RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14682
(322 letters)
>gnl|CDD|187558 cd05247, UDP_G4E_1_SDR_e, UDP-glucose 4 epimerase, subgroup 1,
extended (e) SDRs. UDP-glucose 4 epimerase (aka
UDP-galactose-4-epimerase), is a homodimeric extended
SDR. It catalyzes the NAD-dependent conversion of
UDP-galactose to UDP-glucose, the final step in Leloir
galactose synthesis. This subgroup has the
characteristic active site tetrad and NAD-binding motif
of the extended SDRs. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately 100
amino acids. Extended SDRs are a diverse collection of
proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 323
Score = 347 bits (893), Expect = e-120
Identities = 119/235 (50%), Positives = 151/235 (64%), Gaps = 27/235 (11%)
Query: 1 MQEFKVYHFVFSSSSTVYGTPKFLPFTEDHPTGQGCTNPYGKSKYFVEEILKDLASFKQK 60
M+ V +FVFSSS+ VYG P+ +P TE+ P TNPYG++K VE+IL+DLA
Sbjct: 107 MRAHGVKNFVFSSSAAVYGEPETVPITEEAPLN--PTNPYGRTKLMVEQILRDLA----- 159
Query: 61 LQSLQSSVTQIWLNSVHRSDWHIISLRYFNPVGSHPSGDIGEDPNGIPNNLMPYISQVAV 120
+ + LRYFNP G+HPSG IGEDP IPNNL+PY+ QVA+
Sbjct: 160 ----------------KAPGLNYVILRYFNPAGAHPSGLIGEDPQ-IPNNLIPYVLQVAL 202
Query: 121 GRRKKLMVFGDDYDTKDGSGVRDYIHIMDLAEGHVTALDKLLGGKSQAGFKAYNLGTGTG 180
GRR+KL +FGDDY T DG+ VRDYIH++DLA+ HV AL+KL G G + YNLGTG G
Sbjct: 203 GRREKLAIFGDDYPTPDGTCVRDYIHVVDLADAHVLALEKLENGG---GSEIYNLGTGRG 259
Query: 181 YSVFEMVKAFSEACKKNIPYEVVGRREGDIASSYCDASLAKKELAWEAKYGLDKM 235
YSV E+V+AF + K IPYE+ RR GD AS D S A++EL W+ K L+ M
Sbjct: 260 YSVLEVVEAFEKVSGKPIPYEIAPRRAGDPASLVADPSKAREELGWKPKRDLEDM 314
Score = 96.1 bits (240), Expect = 1e-22
Identities = 38/76 (50%), Positives = 52/76 (68%), Gaps = 10/76 (13%)
Query: 247 ILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETGKPESLKRVENLTGKTVEYH 306
+LVTGGAGYIGSHTVV LLE GY+VVV+DNL N G E+L R+E + +E++
Sbjct: 2 VLVTGGAGYIGSHTVVELLEAGYDVVVLDNLSN-------GHREALPRIEKI---RIEFY 51
Query: 307 EVDILQVSDLREIFSK 322
E DI + L ++F++
Sbjct: 52 EGDIRDRAALDKVFAE 67
>gnl|CDD|177883 PLN02240, PLN02240, UDP-glucose 4-epimerase.
Length = 352
Score = 339 bits (871), Expect = e-116
Identities = 128/237 (54%), Positives = 154/237 (64%), Gaps = 27/237 (11%)
Query: 1 MQEFKVYHFVFSSSSTVYGTPKFLPFTEDHPTGQGCTNPYGKSKYFVEEILKDLASFKQK 60
M + VFSSS+TVYG P+ +P TE+ P TNPYG++K F+EEI +D
Sbjct: 119 MAKHGCKKLVFSSSATVYGQPEEVPCTEEFPLS--ATNPYGRTKLFIEEICRD------- 169
Query: 61 LQSLQSSVTQIWLNSVHRSD--WHIISLRYFNPVGSHPSGDIGEDPNGIPNNLMPYISQV 118
+H SD W II LRYFNPVG+HPSG IGEDP GIPNNLMPY+ QV
Sbjct: 170 ---------------IHASDPEWKIILLRYFNPVGAHPSGRIGEDPKGIPNNLMPYVQQV 214
Query: 119 AVGRRKKLMVFGDDYDTKDGSGVRDYIHIMDLAEGHVTALDKLLGGKSQAGFKAYNLGTG 178
AVGRR +L VFG+DY TKDG+GVRDYIH+MDLA+GH+ AL KL G +AYNLGTG
Sbjct: 215 AVGRRPELTVFGNDYPTKDGTGVRDYIHVMDLADGHIAALRKLF-TDPDIGCEAYNLGTG 273
Query: 179 TGYSVFEMVKAFSEACKKNIPYEVVGRREGDIASSYCDASLAKKELAWEAKYGLDKM 235
G SV EMV AF +A K IP ++ RR GD Y A+KEL W+AKYG+D+M
Sbjct: 274 KGTSVLEMVAAFEKASGKKIPLKLAPRRPGDAEEVYASTEKAEKELGWKAKYGIDEM 330
Score = 98.1 bits (245), Expect = 2e-23
Identities = 37/79 (46%), Positives = 50/79 (63%), Gaps = 10/79 (12%)
Query: 247 ILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETGKPESLKRVENLTG---KTV 303
ILVTGGAGYIGSHTV+ LL GY VVV+DNL N+ E+L+RV+ L G +
Sbjct: 8 ILVTGGAGYIGSHTVLQLLLAGYKVVVIDNLDNSS-------EEALRRVKELAGDLGDNL 60
Query: 304 EYHEVDILQVSDLREIFSK 322
+H+VD+ L ++F+
Sbjct: 61 VFHKVDLRDKEALEKVFAS 79
>gnl|CDD|224012 COG1087, GalE, UDP-glucose 4-epimerase [Cell envelope biogenesis,
outer membrane].
Length = 329
Score = 304 bits (781), Expect = e-103
Identities = 91/236 (38%), Positives = 131/236 (55%), Gaps = 28/236 (11%)
Query: 1 MQEFKVYHFVFSSSSTVYGTPKFLPFTEDHPTGQGCTNPYGKSKYFVEEILKDLASFKQK 60
M + V F+FSS++ VYG P P +E P NPYG+SK EEIL+D A
Sbjct: 105 MLQTGVKKFIFSSTAAVYGEPTTSPISETSPLAP--INPYGRSKLMSEEILRDAAK---- 158
Query: 61 LQSLQSSVTQIWLNSVHRSDWHIISLRYFNPVGSHPSGDIGEDPNGIPNNLMPYISQVAV 120
+ + ++ LRYFN G+ P G +G+ G L+P ++ A+
Sbjct: 159 -----------------ANPFKVVILRYFNVAGACPDGTLGQRYPGA-TLLIPVAAEAAL 200
Query: 121 GRRKKLMVFGDDYDTKDGSGVRDYIHIMDLAEGHVTALDKLLGGKSQAGFKAYNLGTGTG 180
G+R KL +FGDDYDTKDG+ +RDYIH+ DLA+ HV AL L G S +NLG+G G
Sbjct: 201 GKRDKLFIFGDDYDTKDGTCIRDYIHVDDLADAHVLALKYLKEGGSNN---IFNLGSGNG 257
Query: 181 YSVFEMVKAFSEACKKNIPYEVVGRREGDIASSYCDASLAKKELAWEAKY-GLDKM 235
+SV E+++A + ++IP E+ RR GD A D+S A++ L W+ Y L+ +
Sbjct: 258 FSVLEVIEAAKKVTGRDIPVEIAPRRAGDPAILVADSSKARQILGWQPTYDDLEDI 313
Score = 88.4 bits (220), Expect = 5e-20
Identities = 31/76 (40%), Positives = 46/76 (60%), Gaps = 13/76 (17%)
Query: 247 ILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETGKPESLKRVENLTGKTVEYH 306
+LVTGGAGYIGSHTV LL+ G+ VVV+DNL N G +L +++ +++
Sbjct: 3 VLVTGGAGYIGSHTVRQLLKTGHEVVVLDNLSN-------GHKIALLKLQ------FKFY 49
Query: 307 EVDILQVSDLREIFSK 322
E D+L + L +F +
Sbjct: 50 EGDLLDRALLTAVFEE 65
>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 = 281 bits (720), Expect = 9e-94
Identities = 112/236 (47%), Positives = 144/236 (61%), Gaps = 27/236 (11%)
Query: 1 MQEFKVYHFVFSSSSTVYGTPKFLPFTEDHPTGQGCTNPYGKSKYFVEEILKDLASFKQK 60
MQ+ V F+FSSS+ VYG P +P +ED P G NPYG+SK E+IL+DL
Sbjct: 108 MQQAGVKKFIFSSSAAVYGEPSSIPISEDSPLGP--INPYGRSKLMSEQILRDL------ 159
Query: 61 LQSLQSSVTQIWLNSVHRSDWHIISLRYFNPVGSHPSGDIGEDPNGIPNNLMPYISQVAV 120
DW + LRYFN G+HPSGDIGEDP GI + L+PY QVAV
Sbjct: 160 --------------QKADPDWSYVILRYFNVAGAHPSGDIGEDPPGITH-LIPYACQVAV 204
Query: 121 GRRKKLMVFGDDYDTKDGSGVRDYIHIMDLAEGHVTALDKLLGGKSQAGFKAYNLGTGTG 180
G+R KL +FG DY T DG+ VRDYIH+MDLA+ H+ AL+ LL G G YNLG G G
Sbjct: 205 GKRDKLTIFGTDYPTPDGTCVRDYIHVMDLADAHLAALEYLLNG---GGSHVYNLGYGQG 261
Query: 181 YSVFEMVKAFSEACKKNIPYEVVGRREGDIASSYCDASLAKKELAWEAKYG-LDKM 235
+SV E+++AF + K+ P E+ RR GD AS DAS ++EL W+ KY L+++
Sbjct: 262 FSVLEVIEAFKKVSGKDFPVELAPRRPGDPASLVADASKIRRELGWQPKYTDLEEI 317
Score = 75.8 bits (187), Expect = 1e-15
Identities = 36/76 (47%), Positives = 45/76 (59%), Gaps = 9/76 (11%)
Query: 247 ILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETGKPESLKRVENLTGKTVEYH 306
ILVTGGAGYIGSHTV LLE G+ VV++DNL N G E+L R E +T V +
Sbjct: 2 ILVTGGAGYIGSHTVRQLLESGHEVVILDNLSN-------GSREALPRGERIT--PVTFV 52
Query: 307 EVDILQVSDLREIFSK 322
E D+ L +F +
Sbjct: 53 EGDLRDRELLDRLFEE 68
>gnl|CDD|182639 PRK10675, PRK10675, UDP-galactose-4-epimerase; Provisional.
Length = 338
Score = 274 bits (703), Expect = 5e-91
Identities = 124/235 (52%), Positives = 153/235 (65%), Gaps = 24/235 (10%)
Query: 1 MQEFKVYHFVFSSSSTVYGTPKFLPFTEDHPTGQGCTNPYGKSKYFVEEILKDLASFKQK 60
M+ V + +FSSS+TVYG +P+ E PTG +PYGKSK VE+IL DL QK
Sbjct: 111 MRAANVKNLIFSSSATVYGDQPKIPYVESFPTGTP-QSPYGKSKLMVEQILTDL----QK 165
Query: 61 LQSLQSSVTQIWLNSVHRSDWHIISLRYFNPVGSHPSGDIGEDPNGIPNNLMPYISQVAV 120
Q DW I LRYFNPVG+HPSGD+GEDP GIPNNLMPYI+QVAV
Sbjct: 166 AQP----------------DWSIALLRYFNPVGAHPSGDMGEDPQGIPNNLMPYIAQVAV 209
Query: 121 GRRKKLMVFGDDYDTKDGSGVRDYIHIMDLAEGHVTALDKLLGGKSQAGFKAYNLGTGTG 180
GRR L +FG+DY T+DG+GVRDYIH+MDLA+GHV A++KL + G YNLG G G
Sbjct: 210 GRRDSLAIFGNDYPTEDGTGVRDYIHVMDLADGHVAAMEKLAN---KPGVHIYNLGAGVG 266
Query: 181 YSVFEMVKAFSEACKKNIPYEVVGRREGDIASSYCDASLAKKELAWEAKYGLDKM 235
SV ++V AFS+AC K + Y RREGD+ + + DAS A +EL W LD+M
Sbjct: 267 SSVLDVVNAFSKACGKPVNYHFAPRREGDLPAYWADASKADRELNWRVTRTLDEM 321
Score = 73.3 bits (180), Expect = 1e-14
Identities = 34/76 (44%), Positives = 46/76 (60%), Gaps = 7/76 (9%)
Query: 247 ILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETGKPESLKRVENLTGKTVEYH 306
+LVTGG+GYIGSHT V LL++G++VV++DNL N+ K L +E L GK +
Sbjct: 3 VLVTGGSGYIGSHTCVQLLQNGHDVVILDNLCNS-------KRSVLPVIERLGGKHPTFV 55
Query: 307 EVDILQVSDLREIFSK 322
E DI + L EI
Sbjct: 56 EGDIRNEALLTEILHD 71
>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 = 113 bits (285), Expect = 2e-29
Identities = 71/232 (30%), Positives = 100/232 (43%), Gaps = 44/232 (18%)
Query: 3 EFKVYHFVFSSSSTVYGTPKFLPFTEDHPTGQGCTNPYGKSKYFVEEILKDLASFKQKLQ 62
+ V FV++SSS+VYG P +LP EDHP +PY SKY E +L
Sbjct: 106 KAGVKRFVYASSSSVYGDPPYLPKDEDHPPNP--LSPYAVSKYAGEL----YCQVFARLY 159
Query: 63 SLQSSVTQIWLNSVHRSDWHIISLRYFNPVGSHPSGDIGEDPNGIPNNLMP-YISQVAVG 121
L + +SLRYFN G +DPNG ++P +I + G
Sbjct: 160 GLPT-----------------VSLRYFNVYGP------RQDPNGGYAAVIPIFIERALKG 196
Query: 122 RRKKLMVFGDDYDTKDGSGVRDYIHIMDLAEGHVTALDKLLGGKSQAGFKAYNLGTGTGY 181
++GD G RD+ ++ D+ E ++ A GG+ YN+GTG
Sbjct: 197 EP--PTIYGD------GEQTRDFTYVEDVVEANLLAATAGAGGE------VYNIGTGKRT 242
Query: 182 SVFEMVKAFSEACKKNIPYEVVGRREGDIASSYCDASLAKKELAWEAKYGLD 233
SV E+ + E K + R GD+ S D S AKK L WE K +
Sbjct: 243 SVNELAELIREILGKELEPVYAPPRPGDVRHSLADISKAKKLLGWEPKVSFE 294
Score = 57.6 bits (140), Expect = 2e-09
Identities = 32/75 (42%), Positives = 42/75 (56%), Gaps = 11/75 (14%)
Query: 247 ILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETGKPESLKRVENLTGKTVEYH 306
+LVTGGAG+IGSH V LLE G+ V+V+DNL TGK E+L V+ V++
Sbjct: 2 VLVTGGAGFIGSHLVERLLERGHEVIVLDNLS-------TGKKENLPEVKP----NVKFI 50
Query: 307 EVDILQVSDLREIFS 321
E DI + F
Sbjct: 51 EGDIRDDELVEFAFE 65
>gnl|CDD|206121 pfam13950, Epimerase_Csub, UDP-glucose 4-epimerase C-term subunit.
This domain is the very C-terminal subunit of
UDP-glucose 4-epimerase.
Length = 62
Score = 91.0 bits (227), Expect = 2e-23
Identities = 26/47 (55%), Positives = 33/47 (70%)
Query: 189 AFSEACKKNIPYEVVGRREGDIASSYCDASLAKKELAWEAKYGLDKM 235
AF +A K IPYE+V RR GD+A Y D S A+KEL W+A+ GL+ M
Sbjct: 1 AFEKASGKKIPYEIVPRRPGDVAECYADPSKAEKELGWKAERGLEDM 47
>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 = 92.0 bits (229), Expect = 6e-22
Identities = 43/176 (24%), Positives = 72/176 (40%), Gaps = 43/176 (24%)
Query: 1 MQEFKVYHFVFSSSSTVYGTPKFLPFTEDHPTGQGCTNPYGKSKYFVEEILKDLASFKQK 60
+ V FVF+SSS VYG P TED P G +PY +K E +++ A
Sbjct: 101 ARRAGVKRFVFASSSEVYGDVADPPITEDTPLGP--LSPYAAAKLAAERLVEAYA----- 153
Query: 61 LQSLQSSVTQIWLNSVHRSDWHIISLRYFNPVGSHPSGDIGEDPNGIPNNLMPYISQVAV 120
+ LR FN G +P+ +++P + + +
Sbjct: 154 ----------------RAYGLRAVILRLFNVYGPG-------NPDPFVTHVIPALIRRIL 190
Query: 121 GRRKKLMVFGDDYDTKDGSGVRDYIHIMDLAEGHVTALDKLLGGKSQAGFKAYNLG 176
K +++ GD G+ RD++++ D+A + AL+ GG + YN+G
Sbjct: 191 -EGKPILLLGD------GTQRRDFLYVDDVARAILLALEHPDGG------EIYNIG 233
Score = 55.8 bits (135), Expect = 4e-09
Identities = 25/76 (32%), Positives = 36/76 (47%), Gaps = 15/76 (19%)
Query: 247 ILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETGKPESLKRVENLTGKTVEYH 306
ILVTGG G+IGSH V LL+ GY V+ L +R E+L + +H
Sbjct: 1 ILVTGGTGFIGSHLVRRLLQEGYEVI---VLGRR------------RRSESLNTGRIRFH 45
Query: 307 EVDILQVSDLREIFSK 322
E D+ L + ++
Sbjct: 46 EGDLTDPDALERLLAE 61
>gnl|CDD|223528 COG0451, WcaG, Nucleoside-diphosphate-sugar epimerases [Cell
envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 314
Score = 91.2 bits (226), Expect = 5e-21
Identities = 67/238 (28%), Positives = 99/238 (41%), Gaps = 47/238 (19%)
Query: 1 MQEFKVYHFVFSSS-STVYGTPKFLPFTEDHPTGQGCTNPYGKSKYFVEEILKDLASFKQ 59
+ V FVF+SS S VYG P LP ED + NPYG SK E++L+ A
Sbjct: 103 ARAAGVKRFVFASSVSVVYGDPPPLPIDEDLGPPRP-LNPYGVSKLAAEQLLRAYA---- 157
Query: 60 KLQSLQSSVTQIWLNSVHRSDWHIISLRYFNPVGSHPSGDIGEDPNGIPNNLMPYISQVA 119
++ LR FN G G+ P+ + +I Q+
Sbjct: 158 -----------------RLYGLPVVILRPFNVYG------PGDKPDLSSGVVSAFIRQLL 194
Query: 120 VGRRKKLMVFGDDYDTKDGSGVRDYIHIMDLAEGHVTALDKLLGGKSQAGFKAYNLGTGT 179
G ++ DGS RD++++ D+A+ + AL+ GG +N+G+GT
Sbjct: 195 KGEPIIVIGG-------DGSQTRDFVYVDDVADALLLALENPDGG-------VFNIGSGT 240
Query: 180 G-YSVFEMVKAFSEACKKNIPYEVV---GRREGDIASSYCDASLAKKELAWEAKYGLD 233
+V E+ +A +EA P V GRR D S A+ L WE K L+
Sbjct: 241 AEITVRELAEAVAEAVGSKAPLIVYIPLGRRGDLREGKLLDISKARAALGWEPKVSLE 298
Score = 54.9 bits (132), Expect = 1e-08
Identities = 19/34 (55%), Positives = 24/34 (70%)
Query: 247 ILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNA 280
ILVTGGAG+IGSH V LL G++V +D L +
Sbjct: 3 ILVTGGAGFIGSHLVERLLAAGHDVRGLDRLRDG 36
>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 = 89.3 bits (222), Expect = 2e-20
Identities = 62/235 (26%), Positives = 98/235 (41%), Gaps = 44/235 (18%)
Query: 1 MQEFKVYHFVF-SSSSTVYGTPKFLPFTEDHPTGQGCTNPYGKSKYFVEEILKDLASFKQ 59
+ +F SS TVYG P+ LP +E PT YG SK +E+ L Q
Sbjct: 100 CAAAGIGKIIFASSGGTVYGVPEQLPISESDPTLPIS--SYGISKLAIEKYL----RLYQ 153
Query: 60 KLQSLQSSVTQIWLNSVHRSDWHIISLRYFNPVGSHPSGDIGEDPNGIPNNLMPYISQVA 119
L L +V LR NP G G+ P+G + ++++
Sbjct: 154 YLYGLDYTV-----------------LRISNPYGP------GQRPDGKQGVIPIALNKIL 190
Query: 120 VGRRKKLMVFGDDYDTKDGSGVRDYIHIMDLAEGHVTALDKLLGGKSQAGFKAYNLGTGT 179
G + ++G DG +RDYI+I DL E + L +S+ + +N+G+G
Sbjct: 191 RGEP--IEIWG------DGESIRDYIYIDDLVEALMALL------RSKGLEEVFNIGSGI 236
Query: 180 GYSVFEMVKAFSEACKKNIPYEVVGRREGDIASSYCDASLAKKELAWEAKYGLDK 234
GYS+ E++ + +++ R D+ D S A+ EL W K L+
Sbjct: 237 GYSLAELIAEIEKVTGRSVQVIYTPARTTDVPKIVLDISRARAELGWSPKISLED 291
Score = 40.4 bits (95), Expect = 7e-04
Identities = 22/73 (30%), Positives = 31/73 (42%), Gaps = 15/73 (20%)
Query: 247 ILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETGKPESLKRVENLTGKTVEYH 306
+L+ GG G+IGSH V +LLE G V V D + + G V+Y
Sbjct: 2 VLIVGGNGFIGSHLVDALLEEGPQVRVFDRSIPPYELPLGG---------------VDYI 46
Query: 307 EVDILQVSDLREI 319
+ D +DL
Sbjct: 47 KGDYENRADLESA 59
>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 = 73.9 bits (182), Expect = 1e-15
Identities = 46/174 (26%), Positives = 70/174 (40%), Gaps = 43/174 (24%)
Query: 3 EFKVYHFVFSSSSTVYGTPKFLPFTEDHPTGQGCTNPYGKSKYFVEEILKDLASFKQKLQ 62
+ V FV++SS++VYG+P+ LP E+ P +PYG SK E +L+
Sbjct: 70 KAGVKRFVYASSASVYGSPEGLPEEEETPP--RPLSPYGVSKLAAEHLLRSYGE------ 121
Query: 63 SLQSSVTQIWLNSVHRSDWHIISLRYFNPVGSHPSGDIGEDPNGIPNNLMPYISQVAVGR 122
++ LR N G +G+ N+ I + G
Sbjct: 122 ---------------SYGLPVVILRLANVYGPGQ----RPRLDGVVNDF---IRRALEG- 158
Query: 123 RKKLMVFGDDYDTKDGSGVRDYIHIMDLAEGHVTALDKLLGGKSQAGFKAYNLG 176
K L VFG G+ RD+IH+ D+ + AL+ L G YN+G
Sbjct: 159 -KPLTVFG------GGNQTRDFIHVDDVVRAILHALENPLE-----GGGVYNIG 200
Score = 56.9 bits (138), Expect = 1e-09
Identities = 22/31 (70%), Positives = 25/31 (80%)
Query: 247 ILVTGGAGYIGSHTVVSLLEHGYNVVVVDNL 277
ILVTGGAG+IGSH V LLE G+ VVV+D L
Sbjct: 1 ILVTGGAGFIGSHLVRRLLERGHEVVVIDRL 31
>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 = 69.3 bits (170), Expect = 2e-13
Identities = 59/246 (23%), Positives = 95/246 (38%), Gaps = 61/246 (24%)
Query: 1 MQEFKVYHFVFSSSSTVYGTPKFLPFTE----DHPTGQGCTNPYGKSKYFVEEILKDLAS 56
+ F V H V++SSS+VYG +PF+E DHP + Y +K E + +
Sbjct: 114 CRHFGVKHLVYASSSSVYGLNTKMPFSEDDRVDHPI-----SLYAATKKANELMAHTYS- 167
Query: 57 FKQKLQSLQSSVTQIWLNSVHRSDWHIISLRYFNPVGSHPSGDIGEDPNGIPNNLMPYIS 116
H LR+F G P G P+ M
Sbjct: 168 --------------------HLYGIPTTGLRFFTVYG----------PWGRPD--MALFL 195
Query: 117 QV-AVGRRKKLMVFGDDYDTKDGSGVRDYIHIMDLAEGHVTALDKLLGG----------- 164
A+ K + VF D G+ RD+ +I D+ EG V ALD
Sbjct: 196 FTKAILEGKPIDVFND------GNMSRDFTYIDDIVEGVVRALDTPAKPNPNWDAEAPDP 249
Query: 165 -KSQAGFKAYNLGTGTGYSVFEMVKAFSEACKKNIPYEVVGRREGDIASSYCDASLAKKE 223
S A ++ YN+G + + + ++A +A K + ++GD+ +Y D S ++
Sbjct: 250 STSSAPYRVYNIGNNSPVKLMDFIEALEKALGKKAKKNYLPMQKGDVPETYADISKLQRL 309
Query: 224 LAWEAK 229
L ++ K
Sbjct: 310 LGYKPK 315
Score = 48.5 bits (116), Expect = 2e-06
Identities = 27/76 (35%), Positives = 38/76 (50%), Gaps = 8/76 (10%)
Query: 247 ILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVN--ACRVEETGKPESLKRVENLTGKTVE 304
ILVTG AG+IG H LLE G VV +DNL + R++E + E L +
Sbjct: 3 ILVTGAAGFIGFHVAKRLLERGDEVVGIDNLNDYYDVRLKE-ARLELLGKSGGFK----- 56
Query: 305 YHEVDILQVSDLREIF 320
+ + D+ LR +F
Sbjct: 57 FVKGDLEDREALRRLF 72
>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 = 59.6 bits (145), Expect = 3e-10
Identities = 59/238 (24%), Positives = 84/238 (35%), Gaps = 57/238 (23%)
Query: 8 HFVFSSSSTVYGTPKFLPFTEDHPTGQGCT--NPYGKSKYFVEEILKDLA-SFKQKLQSL 64
V +S+S VYGT + +P EDHP +PY SK + + SF
Sbjct: 113 RVVHTSTSEVYGTAQDVPIDEDHPLLYINKPRSPYSASKQGADRLAYSYGRSFG------ 166
Query: 65 QSSVTQIWLNSVHRSDWHIISLRYFNPVGSHPSGDIGEDPNGIPNNLMPYISQVAVGRRK 124
+ + +R FN G P IP ISQ A+G+R
Sbjct: 167 ----LPVTI------------IRPFNTYG--PRQSAR---AVIPT----IISQRAIGQRL 201
Query: 125 KLMVFGDDYDTKDGSGVRDYIHIMDLAEGHVTALD--KLLGGKSQAGFKAYNLGTGTGYS 182
+ DGS RD+ + D A G + LD + +G + N G+G S
Sbjct: 202 INLG--------DGSPTRDFNFVKDTARGFIDILDAIEAVG-------EIINNGSGEEIS 246
Query: 183 VFEMVKAFSE---ACKKNIPYEVV-GRREG--DIASSYCDASLAKKELAWEAKYGLDK 234
+ I Y+ R G ++ D AK+ L WE KY L
Sbjct: 247 IGNPAVELIVEELGEMVLIVYDDHREYRPGYSEVERRIPDIRKAKRLLGWEPKYSLRD 304
Score = 45.8 bits (109), Expect = 1e-05
Identities = 19/63 (30%), Positives = 28/63 (44%), Gaps = 1/63 (1%)
Query: 247 ILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETGKPESLKRVENLTGKTVEYH 306
+LVTG G+IGSH LL G+ V +D N+ R ++G +
