the
Rossmann fold core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 282
Score = 30.3 bits (69), Expect = 1.4
Identities = 11/30 (36%), Positives = 16/30 (53%), Gaps = 1/30 (3%)
Query: 84 RILITGGAGFVGSHLVDKLM-LMGHEVTVV 112
+I I G G +G +V L+ G VTV+
Sbjct: 1 KIAIAGATGTLGGPIVSALLASPGFTVTVL 30
>gnl|CDD|214966 smart01002, AlaDh_PNT_C, Alanine dehydrogenase/PNT, C-terminal
domain. Alanine dehydrogenase catalyzes the
NAD-dependent reversible reductive amination of pyruvate
into alanine.
Length = 149
Score = 29.4 bits (67), Expect = 1.5
Identities = 14/46 (30%), Positives = 21/46 (45%), Gaps = 4/46 (8%)
Query: 84 RILITGGAGFVGSHLVDKLMLMGHEVTVVD-NFFTGRKENVEHWFG 128
++++ G AG VG +G EVTV+D R +E G
Sbjct: 22 KVVVIG-AGVVGLGAAATAKGLGAEVTVLDVR--PARLRQLESLLG 64
>gnl|CDD|240131 cd04861, LigD_Pol_like, LigD_Pol_like: Polymerase (Pol) domain of
bacterial LigD proteins similar to Pseudomonas
aeruginosa (Pae) LigD. The LigD Pol domain belongs to
the archaeal/eukaryal primase (AEP) superfamily. In
prokaryotes, LigD along with Ku is required for
non-homologous end joining (NHEJ)-mediated repair of DNA
double-strand breaks (DSB). NHEJ-mediated DNA DSB repair
is error-prone. PaeLigD is monomeric, containing an
N-terminal phosphoesterase module, a central polymerase
(Pol) domain, and a C-terminal ATP-dependent ligase
domain. Mycobacterium tuberculosis (Mt)LigD, also found
in this group, is monomeric and contains the same
modules but these are arranged differently: an
N-terminal Pol domain, a central phosphoesterase module,
and a C-terminal ligase domain. It has been suggested
that LigD Pol contributes to NHEJ-mediated DNA DSB
repair in vivo, by filling in short 5'-overhangs with
ribonucleotides; the filled in termini would then be
sealed by the associated LigD ligase domain, resulting
in short stretches of RNA incorporated into the genomic
DNA. The PaeLigD Pol domain in vitro, in a
manganese-dependent fashion, catalyzes templated
extensions of 5'-overhang duplex DNA, and nontemplated
single-nucleotide additions to blunt-end duplex DNA; it
preferentially adds single ribonucleotides at blunt DNA
ends. PaeLigD Pol adds a correctly paired rNTP to the
DNA primer termini more rapidly than it does a correctly
paired dNTP; it has higher infidelity as an RNA
polymerase than it does as a DNA polymerase, which is in
keeping with the mutagenic property of NHEJ-mediated DNA
DSB repair. The MtLigD Pol domain similarly is
stimulated by manganese, is error-prone, and prefers
adding rNTPs to dNTPs in vitro. The MtLigD Pol domain
has been shown to prefer DNA gapped substrates
containing a 5'-phosphate group at the gap.
Length = 227
Score = 29.8 bits (68), Expect = 1.8
Identities = 14/44 (31%), Positives = 19/44 (43%), Gaps = 8/44 (18%)
Query: 218 PIGPRACYDEAKRVAETLCYAYAR-HEDLSV-------RVARIF 253
P+ PR +DE + A+ L AR DL R +IF
Sbjct: 149 PLAPRYTWDEVRAFAKALARELARRLPDLFTAEMAKAKRGGKIF 192
>gnl|CDD|234024 TIGR02817, adh_fam_1, zinc-binding alcohol dehydrogenase family
protein. Members of this model form a distinct subset
of the larger family of oxidoreductases that includes
zinc-binding alcohol dehydrogenases and NADPH:quinone
reductases (pfam00107). While some current members of
this family carry designations as putative alginate
lyase, it seems no sequence with a direct
characterization as such is detected by this model
[Energy metabolism, Fermentation].
