RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7590
(358 letters)
>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 = 440 bits (1135), Expect = e-156
Identities = 149/344 (43%), Positives = 203/344 (59%), Gaps = 45/344 (13%)
Query: 7 ILVTGGTGLVGKAIEKIVKEEEKRDDETWIFVSSKEADLSNLESTQQLFSKYKPTHVIHL 66
ILVTG GLVG AI +++ +R E +F +SKE DL++ E+ + F K KP +VIHL
Sbjct: 2 ILVTGHRGLVGSAIVRVL---ARRGYENVVFRTSKELDLTDQEAVRAFFEKEKPDYVIHL 58
Query: 67 AAMVGGLFHNMSHNLDFFRVNMKINDNVLDTSYKQGVKKVVSCLSTCIFPDKTTYPIDET 126
AA VGG+ NM++ DF R N+ INDNV+ +++ GVKK+V S+CI+PD PIDE+
Sbjct: 59 AAKVGGIVANMTYPADFLRDNLLINDNVIHAAHRFGVKKLVFLGSSCIYPDLAPQPIDES 118
Query: 127 MVHNGPPHPSNFGYSHAKRMLDVLNKAYYQQHGVTYTSVIPCNVFGPHDNYNLESSHVIP 186
+ GPP P+N GY+ AKR L +AY +Q+G Y SV+P N++GPHDN++ E+SHVIP
Sbjct: 119 DLLTGPPEPTNEGYAIAKRAGLKLCEAYRKQYGCDYISVMPTNLYGPHDNFDPENSHVIP 178
Query: 187 GLIRKLYDTIEKGKDQSVFESRARFPPGANSFGLDKLDLIPFSLFPFCFTGGDEFKVLGT 246
LIRK + A KL GG E V G+
Sbjct: 179 ALIRKFH--------------EA------------KL------------RGGKEVTVWGS 200
Query: 247 GKPLRQFIYSLDLARLFIWVLREYDSVEPIILSVDEKDEVTIAEVAEAIANAFQFKGRIT 306
G P R+F+YS DLAR +++L YD EPII++V E++I E+AEAIA FKG I
Sbjct: 201 GTPRREFLYSDDLARAIVFLLENYD--EPIIVNVGSGVEISIRELAEAIAEVVGFKGEIV 258
Query: 307 FDTNAADGQLKKTASNRKLRELRGPGFEFTPFQQAVQESVAWFR 350
FDT+ DGQ +K KLR L F FTP +Q ++E+ W+
Sbjct: 259 FDTSKPDGQPRKLLDVSKLRAL--GWFPFTPLEQGIRETYEWYL 300
>gnl|CDD|178326 PLN02725, PLN02725,
GDP-4-keto-6-deoxymannose-3,5-epimerase-4-reductase.
Length = 306
Score = 377 bits (969), Expect = e-131
Identities = 118/350 (33%), Positives = 179/350 (51%), Gaps = 45/350 (12%)
Query: 8 LVTGGTGLVGKAIEKIVKEEEKRDDETWIFVSSKEADLSNLESTQQLFSKYKPTHVIHLA 67
V G GLVG AI + ++ + + KE DL+ + F+K KPT+VI A
Sbjct: 1 FVAGHRGLVGSAIVRKLEALG---FTNLVLRTHKELDLTRQADVEAFFAKEKPTYVILAA 57
Query: 68 AMVGGLFHNMSHNLDFFRVNMKINDNVLDTSYKQGVKKVVSCLSTCIFPDKTTYPIDETM 127
A VGG+ NM++ DF R N++I NV+D +Y+ GVKK++ S+CI+P PI ET
Sbjct: 58 AKVGGIHANMTYPADFIRENLQIQTNVIDAAYRHGVKKLLFLGSSCIYPKFAPQPIPETA 117
Query: 128 VHNGPPHPSNFGYSHAKRMLDVLNKAYYQQHGVTYTSVIPCNVFGPHDNYNLESSHVIPG 187
+ GPP P+N Y+ AK + +AY Q+G S +P N++GPHDN++ E+SHVIP
Sbjct: 118 LLTGPPEPTNEWYAIAKIAGIKMCQAYRIQYGWDAISGMPTNLYGPHDNFHPENSHVIPA 177
Query: 188 LIRKLYDTIEKGKDQSVFESRARFPPGANSFGLDKLDLIPFSLFPFCFTGGDEFKVLGTG 247
LIR+ ++ G + V V G+G
Sbjct: 178 LIRRFHEAKANGAPEVV--------------------------------------VWGSG 199
Query: 248 KPLRQFIYSLDLARLFIWVLREYDSVEPIILSVDEKDEVTIAEVAEAIANAFQFKGRITF 307
PLR+F++ DLA ++++R Y E + +V DEVTI E+AE + F+G + +
Sbjct: 200 SPLREFLHVDDLADAVVFLMRRYSGAEHV--NVGSGDEVTIKELAELVKEVVGFEGELVW 257
Query: 308 DTNAADGQLKKTASNRKLRELRGPGFEFTPFQQAVQESVAWFRENHSVAR 357
DT+ DG +K + KLR L G +F + +QE+ W+ EN+
Sbjct: 258 DTSKPDGTPRKLMDSSKLRSL-GWDPKF-SLKDGLQETYKWYLENYETGG 305
>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 = 177 bits (452), Expect = 3e-54
Identities = 72/280 (25%), Positives = 117/280 (41%), Gaps = 60/280 (21%)
Query: 7 ILVTGGTGLVGKAIEKIVKEEE--------KRDDETWIFVSSK--EADLSNLESTQQLFS 56
ILVTGGTG +G + + + +E +R E+ + E DL++ ++ ++L +
Sbjct: 1 ILVTGGTGFIGSHLVRRLLQEGYEVIVLGRRRRSESLNTGRIRFHEGDLTDPDALERLLA 60
Query: 57 KYKPTHVIHLAAMVGGLFHNMSHNLDFFRVNMKINDNVLDTSYKQGVKKVVSCLSTCIFP 116
+ +P VIHLAA G + DF R N+ +L+ + + GVK+ V S+ ++
Sbjct: 61 EVQPDAVIHLAAQSGV-GASFEDPADFIRANVLGTLRLLEAARRAGVKRFVFASSSEVYG 119
Query: 117 DKTTYPIDETMVHNGPPHPSNFGYSHAKRMLDVLNKAYYQQHGVTYTSVIPCNVFGPHDN 176
D PI E GP P Y+ AK + L +AY + +G+ + NV+GP +
Sbjct: 120 DVADPPITEDTPL-GPLSP----YAAAKLAAERLVEAYARAYGLRAVILRLFNVYGPGN- 173
Query: 177 YNLESSHVIPGLIRKLYDTIEKGKDQSVFESRARFPPGANSFGLDKLDLIPFSLFPFCFT 236
+ +HVIP LIR++ +
Sbjct: 174 PDPFVTHVIPALIRRILE------------------------------------------ 191
Query: 237 GGDEFKVLGTGKPLRQFIYSLDLARLFIWVLREYDSVEPI 276
G +LG G R F+Y D+AR + L D E
Sbjct: 192 -GKPILLLGDGTQRRDFLYVDDVARAILLALEHPDGGEIY 230
>gnl|CDD|223528 COG0451, WcaG, Nucleoside-diphosphate-sugar epimerases [Cell
envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 314
Score = 124 bits (313), Expect = 5e-33
Identities = 88/363 (24%), Positives = 139/363 (38%), Gaps = 65/363 (17%)
Query: 5 KIILVTGGTGLVGKAI-EKIVKEEEK---------RDDETWIFVSSKEADLSNLESTQQL 54
ILVTGG G +G + E+++ D V DL++ + +L
Sbjct: 1 MRILVTGGAGFIGSHLVERLLAAGHDVRGLDRLRDGLDPLLSGVEFVVLDLTDRDLVDEL 60
Query: 55 FSKYKPTHVIHLAAMVGGLFHNMSHNLDFFRVNMKINDNVLDTSYKQGVKKVVSCLST-- 112
K P VIHLAA N S +F VN+ N+L+ + GVK+ V S+
Sbjct: 61 A-KGVPDAVIHLAAQSSVPDSNASDPAEFLDVNVDGTLNLLEAARAAGVKRFV-FASSVS 118
Query: 113 CIFPDKTTYPIDETMVHNGPPHPSNFGYSHAKRMLDVLNKAYYQQHGVTYTSVIPCNVFG 172
++ D PIDE + GPP P N Y +K + L +AY + +G+ + P NV+G
Sbjct: 119 VVYGDPPPLPIDEDL---GPPRPLNP-YGVSKLAAEQLLRAYARLYGLPVVILRPFNVYG 174
Query: 173 PHDNYNLESSHVIPGLIRKLYDTIEKGKDQSVFESRARFPPGANSFGLDKLDLIPFSLFP 232
P D +L SS V+ IR+L
Sbjct: 175 PGDKPDL-SSGVVSAFIRQL---------------------------------------- 193
Query: 233 FCFTGGDEFKVLGTGKPLRQFIYSLDLARLFIWVLREYDSVEPIILSVDEKDEVTIAEVA 292
G + G G R F+Y D+A + L E + E+T+ E+A
Sbjct: 194 --LKGEPIIVIGGDGSQTRDFVYVDDVADALLLAL-ENPDGGVFNIG-SGTAEITVRELA 249
Query: 293 EAIANAFQFKGR-ITFDTNAADGQLKKTASNRKLRELRGPGFE-FTPFQQAVQESVAWFR 350
EA+A A K I + G L++ + G+E ++ + +++ W
Sbjct: 250 EAVAEAVGSKAPLIVYIPLGRRGDLREGKLLDISKARAALGWEPKVSLEEGLADTLEWLL 309
Query: 351 ENH 353
+
Sbjct: 310 KKL 312
>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 = 89.3 bits (222), Expect = 5e-21
Identities = 55/272 (20%), Positives = 93/272 (34%), Gaps = 76/272 (27%)
Query: 7 ILVTGGTGLVGKAI-EKIVKEEEKRDDETWIFVSSKEADLSNLESTQQLFSKYKPTHVIH 65
ILVTGG G +G + ++++ + + V + L V+H
Sbjct: 1 ILVTGGAGFIGSHLVRRLLERGHE------VVV------IDRL------------DVVVH 36
Query: 66 LAAMVGGLFHNMSHNLDFFRVNMKINDNVLDTSYKQGVKKVVSCLSTCIFPDKTTYPIDE 125
LAA+VG + + + F N+ N+L+ + K GVK+ V S ++ P +E
Sbjct: 37 LAALVGVPA-SWDNPDEDFETNVVGTLNLLEAARKAGVKRFVYASSASVYGSPEGLPEEE 95
Query: 126 TMVHNGPPHPSNFGYSHAKRMLDVLNKAYYQQHGVTYTSVIPCNVFGPHDNYNLESSHVI 185
PP P + Y +K + L ++Y + +G+ + NV+GP L V+
Sbjct: 96 ET----PPRPLSP-YGVSKLAAEHLLRSYGESYGLPVVILRLANVYGPGQRPRL--DGVV 148
Query: 186 PGLIRKLYDTIEKGKDQSVFESRARFPPGANSFGLDKLDLIPFSLFPFCFTGGDEFKVLG 245
IR+ G V G
Sbjct: 149 NDFIRRAL-------------------------------------------EGKPLTVFG 165
Query: 246 TGKPLRQFIYSLDLARLFIWVLREYDSVEPII 277
G R FI+ D+ R + L +
Sbjct: 166 GGNQTRDFIHVDDVVRAILHALENPLEGGGVY 197
>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 = 91.8 bits (228), Expect = 6e-21
Identities = 81/370 (21%), Positives = 133/370 (35%), Gaps = 81/370 (21%)
Query: 7 ILVTGGTGLVGKAI-EKIV----------------KEEEKRDDETWIFVSSKEADLSNLE 49
LVTG G +G + E++ + DDE F DL +E
Sbjct: 3 ALVTGAGGFIGSHLAERLKAEGHYVRGADWKSPEHMTQPTDDDE---FHL---VDLREME 56
Query: 50 STQQLFSKYKPTHVIHLAAMVGGLFHNMSHNLDFFRVNMKINDNVLDTSYKQGVKKVVSC 109
+ + HV HLAA +GG+ + S++ N IN N+L+ + GV++ +
Sbjct: 57 NCLKATEGVD--HVFHLAADMGGMGYIQSNHAVIMYNNTLINFNMLEAARINGVERFLFA 114
Query: 110 LSTCIFP-----DKTTYPIDETMVHNGPPHPSNFGYSHAKRMLDVLNKAYYQQHGVTYTS 164
S C++P + T + E P Y K + L + Y + +G+
Sbjct: 115 SSACVYPEFKQLETTVVRLREEDAWPAEPQD---AYGWEKLATERLCQHYNEDYGIETRI 171
Query: 165 VIPCNVFGPHDNYNLESSHVIPGLIRKLYDTIEKGKDQSVFESRARFPPGANSFGLDKLD 224
V N++GP ++ + RK V ++
Sbjct: 172 VRFHNIYGPRGTWDGGREKAPAAMCRK------------VATAK---------------- 203
Query: 225 LIPFSLFPFCFTGGDEFKVLGTGKPLRQFIYSLDLARLFIWVLREYDSVEPIILSVDEKD 284
GD F++ G G R F Y D L E D EP+ L DE
Sbjct: 204 ------------DGDRFEIWGDGLQTRSFTYIDDCVEGLR-RLMESDFGEPVNLGSDE-- 248
Query: 285 EVTIAEVAEAIANAFQFKGRITFDTNAADGQLKKTASNRKLRELRG--PGFEFTPFQQAV 342
V++ E+AE + + I T G + + N L+E G P TP ++ +
Sbjct: 249 MVSMNELAEMVLSFSGKPLEIIHHTPGPQGVRGRNSDNTLLKEELGWEPN---TPLEEGL 305
Query: 343 QESVAWFREN 352
+ + W +E
Sbjct: 306 RITYFWIKEQ 315
>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 = 73.8 bits (182), Expect = 7e-15
Identities = 68/365 (18%), Positives = 129/365 (35%), Gaps = 84/365 (23%)
Query: 7 ILVTGGTGLVGKAI-EKIVKE------------------EEKRDDETWIFVSSKEADLSN 47
+LVTGG G +G + E++++ E + + +I E D+ +
Sbjct: 2 VLVTGGAGFIGSHLVERLLERGHEVIVLDNLSTGKKENLPEVKPNVKFI-----EGDIRD 56
Query: 48 LESTQQLFSKYKPTHVIHLAAMVGGLFHNMSHNLDFFRVNMKINDNVLDTSYKQGVKKVV 107
E + F +V H AA + ++ + VN+ N+L+ + K GVK+ V
Sbjct: 57 DELVEFAFEG--VDYVFHQAAQ-ASVPRSIEDPIKDHEVNVLGTLNLLEAARKAGVKRFV 113
Query: 108 SCLSTCIFPDKTTYPIDETMVHNGPPHPSNFGYSHAKRMLDVLNKAYYQQHGVTYTSVIP 167
S+ ++ D P DE N P P Y+ +K ++ + + + +G+ S+
Sbjct: 114 YASSSSVYGDPPYLPKDEDHPPN-PLSP----YAVSKYAGELYCQVFARLYGLPTVSLRY 168
Query: 168 CNVFGPHDNYNLESSHVIPGLIRKLYDTIEKGKDQSVFESRARFPPGANSFGLDKLDLIP 227
NV+GP + N + VIP I +
Sbjct: 169 FNVYGPRQDPNGGYAAVIPIFIERALK--------------------------------- 195
Query: 228 FSLFPFCFTGGDEFKVLGTGKPLRQFIYSLDLARLFIWVLREYDSVEPIILSVDEKDEVT 287
G+ + G G+ R F Y D+ + + ++ +
Sbjct: 196 ----------GEPPTIYGDGEQTRDFTYVEDVVEANLLAA--TAGAGGEVYNIGTGKRTS 243
Query: 288 IAEVAEAIANAFQFKGRITFDTNAADGQLKKTASNRKLRELRGPGFEFTP---FQQAVQE 344
+ E+AE I + + A K ++L G + P F++ ++
Sbjct: 244 VNELAELIREILGKELEPVYAPPRPGDVRHSLADISKAKKLLG----WEPKVSFEEGLRL 299
Query: 345 SVAWF 349
+V WF