Sbjct: 2 VLVTGADGFIGSHLTERLLREGHEVRALDIY-NSFNSWGLLDNAVHDRFHFISGDVRDAS 60
Query: 307 EVD 309
EV+
Sbjct: 61 EVE 63
>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 = 56.9 bits (138), Expect = 3e-09
Identities = 24/31 (77%), Positives = 25/31 (80%)
Query: 247 ILVTGGAGYIGSHTVVSLLEHGYNVVVVDNL 277
ILVTGGAG+IGSH V LLE G VVVVDNL
Sbjct: 2 ILVTGGAGFIGSHLVDRLLEEGNEVVVVDNL 32
Score = 49.6 bits (119), Expect = 7e-07
Identities = 58/233 (24%), Positives = 92/233 (39%), Gaps = 49/233 (21%)
Query: 1 MQEFKVYHFVFSSSSTVYGTPKFLPFTEDHPTGQGCTNPYGKSKYFVEEILKDLASFKQK 60
M+ V VF+SSSTVYG K +P ED+P + YG SK LA+
Sbjct: 105 MRANGVKRIVFASSSTVYGEAKVIPTPEDYPPLP--ISVYGASK---------LAA---- 149
Query: 61 LQSLQSSVTQIWLNSVHRSDWHIISLRYFNPVGSHPSGDIGEDPNGIPNNLMPYISQVAV 120
++L S+ H + R+ N VG + + D +I+++
Sbjct: 150 -EALISA-------YAHLFGFQAWIFRFANIVGPRSTHGVIYD----------FINKLK- 190
Query: 121 GRRKKLMVFGDDYDTKDGSGVRDYIHIMDLAEGHVTALDKLLGGKSQAGFKAYNLGTGTG 180
+L V G DG + Y+++ D + + A + KS G +NLG
Sbjct: 191 RNPNELEVLG------DGRQRKSYLYVSDCVDAMLLAWE-----KSTEGVNIFNLGNDDT 239
Query: 181 YSVFEMVKAFSEACKKNIPYEVV-GRR--EGDIASSYCDASLAKKELAWEAKY 230
SV E+ + E ++ G R +GD+ D K L W+ +Y
Sbjct: 240 ISVNEIAEIVIEELGLKPRFKYSGGDRGWKGDVPYMRLDIEKLKA-LGWKPRY 291
>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 = 56.2 bits (136), Expect = 4e-09
Identities = 64/238 (26%), Positives = 95/238 (39%), Gaps = 59/238 (24%)
Query: 3 EFKVYHFVFSSSSTVYGTPKFLPFTEDHP-TGQGCTNPYGKSKYFVEEILKDLASFKQKL 61
+ V V +S+S VYGT +++P E HP GQ +PY SK I D
Sbjct: 110 DLGVEKVVHTSTSEVYGTAQYVPIDEKHPLQGQ---SPYSASK-----IGAD-------- 153
Query: 62 QSLQSSVTQIWLNSVHRS-DWHIISLRYFNPVGSHPSGDIGEDPNGIPNNLMPYISQVAV 120
Q+ L S +RS + + +R FN G S IP I+Q+A
Sbjct: 154 --------QLAL-SFYRSFNTPVTIIRPFNTYGPRQSARA-----VIPT----IITQIAS 195
Query: 121 GRRK-KLMVFGDDYDTKDGSGVRDYIHIMDLAEGHVTAL--DKLLGGKSQAGFKAYNLGT 177
G+R+ KL G T RD+ ++ D G + DK +G + N+G+
Sbjct: 196 GKRRIKL---GSLSPT------RDFNYVTDTVRGFIAIAESDKTVG-------EVINIGS 239
Query: 178 GTGYSVFEMVKAFSEACKKNIPYEVVGRREGDIASS----YCDASLAKKELAWEAKYG 231
S+ + VK +E + E R S +CD S K+ W+ KY
Sbjct: 240 NFEISIGDTVKLIAEIMGSEVEIETDEERLRPEKSEVERLWCDNSKIKELTGWQPKYS 297
Score = 42.3 bits (100), Expect = 2e-04
Identities = 24/64 (37%), Positives = 35/64 (54%), Gaps = 2/64 (3%)
Query: 247 ILVTGGAGYIGSHTVVSLLEHGYNVV--VVDNLVNACRVEETGKPESLKRVENLTGKTVE 304
+LVTG G+IGSH V +L+ GY V V+ N N+ +T PE ++E +TG +
Sbjct: 1 VLVTGADGFIGSHLVEALVRQGYEVRAFVLYNSFNSWGWLDTSPPEVKDKIEVVTGDIRD 60
Query: 305 YHEV 308
V
Sbjct: 61 PDSV 64
>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 = 54.4 bits (131), Expect = 2e-08
Identities = 26/53 (49%), Positives = 32/53 (60%), Gaps = 7/53 (13%)
Query: 247 ILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETGKPESLKRVENLT 299
+L+TGGAG IGSH + LLE G+ VVV+DN TG+ E L NLT
Sbjct: 3 VLITGGAGQIGSHLIEHLLERGHQVVVIDNF-------ATGRREHLPDHPNLT 48
Score = 39.0 bits (91), Expect = 0.002
Identities = 26/94 (27%), Positives = 38/94 (40%), Gaps = 8/94 (8%)
Query: 141 VRDYIHIMDLAEGHVTALDKLLGGKSQAGFKAYNLGTGTGYSVFEMVKAFSEACKKNI-- 198
RD++ + DLA ALD G AY+ +G S+ E+ A EA +
Sbjct: 197 RRDFVFVKDLARVVDKALD------GIRGHGAYHFSSGEDVSIKELFDAVVEALDLPLRP 250
Query: 199 PYEVVGRREGDIASSYCDASLAKKELAWEAKYGL 232
EVV D+ S D S ++ W+ L
Sbjct: 251 EVEVVELGPDDVPSILLDPSRTFQDFGWKEFTPL 284
>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 = 53.8 bits (130), Expect = 3e-08
Identities = 26/71 (36%), Positives = 36/71 (50%), Gaps = 15/71 (21%)
Query: 247 ILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETGKPESLK------RVENLTG 300
IL+TGGAG++GSH LLE G+ V+ VDN TG+ +++ E +
Sbjct: 3 ILITGGAGFLGSHLCDRLLEDGHEVICVDNFF-------TGRKRNIEHLIGHPNFEFIRH 55
Query: 301 KTVE--YHEVD 309
E Y EVD
Sbjct: 56 DVTEPLYLEVD 66
Score = 33.4 bits (77), Expect = 0.14
Identities = 56/229 (24%), Positives = 86/229 (37%), Gaps = 55/229 (24%)
Query: 9 FVFSSSSTVYGTPKFLPFTEDH-----PTG-QGCTNPYGKSKYFVEEILKDLASFKQKLQ 62
+ +S+S VYG P+ P E + P G + C Y + K E + +A +Q
Sbjct: 109 VLLASTSEVYGDPEVHPQPESYWGNVNPIGPRSC---YDEGKRVAETLC--MAYHRQ--- 160
Query: 63 SLQSSVTQIWLNSVHRSDWHIISLRYFNPVGS--HPSGDIGEDPNGIPNNLMPYISQVAV 120
H D I R FN G HP+ D + N +I Q
Sbjct: 161 --------------HGVDVRIA--RIFNTYGPRMHPN-----DGRVVSN----FIVQALR 195
Query: 121 GRRKKLMVFGDDYDTKDGSGVRDYIHIMDLAEGHVTALDKLLGGKSQAGFKAYNLGTGTG 180
G + + V+GD G+ R + ++ DL EG L +L+ G NLG
Sbjct: 196 G--EPITVYGD------GTQTRSFQYVSDLVEG----LIRLMNSDYFGG--PVNLGNPEE 241
Query: 181 YSVFEMVKAFSEACKKNIPYEVVGRREGDIASSYCDASLAKKELAWEAK 229
+++ E+ + + + E D D S AK+ L WE K
Sbjct: 242 FTILELAELVKKLTGSKSEIVFLPLPEDDPKRRRPDISKAKELLGWEPK 290
>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 = 51.9 bits (125), Expect = 1e-07
Identities = 23/74 (31%), Positives = 37/74 (50%), Gaps = 5/74 (6%)
Query: 247 ILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETGKPESLKRVENLTGKTVEYH 306
+L+TGGAG+IGS+ L+ G+ V+ DNL+ R G LK G +
Sbjct: 3 VLITGGAGFIGSNLARFFLKQGWEVIGFDNLM---RRGSFGNLAWLKANREDGGVRFVHG 59
Query: 307 EVDILQVSDLREIF 320
++ +DL ++F
Sbjct: 60 DIRNR--NDLEDLF 71
Score = 50.0 bits (120), Expect = 7e-07
Identities = 49/255 (19%), Positives = 83/255 (32%), Gaps = 67/255 (26%)
Query: 9 FVFSSSSTVYG-TPKFLP-------------------FTEDHPTGQGCTNPYGKSKYFVE 48
F+F+S++ VYG P +LP +E P + YG SK +
Sbjct: 120 FIFTSTNKVYGDLPNYLPLEELETRYELAPEGWSPAGISESFPLDFSHS-LYGASKGAAD 178
Query: 49 EILKDLA-SFKQKLQSLQSSVTQIWLNSVHRSDWHIISLRYFNPVGSHPSGDIGEDPNGI 107
+ +++ F K T ++ G+ G +
Sbjct: 179 QYVQEYGRIFGLK--------TVVFRCGCLTGPRQF---------GTEDQGWVA------ 215
Query: 108 PNNLMPYISQVAVGRRKKLMVFGDDYDTKDGSGVRDYIHIMDLAEGHVTALDKLLGGKSQ 167
Y + AV K L +FG G VRD +H DL + +
Sbjct: 216 ------YFLKCAV-TGKPLTIFGYG-----GKQVRDVLHSADLVN----LYLRQFQNPDR 259
Query: 168 AGFKAYNLGTGTGYSV--FEMVKAFSEACKKNIPYEVVGRREGDIASSYCDASLAKKELA 225
+ +N+G G SV E++ E + + R GD D K++
Sbjct: 260 RKGEVFNIGGGRENSVSLLELIALCEEITGRKMESYKDENRPGDQIWYISDIRKIKEKPG 319
Query: 226 WEAKY----GLDKMY 236
W+ + L ++Y
Sbjct: 320 WKPERDPREILAEIY 334
>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 = 51.5 bits (124), Expect = 2e-07
Identities = 45/198 (22%), Positives = 77/198 (38%), Gaps = 45/198 (22%)
Query: 9 FVFSSSSTVYGTPKFLPFTEDHPTGQGCTNPYGKSKYFVEEILKDLASFKQKLQSLQSSV 68
F+++SS+ YG + F E + N YG SK+ L D ++ L
Sbjct: 109 FIYASSAATYGDGE-AGFREG-RELERPLNVYGYSKF-----LFDQYVRRRVLP------ 155
Query: 69 TQIWLNSVHRSDWHIISLRYFNPVGSHPSGDIGEDPNGIPNNLMPYIS-----QVAVGRR 123
++ LRYFN G P M ++ Q+ G
Sbjct: 156 --------EALSAQVVGLRYFNVYG----------PREYHKGKMASVAFHLFNQIKAGGN 197
Query: 124 KKLMVFGDDYDTKDGSGVRDYIHIMDLAEGHVTALDKLLGGKSQAGFKAYNLGTGTGYSV 183
KL + + KDG +RD++++ D+ + ++ L+ + G +NLGTG S
Sbjct: 198 VKLFKSSEGF--KDGEQLRDFVYVKDVVDVNLWLLENGVSG-------IFNLGTGRARSF 248
Query: 184 FEMVKAFSEACKKNIPYE 201
++ A +A K+ E
Sbjct: 249 NDLADAVFKALGKDEKIE 266
Score = 42.7 bits (101), Expect = 1e-04
Identities = 25/73 (34%), Positives = 39/73 (53%), Gaps = 12/73 (16%)
Query: 247 ILVTGGAGYIGSHTVVSLLEHGY-NVVVVDNLVNACR---------VEETGKPESLKRVE 296
I+VTGGAG+IGS+ V +L E G +++VVDNL + + + K + L R+E
Sbjct: 1 IIVTGGAGFIGSNLVKALNERGITDILVVDNLRDGHKFLNLADLVIADYIDKEDFLDRLE 60
Query: 297 NLTGKTVEY--HE 307
+E H+
Sbjct: 61 KGAFGKIEAIFHQ 73
>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 = 50.2 bits (121), Expect = 4e-07
Identities = 24/78 (30%), Positives = 38/78 (48%), Gaps = 10/78 (12%)
Query: 247 ILVTGGAGYIGSHTVVSLLEHGYN--VVVVDNLVNACRVEETGKPESLKRVENLTGKTVE 304
ILVTGGAG+IGS+ V LL + ++ +D L A G E+L+ V +
Sbjct: 3 ILVTGGAGFIGSNFVRYLLNKYPDYKIINLDKLTYA------GNLENLEDVSS--SPRYR 54
Query: 305 YHEVDILQVSDLREIFSK 322
+ + DI + +F +
Sbjct: 55 FVKGDICDAELVDRLFEE 72
Score = 39.8 bits (94), Expect = 0.001
Identities = 60/237 (25%), Positives = 93/237 (39%), Gaps = 56/237 (23%)
Query: 3 EFKVYHFVFSSSSTVYGTPKFLP-FTEDHPTGQGCTNPYGKSKYFVEEILKDLASFKQKL 61
++ V FV S+ VYG FTE P T+PY SK + +++
Sbjct: 114 KYGVKRFVHISTDEVYGDLLDDGEFTETSPLAP--TSPYSASKAAADLLVR--------- 162
Query: 62 QSLQSSVTQIWLNSVHRSDWHIISLRY-FNPVGSHPSGDIGEDPNGIPNNLMPYISQVAV 120
+ HR+ Y V + S + G P P L+P A+
Sbjct: 163 -------------AYHRT--------YGLPVVITRCSNNYG--PYQFPEKLIPLFILNAL 199
Query: 121 GRRKKLMVFGDDYDTKDGSGVRDYIHIMDLAEGHVTALDKLL-GGKSQAGFKAYNLGTGT 179
K L ++GD G VRD++++ D H A++ +L G+ + YN+G G
Sbjct: 200 -DGKPLPIYGD------GLNVRDWLYVED----HARAIELVLEKGRV---GEIYNIGGGN 245
Query: 180 GYSVFEMVKAFSEACKKNIPY-EVVGRREG-DIASSYC-DASLAKKELAWEAKYGLD 233
+ E+VK E K+ V R G D Y D+S ++EL W K +
Sbjct: 246 ELTNLELVKLILELLGKDESLITYVKDRPGHDRR--YAIDSSKIRRELGWRPKVSFE 300
>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 = 50.1 bits (120), Expect = 6e-07
Identities = 29/85 (34%), Positives = 42/85 (49%), Gaps = 9/85 (10%)
Query: 247 ILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETG----KP-----ESLKRVEN 297
+L+ GG GY G T + L + G+ V +VDNLV E G P E L+ +
Sbjct: 3 VLILGGDGYCGWPTALHLSKRGHEVCIVDNLVRRRIDVELGLESLTPIASIHERLRAWKE 62
Query: 298 LTGKTVEYHEVDILQVSDLREIFSK 322
LTGKT+E++ D L E+ +
Sbjct: 63 LTGKTIEFYVGDACDYEFLAELLAS 87
>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 = 49.6 bits (119), Expect = 7e-07
Identities = 44/208 (21%), Positives = 76/208 (36%), Gaps = 49/208 (23%)
Query: 9 FVFSSSSTVYGTPKFLPFTEDHPTGQGCTNPYGKSKYFVEEILKDLASFKQKLQSLQSSV 68
F+++SS+ VYG + N YG SK ++ +
Sbjct: 111 FIYASSAAVYGNGSLGFAEDIETPNLRPLNVYGYSKLLFDQWARRHGK------------ 158
Query: 69 TQIWLNSVHRSDWHIISLRYFNPVGSHPSGDIGEDPNG----IPNNLMPYISQVAVGRRK 124
++ LRYFN G E G + +L Q+ G +
Sbjct: 159 ---------EVLSQVVGLRYFNVYGPR------EYHKGRMASVVFHLFN---QIKAGEKV 200
Query: 125 KLMVFGDDYDTKDGSGVRDYIHIMDLAEGHVTALDKLLGGKSQAGFKAYNLGTGTGYSVF 184
KL D Y DG +RD++++ D+ + ++ L+ S G +N+GTG S
Sbjct: 201 KLFKSSDGY--ADGEQLRDFVYVKDVVKVNLFFLEN--PSVS--GI--FNVGTGRARSFN 252
Query: 185 EMVKAFSEACKKN-------IPYEVVGR 205
++ A +A K P ++ G+
Sbjct: 253 DLASATFKALGKEVKIEYIDFPEDLRGK 280
Score = 43.4 bits (103), Expect = 7e-05
Identities = 20/35 (57%), Positives = 27/35 (77%), Gaps = 1/35 (2%)
Query: 247 ILVTGGAGYIGSHTVVSLLEHGY-NVVVVDNLVNA 280
I+VTGGAG+IGS+ V +L E G +++VVDNL N
Sbjct: 2 IIVTGGAGFIGSNLVKALNERGITDILVVDNLSNG 36
>gnl|CDD|223959 COG1028, FabG, Dehydrogenases with different specificities (related
to short-chain alcohol dehydrogenases) [Secondary
metabolites biosynthesis, transport, and catabolism /
General function prediction only].
Length = 251
Score = 47.1 bits (112), Expect = 4e-06
Identities = 19/78 (24%), Positives = 24/78 (30%), Gaps = 8/78 (10%)
Query: 241 MSNPKFILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETGKPESLKRVENLTG 300
+ K LVTG + IG +L G VVV E ++ G
Sbjct: 2 DLSGKVALVTGASSGIGRAIARALAREGARVVVAARRSEEEAAEAL-----AAAIKEAGG 56
Query: 301 KTVEYHEVDILQVSDLRE 318
D VSD E
Sbjct: 57 GRAAAVAAD---VSDDEE 71
>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 = 47.3 bits (113), Expect = 5e-06
Identities = 14/25 (56%), Positives = 17/25 (68%)
Query: 247 ILVTGGAGYIGSHTVVSLLEHGYNV 271
+LVTG G+I SH V LL+ GY V
Sbjct: 2 VLVTGATGFIASHIVEQLLKAGYKV 26
>gnl|CDD|224013 COG1088, RfbB, dTDP-D-glucose 4,6-dehydratase [Cell envelope
biogenesis, outer membrane].
Length = 340
Score = 46.1 bits (110), Expect = 1e-05
Identities = 26/78 (33%), Positives = 38/78 (48%), Gaps = 10/78 (12%)
Query: 247 ILVTGGAGYIGSHTVVSLLEHG--YNVVVVDNLVNACRVEETGKPESLKRVENLTGKTVE 304
ILVTGGAG+IGS+ V +L +VV +D L A G E+L VE+
Sbjct: 3 ILVTGGAGFIGSNFVRYILNKHPDDHVVNLDKLTYA------GNLENLADVEDSP--RYR 54
Query: 305 YHEVDILQVSDLREIFSK 322
+ + DI + +F +
Sbjct: 55 FVQGDICDRELVDRLFKE 72
Score = 45.7 bits (109), Expect = 2e-05
Identities = 43/142 (30%), Positives = 61/142 (42%), Gaps = 33/142 (23%)
Query: 109 NNLMPY----------ISQVAVGRRKKLMVFGDDYDTKDGSGVRDYIHIMDLAEGHVTAL 158
NN PY I +G K L V+GD G +RD++++ D H A+
Sbjct: 181 NNYGPYQFPEKLIPLMIINALLG--KPLPVYGD------GLQIRDWLYVED----HCRAI 228
Query: 159 DKLLGGKSQAGFKAYNLGTGTGYSVFEMVKAFSEACKKNIP-----YEVVGRREG-DIAS 212
D +L K + G + YN+G G + E+VK E K+ P V R G D
Sbjct: 229 DLVL-TKGKIG-ETYNIGGGNERTNLEVVKTICELLGKDKPDYRDLITFVEDRPGHD--R 284
Query: 213 SYC-DASLAKKELAWEAKYGLD 233
Y DAS K+EL W + +
Sbjct: 285 RYAIDASKIKRELGWRPQETFE 306
>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 = 45.9 bits (109), Expect = 1e-05
Identities = 18/57 (31%), Positives = 24/57 (42%), Gaps = 4/57 (7%)
Query: 245 KFILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETGKPE----SLKRVEN 297
+ LVTG G+IGSH L G+ V D + T E L+ +EN
Sbjct: 1 QRALVTGAGGFIGSHLAERLKAEGHYVRGADWKSPEHMTQPTDDDEFHLVDLREMEN 57
Score = 32.8 bits (75), Expect = 0.23
Identities = 25/104 (24%), Positives = 36/104 (34%), Gaps = 23/104 (22%)
Query: 137 DGSGVRDYIHIMDLAEGHVTALDKLLGGKSQAGFKAYNLGTGTGYSVFEMVKAFSEACKK 196
DG R + +I D EG ++ G NLG+ S+ E+ + K
Sbjct: 213 DGLQTRSFTYIDDCVEGLRRLMESDFGE-------PVNLGSDEMVSMNELAEMVLSFSGK 265
Query: 197 NIPYE--------VVGRREGDIASSYCDASLAKKELAWEAKYGL 232
+ V GR D +L K+EL WE L
Sbjct: 266 PLEIIHHTPGPQGVRGRN--------SDNTLLKEELGWEPNTPL 301
>gnl|CDD|223774 COG0702, COG0702, Predicted nucleoside-diphosphate-sugar epimerases
[Cell envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 275
Score = 44.9 bits (106), Expect = 2e-05
Identities = 12/28 (42%), Positives = 15/28 (53%)
Query: 247 ILVTGGAGYIGSHTVVSLLEHGYNVVVV 274
ILVTG G++G V LL G+ V
Sbjct: 3 ILVTGATGFVGGAVVRELLARGHEVRAA 30
>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 = 44.9 bits (107), Expect = 2e-05
Identities = 17/54 (31%), Positives = 24/54 (44%), Gaps = 7/54 (12%)
Query: 249 VTGGAGYIGSHTVVSLLEHGYNV-VVVDNLVNACRVEETGKPESLKRVENLTGK 301
VTG +G+IGS V LL+ GY V V + + K L +E +
Sbjct: 3 VTGASGFIGSWLVKRLLQRGYTVRATVRDP------GDEKKVAHLLELEGAKER 50
>gnl|CDD|236649 PRK10084, PRK10084, dTDP-glucose 4,6 dehydratase; Provisional.
Length = 352
Score = 44.4 bits (105), Expect = 4e-05
Identities = 29/77 (37%), Positives = 39/77 (50%), Gaps = 9/77 (11%)
Query: 247 ILVTGGAGYIGSHTVVSLLEHGYNVVV-VDNLVNACRVEETGKPESLKRVENLTGKTVEY 305
ILVTGGAG+IGS V ++ + + VV VD L A G ESL V + E
Sbjct: 3 ILVTGGAGFIGSAVVRHIINNTQDSVVNVDKLTYA------GNLESLADVSDSERYVFE- 55
Query: 306 HEVDILQVSDLREIFSK 322
DI ++L IF++
Sbjct: 56 -HADICDRAELDRIFAQ 71
>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 = 43.5 bits (103), Expect = 7e-05
Identities = 25/78 (32%), Positives = 38/78 (48%), Gaps = 10/78 (12%)
Query: 247 ILVTGGAGYIGSHTVVSLLEH--GYNVVVVDNLVNACRVEETGKPESLKRVENLTGKTVE 304
ILVTGGAG+IGS+ V +L V+V+D L A G E+L +E+
Sbjct: 2 ILVTGGAGFIGSNFVRYILNEHPDAEVIVLDKLTYA------GNLENLADLEDNPRYRFV 55
Query: 305 YHEVDILQVSDLREIFSK 322
+ DI + +F++
Sbjct: 56 --KGDIGDRELVSRLFTE 71
Score = 40.4 bits (95), Expect = 7e-04
Identities = 41/139 (29%), Positives = 59/139 (42%), Gaps = 18/139 (12%)
Query: 94 SHPSGDIGEDPNGIPNNLMPYISQVAVGRRKKLMVFGDDYDTKDGSGVRDYIHIMDLAEG 153
+ S + G P P L+P + A+ K L V+GD G VRD++++ D
Sbjct: 175 TRCSNNYG--PYQFPEKLIPLMITNAL-AGKPLPVYGD------GQQVRDWLYVED---- 221
Query: 154 HVTALDK-LLGGKSQAGFKAYNLGTGTGYSVFEMVKAFSEACKKNIPY-EVVGRREGDIA 211
H A+ L G+ YN+G G + E+V+ E K+ V R G
Sbjct: 222 HCRAIYLVLEKGRVGE---TYNIGGGNERTNLEVVETILELLGKDEDLITHVEDRPGHDR 278
Query: 212 SSYCDASLAKKELAWEAKY 230
DAS K+EL W KY
Sbjct: 279 RYAIDASKIKRELGWAPKY 297
>gnl|CDD|212491 cd05233, SDR_c, classical (c) SDRs. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold
(alpha/beta folding pattern with a central beta-sheet),
an NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRs are approximately
350 residues. Sequence identity between different SDR
enzymes are typically in the 15-30% range, but the
enzymes share the Rossmann fold NAD-binding motif and
characteristic NAD-binding and catalytic sequence
patterns. These enzymes catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human prostaglandin dehydrogenase
(PGDH) numbering). In addition to the Tyr and Lys, there
is often an upstream Ser (Ser-138, PGDH numbering)
and/or an Asn (Asn-107, PGDH numbering) contributing to
the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 234
Score = 43.0 bits (102), Expect = 7e-05
Identities = 17/76 (22%), Positives = 25/76 (32%), Gaps = 9/76 (11%)
Query: 247 ILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETGKPESLKRVENLTGKTVEYH 306
LVTG + IG L G VV+ D R EE + G
Sbjct: 1 ALVTGASSGIGRAIARRLAREGAKVVLAD------RNEEALAELAAIEAL---GGNAVAV 51
Query: 307 EVDILQVSDLREIFSK 322
+ D+ D+ + +
Sbjct: 52 QADVSDEEDVEALVEE 67
>gnl|CDD|182998 PRK11150, rfaD, ADP-L-glycero-D-mannoheptose-6-epimerase;
Provisional.
Length = 308
Score = 43.5 bits (103), Expect = 7e-05
Identities = 18/34 (52%), Positives = 26/34 (76%), Gaps = 1/34 (2%)
Query: 247 ILVTGGAGYIGSHTVVSLLEHGYN-VVVVDNLVN 279
I+VTGGAG+IGS+ V +L + G ++VVDNL +
Sbjct: 2 IIVTGGAGFIGSNIVKALNDKGITDILVVDNLKD 35
>gnl|CDD|177856 PLN02206, PLN02206, UDP-glucuronate decarboxylase.