Length = 336
Score = 30.1 bits (68), Expect = 1.8
Identities = 12/18 (66%), Positives = 14/18 (77%)
Query: 82 KRRILITGGAGFVGSHLV 99
KR +LI GGAG VGS L+
Sbjct: 149 KRALLIIGGAGGVGSILI 166
>gnl|CDD|176191 cd05289, MDR_like_2, alcohol dehydrogenase and quinone
reductase-like medium chain degydrogenases/reductases.
Members identified as zinc-dependent alcohol
dehydrogenases and quinone oxidoreductase. QOR catalyzes
the conversion of a quinone + NAD(P)H to a hydroquinone
+ NAD(P)+. Quinones are cyclic diones derived from
aromatic compounds. Membrane bound QOR actin the
respiratory chains of bacteria and mitochondria, while
soluble QOR acts to protect from toxic quinones (e.g.
DT-diaphorase) or as a soluble eye-lens protein in some
vertebrates (e.g. zeta-crystalin). QOR reduces quinones
through a semi-quinone intermediate via a
NAD(P)H-dependent single electron transfer. QOR is a
member of the medium chain dehydrogenase/reductase
family, but lacks the zinc-binding sites of the
prototypical alcohol dehydrogenases of this group.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which has a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES. These
proteins typically form dimers (typically higher plants,
mammals) or tetramers (yeast, bacteria), and have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site and a structural zinc in a lobe of
the catalytic domain. NAD(H) binding occurs in the
cleft between the catalytic and coenzyme-binding domains
at the active site, and coenzyme binding induces a
conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
In human ADH catalysis, the zinc ion helps coordinate
the alcohol, followed by deprotonation of a histidine,
the ribose of NAD, a serine, then the alcohol, which
allows the transfer of a hydride to NAD+, creating NADH
and a zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 309
Score = 29.8 bits (68), Expect = 1.9
Identities = 13/45 (28%), Positives = 18/45 (40%), Gaps = 5/45 (11%)
Query: 80 QSKRRILITGGAGFVGSHLVDKLMLMGHEVTVVDNFFTGRKENVE 124
++ + +LI G AG VGS V G V T N +
Sbjct: 143 KAGQTVLIHGAAGGVGSFAVQLAKARGARVIA-----TASAANAD 182
>gnl|CDD|235630 PRK05865, PRK05865, hypothetical protein; Provisional.
Length = 854
Score = 30.0 bits (67), Expect = 2.1
Identities = 31/119 (26%), Positives = 47/119 (39%), Gaps = 23/119 (19%)
Query: 84 RILITGGAGFVGSHLVDKLMLMGHEVTVVDNFFTGRKENVEHWFGHPNFEIIHQDI---- 139
RI +TG +G +G L +L+ GHEV + + + W +F I DI
Sbjct: 2 RIAVTGASGVLGRGLTARLLSQGHEVVGIA------RHRPDSWPSSADF--IAADIRDAT 53
Query: 140 -VTPLFVEVDEIYHLASPASPPHYMFNPVKTIKTNTIGTINMLGLAKRVGA-KILFAST 196
V D + H A ++ I N GT N+L G +I+F S+
Sbjct: 54 AVESAMTGADVVAHCA-------WVRGRNDHI--NIDGTANVLKAMAETGTGRIVFTSS 103
>gnl|CDD|216396 pfam01262, AlaDh_PNT_C, Alanine dehydrogenase/PNT, C-terminal
domain. This family now also contains the lysine
2-oxoglutarate reductases.
Length = 150
Score = 29.0 bits (66), Expect = 2.1
Identities = 11/49 (22%), Positives = 17/49 (34%), Gaps = 12/49 (24%)
Query: 77 QDYQSKRRILITG------------GAGFVGSHLVDKLMLMGHEVTVVD 113
+ Y +L+ G G G VG +G VT++D
Sbjct: 2 EKYGGGFGMLLGGAGGVPPAKVVVIGGGVVGLGAAATAKGLGAPVTILD 50
>gnl|CDD|215100 PLN00198, PLN00198, anthocyanidin reductase; Provisional.