Sbjct: 300 TVEWF 304
>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 = 68.9 bits (169), Expect = 4e-13
Identities = 88/371 (23%), Positives = 134/371 (36%), Gaps = 81/371 (21%)
Query: 7 ILVTGGTGLVGKAIEKIVKEEEKRDDETWIFVSSKEADLSNLESTQQLFSKYKPTHVIHL 66
ILVTG TG +G + V+ + V S +D L+ + T L
Sbjct: 1 ILVTGATGFLGSNL---VRALLAQGYRVRALVRSG-SDAVLLDGLPVEVVEGDLTDAASL 56
Query: 67 AAMVGG---LFHNMS-------HNLDFFRVNMKINDNVLDTSYKQGVKKVVSCLSTCIFP 116
AA + G +FH + + +R N++ NVLD + + GV++VV S
Sbjct: 57 AAAMKGCDRVFHLAAFTSLWAKDRKELYRTNVEGTRNVLDAALEAGVRRVVHTSSIAALG 116
Query: 117 DKTTYPIDETMVHNGPPHPSNFGYSHAKRM--LDVLNKAYYQQHGVTYTSVIPCNVFGPH 174
IDET N P P++ Y +K + L+VL A V V P VFGP
Sbjct: 117 GPPDGRIDETTPWNERPFPND--YYRSKLLAELEVLEAAAEGLDVV---IVNPSAVFGPG 171
Query: 175 DNYNLESSHVIPGLIRKLYDTIEKGKDQSVFESRARFPPGANSFGLDKLDLIPFSLFPFC 234
D GL Y GK + PPG SF +D D+
Sbjct: 172 DEGP-----TSTGLDVLDYL---NGKLPAY-------PPGGTSF-VDVRDV--------- 206
Query: 235 FTGGDEFKVLG------TGKPLRQFIYS---LDLARLFIWVLREYDSVEPIILSVDEKDE 285
G G+ ++I L +LF + I V
Sbjct: 207 --------AEGHIAAMEKGRRGERYILGGENLSFKQLFETLAE--------ITGVKPPRR 250
Query: 286 VTIAEVAEAIANAFQFKGRITFD------TNAADGQLKKTASNRK-LRELRGPGFEFTPF 338
+ +A+A + K R+T A + S+ K REL G+ P
Sbjct: 251 TIPPWLLKAVAALSELKARLTGKPPLLTPRTARVLRRNYLYSSDKARREL---GYSPRPL 307
Query: 339 QQAVQESVAWF 349
++A+++++AW
Sbjct: 308 EEALRDTLAWL 318
>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 = 63.1 bits (154), Expect = 4e-11
Identities = 75/379 (19%), Positives = 129/379 (34%), Gaps = 97/379 (25%)
Query: 7 ILVTGGTGLVGKAI-EKIVKEEEK---------RDDETWIFVSSKE-ADLSNLESTQQLF 55
+LVTG G +G + E++++E + + + + + + +
Sbjct: 2 VLVTGADGFIGSHLTERLLREGHEVRALDIYNSFNSWGLLDNAVHDRFHFISGDVRDASE 61
Query: 56 SKY--KPTH-VIHLAAMVGGLFHNMSHN--LDFFRVNMKINDNVLDTSYKQGVKKVVSCL 110
+Y K V HLAA++ + S+ L + N+ NVL+ + K+VV
Sbjct: 62 VEYLVKKCDVVFHLAALIAIPY---SYTAPLSYVETNVFGTLNVLEAACVLYRKRVVH-T 117
Query: 111 STC-IFPDKTTYPIDETMVHNGPPHPS------NFGYSHAKRMLDVLNKAYYQQHGVTYT 163
ST ++ PIDE HP YS +K+ D L +Y + G+ T
Sbjct: 118 STSEVYGTAQDVPIDED-------HPLLYINKPRSPYSASKQGADRLAYSYGRSFGLPVT 170
Query: 164 SVIPCNVFGPHDNYNLESSHVIPGLIRKLYDTIEKGKDQSVFESRARFPPGANSFGLDKL 223
+ P N +GP + VIP +I +
Sbjct: 171 IIRPFNTYGP----RQSARAVIPTIISQRAIGQRLIN----------------------- 203
Query: 224 DLIPFSLFPFCFTGGDEFKVLGTGKPLRQFIYSLDLARLFIWVLREYDSV-EPI------ 276
LG G P R F + D AR FI +L ++V E I
Sbjct: 204 --------------------LGDGSPTRDFNFVKDTARGFIDILDAIEAVGEIINNGSGE 243
Query: 277 ILSVDEKDEVTIAEVAEAIANAFQFKGRITFDTNAADGQLKKTASNRKLRELRGPGFEFT 336
+S+ I E + R + + RK + L G +
Sbjct: 244 EISIGNPAVELIVEELGEMVLIVYDDHREYRPGYSEVERRI--PDIRKAKRLLG----WE 297
Query: 337 P---FQQAVQESVAWFREN 352
P + ++E++ WF++
Sbjct: 298 PKYSLRDGLRETIEWFKDQ 316
>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 = 61.2 bits (149), Expect = 2e-10
Identities = 56/220 (25%), Positives = 95/220 (43%), Gaps = 29/220 (13%)
Query: 7 ILVTGGTGLVG---------KAIEKIV-------KEEEKRDDETWIFVSSKEADLSNLES 50
ILVTGG G +G E ++ E E V+ E DL + E
Sbjct: 2 ILVTGGAGYIGSHTVRQLLESGHEVVILDNLSNGSREALPRGERITPVTFVEGDLRDREL 61
Query: 51 TQQLFSKYKPTHVIHLAAMVGGLFHNMSHNLDFFRVNMKINDNVLDTSYKQGVKKVVSCL 110
+LF ++K VIH A ++ + ++ L ++R N+ N+L+ + GVKK +
Sbjct: 62 LDRLFEEHKIDAVIHFAGLI-AVGESVQKPLKYYRNNVVGTLNLLEAMQQAGVKKFIFSS 120
Query: 111 STCIFPDKTTYPIDETMVHNGPPHPSN-FGYSH--AKRMLDVLNKAYYQQHGVTYTSVIP 167
S ++ + ++ PI E P P N +G S ++++L L KA +Y +
Sbjct: 121 SAAVYGEPSSIPISEDS----PLGPINPYGRSKLMSEQILRDLQKA---DPDWSYVILRY 173
Query: 168 CNVFGPHDNYNL-ESSHVIPGLIRKLYDTIEKGKDQ-SVF 205
NV G H + ++ E I LI +D+ ++F
Sbjct: 174 FNVAGAHPSGDIGEDPPGITHLIPYACQVAVGKRDKLTIF 213
>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 = 59.1 bits (144), Expect = 7e-10
Identities = 49/210 (23%), Positives = 86/210 (40%), Gaps = 46/210 (21%)
Query: 7 ILVTGGTGLVG---------------------KAIEKIVKEEEKRDDETWIFVSSKEADL 45
+LVTGG G +G + + EK E F E D+
Sbjct: 2 VLVTGGAGYIGSHTVVELLEAGYDVVVLDNLSNGHREALPRIEKIRIE---FY---EGDI 55
Query: 46 SNLESTQQLFSKYKPTHVIHLAAM--VGGLFHNMSHNLDFFRVNMKINDNVLDTSYKQGV 103
+ + ++F+++K VIH AA+ VG ++ L ++ N+ N+L+ GV
Sbjct: 56 RDRAALDKVFAEHKIDAVIHFAALKAVG---ESVQKPLKYYDNNVVGTLNLLEAMRAHGV 112
Query: 104 KKVV-SCLSTC-IFPDKTTYPIDETMVHNGPPHPSNFGYSHAKRMLDVLNKAYYQQHGVT 161
K V S S+ ++ + T PI E P +P+N Y K M++ + + + G+
Sbjct: 113 KNFVFS--SSAAVYGEPETVPITEEA----PLNPTN-PYGRTKLMVEQILRDLAKAPGLN 165
Query: 162 YTSVIPCNVFGPHDN-----YNLESSHVIP 186
Y + N G H + +++IP
Sbjct: 166 YVILRYFNPAGAHPSGLIGEDPQIPNNLIP 195
>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 = 58.7 bits (143), Expect = 9e-10
Identities = 82/382 (21%), Positives = 139/382 (36%), Gaps = 103/382 (26%)
Query: 7 ILVTGGTGLVGKA-IEKIVKE---------------------EEKRDDETWIFVSSKEAD 44
ILVTGG G +G + ++ + E+ + FV + D
Sbjct: 3 ILVTGGAGFIGSNFVRYLLNKYPDYKIINLDKLTYAGNLENLEDVSSSPRYRFV---KGD 59
Query: 45 LSNLESTQQLFSKYKPTHVIHLAAMVGGLFHNMSHN-------LDFFRVNMKINDNVLDT 97
+ + E +LF + K VIH AA SH F R N+ +L+
Sbjct: 60 ICDAELVDRLFEEEKIDAVIHFAAE--------SHVDRSISDPEPFIRTNVLGTYTLLEA 111
Query: 98 SYKQGVKKVVSCLSTCIFPDKTTYPIDET--MVHNGPPHPSNFGYSHAKRMLDVLNKAYY 155
+ K GVK+ V +ST D+ + + P P++ YS +K D+L +AY+
Sbjct: 112 ARKYGVKRFVH-IST----DEVYGDLLDDGEFTETSPLAPTS-PYSASKAAADLLVRAYH 165
Query: 156 QQHGVTYTSVIPCNVFGPHDNYNLESSHVIPGLIRKLYDTIEKGKDQSVFESRARFPPGA 215
+ +G+ N +GP+ +IP I
Sbjct: 166 RTYGLPVVITRCSNNYGPYQF----PEKLIPLFILNA----------------------- 198
Query: 216 NSFGLDKLDLIPFSLFPFCFTGGDEFKVLGTGKPLRQFIYSLDLARLFIWVLREYDSVEP 275
LD L + G G +R ++Y D AR VL + E
Sbjct: 199 ----LDGKPL----------------PIYGDGLNVRDWLYVEDHARAIELVLEKGRVGE- 237
Query: 276 IILSVDEKDEVTIAEVAEAIANAF-QFKGRITF--DTNAADGQLKKTASNRKLRELRGPG 332
I ++ +E+T E+ + I + + IT+ D D + +S K+R G
Sbjct: 238 -IYNIGGGNELTNLELVKLILELLGKDESLITYVKDRPGHDRRYAIDSS--KIRRELGW- 293
Query: 333 FEFTPFQQAVQESVAWFRENHS 354
F++ ++++V W+ EN
Sbjct: 294 RPKVSFEEGLRKTVRWYLENRW 315
>gnl|CDD|224012 COG1087, GalE, UDP-glucose 4-epimerase [Cell envelope biogenesis,
outer membrane].
Length = 329
Score = 58.3 bits (142), Expect = 1e-09
Identities = 47/201 (23%), Positives = 82/201 (40%), Gaps = 31/201 (15%)
Query: 7 ILVTGGTGLVGK--AIEKIVKEEE----------KRDDETWIFVSSKEADLSNLESTQQL 54
+LVTGG G +G + + E + + E DL + +
Sbjct: 3 VLVTGGAGYIGSHTVRQLLKTGHEVVVLDNLSNGHKIALLKLQFKFYEGDLLDRALLTAV 62
Query: 55 FSKYKPTHVIHLAAM--VGGLFHNMSHNLDFFRVNMKINDNVLDTSYKQGVKKVV-SCLS 111
F + K V+H AA VG ++ + L ++ N+ N+++ + GVKK + S S
Sbjct: 63 FEENKIDAVVHFAASISVG---ESVQNPLKYYDNNVVGTLNLIEAMLQTGVKKFIFS--S 117
Query: 112 TC-IFPDKTTYPIDETMVHNGPPHPSNFGYSHAKRMLDVLNKAYYQQHGVTYTSVIPCNV 170
T ++ + TT PI ET P P N Y +K M + + + + + + NV
Sbjct: 118 TAAVYGEPTTSPISETS----PLAPIN-PYGRSKLMSEEILRDAAKANPFKVVILRYFNV 172
Query: 171 FGPHDNYNL-ES----SHVIP 186
G + L + + +IP
Sbjct: 173 AGACPDGTLGQRYPGATLLIP 193
>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 = 57.1 bits (138), Expect = 4e-09
Identities = 53/226 (23%), Positives = 91/226 (40%), Gaps = 41/226 (18%)
Query: 7 ILVTGGTGLVGKAIEKIVKEEEKRDDETWIFVSSKEA--------------DLSNLESTQ 52
+LVTGG+G G+ + K + E ++ EA D+++ +
Sbjct: 2 VLVTGGSGFFGERLVKQLLERGGTYVRSFDIAPPGEALSAWQHPNIEFLKGDITDRNDVE 61
Query: 53 QLFSKYKPTHVIHLAAMVGGLFHNMSHNLD-FFRVNMKINDNVLDTSYKQGVKKVV-SCL 110
Q S V H AA+V D ++ VN+ NVLD + GV+K V +
Sbjct: 62 QALSGA--DCVFHTAAIVPLA-----GPRDLYWEVNVGGTQNVLDACQRCGVQKFVYTSS 114
Query: 111 STCIFPDKTTYPIDETMVHNGPPHPS--NFGYSHAKRMLDVLNKAYYQQHGVTYTSVIPC 168
S+ IF + + DET+ P+P + Y+ K + +++ + + ++ P
Sbjct: 115 SSVIFGGQNIHNGDETL-----PYPPLDSDMYAETKAIAEIIVLEANGRDDLLTCALRPA 169
Query: 169 NVFGPHDNYNLESSHVIPGLIRKLYDTIEKGKDQSVFES-RARFPP 213
+FGP D GL+ L++ EKG + VF
Sbjct: 170 GIFGPGD----------QGLVPILFEWAEKGLVKFVFGRGNNLVDF 205
>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 = 56.1 bits (136), Expect = 6e-09
Identities = 44/213 (20%), Positives = 87/213 (40%), Gaps = 33/213 (15%)
Query: 7 ILVTGGTGLVGKAIEKIVKEEEKRDDETWIFVSSKEA-----DLSNLESTQQLFSKYKPT 61
IL+TG TG++G+A+ +++KE I A DL++ ++ ++ YKP
Sbjct: 2 ILITGATGMLGRALVRLLKE----RGYEVIGTGRSRASLFKLDLTDPDAVEEAIRDYKPD 57
Query: 62 HVIHLAAMVGGLFHNMSHNLDF-FRVNMKINDNVLDTSYKQGVKKVVSCLST-CIFPDKT 119
+I+ AA + + +RVN+ +N+ + + G + + +ST +F D
Sbjct: 58 VIINCAAYTR--VDKCESDPELAYRVNVLAPENLARAAKEVGARLIH--ISTDYVF-DGK 112
Query: 120 TYPIDETMVHNGPPHPSNFGYSHAKRMLDVLNKAYYQQHGVTYTSVIPCNVFGPHDNYNL 179
P E P+P N Y +K + +V ++ + TS + +G N
Sbjct: 113 KGPYKEE----DAPNPLNV-YGKSKLLGEVAVLNANPRYLILRTSWL----YGELKNGE- 162
Query: 180 ESSHVIPGLIRKLYDTIEKGKDQSVFESRARFP 212
+ + + K+ +V + P
Sbjct: 163 -------NFVEWMLRLAAERKEVNVVHDQIGSP 188
>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 = 55.3 bits (134), Expect = 1e-08
Identities = 57/230 (24%), Positives = 91/230 (39%), Gaps = 58/230 (25%)
Query: 5 KIILVTGGTGLVGKAI-EKIVKEEEKR-----DDETWIFVSSKE--------------AD 44
K ILVTGG G +G + +I+K K+ DE + +E D
Sbjct: 3 KTILVTGGAGSIGSELVRQILKFGPKKLIVFDRDENKLHELVRELRSRFPHDKLRFIIGD 62
Query: 45 LSNLESTQQLFSKYKPTHVIHLAAMVGGLFH--NMSHN-LDFFRVNMKINDNVLDTSYKQ 101
+ + E ++ F + P V H AA L H +M N + + N+ NV+D + +