Length = 442
Score = 43.4 bits (102), Expect = 8e-05
Identities = 17/31 (54%), Positives = 24/31 (77%)
Query: 247 ILVTGGAGYIGSHTVVSLLEHGYNVVVVDNL 277
++VTGGAG++GSH V L+ G +V+VVDN
Sbjct: 122 VVVTGGAGFVGSHLVDRLMARGDSVIVVDNF 152
Score = 41.1 bits (96), Expect = 5e-04
Identities = 60/227 (26%), Positives = 90/227 (39%), Gaps = 42/227 (18%)
Query: 9 FVFSSSSTVYGTPKFLPFTEDHPTGQGCTNPYGKSKYFVEEILKDLASFKQKLQSLQSSV 68
F+ +S+S VYG P P E T G NP G + E K+ ++L
Sbjct: 228 FLLTSTSEVYGDPLQHPQVE---TYWGNVNPIGVRSCYDEG--------KRTAETLTMDY 276
Query: 69 TQIWLNSVHR-SDWHIISLRYFNPVGSHPSGDIGEDPNGIPNNLMPYISQVAVGRRKKLM 127
HR ++ + R FN G D G + +N +++Q R++ L
Sbjct: 277 --------HRGANVEVRIARIFNTYGPRMCIDDGR----VVSN---FVAQAL--RKEPLT 319
Query: 128 VFGDDYDTKDGSGVRDYIHIMDLAEGHVTALDKLLGGKSQAGFKAYNLGTGTGYSVFEMV 187
V+GD G R + + DL EG L +L+ G+ F NLG +++ E+
Sbjct: 320 VYGD------GKQTRSFQFVSDLVEG----LMRLMEGEHVGPF---NLGNPGEFTMLELA 366
Query: 188 KAFSEACKKNIPYEVVGRREGDIASSYCDASLAKKELAWEAKYGLDK 234
K E N E E D D + AK+ L WE K L +
Sbjct: 367 KVVQETIDPNAKIEFRPNTEDDPHKRKPDITKAKELLGWEPKVSLRQ 413
>gnl|CDD|215310 PLN02572, PLN02572, UDP-sulfoquinovose synthase.
Length = 442
Score = 43.2 bits (102), Expect = 1e-04
Identities = 29/90 (32%), Positives = 42/90 (46%), Gaps = 9/90 (10%)
Query: 242 SNPKFILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETG----KP-----ESL 292
S K ++V GG GY G T + L + GY V +VDNL + G P E +
Sbjct: 45 SKKKKVMVIGGDGYCGWATALHLSKRGYEVAIVDNLCRRLFDHQLGLDSLTPIASIHERV 104
Query: 293 KRVENLTGKTVEYHEVDILQVSDLREIFSK 322
+R + ++GK +E + DI L E F
Sbjct: 105 RRWKEVSGKEIELYVGDICDFEFLSEAFKS 134
>gnl|CDD|212492 cd05327, retinol-DH_like_SDR_c_like, retinol dehydrogenase
(retinol-DH), Light dependent Protochlorophyllide
(Pchlide) OxidoReductase (LPOR) and related proteins,
classical (c) SDRs. Classical SDR subgroup containing
retinol-DHs, LPORs, and related proteins. Retinol is
processed by a medium chain alcohol dehydrogenase
followed by retinol-DHs. Pchlide reductases act in
chlorophyll biosynthesis. There are distinct enzymes
that catalyze Pchlide reduction in light or dark
conditions. Light-dependent reduction is via an
NADP-dependent SDR, LPOR. Proteins in this subfamily
share the glycine-rich NAD-binding motif of the
classical SDRs, have a partial match to the canonical
active site tetrad, but lack the typical active site
Ser. This subgroup includes the human proteins: retinol
dehydrogenase -12, -13 ,and -14, dehydrogenase/reductase
SDR family member (DHRS)-12 , -13 and -X (a DHRS on
chromosome X), and WWOX (WW domain-containing
oxidoreductase), as well as a Neurospora crassa SDR
encoded by the blue light inducible bli-4 gene. SDRs are
a functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold (alpha/beta folding pattern with a central
beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRs are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes catalyze a
wide range of activities including the metabolism of
steroids, cofactors, carbohydrates, lipids, aromatic
compounds, and amino acids, and act in redox sensing.
Classical SDRs have an TGXXX[AG]XG cofactor binding
motif and a YXXXK active site motif, with the Tyr
residue of the active site motif serving as a critical
catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 269
Score = 43.0 bits (102), Expect = 1e-04
Identities = 20/75 (26%), Positives = 35/75 (46%), Gaps = 9/75 (12%)
Query: 245 KFILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETGKPESLKRVENLTGKTVE 304
K +++TG IG T L + G +V++ ACR EE G+ + + + VE
Sbjct: 2 KVVVITGANSGIGKETARELAKRGAHVII------ACRNEEKGEEAAAEIKKETGNAKVE 55
Query: 305 YHEVDILQVSDLREI 319
++D +S L +
Sbjct: 56 VIQLD---LSSLASV 67
>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 = 42.7 bits (101), Expect = 1e-04
Identities = 23/78 (29%), Positives = 37/78 (47%), Gaps = 7/78 (8%)
Query: 245 KFILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETGKPESLKRVENLTGKTVE 304
K IL+TG AG IG +LL G +++ D +NA +E+ + + NL V
Sbjct: 3 KIILITGAAGLIGKAFCKALLSAGARLILAD--INAPALEQLK-----EELTNLYKNRVI 55
Query: 305 YHEVDILQVSDLREIFSK 322
E+DI ++E+
Sbjct: 56 ALELDITSKESIKELIES 73
>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 = 42.7 bits (101), Expect = 1e-04
Identities = 19/74 (25%), Positives = 26/74 (35%), Gaps = 13/74 (17%)
Query: 247 ILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETGKPESLKRVENLTGKTVEYH 306
+LVTG GY+G V LL+ G+ V R E K + + V
Sbjct: 1 VLVTGATGYVGGRLVPRLLQEGHQVRA------LVRSPE-------KLADRPWSERVTVV 47
Query: 307 EVDILQVSDLREIF 320
D+ LR
Sbjct: 48 RGDLEDPESLRAAL 61
>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 = 42.6 bits (101), Expect = 1e-04
Identities = 49/244 (20%), Positives = 83/244 (34%), Gaps = 63/244 (25%)
Query: 9 FVFSSSSTVYGTPKFLPFTED---HPTGQGCTNPYGKSKYFVEEILKDLASFKQKLQSLQ 65
F +SSS YG + LP +E P +PY SK + +
Sbjct: 119 FYQASSSEEYGKVQELPQSETTPFRPR-----SPYAVSKLYAD----------------- 156
Query: 66 SSVTQIWL--NSVHRSDWHIISLRYFNPVGSHPSGDIGEDPNGIPNNLMPYISQVAVGRR 123
W+ N ++ R FN H + + ++++ G +
Sbjct: 157 ------WITRNYREAYGLFAVNGRLFN----HEG--PRRGETFVTRKITRQVARIKAGLQ 204
Query: 124 KKLMVFGDDYDTKDG--SGVRDYIHIMDLAEGHVTALDKLLGGKSQAGFKAYNLGTGTGY 181
L + G RD+ D E + LL + + Y + TG +
Sbjct: 205 PVLKL---------GNLDAKRDWGDARDYVEAY-----WLLLQQGEPD--DYVIATGETH 248
Query: 182 SVFEMV-KAFSEACKKNIPYEVVGR---REGDIASSYCDASLAKKELAWEAKYGLDKMYL 237
SV E V AF E+ + R ++ D S A++EL W+ + ++ L
Sbjct: 249 SVREFVELAFEESGLTGDIEVEIDPRYFRPTEVDLLLGDPSKAREELGWKPEVSFEE--L 306
Query: 238 QRDM 241
R+M
Sbjct: 307 VREM 310
Score = 31.0 bits (71), Expect = 0.66
Identities = 21/78 (26%), Positives = 30/78 (38%), Gaps = 11/78 (14%)
Query: 247 ILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETGKPESLKRVENLTG--KTVE 304
L+TG G GS+ LLE GY V R + + R+++L +
Sbjct: 2 ALITGITGQDGSYLAEFLLEKGYEVHG------IVRRSSSF---NTDRIDHLYINKDRIT 52
Query: 305 YHEVDILQVSDLREIFSK 322
H D+ S LR K
Sbjct: 53 LHYGDLTDSSSLRRAIEK 70
>gnl|CDD|187584 cd05323, ADH_SDR_c_like, insect type alcohol dehydrogenase
(ADH)-like, classical (c) SDRs. This subgroup contains
insect type ADH, and 15-hydroxyprostaglandin
dehydrogenase (15-PGDH) type I; these proteins are
classical SDRs. ADH catalyzes the NAD+-dependent
oxidation of alcohols to aldehydes/ketones. This
subgroup is distinct from the zinc-dependent alcohol
dehydrogenases of the medium chain
dehydrogenase/reductase family, and evolved in fruit
flies to allow the digestion of fermenting fruit.
15-PGDH catalyzes the NAD-dependent interconversion of
(5Z,13E)-(15S)-11alpha,15-dihydroxy-9-oxoprost-13-enoate
and (5Z,13E)-11alpha-hydroxy-9,15-dioxoprost-13-enoate,
and has a typical SDR glycine-rich NAD-binding motif,
which is not fully present in ADH. 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 = 244
Score = 41.9 bits (99), Expect = 2e-04
Identities = 21/78 (26%), Positives = 30/78 (38%), Gaps = 8/78 (10%)
Query: 245 KFILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETGKPESLKRVENLTGKTVE 304
K ++TGGA IG T LL+ G V ++D R E G L+
Sbjct: 1 KVAIITGGASGIGLATAKLLLKKGAKVAILD------RNENPGAAAELQ--AINPKVKAT 52
Query: 305 YHEVDILQVSDLREIFSK 322
+ + D+ L F K
Sbjct: 53 FVQCDVTSWEQLAAAFKK 70
>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 = 41.5 bits (98), Expect = 2e-04
Identities = 13/27 (48%), Positives = 14/27 (51%)
Query: 247 ILVTGGAGYIGSHTVVSLLEHGYNVVV 273
LVTG A IG +L GY VVV
Sbjct: 3 ALVTGAAKRIGRAIAEALAAEGYRVVV 29
>gnl|CDD|165812 PLN02166, PLN02166, dTDP-glucose 4,6-dehydratase.
Length = 436
Score = 42.3 bits (99), Expect = 2e-04
Identities = 21/46 (45%), Positives = 29/46 (63%), Gaps = 7/46 (15%)
Query: 247 ILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETGKPESL 292
I+VTGGAG++GSH V L+ G V+V+DN TG+ E+L
Sbjct: 123 IVVTGGAGFVGSHLVDKLIGRGDEVIVIDNFF-------TGRKENL 161
Score = 40.0 bits (93), Expect = 0.001
Identities = 56/225 (24%), Positives = 88/225 (39%), Gaps = 42/225 (18%)
Query: 9 FVFSSSSTVYGTPKFLPFTEDHPTGQGCTNPYGKSKYFVEEILKDLASFKQKLQSLQSSV 68
F+ +S+S VYG P P E T G NP G+ + E K+ ++L
Sbjct: 229 FLLTSTSEVYGDPLEHPQKE---TYWGNVNPIGERSCYDEG--------KRTAETLAM-- 275
Query: 69 TQIWLNSVHR-SDWHIISLRYFNPVGSHPSGDIGEDPNGIPNNLMPYISQVAVGRRKKLM 127
HR + + R FN G D G + +N +++Q R++ +
Sbjct: 276 ------DYHRGAGVEVRIARIFNTYGPRMCLDDGR----VVSN---FVAQTI--RKQPMT 320
Query: 128 VFGDDYDTKDGSGVRDYIHIMDLAEGHVTALDKLLGGKSQAGFKAYNLGTGTGYSVFEMV 187
V+G DG R + ++ DL +G V L+ G+ F NLG +++ E+
Sbjct: 321 VYG------DGKQTRSFQYVSDLVDGLVA----LMEGEHVGPF---NLGNPGEFTMLELA 367
Query: 188 KAFSEACKKNIPYEVVGRREGDIASSYCDASLAKKELAWEAKYGL 232
+ E + E D D S AK+ L WE K L
Sbjct: 368 EVVKETIDSSATIEFKPNTADDPHKRKPDISKAKELLNWEPKISL 412
>gnl|CDD|185103 PRK15181, PRK15181, Vi polysaccharide biosynthesis protein TviC;
Provisional.
Length = 348
Score = 42.0 bits (98), Expect = 2e-04
Identities = 57/241 (23%), Positives = 103/241 (42%), Gaps = 57/241 (23%)
Query: 6 VYHFVFSSSSTVYGTPKFLPFTEDHPTGQGCTNPYGKSKYFVEEILKDLASFKQKLQSLQ 65
V F +++SS+ YG LP E+ G+ + PY +KY
Sbjct: 133 VSSFTYAASSSTYGDHPDLPKIEER-IGRPLS-PYAVTKY-------------------- 170
Query: 66 SSVTQIWLNSVHRS-DWHIISLRYFNPVGSHPSGDIGEDPNGIPNNLMPYISQVAVGRRK 124
V +++ + RS +++ I LRYFN G ++PNG + ++P R
Sbjct: 171 --VNELYADVFARSYEFNAIGLRYFNVFGRR------QNPNGAYSAVIP---------RW 213
Query: 125 KLMVFGDD--YDTKDGSGVRDYIHIMDLAEGH-VTALDKLLGGKSQAGFKAYNLGTGTGY 181
L + D+ Y DGS RD+ +I ++ + + ++A L K+ K YN+ G
Sbjct: 214 ILSLLKDEPIYINGDGSTSRDFCYIENVIQANLLSATTNDLASKN----KVYNVAVGDRT 269
Query: 182 SVFEMVKAF--------SEACKKNIPYEVVGRREGDIASSYCDASLAKKELAWEAKYGLD 233
S+ E+ +E + Y+ R+GD+ S D + K L++E ++ +
Sbjct: 270 SLNELYYLIRDGLNLWRNEQSRAEPIYKDF--RDGDVKHSQADITKIKTFLSYEPEFDIK 327
Query: 234 K 234
+
Sbjct: 328 E 328
>gnl|CDD|223377 COG0300, DltE, Short-chain dehydrogenases of various substrate
specificities [General function prediction only].
Length = 265
Score = 41.5 bits (98), Expect = 3e-04
Identities = 24/81 (29%), Positives = 36/81 (44%), Gaps = 9/81 (11%)
Query: 241 MSNPKFILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETGKPESL-KRVENLT 299
K L+TG + IG+ L GYN+++V R E+ K E+L K +E+ T
Sbjct: 3 PMKGKTALITGASSGIGAELAKQLARRGYNLILVA------RRED--KLEALAKELEDKT 54
Query: 300 GKTVEYHEVDILQVSDLREIF 320
G VE D+ L +
Sbjct: 55 GVEVEVIPADLSDPEALERLE 75
>gnl|CDD|236241 PRK08324, PRK08324, short chain dehydrogenase; Validated.
Length = 681
Score = 41.8 bits (99), Expect = 4e-04
Identities = 22/54 (40%), Positives = 24/54 (44%), Gaps = 13/54 (24%)
Query: 227 EAKYGLDKMYLQRDMSNPKF-----ILVTGGAGYIGSHTVVSLLEHGYNVVVVD 275
+AK LQR M PK LVTG AG IG T L G VV+ D
Sbjct: 408 QAK-------LQR-MPKPKPLAGKVALVTGAAGGIGKATAKRLAAEGACVVLAD 453
>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 = 40.7 bits (96), Expect = 5e-04
Identities = 21/72 (29%), Positives = 29/72 (40%), Gaps = 14/72 (19%)
Query: 247 ILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETGKPESLKRVENLTGKTVEYH 306
ILVTG G++GS+ V +LL GY V + V L + VE
Sbjct: 1 ILVTGATGFLGSNLVRALLAQGYRVRAL--------VRSGSDAVLLDGLP------VEVV 46
Query: 307 EVDILQVSDLRE 318
E D+ + L
Sbjct: 47 EGDLTDAASLAA 58
>gnl|CDD|236399 PRK09186, PRK09186, flagellin modification protein A; Provisional.
Length = 256
Score = 40.4 bits (95), Expect = 6e-04
Identities = 28/82 (34%), Positives = 38/82 (46%), Gaps = 6/82 (7%)
Query: 241 MSNPKFILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETGKPESLKRVENLTG 300
M K IL+TG G IGS V ++LE G V+ D ++ + E ESL +
Sbjct: 1 MLKGKTILITGAGGLIGSALVKAILEAGGIVIAAD--IDKEALNE--LLESLG--KEFKS 54
Query: 301 KTVEYHEVDILQVSDLREIFSK 322
K + E+DI L E SK
Sbjct: 55 KKLSLVELDITDQESLEEFLSK 76
>gnl|CDD|215146 PLN02260, PLN02260, probable rhamnose biosynthetic enzyme.
Length = 668
Score = 40.9 bits (96), Expect = 7e-04
Identities = 17/36 (47%), Positives = 23/36 (63%), Gaps = 2/36 (5%)
Query: 244 PKFILVTGGAGYIGSHTVVSLLEH--GYNVVVVDNL 277
PK IL+TG AG+I SH L+ + Y +VV+D L
Sbjct: 6 PKNILITGAAGFIASHVANRLIRNYPDYKIVVLDKL 41
Score = 31.3 bits (71), Expect = 0.84
Identities = 25/75 (33%), Positives = 35/75 (46%), Gaps = 15/75 (20%)
Query: 104 PNGIPNNLMPYISQVAVGRRKKLMVFGDDYDTKDGSGVRDYIHIMDLAEGHVTALDK-LL 162
PN P L+P +A+ + K L + GD GS VR Y++ D+AE L K +
Sbjct: 192 PNQFPEKLIPKFILLAM-QGKPLPIHGD------GSNVRSYLYCEDVAEAFEVVLHKGEV 244
Query: 163 GGKSQAGFKAYNLGT 177
G YN+GT
Sbjct: 245 GH-------VYNIGT 252
>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 = 40.3 bits (94), Expect = 8e-04
Identities = 14/25 (56%), Positives = 18/25 (72%)
Query: 247 ILVTGGAGYIGSHTVVSLLEHGYNV 271
+LVTG +G++ SH V LLE GY V
Sbjct: 1 VLVTGASGFVASHVVEQLLERGYKV 25
>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 = 39.9 bits (94), Expect = 8e-04
Identities = 22/73 (30%), Positives = 32/73 (43%), Gaps = 11/73 (15%)
Query: 247 ILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETGKPESLKRVENLTGKTVEYH 306
+L+TGG IG + + G VV++D +N EET K G V Y+
Sbjct: 2 VLITGGGSGIGRLLALEFAKRGAKVVILD--INEKGAEET-ANNVRK-----AGGKVHYY 53
Query: 307 EVDILQVSDLREI 319
+ D VS E+
Sbjct: 54 KCD---VSKREEV 63
>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 = 39.5 bits (93), Expect = 9e-04
Identities = 12/28 (42%), Positives = 16/28 (57%)
Query: 247 ILVTGGAGYIGSHTVVSLLEHGYNVVVV 274
+LV G G +G H V LL+ GY V +
Sbjct: 2 VLVVGATGKVGRHVVRELLDRGYQVRAL 29
>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 = 39.3 bits (92), Expect = 0.002
Identities = 21/52 (40%), Positives = 24/52 (46%), Gaps = 5/52 (9%)
Query: 6 VYHFVFSSSSTVYGTPKF-LPFTE-DHPTGQGCTNPYGKSKYFVEEILKDLA 55
V FVF SS V G PF E D P Q + YG+SK E L +L
Sbjct: 102 VKRFVFLSSVKVNGEGTVGAPFDETDPPAPQ---DAYGRSKLEAERALLELG 150
Score = 35.0 bits (81), Expect = 0.041
Identities = 16/35 (45%), Positives = 19/35 (54%), Gaps = 1/35 (2%)
Query: 247 ILVTGGAGYIGSHTVVSLLEHGYNVVV-VDNLVNA 280
+LVTG G+IG V LL G V + V N NA
Sbjct: 2 VLVTGANGFIGRALVDKLLSRGEEVRIAVRNAENA 36
>gnl|CDD|131680 TIGR02632, RhaD_aldol-ADH, rhamnulose-1-phosphate aldolase/alcohol
dehydrogenase.
Length = 676
Score = 39.1 bits (91), Expect = 0.003
Identities = 27/86 (31%), Positives = 37/86 (43%), Gaps = 10/86 (11%)
Query: 206 REGDIASSYCDASLAKKELAWEAKYGLDKMYLQRDMSNPK-----FILVTGGAGYIGSHT 260
R + S Y SL ++E A++ +Y + R M K VTGGAG IG T
Sbjct: 374 RGAEAVSEY--VSLPEQE-AFDIEYWPLEEAKLRRMPKEKTLARRVAFVTGGAGGIGRET 430
Query: 261 VVSLLEHGYNVVVVDNLVNACRVEET 286
L G +VV+ D +N E
Sbjct: 431 ARRLAAEGAHVVLAD--LNLEAAEAV 454
>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 = 38.1 bits (89), Expect = 0.003
Identities = 23/73 (31%), Positives = 30/73 (41%), Gaps = 13/73 (17%)
Query: 248 LVTGGAGYIGSHTVVSLLEHG--YNVVVVDNLVNACRVEETGKPESLKRVENLTGKTVEY 305
LVTGG G++G H V LL G V V D E +++ +T Y
Sbjct: 1 LVTGGGGFLGRHIVRLLLREGELQEVRVFD------LRFSPELLEDFSKLQVIT-----Y 49
Query: 306 HEVDILQVSDLRE 318
E D+ DLR
Sbjct: 50 IEGDVTDKQDLRR 62
>gnl|CDD|180439 PRK06171, PRK06171, sorbitol-6-phosphate 2-dehydrogenase;
Provisional.
Length = 266
Score = 37.7 bits (88), Expect = 0.004
Identities = 16/31 (51%), Positives = 19/31 (61%)
Query: 245 KFILVTGGAGYIGSHTVVSLLEHGYNVVVVD 275
K I+VTGG+ IG V LL +G NVV D
Sbjct: 10 KIIIVTGGSSGIGLAIVKELLANGANVVNAD 40
>gnl|CDD|237218 PRK12825, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 249
Score = 37.9 bits (89), Expect = 0.004
Identities = 20/75 (26%), Positives = 32/75 (42%), Gaps = 7/75 (9%)
Query: 245 KFILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETGKPESLKRVENLTGKTVE 304
+ LVTG A +G + L G +VVV R +E E ++ VE L G+ +
Sbjct: 7 RVALVTGAARGLGRAIALRLARAGADVVVH------YRSDEEAAEELVEAVEAL-GRRAQ 59
Query: 305 YHEVDILQVSDLREI 319
+ D+ + L
Sbjct: 60 AVQADVTDKAALEAA 74
>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 = 38.0 bits (89), Expect = 0.004
Identities = 10/28 (35%), Positives = 15/28 (53%)
Query: 247 ILVTGGAGYIGSHTVVSLLEHGYNVVVV 274
+ V G G+IG + V L + G V+V
Sbjct: 3 VTVFGATGFIGRYVVNRLAKRGSQVIVP 30
>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 = 37.0 bits (86), Expect = 0.004
Identities = 17/74 (22%), Positives = 27/74 (36%), Gaps = 14/74 (18%)
Query: 247 ILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETGKPESLKRVENLTGKTVEYH 306
IL+ G G+IG LLE G+ V ++ KR+ + V
Sbjct: 1 ILILGATGFIGRALARELLEQGHEVTLLVRNT--------------KRLSKEDQEPVAVV 46
Query: 307 EVDILQVSDLREIF 320
E D+ + L +
Sbjct: 47 EGDLRDLDSLSDAV 60
>gnl|CDD|181668 PRK09135, PRK09135, pteridine reductase; Provisional.
Length = 249
Score = 37.6 bits (88), Expect = 0.005
Identities = 12/34 (35%), Positives = 17/34 (50%)
Query: 240 DMSNPKFILVTGGAGYIGSHTVVSLLEHGYNVVV 273
+ K L+TGGA IG+ +L GY V +
Sbjct: 2 MTDSAKVALITGGARRIGAAIARTLHAAGYRVAI 35
>gnl|CDD|183489 PRK12384, PRK12384, sorbitol-6-phosphate dehydrogenase;
Provisional.
Length = 259
Score = 37.3 bits (87), Expect = 0.005
Identities = 22/83 (26%), Positives = 32/83 (38%), Gaps = 16/83 (19%)
Query: 245 KFILVTGGAGYIGSHTVVSLLEHGYNVVVVD-NLVNACRV-----EETGKPESL------ 292
+ +V GG +G+ L E GY V V D N A V E G+ +
Sbjct: 3 QVAVVIGGGQTLGAFLCHGLAEEGYRVAVADINSEKAANVAQEINAEYGEGMAYGFGADA 62
Query: 293 ---KRVENLTGKTVE-YHEVDIL 311
+ V L+ E + VD+L
Sbjct: 63 TSEQSVLALSRGVDEIFGRVDLL 85
>gnl|CDD|182313 PRK10217, PRK10217, dTDP-glucose 4,6-dehydratase; Provisional.
Length = 355
Score = 37.3 bits (86), Expect = 0.007
Identities = 27/79 (34%), Positives = 41/79 (51%), Gaps = 9/79 (11%)
Query: 245 KFILVTGGAGYIGSHTVVSLLEHGYN-VVVVDNLVNACRVEETGKPESLKRVENLTGKTV 303
+ IL+TGGAG+IGS V ++ + VVVVD L A G SL V +
Sbjct: 2 RKILITGGAGFIGSALVRYIINETSDAVVVVDKLTYA------GNLMSLAPVAQ--SERF 53
Query: 304 EYHEVDILQVSDLREIFSK 322
+ +VDI ++L +F++
Sbjct: 54 AFEKVDICDRAELARVFTE 72
>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 = 36.7 bits (85), Expect = 0.007
Identities = 20/77 (25%), Positives = 31/77 (40%), Gaps = 3/77 (3%)
Query: 247 ILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETGKPESLKRVENLTGKTVE-Y 305
+LVTGG+G IG L G V+V V + R+ +LTG +E
Sbjct: 1 VLVTGGSGGIGGAIARWLASRGSPKVLV-VSRRDVVVHNAAILD-DGRLIDLTGSRIERA 58
Query: 306 HEVDILQVSDLREIFSK 322
+++ L E +
Sbjct: 59 IRANVVGTRRLLEAARE 75
>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 = 37.3 bits (87), Expect = 0.008
Identities = 14/26 (53%), Positives = 16/26 (61%)
Query: 248 LVTGGAGYIGSHTVVSLLEHGYNVVV 273
LVTG G++GS V LLE G V V
Sbjct: 4 LVTGATGFVGSAVVRLLLEQGEEVRV 29
>gnl|CDD|187629 cd05371, HSD10-like_SDR_c, 17hydroxysteroid dehydrogenase type 10
(HSD10)-like, classical (c) SDRs. HSD10, also known as
amyloid-peptide-binding alcohol dehydrogenase (ABAD),
was previously identified as a L-3-hydroxyacyl-CoA
dehydrogenase, HADH2. In fatty acid metabolism, HADH2
catalyzes the third step of beta-oxidation, the
conversion of a hydroxyl to a keto group in the
NAD-dependent oxidation of L-3-hydroxyacyl CoA. In
addition to alcohol dehydrogenase and HADH2 activites,
HSD10 has steroid dehydrogenase activity. Although the
mechanism is unclear, HSD10 is implicated in the
formation of amyloid beta-petide in the brain (which is
linked to the development of Alzheimer's disease).
Although HSD10 is normally concentrated in the
mitochondria, in the presence of amyloid beta-peptide it
translocates into the plasma membrane, where it's action
may generate cytotoxic aldehydes and may lower estrogen
levels through its use of 17-beta-estradiol as a
substrate. HSD10 is a member of the SRD family, but
differs from other SDRs by the presence of two
insertions of unknown 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 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 = 252
Score = 36.5 bits (85), Expect = 0.010
Identities = 19/76 (25%), Positives = 30/76 (39%), Gaps = 12/76 (15%)
Query: 247 ILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETGKPESLKRVENLTGKTVEYH 306
+VTGGA +G TV LL G VV++D G+ + G +
Sbjct: 5 AVVTGGASGLGLATVERLLAQGAKVVILD------LPNSPGETVA------KLGDNCRFV 52
Query: 307 EVDILQVSDLREIFSK 322
VD+ D++ +
Sbjct: 53 PVDVTSEKDVKAALAL 68
>gnl|CDD|187640 cd08935, mannonate_red_SDR_c, putative D-mannonate oxidoreductase,
classical (c) SDR. D-mannonate oxidoreductase catalyzes
the NAD-dependent interconversion of D-mannonate and
D-fructuronate. This subgroup includes Bacillus
subtitils UxuB/YjmF, a putative D-mannonate
oxidoreductase; the B. subtilis UxuB gene is part of a
putative ten-gene operon (the Yjm operon) involved in
hexuronate catabolism. Escherichia coli UxuB does not
belong to this subgroup. This subgroup has a canonical
active site tetrad and a typical Gly-rich NAD-binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold (alpha/beta folding
pattern with a central beta-sheet), an NAD(P)(H)-binding
region, and a structurally diverse C-terminal region.