Length = 338
Score = 29.9 bits (67), Expect = 2.2
Identities = 32/137 (23%), Positives = 54/137 (39%), Gaps = 25/137 (18%)
Query: 80 QSKRRILITGGAGFVGSHLVDKLMLMGHEV-TVVDNFFTGRKENVEHWFGHPNF------ 132
K+ + GG GF+ S L+ L+ G+ V T V + +K + H
Sbjct: 7 TGKKTACVIGGTGFLASLLIKLLLQKGYAVNTTVRDPENQKK--IAHLRALQELGDLKIF 64
Query: 133 --EIIHQDIVTPLFVEVDEIYHLASPAS-----PPHYMFNPVKTIKTNTIGTINMLGL-- 183
++ ++ D ++H+A+P + P + M IK G N+L
Sbjct: 65 GADLTDEESFEAPIAGCDLVFHVATPVNFASEDPENDM------IKPAIQGVHNVLKACA 118
Query: 184 -AKRVGAKILFASTSEV 199
AK V IL +S + V
Sbjct: 119 KAKSVKRVILTSSAAAV 135
>gnl|CDD|187598 cd05339, 17beta-HSDXI-like_SDR_c, human 17-beta-hydroxysteroid
dehydrogenase XI-like, classical (c) SDRs.
17-beta-hydroxysteroid dehydrogenases (17betaHSD) are a
group of isozymes that catalyze activation and
inactivation of estrogen and androgens. 17betaHSD type
XI, a classical SDR, preferentially converts
3alpha-adiol to androsterone but not numerous other
tested steroids. This subgroup of classical SDRs also
includes members identified as retinol dehydrogenases,
which convert retinol to retinal, a property that
overlaps with 17betaHSD activity. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold (alpha/beta folding pattern with a central
beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRS are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes have a
3-glycine N-terminal NAD(P)(H)-binding pattern
(typically, TGxxxGxG in classical SDRs and TGxxGxxG in
extended SDRs), while substrate binding is in the
C-terminal region. A critical catalytic Tyr residue
(Tyr-151, human 15-hydroxyprostaglandin dehydrogenase
(15-PGDH) numbering), is often found in a conserved
YXXXK pattern. In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) or additional
Ser, contributing to the active site. Substrates for
these enzymes include sugars, steroids, alcohols, and
aromatic compounds. The standard reaction mechanism is a
proton relay involving the conserved Tyr and Lys, as
well as Asn (or Ser). Some SDR family members, including
17 beta-hydroxysteroid dehydrogenase contain an
additional helix-turn-helix motif that is not generally
found among SDRs.
Length = 243
Score = 29.5 bits (67), Expect = 2.4
Identities = 10/29 (34%), Positives = 16/29 (55%)
Query: 85 ILITGGAGFVGSHLVDKLMLMGHEVTVVD 113
+LITGG +G L + G +V ++D
Sbjct: 2 VLITGGGSGIGRLLALEFAKRGAKVVILD 30
>gnl|CDD|99959 cd01635, Glycosyltransferase_GTB_type, Glycosyltransferases
catalyze the transfer of sugar moieties from activated
donor molecules to specific acceptor molecules, forming
glycosidic bonds. The acceptor molecule can be a lipid,
a protein, a heterocyclic compound, or another
carbohydrate residue. The structures of the formed
glycoconjugates are extremely diverse, reflecting a wide
range of biological functions. The members of this
family share a common GTB topology, one of the two
protein topologies observed for
nucleotide-sugar-dependent glycosyltransferases. GTB
proteins have distinct N- and C- terminal domains each
containing a typical Rossmann fold. The two domains have
high structural homology despite minimal sequence
homology. The large cleft that separates the two domains
includes the catalytic center and permits a high degree
of flexibility.
Length = 229
Score = 29.5 bits (66), Expect = 2.5
Identities = 12/50 (24%), Positives = 16/50 (32%), Gaps = 4/50 (8%)
Query: 87 ITGGAGFVGSHLVDKLMLMGHEVTVVDNFFTGRKENVEHWFGHPNFEIIH 136
GG V L L GHEV VV + +++H
Sbjct: 11 GGGGVELVLLDLAKALARRGHEVEVV----ALLLLLLLRILRGFKPDVVH 56
>gnl|CDD|226476 COG3967, DltE, Short-chain dehydrogenase involved in D-alanine
esterification of lipoteichoic acid and wall teichoic
acid (D-alanine transfer protein) [Cell envelope
biogenesis, outer membrane].