Sbjct: 63 VRDKERLRRAFKERGPDIVFHAAA----LKHVPSMEDNPEEAIKTNVLGTKNVIDAAIEN 118
Query: 102 GVKKVVSCLSTCIFPDKTTYPIDETMVHNGPPHPSNFGYSHAKRMLDVLNKAYYQQHGVT 161
GV+K V C+ST DK P+ N KR+ + L A + T
Sbjct: 119 GVEKFV-CIST----DKAVNPV-------------NV-MGATKRVAEKLLLAKNEYSSST 159
Query: 162 -YTSVIPCNVFGPHDNYNLESSHVIPGLIRKLYDTIEKGKDQSVFESRAR 210
+++V NV G V+P ++ I+KG +V +
Sbjct: 160 KFSTVRFGNVLG-------SRGSVLPLFKKQ----IKKGGPLTVTDPDMT 198
>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 = 53.9 bits (130), Expect = 3e-08
Identities = 42/184 (22%), Positives = 73/184 (39%), Gaps = 25/184 (13%)
Query: 7 ILVTGGTGLVGKA----------IEKIVKEEEKRDDETWIFVSSKEADLSNLESTQQLFS 56
ILVTG G +G+ + + + +R + V D+ + + +F
Sbjct: 1 ILVTGAAGGLGRLLARRLAASPRVIGVDGLDRRRPPGSPPKVEYVRLDIRDPAA-ADVFR 59
Query: 57 KYKPTHVIHLAAMVGGLFHNMSHNLDFFRVNMKINDNVLDTSYKQGVKKVVSCLSTCIF- 115
+ + V+HLA ++ R+N+ NVLD GV +VV S ++
Sbjct: 60 EREADAVVHLAFILDPPRDGAER----HRINVDGTQNVLDACAAAGVPRVVVTSSVAVYG 115
Query: 116 --PDKTTYPIDETMVHNGPPHPS-NFGYSHAKRMLDVLNKAYYQQH-GVTYTSVIPCNVF 171
PD P+ E + P S F YS K ++ L + ++H + T + P +
Sbjct: 116 AHPDNPA-PLTE----DAPLRGSPEFAYSRDKAEVEQLLAEFRRRHPELNVTVLRPATIL 170
Query: 172 GPHD 175
GP
Sbjct: 171 GPGT 174
>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 = 52.7 bits (127), Expect = 8e-08
Identities = 49/187 (26%), Positives = 77/187 (41%), Gaps = 24/187 (12%)
Query: 7 ILVTGGTGLVGKAIEK--IVKEEEKR---DDETWIFVSSKEADLSNLESTQQLFSKYKPT 61
+LVTG G +G+A+ + + EE R + S A+L +++S LF
Sbjct: 2 VLVTGANGFIGRALVDKLLSRGEEVRIAVRNAENAEPSVVLAELPDIDSFTDLFLGV--D 59
Query: 62 HVIHLAAMVGGLFHNMSHN-----LDFFRVNMKINDNVLDTSYKQGVKKVVSCLST--CI 114
V+HLAA V H M+ D+ +VN ++ + + +QGVK+ V LS+
Sbjct: 60 AVVHLAARV----HVMNDQGADPLSDYRKVNTELTRRLARAAARQGVKRFVF-LSSVKVN 114
Query: 115 FPDKTTYPIDETMVHNGPPHPSNFGYSHAKRMLDVLNKAYYQQHGVTYTSVIPCNVFGPH 174
P DET PP P + Y +K + G+ + P V+GP
Sbjct: 115 GEGTVGAPFDETD----PPAPQD-AYGRSKLEAERALLELGASDGMEVVILRPPMVYGPG 169
Query: 175 DNYNLES 181
N
Sbjct: 170 VRGNFAR 176
>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 = 52.7 bits (127), Expect = 8e-08
Identities = 55/195 (28%), Positives = 83/195 (42%), Gaps = 36/195 (18%)
Query: 8 LVTGGTGLVGKAIEK-IVKEEEKRDDETW--IFVSSKEADLSNLE----------STQQL 54
LVTGG G +G+ I + +++E E ++ + F D S L+ Q L
Sbjct: 1 LVTGGGGFLGRHIVRLLLREGELQEVRVFDLRFSPELLEDFSKLQVITYIEGDVTDKQDL 60
Query: 55 FSKYKPTH-VIHLAA--MVGGLFHNMSHNLDFFRVNMKINDNVLDTSYKQGVKKVVSCLS 111
+ + VIH AA V G + + +VN+K NVLD K GV+ +V S
Sbjct: 61 RRALQGSDVVIHTAAIIDVFGKAYRDT----IMKVNVKGTQNVLDACVKAGVRVLVYTSS 116
Query: 112 -TCIFPDKTTYPI---DETMVHNGPPHPSNFG--YSHAKRMLD--VL--NKAYYQQHGVT 161
+ P+ PI DET P+ S Y +K + + VL N + + G
Sbjct: 117 MEVVGPNSYGQPIVNGDETT-----PYESTHQDPYPESKALAEKLVLKANGSTLKNGGRL 171
Query: 162 YTSVI-PCNVFGPHD 175
YT + P +FG D
Sbjct: 172 YTCALRPAGIFGEGD 186
>gnl|CDD|217199 pfam02719, Polysacc_synt_2, Polysaccharide biosynthesis protein.
This is a family of diverse bacterial polysaccharide
biosynthesis proteins including the CapD protein, WalL
protein mannosyl-transferase and several putative
epimerases (e.g. WbiI).
Length = 280
Score = 52.5 bits (127), Expect = 9e-08
Identities = 33/139 (23%), Positives = 61/139 (43%), Gaps = 30/139 (21%)
Query: 7 ILVTGGTGLVGKAI-EKIVKEEEKR-----DDETWIFVSSKE--------------ADLS 46
+LVTGG G +G + +I+K K+ DE ++ +E D+
Sbjct: 1 VLVTGGGGSIGSELCRQILKFNPKKIILFSRDEFKLYEIRQELRQEYNDPKLRFFIGDVR 60
Query: 47 NLESTQQLFSKYKPTHVIHLAAM--VGGLFHNMSHNLDFFRVNMKINDNVLDTSYKQGVK 104
+ E ++ ++ V H AA+ V + +N ++ + N+ +NV + + + GV+
Sbjct: 61 DRERLERAMEQHGVDTVFHAAALKHVPLVEYNP---MEAIKTNVLGTENVAEAAIENGVE 117
Query: 105 KVVSCLSTCIFPDKTTYPI 123
K V +ST DK P
Sbjct: 118 KFV-LIST----DKAVNPT 131
>gnl|CDD|224016 COG1091, RfbD, dTDP-4-dehydrorhamnose reductase [Cell envelope
biogenesis, outer membrane].
Length = 281
Score = 51.9 bits (125), Expect = 1e-07
Identities = 40/179 (22%), Positives = 73/179 (40%), Gaps = 34/179 (18%)
Query: 7 ILVTGGTGLVGKAIEKIVKEEEKRDDETWIFVSSKEADLSNLESTQQLFSKYKPTHVIHL 66
IL+TG G +G + + + E + I E D+++ ++ ++ + +P VI+
Sbjct: 3 ILITGANGQLGTELRRALPGEFE-----VIATDRAELDITDPDAVLEVIRETRPDVVINA 57
Query: 67 AAMVGGLFHNMSHNLDF--------FRVNMKINDNVLDTSYKQGVKKVVSCLST-CIFPD 117
AA +D F VN +N+ + + G + V +ST +F
Sbjct: 58 AAY---------TAVDKAESEPELAFAVNATGAENLARAAAEVGARLVH--ISTDYVFDG 106
Query: 118 KTTYPIDETMVHNGPPHPSNFGYSHAKRMLDVLNKAYYQQHGVTYTSVIPCNVFGPHDN 176
+ P ET P+P N Y +K + +A +H + TS V+G + N
Sbjct: 107 EKGGPYKET----DTPNPLNV-YGRSKLAGEEAVRAAGPRHLILRTSW----VYGEYGN 156
>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 = 51.8 bits (125), Expect = 2e-07
Identities = 17/62 (27%), Positives = 32/62 (51%), Gaps = 4/62 (6%)
Query: 7 ILVTGGTGLVGKAIEKIVKEEEKRDDETWIFVSSKEADLSNLESTQQLFSKYKPTHVIHL 66
ILVTG G +G+ + +++ E + + E DL++ E+ L + +P V++
Sbjct: 1 ILVTGANGQLGRELTRLLAER----GVEVVALDRPELDLTDPEAVAALVREARPDVVVNA 56
Query: 67 AA 68
AA
Sbjct: 57 AA 58
>gnl|CDD|224011 COG1086, COG1086, Predicted nucleoside-diphosphate sugar epimerases
[Cell envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 588
Score = 50.7 bits (122), Expect = 6e-07
Identities = 53/225 (23%), Positives = 84/225 (37%), Gaps = 58/225 (25%)
Query: 1 MAEEKIILVTGGTGLVGKAI-EKIVKEEEKR-----DDETWIFVSSKE------------ 42
M K +LVTGG G +G + +I+K K DE +++ E
Sbjct: 247 MLTGKTVLVTGGGGSIGSELCRQILKFNPKEIILFSRDEYKLYLIDMELREKFPELKLRF 306
Query: 43 --ADLSNLESTQQLFSKYKPTHVIHLAAM--VGGLFHNMSHNLDFFRVNMKINDNVLDTS 98
D+ + + ++ +K V H AA+ V + +N + + N+ +NV + +
Sbjct: 307 YIGDVRDRDRVERAMEGHKVDIVFHAAALKHVPLVEYNP---EEAIKTNVLGTENVAEAA 363
Query: 99 YKQGVKKVVSCLSTCIFPDKTTYPIDETMVHNGPPHPSNFGYSHAKRMLDVLNKAY---Y 155
K GVKK V +ST DK P + KR+ + L +A
Sbjct: 364 IKNGVKKFV-LIST----DKAVNPTNV--------------MGATKRLAEKLFQAANRNV 404
Query: 156 QQHGVTYTSVIPCNVFGPHDNYNLESSHVIPGLIRKLYDTIEKGK 200
G + V NV G VIP L +K I +G
Sbjct: 405 SGTGTRFCVVRFGNVLG-------SRGSVIP-LFKKQ---IAEGG 438
>gnl|CDD|200381 TIGR04130, FnlA, UDP-N-acetylglucosamine
4,6-dehydratase/5-epimerase. The FnlA enzyme is the
first step in the biosynthesis of UDP-FucNAc from
UDP-GlcNAc in E. coli (along with FnlB and FnlC). The
proteins identified by this model include FnlA homologs
in the O-antigen clusters of O4, O25, O26, O29 (Shigella
D11), O118, O145 and O172 serotype strains, all of which
produce O-antigens containing FucNAc (or the further
modified FucNAm). A homolog from Pseudomonas aerugiosa
serotype O11, WbjB, also involved in the biosynthesis of
UDP-FucNAc has been characterized and is now believed to
carry out both the initial 4,6-dehydratase reaction and
the subsequent epimerization of the resulting methyl
group at C-5. A phylogenetic tree of related sequences
shows a distinct clade of enzymes involved in the
biosynthesis of UDP-QuiNAc (Qui=qinovosamine). This
clade appears to be descendant from the common ancestor
of the Pseudomonas and E. coli fucose-biosynthesis
enzymes. It has been hypothesized that the first step in
the biosynthesis of these two compounds may be the same,
and thus that these enzymes all have the same function.
At present, lacking sufficient confirmation of this, the
current model trusted cutoff only covers the tree
segment surrounding the E. coli genes. The clades
containing the Pseudomonas and QuiNAc biosynthesis
enzymes score above the noise cutoff. Immediately below
the noise cutoff are enzymes involved in the
biosynthesis of UDP-RhaNAc (Rha=rhamnose), which again
may or may not produce the same product.
Length = 337
Score = 48.4 bits (115), Expect = 2e-06
Identities = 41/137 (29%), Positives = 72/137 (52%), Gaps = 18/137 (13%)
Query: 1 MAEEKIILVTGGTGLVGKAI-----EKIVKE-------EEKRDDETWIFVSSK-EADLSN 47
M ++KI+L+TGGTG G A+ + +KE E+K+DD + +SK + + +
Sbjct: 1 MFKDKILLITGGTGSFGNAVLRRFLDTDIKEIRIFSRDEKKQDDMRKKYNNSKLKFYIGD 60
Query: 48 LESTQQLFSKYKPTHVIHLAAMVGGLFHNMSHNLDFFRVNMKINDNVLDTSYKQGVKKVV 107
+ + + + + I+ AA + + H ++ + N+ +NVL+ + GVK+VV
Sbjct: 61 VRDYRSILNATRGVDFIYHAAALKQVPSCEFHPMEAVKTNVLGTENVLEAAIANGVKRVV 120
Query: 108 SCLSTCIFPDKTTYPID 124
CLST DK YPI+
Sbjct: 121 -CLST----DKAVYPIN 132
>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 = 46.6 bits (111), Expect = 8e-06
Identities = 49/202 (24%), Positives = 94/202 (46%), Gaps = 39/202 (19%)
Query: 8 LVTGGTGLVGKA-IEKIVKEEE------------KRDDETWIFVSSKEADLSNLESTQQL 54
LV GG+G +G+ +E++++ + D + V DL++ + ++
Sbjct: 3 LVVGGSGFLGRHLVEQLLRRGNPTVHVFDIRPTFELDPSSSGRVQFHTGDLTDPQDLEKA 62
Query: 55 FSKYKPTHVIHLAAMVGGLFHNMSHNLDFFRVNMKINDNVLDTSYKQGVKKVVSCLS-TC 113
F++ P V H A+ G S++ +++VN++ NV++ K GVKK+V S +
Sbjct: 63 FNEKGPNVVFHTASPDHG-----SNDDLYYKVNVQGTRNVIEACRKCGVKKLVYTSSASV 117
Query: 114 IFPDKTTYPIDETMVHNGPPHPSNF--GYSHAK----RMLDVLNKAYYQQHGVTYTSVIP 167
+F + DE++ P+P Y+ K ++ VL KA + G+ ++ P
Sbjct: 118 VFNGQDIINGDESL-----PYPDKHQDAYNETKALAEKL--VL-KANDPESGLLTCALRP 169
Query: 168 CNVFGPHDNYNLESSHVIPGLI 189
+FGP D ++PGL+
Sbjct: 170 AGIFGPGD------RQLVPGLL 185
>gnl|CDD|224013 COG1088, RfbB, dTDP-D-glucose 4,6-dehydratase [Cell envelope
biogenesis, outer membrane].