Classical SDRs are typically about 250 residues long,
while extended SDRs are approximately 350 residues.
Sequence identity between different SDR enzymes are
typically in the 15-30% range, but the enzymes share the
Rossmann fold NAD-binding motif and characteristic
NAD-binding and catalytic sequence patterns. These
enzymes 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 = 271
Score = 36.3 bits (84), Expect = 0.014
Identities = 16/74 (21%), Positives = 30/74 (40%), Gaps = 8/74 (10%)
Query: 245 KFILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETGKPESLKRVENLTGKTVE 304
K ++TGG G +G +L + G V + N + ++ K + L G+ +
Sbjct: 6 KVAVITGGTGVLGGAMARALAQAGAKVAALG--RNQEKGDKV-----AKEITALGGRAIA 58
Query: 305 YHEVDILQVSDLRE 318
D+L + L
Sbjct: 59 L-AADVLDRASLER 71
>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 = 36.3 bits (84), Expect = 0.017
Identities = 19/72 (26%), Positives = 28/72 (38%), Gaps = 13/72 (18%)
Query: 247 ILVTGGAGYIGSHTVVSLLE-HGYNVVVVDNLVNACRVEETGKPESLKRVENLTGKTVEY 305
+LVTGG+G+ G V LLE G V D + P +E+
Sbjct: 2 VLVTGGSGFFGERLVKQLLERGGTYVRSFDIAPPGEALSAWQHPN------------IEF 49
Query: 306 HEVDILQVSDLR 317
+ DI +D+
Sbjct: 50 LKGDITDRNDVE 61
>gnl|CDD|187578 cd05269, TMR_SDR_a, triphenylmethane reductase (TMR)-like proteins,
NMRa-like, atypical (a) SDRs. TMR is an atypical
NADP-binding protein of the SDR family. It lacks the
active site residues of the SDRs but has a glycine rich
NAD(P)-binding motif that matches the extended SDRs.
Proteins in this subgroup however, are more similar in
length to the classical SDRs. TMR was identified as a
reducer of triphenylmethane dyes, important
environmental pollutants. This subgroup also includes
Escherichia coli NADPH-dependent quinine oxidoreductase
(QOR2), which catalyzes two-electron reduction of
quinone; but is unlikely to play a major role in
protecting against quinone cytotoxicity. Atypical SDRs
are distinct from classical SDRs. Atypical SDRs include
biliverdin IX beta reductase (BVR-B,aka flavin
reductase), NMRa (a negative transcriptional regulator
of various fungi), progesterone 5-beta-reductase like
proteins, phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. In addition to the
Rossmann fold core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 272
Score = 36.1 bits (84), Expect = 0.017
Identities = 17/50 (34%), Positives = 21/50 (42%), Gaps = 6/50 (12%)
Query: 247 ILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETGKPESLKRVE 296
ILVTG G +G+ V LL +VV R E K + VE
Sbjct: 1 ILVTGATGKLGTAVVELLLAKVASVVA------LVRNPEKAKAFAADGVE 44
Score = 29.5 bits (67), Expect = 2.0
Identities = 19/59 (32%), Positives = 23/59 (38%), Gaps = 5/59 (8%)
Query: 149 DLAEGHVTALDKLLGGKSQAGFKAYNLGTGTGYSVFEMVKAFSEACKKNIPYEVVGRRE 207
D+AE AL + G K YNL S E+ SEA K + Y V E
Sbjct: 171 DIAEAAAAALTE----PGHEG-KVYNLTGPEALSYAELAAILSEALGKPVRYVPVSPDE 224
>gnl|CDD|183773 PRK12824, PRK12824, acetoacetyl-CoA reductase; Provisional.
Length = 245
Score = 35.9 bits (83), Expect = 0.018
Identities = 15/42 (35%), Positives = 17/42 (40%)
Query: 243 NPKFILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVE 284
K LVTG IGS LL GY V+ N C +
Sbjct: 1 MKKIALVTGAKRGIGSAIARELLNDGYRVIATYFSGNDCAKD 42
>gnl|CDD|212493 cd08932, HetN_like_SDR_c, HetN oxidoreductase-like, classical (c)
SDR. This subgroup includes Anabaena sp. strain PCC
7120 HetN, a putative oxidoreductase involved in
heterocyst differentiation, and related proteins. SDRs
are a functionally diverse family of oxidoreductases
that have a single domain with a structurally conserved
Rossmann fold (alpha/beta folding pattern with a central
beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRs are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes catalyze a
wide range of activities including the metabolism of
steroids, cofactors, carbohydrates, lipids, aromatic
compounds, and amino acids, and act in redox sensing.
Classical SDRs have an TGXXX[AG]XG cofactor binding
motif and a YXXXK active site motif, with the Tyr
residue of the active site motif serving as a critical
catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 223
Score = 35.8 bits (83), Expect = 0.019
Identities = 17/73 (23%), Positives = 23/73 (31%), Gaps = 12/73 (16%)
Query: 245 KFILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETGKPESLKRVENLTGKTVE 304
K LVTG + IG +L GY V + + + +G VE
Sbjct: 1 KVALVTGASRGIGIEIARALARDGYRVSL------------GLRNPEDLAALSASGGDVE 48
Query: 305 YHEVDILQVSDLR 317
D D R
Sbjct: 49 AVPYDARDPEDAR 61
>gnl|CDD|180408 PRK06114, PRK06114, short chain dehydrogenase; Provisional.
Length = 254
Score = 35.5 bits (82), Expect = 0.021
Identities = 17/71 (23%), Positives = 28/71 (39%), Gaps = 7/71 (9%)
Query: 248 LVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETGKPESLKRVENLTGKTVEYHE 307
VTG IG + L + G +V + D + G E+ + +E G+
Sbjct: 12 FVTGAGSGIGQRIAIGLAQAGADVALFD------LRTDDGLAETAEHIEAA-GRRAIQIA 64
Query: 308 VDILQVSDLRE 318
D+ +DLR
Sbjct: 65 ADVTSKADLRA 75
>gnl|CDD|178263 PLN02657, PLN02657, 3,8-divinyl protochlorophyllide a 8-vinyl
reductase.
Length = 390
Score = 35.9 bits (83), Expect = 0.022
Identities = 22/62 (35%), Positives = 28/62 (45%), Gaps = 4/62 (6%)
Query: 247 ILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETGKPESLKRVENLTGKTVEYH 306
+LV G GYIG V L+ GYNVV V + R GK + L G V +
Sbjct: 63 VLVVGATGYIGKFVVRELVRRGYNVVAVAREKSGIR----GKNGKEDTKKELPGAEVVFG 118
Query: 307 EV 308
+V
Sbjct: 119 DV 120
>gnl|CDD|178298 PLN02695, PLN02695, GDP-D-mannose-3',5'-epimerase.
Length = 370
Score = 35.6 bits (82), Expect = 0.025
Identities = 10/29 (34%), Positives = 15/29 (51%)
Query: 247 ILVTGGAGYIGSHTVVSLLEHGYNVVVVD 275
I +TG G+I SH L G+ ++ D
Sbjct: 24 ICITGAGGFIASHIARRLKAEGHYIIASD 52
>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 = 35.1 bits (81), Expect = 0.029
Identities = 23/80 (28%), Positives = 31/80 (38%), Gaps = 13/80 (16%)
Query: 245 KFILVTGGAGYIGSHTVVSLLEHGYNVVVVD---NLVNACRVEETGKPESLKRVENLT-- 299
K LVTGGA IG L G VVV D + G P +L ++T
Sbjct: 2 KVALVTGGASGIGLAIAKRLAAEGAAVVVADIDPEIAEKVAEAAQGGPRALGVQCDVTSE 61
Query: 300 -------GKTV-EYHEVDIL 311
+ V E+ +DI+
Sbjct: 62 AQVQSAFEQAVLEFGGLDIV 81
>gnl|CDD|187553 cd05242, SDR_a8, atypical (a) SDRs, subgroup 8. This subgroup
contains atypical SDRs of unknown function. Proteins in
this subgroup have a glycine-rich NAD(P)-binding motif
consensus that resembles that of the extended SDRs,
(GXXGXXG or GGXGXXG), but lacks the characteristic
active site residues of the SDRs. A Cys often replaces
the usual Lys of the YXXXK active site motif, while the
upstream Ser is generally present and Arg replaces the
usual Asn. Atypical SDRs generally lack the catalytic
residues characteristic of the SDRs, and their
glycine-rich NAD(P)-binding motif is often different
from the forms normally seen in classical or extended
SDRs. Atypical SDRs include biliverdin IX beta reductase
(BVR-B,aka flavin reductase), NMRa (a negative
transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. In addition to the
Rossmann fold core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 296
Score = 35.3 bits (82), Expect = 0.031
Identities = 18/68 (26%), Positives = 28/68 (41%), Gaps = 11/68 (16%)
Query: 247 ILVTGGAGYIGSHTVVSLLEHGYNVVVV-----DNLVNACRVE---ETGKPESLKRVE-- 296
I++TGG G+IG L G+ VVV+ A + + P L +
Sbjct: 2 IVITGGTGFIGRALTRRLTAAGHEVVVLSRRPGKAEGLAEVITWDGLSLGPWELPGADAV 61
Query: 297 -NLTGKTV 303
NL G+ +
Sbjct: 62 INLAGEPI 69
>gnl|CDD|187572 cd05262, SDR_a7, atypical (a) SDRs, subgroup 7. This subgroup
contains atypical SDRs of unknown function. Members of
this subgroup have a glycine-rich NAD(P)-binding motif
consensus that matches the extended SDRs, TGXXGXXG, but
lacks the characteristic active site residues of the
SDRs. This subgroup has basic residues (HXXXR) in place
of the active site motif YXXXK, these may have a
catalytic role. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and their
glycine-rich NAD(P)-binding motif is often different
from the forms normally seen in classical or extended
SDRs. Atypical SDRs include biliverdin IX beta reductase
(BVR-B,aka flavin reductase), NMRa (a negative
transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. In addition to the
Rossmann fold core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 291
Score = 35.4 bits (82), Expect = 0.031
Identities = 12/26 (46%), Positives = 16/26 (61%)
Query: 247 ILVTGGAGYIGSHTVVSLLEHGYNVV 272
+ VTG G+IGS V L+ G+ VV
Sbjct: 3 VFVTGATGFIGSAVVRELVAAGHEVV 28
>gnl|CDD|131468 TIGR02415, 23BDH, acetoin reductases. One member of this family,
as characterized in Klebsiella terrigena, is described
as able to interconvert acetoin + NADH with
meso-2,3-butanediol + NAD(+). It is also called capable
of irreversible reduction of diacetyl with NADH to
acetoin. Blomqvist, et al. decline to specify either EC
1.1.1.4 which is (R,R)-butanediol dehydrogenase, or EC
1.1.1.5, which is acetoin dehydrogenase without a
specified stereochemistry, for this enzyme. This enzyme
is a homotetramer in the family of short chain
dehydrogenases (pfam00106). Another member of this
family, from Corynebacterium glutamicum, is called
L-2,3-butanediol dehydrogenase (PMID:11577733) [Energy
metabolism, Fermentation].
Length = 254
Score = 35.1 bits (81), Expect = 0.032
Identities = 27/77 (35%), Positives = 34/77 (44%), Gaps = 11/77 (14%)
Query: 245 KFILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETGKPESLKRVENLTGKTVE 304
K LVTGGA IG L + G+ V V D + E E+ K + GK V
Sbjct: 1 KVALVTGGAQGIGKGIAERLAKDGFAVAVAD-------LNEETAKETAKEINQAGGKAVA 53
Query: 305 YHEVDILQVSDLREIFS 321
Y L VSD ++FS
Sbjct: 54 Y----KLDVSDKDQVFS 66
>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 = 35.1 bits (81), Expect = 0.037
Identities = 17/46 (36%), Positives = 21/46 (45%), Gaps = 4/46 (8%)
Query: 9 FVFSSSSTVYGTPKFLPFTED-HPTGQGCTNPYGKSKYFVEEILKD 53
FVF+SS VYG P P T+ + YG K E +L D
Sbjct: 112 FVFTSSLAVYGLPLPNPVTDHTALDPA---SSYGAQKAMCELLLND 154
>gnl|CDD|224014 COG1089, Gmd, GDP-D-mannose dehydratase [Cell envelope biogenesis,
outer membrane].
Length = 345
Score = 35.0 bits (81), Expect = 0.038
Identities = 21/93 (22%), Positives = 36/93 (38%), Gaps = 24/93 (25%)
Query: 173 YNLGTGTGYSVFEMV-KAFS------------------EACKKNIPYEVVGR--REGDIA 211
Y + TG +SV E V AF +A I E+ R R ++
Sbjct: 247 YVIATGETHSVREFVELAFEMVGIDLEWEGTGVDEKGVDAKTGKIIVEIDPRYFRPAEVD 306
Query: 212 SSYCDASLAKKELAWEAKYGLD---KMYLQRDM 241
D + AK++L W + L+ + ++ D+
Sbjct: 307 LLLGDPTKAKEKLGWRPEVSLEELVREMVEADL 339
>gnl|CDD|187656 cd08953, KR_2_SDR_x, ketoreductase (KR), subgroup 2, complex (x)
SDRs. Ketoreductase, a module of the multidomain
polyketide synthase (PKS), has 2 subdomains, each
corresponding to a SDR family monomer. The C-terminal
subdomain catalyzes the NADPH-dependent reduction of the
beta-carbonyl of a polyketide to a hydroxyl group, a
step in the biosynthesis of polyketides, such as
erythromycin. The N-terminal subdomain, an interdomain
linker, is a truncated Rossmann fold which acts to
stabilizes the catalytic subdomain. Unlike typical SDRs,
the isolated domain does not oligomerize but is composed
of 2 subdomains, each resembling an SDR monomer. The
active site resembles that of typical SDRs, except that
the usual positions of the catalytic Asn and Tyr are
swapped, so that the canonical YXXXK motif changes to
YXXXN. Modular PKSs are multifunctional structures in
which the makeup recapitulates that found in (and may
have evolved from) FAS. Polyketide synthesis also
proceeds via the addition of 2-carbon units as in fatty
acid synthesis. The complex SDR NADP-binding motif,
GGXGXXG, is often present, but is not strictly conserved
in each instance of the module. This subfamily includes
both KR domains of the Bacillus subtilis Pks J,-L, and
PksM, and all three KR domains of PksN, components of
the megacomplex bacillaene synthase, which synthesizes
the antibiotic bacillaene. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold
(alpha/beta folding pattern with a central beta-sheet),
an NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRs are approximately
350 residues. Sequence identity between different SDR
enzymes are typically in the 15-30% range, but the
enzymes share the Rossmann fold NAD-binding motif and
characteristic NAD-binding and catalytic sequence
patterns. These enzymes catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human prostaglandin dehydrogenase
(PGDH) numbering). In addition to the Tyr and Lys, there
is often an upstream Ser (Ser-138, PGDH numbering)
and/or an Asn (Asn-107, PGDH numbering) contributing to
the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type KRs have a TGXXXGX(1-2)G
NAD(P)-binding motif. Some atypical SDRs have lost
catalytic activity and/or have an unusual NAD(P)-binding
motif and missing or unusual active site residues.
Reactions catalyzed within the SDR family include
isomerization, decarboxylation, epimerization, C=N bond
reduction, dehydratase activity, dehalogenation,
Enoyl-CoA reduction, and carbonyl-alcohol
oxidoreduction.
Length = 436
Score = 35.0 bits (81), Expect = 0.041
Identities = 25/74 (33%), Positives = 33/74 (44%), Gaps = 15/74 (20%)
Query: 248 LVTGGAGYIGSHTVVSLLEH-GYNVVVVDNLVNACRV----EETGKPESLKRVENLTGKT 302
LVTGGAG IG +L G +V++ R EE K ++L +E L G
Sbjct: 209 LVTGGAGGIGRALARALARRYGARLVLLG------RSPLPPEEEWKAQTLAALEAL-GAR 261
Query: 303 VEYHEVDILQVSDL 316
V Y D V+D
Sbjct: 262 VLYISAD---VTDA 272
>gnl|CDD|187594 cd05333, BKR_SDR_c, beta-Keto acyl carrier protein reductase (BKR),
involved in Type II FAS, classical (c) SDRs. This
subgroup includes the Escherichai coli K12 BKR, FabG.
BKR catalyzes the NADPH-dependent reduction of ACP in
the first reductive step of de novo fatty acid synthesis
(FAS). FAS consists of four elongation steps, which are
repeated to extend the fatty acid chain through the
addition of two-carbo units from malonyl acyl-carrier
protein (ACP): condensation, reduction, dehydration, and
a final reduction. Type II FAS, typical of plants and
many bacteria, maintains these activities on discrete
polypeptides, while type I FAS utilizes one or two
multifunctional polypeptides. BKR resembles enoyl
reductase, which catalyzes the second reduction step in
FAS. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with
structurally conserved Rossmann fold (alpha/beta folding
pattern with a central beta-sheet) 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: TGxxxGxG in classical SDRs. 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 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. 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-151 and
Lys-155, and well as Asn-111 (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 = 240
Score = 34.8 bits (81), Expect = 0.042
Identities = 22/84 (26%), Positives = 25/84 (29%), Gaps = 20/84 (23%)
Query: 245 KFILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEET----------------GK 288
K LVTG + IG + L G V V D A
Sbjct: 1 KVALVTGASRGIGRAIALRLAAEGAKVAVTDRSEEAAAETVEEIKALGGNAAALEADVSD 60
Query: 289 PESLKRVENLTGKTVEYH-EVDIL 311
E+ VE L K VDIL
Sbjct: 61 REA---VEALVEKVEAEFGPVDIL 81
>gnl|CDD|217692 pfam03721, UDPG_MGDP_dh_N, UDP-glucose/GDP-mannose dehydrogenase
family, NAD binding domain. The UDP-glucose/GDP-mannose
dehydrogenaseses are a small group of enzymes which
possesses the ability to catalyze the NAD-dependent
2-fold oxidation of an alcohol to an acid without the
release of an aldehyde intermediate.
Length = 188
Score = 34.1 bits (79), Expect = 0.045
Identities = 14/34 (41%), Positives = 22/34 (64%), Gaps = 2/34 (5%)
Query: 252 GAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEE 285
G GY+G T V L E G++VV VD +N ++++
Sbjct: 7 GLGYVGLPTAVCLAEIGHDVVGVD--INQSKIDK 38
>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 = 34.9 bits (81), Expect = 0.045
Identities = 11/28 (39%), Positives = 17/28 (60%)
Query: 247 ILVTGGAGYIGSHTVVSLLEHGYNVVVV 274
IL+TGG G+IG L + G+ V ++
Sbjct: 1 ILITGGTGFIGRALTQRLTKRGHEVTIL 28
>gnl|CDD|187602 cd05344, BKR_like_SDR_like, putative beta-ketoacyl acyl carrier
protein [ACP] reductase (BKR)-like, SDR. This subgroup
resembles the SDR family, but does not have a perfect
match to the NAD-binding motif or the catalytic tetrad
characteristic of the SDRs. It includes the SDRs, Q9HYA2
from Pseudomonas aeruginosa PAO1 and APE0912 from
Aeropyrum pernix K1. BKR catalyzes the NADPH-dependent
reduction of ACP in the first reductive step of de novo
fatty acid synthesis (FAS). FAS consists of four
elongation steps, which are repeated to extend the fatty
acid chain through the addition of two-carbo units from
malonyl acyl-carrier protein (ACP): condensation,
reduction, dehydration, and a final reduction. Type II
FAS, typical of plants and many bacteria, maintains
these activities on discrete polypeptides, while type I
FAS utilizes one or two multifunctional polypeptides.
BKR resembles enoyl reductase, which catalyzes the
second reduction step in FAS. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold
(alpha/beta folding pattern with a central beta-sheet),
an NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRS are approximately
350 residues. Sequence identity between different SDR
enzymes are typically in the 15-30% range, but the
enzymes share the Rossmann fold NAD-binding motif and
characteristic NAD-binding and catalytic sequence
patterns. These enzymes have a 3-glycine N-terminal
NAD(P)(H)-binding pattern (typically, TGxxxGxG in
classical SDRs and TGxxGxxG in extended SDRs), while
substrate binding is in the C-terminal region. A
critical catalytic Tyr residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering), is often found in a conserved YXXXK pattern.
In addition to the Tyr and Lys, there is often an
upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn
(Asn-107, 15-PGDH numbering) or additional Ser,
contributing to the active site. Substrates for these
enzymes include sugars, steroids, alcohols, and aromatic
compounds. The standard reaction mechanism is a proton
relay involving the conserved Tyr and Lys, as well as
Asn (or Ser). Some SDR family members, including 17
beta-hydroxysteroid dehydrogenase contain an additional
helix-turn-helix motif that is not generally found among
SDRs.
Length = 253
Score = 34.6 bits (80), Expect = 0.047
Identities = 20/80 (25%), Positives = 28/80 (35%), Gaps = 18/80 (22%)
Query: 248 LVTGGAGYIGSHTVVSLLEHGYNVVVV----DNLVNAC------------RVEETGKPES 291
LVT + IG +L G V + +NL A V + PE
Sbjct: 5 LVTAASSGIGLAIARALAREGARVAICARNRENLERAASELRAGGAGVLAVVADLTDPED 64
Query: 292 LKRVENLTGKTVEYHEVDIL 311
+ R+ G + VDIL
Sbjct: 65 IDRLVEKAGDA--FGRVDIL 82
>gnl|CDD|237100 PRK12429, PRK12429, 3-hydroxybutyrate dehydrogenase; Provisional.
Length = 258
Score = 34.5 bits (80), Expect = 0.051
Identities = 22/80 (27%), Positives = 29/80 (36%), Gaps = 13/80 (16%)
Query: 241 MSNPKFILVTGGAGYIGSHTVVSLLEHGYNVVVVD-NLVNACRVEETGKPESLKRVENLT 299
M K LVTG A IG ++L + G VV+ D N A E +
Sbjct: 1 MLKGKVALVTGAASGIGLEIALALAKEGAKVVIADLNDEAAAAAAEALQKA--------- 51
Query: 300 GKTVEYHEVDILQVSDLREI 319
G +D V+D I
Sbjct: 52 GGKAIGVAMD---VTDEEAI 68
>gnl|CDD|181139 PRK07832, PRK07832, short chain dehydrogenase; Provisional.
Length = 272
Score = 34.6 bits (80), Expect = 0.051
Identities = 18/66 (27%), Positives = 27/66 (40%), Gaps = 7/66 (10%)
Query: 245 KFILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETGKPESLKRVENLTGKTVE 304
K VTG A IG T + L G + + D +A + +T + L G E
Sbjct: 1 KRCFVTGAASGIGRATALRLAAQGAELFLTD--RDADGLAQT-----VADARALGGTVPE 53
Query: 305 YHEVDI 310
+ +DI
Sbjct: 54 HRALDI 59
>gnl|CDD|178484 PLN02896, PLN02896, cinnamyl-alcohol dehydrogenase.
Length = 353
Score = 34.8 bits (80), Expect = 0.054
Identities = 14/23 (60%), Positives = 15/23 (65%)
Query: 249 VTGGAGYIGSHTVVSLLEHGYNV 271
VTG GYIGS V LL+ GY V
Sbjct: 15 VTGATGYIGSWLVKLLLQRGYTV 37
>gnl|CDD|187587 cd05326, secoisolariciresinol-DH_like_SDR_c, secoisolariciresinol
dehydrogenase (secoisolariciresinol-DH)-like, classical
(c) SDRs. Podophyllum secoisolariciresinol-DH is a homo
tetrameric, classical SDR that catalyzes the
NAD-dependent conversion of (-)-secoisolariciresinol to
(-)-matairesinol via a (-)-lactol intermediate.
(-)-Matairesinol is an intermediate to various
8'-lignans, including the cancer-preventive mammalian
lignan, and those involved in vascular plant defense.
This subgroup also includes rice momilactone A synthase
which catalyzes the conversion of
3beta-hydroxy-9betaH-pimara-7,15-dien-19,6beta-olide
into momilactone A, Arabidopsis ABA2 which during
abscisic acid (ABA) biosynthesis, catalyzes the
conversion of xanthoxin to abscisic aldehyde and, maize
Tasselseed2 which participate in the maize sex
determination pathway. SDRs are a functionally diverse
family of oxidoreductases that have a single domain with
a structurally conserved Rossmann fold (alpha/beta
folding pattern with a central beta-sheet), an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRs are approximately
350 residues. Sequence identity between different SDR
enzymes are typically in the 15-30% range, but the
enzymes share the Rossmann fold NAD-binding motif and
characteristic NAD-binding and catalytic sequence
patterns. These enzymes catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, 15-hydroxyprostaglandin dehydrogenase
(15-PGDH) numbering). In addition to the Tyr and Lys,
there is often an upstream Ser (Ser-138, 15-PGDH
numbering) and/or an Asn (Asn-107, 15-PGDH numbering)
contributing to the active site; while substrate binding
is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. Extended SDRs have additional
elements in the C-terminal region, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Some atypical SDRs have lost catalytic activity and/or
have an unusual NAD(P)-binding motif and missing or
unusual active site residues. Reactions catalyzed within
the SDR family include isomerization, decarboxylation,
epimerization, C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 249
Score = 34.4 bits (79), Expect = 0.055
Identities = 13/31 (41%), Positives = 17/31 (54%)
Query: 245 KFILVTGGAGYIGSHTVVSLLEHGYNVVVVD 275
K ++TGGA IG T +HG VV+ D
Sbjct: 5 KVAIITGGASGIGEATARLFAKHGARVVIAD 35
>gnl|CDD|178268 PLN02662, PLN02662, cinnamyl-alcohol dehydrogenase family protein.
Length = 322
Score = 34.3 bits (79), Expect = 0.060
Identities = 14/27 (51%), Positives = 17/27 (62%)
Query: 245 KFILVTGGAGYIGSHTVVSLLEHGYNV 271
K + VTG +GYI S V LL+ GY V
Sbjct: 5 KVVCVTGASGYIASWLVKLLLQRGYTV 31
>gnl|CDD|211705 TIGR01963, PHB_DH, 3-hydroxybutyrate dehydrogenase. This model
represents a subfamily of the short chain
dehydrogenases. Characterized members so far as
3-hydroxybutyrate dehydrogenases and are found in
species that accumulate ester polmers called
polyhydroxyalkanoic acids (PHAs) under certain
conditions. Several members of the family are from
species not known to accumulate PHAs, including
Oceanobacillus iheyensis and Bacillus subtilis. However,
polymer formation is not required for there be a role
for 3-hydroxybutyrate dehydrogenase; it may be members
of this family have the same function in those species.
Length = 255
Score = 34.3 bits (79), Expect = 0.062
Identities = 25/76 (32%), Positives = 29/76 (38%), Gaps = 11/76 (14%)
Query: 244 PKFILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETGKPESLKRVENLTGKTV 303
K LVTG A IG +L G NVVV D E G + K + G V
Sbjct: 1 GKTALVTGAASGIGLAIARALAAAGANVVVND-------FGEEGAEAAAKVAGDAGGS-V 52
Query: 304 EYHEVDILQVSDLREI 319
Y D V+ EI
Sbjct: 53 IYLPAD---VTKEDEI 65
>gnl|CDD|187632 cd05374, 17beta-HSD-like_SDR_c, 17beta hydroxysteroid
dehydrogenase-like, classical (c) SDRs.