Length = 245
Score = 29.3 bits (66), Expect = 2.6
Identities = 14/37 (37%), Positives = 20/37 (54%), Gaps = 5/37 (13%)
Query: 85 ILITGGAGFVGSHLVDKLMLMGHEVTVVDNFFTGRKE 121
ILITGGA +G L + + +G+ V + GR E
Sbjct: 8 ILITGGASGIGLALAKRFLELGNTVII-----CGRNE 39
>gnl|CDD|224657 COG1743, COG1743, Adenine-specific DNA methylase containing a
Zn-ribbon [DNA replication, recombination, and repair].
Length = 875
Score = 29.8 bits (67), Expect = 2.6
Identities = 22/97 (22%), Positives = 35/97 (36%), Gaps = 9/97 (9%)
Query: 43 RGDLNFA------NERIKILEEKLKSLDVRIPKKYPSVKFQDYQSKRRILITGGAGFVGS 96
RGDL F ER ++ E+L+ P+ + ++ R + I G +
Sbjct: 288 RGDLIFEPATDEDLERFELAREELREEWEEADDDVPTEEIPRGENPRGVRIYGIWDW--Y 345
Query: 97 HLVDKLMLMGHEVTVVDNFFTGRKENVEHWFGHPNFE 133
L + L+ V V K+ E W FE
Sbjct: 346 KLFNPRQLLAL-VKFVRLIREVGKKIEEGWAAERAFE 381
>gnl|CDD|187628 cd05370, SDR_c2, classical (c) SDR, subgroup 2. Short-chain
dehydrogenases/reductases (SDRs, aka Tyrosine-dependent
oxidoreductases) 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 = 228
Score = 29.2 bits (66), Expect = 2.8
Identities = 14/39 (35%), Positives = 20/39 (51%), Gaps = 5/39 (12%)
Query: 83 RRILITGGAGFVGSHLVDKLMLMGHEVTVVDNFFTGRKE 121
+LITGG +G L K + G+ V + TGR+E
Sbjct: 6 NTVLITGGTSGIGLALARKFLEAGNTVII-----TGRRE 39
>gnl|CDD|183775 PRK12826, PRK12826, 3-ketoacyl-(acyl-carrier-protein) reductase;
Reviewed.
Length = 251
Score = 29.1 bits (66), Expect = 2.9
Identities = 13/31 (41%), Positives = 17/31 (54%)
Query: 83 RRILITGGAGFVGSHLVDKLMLMGHEVTVVD 113
R L+TG A +G + +L G EV VVD
Sbjct: 7 RVALVTGAARGIGRAIAVRLAADGAEVIVVD 37
>gnl|CDD|215370 PLN02686, PLN02686, cinnamoyl-CoA reductase.
Length = 367
Score = 29.4 bits (66), Expect = 3.0
Identities = 11/30 (36%), Positives = 19/30 (63%)
Query: 83 RRILITGGAGFVGSHLVDKLMLMGHEVTVV 112
R + +TGG F+G +VD+L+ G+ V +
Sbjct: 54 RLVCVTGGVSFLGLAIVDRLLRHGYSVRIA 83
>gnl|CDD|132368 TIGR03325, BphB_TodD, cis-2,3-dihydrobiphenyl-2,3-diol
dehydrogenase. Members of this family occur as the BphD
protein of biphenyl catabolism and as the TodD protein
of toluene catabolism. Members catalyze the second step
in each pathway and proved interchangeable when tested;
the first and fourth enzymes in each pathway confer
metabolic specificity. In the context of biphenyl
degradation, the enzyme acts as
cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase (EC
1.3.1.56), while in toluene degradation it acts as
cis-toluene dihydrodiol dehydrogenase.
Length = 262
Score = 29.0 bits (65), Expect = 3.1
Identities = 12/29 (41%), Positives = 19/29 (65%)
Query: 85 ILITGGAGFVGSHLVDKLMLMGHEVTVVD 113
+L+TGGA +G +VD+ + G V V+D
Sbjct: 8 VLVTGGASGLGRAIVDRFVAEGARVAVLD 36
>gnl|CDD|224996 COG2085, COG2085, Predicted dinucleotide-binding enzymes [General
function prediction only].