Length = 340
Score = 44.9 bits (107), Expect = 3e-05
Identities = 47/207 (22%), Positives = 76/207 (36%), Gaps = 64/207 (30%)
Query: 7 ILVTGGTGLVGKA-IEKIVKEEEKR---------------------DDETWIFVSSKEAD 44
ILVTGG G +G + I+ + D + FV + D
Sbjct: 3 ILVTGGAGFIGSNFVRYILNKHPDDHVVNLDKLTYAGNLENLADVEDSPRYRFV---QGD 59
Query: 45 LSNLESTQQLFSKYKPTHVIHLAAMVGGLFHNMSHN-------LDFFRVNMKINDNVLDT 97
+ + E +LF +Y+P V+H AA SH F + N+ +L+
Sbjct: 60 ICDRELVDRLFKEYQPDAVVHFAA--------ESHVDRSIDGPAPFIQTNVVGTYTLLEA 111
Query: 98 S--YKQGVKKV-VS--------CLSTCIFPDKTTYPIDETMVHNGPPHPSNFGYSHAKRM 146
+ Y + +S L F + T Y +PS+ YS +K
Sbjct: 112 ARKYWGKFRFHHISTDEVYGDLGLDDDAFTETTPY------------NPSS-PYSASKAA 158
Query: 147 LDVLNKAYYQQHGVTYTSVIPCNVFGP 173
D+L +AY + +G+ T N +GP
Sbjct: 159 SDLLVRAYVRTYGLPATITRCSNNYGP 185
>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 = 44.2 bits (105), Expect = 5e-05
Identities = 50/201 (24%), Positives = 78/201 (38%), Gaps = 28/201 (13%)
Query: 7 ILVTGGTGLVGK-AIEKIVKEEEK----------RDDETWIFVSSKEADL--SNLESTQQ 53
ILVTGG G +G ++++++E + R + +K +L T
Sbjct: 2 ILVTGGAGFIGSHLVDRLLEEGNEVVVVDNLSSGRRENIEPEFENKAFRFVKRDLLDTAD 61
Query: 54 LFSKYKPTHVIHLAAMVGGLFHNMSHNLDF-FRVNMKINDNVLDTSYKQGVKKVVSCLST 112
+K V HLAA + + D N+ NVL+ GVK++V S+
Sbjct: 62 KVAKKDGDTVFHLAANPD--VRLGATDPDIDLEENVLATYNVLEAMRANGVKRIVFASSS 119
Query: 113 CIFPDKTTYPIDETMVHNGPPHPSNFGYSHAKRMLDVLNKAYYQQHGVTYTSVIPCNVFG 172
++ + P E + PP P + Y +K + L AY G N+ G
Sbjct: 120 TVYGEAKVIPTPE----DYPPLPISV-YGASKLAAEALISAYAHLFGFQAWIFRFANIVG 174
Query: 173 PHDNYNLESSH-VIPGLIRKL 192
P S+H VI I KL
Sbjct: 175 P------RSTHGVIYDFINKL 189
>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 = 44.0 bits (104), Expect = 6e-05
Identities = 44/212 (20%), Positives = 80/212 (37%), Gaps = 39/212 (18%)
Query: 8 LVTGGTGLVGKAIEKIVKEEEKRDDETWIFVSSKEADLSNLESTQQLFSKY-------KP 60
LVTGG G +G+ I +++ E ++ E + + +L Q + K
Sbjct: 3 LVTGGGGFLGQHIIRLLLERKEELKEIRVLDKAFGPELIEHFEKSQGKTYVTDIEGDIKD 62
Query: 61 THVIHLA-AMVGGLFHNMS--------HNLDFFRVNMKINDNVLDTSYKQGVKKVV--SC 109
+ A V + H + + + VN+ VL+ + VK++V S
Sbjct: 63 LSFLFRACQGVSVVIHTAAIVDVFGPPNYEELEEVNVNGTQAVLEACVQNNVKRLVYTSS 122
Query: 110 LSTCIFPDKTTYPI----DETMVHNGPPHPSNFGYSHAKRMLD--VL--NKAYYQQHGVT 161
+ P+ PI ++T + P Y+ +K + + VL N A +Q G
Sbjct: 123 IEVA-GPNFKGRPIFNGVEDTPYEDTSTPP----YASSKLLAENIVLNANGAPLKQGGYL 177
Query: 162 YTSVI-PCNVFGPHDNYNLESSHVIPGLIRKL 192
T + P ++G E SH + + L
Sbjct: 178 VTCALRPMYIYG-------EGSHFLTEIFDFL 202
>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 = 41.6 bits (98), Expect = 2e-04
Identities = 39/177 (22%), Positives = 66/177 (37%), Gaps = 34/177 (19%)
Query: 7 ILVTGGTGLVGKAIEK-----------IVKEEEKRDDETWIFVSSKEADLSNLESTQQLF 55
IL+ G TG +G+A+ + +V+ ++ E V+ E DL +L+S
Sbjct: 1 ILILGATGFIGRALARELLEQGHEVTLLVRNTKRLSKEDQEPVAVVEGDLRDLDSLSDAV 60
Query: 56 SKYKPTHVIHLAAMVGGLFHNMSHNLDFFRVNMKINDNVLDTSYKQGVKKVVSCLSTCIF 115
VIHLA G + + + NVL+ + + GVK + S +
Sbjct: 61 Q--GVDVVIHLA----GAPRDTRDFCEVDVEGTR---NVLEAAKEAGVKHFIFISSLGAY 111
Query: 116 PDKTTYPIDETMVHNGPPHPSNFGYSHAKRMLDVLNKAYYQQHGVTYTSVIPCNVFG 172
D P PS+ Y K + + + + YT V P ++G
Sbjct: 112 GDLHEE---------TEPSPSSP-YLAVKAKTEAVLREA----SLPYTIVRPGVIYG 154
>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 = 41.9 bits (99), Expect = 3e-04
Identities = 75/364 (20%), Positives = 138/364 (37%), Gaps = 77/364 (21%)
Query: 5 KIILVTGGTGLVGKAI-EKIVKEEEK---RDDETWIFVSSKEADLSNLES---------- 50
K IL+TGG G +G + ++++++ + D+ F + ++ ++ +L
Sbjct: 1 KRILITGGAGFLGSHLCDRLLEDGHEVICVDN----FFTGRKRNIEHLIGHPNFEFIRHD 56
Query: 51 -TQQLFSKYKPTHVIHLAAMVGGLFHNMSHNLDFFRVNMKINDNVLDTSYKQGVKKVVSC 109
T+ L+ + + HLA H + + + N+ N+L + + G + +++
Sbjct: 57 VTEPLYLEVD--QIYHLACPASP-VHYQYNPIKTLKTNVLGTLNMLGLAKRVGARVLLAS 113
Query: 110 LSTCIFPDKTTYPIDETMVHNGPPHPSNFGYSHAKRMLDVLNKAYYQQHGVTYTSVIPCN 169
S ++ D +P E+ N P Y KR+ + L AY++QHGV N
Sbjct: 114 TSE-VYGDPEVHPQPESYWGNVNPIGPRSCYDEGKRVAETLCMAYHRQHGVDVRIARIFN 172
Query: 170 VFGP--HDNYNLESSHVIPGLIRKLYDTIEKGKDQSVFESRARFPPGANSFGLDKLDLIP 227
+GP H N V+ I + +G+ +V+
Sbjct: 173 TYGPRMHPND----GRVVSNFIVQAL----RGEPITVY---------------------- 202
Query: 228 FSLFPFCFTGGDEFKVLGTGKPLRQFIYSLDLARLFIWVLREYDSVEPIILSVDEKDEVT 287
G G R F Y DL I ++ P+ L E E T
Sbjct: 203 -----------------GDGTQTRSFQYVSDLVEGLIRLMNSDYFGGPVNLGNPE--EFT 243
Query: 288 IAEVAEAIANAFQFKGRITFDTNAADGQLKKTASNRKLRELRGPGFEFT-PFQQAVQESV 346
I E+AE + K I F D ++ K +EL G+E P ++ ++ ++
Sbjct: 244 ILELAELVKKLTGSKSEIVFLPLPEDDPKRRRPDISKAKELL--GWEPKVPLEEGLRRTI 301
Query: 347 AWFR 350
+FR
Sbjct: 302 EYFR 305
>gnl|CDD|178298 PLN02695, PLN02695, GDP-D-mannose-3',5'-epimerase.
Length = 370
Score = 40.9 bits (96), Expect = 6e-04
Identities = 34/133 (25%), Positives = 61/133 (45%), Gaps = 24/133 (18%)
Query: 2 AEEKI-ILVTGGTGLVGKAIEKIVKEEE--------KRDDETWIFVSSKE-------ADL 45
EK+ I +TG G + I + +K E K+++ +S DL
Sbjct: 18 PSEKLRICITGAGGFIASHIARRLKAEGHYIIASDWKKNE----HMSEDMFCHEFHLVDL 73
Query: 46 SNLESTQQLFSKYKPTHVIHLAAMVGGL-FHNMSHNLDFFRVNMKINDNVLDTSYKQGVK 104
+E+ ++ HV +LAA +GG+ F +H++ + N I+ N+L+ + GVK
Sbjct: 74 RVMENCLKVTKGVD--HVFNLAADMGGMGFIQSNHSVIMYN-NTMISFNMLEAARINGVK 130
Query: 105 KVVSCLSTCIFPD 117
+ S CI+P+
Sbjct: 131 RFFYASSACIYPE 143
>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 = 39.3 bits (92), Expect = 0.002
Identities = 45/195 (23%), Positives = 78/195 (40%), Gaps = 39/195 (20%)
Query: 7 ILVTGGTGLVGKA-IEKIVKEEEKR---------------------DDETWIFVSSKEAD 44
ILVTGG G +G + I+ E D+ + FV + D
Sbjct: 2 ILVTGGAGFIGSNFVRYILNEHPDAEVIVLDKLTYAGNLENLADLEDNPRYRFV---KGD 58
Query: 45 LSNLESTQQLFSKYKPTHVIHLAAMVGGLFH---NMSHNLDFFRVNMKINDNVLDTSYKQ 101
+ + E +LF++++P V+H AA H ++S F N+ +L+ K
Sbjct: 59 IGDRELVSRLFTEHQPDAVVHFAAES----HVDRSISGPAAFIETNVVGTYTLLEAVRKY 114
Query: 102 GVKKVVSCLSTCIFPDKTTYPI--DETMVHNGPPHPSNFGYSHAKRMLDVLNKAYYQQHG 159
+ +ST D+ + + P PS+ YS +K D L +AY++ +G
Sbjct: 115 WHEFRFHHIST----DEVYGDLEKGDAFTETTPLAPSS-PYSASKAASDHLVRAYHRTYG 169
Query: 160 VTYTSVIPCNVFGPH 174
+ N +GP+
Sbjct: 170 LPALITRCSNNYGPY 184
>gnl|CDD|235500 PRK05557, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Validated.
Length = 248
Score = 38.6 bits (91), Expect = 0.003
Identities = 23/116 (19%), Positives = 45/116 (38%), Gaps = 28/116 (24%)
Query: 1 MAEEKIILVTGGTGLVGKAI-EKIVKEE---------EKRDDETWI---------FVSSK 41
E K+ LVTG + +G+AI E++ + + E + ++ +
Sbjct: 2 SLEGKVALVTGASRGIGRAIAERLAAQGANVVINYASSEAGAEALVAEIGALGGKALAVQ 61
Query: 42 EADLSNLESTQQLFSKYKPTH-----VIHLAA-MVGGLFHNMSHNLDFFRVNMKIN 91
D+S+ ES ++ + K +++ A L M D+ RV + N
Sbjct: 62 -GDVSDAESVERAVDEAKAEFGGVDILVNNAGITRDNLLMRMKEE-DWDRV-IDTN 114
>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 = 38.1 bits (89), Expect = 0.005
Identities = 33/132 (25%), Positives = 64/132 (48%), Gaps = 5/132 (3%)
Query: 42 EADLSNLESTQQLFSKYKPTHVIHLAAMVGGLFHNMSHNLDFFRVNMKINDNVLDTSYKQ 101
+ DL + E+ ++LF ++ VIHLAA G+ +++ + + N+ N+L+
Sbjct: 59 KGDLEDREALRRLFKDHEFDAVIHLAAQ-AGVRYSLENPHAYVDSNIVGFLNLLELCRHF 117
Query: 102 GVKKVVSCLSTCIFPDKTTYPIDETMVHNGPPHPSNFGYSHAKRMLDVLNKAYYQQHGVT 161
GVK +V S+ ++ T P E + HP + Y+ K+ +++ Y +G+
Sbjct: 118 GVKHLVYASSSSVYGLNTKMPFSE---DDRVDHPISL-YAATKKANELMAHTYSHLYGIP 173
Query: 162 YTSVIPCNVFGP 173
T + V+GP
Sbjct: 174 TTGLRFFTVYGP 185
>gnl|CDD|200085 TIGR01214, rmlD, dTDP-4-dehydrorhamnose reductase. This enzyme
catalyzes the last of 4 steps in making dTDP-rhamnose,
a precursor of LPS core antigen, O-antigen, etc [Cell
envelope, Biosynthesis and degradation of surface
polysaccharides and lipopolysaccharides].
Length = 287
Score = 37.8 bits (88), Expect = 0.005
Identities = 15/64 (23%), Positives = 34/64 (53%), Gaps = 4/64 (6%)
Query: 7 ILVTGGTGLVGKAIEKIVKEEEKRDDETWIFVSSKEADLSNLESTQQLFSKYKPTHVIHL 66
IL+TG G +G+ + + + E + + ++ + DL++ E+ ++L +P V++
Sbjct: 2 ILITGANGQLGRELVQQLSPEGRV----VVALTRSQLDLTDPEALERLLRAIRPDAVVNT 57
Query: 67 AAMV 70
AA
Sbjct: 58 AAYT 61
>gnl|CDD|236649 PRK10084, PRK10084, dTDP-glucose 4,6 dehydratase; Provisional.
Length = 352
Score = 37.5 bits (87), Expect = 0.008
Identities = 22/83 (26%), Positives = 38/83 (45%), Gaps = 24/83 (28%)
Query: 7 ILVTGGTGLVGKA-IEKIVKEEEKR--------------------DDETWIFVSSKEADL 45
ILVTGG G +G A + I+ + D E ++F + AD+
Sbjct: 3 ILVTGGAGFIGSAVVRHIINNTQDSVVNVDKLTYAGNLESLADVSDSERYVF---EHADI 59
Query: 46 SNLESTQQLFSKYKPTHVIHLAA 68
+ ++F++++P V+HLAA
Sbjct: 60 CDRAELDRIFAQHQPDAVMHLAA 82
>gnl|CDD|178377 PLN02778, PLN02778, 3,5-epimerase/4-reductase.