17beta-hydroxysteroid dehydrogenases are a group of
isozymes that catalyze activation and inactivation of
estrogen and androgens. 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 = 248
Score = 34.1 bits (79), Expect = 0.063
Identities = 10/28 (35%), Positives = 16/28 (57%)
Query: 245 KFILVTGGAGYIGSHTVVSLLEHGYNVV 272
K +L+TG + IG ++L GY V+
Sbjct: 1 KVVLITGCSSGIGLALALALAAQGYRVI 28
>gnl|CDD|219957 pfam08659, KR, KR domain. This enzymatic domain is part of
bacterial polyketide synthases and catalyzes the first
step in the reductive modification of the beta-carbonyl
centres in the growing polyketide chain. It uses NADPH
to reduce the keto group to a hydroxy group.
Length = 181
Score = 33.6 bits (78), Expect = 0.067
Identities = 20/76 (26%), Positives = 28/76 (36%), Gaps = 8/76 (10%)
Query: 248 LVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETGKPESLKRVENLT--GKTVEY 305
LVTGG G +G L E G +LV R PE+ + L G V
Sbjct: 4 LVTGGLGGLGLELARWLAERG-----ARHLVLLSRSGAPD-PEAEALLAELEARGAEVTV 57
Query: 306 HEVDILQVSDLREIFS 321
D+ +R + +
Sbjct: 58 VACDVSDRDAVRALLA 73
>gnl|CDD|236216 PRK08277, PRK08277, D-mannonate oxidoreductase; Provisional.
Length = 278
Score = 34.1 bits (79), Expect = 0.071
Identities = 17/76 (22%), Positives = 28/76 (36%), Gaps = 12/76 (15%)
Query: 245 KFILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETGKPESLKRVENLT--GKT 302
K ++TGG G +G L G V ++D R +E + V + G
Sbjct: 11 KVAVITGGGGVLGGAMAKELARAGAKVAILD------RNQEKAE----AVVAEIKAAGGE 60
Query: 303 VEYHEVDILQVSDLRE 318
+ D+L L +
Sbjct: 61 ALAVKADVLDKESLEQ 76
>gnl|CDD|191263 pfam05368, NmrA, NmrA-like family. NmrA is a negative
transcriptional regulator involved in the
post-translational modification of the transcription
factor AreA. NmrA is part of a system controlling
nitrogen metabolite repression in fungi. This family
only contains a few sequences as iteration results in
significant matches to other Rossmann fold families.
Length = 232
Score = 33.8 bits (78), Expect = 0.077
Identities = 11/25 (44%), Positives = 14/25 (56%)
Query: 247 ILVTGGAGYIGSHTVVSLLEHGYNV 271
ILV G GY G V + L+ G+ V
Sbjct: 1 ILVFGATGYQGGSVVRASLKAGHPV 25
>gnl|CDD|216400 pfam01266, DAO, FAD dependent oxidoreductase. This family includes
various FAD dependent oxidoreductases:
Glycerol-3-phosphate dehydrogenase EC:1.1.99.5,
Sarcosine oxidase beta subunit EC:1.5.3.1, D-alanine
oxidase EC:1.4.99.1, D-aspartate oxidase EC:1.4.3.1.
Length = 234
Score = 33.8 bits (78), Expect = 0.080
Identities = 7/24 (29%), Positives = 12/24 (50%)
Query: 252 GAGYIGSHTVVSLLEHGYNVVVVD 275
G G +G T L G +V +++
Sbjct: 6 GGGIVGLSTAYELARRGLSVTLLE 29
>gnl|CDD|235546 PRK05653, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Validated.
Length = 246
Score = 33.6 bits (78), Expect = 0.082
Identities = 14/42 (33%), Positives = 17/42 (40%), Gaps = 2/42 (4%)
Query: 245 KFILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEET 286
K LVTG + IG + L G VV+ D N E
Sbjct: 6 KTALVTGASRGIGRAIALRLAADGAKVVIYD--SNEEAAEAL 45
>gnl|CDD|213929 TIGR04316, dhbA_paeA, 2,3-dihydro-2,3-dihydroxybenzoate
dehydrogenase. Members of this family are
2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase (EC
1.3.1.28), the third enzyme in the biosynthesis of
2,3-dihydroxybenzoic acid (DHB) from chorismate. The
first two enzymes are isochorismate synthase (EC
5.4.4.2) and isochorismatase (EC 3.3.2.1). Synthesis is
often followed by adenylation by the enzyme DHBA-AMP
ligase (EC 2.7.7.58) to activate (DHB) for a
non-ribosomal peptide synthetase.
Length = 250
Score = 33.8 bits (78), Expect = 0.086
Identities = 18/72 (25%), Positives = 27/72 (37%), Gaps = 8/72 (11%)
Query: 248 LVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETGKPESLKRVENLTGKTVEYHE 307
LVTG A IG +L E G V VD E + L G ++
Sbjct: 2 LVTGAAQGIGYAVARALAEAGARVAAVD-----RNFE---QLLELVADLRRYGYPFATYK 53
Query: 308 VDILQVSDLREI 319
+D+ + + E+
Sbjct: 54 LDVADSAAVDEV 65
>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 = 33.9 bits (78), Expect = 0.098
Identities = 22/63 (34%), Positives = 31/63 (49%), Gaps = 6/63 (9%)
Query: 247 ILVTGGAGYIGSHTVVSLLEHGYNVVVV----DNLVNACRVEETGKPESLKRVENLTGKT 302
+ VTGG G++G H V LLE+G+ V+V+ R+EE G RV L G
Sbjct: 1 VFVTGGTGFLGRHLVKRLLENGFKVLVLVRSESLGEAHERIEEAGLE--ADRVRVLEGDL 58
Query: 303 VEY 305
+
Sbjct: 59 TQP 61
Score = 30.4 bits (69), Expect = 1.2
Identities = 13/49 (26%), Positives = 24/49 (48%)
Query: 8 HFVFSSSSTVYGTPKFLPFTEDHPTGQGCTNPYGKSKYFVEEILKDLAS 56
F + S++ V G + + GQ NPY +SK E++++ A+
Sbjct: 118 RFHYVSTAYVAGNREGNIRETELNPGQNFKNPYEQSKAEAEQLVRAAAT 166
>gnl|CDD|187627 cd05369, TER_DECR_SDR_a, Trans-2-enoyl-CoA reductase (TER) and
2,4-dienoyl-CoA reductase (DECR), atypical (a) SDR.
TTER is a peroxisomal protein with a proposed role in
fatty acid elongation. Fatty acid synthesis is known to
occur in the both endoplasmic reticulum and
mitochondria; peroxisomal TER has been proposed as an
additional fatty acid elongation system, it reduces the
double bond at C-2 as the last step of elongation. This
system resembles the mitochondrial system in that
acetyl-CoA is used as a carbon donor. TER may also
function in phytol metabolism, reducting phytenoyl-CoA
to phytanoyl-CoA in peroxisomes. DECR processes double
bonds in fatty acids to increase their utility in fatty
acid metabolism; it reduces 2,4-dienoyl-CoA to an
enoyl-CoA. DECR is active in mitochondria and
peroxisomes. This subgroup has the Gly-rich NAD-binding
motif of the classical SDR family, but does not display
strong identity to the canonical active site tetrad, and
lacks the characteristic Tyr at the usual position. 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 = 249
Score = 33.7 bits (78), Expect = 0.098
Identities = 19/85 (22%), Positives = 31/85 (36%), Gaps = 21/85 (24%)
Query: 245 KFILVTGGAGYIGSHTVVSLLEHGYNVVVV----DNLVNACR-VEETG------------ 287
K +TGG IG + E G +V + + L A +
Sbjct: 4 KVAFITGGGTGIGKAIAKAFAELGASVAIAGRKPEVLEAAAEEISSATGGRAHPIQCDVR 63
Query: 288 KPESLKRVENLTGKTVEYH-EVDIL 311
PE+ VE +T++ ++DIL
Sbjct: 64 DPEA---VEAAVDETLKEFGKIDIL 85
>gnl|CDD|181517 PRK08642, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 253
Score = 33.5 bits (77), Expect = 0.10
Identities = 10/29 (34%), Positives = 16/29 (55%)
Query: 245 KFILVTGGAGYIGSHTVVSLLEHGYNVVV 273
+ +LVTGG+ +G+ + G VVV
Sbjct: 6 QTVLVTGGSRGLGAAIARAFAREGARVVV 34
>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 = 33.7 bits (78), Expect = 0.10
Identities = 19/45 (42%), Positives = 23/45 (51%), Gaps = 13/45 (28%)
Query: 247 ILVTGGAGYIGSHTVVSLLEH-GYNVVVVDNLVNACRVEETGKPE 290
+LVTG AG +GS V+LL GY VV TG+PE
Sbjct: 150 VLVTGAAGGVGS-VAVALLARLGYEVVAS-----------TGRPE 182
>gnl|CDD|224015 COG1090, COG1090, Predicted nucleoside-diphosphate sugar epimerase
[General function prediction only].
Length = 297
Score = 33.8 bits (78), Expect = 0.11
Identities = 11/28 (39%), Positives = 16/28 (57%)
Query: 247 ILVTGGAGYIGSHTVVSLLEHGYNVVVV 274
IL+TGG G IG L + G+ V ++
Sbjct: 1 ILITGGTGLIGRALTARLRKGGHQVTIL 28
>gnl|CDD|183833 PRK12939, PRK12939, short chain dehydrogenase; Provisional.
Length = 250
Score = 33.4 bits (77), Expect = 0.12
Identities = 18/76 (23%), Positives = 27/76 (35%), Gaps = 8/76 (10%)
Query: 245 KFILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETGKPESLKRVENLTGKTVE 304
K LVTG A +G+ +L E G V D A E +L+ G
Sbjct: 8 KRALVTGAARGLGAAFAEALAEAGATVAFND--GLAAEARELA--AALEA----AGGRAH 59
Query: 305 YHEVDILQVSDLREIF 320
D+ + ++ F
Sbjct: 60 AIAADLADPASVQRFF 75
>gnl|CDD|215370 PLN02686, PLN02686, cinnamoyl-CoA reductase.
Length = 367
Score = 33.6 bits (77), Expect = 0.12
Identities = 15/43 (34%), Positives = 24/43 (55%), Gaps = 1/43 (2%)
Query: 244 PKFILVTGGAGYIGSHTVVSLLEHGYNV-VVVDNLVNACRVEE 285
+ + VTGG ++G V LL HGY+V + VD + ++ E
Sbjct: 53 ARLVCVTGGVSFLGLAIVDRLLRHGYSVRIAVDTQEDKEKLRE 95
>gnl|CDD|235628 PRK05855, PRK05855, short chain dehydrogenase; Validated.
Length = 582
Score = 33.8 bits (78), Expect = 0.12
Identities = 13/42 (30%), Positives = 19/42 (45%), Gaps = 2/42 (4%)
Query: 245 KFILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEET 286
K ++VTG IG T ++ G VV D ++ E T
Sbjct: 316 KLVVVTGAGSGIGRETALAFAREGAEVVASD--IDEAAAERT 355
>gnl|CDD|215720 pfam00106, adh_short, short chain dehydrogenase. This family
contains a wide variety of dehydrogenases.
Length = 167
Score = 32.5 bits (75), Expect = 0.13
Identities = 16/74 (21%), Positives = 22/74 (29%), Gaps = 5/74 (6%)
Query: 247 ILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETGKPESLKRVENLTGKTVEYH 306
+L+TGG G +G L G +LV R L G V
Sbjct: 3 VLITGGTGGLGLALARWLAAEG-----ARHLVLVSRRGPAPGAAELVAELEALGAEVTVA 57
Query: 307 EVDILQVSDLREIF 320
D+ L +
Sbjct: 58 ACDVADRDALAALL 71
>gnl|CDD|178256 PLN02650, PLN02650, dihydroflavonol-4-reductase.
Length = 351
Score = 33.6 bits (77), Expect = 0.13
Identities = 14/25 (56%), Positives = 18/25 (72%)
Query: 247 ILVTGGAGYIGSHTVVSLLEHGYNV 271
+ VTG +G+IGS V+ LLE GY V
Sbjct: 8 VCVTGASGFIGSWLVMRLLERGYTV 32
>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 = 33.4 bits (77), Expect = 0.14
Identities = 22/49 (44%), Positives = 28/49 (57%), Gaps = 9/49 (18%)
Query: 195 KKNIP-----YEVVGRREGDIASSY---CDASLAKKELAWEAKYGLDKM 235
KK+IP YEV RR+ IA S+ D S A+K+ W+ KY LD M
Sbjct: 253 KKHIPEFQITYEVDPRRQA-IADSWPMSLDDSNARKDWGWKHKYDLDSM 300
>gnl|CDD|180586 PRK06483, PRK06483, dihydromonapterin reductase; Provisional.
Length = 236
Score = 33.0 bits (76), Expect = 0.15
Identities = 13/33 (39%), Positives = 15/33 (45%), Gaps = 2/33 (6%)
Query: 241 MSNPKFILVTGGAGYIGSHTVVSLLEHGYNVVV 273
M P IL+TG IG LL G V+V
Sbjct: 1 MPAP--ILITGAGQRIGLALAWHLLAQGQPVIV 31
>gnl|CDD|180150 PRK05586, PRK05586, biotin carboxylase; Validated.
Length = 447
Score = 33.1 bits (76), Expect = 0.16
Identities = 23/76 (30%), Positives = 38/76 (50%), Gaps = 10/76 (13%)
Query: 172 AYNLGTGTGYSVFEMVKAFSEACKKNIPYEVVGRREGDIASSYCDASLAKKELAWEAKYG 231
A + GY V MVKA + + I + R E ++ ++ + AK E +A +G
Sbjct: 144 ALEIAKEIGYPV--MVKASAGGGGRGIR---IVRSEEELIKAF---NTAKSEA--KAAFG 193
Query: 232 LDKMYLQRDMSNPKFI 247
D MY+++ + NPK I
Sbjct: 194 DDSMYIEKFIENPKHI 209
>gnl|CDD|235506 PRK05565, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 247
Score = 32.9 bits (76), Expect = 0.16
Identities = 24/83 (28%), Positives = 37/83 (44%), Gaps = 17/83 (20%)
Query: 245 KFILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEET--------GKPESLK--- 293
K +VTG +G IG L + G VV+ ++ N +E G ++K
Sbjct: 6 KVAIVTGASGGIGRAIAELLAKEGAKVVIAYDI-NEEAAQELLEEIKEEGGDAIAVKADV 64
Query: 294 ----RVENLTGKTVE-YHEVDIL 311
VENL + VE + ++DIL
Sbjct: 65 SSEEDVENLVEQIVEKFGKIDIL 87
>gnl|CDD|168574 PRK06484, PRK06484, short chain dehydrogenase; Validated.
Length = 520
Score = 33.3 bits (76), Expect = 0.17
Identities = 15/38 (39%), Positives = 17/38 (44%)
Query: 245 KFILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACR 282
+ +LVTG AG IG G VVV D V R
Sbjct: 6 RVVLVTGAAGGIGRAACQRFARAGDQVVVADRNVERAR 43
>gnl|CDD|187561 cd05251, NmrA_like_SDR_a, NmrA (a transcriptional regulator) and
HSCARG (an NADPH sensor) like proteins, atypical (a)
SDRs. NmrA and HSCARG like proteins. NmrA is a negative
transcriptional regulator of various fungi, involved in
the post-translational modulation of the GATA-type
transcription factor AreA. NmrA lacks the canonical
GXXGXXG NAD-binding motif and has altered residues at
the catalytic triad, including a Met instead of the
critical Tyr residue. NmrA may bind nucleotides but
appears to lack any dehydrogenase activity. HSCARG has
been identified as a putative NADP-sensing molecule, and
redistributes and restructures in response to NADPH/NADP
ratios. Like NmrA, it lacks most of the active site
residues of the SDR family, but has an NAD(P)-binding
motif similar to the extended SDR family, GXXGXXG. SDRs
are a functionally diverse family of oxidoreductases
that have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Atypical SDRs
are distinct from classical SDRs. Classical SDRs have an
TGXXX[AG]XG cofactor binding motif and a YXXXK active
site motif, with the Tyr residue of the active site
motif serving as a critical catalytic residue (Tyr-151,
human 15-hydroxyprostaglandin dehydrogenase numbering).
In addition to the Tyr and Lys, there is often an
upstream Ser and/or an Asn, contributing to the active
site; while substrate binding is in the C-terminal
region, which determines specificity. The standard
reaction mechanism is a 4-pro-S hydride transfer and
proton relay involving the conserved Tyr and Lys, a
water molecule stabilized by Asn, and nicotinamide. In
addition to the Rossmann fold core region typical of all
SDRs, extended SDRs have a less conserved C-terminal
extension of approximately 100 amino acids, and
typically have a TGXXGXXG cofactor binding motif.
Complex (multidomain) SDRs such as ketoreductase domains
of fatty acid synthase have a GGXGXXG NAD(P)-binding
motif and an altered active site motif (YXXXN). Fungal
type ketoacyl reductases have a TGXXXGX(1-2)G
NAD(P)-binding motif.
Length = 242
Score = 32.6 bits (75), Expect = 0.17
Identities = 19/76 (25%), Positives = 25/76 (32%), Gaps = 13/76 (17%)
Query: 247 ILVTGGAGYIGSHTVVSLLEH-GYNVVVVDNLVNACRVEETGKPESLKRVENLTGKTVEY 305
ILV G G G V +LL+ G+ V + T P S L VE
Sbjct: 1 ILVFGATGKQGGSVVRALLKDPGFKVRAL-----------TRDPSSPAAKA-LAAPGVEV 48
Query: 306 HEVDILQVSDLREIFS 321
+ D+ L
Sbjct: 49 VQGDLDDPESLEAALK 64
>gnl|CDD|183775 PRK12826, PRK12826, 3-ketoacyl-(acyl-carrier-protein) reductase;
Reviewed.
Length = 251
Score = 33.0 bits (76), Expect = 0.18
Identities = 17/48 (35%), Positives = 21/48 (43%), Gaps = 3/48 (6%)
Query: 239 RDMSNPKFILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEET 286
RD+ + LVTG A IG V L G V+VVD + T
Sbjct: 2 RDLEG-RVALVTGAARGIGRAIAVRLAADGAEVIVVD--ICGDDAAAT 46
>gnl|CDD|236389 PRK09134, PRK09134, short chain dehydrogenase; Provisional.
Length = 258
Score = 32.6 bits (75), Expect = 0.18
Identities = 14/35 (40%), Positives = 19/35 (54%)
Query: 239 RDMSNPKFILVTGGAGYIGSHTVVSLLEHGYNVVV 273
M+ P+ LVTG A IG + L HG++V V
Sbjct: 4 MSMAAPRAALVTGAARRIGRAIALDLAAHGFDVAV 38
>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 = 32.6 bits (75), Expect = 0.21
Identities = 16/30 (53%), Positives = 20/30 (66%)
Query: 245 KFILVTGGAGYIGSHTVVSLLEHGYNVVVV 274
K ILVTGGAG IGS V +L+ G ++V
Sbjct: 3 KTILVTGGAGSIGSELVRQILKFGPKKLIV 32
>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 = 32.7 bits (75), Expect = 0.21
Identities = 16/73 (21%), Positives = 24/73 (32%), Gaps = 16/73 (21%)
Query: 247 ILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETGKPESLKRVENLTGKTVEYH 306
V G +G IG L G++V +V S ++ L G VE
Sbjct: 2 AHVLGASGPIGREVARELRRRGWDVRLVS--------------RSGSKLAWLPG--VEIV 45
Query: 307 EVDILQVSDLREI 319
D + S +
Sbjct: 46 AADAMDASSVIAA 58
>gnl|CDD|235975 PRK07231, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 251
Score = 32.5 bits (75), Expect = 0.24
Identities = 14/45 (31%), Positives = 17/45 (37%), Gaps = 6/45 (13%)
Query: 245 KFILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETGKP 289
K +VTG + IG G VVV D R EE +
Sbjct: 6 KVAIVTGASSGIGEGIARRFAAEGARVVVTD------RNEEAAER 44
>gnl|CDD|187643 cd08939, KDSR-like_SDR_c, 3-ketodihydrosphingosine reductase (KDSR)
and related proteins, classical (c) SDR. These proteins
include members identified as KDSR, ribitol type
dehydrogenase, and others. The group shows strong
conservation of the active site tetrad and glycine rich
NAD-binding motif of the classical SDRs. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold (alpha/beta folding pattern with a central
beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRs are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes catalyze a
wide range of activities including the metabolism of
steroids, cofactors, carbohydrates, lipids, aromatic
compounds, and amino acids, and act in redox sensing.
Classical SDRs have an TGXXX[AG]XG cofactor binding
motif and a YXXXK active site motif, with the Tyr
residue of the active site motif serving as a critical
catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 239
Score = 32.2 bits (74), Expect = 0.25
Identities = 20/70 (28%), Positives = 32/70 (45%), Gaps = 12/70 (17%)
Query: 245 KFILVTGGAGYIGSHTVVSLLEHGYNVVVV----DNLVNACRVEETGKPESLKRVENLTG 300
K +L+TGG+ IG L++ G NV++V L A E ++ N +G
Sbjct: 2 KHVLITGGSSGIGKALAKELVKEGANVIIVARSESKLEEAV--------EEIEAEANASG 53
Query: 301 KTVEYHEVDI 310
+ V Y D+
Sbjct: 54 QKVSYISADL 63
>gnl|CDD|187575 cd05265, SDR_a1, atypical (a) SDRs, subgroup 1. Atypical SDRs in
this subgroup are poorly defined and have been
identified putatively as isoflavones reductase, sugar
dehydratase, mRNA binding protein etc. Atypical SDRs are
distinct from classical SDRs. Members of this subgroup
retain the canonical active site triad (though not the
upstream Asn found in most SDRs) but have an unusual
putative glycine-rich NAD(P)-binding motif, GGXXXXG, in
the usual location. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and their
glycine-rich NAD(P)-binding motif is often different
from the forms normally seen in classical or extended
SDRs. Atypical SDRs include biliverdin IX beta reductase
(BVR-B,aka flavin reductase), NMRa (a negative
transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. In addition to the
Rossmann fold core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 250
Score = 32.3 bits (74), Expect = 0.27
Identities = 35/194 (18%), Positives = 64/194 (32%), Gaps = 52/194 (26%)
Query: 5 KVYHFVFSSSSTVYGTPK-----FLPFTEDHPTGQGCTNPYGKSKYFVEEILKDLASFKQ 59
+V ++F SS++VY P P E G YG+ K E++L + A+F
Sbjct: 89 RVKQYIFISSASVYLKPGRVITESTPLREPDAVGLSDPWDYGRGKRAAEDVLIEAAAF-- 146
Query: 60 KLQSLQSSVTQIWLNSVHRSDWHIISLRYFNPVGSHPSGDIGEDPNGIPNNLMPYISQVA 119
++ + R + L P+ +P
Sbjct: 147 PYTIVRPPYIYGPGDYTGRLAYFFDRLARGRPI-------------LVPG---------- 183
Query: 120 VGRRKKLMVFGDDYDTKDGSGVRDYIHIMDLAEGHVTALDKLLGGKSQAGFKAYNLGTGT 179
DG + +IH+ DLA + A G +A +N+
Sbjct: 184 -----------------DGHSLVQFIHVKDLARALLGAA-----GNPKAIGGIFNITGDE 221
Query: 180 GYSVFEMVKAFSEA 193
+ E+++A ++A
Sbjct: 222 AVTWDELLEACAKA 235
Score = 31.5 bits (72), Expect = 0.43
Identities = 12/27 (44%), Positives = 16/27 (59%)
Query: 247 ILVTGGAGYIGSHTVVSLLEHGYNVVV 273
IL+ GG +IG V LL G++V V
Sbjct: 3 ILIIGGTRFIGKALVEELLAAGHDVTV 29
>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 = 32.2 bits (74), Expect = 0.27
Identities = 14/28 (50%), Positives = 15/28 (53%)
Query: 247 ILVTGGAGYIGSHTVVSLLEHGYNVVVV 274
ILVTG G +GS V L GY VV
Sbjct: 2 ILVTGHRGLVGSAIVRVLARRGYENVVF 29
>gnl|CDD|187585 cd05324, carb_red_PTCR-like_SDR_c, Porcine testicular carbonyl
reductase (PTCR)-like, classical (c) SDRs. PTCR is a
classical SDR which catalyzes the NADPH-dependent
reduction of ketones on steroids and prostaglandins.
Unlike most SDRs, PTCR functions as a monomer. This
subgroup also includes human carbonyl reductase 1 (CBR1)
and CBR3. CBR1 is an NADPH-dependent SDR with broad
substrate specificity and may be responsible for the in
vivo reduction of quinones, prostaglandins, and other
carbonyl-containing compounds. In addition it includes
poppy NADPH-dependent salutaridine reductase which
catalyzes the stereospecific reduction of salutaridine
to 7(S)-salutaridinol in the biosynthesis of morphine,
and Arabidopsis SDR1,a menthone reductase, which
catalyzes the reduction of menthone to neomenthol, a
compound with antimicrobial activity; SDR1 can also
carry out neomenthol oxidation. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold
(alpha/beta folding pattern with a central beta-sheet),
an NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRs are approximately
350 residues. Sequence identity between different SDR
enzymes are typically in the 15-30% range, but the
enzymes share the Rossmann fold NAD-binding motif and
characteristic NAD-binding and catalytic sequence
patterns. These enzymes catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, 15-hydroxyprostaglandin dehydrogenase
(15-PGDH) numbering). In addition to the Tyr and Lys,
there is often an upstream Ser (Ser-138, 15-PGDH
numbering) and/or an Asn (Asn-107, 15-PGDH numbering)
contributing to the active site; while substrate binding
is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. Extended SDRs have additional
elements in the C-terminal region, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Some atypical SDRs have lost catalytic activity and/or
have an unusual NAD(P)-binding motif and missing or
unusual active site residues. Reactions catalyzed within
the SDR family include isomerization, decarboxylation,
epimerization, C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 225
Score = 32.2 bits (74), Expect = 0.28
Identities = 18/66 (27%), Positives = 32/66 (48%), Gaps = 7/66 (10%)
Query: 245 KFILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETGKPESLKRVENLTGKTVE 304
K LVTG IG V L + G V++ R E G+ +++++ G +V
Sbjct: 1 KVALVTGANRGIGFEIVRQLAKSGPGTVIL-----TARDVERGQ-AAVEKLRA-EGLSVR 53
Query: 305 YHEVDI 310
+H++D+
Sbjct: 54 FHQLDV 59
>gnl|CDD|187612 cd05354, SDR_c7, classical (c) SDR, subgroup 7. These proteins are
members of the classical SDR family, with a canonical
active site triad (and also an active site Asn) and a
typical Gly-rich NAD-binding motif. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold (alpha/beta folding pattern with a central
beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRS are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes have a
3-glycine N-terminal NAD(P)(H)-binding pattern
(typically, TGxxxGxG in classical SDRs and TGxxGxxG in
extended SDRs), while substrate binding is in the
C-terminal region. A critical catalytic Tyr residue
(Tyr-151, human 15-hydroxyprostaglandin dehydrogenase
(15-PGDH) numbering), is often found in a conserved
YXXXK pattern. In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) or additional
Ser, contributing to the active site. Substrates for
these enzymes include sugars, steroids, alcohols, and
aromatic compounds. The standard reaction mechanism is a
proton relay involving the conserved Tyr and Lys, as
well as Asn (or Ser). Some SDR family members, including
17 beta-hydroxysteroid dehydrogenase contain an
additional helix-turn-helix motif that is not generally
found among SDRs.