Length = 211
Score = 28.8 bits (65), Expect = 3.3
Identities = 12/30 (40%), Positives = 15/30 (50%), Gaps = 1/30 (3%)
Query: 82 KRRILITGGAGFVGSHLVDKLMLMGHEVTV 111
I I G G +GS L +L GHEV +
Sbjct: 1 MMIIAI-IGTGNIGSALALRLAKAGHEVII 29
>gnl|CDD|133419 cd00650, LDH_MDH_like, NAD-dependent, lactate dehydrogenase-like,
2-hydroxycarboxylate dehydrogenase family. Members of
this family include ubiquitous enzymes like L-lactate
dehydrogenases (LDH), L-2-hydroxyisocaproate
dehydrogenases, and some malate dehydrogenases (MDH).
LDH catalyzes the last step of glycolysis in which
pyruvate is converted to L-lactate. MDH is one of the
key enzymes in the citric acid cycle, facilitating both
the conversion of malate to oxaloacetate and
replenishing levels of oxalacetate by reductive
carboxylation of pyruvate. The LDH/MDH-like proteins are
part of the NAD(P)-binding Rossmann fold superfamily,
which includes a wide variety of protein families
including the NAD(P)-binding domains of alcohol
dehydrogenases, tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate dehydrogenases,
formate/glycerate dehydrogenases, siroheme synthases,
6-phosphogluconate dehydrogenases, aminoacid
dehydrogenases, repressor rex, and NAD-binding potassium
channel domains, among others.
Length = 263
Score = 29.2 bits (66), Expect = 3.4
Identities = 10/35 (28%), Positives = 15/35 (42%), Gaps = 4/35 (11%)
Query: 85 ILITGGAGFVGSHLV----DKLMLMGHEVTVVDNF 115
I + G G VG L D +L+ E+ + D
Sbjct: 1 IAVIGAGGNVGPALAFGLADGSVLLAIELVLYDID 35
>gnl|CDD|179902 PRK04965, PRK04965, NADH:flavorubredoxin oxidoreductase;
Provisional.
Length = 377
Score = 29.1 bits (66), Expect = 3.5
Identities = 14/38 (36%), Positives = 21/38 (55%), Gaps = 1/38 (2%)
Query: 77 QDYQSKRRILITGGAGFVGSHLVDKLMLMGHEVTVVDN 114
+ +R+L+ GG G +G+ L L G VT+VDN
Sbjct: 136 TQLRDAQRVLVVGG-GLIGTELAMDLCRAGKAVTLVDN 172
>gnl|CDD|223411 COG0334, GdhA, Glutamate dehydrogenase/leucine dehydrogenase [Amino
acid transport and metabolism].
Length = 411
Score = 29.1 bits (66), Expect = 3.6
Identities = 9/24 (37%), Positives = 13/24 (54%)
Query: 90 GAGFVGSHLVDKLMLMGHEVTVVD 113
G G VG + +KL +G +V V
Sbjct: 214 GFGNVGQYAAEKLHELGAKVVAVS 237
>gnl|CDD|236399 PRK09186, PRK09186, flagellin modification protein A; Provisional.
Length = 256
Score = 28.8 bits (65), Expect = 3.9
Identities = 17/63 (26%), Positives = 25/63 (39%), Gaps = 3/63 (4%)
Query: 83 RRILITGGAGFVGSHLVDKLMLMGHEVTVVD---NFFTGRKENVEHWFGHPNFEIIHQDI 139
+ ILITG G +GS LV ++ G V D E++ F ++ DI
Sbjct: 5 KTILITGAGGLIGSALVKAILEAGGIVIAADIDKEALNELLESLGKEFKSKKLSLVELDI 64
Query: 140 VTP 142
Sbjct: 65 TDQ 67
>gnl|CDD|237249 PRK12891, PRK12891, allantoate amidohydrolase; Reviewed.
Length = 414
Score = 29.0 bits (65), Expect = 3.9
Identities = 20/79 (25%), Positives = 28/79 (35%), Gaps = 14/79 (17%)
Query: 183 LAKRVGAKILFASTSEVYGDPEVHPQPETYWGHVNPIG--PRACYDEAKRVAETLCYAYA 240
A RV + L+AS + P G R + R A L A+A
Sbjct: 3 RAPRVDGERLWASLERMAQI------------GATPKGGVCRLALTDGDREARDLFVAWA 50
Query: 241 RHEDLSVRVARIFNTYGPR 259
R +VRV + N + R
Sbjct: 51 RDAGCTVRVDAMGNLFARR 69
>gnl|CDD|183773 PRK12824, PRK12824, acetoacetyl-CoA reductase; Provisional.