Length = 298
Score = 37.4 bits (87), Expect = 0.008
Identities = 38/157 (24%), Positives = 62/157 (39%), Gaps = 16/157 (10%)
Query: 4 EKIILVTGGTGLVGKAIEKIVKEEEKRDDETWIFVSSKEADLSNLESTQQLFSKYKPTHV 63
L+ G TG +G + K+ +E+ I L N S + KPTHV
Sbjct: 9 TLKFLIYGKTGWIGGLLGKLCQEQG-------IDFHYGSGRLENRASLEADIDAVKPTHV 61
Query: 64 IHLAAMVGGLFHNM----SHNLDFFRVNMKINDNVLDTSYKQGVKKVVSCLSTCIFPDKT 119
+ A + G N+ SH ++ R N+ + D ++G+ + CIF
Sbjct: 62 FNAAGVTGR--PNVDWCESHKVETIRANVVGTLTLADVCRERGLVLTNYA-TGCIFEYDD 118
Query: 120 TYPIDETMVHNGPPHPSNFG--YSHAKRMLDVLNKAY 154
+P+ + P+ G YS K M++ L K Y
Sbjct: 119 AHPLGSGIGFKEEDTPNFTGSFYSKTKAMVEELLKNY 155
>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 = 37.4 bits (87), Expect = 0.008
Identities = 41/141 (29%), Positives = 62/141 (43%), Gaps = 25/141 (17%)
Query: 1 MAEEKIILVTGGTGLVGKAIEKIVKEEEK--------RDD-ETWIFVSSKEAD-----LS 46
M K IL+TGGTG GKA + E RD+ + W A +
Sbjct: 1 MFNNKSILITGGTGSFGKAFISRLLENYNPKKIIIYSRDELKQWEMQQKFPAPCLRFFIG 60
Query: 47 NLESTQQLFSKYKPT-HVIHLAAM--VGGLFHNMSHNLDFFRVNMKINDNVLDTSYKQGV 103
++ ++L + +V+H AA+ V +N + R N+ NV+D + GV
Sbjct: 61 DVRDKERLTRALRGVDYVVHAAALKQVPAAEYN---PFECIRTNINGAQNVIDAAIDNGV 117
Query: 104 KKVVSCLSTCIFPDKTTYPID 124
K+VV+ LST DK PI+
Sbjct: 118 KRVVA-LST----DKAANPIN 133
>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 = 36.9 bits (86), Expect = 0.012
Identities = 20/66 (30%), Positives = 35/66 (53%), Gaps = 3/66 (4%)
Query: 288 IAEVAEAIANAFQFKGRITFDTNAADGQLKKTASNRKLRELRGPGFEFTPFQQAVQESVA 347
+A AEA+A + R+T D + +S + +REL G+ P ++A++++V
Sbjct: 264 VAWGAEALARLTGKEPRVTVDGVRMAKKKMFFSSAKAVREL---GYRQRPAREALRDAVE 320
Query: 348 WFRENH 353
WFR N
Sbjct: 321 WFRANG 326
>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 = 36.2 bits (84), Expect = 0.017
Identities = 39/169 (23%), Positives = 65/169 (38%), Gaps = 25/169 (14%)
Query: 7 ILVTGGTGLVG----------KAIEKIV---KEEEKRDDETWIFVSSKEADLSNLESTQQ 53
+L+TG +G VG E+++ K V+ DL+ +
Sbjct: 3 VLITGASGFVGQRLAERLLSDVPNERLILIDVVSPKAPSGAPR-VTQIAGDLAVPALIEA 61
Query: 54 LFSKYKPTHVIHLAAMVGGLFHNMSHNLDFFRVNMKINDNVLDTSYKQG-VKKVVSCLST 112
L +P V HLAA+V G + +RVN+ N+L+ K G + V S
Sbjct: 62 LA-NGRPDVVFHLAAIVSG--GAEADFDLGYRVNVDGTRNLLEALRKNGPKPRFVFTSSL 118
Query: 113 CIFPDKTTYPI-DETMVHNGPPHPSNFGYSHAKRMLDVLNKAYYQQHGV 160
++ P+ D T P++ Y K M ++L Y ++ V
Sbjct: 119 AVYGLPLPNPVTDHT-----ALDPAS-SYGAQKAMCELLLNDYSRRGFV 161
>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 = 36.1 bits (84), Expect = 0.019
Identities = 27/113 (23%), Positives = 51/113 (45%), Gaps = 21/113 (18%)
Query: 7 ILVTGGTGLVGKAIEKIVKEE-----------EKRDDETWIFVSSKEADLSNLESTQQLF 55
IL+TGG G +G + K++++ K + + D+ + +S +++
Sbjct: 2 ILITGGLGQIGSELAKLLRKRYGKDNVIASDIRKPPAHVVLSGPFEYLDVLDFKSLEEIV 61
Query: 56 SKYKPTHVIHLAAM---VGGLFHNMSHNLDF-FRVNMKINDNVLDTSYKQGVK 104
+K T +IHLAA+ VG N + VNM NVL+ + + ++
Sbjct: 62 VNHKITWIIHLAALLSAVG------EKNPPLAWDVNMNGLHNVLELAREHNLR 108
>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 = 36.1 bits (84), Expect = 0.022
Identities = 60/276 (21%), Positives = 102/276 (36%), Gaps = 64/276 (23%)
Query: 62 HVIHLAAMVGGLFHNMSHNLDFFRVNMKINDNVLDTSYKQGVKKVVSCLSTCIFPDKTTY 121
V HLAA++ + ++ + + N+ NVL + GV+KVV ++ ++
Sbjct: 73 VVFHLAALIAIPYSYIAPD-SYVDTNVTGTLNVLQAARDLGVEKVVHTSTSEVYGTAQYV 131
Query: 122 PIDETMVHNGPPHPSN--FGYSHAKRMLDVLNKAYYQQHGVTYTSVIPCNVFGPHDNYNL 179
PIDE HP YS +K D L ++Y+ T + P N +GP
Sbjct: 132 PIDEK-------HPLQGQSPYSASKIGADQLALSFYRSFNTPVTIIRPFNTYGPR----- 179
Query: 180 ESSH-VIPGLIRKLYDTIEKGKDQSVFESRARFPPGANSFGLDKLDLIPFSLFPFCFTGG 238
+S+ VIP +I ++ G
Sbjct: 180 QSARAVIPTIITQI-------------------------------------------ASG 196
Query: 239 DEFKVLGTGKPLRQFIYSLDLARLFIWVLREYDSVEPIILSVDEKDEVTIAEVAEAIANA 298
LG+ P R F Y D R FI + +V +I ++ E++I + + IA
Sbjct: 197 KRRIKLGSLSPTRDFNYVTDTVRGFIAIAESDKTVGEVI-NIGSNFEISIGDTVKLIAEI 255
Query: 299 FQFKGRITFDTN---AADGQLKKT-ASNRKLRELRG 330
+ I D ++++ N K++EL G
Sbjct: 256 MGSEVEIETDEERLRPEKSEVERLWCDNSKIKELTG 291
>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 = 35.8 bits (83), Expect = 0.024
Identities = 26/103 (25%), Positives = 44/103 (42%), Gaps = 27/103 (26%)
Query: 3 EEKIILVTGGTGLVGKAIEKIVKE---------------EEKRDDETWIF---VSSKEAD 44
E+KIIL+TG GL+GKA K + E+ +++ T ++ V + E D
Sbjct: 1 EDKIILITGAAGLIGKAFCKALLSAGARLILADINAPALEQLKEELTNLYKNRVIALELD 60
Query: 45 LSNLESTQQLFSKYKPTH-----VIHLAAMV----GGLFHNMS 78
+++ ES ++L Y +I+ A G F
Sbjct: 61 ITSKESIKELIESYLEKFGRIDILINNAYPSPKVWGSRFEEFP 103
>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 = 34.5 bits (80), Expect = 0.046
Identities = 40/173 (23%), Positives = 61/173 (35%), Gaps = 36/173 (20%)
Query: 7 ILVTGGTGLVGKAIEK-----------IVKEEEKRDDETWIFVSSKEADLSNLESTQQLF 55
+LV G TG VG+ + + +V++ + + DL++ ES
Sbjct: 2 VLVVGATGKVGRHVVRELLDRGYQVRALVRDPSQAEKLEAAGAEVVVGDLTDAESLAAAL 61
Query: 56 SKYKPTHVIHLAAMVGGLFHNMSHNLDFFRVNMKINDNVLDTSYKQGVKKVVSCLSTCIF 115
VI A G V+ N N++D + K GVK+ V L + I
Sbjct: 62 --EGIDAVISAAGSGGKGG------PRTEAVDYDGNINLIDAAKKAGVKRFV--LVSSIG 111
Query: 116 PDKTTYPIDETMVHNGPPHPSNFGYSHAKRMLDVLNKAYYQQHGVTYTSVIPC 168
DK P + Y AKR + Y + G+ YT V P
Sbjct: 112 ADKP-----------SHPLEALGPYLDAKRKAE----DYLRASGLDYTIVRPG 149
>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 = 0.047
Identities = 18/67 (26%), Positives = 24/67 (35%), Gaps = 9/67 (13%)
Query: 7 ILVTGGTGLVGKAIEKIVKEEEKRDDETWIFVSSKEA---DLSNLESTQQLFSKYKPT-- 61
IL+TGGTG +G+A + + KR E I S
Sbjct: 1 ILITGGTGFIGRA---LTQRLTKRGHEVTILTRSPPPGANTKWEGYKPWAGEDADSLEGA 57
Query: 62 -HVIHLA 67
VI+LA
Sbjct: 58 DAVINLA 64
>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 = 34.7 bits (80), Expect = 0.053
Identities = 22/90 (24%), Positives = 36/90 (40%), Gaps = 33/90 (36%)
Query: 7 ILVTGGTGLVGKAIEKIVKEEEKRDDETWIFVSSK----------------------EAD 44
+ VTGGTG +G+ +VK + + + V S+ E D
Sbjct: 1 VFVTGGTGFLGRH---LVKRLLENGFKVLVLVRSESLGEAHERIEEAGLEADRVRVLEGD 57
Query: 45 LS------NLESTQQLFSKYKPTHVIHLAA 68
L+ + ++++L K HVIH AA
Sbjct: 58 LTQPNLGLSAAASRELAGKV--DHVIHCAA 85
>gnl|CDD|187562 cd05252, CDP_GD_SDR_e, CDP-D-glucose 4,6-dehydratase, extended (e)
SDRs. This subgroup contains CDP-D-glucose
4,6-dehydratase, an extended SDR, which catalyzes the
conversion of CDP-D-glucose to
CDP-4-keto-6-deoxy-D-glucose. This subgroup has the
characteristic active site tetrad and NAD-binding motif
of the extended SDRs. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately 100
amino acids. Extended SDRs are a diverse collection of
proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 336
Score = 34.6 bits (80), Expect = 0.059
Identities = 52/220 (23%), Positives = 88/220 (40%), Gaps = 50/220 (22%)
Query: 5 KIILVTGGTGLVGKAIEKIVKE-------------------EEKRDDETWIFVSSKEADL 45
K +LVTG TG G + ++E E D +SS D+
Sbjct: 5 KRVLVTGHTGFKGSWLSLWLQELGAKVIGYSLDPPTNPNLFELANLDNK---ISSTRGDI 61
Query: 46 SNLESTQQLFSKYKPTHVIHLAA--MVGGLFHNMSHNLDFFRVNMKINDNVLDTSYKQG- 102
+L + ++ +Y+P V HLAA +V + + ++ F N+ N+L+ + G
Sbjct: 62 RDLNALREAIREYEPEIVFHLAAQPLVRLSYKD---PVETFETNVMGTVNLLEAIRETGS 118
Query: 103 VKKVVSCLSTCIFPDKTT---YPIDETMVHNGPPHPSNFGYSHAKRMLDVLNKAY----- 154
VK VV+ S + +K Y ++ + G P YS +K +++ +Y
Sbjct: 119 VKAVVNVTSDKCYENKEWGWGYRENDPL---GGHDP----YSSSKGCAELIISSYRNSFF 171
Query: 155 ----YQQHGVTYTSVIPCNVFGPHDNYNLESSHVIPGLIR 190
Y +HG+ S NV G D ++P IR
Sbjct: 172 NPENYGKHGIAIASARAGNVIGGGD---WAEDRIVPDCIR 208
>gnl|CDD|165812 PLN02166, PLN02166, dTDP-glucose 4,6-dehydratase.
Length = 436
Score = 35.0 bits (80), Expect = 0.062
Identities = 28/86 (32%), Positives = 35/86 (40%), Gaps = 3/86 (3%)
Query: 243 VLGTGKPLRQFIYSLDLARLFIWVLREYDSVEPIILSVDEKDEVTIAEVAEAIANAFQFK 302
V G GK R F Y DL + L E + V P L E T+ E+AE +
Sbjct: 321 VYGDGKQTRSFQYVSDLVDGLV-ALMEGEHVGPFNLG--NPGEFTMLELAEVVKETIDSS 377
Query: 303 GRITFDTNAADGQLKKTASNRKLREL 328
I F N AD K+ K +EL
Sbjct: 378 ATIEFKPNTADDPHKRKPDISKAKEL 403
>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 = 34.4 bits (79), Expect = 0.071
Identities = 40/183 (21%), Positives = 74/183 (40%), Gaps = 30/183 (16%)
Query: 7 ILVTGGTGLVGKAI--------EKIV--------KEEEKRDDETWIFVSSKEADLSNLES 50
+L+TGG G +G + ++V + E D V AD + ++
Sbjct: 3 VLITGGAGQIGSHLIEHLLERGHQVVVIDNFATGRREHLPDHPNLTVVEGSIADKALVD- 61
Query: 51 TQQLFSKYKPTHVIHLAAMVGGLFHNMSHNLDFFRVNMKINDNVLDTSYKQGVKKVVSCL 110
+LF +KP V+H AA + + + N+ NV+ + K GVK+++
Sbjct: 62 --KLFGDFKPDAVVHTAAA----YKDPDDWYEDTLTNVVGGANVVQAAKKAGVKRLIYFQ 115
Query: 111 STCIFPDKTTYPIDETMVHNGPPHPSNFGYSHAKRMLDVLNKAYYQQHGVTYTSVIPCNV 170
+ + K P+ + + + P P Y+ +K + Y + GV + + NV
Sbjct: 116 TALCYGLK---PMQQPIRLDHPRAPPGSSYAISK----TAGEYYLELSGVDFVTFRLANV 168
Query: 171 FGP 173
GP
Sbjct: 169 TGP 171
>gnl|CDD|187571 cd05261, CAPF_like_SDR_e, capsular polysaccharide assembling
protein (CAPF) like, extended (e) SDRs. This subgroup
of extended SDRs, includes some members which have been
identified as capsular polysaccharide assembling
proteins, such as Staphylococcus aureus Cap5F which is
involved in the biosynthesis of N-acetyl-l-fucosamine, a
constituent of surface polysaccharide structures of S.
aureus. This subgroup has the characteristic active site
tetrad and NAD-binding motif of extended SDRs. Extended
SDRs are distinct from classical SDRs. In addition to
the Rossmann fold (alpha/beta folding pattern with a
central beta-sheet) core region typical of all SDRs,
extended SDRs have a less conserved C-terminal extension
of approximately 100 amino acids. Extended SDRs are a
diverse collection of proteins, and include isomerases,
epimerases, oxidoreductases, and lyases; they typically
have a TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 248
Score = 33.9 bits (78), Expect = 0.081
Identities = 45/176 (25%), Positives = 71/176 (40%), Gaps = 39/176 (22%)
Query: 7 ILVTGGTGLVGKAIEKIVKEEEKRDDETWIFVSSKEADLSNLESTQQLFSKYKPTHVIHL 66
IL+TG G +GK + I + +E++DD+ IF +E+D S L+ Q + HL
Sbjct: 3 ILITGAKGFIGKNL--IARLKEQKDDD--IFFYDRESDESELDDFLQ-----GADFIFHL 53
Query: 67 AAMVGGLFHNMSHNLDFFRVNMKINDNVLDTSYKQGVKKVVSCLSTCIFPDKTTYPIDET 126
A + +F N+ + + +LD + G KK LS+ I
Sbjct: 54 AGVNRPK-----DEAEFESGNVGLTERLLDALTRNG-KKPPILLSSSIQAAL-------- 99
Query: 127 MVHNGPPHPSNFGYSHAKRMLDVLNKAYYQQHGVTYTSVIPCNVFG----PHDNYN 178
+ P Y +K + L + Y ++ G NVFG P NYN
Sbjct: 100 ---DNP-------YGKSKLAAEELLQEYARETGAPVYIYRLPNVFGKWCRP--NYN 143
>gnl|CDD|222146 pfam13460, NAD_binding_10, NADH(P)-binding.
Length = 182
Score = 33.1 bits (76), Expect = 0.12
Identities = 34/181 (18%), Positives = 56/181 (30%), Gaps = 47/181 (25%)
Query: 7 ILVTGGTGLVGKAIEKIVKEEEKRDDETWIFVSSKEA-----------DLSNLESTQQLF 55
I V G TG G+ +VKE R + + DL +L +
Sbjct: 1 IAVIGATGKTGRR---LVKELLARGHQVTALSRNPSKAPAPGVTPVQKDLFDLADLAEAL 57
Query: 56 SKYKPTHVIHLAAMVGGLFHNMSHNLDFFRVNMKINDNVLDTSYKQGVKK--VVSCLSTC 113
+ V+ + D ++LD + + GV++ VVS
Sbjct: 58 AGVD--AVVDAFG---------ARPDDS-----DGVKHLLDAAARAGVRRIVVVSAAGLY 101
Query: 114 IFPDKTTYPIDETMVHNGPPHPSNFGYSHAKR-MLDVLNKAYYQQHGVTYTSVIPCNVFG 172
T D P Y+ AK ++L + G+ +T V P +F
Sbjct: 102 RDEPGTFRLDD---------APLFPPYARAKAAAEELL-----RASGLDWTIVRPGALFD 147
Query: 173 P 173
Sbjct: 148 E 148
>gnl|CDD|236399 PRK09186, PRK09186, flagellin modification protein A;
Provisional.
Length = 256
Score = 33.4 bits (77), Expect = 0.13
Identities = 19/78 (24%), Positives = 33/78 (42%), Gaps = 21/78 (26%)
Query: 1 MAEEKIILVTGGTGLVGKAIEKIV--------------------KEEEKRDDETWIFVSS 40
M + K IL+TG GL+G A+ K + E ++ ++ S
Sbjct: 1 MLKGKTILITGAGGLIGSALVKAILEAGGIVIAADIDKEALNELLESLGKEFKSKKL-SL 59
Query: 41 KEADLSNLESTQQLFSKY 58
E D+++ ES ++ SK
Sbjct: 60 VELDITDQESLEEFLSKS 77
>gnl|CDD|182313 PRK10217, PRK10217, dTDP-glucose 4,6-dehydratase; Provisional.
Length = 355
Score = 33.9 bits (77), Expect = 0.13
Identities = 20/85 (23%), Positives = 38/85 (44%), Gaps = 24/85 (28%)
Query: 5 KIILVTGGTGLVGKAIEK-IVKEEEKR--------------------DDETWIFVSSKEA 43
+ IL+TGG G +G A+ + I+ E E + F ++
Sbjct: 2 RKILITGGAGFIGSALVRYIINETSDAVVVVDKLTYAGNLMSLAPVAQSERFAF---EKV 58
Query: 44 DLSNLESTQQLFSKYKPTHVIHLAA 68
D+ + ++F++++P V+HLAA
Sbjct: 59 DICDRAELARVFTEHQPDCVMHLAA 83
>gnl|CDD|235506 PRK05565, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 247
Score = 33.3 bits (77), Expect = 0.14
Identities = 23/113 (20%), Positives = 42/113 (37%), Gaps = 26/113 (23%)
Query: 3 EEKIILVTGGTGLVGKAI------------------EKIVKEEEKRDDETWIFVSSKEAD 44
K+ +VTG +G +G+AI E+ +E + E + +AD
Sbjct: 4 MGKVAIVTGASGGIGRAIAELLAKEGAKVVIAYDINEEAAQELLEEIKEEGGDAIAVKAD 63
Query: 45 LSNLESTQQLFS----KYKPTHVIHLAA--MVGGLFHNMSHNL--DFFRVNMK 89
+S+ E + L K+ ++ A GL +M+ VN+
Sbjct: 64 VSSEEDVENLVEQIVEKFGKIDILVNNAGISNFGLVTDMTDEEWDRVIDVNLT 116
>gnl|CDD|224015 COG1090, COG1090, Predicted nucleoside-diphosphate sugar
epimerase [General function prediction only].