Length = 235
Score = 32.0 bits (73), Expect = 0.28
Identities = 24/75 (32%), Positives = 28/75 (37%), Gaps = 13/75 (17%)
Query: 245 KFILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETGKPESLKRVENLTGKTVE 304
K +LVTG IG V SLL HG V A R P S + G V
Sbjct: 4 KTVLVTGANRGIGKAFVESLLAHGAKKVYA-----AVR-----DPGSAAHLVAKYGDKVV 53
Query: 305 YHEVDILQVSDLREI 319
+D V+D I
Sbjct: 54 PLRLD---VTDPESI 65
>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 = 32.2 bits (74), Expect = 0.29
Identities = 12/30 (40%), Positives = 15/30 (50%)
Query: 247 ILVTGGAGYIGSHTVVSLLEHGYNVVVVDN 276
IL+TG G +G V L E GY V+
Sbjct: 2 ILITGATGMLGRALVRLLKERGYEVIGTGR 31
Score = 31.1 bits (71), Expect = 0.68
Identities = 12/46 (26%), Positives = 19/46 (41%), Gaps = 3/46 (6%)
Query: 8 HFVFSSSSTVYGTPKFLPFTEDHPTGQGCTNPYGKSKYFVEEILKD 53
+ S+ V+ K P+ E+ N YGKSK E + +
Sbjct: 99 RLIHISTDYVFDGKK-GPYKEEDAPN--PLNVYGKSKLLGEVAVLN 141
>gnl|CDD|187555 cd05244, BVR-B_like_SDR_a, biliverdin IX beta reductase (BVR-B, aka
flavin reductase)-like proteins; atypical (a) SDRs.
Human BVR-B catalyzes pyridine nucleotide-dependent
production of bilirubin-IX beta during fetal
development; in the adult BVR-B has flavin and ferric
reductase activities. Human BVR-B catalyzes the
reduction of FMN, FAD, and riboflavin. Recognition of
flavin occurs mostly by hydrophobic interactions,
accounting for the broad substrate specificity. Atypical
SDRs are distinct from classical SDRs. BVR-B does not
share the key catalytic triad, or conserved tyrosine
typical of SDRs. The glycine-rich NADP-binding motif of
BVR-B is GXXGXXG, which is similar but not identical to
the pattern seen in extended SDRs. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Atypical SDRs include
biliverdin IX beta reductase (BVR-B,aka flavin
reductase), NMRa (a negative transcriptional regulator
of various fungi), progesterone 5-beta-reductase like
proteins, phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. In addition to the
Rossmann fold core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 207
Score = 31.8 bits (73), Expect = 0.29
Identities = 9/43 (20%), Positives = 17/43 (39%), Gaps = 2/43 (4%)
Query: 247 ILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETGKP 289
I + G G GS V L G+ V + + + ++ +
Sbjct: 2 IAIIGATGRTGSAIVREALARGHEVTAL--VRDPAKLPAEHEK 42
>gnl|CDD|214833 smart00822, PKS_KR, This enzymatic domain is part of bacterial
polyketide synthases. It catalyses the first step in
the reductive modification of the beta-carbonyl centres
in the growing polyketide chain. It uses NADPH to reduce
the keto group to a hydroxy group.
Length = 180
Score = 31.3 bits (72), Expect = 0.34
Identities = 19/73 (26%), Positives = 24/73 (32%), Gaps = 8/73 (10%)
Query: 248 LVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACR--VEETGKPESLKRVENLTGKTVEY 305
L+TGG G +G L E G LV R + G L +E G V
Sbjct: 4 LITGGLGGLGRALARWLAERG-----ARRLVLLSRSGPDAPGAAALLAELEAA-GARVTV 57
Query: 306 HEVDILQVSDLRE 318
D+ L
Sbjct: 58 VACDVADRDALAA 70
>gnl|CDD|177895 PLN02253, PLN02253, xanthoxin dehydrogenase.
Length = 280
Score = 32.1 bits (73), Expect = 0.35
Identities = 15/31 (48%), Positives = 17/31 (54%)
Query: 245 KFILVTGGAGYIGSHTVVSLLEHGYNVVVVD 275
K LVTGGA IG V +HG V +VD
Sbjct: 19 KVALVTGGATGIGESIVRLFHKHGAKVCIVD 49
>gnl|CDD|235924 PRK07063, PRK07063, short chain dehydrogenase; Provisional.
Length = 260
Score = 31.9 bits (73), Expect = 0.37
Identities = 16/78 (20%), Positives = 27/78 (34%), Gaps = 6/78 (7%)
Query: 245 KFILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETGKPESLKRVENLTGKTVE 304
K LVTG A IG+ + G V + D ++A E ++ G V
Sbjct: 8 KVALVTGAAQGIGAAIARAFAREGAAVALAD--LDAALAERAAA----AIARDVAGARVL 61
Query: 305 YHEVDILQVSDLREIFSK 322
D+ + + +
Sbjct: 62 AVPADVTDAASVAAAVAA 79
>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 = 31.9 bits (73), Expect = 0.38
Identities = 19/95 (20%), Positives = 39/95 (41%), Gaps = 4/95 (4%)
Query: 141 VRDYIHIMDLAEGHVTALDKLLGGKSQAGFKAYNLGTGT--GYSVFEMVKAFSEACKKN- 197
+R + H+++ G++ +KL + +A+N G +V E+V+A + ++
Sbjct: 224 IRPWQHVLEPLSGYLLLAEKLYERGEEYA-EAWNFGPDDEDAVTVLELVEAMARYWGEDA 282
Query: 198 IPYEVVGRREGDIASSYCDASLAKKELAWEAKYGL 232
+ D S AK L W ++ L
Sbjct: 283 RWDLDGNSHPHEANLLKLDCSKAKTMLGWRPRWNL 317
>gnl|CDD|223643 COG0569, TrkA, K+ transport systems, NAD-binding component
[Inorganic ion transport and metabolism].
Length = 225
Score = 31.5 bits (72), Expect = 0.39
Identities = 13/32 (40%), Positives = 19/32 (59%), Gaps = 2/32 (6%)
Query: 245 KFILVTGGAGYIGSHTVVSLLEHGYNVVVVDN 276
K I++ GAG +G L E G+NVV++D
Sbjct: 2 KIIII--GAGRVGRSVARELSEEGHNVVLIDR 31
>gnl|CDD|177862 PLN02214, PLN02214, cinnamoyl-CoA reductase.
Length = 342
Score = 32.0 bits (72), Expect = 0.41
Identities = 17/34 (50%), Positives = 21/34 (61%), Gaps = 2/34 (5%)
Query: 240 DMSNP--KFILVTGGAGYIGSHTVVSLLEHGYNV 271
D+++P K + VTG GYI S V LLE GY V
Sbjct: 4 DVASPAGKTVCVTGAGGYIASWIVKILLERGYTV 37
>gnl|CDD|222146 pfam13460, NAD_binding_10, NADH(P)-binding.
Length = 182
Score = 31.1 bits (71), Expect = 0.41
Identities = 10/28 (35%), Positives = 12/28 (42%)
Query: 247 ILVTGGAGYIGSHTVVSLLEHGYNVVVV 274
I V G G G V LL G+ V +
Sbjct: 1 IAVIGATGKTGRRLVKELLARGHQVTAL 28
>gnl|CDD|187617 cd05359, ChcA_like_SDR_c, 1-cyclohexenylcarbonyl_coenzyme
A_reductase (ChcA)_like, classical (c) SDRs. This
subgroup contains classical SDR proteins, including
members identified as 1-cyclohexenylcarbonyl coenzyme A
reductase. ChcA of Streptomyces collinus is implicated
in the final reduction step of shikimic acid to
ansatrienin. ChcA shows sequence similarity to the SDR
family of NAD-binding proteins, but it lacks the
conserved Tyr of the characteristic catalytic site. This
subgroup also contains the NADH-dependent
enoyl-[acyl-carrier-protein(ACP)] reductase FabL from
Bacillus subtilis. This enzyme participates in bacterial
fatty acid synthesis, in type II fatty-acid synthases
and catalyzes the last step in each elongation cycle.
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 = 242
Score = 31.6 bits (72), Expect = 0.44
Identities = 22/74 (29%), Positives = 34/74 (45%), Gaps = 7/74 (9%)
Query: 248 LVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETGKPESLKRVENLTGKTVEYHE 307
LVTGG+ IG + L E G +VV +N + ++ E +E L G
Sbjct: 2 LVTGGSRGIGKAIALRLAERGADVV-----INYRKSKDAAA-EVAAEIEEL-GGKAVVVR 54
Query: 308 VDILQVSDLREIFS 321
D+ Q D+ E+F+
Sbjct: 55 ADVSQPQDVEEMFA 68
>gnl|CDD|238245 cd00431, cysteine_hydrolases, Cysteine hydrolases; This family
contains amidohydrolases, like CSHase
(N-carbamoylsarcosine amidohydrolase), involved in
creatine metabolism and nicotinamidase, converting
nicotinamide to nicotinic acid and ammonia in the
pyridine nucleotide cycle. It also contains
isochorismatase, an enzyme that catalyzes the conversion
of isochorismate to 2,3-dihydroxybenzoate and pyruvate,
via the hydrolysis of the vinyl ether bond, and other
related enzymes with unknown function.
Length = 161
Score = 31.1 bits (71), Expect = 0.45
Identities = 11/29 (37%), Positives = 15/29 (51%), Gaps = 1/29 (3%)
Query: 247 ILVTGGAGYIG-SHTVVSLLEHGYNVVVV 274
++V G A I T L+ GY V+VV
Sbjct: 113 LVVCGIATDICVLATARDALDLGYRVIVV 141
>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 = 31.6 bits (72), Expect = 0.47
Identities = 18/49 (36%), Positives = 23/49 (46%), Gaps = 4/49 (8%)
Query: 6 VYHFVFSSSSTVYGT--PKFLPFTEDHPTGQGCTN-PYGKSKYFVEEIL 51
V V +SS VYG P TED P +G Y + K VE++L
Sbjct: 102 VPRVVVTSSVAVYGAHPDNPAPLTEDAPL-RGSPEFAYSRDKAEVEQLL 149
Score = 30.8 bits (70), Expect = 1.00
Identities = 20/64 (31%), Positives = 25/64 (39%), Gaps = 15/64 (23%)
Query: 247 ILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETGKPESLKRVENLTGKTVEYH 306
ILVTG AG +G + L V+ VD L R P+ VEY
Sbjct: 1 ILVTGAAGGLG-RLLARRLAASPRVIGVDGL--DRRRPPGSPPK------------VEYV 45
Query: 307 EVDI 310
+DI
Sbjct: 46 RLDI 49
>gnl|CDD|236209 PRK08265, PRK08265, short chain dehydrogenase; Provisional.
Length = 261
Score = 31.5 bits (72), Expect = 0.50
Identities = 13/31 (41%), Positives = 18/31 (58%)
Query: 245 KFILVTGGAGYIGSHTVVSLLEHGYNVVVVD 275
K +VTGGA IG+ +L+ G V +VD
Sbjct: 7 KVAIVTGGATLIGAAVARALVAAGARVAIVD 37
>gnl|CDD|235794 PRK06398, PRK06398, aldose dehydrogenase; Validated.
Length = 258
Score = 31.3 bits (71), Expect = 0.50
Identities = 24/73 (32%), Positives = 37/73 (50%), Gaps = 9/73 (12%)
Query: 245 KFILVTGGAGYIGSHTVVSLLEHGYNVVVVD------NLVNACRVEETGKPESLKRVENL 298
K +VTGG+ IG V L E G NV+ D N V+ +V+ + K + +K ++ +
Sbjct: 7 KVAIVTGGSQGIGKAVVNRLKEEGSNVINFDIKEPSYNDVDYFKVDVSNKEQVIKGIDYV 66
Query: 299 TGKTVEYHEVDIL 311
K Y +DIL
Sbjct: 67 ISK---YGRIDIL 76
>gnl|CDD|236145 PRK08063, PRK08063, enoyl-(acyl carrier protein) reductase;
Provisional.
Length = 250
Score = 31.2 bits (71), Expect = 0.55
Identities = 12/30 (40%), Positives = 16/30 (53%)
Query: 245 KFILVTGGAGYIGSHTVVSLLEHGYNVVVV 274
K LVTG + IG + L E GY++ V
Sbjct: 5 KVALVTGSSRGIGKAIALRLAEEGYDIAVN 34
>gnl|CDD|223737 COG0665, DadA, Glycine/D-amino acid oxidases (deaminating) [Amino
acid transport and metabolism].
Length = 387
Score = 31.4 bits (71), Expect = 0.63
Identities = 8/24 (33%), Positives = 12/24 (50%)
Query: 252 GAGYIGSHTVVSLLEHGYNVVVVD 275
G G +G L E G +V V++
Sbjct: 11 GGGIVGLSAAYYLAERGADVTVLE 34
>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 = 31.1 bits (71), Expect = 0.63
Identities = 14/28 (50%), Positives = 16/28 (57%)
Query: 247 ILVTGGAGYIGSHTVVSLLEHGYNVVVV 274
ILVTG G IGS +LLE G V +
Sbjct: 1 ILVTGATGRIGSKVATTLLEAGRPVRAL 28
>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 = 31.2 bits (71), Expect = 0.64
Identities = 21/76 (27%), Positives = 35/76 (46%), Gaps = 14/76 (18%)
Query: 248 LVTGGAGYIGSHTVVSLLEHG-YNVVVVDNLVNACRVEETGKPESLKRVENLTGKTVEYH 306
LV GG+G++G H V LL G V V D + + + +G+ V++H
Sbjct: 3 LVVGGSGFLGRHLVEQLLRRGNPTVHVFDIR------------PTFELDPSSSGR-VQFH 49
Query: 307 EVDILQVSDLREIFSK 322
D+ DL + F++
Sbjct: 50 TGDLTDPQDLEKAFNE 65
>gnl|CDD|187610 cd05352, MDH-like_SDR_c, mannitol dehydrogenase (MDH)-like,
classical (c) SDRs. NADP-mannitol dehydrogenase
catalyzes the conversion of fructose to mannitol, an
acyclic 6-carbon sugar. MDH is a tetrameric member of
the SDR family. This subgroup also includes various
other tetrameric SDRs, including Pichia stipitis
D-arabinitol dehydrogenase (aka polyol dehydrogenase),
Candida albicans Sou1p, a sorbose reductase, and Candida
parapsilosis (S)-specific carbonyl reductase (SCR, aka
S-specific alcohol dehydrogenase) which catalyzes the
enantioselective reduction of 2-hydroxyacetophenone into
(S)-1-phenyl-1,2-ethanediol. 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).
Length = 252
Score = 31.1 bits (71), Expect = 0.68
Identities = 15/78 (19%), Positives = 31/78 (39%), Gaps = 7/78 (8%)
Query: 245 KFILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETGKPESLKRVENLTGKTVE 304
K +VTGG+ IG +L E G +V ++ N + + + G +
Sbjct: 9 KVAIVTGGSRGIGLAIARALAEAGADVAIIYN-----SAPRAEEKA--EELAKKYGVKTK 61
Query: 305 YHEVDILQVSDLREIFSK 322
++ D+ + + F +
Sbjct: 62 AYKCDVSSQESVEKTFKQ 79
>gnl|CDD|187569 cd05259, PCBER_SDR_a, phenylcoumaran benzylic ether reductase
(PCBER) like, atypical (a) SDRs. PCBER and
pinoresinol-lariciresinol reductases are NADPH-dependent
aromatic alcohol reductases, and are atypical members of
the SDR family. Other proteins in this subgroup are
identified as eugenol synthase. These proteins contain
an N-terminus characteristic of NAD(P)-binding proteins
and a small C-terminal domain presumed to be involved in
substrate binding, but they do not have the conserved
active site Tyr residue typically found in SDRs.
Numerous other members have unknown functions. The
glycine rich NADP-binding motif in this subgroup is of 2
forms: GXGXXG and G[GA]XGXXG; it tends to be atypical
compared with the forms generally seen in classical or
extended SDRs. The usual SDR active site tetrad is not
present, but a critical active site Lys at the usual SDR
position has been identified in various members, though
other charged and polar residues are found at this
position in this subgroup. Atypical SDR-related proteins
retain the Rossmann fold of the SDRs, but have limited
sequence identity and generally lack the catalytic
properties of the archetypical members. Atypical SDRs
include biliverdin IX beta reductase (BVR-B,aka flavin
reductase), NMRa (a negative transcriptional regulator
of various fungi), progesterone 5-beta-reductase like
proteins, phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. In addition to the
Rossmann fold core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 282
Score = 31.1 bits (71), Expect = 0.70
Identities = 17/76 (22%), Positives = 24/76 (31%), Gaps = 14/76 (18%)
Query: 247 ILVTGGAGYIGSHTVVSLLEH-GYNVVVVDNLVNACRVEETGKPESLKRVENLTGKTVEY 305
I + G G +G V +LL G+ V V+ +P S E V+
Sbjct: 2 IAIAGATGTLGGPIVSALLASPGFTVTVL------------TRPSSTSSNEFQP-SGVKV 48
Query: 306 HEVDILQVSDLREIFS 321
VD L
Sbjct: 49 VPVDYASHESLVAALK 64
>gnl|CDD|216156 pfam00857, Isochorismatase, Isochorismatase family. This family
are hydrolase enzymes.
Length = 173
Score = 30.4 bits (69), Expect = 0.77
Identities = 11/36 (30%), Positives = 17/36 (47%), Gaps = 4/36 (11%)
Query: 247 ILVTGGAGYIG-SHTVVSLLEHGYNVVVVDNLVNAC 281
+++ G A + T + GY VVVV +AC
Sbjct: 114 LVLAGVATDVCVLSTARDAFDRGYEVVVV---SDAC 146
>gnl|CDD|187653 cd08950, KR_fFAS_SDR_c_like, ketoacyl reductase (KR) domain of
fungal-type fatty acid synthase (fFAS), classical
(c)-like SDRs. KR domain of fungal-type fatty acid
synthase (FAS), type I. Fungal-type FAS is a
heterododecameric FAS composed of alpha and beta
multifunctional polypeptide chains. The KR, an SDR
family member, is located centrally in the alpha chain.
KR catalyzes the NADP-dependent reduction of
ketoacyl-ACP to hydroxyacyl-ACP. KR shares the critical
active site Tyr of the Classical SDR and has partial
identity of the active site tetrad, but the upstream Asn
is replaced in KR by Met. As in other SDRs, there is a
glycine rich NAD-binding motif, but the pattern found in
KR does not match the classical SDRs, and is not
strictly conserved within this group. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold (alpha/beta folding pattern with a central
beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRs are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes catalyze a
wide range of activities including the metabolism of
steroids, cofactors, carbohydrates, lipids, aromatic
compounds, and amino acids, and act in redox sensing.
Classical SDRs have an TGXXX[AG]XG cofactor binding
motif and a YXXXK active site motif, with the Tyr
residue of the active site motif serving as a critical
catalytic residue (Tyr-151, human prostaglandin
dehydrogenase (PGDH) numbering). In addition to the Tyr
and Lys, there is often an upstream Ser (Ser-138, PGDH
numbering) and/or an Asn (Asn-107, PGDH numbering)
contributing to the active site; while substrate binding
is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. Extended SDRs have additional
elements in the C-terminal region, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type KRs have
a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 259
Score = 30.6 bits (70), Expect = 0.84
Identities = 15/30 (50%), Positives = 17/30 (56%), Gaps = 1/30 (3%)
Query: 245 KFILVTG-GAGYIGSHTVVSLLEHGYNVVV 273
K LVTG G G IG+ V LL G V+V
Sbjct: 8 KVALVTGAGPGSIGAEVVAGLLAGGATVIV 37
>gnl|CDD|178569 PLN02989, PLN02989, cinnamyl-alcohol dehydrogenase family protein.
Length = 325
Score = 30.8 bits (69), Expect = 1.1
Identities = 13/27 (48%), Positives = 16/27 (59%)
Query: 245 KFILVTGGAGYIGSHTVVSLLEHGYNV 271
K + VTG +GYI S V LL GY +
Sbjct: 6 KVVCVTGASGYIASWIVKLLLFRGYTI 32
>gnl|CDD|237219 PRK12827, PRK12827, short chain dehydrogenase; Provisional.
Length = 249
Score = 30.5 bits (69), Expect = 1.1
Identities = 14/38 (36%), Positives = 21/38 (55%)
Query: 247 ILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVE 284
+L+TGG+G +G V L G +V+V+D R E
Sbjct: 9 VLITGGSGGLGRAIAVRLAADGADVIVLDIHPMRGRAE 46
>gnl|CDD|214020 cd12955, SKA2, Spindle and kinetochore-associated protein 2.
SKA2, also called FAM33A, is a component of the SKA
complex, which is formed by the association of three
subunits (SKA1, SKA2, annd SKA3). The SKA complex is
essential for accurate cell division. It functions with
the Ndc80 network to establish stable
kinetochore-microtubule interactions, which are crucial
for the highly orchestrated chromosome movements during
mitosis. The biological unit is a W-shaped homodimer of
the three-subunit complex. SKA2 has also been
identified as a glucocorticoid receptor-interacting
protein and may be involved in regulating cancer cell
proliferation.
Length = 116
Score = 29.3 bits (66), Expect = 1.1
Identities = 12/46 (26%), Positives = 21/46 (45%), Gaps = 8/46 (17%)
Query: 26 FTEDHPTGQGCTNPYGKSKYFVEEILKDLASFKQKLQSLQSSVTQI 71
F E+ P G NP E+L+ L++ K + +L + +I
Sbjct: 26 FKENSPESAGEKNPV--------ELLERLSAIKSRYSTLCAQAEEI 63
>gnl|CDD|223749 COG0677, WecC, UDP-N-acetyl-D-mannosaminuronate dehydrogenase [Cell
envelope biogenesis, outer membrane].
Length = 436
Score = 30.7 bits (70), Expect = 1.1
Identities = 10/34 (29%), Positives = 18/34 (52%), Gaps = 2/34 (5%)
Query: 252 GAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEE 285
G GY+G + G+ V+ VD +N +V++
Sbjct: 16 GLGYVGLPLAAAFASAGFKVIGVD--INQKKVDK 47
>gnl|CDD|226674 COG4221, COG4221, Short-chain alcohol dehydrogenase of unknown
specificity [General function prediction only].
Length = 246
Score = 30.3 bits (69), Expect = 1.1
Identities = 18/70 (25%), Positives = 28/70 (40%), Gaps = 10/70 (14%)
Query: 241 MSNPKFILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETGKPESLKRVENLTG 300
K L+TG + IG T +L E G VV+ R EE + E+L + +
Sbjct: 3 TLKGKVALITGASSGIGEATARALAEAGAKVVLAA------RREE--RLEALA--DEIGA 52
Query: 301 KTVEYHEVDI 310
+D+
Sbjct: 53 GAALALALDV 62
>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 = 29.9 bits (68), Expect = 1.2
Identities = 10/28 (35%), Positives = 13/28 (46%)
Query: 247 ILVTGGAGYIGSHTVVSLLEHGYNVVVV 274
I+V G G IG L HG+ V+
Sbjct: 1 IIVIGATGTIGLAVAQLLSAHGHEVITA 28
>gnl|CDD|235725 PRK06179, PRK06179, short chain dehydrogenase; Provisional.
Length = 270
Score = 30.3 bits (69), Expect = 1.2
Identities = 15/32 (46%), Positives = 16/32 (50%)
Query: 241 MSNPKFILVTGGAGYIGSHTVVSLLEHGYNVV 272
MSN K LVTG + IG T L GY V
Sbjct: 1 MSNSKVALVTGASSGIGRATAEKLARAGYRVF 32
>gnl|CDD|181297 PRK08217, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 253
Score = 30.3 bits (69), Expect = 1.2
Identities = 17/78 (21%), Positives = 34/78 (43%), Gaps = 8/78 (10%)
Query: 245 KFILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETGKPESLKRVENLTGKTVE 304
K I++TGGA +G L + G + ++D +N ++EE + L +
Sbjct: 6 KVIVITGGAQGLGRAMAEYLAQKGAKLALID--LNQEKLEEA-----VAECGALGTEVRG 58
Query: 305 YHEVDILQVSDLREIFSK 322
Y ++ D+ F++
Sbjct: 59 Y-AANVTDEEDVEATFAQ 75
>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 = 30.4 bits (69), Expect = 1.3
Identities = 16/54 (29%), Positives = 24/54 (44%), Gaps = 7/54 (12%)
Query: 5 KVYHFVFSSSSTV------YGTPKFLPFTEDHPTGQGCTNPYGKSKYFVEEILK 52
K H+V SS S T F + GQG YG+SK+ E++++
Sbjct: 128 KPLHYV-SSISVGETEYYSNFTVDFDEISPTRNVGQGLAGGYGRSKWVAEKLVR 180
>gnl|CDD|235962 PRK07201, PRK07201, short chain dehydrogenase; Provisional.
Length = 657
Score = 30.7 bits (70), Expect = 1.3
Identities = 19/55 (34%), Positives = 24/55 (43%), Gaps = 12/55 (21%)
Query: 248 LVTGGAGYIGSHTVVSLLEHGYNVVV-VDNLVNACRVEETGKPESLKRVENLTGK 301
VTGG G+IG V LL+ V V LV + +SL R+E L
Sbjct: 4 FVTGGTGFIGRRLVSRLLDRRREATVHV--LV---------RRQSLSRLEALAAY 47
>gnl|CDD|187624 cd05366, meso-BDH-like_SDR_c, meso-2,3-butanediol
dehydrogenase-like, classical (c) SDRs. 2,3-butanediol
dehydrogenases (BDHs) catalyze the NAD+ dependent
conversion of 2,3-butanediol to acetonin; BDHs are
classified into types according to their
stereospecificity as to substrates and products.
Included in this subgroup are Klebsiella pneumonia
meso-BDH which catalyzes meso-2,3-butanediol to
D(-)-acetonin, and Corynebacterium glutamicum L-BDH
which catalyzes lX+)-2,3-butanediol to L(+)-acetonin.
This subgroup is comprised of classical SDRs with the
characteristic catalytic triad and NAD-binding motif.
SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold (alpha/beta folding
pattern with a central beta-sheet), an NAD(P)(H)-binding
region, and a structurally diverse C-terminal region.
Classical SDRs are typically about 250 residues long,
while extended SDRs are approximately 350 residues.
Sequence identity between different SDR enzymes are
typically in the 15-30% range, but the enzymes share the
Rossmann fold NAD-binding motif and characteristic
NAD-binding and catalytic sequence patterns. These
enzymes 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 = 257
Score = 30.0 bits (68), Expect = 1.4
Identities = 11/32 (34%), Positives = 16/32 (50%)
Query: 245 KFILVTGGAGYIGSHTVVSLLEHGYNVVVVDN 276
K ++TG A IG L G+N+V+ D
Sbjct: 3 KVAIITGAAQGIGRAIAERLAADGFNIVLADL 34
>gnl|CDD|187655 cd08952, KR_1_SDR_x, ketoreductase (KR), subgroup 1, complex (x)
SDRs. Ketoreductase, a module of the multidomain
polyketide synthase (PKS), has 2 subdomains, each
corresponding to a SDR family monomer. The C-terminal
subdomain catalyzes the NADPH-dependent reduction of the
beta-carbonyl of a polyketide to a hydroxyl group, a
step in the biosynthesis of polyketides, such as
erythromycin. The N-terminal subdomain, an interdomain
linker, is a truncated Rossmann fold which acts to
stabilizes the catalytic subdomain. Unlike typical SDRs,
the isolated domain does not oligomerize but is composed
of 2 subdomains, each resembling an SDR monomer. The
active site resembles that of typical SDRs, except that
the usual positions of the catalytic Asn and Tyr are
swapped, so that the canonical YXXXK motif changes to
YXXXN. Modular PKSs are multifunctional structures in
which the makeup recapitulates that found in (and may
have evolved from) FAS. Polyketide synthesis also
proceeds via the addition of 2-carbon units as in fatty
acid synthesis. The complex SDR NADP-binding motif,
GGXGXXG, is often present, but is not strictly conserved
in each instance of the module. This subfamily includes
KR domains found in many multidomain PKSs, including six
of seven Sorangium cellulosum PKSs (encoded by
spiDEFGHIJ) which participate in the synthesis of the
polyketide scaffold of the cytotoxic spiroketal
polyketide spirangien. These seven PKSs have either a
single PKS module (SpiF), two PKR modules
(SpiD,-E,-I,-J), or three PKS modules (SpiG,-H). This
subfamily includes the single KR domain of SpiF, the
first KR domains of SpiE,-G,H,-I,and #J, the third KR
domain of SpiG, and the second KR domain of SpiH. The
second KR domains of SpiE,-G, I, and #J, and the KR
domains of SpiD, belong to a different KR_FAS_SDR
subfamily. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold (alpha/beta folding
pattern with a central beta-sheet), an NAD(P)(H)-binding
region, and a structurally diverse C-terminal region.