Length = 245
Score = 29.0 bits (65), Expect = 4.0
Identities = 14/51 (27%), Positives = 25/51 (49%), Gaps = 3/51 (5%)
Query: 82 KRRILITGGAGFVGSHLVDKLMLMGHEVTVVDNFFTGRKENVEHWFGHPNF 132
K+ L+TG +GS + +L+ G+ V+ +F+G + WF F
Sbjct: 2 KKIALVTGAKRGIGSAIARELLNDGY--RVIATYFSGNDCAKD-WFEEYGF 49
>gnl|CDD|215072 PLN00141, PLN00141, Tic62-NAD(P)-related group II protein;
Provisional.
Length = 251
Score = 28.7 bits (64), Expect = 4.3
Identities = 26/125 (20%), Positives = 50/125 (40%), Gaps = 16/125 (12%)
Query: 80 QSKRRILITGGAGFVGSHLVDKLMLMGHEV----TVVDNFFTGRKENVEHWFGHPNFEII 135
+ + + G G G +V++L+ G V VD T ++ P+ +I+
Sbjct: 15 VKTKTVFVAGATGRTGKRIVEQLLAKGFAVKAGVRDVDKAKTSLPQD-------PSLQIV 67
Query: 136 HQDIVTPLFVEVDEIYHLASP---ASPPHYMFNPVKTIKTNTIGTINMLGLAKRVGAK-- 190
D+ V+ I + A+ F+P K + GT+N++ ++ G
Sbjct: 68 RADVTEGSDKLVEAIGDDSDAVICATGFRRSFDPFAPWKVDNFGTVNLVEACRKAGVTRF 127
Query: 191 ILFAS 195
IL +S
Sbjct: 128 ILVSS 132
>gnl|CDD|131367 TIGR02314, ABC_MetN, D-methionine ABC transporter, ATP-binding
protein. Members of this family are the ATP-binding
protein of the D-methionine ABC transporter complex.
Known members belong to the Proteobacteria.
Length = 343
Score = 28.7 bits (64), Expect = 4.5
Identities = 15/64 (23%), Positives = 27/64 (42%)
Query: 96 SHLVDKLMLMGHEVTVVDNFFTGRKENVEHWFGHPNFEIIHQDIVTPLFVEVDEIYHLAS 155
+H +D + + V V+ N + V F HP + + I + L + + E Y
Sbjct: 198 THEMDVVKRICDCVAVISNGELIEQGTVSEIFSHPKTPLAQKFIRSTLHLSIPEDYQERL 257
Query: 156 PASP 159
A+P
Sbjct: 258 QATP 261
>gnl|CDD|216180 pfam00899, ThiF, ThiF family. This family contains a repeated
domain in ubiquitin activating enzyme E1 and members of
the bacterial ThiF/MoeB/HesA family.
Length = 134
Score = 27.5 bits (62), Expect = 5.8
Identities = 12/32 (37%), Positives = 19/32 (59%), Gaps = 2/32 (6%)
Query: 84 RILITGGAGFVGSHLVDKLMLMG-HEVTVVDN 114
R+L+ G AG +GS + L G ++T+VD
Sbjct: 3 RVLVVG-AGGLGSPAAEYLARAGVGKLTLVDF 33
>gnl|CDD|184746 PRK14562, PRK14562, haloacid dehalogenase superfamily protein;
Provisional.
Length = 204
Score = 27.9 bits (63), Expect = 6.0
Identities = 12/37 (32%), Positives = 19/37 (51%), Gaps = 1/37 (2%)
Query: 43 RGDLNFANERIKILEEKLKSLDVRIPKKYPSVKFQDY 79
RGD A + +K EE +K L + K +P + + Y
Sbjct: 43 RGDFEEAEKLLKEAEELVKELKELL-KDHPELYYAGY 78
>gnl|CDD|168574 PRK06484, PRK06484, short chain dehydrogenase; Validated.