Length = 297
Score = 33.4 bits (77), Expect = 0.14
Identities = 19/67 (28%), Positives = 26/67 (38%), Gaps = 9/67 (13%)
Query: 7 ILVTGGTGLVGKAIEKIVKEEEKRDDETWIFVSSKEADLSNLESTQQL---FSKYKPTH- 62
IL+TGGTGL+G+A + K + I NL L +
Sbjct: 1 ILITGGTGLIGRA---LTARLRKGGHQVTILTRRPPKASQNLHPNVTLWEGLADALTLGI 57
Query: 63 --VIHLA 67
VI+LA
Sbjct: 58 DAVINLA 64
>gnl|CDD|233775 TIGR02197, heptose_epim, ADP-L-glycero-D-manno-heptose-6-epimerase.
This family consists of examples of
ADP-L-glycero-D-mannoheptose-6-epimerase, an enzyme
involved in biosynthesis of the inner core of
lipopolysaccharide (LPS) for Gram-negative bacteria.
This enzyme is homologous to UDP-glucose 4-epimerase
(TIGR01179) and belongs to the NAD dependent
epimerase/dehydratase family (pfam01370) [Cell envelope,
Biosynthesis and degradation of surface polysaccharides
and lipopolysaccharides].
Length = 314
Score = 33.4 bits (77), Expect = 0.16
Identities = 49/237 (20%), Positives = 82/237 (34%), Gaps = 56/237 (23%)
Query: 7 ILVTGGTGLVGKAIEKIVKEEEK---------RDDETWI-FVS-------SKEADLSNLE 49
I+VTGG G +G + K + E RD ++ KE L LE
Sbjct: 1 IIVTGGAGFIGSNLVKALNERGITDILVVDNLRDGHKFLNLADLVIADYIDKEDFLDRLE 60
Query: 50 STQQLFSKYKPTHVIHLAAMVGGLFHN----MSHNLDFFRVNMKINDNVLDTSYKQGVKK 105
+ K + H A + M +N + + +LD ++G+
Sbjct: 61 KG----AFGKIEAIFHQGACSDTTETDGEYMMENNYQYSK-------RLLDWCAEKGI-P 108
Query: 106 VVSCLSTCIFPDKTTYPIDETMVHNGPPHPSN-FGYSHAKRMLDVLNKAY-------YQQ 157
+ S + D E P N +GYS K + D + Q
Sbjct: 109 FIYASSAATYGD-GEAGFREG---RELERPLNVYGYS--KFLFDQYVRRRVLPEALSAQV 162
Query: 158 HGVTYTSVIPCNVFGPHDNYNLESSHVIPGLIRKLYDTIEKGKDQSVFESRARFPPG 214
G+ Y NV+GP + + + + V L++ I+ G + +F+S F G
Sbjct: 163 VGLRYF-----NVYGPREYHKGKMASV----AFHLFNQIKAGGNVKLFKSSEGFKDG 210
>gnl|CDD|187652 cd08948, 5beta-POR_like_SDR_a, progesterone 5-beta-reductase-like
proteins (5beta-POR), atypical (a) SDRs. 5beta-POR
catalyzes the reduction of progesterone to
5beta-pregnane-3,20-dione in Digitalis plants. This
subgroup of atypical-extended SDRs, shares the structure
of an extended SDR, but has a different glycine-rich
nucleotide binding motif (GXXGXXG) and lacks the YXXXK
active site motif of classical and extended SDRs.
Tyr-179 and Lys 147 are present in the active site, but
not in the usual SDR configuration. Given these
differences, it has been proposed that this subfamily
represents a new SDR class. Other atypical SDRs include
biliverdin IX beta reductase (BVR-B,aka flavin
reductase), NMRa (a negative transcriptional regulator
of various fungi), 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 = 308
Score = 33.4 bits (77), Expect = 0.17
Identities = 38/208 (18%), Positives = 58/208 (27%), Gaps = 58/208 (27%)
Query: 8 LVTGGTGLVGKAI-----------EKIV-----KEEEKRDDETWIFVSSKEADLSNLEST 51
LV G TG+ G A+ K+ + D + DL + T
Sbjct: 3 LVVGATGISGWALVEHLLSDPGTWWKVYGLSRRPLPTEDDPRLVEHIG---IDLLDPADT 59
Query: 52 --QQLFSKY-KPTHVIHLAAMVGGLFHNMSHNLDF---FRVNMKINDNVLDTSYKQGVKK 105
+ THV + A D VN + N LD ++
Sbjct: 60 VLRAKLPGLEDVTHVFYAA---------YIERPDEAELVEVNGAMLRNFLD-----ALEP 105
Query: 106 VVSCLSTCI-----------FPDKTTYPIDETMVHNGPPHPS-NFGYSHAKRMLDVLNKA 153
L + T +E + P NF Y D+L
Sbjct: 106 ASPNLKHVVLQTGTKHYGVHLGPFKTPRPEEPAREDPPRLLPPNFYY----DQEDLL-FE 160
Query: 154 YYQQHGVTYTSVIPCNVFGP-HDN-YNL 179
+ G T++ + P + G N NL
Sbjct: 161 AAKGKGWTWSVLRPDAIIGFAPGNAMNL 188
>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 = 33.1 bits (76), Expect = 0.20
Identities = 27/113 (23%), Positives = 41/113 (36%), Gaps = 21/113 (18%)
Query: 7 ILVTGGTGLVGK-----------AIEKIVKEEEKRDDETWI-FVSSKEADLSNLESTQQL 54
+LVTG TG VG + +V+ EK D W V+ DL + ES +
Sbjct: 1 VLVTGATGYVGGRLVPRLLQEGHQVRALVRSPEKLADRPWSERVTVVRGDLEDPESLRAA 60
Query: 55 FSKYKPTHVIHLAAMVGGLFHNMSHNLDFFRVNMKINDNVLDTSYKQGVKKVV 107
L H+M DF + + N + GVK+++
Sbjct: 61 LEG---------IDTAYYLVHSMGSGGDFEEADRRAARNFARAARAAGVKRII 104
>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 = 32.6 bits (75), Expect = 0.25
Identities = 35/164 (21%), Positives = 53/164 (32%), Gaps = 39/164 (23%)
Query: 7 ILVTGGTGLVGK-----AIEK------------------IVKEEEKRDDETWIFVSSKEA 43
L+TG TG G +EK I +D T
Sbjct: 2 ALITGITGQDGSYLAEFLLEKGYEVHGIVRRSSSFNTDRIDHLYINKDRITLH-----YG 56
Query: 44 DLSNLESTQQLFSKYKPTHVIHLAAM--VGGLFHNMSHNLDFFRVNMKINDNVLDTSYKQ 101
DL++ S ++ K +P + HLAA V F + VN N+L+
Sbjct: 57 DLTDSSSLRRAIEKVRPDEIYHLAAQSHVKVSFDD---PEYTAEVNAVGTLNLLEAIRIL 113
Query: 102 GVK-KVVSCLSTCIFPDKTTYPIDETMVHNGPPHPSNFGYSHAK 144
G+ + S+ + P ET P P Y+ +K
Sbjct: 114 GLDARFYQASSSEEYGKVQELPQSETTPFR-PRSP----YAVSK 152
>gnl|CDD|187547 cd05236, FAR-N_SDR_e, fatty acyl CoA reductases (FARs), extended
(e) SDRs. SDRs are Rossmann-fold NAD(P)H-binding
proteins, many of which may function as fatty acyl CoA
reductases (FAR), acting on medium and long chain fatty
acids, and have been reported to be involved in diverse
processes such as biosynthesis of insect pheromones,
plant cuticular wax production, and mammalian wax
biosynthesis. In Arabidopsis thaliana, proteins with
this particular architecture have also been identified
as the MALE STERILITY 2 (MS2) gene product, which is
implicated in male gametogenesis. Mutations in MS2
inhibit the synthesis of exine (sporopollenin),
rendering plants unable to reduce pollen wall fatty
acids to corresponding alcohols. This N-terminal domain
shares the catalytic triad (but not the upstream Asn)
and characteristic NADP-binding motif of the extended
SDR family. Extended SDRs are distinct from classical
SDRs. In addition to the Rossmann fold (alpha/beta
folding pattern with a central beta-sheet) core region
typical of all SDRs, extended SDRs have a less
conserved C-terminal extension of approximately 100
amino acids. Extended SDRs are a diverse collection of
proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and
their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 320
Score = 32.3 bits (74), Expect = 0.31
Identities = 10/23 (43%), Positives = 17/23 (73%), Gaps = 1/23 (4%)
Query: 5 KIILVTGGTGLVGKAI-EKIVKE 26
K +L+TG TG +GK + EK+++
Sbjct: 1 KSVLITGATGFLGKVLLEKLLRS 23
>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 = 31.8 bits (73), Expect = 0.31
Identities = 14/55 (25%), Positives = 23/55 (41%), Gaps = 8/55 (14%)
Query: 7 ILVTGGTGLVGKAIEKIVKEEEKRDDETWIFVSSK----EADLSNLESTQQLFSK 57
I+V G TG +G A + + E I + D+++ S + LF K
Sbjct: 1 IIVIGATGTIGLA---VAQLLSAHGHEV-ITAGRSSGDYQVDITDEASIKALFEK 51
>gnl|CDD|188824 cd09440, LIM1_SF3, The first Lim domain of pollen specific protein
SF3. The first Lim domain of pollen specific protein
SF3: SF3 is a Lim protein that is found exclusively in
mature plant pollen grains. It contains two LIM domains.
The exact function of SF3 is unknown. It may be a
transcription factor required for the expression of late
pollen genes. It is possible that SF3 protein is
involved in controlling pollen-specific processes such
as male gamete maturation, pollen tube formation, or
even fertilization. As in other LIM domains, this domain
family is 50-60 amino acids in size and shares two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein.
Length = 63
Score = 29.7 bits (67), Expect = 0.36
Identities = 18/50 (36%), Positives = 21/50 (42%), Gaps = 2/50 (4%)
Query: 113 CIFPDKTTYPIDETMVHNGPPHPSNFGYSHAKRMLDVLNKAYYQQHGVTY 162
C DKT Y +D+ H S F SH K L + N Y GV Y
Sbjct: 5 CKACDKTVYLVDQLSADGVVYHKSCFRCSHCKGTLKLSN--YSSMEGVLY 52
>gnl|CDD|237253 PRK12898, secA, preprotein translocase subunit SecA; Reviewed.
Length = 656
Score = 32.7 bits (75), Expect = 0.37
Identities = 18/67 (26%), Positives = 32/67 (47%), Gaps = 7/67 (10%)
Query: 269 EYDSV------EPIILSVDEKDEVTIAEVAEAIANAFQFKGRITFDTNAADGQLKKTASN 322
E DSV P+I+S K+ +A+ A Q K + +AA+ +++ T +
Sbjct: 250 EADSVLIDEARTPLIISAPAKEADEAEVYRQALELAAQLKEGEDYTIDAAEKRIELTEAG 309
Query: 323 R-KLREL 328
R ++ EL
Sbjct: 310 RARIAEL 316
>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 = 32.1 bits (73), Expect = 0.37
Identities = 32/203 (15%), Positives = 60/203 (29%), Gaps = 54/203 (26%)
Query: 1 MAEEKIILVTGGTGLVGKAI-----------------------EKIVKEEEKRDDETWIF 37
K+ LVTG + +G+AI E + ++
Sbjct: 2 DLSGKVALVTGASSGIGRAIARALAREGARVVVAARRSEEEAAEALAAAIKEAGGGRAAA 61
Query: 38 VSSKEADLSN-LESTQQLF----SKYKPTHVIHLAAMVG---GLFHNMSHN--LDFFRVN 87
V AD+S+ ES + L ++ ++ A + ++ VN
Sbjct: 62 V---AADVSDDEESVEALVAAAEEEFGRIDILVNNAGIAGPDAPLEELTEEDWDRVIDVN 118
Query: 88 MKINDNVLDTSYKQGVKKVVSCLSTCIFPDKTTYPIDETMVHNGPPHPSNFGYSHAKRML 147
+ + + K+ + +S+ V P Y+ +K L
Sbjct: 119 LLGAFLLTRAALPLMKKQRIVNISS---------------VAGLGGPPGQAAYAASKAAL 163
Query: 148 DVLNKAY---YQQHGVTYTSVIP 167
L KA G+ +V P
Sbjct: 164 IGLTKALALELAPRGIRVNAVAP 186
>gnl|CDD|223774 COG0702, COG0702, Predicted nucleoside-diphosphate-sugar epimerases
[Cell envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 275
Score = 32.2 bits (73), Expect = 0.39
Identities = 24/108 (22%), Positives = 35/108 (32%), Gaps = 10/108 (9%)
Query: 7 ILVTGGTGLVGKAIEKIVKEEEKRDDETWIFVSSKEADLSNLESTQQLFSKYKPTHVIHL 66
ILVTG TG VG A +V+E R E V + EA + + + + +
Sbjct: 3 ILVTGATGFVGGA---VVRELLARGHEVRAAVRNPEAAAALAGGVEVVLGDLRDPKSLVA 59
Query: 67 AA-------MVGGLFHNMSHNLDFFRVNMKINDNVLDTSYKQGVKKVV 107
A ++ GL + K GV V
Sbjct: 60 GAKGVDGVLLISGLLDGSDAFRAVQVTAVVRAAEAAGAGVKHGVSLSV 107
>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 = 31.8 bits (73), Expect = 0.46
Identities = 15/85 (17%), Positives = 31/85 (36%), Gaps = 27/85 (31%)
Query: 5 KIILVTGGTGLVGKAI---------------------EKIVKEEEKRDDETWIFVSSKEA 43
K++++TG +GK E+ E +K + V +
Sbjct: 2 KVVVITGANSGIGKETARELAKRGAHVIIACRNEEKGEEAAAEIKKETGNAKVEV--IQL 59
Query: 44 DLSNLESTQQLF----SKYKPTHVI 64
DLS+L S +Q +++ ++
Sbjct: 60 DLSSLASVRQFAEEFLARFPRLDIL 84
>gnl|CDD|236057 PRK07578, PRK07578, short chain dehydrogenase; Provisional.