Classical SDRs are typically about 250 residues long,
while extended SDRs are approximately 350 residues.
Sequence identity between different SDR enzymes are
typically in the 15-30% range, but the enzymes share the
Rossmann fold NAD-binding motif and characteristic
NAD-binding and catalytic sequence patterns. These
enzymes catalyze a wide range of activities including
the metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
prostaglandin dehydrogenase (PGDH) numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser (Ser-138, PGDH numbering) and/or an Asn (Asn-107,
PGDH numbering) contributing to the active site; while
substrate binding is in the C-terminal region, which
determines specificity. The standard reaction mechanism
is a 4-pro-S hydride transfer and proton relay involving
the conserved Tyr and Lys, a water molecule stabilized
by Asn, and nicotinamide. Extended SDRs have additional
elements in the C-terminal region, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type KRs have
a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 480
Score = 30.2 bits (69), Expect = 1.6
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 247 ILVTGGAGYIGSHTVVSLLEHG 268
+LVTGG G +G+H L G
Sbjct: 233 VLVTGGTGALGAHVARWLARRG 254
>gnl|CDD|180343 PRK05993, PRK05993, short chain dehydrogenase; Provisional.
Length = 277
Score = 30.0 bits (68), Expect = 1.7
Identities = 15/57 (26%), Positives = 24/57 (42%), Gaps = 11/57 (19%)
Query: 241 MSNPKFILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETGKPESLKRVEN 297
M + IL+TG + IG++ +L G+ V CR K E + +E
Sbjct: 1 MDMKRSILITGCSSGIGAYCARALQSDGWRVFA------TCR-----KEEDVAALEA 46
>gnl|CDD|235712 PRK06138, PRK06138, short chain dehydrogenase; Provisional.
Length = 252
Score = 29.7 bits (67), Expect = 1.7
Identities = 19/80 (23%), Positives = 27/80 (33%), Gaps = 13/80 (16%)
Query: 245 KFILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNA-----CRVEETGKPE-------SL 292
+ +VTG IG T G VVV D A + G+ S
Sbjct: 6 RVAIVTGAGSGIGRATAKLFAREGARVVVADRDAEAAERVAAAIAAGGRAFARQGDVGSA 65
Query: 293 KRVENLTGKTV-EYHEVDIL 311
+ VE L + +D+L
Sbjct: 66 EAVEALVDFVAARWGRLDVL 85
>gnl|CDD|234094 TIGR03026, NDP-sugDHase, nucleotide sugar dehydrogenase. Enzymes
in this family catalyze the NAD-dependent
alcohol-to-acid oxidation of nucleotide-linked sugars.
Examples include UDP-glucose 6-dehydrogenase (1.1.1.22)
, GDP-mannose 6-dehydrogenase (1.1.1.132) ,
UDP-N-acetylglucosamine 6-dehydrogenase (1.1.1.136),
UDP-N-acetyl-D-galactosaminuronic acid dehydrogenase and
UDP-N-acetyl-D-mannosaminuronic acid dehydrogenase.
These enzymes are most often involved in the
biosynthesis of polysaccharides and are often found in
operons devoted to that purpose. All of these enzymes
contain three Pfam domains, pfam03721, pfam00984, and
pfam03720 for the N-terminal, central, and C-terminal
regions respectively.
Length = 409
Score = 29.9 bits (68), Expect = 1.7
Identities = 14/52 (26%), Positives = 22/52 (42%), Gaps = 8/52 (15%)
Query: 252 GAGYIGSHTVVSLLEHGYNVVVVD------NLVNA--CRVEETGKPESLKRV 295
G GY+G L + G++V VD + +N + E G E L +
Sbjct: 7 GLGYVGLPLAALLADLGHDVTGVDIDQEKVDKLNKGKSPIYEPGLDELLAKA 58
>gnl|CDD|216949 pfam02254, TrkA_N, TrkA-N domain. This domain is found in a wide
variety of proteins. These protein include potassium
channels, phosphoesterases, and various other
transporters. This domain binds to NAD.
Length = 116
Score = 28.7 bits (65), Expect = 1.8
Identities = 18/68 (26%), Positives = 23/68 (33%), Gaps = 14/68 (20%)
Query: 252 GAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETGKPESLKRVENLTGKTVEYHEVDIL 311
G G +G L E G +VVV+D +RVE L + V D
Sbjct: 5 GYGRVGRSLAEELREGGPDVVVIDK--------------DPERVEELREEGVPVVVGDAT 50
Query: 312 QVSDLREI 319
L E
Sbjct: 51 DEEVLEEA 58
>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 = 29.8 bits (67), Expect = 1.8
Identities = 25/71 (35%), Positives = 34/71 (47%), Gaps = 9/71 (12%)
Query: 248 LVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRV-EETGKPESLKRVENLTGKT-VEY 305
LVTGG G++G H + LLE + RV ++ PE ++ E GKT V
Sbjct: 3 LVTGGGGFLGQHIIRLLLER-------KEELKEIRVLDKAFGPELIEHFEKSQGKTYVTD 55
Query: 306 HEVDILQVSDL 316
E DI +S L
Sbjct: 56 IEGDIKDLSFL 66
Score = 29.0 bits (65), Expect = 3.4
Identities = 20/61 (32%), Positives = 25/61 (40%), Gaps = 6/61 (9%)
Query: 6 VYHFVFSSSSTVYGTP-KFLPF---TEDHPTGQGCTNPYGKSKYFVEEILKDLASFKQKL 61
V V++SS V G K P ED P T PY SK E I+ L + L
Sbjct: 114 VKRLVYTSSIEVAGPNFKGRPIFNGVEDTPYEDTSTPPYASSKLLAENIV--LNANGAPL 171
Query: 62 Q 62
+
Sbjct: 172 K 172
>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 = 29.7 bits (67), Expect = 1.8
Identities = 15/31 (48%), Positives = 18/31 (58%), Gaps = 1/31 (3%)
Query: 241 MSNPKFILVTGGAGYIGSHTVVSLLEHGYNV 271
M N K IL+TGG G G + LLE+ YN
Sbjct: 1 MFNNKSILITGGTGSFGKAFISRLLEN-YNP 30
>gnl|CDD|187662 cd09761, A3DFK9-like_SDR_c, Clostridium thermocellum A3DFK9-like, a
putative carbohydrate or polyalcohol metabolizing SDR,
classical (c) SDRs. This subgroup includes a putative
carbohydrate or polyalcohol metabolizing SDR (A3DFK9)
from Clostridium thermocellum. Its members have a
TGXXXGXG classical-SDR glycine-rich NAD-binding motif,
and some have a canonical SDR active site tetrad (A3DFK9
lacks the upstream Asn). 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 = 242
Score = 29.5 bits (66), Expect = 1.9
Identities = 19/78 (24%), Positives = 26/78 (33%), Gaps = 11/78 (14%)
Query: 245 KFILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNA-CRVEETGKPE---------SLKR 294
K +VTGG IG + LE G VV D E P
Sbjct: 2 KVAIVTGGGHGIGKQICLDFLEAGDKVVFADIDEERGADFAEAEGPNLFFVHGDVADETL 61
Query: 295 VENLTGKTVE-YHEVDIL 311
V+ + +E +D+L
Sbjct: 62 VKFVVYAMLEKLGRIDVL 79
>gnl|CDD|181335 PRK08264, PRK08264, short chain dehydrogenase; Validated.
Length = 238
Score = 29.5 bits (67), Expect = 1.9
Identities = 11/24 (45%), Positives = 12/24 (50%)
Query: 245 KFILVTGGAGYIGSHTVVSLLEHG 268
K +LVTG IG V LL G
Sbjct: 7 KVVLVTGANRGIGRAFVEQLLARG 30
>gnl|CDD|180462 PRK06198, PRK06198, short chain dehydrogenase; Provisional.
Length = 260
Score = 29.6 bits (67), Expect = 2.1
Identities = 19/77 (24%), Positives = 30/77 (38%), Gaps = 7/77 (9%)
Query: 243 NPKFILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETGKPESLKRVENLTGKT 302
+ K LVTGG +G+ + E G +V+ R E G E+ G
Sbjct: 5 DGKVALVTGGTQGLGAAIARAFAERGAAGLVI-----CGRNAEKG--EAQAAELEALGAK 57
Query: 303 VEYHEVDILQVSDLREI 319
+ + D+ V D R +
Sbjct: 58 AVFVQADLSDVEDCRRV 74
>gnl|CDD|180440 PRK06172, PRK06172, short chain dehydrogenase; Provisional.
Length = 253
Score = 29.3 bits (66), Expect = 2.3
Identities = 15/31 (48%), Positives = 17/31 (54%)
Query: 245 KFILVTGGAGYIGSHTVVSLLEHGYNVVVVD 275
K LVTGGA IG T ++ G VVV D
Sbjct: 8 KVALVTGGAAGIGRATALAFAREGAKVVVAD 38
>gnl|CDD|187638 cd08933, RDH_SDR_c, retinal dehydrogenase-like, classical (c) SDR.
These classical SDRs includes members identified as
retinol dehydrogenases, which convert retinol to
retinal, a property that overlaps with 17betaHSD
activity. 17beta-dehydrogenases are a group of isozymes
that catalyze activation and inactivation of estrogen
and androgens, and include members of the short-chain
dehydrogenases/reductase family. 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 = 261
Score = 29.4 bits (66), Expect = 2.3
Identities = 21/79 (26%), Positives = 38/79 (48%), Gaps = 9/79 (11%)
Query: 245 KFILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETGKPESLKRVENLTGK-TV 303
K ++VTGG+ IG V + +E+G VV R E G+ +L+ N G +
Sbjct: 10 KVVIVTGGSRGIGRGIVRAFVENGAKVVFCA------RGEAAGQ--ALESELNRAGPGSC 61
Query: 304 EYHEVDILQVSDLREIFSK 322
++ D+ + D++ + S
Sbjct: 62 KFVPCDVTKEEDIKTLISV 80
>gnl|CDD|187616 cd05358, GlcDH_SDR_c, glucose 1 dehydrogenase (GlcDH), classical
(c) SDRs. GlcDH, is a tetrameric member of the SDR
family, it catalyzes the NAD(P)-dependent oxidation of
beta-D-glucose to D-glucono-delta-lactone. GlcDH has a
typical NAD-binding site glycine-rich pattern as well as
the canonical active site tetrad (YXXXK motif plus
upstream Ser and Asn). SDRs are a functionally diverse
family of oxidoreductases that have a single domain with
a structurally conserved Rossmann fold (alpha/beta
folding pattern with a central beta-sheet), an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRS are approximately
350 residues. Sequence identity between different SDR
enzymes are typically in the 15-30% range, but the
enzymes share the Rossmann fold NAD-binding motif and
characteristic NAD-binding and catalytic sequence
patterns. These enzymes have a 3-glycine N-terminal
NAD(P)(H)-binding pattern (typically, TGxxxGxG in
classical SDRs and TGxxGxxG in extended SDRs), while
substrate binding is in the C-terminal region. A
critical catalytic Tyr residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering), is often found in a conserved YXXXK pattern.
In addition to the Tyr and Lys, there is often an
upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn
(Asn-107, 15-PGDH numbering) or additional Ser,
contributing to the active site. Substrates for these
enzymes include sugars, steroids, alcohols, and aromatic
compounds. The standard reaction mechanism is a proton
relay involving the conserved Tyr and Lys, as well as
Asn (or Ser). Some SDR family members, including 17
beta-hydroxysteroid dehydrogenase contain an additional
helix-turn-helix motif that is not generally found among
SDRs.
Length = 253
Score = 29.3 bits (66), Expect = 2.4
Identities = 22/78 (28%), Positives = 36/78 (46%), Gaps = 7/78 (8%)
Query: 245 KFILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETGKPESLKRVENLTGKTVE 304
K LVTG + IG + L G NVVV N R +E E ++ ++ + GK +
Sbjct: 4 KVALVTGASSGIGKAIAIRLATAGANVVV--NY----RSKEDAAEEVVEEIKAVGGKAI- 56
Query: 305 YHEVDILQVSDLREIFSK 322
+ D+ + D+ +F
Sbjct: 57 AVQADVSKEEDVVALFQS 74
>gnl|CDD|217556 pfam03435, Saccharop_dh, Saccharopine dehydrogenase. This family
comprised of three structural domains that can not be
separated in the linear sequence. In some organisms this
enzyme is found as a bifunctional polypeptide with
lysine ketoglutarate reductase. The saccharopine
dehydrogenase can also function as a saccharopine
reductase.
Length = 380
Score = 29.6 bits (67), Expect = 2.4
Identities = 15/72 (20%), Positives = 20/72 (27%), Gaps = 11/72 (15%)
Query: 252 GAGYIGSHTVVSLLEHG-YNVVVVDNLVNACRVEETGKPESLKRVENLTGKTVEYHEVDI 310
GAG +G L HG + V A R E + G VD
Sbjct: 5 GAGGVGQGVAPLLARHGDLEITV------ADRSLEKAQ----ALAAPKLGLRFIAIAVDA 54
Query: 311 LQVSDLREIFSK 322
L + +
Sbjct: 55 DNYEALVALLKE 66
>gnl|CDD|183778 PRK12829, PRK12829, short chain dehydrogenase; Provisional.
Length = 264
Score = 29.3 bits (66), Expect = 2.5
Identities = 13/29 (44%), Positives = 15/29 (51%)
Query: 247 ILVTGGAGYIGSHTVVSLLEHGYNVVVVD 275
+LVTGGA IG + E G V V D
Sbjct: 14 VLVTGGASGIGRAIAEAFAEAGARVHVCD 42
>gnl|CDD|236094 PRK07774, PRK07774, short chain dehydrogenase; Provisional.
Length = 250
Score = 29.3 bits (66), Expect = 2.5
Identities = 14/31 (45%), Positives = 17/31 (54%)
Query: 245 KFILVTGGAGYIGSHTVVSLLEHGYNVVVVD 275
K +VTG AG IG +L G +VVV D
Sbjct: 7 KVAIVTGAAGGIGQAYAEALAREGASVVVAD 37
>gnl|CDD|187672 cd09812, 3b-HSD_like_1_SDR_e, 3beta-hydroxysteroid dehydrogenase
(3b-HSD)-like, subgroup1, extended (e) SDRs. An
uncharacterized subgroup of the 3b-HSD-like extended-SDR
family. Proteins in this subgroup 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. 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 = 339
Score = 29.4 bits (66), Expect = 2.6
Identities = 11/29 (37%), Positives = 18/29 (62%)
Query: 247 ILVTGGAGYIGSHTVVSLLEHGYNVVVVD 275
+L+TGG GY G +L + G +V++ D
Sbjct: 2 VLITGGGGYFGFRLGCALAKSGVHVILFD 30
>gnl|CDD|132250 TIGR03206, benzo_BadH, 2-hydroxycyclohexanecarboxyl-CoA
dehydrogenase. Members of this protein family are the
enzyme 2-hydroxycyclohexanecarboxyl-CoA dehydrogenase.
The enzymatic properties were confirmed experimentally
in Rhodopseudomonas palustris; the enzyme is
homotetrameric, and not sensitive to oxygen. This enzyme
is part of proposed pathway for degradation of
benzoyl-CoA to 3-hydroxypimeloyl-CoA that differs from
the analogous in Thauera aromatica. It also may occur in
degradation of the non-aromatic compound
cyclohexane-1-carboxylate.
Length = 250
Score = 29.1 bits (65), Expect = 2.6
Identities = 14/31 (45%), Positives = 15/31 (48%)
Query: 245 KFILVTGGAGYIGSHTVVSLLEHGYNVVVVD 275
K +VTGG G IG T E G V V D
Sbjct: 4 KTAIVTGGGGGIGGATCRRFAEEGAKVAVFD 34
>gnl|CDD|131732 TIGR02685, pter_reduc_Leis, pteridine reductase. Pteridine
reductase is an enzyme used by trypanosomatids
(including Trypanosoma cruzi and Leishmania major) to
obtain reduced pteridines by salvage rather than
biosynthetic pathways. Enzymes in T. cruzi described as
pteridine reductase 1 (PTR1) and pteridine reductase 2
(PTR2) have different activity profiles. PTR1 is more
active with with fully oxidized biopterin and folate
than with reduced forms, while PTR2 reduces
dihydrobiopterin and dihydrofolate but not oxidized
pteridines. T. cruzi PTR1 and PTR2 are more similar to
each other in sequence than either is to the pteridine
reductase of Leishmania major, and all are included in
this family.
Length = 267
Score = 29.1 bits (65), Expect = 2.6
Identities = 13/26 (50%), Positives = 17/26 (65%)
Query: 248 LVTGGAGYIGSHTVVSLLEHGYNVVV 273
+VTG A IGS V+L + GY VV+
Sbjct: 5 VVTGAAKRIGSSIAVALHQEGYRVVL 30
>gnl|CDD|235935 PRK07109, PRK07109, short chain dehydrogenase; Provisional.
Length = 334
Score = 29.5 bits (67), Expect = 2.6
Identities = 9/56 (16%), Positives = 21/56 (37%), Gaps = 5/56 (8%)
Query: 237 LQRDMSNPKFILVTGGAGYIGSHTVVSLLEHGYNVVVV----DNLVNACR-VEETG 287
+ + +++TG + +G T + G VV++ + L + G
Sbjct: 1 MMLKPIGRQVVVITGASAGVGRATARAFARRGAKVVLLARGEEGLEALAAEIRAAG 56
>gnl|CDD|235500 PRK05557, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Validated.
Length = 248
Score = 29.0 bits (66), Expect = 2.7
Identities = 17/78 (21%), Positives = 25/78 (32%), Gaps = 7/78 (8%)
Query: 245 KFILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETGKPESLKRVENLTGKTVE 304
K LVTG + IG L G NVV+ E G + + L G
Sbjct: 6 KVALVTGASRGIGRAIAERLAAQGANVVI------NYASSEAGAEALVAEIGAL-GGKAL 58
Query: 305 YHEVDILQVSDLREIFSK 322
+ D+ + +
Sbjct: 59 AVQGDVSDAESVERAVDE 76
>gnl|CDD|187606 cd05348, BphB-like_SDR_c,
cis-biphenyl-2,3-dihydrodiol-2,3-dehydrogenase
(BphB)-like, classical (c) SDRs.
cis-biphenyl-2,3-dihydrodiol-2,3-dehydrogenase (BphB) is
a classical SDR, it is of particular importance for its
role in the degradation of biphenyl/polychlorinated
biphenyls(PCBs); PCBs are a significant source of
environmental contamination. This subgroup also includes
Pseudomonas putida F1
cis-biphenyl-1,2-dihydrodiol-1,2-dehydrogenase (aka
cis-benzene glycol dehydrogenase, encoded by the bnzE
gene), which participates in benzene metabolism. In
addition it includes Pseudomonas sp. C18 putative
1,2-dihydroxy-1,2-dihydronaphthalene dehydrogenase (aka
dibenzothiophene dihydrodiol dehydrogenase, encoded by
the doxE gene) which participates in an upper
naphthalene catabolic pathway. 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 = 257
Score = 29.2 bits (66), Expect = 2.7
Identities = 13/45 (28%), Positives = 20/45 (44%), Gaps = 2/45 (4%)
Query: 241 MSNPKFILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEE 285
+ L+TGG +G V + G V V+D +A +V E
Sbjct: 1 WLKGEVALITGGGSGLGRALVERFVAEGAKVAVLD--RSAEKVAE 43
>gnl|CDD|233590 TIGR01830, 3oxo_ACP_reduc, 3-oxoacyl-(acyl-carrier-protein)
reductase. This model represents 3-oxoacyl-[ACP]
reductase, also called 3-ketoacyl-acyl carrier protein
reductase, an enzyme of fatty acid biosynthesis [Fatty
acid and phospholipid metabolism, Biosynthesis].
Length = 239
Score = 29.1 bits (66), Expect = 2.8
Identities = 16/75 (21%), Positives = 31/75 (41%), Gaps = 7/75 (9%)
Query: 248 LVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETGKPESLKRVENLTGKTVEYHE 307
LVTG + IG + L + G V++ R E G E ++ ++ K +
Sbjct: 2 LVTGASRGIGRAIALKLAKEGAKVIITY------RSSEEGAEEVVEELKAYGVKALGV-V 54
Query: 308 VDILQVSDLREIFSK 322
D+ D++ + +
Sbjct: 55 CDVSDREDVKAVVEE 69
>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 = 29.1 bits (66), Expect = 3.0
Identities = 13/29 (44%), Positives = 15/29 (51%)
Query: 247 ILVTGGAGYIGSHTVVSLLEHGYNVVVVD 275
ILVTG G +G L E G VV +D
Sbjct: 1 ILVTGANGQLGRELTRLLAERGVEVVALD 29
>gnl|CDD|224011 COG1086, COG1086, Predicted nucleoside-diphosphate sugar epimerases
[Cell envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 588
Score = 29.2 bits (66), Expect = 3.1
Identities = 11/30 (36%), Positives = 17/30 (56%)
Query: 245 KFILVTGGAGYIGSHTVVSLLEHGYNVVVV 274
K +LVTGG G IGS +L+ +++
Sbjct: 251 KTVLVTGGGGSIGSELCRQILKFNPKEIIL 280
>gnl|CDD|218636 pfam05557, MAD, Mitotic checkpoint protein. This family consists
of several eukaryotic mitotic checkpoint (Mitotic arrest
deficient or MAD) proteins. The mitotic spindle
checkpoint monitors proper attachment of the bipolar
spindle to the kinetochores of aligned sister chromatids
and causes a cell cycle arrest in prometaphase when
failures occur. Multiple components of the mitotic
spindle checkpoint have been identified in yeast and
higher eukaryotes. In S.cerevisiae, the existence of a
Mad1-dependent complex containing Mad2, Mad3, Bub3 and
Cdc20 has been demonstrated.
Length = 722
Score = 29.5 bits (66), Expect = 3.1
Identities = 14/30 (46%), Positives = 17/30 (56%)
Query: 48 EEILKDLASFKQKLQSLQSSVTQIWLNSVH 77
EE K+LA ++KLQSL S NSV
Sbjct: 202 EECQKELAEAEKKLQSLTSEQASSADNSVK 231
>gnl|CDD|235739 PRK06200, PRK06200, 2,3-dihydroxy-2,3-dihydrophenylpropionate
dehydrogenase; Provisional.
Length = 263
Score = 28.8 bits (65), Expect = 3.2
Identities = 11/29 (37%), Positives = 14/29 (48%)
Query: 247 ILVTGGAGYIGSHTVVSLLEHGYNVVVVD 275
L+TGG IG V L G V V++
Sbjct: 9 ALITGGGSGIGRALVERFLAEGARVAVLE 37
>gnl|CDD|187596 cd05337, BKR_1_SDR_c, putative beta-ketoacyl acyl carrier protein
[ACP] reductase (BKR), subgroup 1, classical (c) SDR.
This subgroup includes Escherichia coli CFT073 FabG. The
Escherichai coli K12 BKR, FabG, belongs to a different
subgroup. BKR catalyzes the NADPH-dependent reduction of
ACP in the first reductive step of de novo fatty acid
synthesis (FAS). FAS consists of four elongation steps,
which are repeated to extend the fatty acid chain
through the addition of two-carbo units from malonyl
acyl-carrier protein (ACP): condensation, reduction,
dehydration, and a final reduction. Type II FAS, typical
of plants and many bacteria, maintains these activities
on discrete polypeptides, while type I FAS utilizes one
or two multifunctional polypeptides. BKR resembles enoyl
reductase, which catalyzes the second reduction step in
FAS. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with
structurally conserved Rossmann fold (alpha/beta folding
pattern with a central beta-sheet) 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: TGxxxGxG in classical SDRs. 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 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. 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-151 and
Lys-155, and well as Asn-111 (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 = 255
Score = 29.0 bits (65), Expect = 3.3
Identities = 17/72 (23%), Positives = 30/72 (41%), Gaps = 7/72 (9%)
Query: 248 LVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETGKPESLKRVENLTGKTVEYHE 307
+VTG + IG L G+++ + D + + E E L G+ Y +
Sbjct: 5 IVTGASRGIGRAIATELAARGFDIAINDL-PDDDQATEVVA-EVLA-----AGRRAIYFQ 57
Query: 308 VDILQVSDLREI 319
DI ++SD +
Sbjct: 58 ADIGELSDHEAL 69
>gnl|CDD|223534 COG0458, CarB, Carbamoylphosphate synthase large subunit (split
gene in MJ) [Amino acid transport and metabolism /
Nucleotide transport and metabolism].
Length = 400
Score = 29.2 bits (66), Expect = 3.3
Identities = 12/34 (35%), Positives = 16/34 (47%)
Query: 242 SNPKFILVTGGAGYIGSHTVVSLLEHGYNVVVVD 275
S P I Y G+ +L E GY VV+V+
Sbjct: 3 SGPIVIGQAAEFDYSGTQACKALKEEGYGVVLVN 36
>gnl|CDD|180817 PRK07060, PRK07060, short chain dehydrogenase; Provisional.
Length = 245
Score = 28.9 bits (65), Expect = 3.3
Identities = 16/45 (35%), Positives = 20/45 (44%), Gaps = 2/45 (4%)
Query: 245 KFILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRV--EETG 287
K +LVTG + IG V+L + G VV A ETG
Sbjct: 10 KSVLVTGASSGIGRACAVALAQRGARVVAAARNAAALDRLAGETG 54
>gnl|CDD|187645 cd08941, 3KS_SDR_c, 3-keto steroid reductase, classical (c) SDRs.
3-keto steroid reductase (in concert with other enzymes)
catalyzes NADP-dependent sterol C-4 demethylation, as
part of steroid biosynthesis. 3-keto reductase is a
classical SDR, with a well conserved canonical active
site tetrad and fairly well conserved characteristic
NAD-binding motif. SDRs are a functionally diverse
family of oxidoreductases that have a single domain with
a structurally conserved Rossmann fold (alpha/beta
folding pattern with a central beta-sheet), an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRs are approximately
350 residues. Sequence identity between different SDR
enzymes are typically in the 15-30% range, but the
enzymes share the Rossmann fold NAD-binding motif and
characteristic NAD-binding and catalytic sequence
patterns. These enzymes 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 = 290
Score = 28.9 bits (65), Expect = 3.3
Identities = 20/84 (23%), Positives = 32/84 (38%), Gaps = 16/84 (19%)
Query: 245 KFILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETGKPESLKRVENLTGKTVE 304
K +LVTG +G LL + L+ ACR +L+R E +
Sbjct: 2 KVVLVTGANSGLGLAICERLLA-EDDENPELTLILACR--------NLQRAEAACRALLA 52
Query: 305 YH-----EVDILQV--SDLREIFS 321
H D + V S++ +F+
Sbjct: 53 SHPDARVVFDYVLVDLSNMVSVFA 76
>gnl|CDD|178567 PLN02986, PLN02986, cinnamyl-alcohol dehydrogenase family protein.