Length = 520
Score = 28.7 bits (64), Expect = 6.1
Identities = 12/45 (26%), Positives = 19/45 (42%)
Query: 80 QSKRRILITGGAGFVGSHLVDKLMLMGHEVTVVDNFFTGRKENVE 124
R +L+TG AG +G + G +V V D +E +
Sbjct: 3 AQSRVVLVTGAAGGIGRAACQRFARAGDQVVVADRNVERARERAD 47
>gnl|CDD|236982 PRK11784, PRK11784, tRNA 2-selenouridine synthase; Provisional.
Length = 345
Score = 28.3 bits (64), Expect = 6.8
Identities = 10/35 (28%), Positives = 15/35 (42%)
Query: 242 HEDLSVRVARIFNTYGPRMHMNDGRVVSNFIIQAL 276
L RV R+ Y RMH + ++ +AL
Sbjct: 243 EAPLEERVERLLEDYVLRMHAAGFQAYPEYLAEAL 277
>gnl|CDD|187615 cd05357, PR_SDR_c, pteridine reductase (PR), classical (c) SDRs.
Pteridine reductases (PRs), members of the SDR family,
catalyzes the NAD-dependent reduction of folic acid,
dihydrofolate and related compounds. In Leishmania,
pteridine reductase (PTR1) acts to circumvent the
anti-protozoan drugs that attack dihydrofolate reductase
activity. Proteins in this subgroup have an N-terminal
NAD-binding motif and a YxxxK active site motif, but
have an Asp instead of the usual upstream catalytic Ser.
SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold (alpha/beta folding
pattern with a central beta-sheet), an NAD(P)(H)-binding
region, and a structurally diverse C-terminal region.
Classical SDRs are typically about 250 residues long,
while extended SDRS are approximately 350 residues.
Sequence identity between different SDR enzymes are
typically in the 15-30% range, but the enzymes share the
Rossmann fold NAD-binding motif and characteristic
NAD-binding and catalytic sequence patterns. These
enzymes have a 3-glycine N-terminal NAD(P)(H)-binding
pattern (typically, TGxxxGxG in classical SDRs and
TGxxGxxG in extended SDRs), while substrate binding is
in the C-terminal region. A critical catalytic Tyr
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase (15-PGDH) numbering), is often found in a
conserved YXXXK pattern. In addition to the Tyr and Lys,
there is often an upstream Ser (Ser-138, 15-PGDH
numbering) and/or an Asn (Asn-107, 15-PGDH numbering) or
additional Ser, contributing to the active site.
Substrates for these enzymes include sugars, steroids,
alcohols, and aromatic compounds. The standard reaction
mechanism is a proton relay involving the conserved Tyr
and Lys, as well as Asn (or Ser). Some SDR family
members, including 17 beta-hydroxysteroid dehydrogenase
contain an additional helix-turn-helix motif that is not
generally found among SDRs.
Length = 234
Score = 28.0 bits (63), Expect = 7.5
Identities = 9/27 (33%), Positives = 14/27 (51%)
Query: 85 ILITGGAGFVGSHLVDKLMLMGHEVTV 111
L+TG A +G + + L G+ V V
Sbjct: 3 ALVTGAAKRIGRAIAEALAAEGYRVVV 29
>gnl|CDD|187647 cd08943, R1PA_ADH_SDR_c, rhamnulose-1-phosphate aldolase/alcohol
dehydrogenase, classical (c) SDRs. This family has
bifunctional proteins with an N-terminal aldolase and a
C-terminal classical SDR domain. One member is
identified as a rhamnulose-1-phosphate aldolase/alcohol
dehydrogenase. The SDR domain has a canonical SDR
glycine-rich NAD(P) binding motif and a match to the
characteristic active site triad. However, it lacks an
upstream active site Asn typical of 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 = 250
Score = 28.1 bits (63), Expect = 7.5
Identities = 11/28 (39%), Positives = 15/28 (53%)
Query: 86 LITGGAGFVGSHLVDKLMLMGHEVTVVD 113
L+TGGA +G + +L G V V D
Sbjct: 5 LVTGGASGIGLAIAKRLAAEGAAVVVAD 32
>gnl|CDD|221927 pfam13116, DUF3971, Protein of unknown function. Some members of
this family are related to the AsmA family proteins.