Length = 199
Score = 31.3 bits (72), Expect = 0.47
Identities = 12/60 (20%), Positives = 25/60 (41%), Gaps = 16/60 (26%)
Query: 5 KIILVTGGTGLVGKAIEK-------IVKEEEKRDDETWIFVSSKEADLSNLESTQQLFSK 57
KI+++ G +G +G+A+ ++ D D+++ S + LF K
Sbjct: 2 KILVI-GASGTIGRAVVAELSKRHEVITAGRSSGDVQ--------VDITDPASIRALFEK 52
>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 = 32.0 bits (73), Expect = 0.53
Identities = 31/148 (20%), Positives = 55/148 (37%), Gaps = 19/148 (12%)
Query: 42 EADLSNLESTQQLFSKYKPTHVIHLAAMVGGLFHNMSHNLDFFRVNMKINDNVLDT-SYK 100
D + E +L + ++P V+H A + + N ++NV+ T +
Sbjct: 72 VGDACDYEFLAELLASHEPDAVVHFAEQRSAPYSMIDRE----HANYTQHNNVIGTLNLL 127
Query: 101 QGVKKVV-SC----LSTCIFPDKTTYPIDE---TMVHNGP----PHPSNFG-YSHAKRML 147
+K+ C L T I E T+ HNG P+P G + H ++
Sbjct: 128 FAIKEFDPDCHLVKLGTMGEYGTPNIDIPEGYITIEHNGRRDTLPYPKQAGSWYHLSKVH 187
Query: 148 DVLNKAYY-QQHGVTYTSVIPCNVFGPH 174
D N + + G+ T + V+G
Sbjct: 188 DSHNIMFACKAWGIRITDLNQGVVYGTK 215
>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 = 31.0 bits (71), Expect = 0.74
Identities = 19/70 (27%), Positives = 30/70 (42%), Gaps = 17/70 (24%)
Query: 5 KIILVTGGTGLVGKAIEK---------IV---KEEEKRDDETWIF-----VSSKEADLSN 47
K+ LVTG + +G+AI V EE + I ++ EAD+S+
Sbjct: 1 KVALVTGASRGIGRAIALRLAAEGAKVAVTDRSEEAAAETVEEIKALGGNAAALEADVSD 60
Query: 48 LESTQQLFSK 57
E+ + L K
Sbjct: 61 REAVEALVEK 70
>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 = 30.7 bits (70), Expect = 0.93
Identities = 39/177 (22%), Positives = 68/177 (38%), Gaps = 17/177 (9%)
Query: 7 ILVTGGTGLVGKAIEKIVKEEE------KRDDETWIF-VSSKEADLSNLESTQQLFSKYK 59
+L+ GG G +G + + EE R + + + + E+ L S
Sbjct: 2 VLIVGGNGFIGSHLVDALLEEGPQVRVFDRSIPPYELPLGGVDYIKGDYENRADLESALV 61
Query: 60 PTH-VIHLAAMVGGLFHNMSHNLDFFRVNMKINDNVLDTSYKQGVKKVV--SCLSTCIFP 116
VIHLA+ N + LD N+ +L+ G+ K++ S T ++
Sbjct: 62 GIDTVIHLASTTNPATSNKNPILDIQT-NVAPTVQLLEACAAAGIGKIIFASSGGT-VYG 119
Query: 117 DKTTYPIDETMVHNGPPHPSNFGYSHAKRMLDVLNKAYYQQHGVTYTSVIPCNVFGP 173
PI E + P P Y +K ++ + Y +G+ YT + N +GP
Sbjct: 120 VPEQLPISE----SDPTLP-ISSYGISKLAIEKYLRLYQYLYGLDYTVLRISNPYGP 171
>gnl|CDD|235962 PRK07201, PRK07201, short chain dehydrogenase; Provisional.
Length = 657
Score = 30.7 bits (70), Expect = 1.2
Identities = 20/87 (22%), Positives = 33/87 (37%), Gaps = 30/87 (34%)
Query: 8 LVTGGTGLVGKA-IEKIVKEEEKRDDETWIFVSSKEADLSNLE----------------- 49
VTGGTG +G+ + +++ + +R+ + V + LS LE
Sbjct: 4 FVTGGTGFIGRRLVSRLL--DRRREATVHVLV--RRQSLSRLEALAAYWGADRVVPLVGD 59
Query: 50 --------STQQLFSKYKPTHVIHLAA 68
S + HV+HLAA
Sbjct: 60 LTEPGLGLSEADIAELGDIDHVVHLAA 86
>gnl|CDD|223336 COG0258, Exo, 5'-3' exonuclease (including N-terminal domain of
PolI) [DNA replication, recombination, and repair].
Length = 310
Score = 30.4 bits (69), Expect = 1.3
Identities = 13/44 (29%), Positives = 22/44 (50%)
Query: 267 LREYDSVEPIILSVDEKDEVTIAEVAEAIANAFQFKGRITFDTN 310
L+EY S+E + ++D + T ++ E AF K T T+
Sbjct: 215 LQEYGSLEGLYENLDIIKKKTREKLLEDKEKAFLSKPLATIKTD 258
>gnl|CDD|187658 cd08955, KR_2_FAS_SDR_x, beta-ketoacyl reductase (KR) domain of
fatty acid synthase (FAS), subgroup 2, complex (x).
Ketoreductase, a module of the multidomain polyketide
synthase, has 2 subdomains, each corresponding to a
short-chain dehydrogenases/reductase (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 oligomerizes but is composed of 2
subdomains, each resembling an SDR monomer. In some
instances, as in porcine FAS, an enoyl reductase (a
Rossman fold NAD binding domain of the MDR family)
module is inserted between the sub-domains. The active
site resembles that of typical SDRs, except that the
usual positions of the catalytic asparagine and tyrosine
are swapped, so that the canonical YXXXK motif changes
to YXXXN. Modular polyketide synthases are
multifunctional structures in which the makeup
recapitulates that found in (and may have evolved from)
fatty acid synthase. In some instances, such as
porcine FAS , an enoyl reductase module is inserted
between the sub-domains. Fatty acid synthesis occurs via
the stepwise elongation of a chain (which is attached to
acyl carrier protein, ACP) with 2-carbon units.
Eukaryotic systems consists of large, multifunctional
synthases (type I) while bacterial, type II systems, use
single function proteins. Fungal fatty acid synthesis
uses dodecamer of 6 alpha and 6 beta subunits. In
mammalian type FAS cycles, ketoacyl synthase forms
acetoacetyl-ACP which is reduced by the NADP-dependent
beta-ketoacyl reductase (KR), forming
beta-hydroxyacyl-ACP, which is in turn dehydrated by
dehydratase to a beta-enoyl intermediate, which is
reduced by NADP-dependent beta-enoyl reductase (ER).
Polyketide syntheses 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 the KR domain of the
Lyngbya majuscule Jam J, -K, and #L which are encoded
on the jam gene cluster and are involved in the
synthesis of the Jamaicamides (neurotoxins); Lyngbya
majuscule Jam P belongs to a different KR_FAS_SDR_x
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 = 376
Score = 30.3 bits (69), Expect = 1.5
Identities = 14/69 (20%), Positives = 28/69 (40%), Gaps = 10/69 (14%)
Query: 7 ILVTGGTGLVGKAIEKIVKEEEKRDDETWIFVSSKEADLSNLESTQQLFSKYKPT----- 61
+++TG A + I E E V AD+S+ ++ ++ + +
Sbjct: 177 LVLTGRRAPSAAARQAIAALE-----EAGAEVVVLAADVSDRDALAAALAQIRASLPPLR 231
Query: 62 HVIHLAAMV 70
VIH A ++
Sbjct: 232 GVIHAAGVL 240
>gnl|CDD|224428 COG1511, COG1511, Predicted membrane protein [Function unknown].
Length = 780
Score = 30.6 bits (69), Expect = 1.5
Identities = 12/36 (33%), Positives = 18/36 (50%), Gaps = 3/36 (8%)
Query: 12 GTGLVGKAI---EKIVKEEEKRDDETWIFVSSKEAD 44
G GK + + +VK +K W FVS +EA+
Sbjct: 59 GATFNGKKVNIGDDLVKTLKKNKSLDWHFVSREEAE 94
>gnl|CDD|178047 PLN02427, PLN02427, UDP-apiose/xylose synthase.
Length = 386
Score = 30.2 bits (68), Expect = 1.7
Identities = 18/65 (27%), Positives = 32/65 (49%), Gaps = 7/65 (10%)
Query: 124 DETMVHNGPPHPSNFGYSHAKRMLDVLNKAYYQQHGVTYTSVIPCNVFGPHDNYNLESSH 183
DE+ G + Y+ AK++++ L A ++G+ +T V P N GP ++
Sbjct: 166 DESPCIFGSIEKQRWSYACAKQLIERLIYAEGAENGLEFTIVRPFNWIGPRMDF------ 219
Query: 184 VIPGL 188
IPG+
Sbjct: 220 -IPGI 223
>gnl|CDD|177856 PLN02206, PLN02206, UDP-glucuronate decarboxylase.
Length = 442
Score = 30.3 bits (68), Expect = 1.8
Identities = 26/88 (29%), Positives = 36/88 (40%), Gaps = 3/88 (3%)
Query: 243 VLGTGKPLRQFIYSLDLARLFIWVLREYDSVEPIILSVDEKDEVTIAEVAEAIANAFQFK 302
V G GK R F + DL + L E + V P L E T+ E+A+ +
Sbjct: 320 VYGDGKQTRSFQFVSDLVEGLM-RLMEGEHVGPFNLG--NPGEFTMLELAKVVQETIDPN 376
Query: 303 GRITFDTNAADGQLKKTASNRKLRELRG 330
+I F N D K+ K +EL G
Sbjct: 377 AKIEFRPNTEDDPHKRKPDITKAKELLG 404
>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 = 29.6 bits (67), Expect = 2.3
Identities = 71/376 (18%), Positives = 133/376 (35%), Gaps = 91/376 (24%)
Query: 7 ILVTGGTGLVGKAIEKIVKEEEKRDDETWIFV------SSKEADLSNLESTQQL------ 54
I+VTGG G +G + K + E D I V K +L L+ +
Sbjct: 2 IIVTGGAGFIGSNLVKALNERGITD----ILVVDNLSNGEKFKNLVGLKIADYIDKDDFK 57
Query: 55 ------FSKYKPTHVIHLAAMVGGLFHN----MSHNLDFFRVNMKINDNVLDTSYKQGVK 104
+K + H A + M +N + + +L ++ ++
Sbjct: 58 DWVRKGDENFKIEAIFHQGACSDTTETDGKYMMDNNYQYTK-------ELLHYCLEKKIR 110
Query: 105 KVVSCLSTCIFPDKTTYPIDETMVHNGPPHPSN-FGYSHAKRMLDVLNKAYYQQHGVTYT 163
+ S ++ + + ++ N P N +GYS K + D + ++HG
Sbjct: 111 -FIYASSAAVYGNGSLGFAEDIETPN--LRPLNVYGYS--KLLFD----QWARRHGKEVL 161
Query: 164 SVIPC----NVFGPHDNYNLESSHVIPGLIRKLYDTIEKGKDQSVFESRARFPPGANSFG 219
S + NV+GP + + + V + L++ I+ G+ +F+S + G
Sbjct: 162 SQVVGLRYFNVYGPREYHKGRMASV----VFHLFNQIKAGEKVKLFKSSDGYADG----- 212
Query: 220 LDKLDLIPFSLFPFCFTGGDEFKVLGTGKPLRQFIYSLDLARLFIWVLREYDSVEPIILS 279
E LR F+Y D+ ++ ++ L E SV I +
Sbjct: 213 --------------------EQ--------LRDFVYVKDVVKVNLFFL-ENPSVSG-IFN 242
Query: 280 VDEKDEVTIAEVAEAIANAFQFKGRITFDTNAADGQLK----KTASNRKLRELRGPGFEF 335
V + ++A A A + +I + D + K A KLR G EF
Sbjct: 243 VGTGRARSFNDLASATFKALGKEVKIEYIDFPEDLRGKYQSFTEADISKLRAA-GYTKEF 301
Query: 336 TPFQQAVQESVAWFRE 351
++ V++ V +
Sbjct: 302 HSLEEGVKDYVKNYLA 317
>gnl|CDD|188169 TIGR01829, AcAcCoA_reduct, acetoacetyl-CoA reductase. This model
represent acetoacetyl-CoA reductase, a member of the
family short-chain-alcohol dehydrogenases. Note that,
despite the precision implied by the enzyme name, the
reaction of EC 1.1.1.36 is defined more generally as
(R)-3-hydroxyacyl-CoA + NADP+ = 3-oxoacyl-CoA + NADPH.
Members of this family may act in the biosynthesis of
poly-beta-hydroxybutyrate (e.g. Rhizobium meliloti) and
related poly-beta-hydroxyalkanoates. Note that the
member of this family from Azospirillum brasilense,
designated NodG, appears to lack acetoacetyl-CoA
reductase activity and to act instead in the production
of nodulation factor. This family is downgraded to
subfamily for this NodG. Other proteins designated
NodG, as from Rhizobium, belong to related but distinct
protein families.
Length = 242
Score = 29.3 bits (66), Expect = 2.5
Identities = 18/75 (24%), Positives = 29/75 (38%), Gaps = 26/75 (34%)
Query: 5 KIILVTGGTGLVGKAI----------------------EKIVKEEEKRDDETWIFVSSKE 42
+I LVTGG G +G AI E ++E+ + + E
Sbjct: 1 RIALVTGGMGGIGTAICQRLAKDGYRVAANCGPNEERAEAWLQEQGALGFDFRVV----E 56
Query: 43 ADLSNLESTQQLFSK 57
D+S+ ES + +K
Sbjct: 57 GDVSSFESCKAAVAK 71
>gnl|CDD|188825 cd09441, LIM2_SF3, The second Lim domain of pollen specific protein
SF3. The second Lim domain of pollen specific protein
SF3: SF3 is a Lim protein that is found exclusively in
mature plant pollen grains. It contains two LIM domains.
The exact function of SF3 is unknown. It may be a
transcription factor required for the expression of late
pollen genes. It is possible that SF3 protein is
involved in controlling pollen-specific processes such
as male gamete maturation, pollen tube formation, or
even fertilization. As in other LIM domains, this domain
family is 50-60 amino acids in size and shares two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein.
Length = 61
Score = 27.0 bits (60), Expect = 2.5
Identities = 12/30 (40%), Positives = 15/30 (50%)
Query: 113 CIFPDKTTYPIDETMVHNGPPHPSNFGYSH 142
C+ KT YPI++ V H S F SH
Sbjct: 1 CVACGKTVYPIEKVTVEGTSYHKSCFKCSH 30
>gnl|CDD|178484 PLN02896, PLN02896, cinnamyl-alcohol dehydrogenase.
Length = 353
Score = 29.4 bits (66), Expect = 2.7
Identities = 53/214 (24%), Positives = 81/214 (37%), Gaps = 50/214 (23%)
Query: 9 VTGGTGLVGKAIEKIVKEEEKRDDETWIFVSSKEADLSNLESTQQLFSKYKPTHVIHL-- 66
VTG TG +G + K++ + A L + + L SK+K + L
Sbjct: 15 VTGATGYIGSWLVKLLLQRGYT----------VHATLRDPAKSLHLLSKWKEGDRLRLFR 64
Query: 67 ----------AAMVG--GLFH---------NMSHNLDFFRVNMKIND-------NVLDTS 98
A+ G G+FH + HN V K+ D NVL +
Sbjct: 65 ADLQEEGSFDEAVKGCDGVFHVAASMEFDVSSDHNNIEEYVQSKVIDPAIKGTLNVLKSC 124
Query: 99 YKQG-VKKVV--SCLSTCIFPDKT---TYPIDET----MVHNGPPHPSNFGYSHAKRMLD 148
K VK+VV S +ST D +DET + H S + Y +K + +
Sbjct: 125 LKSKTVKRVVFTSSISTLTAKDSNGRWRAVVDETCQTPIDHVWNTKASGWVYVLSKLLTE 184
Query: 149 VLNKAYYQQHGVTYTSVIPCNVFGPHDNYNLESS 182
Y +++G+ SVI V GP ++ SS
Sbjct: 185 EAAFKYAKENGIDLVSVITTTVAGPFLTPSVPSS 218
>gnl|CDD|187628 cd05370, SDR_c2, classical (c) SDR, subgroup 2. Short-chain
dehydrogenases/reductases (SDRs, aka Tyrosine-dependent
oxidoreductases) are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold (alpha/beta
folding pattern with a central beta-sheet), an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRs are
approximately 350 residues. Sequence identity between
different SDR enzymes are typically in the 15-30%
range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes catalyze a
wide range of activities including the metabolism of
steroids, cofactors, carbohydrates, lipids, aromatic
compounds, and amino acids, and act in redox sensing.
Classical SDRs have an TGXXX[AG]XG cofactor binding
motif and a YXXXK active site motif, with the Tyr
residue of the active site motif serving as a critical
catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 228
Score = 29.2 bits (66), Expect = 2.8
Identities = 15/71 (21%), Positives = 27/71 (38%), Gaps = 13/71 (18%)
Query: 5 KIILVTGGTGLVGKAIEK----------IVKEEEKRDDET---WIFVSSKEADLSNLEST 51
+L+TGGT +G A+ + I E+R E + + D+ + ES
Sbjct: 6 NTVLITGGTSGIGLALARKFLEAGNTVIITGRREERLAEAKKELPNIHTIVLDVGDAESV 65
Query: 52 QQLFSKYKPTH 62
+ L +
Sbjct: 66 EALAEALLSEY 76
>gnl|CDD|183375 PRK11908, PRK11908, NAD-dependent epimerase/dehydratase family
protein; Provisional.