Length = 322
Score = 28.8 bits (64), Expect = 3.3
Identities = 14/27 (51%), Positives = 16/27 (59%)
Query: 245 KFILVTGGAGYIGSHTVVSLLEHGYNV 271
K + VTG +GYI S V LL GY V
Sbjct: 6 KLVCVTGASGYIASWIVKLLLLRGYTV 32
>gnl|CDD|224254 COG1335, PncA, Amidases related to nicotinamidase [Secondary
metabolites biosynthesis, transport, and catabolism].
Length = 205
Score = 28.7 bits (64), Expect = 3.5
Identities = 10/37 (27%), Positives = 15/37 (40%), Gaps = 4/37 (10%)
Query: 247 ILVTGGAGYIG-SHTVVSLLEHGYNVVVVDNLVNACR 282
++V G A I T + GY V +V +A
Sbjct: 136 VVVCGIATDICVLATARDAFDLGYQVTLV---EDATA 169
>gnl|CDD|180617 PRK06550, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 235
Score = 28.8 bits (65), Expect = 3.6
Identities = 12/31 (38%), Positives = 15/31 (48%)
Query: 245 KFILVTGGAGYIGSHTVVSLLEHGYNVVVVD 275
K +L+TG A IG + L G V VD
Sbjct: 6 KTVLITGAASGIGLAQARAFLAQGAQVYGVD 36
>gnl|CDD|187601 cd05343, Mgc4172-like_SDR_c, human Mgc4172-like, classical (c)
SDRs. Human Mgc4172-like proteins, putative SDRs. These
proteins are members of the SDR family, with a canonical
active site tetrad and a typical Gly-rich NAD-binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold (alpha/beta folding
pattern with a central beta-sheet), an NAD(P)(H)-binding
region, and a structurally diverse C-terminal region.
Classical SDRs are typically about 250 residues long,
while extended SDRs are approximately 350 residues.
Sequence identity between different SDR enzymes are
typically in the 15-30% range, but the enzymes share the
Rossmann fold NAD-binding motif and characteristic
NAD-binding and catalytic sequence patterns. These
enzymes 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 = 28.6 bits (64), Expect = 3.6
Identities = 18/85 (21%), Positives = 32/85 (37%), Gaps = 21/85 (24%)
Query: 245 KFILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETGKPESLKRVENLTG--KT 302
+ LVTG + IG+ +L++HG VV G + ++E L ++
Sbjct: 7 RVALVTGASVGIGAAVARALVQHGMKVV--------------GCARRVDKIEALAAECQS 52
Query: 303 VEYHE-----VDILQVSDLREIFSK 322
Y D+ + +FS
Sbjct: 53 AGYPTLFPYQCDLSNEEQILSMFSA 77
>gnl|CDD|177093 CHL00194, ycf39, Ycf39; Provisional.
Length = 317
Score = 28.8 bits (65), Expect = 3.7
Identities = 21/67 (31%), Positives = 29/67 (43%), Gaps = 12/67 (17%)
Query: 247 ILVTGGAGYIGSHTVVSLLEHGYNV-VVVDNLVNACRVEETGK---------PESLKRVE 296
+LV G G +G V L+ GY V +V NL A ++E G PE+L
Sbjct: 3 LLVIGATGTLGRQIVRQALDEGYQVRCLVRNLRKASFLKEWGAELVYGDLSLPETLP--P 60
Query: 297 NLTGKTV 303
+ G T
Sbjct: 61 SFKGVTA 67
>gnl|CDD|176214 cd08252, AL_MDR, Arginate lyase and other MDR family members. This
group contains a structure identified as an arginate
lyase. Other members are identified quinone reductases,
alginate lyases, and other proteins related to the
zinc-dependent dehydrogenases/reductases. QOR catalyzes
the conversion of a quinone and NAD(P)H to a
hydroquinone and NAD(P+. Quinones are cyclic diones
derived from aromatic compounds. Membrane bound QOR acts
in 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.
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. 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 = 336
Score = 28.6 bits (65), Expect = 4.0
Identities = 15/35 (42%), Positives = 22/35 (62%), Gaps = 3/35 (8%)
Query: 225 AWEAKYGLDKMYLQRDMSN-PKFILVTGGAGYIGS 258
AWEA + D++ + D N K +L+ GGAG +GS
Sbjct: 132 AWEALF--DRLGISEDAENEGKTLLIIGGAGGVGS 164
>gnl|CDD|235876 PRK06849, PRK06849, hypothetical protein; Provisional.
Length = 389
Score = 28.9 bits (65), Expect = 4.0
Identities = 9/37 (24%), Positives = 16/37 (43%)
Query: 241 MSNPKFILVTGGAGYIGSHTVVSLLEHGYNVVVVDNL 277
M+ K +L+TG G+ V++ D+L
Sbjct: 1 MNTKKTVLITGARAPAALELARLFHNAGHTVILADSL 37
>gnl|CDD|237188 PRK12745, PRK12745, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 256
Score = 28.4 bits (64), Expect = 4.3
Identities = 16/68 (23%), Positives = 29/68 (42%), Gaps = 7/68 (10%)
Query: 248 LVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETGKPESLKRVENLTGKTVEYHE 307
LVTGG IG +L G+++ + D R ++ + + + L G V +
Sbjct: 6 LVTGGRRGIGLGIARALAAAGFDLAIND------RPDDEELAATQQELRAL-GVEVIFFP 58
Query: 308 VDILQVSD 315
D+ +S
Sbjct: 59 ADVADLSA 66
>gnl|CDD|187591 cd05330, cyclohexanol_reductase_SDR_c, cyclohexanol reductases,
including levodione reductase, classical (c) SDRs.
Cyloclohexanol reductases,including
(6R)-2,2,6-trimethyl-1,4-cyclohexanedione (levodione)
reductase of Corynebacterium aquaticum, catalyze the
reversible oxidoreduction of hydroxycyclohexanone
derivatives. 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 = 257
Score = 28.6 bits (64), Expect = 4.3
Identities = 16/57 (28%), Positives = 23/57 (40%)
Query: 245 KFILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETGKPESLKRVENLTGK 301
K +L+TGG +G T V L + G + +VD + E E L K
Sbjct: 4 KVVLITGGGSGLGLATAVRLAKEGAKLSLVDLNEEGLEAAKAALLEIAPDAEVLLIK 60
>gnl|CDD|237220 PRK12828, PRK12828, short chain dehydrogenase; Provisional.
Length = 239
Score = 28.6 bits (64), Expect = 4.4
Identities = 10/31 (32%), Positives = 15/31 (48%)
Query: 245 KFILVTGGAGYIGSHTVVSLLEHGYNVVVVD 275
K + +TGG G +G T L G V ++
Sbjct: 8 KVVAITGGFGGLGRATAAWLAARGARVALIG 38
>gnl|CDD|201726 pfam01320, Colicin_Pyocin, Colicin immunity protein / pyocin
immunity protein.
Length = 85
Score = 26.8 bits (60), Expect = 4.5
Identities = 10/48 (20%), Positives = 19/48 (39%), Gaps = 5/48 (10%)
Query: 56 SFKQKLQSLQSS-----VTQIWLNSVHRSDWHIISLRYFNPVGSHPSG 98
K+K+ S V +I+ + + H + +F + HP G
Sbjct: 2 ELKKKISDYTESEFLEFVKEIFNAELDTEEEHDDLVEHFEKITEHPDG 49
>gnl|CDD|181126 PRK07806, PRK07806, short chain dehydrogenase; Provisional.
Length = 248
Score = 28.5 bits (64), Expect = 4.6
Identities = 13/34 (38%), Positives = 16/34 (47%)
Query: 240 DMSNPKFILVTGGAGYIGSHTVVSLLEHGYNVVV 273
K LVTG + IG+ T L G +VVV
Sbjct: 2 GDLPGKTALVTGSSRGIGADTAKILAGAGAHVVV 35
>gnl|CDD|236190 PRK08220, PRK08220, 2,3-dihydroxybenzoate-2,3-dehydrogenase;
Validated.
Length = 252
Score = 28.3 bits (64), Expect = 4.7
Identities = 13/36 (36%), Positives = 18/36 (50%), Gaps = 1/36 (2%)
Query: 240 DMSNPKFILVTGGAGYIGSHTVVSLLEHGYNVVVVD 275
D S K + VTG A IG ++ +E G V+ D
Sbjct: 5 DFSG-KTVWVTGAAQGIGYAVALAFVEAGAKVIGFD 39
>gnl|CDD|223677 COG0604, Qor, NADPH:quinone reductase and related Zn-dependent
oxidoreductases [Energy production and conversion /
General function prediction only].
Length = 326
Score = 28.5 bits (64), Expect = 4.7
Identities = 17/67 (25%), Positives = 25/67 (37%), Gaps = 12/67 (17%)
Query: 245 KFILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETGKPESLKRVENLTGK-TV 303
+ +LV G AG +GS + G VV V E L+ ++ L +
Sbjct: 144 ETVLVHGAAGGVGSAAIQLAKALGATVVAV-----------VSSSEKLELLKELGADHVI 192
Query: 304 EYHEVDI 310
Y E D
Sbjct: 193 NYREEDF 199
>gnl|CDD|181198 PRK08017, PRK08017, oxidoreductase; Provisional.
Length = 256
Score = 28.5 bits (64), Expect = 4.8
Identities = 17/54 (31%), Positives = 26/54 (48%), Gaps = 11/54 (20%)
Query: 245 KFILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETGKPESLKRVENL 298
K +L+TG + IG + L GY V+ ACR KP+ + R+ +L
Sbjct: 3 KSVLITGCSSGIGLEAALELKRRGYRVLA------ACR-----KPDDVARMNSL 45
>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 = 28.3 bits (64), Expect = 4.9
Identities = 17/45 (37%), Positives = 21/45 (46%), Gaps = 13/45 (28%)
Query: 247 ILVTGGAGYIGSHTVVSLLEH-GYNVVVVDNLVNACRVEETGKPE 290
+LVTG G +GS V++L GY VV TGK E
Sbjct: 149 VLVTGATGGVGS-LAVAILSKLGYEVVAS-----------TGKAE 181
>gnl|CDD|223936 COG1004, Ugd, Predicted UDP-glucose 6-dehydrogenase [Cell envelope
biogenesis, outer membrane].
Length = 414
Score = 28.7 bits (65), Expect = 5.0
Identities = 12/28 (42%), Positives = 15/28 (53%)
Query: 252 GAGYIGSHTVVSLLEHGYNVVVVDNLVN 279
G GY+G T L E G+ VV VD +
Sbjct: 7 GTGYVGLVTGACLAELGHEVVCVDIDES 34
>gnl|CDD|203999 pfam08608, Wyosine_form, Wyosine base formation. Some proteins in
this family appear to be important in wyosine base
formation in a subset of phenylalanine specific tRNAs.
It has been proposed that they participates in
converting tRNA(Phe)-m(1)G(37) to tRNA(Phe)-yW.
Length = 62
Score = 26.0 bits (58), Expect = 5.1
Identities = 14/47 (29%), Positives = 18/47 (38%), Gaps = 13/47 (27%)
Query: 171 KAYNLGTGTGYSVF----------EMVKAFSEACKKNIPYEVVGRRE 207
KAY GYS E V F +A +++ Y V RE
Sbjct: 10 KAY---MHVGYSRNRLTMGNMPAHEEVLEFCKALAEHLGYLVTQERE 53
>gnl|CDD|181199 PRK08020, ubiF, 2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol
hydroxylase; Reviewed.
Length = 391
Score = 28.4 bits (64), Expect = 5.1
Identities = 10/36 (27%), Positives = 21/36 (58%)
Query: 241 MSNPKFILVTGGAGYIGSHTVVSLLEHGYNVVVVDN 276
M+N + G G +G+ + L +HG++V V+++
Sbjct: 1 MTNQPTDIAIVGGGMVGAALALGLAQHGFSVAVLEH 36
>gnl|CDD|187607 cd05349, BKR_2_SDR_c, putative beta-ketoacyl acyl carrier protein
[ACP]reductase (BKR), subgroup 2, classical (c) SDR.
This subgroup includes Rhizobium sp. NGR234 FabG1. The
Escherichai coli K12 BKR, FabG, belongs to a different
subgroup. BKR catalyzes the NADPH-dependent reduction of
ACP in the first reductive step of de novo fatty acid
synthesis (FAS). FAS consists of four elongation steps,
which are repeated to extend the fatty acid chain
through the addition of two-carbo units from malonyl
acyl-carrier protein (ACP): condensation, reduction,
dehydration, and a final reduction. Type II FAS, typical
of plants and many bacteria, maintains these activities
on discrete polypeptides, while type I FAS utilizes one
or two multifunctional polypeptides. BKR resembles enoyl
reductase, which catalyzes the second reduction step in
FAS. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold (alpha/beta folding
pattern with a central beta-sheet), an NAD(P)(H)-binding
region, and a structurally diverse C-terminal region.
Classical SDRs are typically about 250 residues long,
while extended SDRS are approximately 350 residues.
Sequence identity between different SDR enzymes are
typically in the 15-30% range, but the enzymes share the
Rossmann fold NAD-binding motif and characteristic
NAD-binding and catalytic sequence patterns. These
enzymes have a 3-glycine N-terminal NAD(P)(H)-binding
pattern (typically, TGxxxGxG in classical SDRs and
TGxxGxxG in extended SDRs), while substrate binding is
in the C-terminal region. A critical catalytic Tyr
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase (15-PGDH) numbering), is often found in a
conserved YXXXK pattern. In addition to the Tyr and Lys,
there is often an upstream Ser (Ser-138, 15-PGDH
numbering) and/or an Asn (Asn-107, 15-PGDH numbering) or
additional Ser, contributing to the active site.
Substrates for these enzymes include sugars, steroids,
alcohols, and aromatic compounds. The standard reaction
mechanism is a proton relay involving the conserved Tyr
and Lys, as well as Asn (or Ser). Some SDR family
members, including 17 beta-hydroxysteroid dehydrogenase
contain an additional helix-turn-helix motif that is not
generally found among SDRs.
Length = 246
Score = 28.2 bits (63), Expect = 5.4
Identities = 10/29 (34%), Positives = 15/29 (51%)
Query: 245 KFILVTGGAGYIGSHTVVSLLEHGYNVVV 273
+ +LVTG + +G+ S G VVV
Sbjct: 1 QVVLVTGASRGLGAAIARSFAREGARVVV 29
>gnl|CDD|236126 PRK07899, rpsA, 30S ribosomal protein S1; Reviewed.
Length = 486
Score = 28.5 bits (64), Expect = 5.4
Identities = 15/41 (36%), Positives = 23/41 (56%), Gaps = 2/41 (4%)
Query: 115 ISQVAVGRRKKLMVFGDDYDTKDGSGVRDYIHIMDLAEGHV 155
I Q+ G+ KL+ FG ++G + +HI +LAE HV
Sbjct: 293 IGQIVPGKVTKLVPFGAFVRVEEG--IEGLVHISELAERHV 331
>gnl|CDD|181508 PRK08628, PRK08628, short chain dehydrogenase; Provisional.
Length = 258
Score = 28.4 bits (64), Expect = 5.4
Identities = 12/32 (37%), Positives = 17/32 (53%)
Query: 245 KFILVTGGAGYIGSHTVVSLLEHGYNVVVVDN 276
K ++VTGGA IG+ + L E G V+
Sbjct: 8 KVVIVTGGASGIGAAISLRLAEEGAIPVIFGR 39
>gnl|CDD|180371 PRK06057, PRK06057, short chain dehydrogenase; Provisional.
Length = 255
Score = 28.2 bits (63), Expect = 5.8
Identities = 12/27 (44%), Positives = 13/27 (48%)
Query: 249 VTGGAGYIGSHTVVSLLEHGYNVVVVD 275
+TGG IG T L G VVV D
Sbjct: 12 ITGGGSGIGLATARRLAAEGATVVVGD 38
>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 = 28.3 bits (64), Expect = 6.1
Identities = 17/44 (38%), Positives = 21/44 (47%), Gaps = 11/44 (25%)
Query: 247 ILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETGKPE 290
+LVTG G +GS V L + GY VV + TGK E
Sbjct: 150 VLVTGATGGVGSIAVAILAKLGYTVVAL-----------TGKEE 182
>gnl|CDD|181136 PRK07825, PRK07825, short chain dehydrogenase; Provisional.
Length = 273
Score = 28.0 bits (63), Expect = 6.3
Identities = 14/43 (32%), Positives = 21/43 (48%), Gaps = 2/43 (4%)
Query: 245 KFILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETG 287
K + +TGGA IG T +L G V + D ++ +ET
Sbjct: 6 KVVAITGGARGIGLATARALAALGARVAIGD--LDEALAKETA 46
>gnl|CDD|215789 pfam00208, ELFV_dehydrog, Glutamate/Leucine/Phenylalanine/Valine
dehydrogenase.
Length = 237
Score = 27.9 bits (63), Expect = 6.5
Identities = 22/80 (27%), Positives = 28/80 (35%), Gaps = 18/80 (22%)
Query: 249 VTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETG-KPESLK--------RVENLT 299
G G +GS+ LLE G VV V + + + G E L RV
Sbjct: 36 AVQGFGNVGSYAAEKLLELGAKVVAVSD-SSGYIYDPNGIDIEELLELKEEGGGRVVEYA 94
Query: 300 GKTVEYH--------EVDIL 311
G EY + DIL
Sbjct: 95 GSGAEYISGEELWEIDCDIL 114
>gnl|CDD|235925 PRK07067, PRK07067, sorbitol dehydrogenase; Provisional.
Length = 257
Score = 27.7 bits (62), Expect = 6.9
Identities = 13/42 (30%), Positives = 16/42 (38%), Gaps = 2/42 (4%)
Query: 245 KFILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEET 286
K L+TG A IG L G VV+ D + R
Sbjct: 7 KVALLTGAASGIGEAVAERYLAEGARVVIAD--IKPARARLA 46
>gnl|CDD|187642 cd08937, DHB_DH-like_SDR_c,
1,6-dihydroxycyclohexa-2,4-diene-1-carboxylate
dehydrogenase (DHB DH)-like, classical (c) SDR. DHB DH
(aka 1,2-dihydroxycyclohexa-3,5-diene-1-carboxylate
dehydrogenase) catalyzes the NAD-dependent conversion of
1,2-dihydroxycyclohexa-3,4-diene carboxylate to a
catechol. This subgroup also contains Pseudomonas putida
F1 CmtB, 2,3-dihydroxy-2,3-dihydro-p-cumate
dehydrogenase, the second enzyme in the pathway for
catabolism of p-cumate catabolism. This subgroup shares
the glycine-rich NAD-binding motif of the classical SDRs
and shares the same catalytic triad; however, the
upstream Asn implicated in cofactor binding or catalysis
in other SDRs is generally substituted by a 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 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 = 256
Score = 27.9 bits (62), Expect = 6.9
Identities = 12/31 (38%), Positives = 16/31 (51%)
Query: 245 KFILVTGGAGYIGSHTVVSLLEHGYNVVVVD 275
K ++VTG A IG L G V++VD
Sbjct: 5 KVVVVTGAAQGIGRGVAERLAGEGARVLLVD 35
>gnl|CDD|176178 cd05188, MDR, Medium chain reductase/dehydrogenase
(MDR)/zinc-dependent alcohol dehydrogenase-like family.
The medium chain reductase/dehydrogenases
(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. ADH-like proteins
typically form dimers (typically higher plants, mammals)
or tetramers (yeast, bacteria), and generally 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. 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. Other MDR members have only
a catalytic zinc, and some contain no coordinated zinc.
Length = 271
Score = 28.1 bits (63), Expect = 7.0
Identities = 9/29 (31%), Positives = 12/29 (41%), Gaps = 1/29 (3%)
Query: 247 ILVTGGAGYIGSHTVVSLLEHGYNVVVVD 275
+LV G G +G G V+V D
Sbjct: 138 VLVLGAGG-VGLLAAQLAKAAGARVIVTD 165
>gnl|CDD|181162 PRK07904, PRK07904, short chain dehydrogenase; Provisional.
Length = 253
Score = 27.7 bits (62), Expect = 7.0
Identities = 16/69 (23%), Positives = 31/69 (44%), Gaps = 5/69 (7%)
Query: 243 NPKFILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETGKPESLKRVENLTGKT 302
NP+ IL+ GG IG L++ VV+ A ++ + ++ +++ +
Sbjct: 7 NPQTILLLGGTSEIGLAICERYLKNAPARVVL-----AALPDDPRRDAAVAQMKAAGASS 61
Query: 303 VEYHEVDIL 311
VE + D L
Sbjct: 62 VEVIDFDAL 70
>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 = 28.1 bits (63), Expect = 7.5
Identities = 22/64 (34%), Positives = 30/64 (46%), Gaps = 7/64 (10%)
Query: 240 DMSNPKFILVTGGAGYIGSHTVVSLLEHGYNVVV-VDNLVNACRVEETGKPESLKRVENL 298
D S P + +TG G++GS + LL N V V A + EE G L+R+
Sbjct: 967 DASTPITVFLTGATGFLGSFILRDLLTRRSNSNFKVFAHVRA-KSEEAG----LERLRK- 1020
Query: 299 TGKT 302
TG T
Sbjct: 1021 TGTT 1024
>gnl|CDD|187620 cd05362, THN_reductase-like_SDR_c,
tetrahydroxynaphthalene/trihydroxynaphthalene
reductase-like, classical (c) SDRs.
1,3,6,8-tetrahydroxynaphthalene reductase (4HNR) of
Magnaporthe grisea and the related
1,3,8-trihydroxynaphthalene reductase (3HNR) are typical
members of the SDR family containing the canonical
glycine rich NAD(P)-binding site and active site tetrad,
and function in fungal melanin biosynthesis. This
subgroup also includes an SDR from Norway spruce that
may function to protect against both biotic and abitoic
stress. 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 = 243
Score = 27.6 bits (62), Expect = 8.6
Identities = 12/29 (41%), Positives = 14/29 (48%)
Query: 245 KFILVTGGAGYIGSHTVVSLLEHGYNVVV 273
K LVTG + IG L G +VVV
Sbjct: 4 KVALVTGASRGIGRAIAKRLARDGASVVV 32
>gnl|CDD|180669 PRK06720, PRK06720, hypothetical protein; Provisional.
Length = 169
Score = 27.2 bits (60), Expect = 8.6
Identities = 13/31 (41%), Positives = 18/31 (58%)
Query: 245 KFILVTGGAGYIGSHTVVSLLEHGYNVVVVD 275
K +VTGG IG +T + L + G V+V D
Sbjct: 17 KVAIVTGGGIGIGRNTALLLAKQGAKVIVTD 47
>gnl|CDD|234556 TIGR04345, ovoA_Cterm, putative 4-mercaptohistidine
N1-methyltranferase. Ovothiol A is
N1-methyl-4-mercaptohistidine. In the absence of
S-adenosylmethione, a methyl donor, the intermediate
produced is 4-mercaptohistidine. In both Erwinia
tasmaniensis and Trypanosoma cruzi, a protein occurs
with 5-histidylcysteine sulfoxide synthase activity, but
these two enzymes and most homologs share an additional
C-terminal methyltransferase domain. Thus OvoA may be a
bifunctional enzyme with 5-histidylcysteine sulfoxide
synthase and 4-mercaptohistidine N1-methyltranferase
activity. This model describes C-terminal putative
4-mercaptohistidine N1-methyltranferase domain
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Glutathione and analogs].
Length = 242
Score = 27.6 bits (62), Expect = 8.9
Identities = 25/127 (19%), Positives = 50/127 (39%), Gaps = 47/127 (37%)
Query: 171 KAYNLGTGTGYSVFEMVKAFSE---------------ACKKN--IPYEVVGRREGDIASS 213
+A ++G G + FE+ + F E A K+ + Y + + EG++ S
Sbjct: 44 RALDIGCAVGRASFELARYFDEVDGIDFSARFIRPAVALKERGSLRYAL--KEEGEL-VS 100
Query: 214 YCDASLAKKELAWEAKYGLDKM-YLQRDMSN--PKFILVTGGAGYIGSHTVVSLLEHGYN 270
+ + +L+ +L + D++ + Q D N P F GY+
Sbjct: 101 FKEVTLS--DLGLDEVR--DRVSFFQGDACNLKPHF--------------------TGYD 136
Query: 271 VVVVDNL 277
+++ NL
Sbjct: 137 LILAANL 143
>gnl|CDD|181077 PRK07677, PRK07677, short chain dehydrogenase; Provisional.
Length = 252
Score = 27.3 bits (61), Expect = 9.0
Identities = 12/44 (27%), Positives = 20/44 (45%), Gaps = 2/44 (4%)
Query: 245 KFILVTGGAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETGK 288
K +++TGG+ +G E G NVV+ ++EE
Sbjct: 2 KVVIITGGSSGMGKAMAKRFAEEGANVVITGR--TKEKLEEAKL 43
>gnl|CDD|180822 PRK07069, PRK07069, short chain dehydrogenase; Validated.
Length = 251
Score = 27.4 bits (61), Expect = 9.5
Identities = 9/29 (31%), Positives = 13/29 (44%)
Query: 248 LVTGGAGYIGSHTVVSLLEHGYNVVVVDN 276
+TG AG +G + E G V + D
Sbjct: 3 FITGAAGGLGRAIARRMAEQGAKVFLTDI 31
>gnl|CDD|202367 pfam02737, 3HCDH_N, 3-hydroxyacyl-CoA dehydrogenase, NAD binding
domain. This family also includes lambda crystallin.
Length = 180
Score = 27.1 bits (61), Expect = 9.6
Identities = 14/67 (20%), Positives = 26/67 (38%), Gaps = 7/67 (10%)
Query: 252 GAGYIGSHTVVSLLEHGYNVVVVDNLVNACRVEETGKPESLKRVENLTGKTVEYHEVDIL 311
GAG +G+ G VV+VD ++ +E ++ R+E + VE +
Sbjct: 6 GAGTMGAGIAQVFARAGLEVVLVD--ISEEALE-----KARARIEKSLARLVEKGRITEE 58
Query: 312 QVSDLRE 318
+
Sbjct: 59 DADAVLA 65
>gnl|CDD|107305 cd06310, PBP1_ABC_sugar_binding_like_2, Periplasmic sugar-binding
domain of uncharacterized ABC-type transport systems.
Periplasmic sugar-binding domain of uncharacterized
ABC-type transport systems that share homology with a
family of pentose/hexose sugar-binding proteins of the
type I periplasmic binding protein superfamily, which
consists of two domains connected by a three-stranded
hinge. The substrate specificity of this group is not
known, but it is predicted to be involved in the
transport of sugar-containing molecules and chemotaxis.
Length = 273
Score = 27.6 bits (62), Expect = 9.9
Identities = 15/60 (25%), Positives = 27/60 (45%), Gaps = 5/60 (8%)
Query: 157 ALDKLLGGKSQAGFKAYNLGTGTGYSVFEMVKAFSEACKKNIPYEVVGRR--EGDIASSY 214
AL +LLG K + ++ G+ T + + F E K+ E+V + + D A +
Sbjct: 115 ALAELLGKKGKVAVISFVPGSSTT---DQREEGFLEGLKEYPGIEIVATQYSDSDYAKAL 171
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
0.317 0.135 0.401
Gapped
Lambda K H
0.267 0.0845 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 16,730,477
Number of extensions: 1612543
Number of successful extensions: 2124
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2056
Number of HSP's successfully gapped: 293
Length of query: 322
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 225
Effective length of database: 6,635,264
Effective search space: 1492934400
Effective search space used: 1492934400
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 59 (26.3 bits)