Length = 289
Score = 28.0 bits (63), Expect = 8.0
Identities = 15/50 (30%), Positives = 19/50 (38%), Gaps = 11/50 (22%)
Query: 26 VRYDDNVLEDSPLITRLRGDLNFANERIKI-------LEEKLKSLDVRIP 68
+++D D P IT L DL F N + I L V IP
Sbjct: 67 LKFD----PDWPAITDLNADLLFKNNGLDIDANSAKLQGVTLDGSTVVIP 112
>gnl|CDD|238760 cd01483, E1_enzyme_family, Superfamily of activating enzymes (E1)
of the ubiquitin-like proteins. This family includes
classical ubiquitin-activating enzymes E1,
ubiquitin-like (ubl) activating enzymes and other
mechanistic homologes, like MoeB, Thif1 and others. The
common reaction mechanism catalyzed by MoeB, ThiF and
the E1 enzymes begins with a nucleophilic attack of the
C-terminal carboxylate of MoaD, ThiS and ubiquitin,
respectively, on the alpha-phosphate of an ATP molecule
bound at the active site of the activating enzymes,
leading to the formation of a high-energy acyladenylate
intermediate and subsequently to the formation of a
thiocarboxylate at the C termini of MoaD and ThiS.
Length = 143
Score = 27.2 bits (61), Expect = 8.0
Identities = 10/32 (31%), Positives = 18/32 (56%), Gaps = 2/32 (6%)
Query: 84 RILITGGAGFVGSHLVDKLMLMGH-EVTVVDN 114
R+L+ G G +GS + L G ++T++D
Sbjct: 1 RVLLVG-LGGLGSEIALNLARSGVGKITLIDF 31
>gnl|CDD|219686 pfam07992, Pyr_redox_2, Pyridine nucleotide-disulphide
oxidoreductase. This family includes both class I and
class II oxidoreductases and also NADH oxidases and
peroxidases. This domain is actually a small NADH
binding domain within a larger FAD binding domain.
Length = 283
Score = 27.7 bits (62), Expect = 9.2
Identities = 13/31 (41%), Positives = 21/31 (67%), Gaps = 1/31 (3%)
Query: 83 RRILITGGAGFVGSHLVDKLMLMGHEVTVVD 113
+R+++ GG G++G L L +G EVTVV+
Sbjct: 143 KRVVVVGG-GYIGLELAAALAKLGKEVTVVE 172
>gnl|CDD|235633 PRK05872, PRK05872, short chain dehydrogenase; Provisional.
Length = 296
Score = 27.6 bits (62), Expect = 9.3
Identities = 9/31 (29%), Positives = 19/31 (61%)
Query: 83 RRILITGGAGFVGSHLVDKLMLMGHEVTVVD 113
+ +++TG A +G+ L +L G ++ +VD
Sbjct: 10 KVVVVTGAARGIGAELARRLHARGAKLALVD 40
>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 = 27.7 bits (62), Expect = 9.7
Identities = 11/33 (33%), Positives = 16/33 (48%)
Query: 81 SKRRILITGGAGFVGSHLVDKLMLMGHEVTVVD 113
+ ILITG AG +G L+ G + + D
Sbjct: 1 EDKIILITGAAGLIGKAFCKALLSAGARLILAD 33
>gnl|CDD|184316 PRK13771, PRK13771, putative alcohol dehydrogenase; Provisional.
Length = 334
Score = 27.7 bits (62), Expect = 9.8
Identities = 20/81 (24%), Positives = 32/81 (39%), Gaps = 21/81 (25%)
Query: 48 FANERIKILEEKLKSLDVRIPKK----------------YPSVKFQDYQSKRRILITGGA 91
FA E K+ K+ SL V++P Y ++ + +L+TG
Sbjct: 118 FA-EYAKV---KVTSL-VKVPPNVSDEGAVIVPCVTGMVYRGLRRAGVKKGETVLVTGAG 172
Query: 92 GFVGSHLVDKLMLMGHEVTVV 112
G VG H + +G +V V
Sbjct: 173 GGVGIHAIQVAKALGAKVIAV 193
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 0.137 0.416
Gapped
Lambda K H
0.267 0.0831 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 18,692,376
Number of extensions: 1829420
Number of successful extensions: 2305
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2167
Number of HSP's successfully gapped: 184
Length of query: 360
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 262
Effective length of database: 6,590,910
Effective search space: 1726818420
Effective search space used: 1726818420
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 60 (26.7 bits)