Length = 347
Score = 29.3 bits (66), Expect = 3.4
Identities = 11/34 (32%), Positives = 20/34 (58%)
Query: 140 YSHAKRMLDVLNKAYYQQHGVTYTSVIPCNVFGP 173
Y+ +K+++D + AY + G+ +T P N GP
Sbjct: 149 YACSKQLMDRVIWAYGMEEGLNFTLFRPFNWIGP 182
>gnl|CDD|215146 PLN02260, PLN02260, probable rhamnose biosynthetic enzyme.
Length = 668
Score = 29.3 bits (66), Expect = 3.6
Identities = 36/154 (23%), Positives = 67/154 (43%), Gaps = 18/154 (11%)
Query: 8 LVTGGTGLVGKAIEKIVKEEEKRDDETWIFVSSKEADLSNLESTQQLFSKYKPTHVIHLA 67
L+ G TG +G + K+ +++ + + + D S+L + + KPTHV + A
Sbjct: 384 LIYGRTGWIGGLLGKLCEKQGIA----YEYGKGRLEDRSSLLADIR---NVKPTHVFNAA 436
Query: 68 AMVGGLFHNM----SHNLDFFRVNMKINDNVLDTSYKQGVKKVVSCLSTCIFPDKTTYPI 123
+ G N+ SH ++ R N+ + D + G+ +++ + CIF +P
Sbjct: 437 GVTGR--PNVDWCESHKVETIRANVVGTLTLADVCRENGL-LMMNFATGCIFEYDAKHPE 493
Query: 124 DETMVHNGPPHPSNFG---YSHAKRMLDVLNKAY 154
+ P NF YS K M++ L + Y
Sbjct: 494 GSGIGFKEEDKP-NFTGSFYSKTKAMVEELLREY 526
>gnl|CDD|180576 PRK06463, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 255
Score = 29.0 bits (65), Expect = 3.9
Identities = 12/30 (40%), Positives = 19/30 (63%), Gaps = 1/30 (3%)
Query: 1 MAEEKIILVTGGTGLVGKAI-EKIVKEEEK 29
+ K+ L+TGGT +G+AI E ++E K
Sbjct: 4 RFKGKVALITGGTRGIGRAIAEAFLREGAK 33
>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 = 28.8 bits (65), Expect = 3.9
Identities = 9/14 (64%), Positives = 11/14 (78%)
Query: 7 ILVTGGTGLVGKAI 20
ILVTG TG +G A+
Sbjct: 1 ILVTGATGKLGTAV 14
>gnl|CDD|226466 COG3957, COG3957, Phosphoketolase [Carbohydrate transport and
metabolism].
Length = 793
Score = 29.3 bits (66), Expect = 4.1
Identities = 22/96 (22%), Positives = 34/96 (35%), Gaps = 16/96 (16%)
Query: 207 SRARFPPGANSFGLDKLDLIPFSLFPFCFTGGDEFKVLGTGKPLRQFIYSLDLAR----- 261
R FPP AN+ +++ C ++ V+ K R +++ A
Sbjct: 559 VRVYFPPDANTL---------LAVYDHCLRSRNKINVIVASKQPRPQWLTMEQAEKHCTD 609
Query: 262 -LFIWVLREYDSVEPIILSVDEKDEVTIAEVAEAIA 296
IW D EP ++ D TI EV A
Sbjct: 610 GAGIWEWASGDDGEPDVVMACAGDVPTI-EVLAAAQ 644
>gnl|CDD|215279 PLN02503, PLN02503, fatty acyl-CoA reductase 2.
Length = 605
Score = 29.1 bits (65), Expect = 4.1
Identities = 21/66 (31%), Positives = 32/66 (48%), Gaps = 11/66 (16%)
Query: 5 KIILVTGGTGLVGKA-IEKIVKEEEKRDDETWIFV----SSKEADLSNLES---TQQLFS 56
K L+TG TG + K IEKI++ D I++ KEA + L++ +LF
Sbjct: 120 KNFLITGATGFLAKVLIEKILRTNP---DVGKIYLLIKAKDKEAAIERLKNEVIDAELFK 176
Query: 57 KYKPTH 62
+ TH
Sbjct: 177 CLQETH 182
>gnl|CDD|181508 PRK08628, PRK08628, short chain dehydrogenase; Provisional.
Length = 258
Score = 28.8 bits (65), Expect = 4.1
Identities = 10/25 (40%), Positives = 17/25 (68%)
Query: 3 EEKIILVTGGTGLVGKAIEKIVKEE 27
++K+++VTGG +G AI + EE
Sbjct: 6 KDKVVIVTGGASGIGAAISLRLAEE 30
>gnl|CDD|236156 PRK08125, PRK08125, bifunctional UDP-glucuronic acid
decarboxylase/UDP-4-amino-4-deoxy-L-arabinose
formyltransferase; Validated.
Length = 660
Score = 29.2 bits (66), Expect = 4.3
Identities = 24/66 (36%), Positives = 35/66 (53%), Gaps = 4/66 (6%)
Query: 131 GPPHPSNFGYSHAKRMLDVLNKAYYQQHGVTYTSVIPCNVFGPH-DNYN---LESSHVIP 186
GP + + YS +K++LD + AY ++ G+ +T P N GP DN N + SS I
Sbjct: 454 GPINKQRWIYSVSKQLLDRVIWAYGEKEGLRFTLFRPFNWMGPRLDNLNAARIGSSRAIT 513
Query: 187 GLIRKL 192
LI L
Sbjct: 514 QLILNL 519
>gnl|CDD|225255 COG2380, COG2380, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 327
Score = 28.8 bits (64), Expect = 4.6
Identities = 19/97 (19%), Positives = 34/97 (35%), Gaps = 5/97 (5%)
Query: 199 GKDQSVFESRARFPPGANSFGL-DKLDLIPFSLFPFCFTGGDEFKVLGTGKPLRQFIYSL 257
G +++F + P L TGG +FKV GK + L
Sbjct: 89 GGRKALFLD-DKPPVAERVLAFSQDAPEEGARLSRNEETGGLDFKVGREGKDAMAAVDKL 147
Query: 258 DLARLFIWVLREYDSVEPIILSVDEKDEVTIAEVAEA 294
+ +L I R+ + L++ KD + + +
Sbjct: 148 -MLQLEIEESRQIAHEDGEALAL--KDGLALQDGPFE 181
>gnl|CDD|187647 cd08943, R1PA_ADH_SDR_c, rhamnulose-1-phosphate aldolase/alcohol
dehydrogenase, classical (c) SDRs. This family has
bifunctional proteins with an N-terminal aldolase and a
C-terminal classical SDR domain. One member is
identified as a rhamnulose-1-phosphate aldolase/alcohol
dehydrogenase. The SDR domain has a canonical SDR
glycine-rich NAD(P) binding motif and a match to the
characteristic active site triad. However, it lacks an
upstream active site Asn typical of SDRs. SDRs are a
functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold (alpha/beta folding pattern with a
central beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRs are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes catalyze a
wide range of activities including the metabolism of
steroids, cofactors, carbohydrates, lipids, aromatic
compounds, and amino acids, and act in redox sensing.
Classical SDRs have an TGXXX[AG]XG cofactor binding
motif and a YXXXK active site motif, with the Tyr
residue of the active site motif serving as a critical
catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 250
Score = 28.5 bits (64), Expect = 4.9
Identities = 11/24 (45%), Positives = 14/24 (58%)
Query: 5 KIILVTGGTGLVGKAIEKIVKEEE 28
K+ LVTGG +G AI K + E
Sbjct: 2 KVALVTGGASGIGLAIAKRLAAEG 25
>gnl|CDD|222238 pfam13580, SIS_2, SIS domain. SIS (Sugar ISomerase) domains are
found in many phosphosugar isomerases and phosphosugar
binding proteins. SIS domains are also found in proteins
that regulate the expression of genes involved in
synthesis of phosphosugars.
Length = 138
Score = 27.9 bits (63), Expect = 5.1
Identities = 10/36 (27%), Positives = 21/36 (58%)
Query: 270 YDSVEPIILSVDEKDEVTIAEVAEAIANAFQFKGRI 305
+D + ++ V+E + I + A+ IA+A + G+I
Sbjct: 3 FDEISALLERVEETEAEAIEKAADLIADALKNGGKI 38
>gnl|CDD|221753 pfam12753, Nro1, Nuclear pore complex subunit Nro1. In fission
yeast, this protein is a positive regulator of the
stability of Sre1N, the sterol regulatory
element-binding protein which is an ER membrane-bound
transcription factor that controls adaptation to low
oxygen-growth. In addition, the fission yeast Nro1 is a
direct inhibitor of a protein that inhibits SreN1
degradation, Ofd1 (an oxoglutamate deoxygenase). The
outcome of this reactivity is that Ofd1 acts as an
oxygen sensor that regulates the binding of Nro1 to Ofd1
to control the stability of Sre1N. Solution of the
structure of Nro1 reveals it to be made up of a number
of TPR coils.
Length = 401
Score = 28.7 bits (64), Expect = 5.3
Identities = 18/44 (40%), Positives = 27/44 (61%), Gaps = 3/44 (6%)
Query: 13 TGLVGKAIEKIVKEEEKRDDETWIFVSSKEADLSNL---ESTQQ 53
L+ KA+E + K E++ D ETW+ V+ DL NL ES++Q
Sbjct: 328 QSLIKKALEYLKKAEDEDDPETWVDVAEAMIDLGNLYDVESSEQ 371
>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 = 28.4 bits (64), Expect = 5.6
Identities = 25/114 (21%), Positives = 46/114 (40%), Gaps = 4/114 (3%)
Query: 238 GDEFKVLGTGKP-LRQFIYSLDLARLFIWVLREYDSVEPIILSVDEKDE--VTIAEVAEA 294
G + G G +R ++S DL L++ + D + + ++ E V++ E+
Sbjct: 224 GKPLTIFGYGGKQVRDVLHSADLVNLYLRQFQNPDRRKGEVFNIGGGRENSVSLLELIAL 283
Query: 295 IANAFQFKGRITFDTNAADGQLKKTASNRKLRELRGPGFEFTPFQQAVQESVAW 348
K D N Q+ + RK++E G E P ++ + E AW
Sbjct: 284 CEEITGRKMESYKDENRPGDQIWYISDIRKIKEKPGWKPERDP-REILAEIYAW 336
>gnl|CDD|233954 TIGR02622, CDP_4_6_dhtase, CDP-glucose 4,6-dehydratase. Members
of this protein family are CDP-glucose 4,6-dehydratase
from a variety of Gram-negative and Gram-positive
bacteria. Members typically are encoded next to a gene
that encodes a glucose-1-phosphate
cytidylyltransferase, which produces the substrate,
CDP-D-glucose, used by this enzyme to produce
CDP-4-keto-6-deoxyglucose [Cell envelope, Biosynthesis
and degradation of surface polysaccharides and
lipopolysaccharides].
Length = 349
Score = 28.4 bits (64), Expect = 5.6
Identities = 8/26 (30%), Positives = 15/26 (57%)
Query: 43 ADLSNLESTQQLFSKYKPTHVIHLAA 68
D+ + ++ +++KP V HLAA
Sbjct: 59 GDIRDAAKLRKAIAEFKPEIVFHLAA 84
>gnl|CDD|215720 pfam00106, adh_short, short chain dehydrogenase. This family
contains a wide variety of dehydrogenases.
Length = 167
Score = 27.9 bits (63), Expect = 6.2
Identities = 18/113 (15%), Positives = 38/113 (33%), Gaps = 28/113 (24%)
Query: 5 KIILVTGGTGLVGKAI-EKIVKE-----------------EEKRDD--ETWIFVSSKEAD 44
+L+TGGTG +G A+ + E E + V+ D
Sbjct: 1 GTVLITGGTGGLGLALARWLAAEGARHLVLVSRRGPAPGAAELVAELEALGAEVTVAACD 60
Query: 45 LSNLESTQQLFSKYKPTH-----VIHLAAMVG-GLFHNMSHNLDFFRVNMKIN 91
+++ ++ L + V+H A ++ G ++ + F +
Sbjct: 61 VADRDALAALLAALPAALGPLDGVVHNAGVLDDGPLEELT--PERFERVLAPK 111
>gnl|CDD|151051 pfam10491, Nrf1_DNA-bind, NLS-binding and DNA-binding and
dimerisation domains of Nrf1. In Drosophila, the erect
wing (ewg) protein is required for proper development of
the central nervous system and the indirect flight
muscles. The fly ewg gene encodes a novel DNA-binding
domain that is also found in four genes previously
identified in sea urchin, chicken, zebrafish, and human.
Nuclear respiratory factor-1 is a transcriptional
activator that has been implicated in the nuclear
control of respiratory chain expression in vertebrates.
The first 26 amino acids of nuclear respiratory factor-1
are required for the binding of dynein light chain. The
interaction with dynein light chain is observed for both
ewg and Nrf-1, transcription factors that are
structurally and functionally similar between humans and
Drosophila. The highest level of expression of both ewg
and Nrf-1 was found in the central nervous system,
somites, first branchial arch, optic vesicle, and otic
vesicle. In the mouse Nrf-1 protein, there is also an
NLS domain at 88-116, and a DNA binding and dimerisation
domain at 127-282. Ewg is a site-specific
transcriptional activator, and evolutionarily conserved
regions of ewg contribute both positively and negatively
to transcriptional activity.
Length = 214
Score = 28.0 bits (62), Expect = 6.4
Identities = 19/53 (35%), Positives = 27/53 (50%), Gaps = 5/53 (9%)
Query: 292 AEAIANAFQFKGRITFDTNAADGQLKKTASNRKLRELRGPGFEFTPF--QQAV 342
A AIA + K +F+TN + ++K R LR+LR E+ QQAV
Sbjct: 8 AAAIATGKKRKRPHSFETNPS---IRKRQQTRLLRKLRATIDEYATRVGQQAV 57
>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 = 28.0 bits (63), Expect = 6.9
Identities = 22/69 (31%), Positives = 30/69 (43%), Gaps = 3/69 (4%)
Query: 238 GDEFKVLGTGKPLRQFIYSLDLARLFIWVLREYDSV-EPIILSVDEKDEVTIAEVAEAIA 296
G V G G L QFI+ DLAR + ++ ++ DE VT E+ EA A
Sbjct: 176 GRPILVPGDGHSLVQFIHVKDLARALLGAAGNPKAIGGIFNITGDEA--VTWDELLEACA 233
Query: 297 NAFQFKGRI 305
A + I
Sbjct: 234 KALGKEAEI 242
>gnl|CDD|181077 PRK07677, PRK07677, short chain dehydrogenase; Provisional.
Length = 252
Score = 28.1 bits (63), Expect = 7.0
Identities = 10/23 (43%), Positives = 17/23 (73%)
Query: 5 KIILVTGGTGLVGKAIEKIVKEE 27
K++++TGG+ +GKA+ K EE
Sbjct: 2 KVVIITGGSSGMGKAMAKRFAEE 24
>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 = 28.0 bits (63), Expect = 7.3
Identities = 8/13 (61%), Positives = 12/13 (92%)
Query: 7 ILVTGGTGLVGKA 19
I++TGGTG +G+A
Sbjct: 2 IVITGGTGFIGRA 14
>gnl|CDD|183773 PRK12824, PRK12824, acetoacetyl-CoA reductase; Provisional.
Length = 245
Score = 27.8 bits (62), Expect = 7.4
Identities = 22/99 (22%), Positives = 36/99 (36%), Gaps = 24/99 (24%)
Query: 5 KIILVTGGTGLVGKAIEK------------------IVKEEEKRDDETWIFVSSKEADLS 46
KI LVTG +G AI + K+ + T V KE D++
Sbjct: 3 KIALVTGAKRGIGSAIARELLNDGYRVIATYFSGNDCAKDWFEEYGFTEDQVRLKELDVT 62
Query: 47 NLESTQQLFSK----YKPTHVIHLAAMV--GGLFHNMSH 79
+ E + ++ P ++ A + +F MSH
Sbjct: 63 DTEECAEALAEIEEEEGPVDILVNNAGITRDSVFKRMSH 101
>gnl|CDD|180439 PRK06171, PRK06171, sorbitol-6-phosphate 2-dehydrogenase;
Provisional.
Length = 266
Score = 28.1 bits (63), Expect = 7.7
Identities = 13/24 (54%), Positives = 17/24 (70%), Gaps = 3/24 (12%)
Query: 3 EEKIILVTGGTGLVGKAIEKIVKE 26
+ KII+VTGG+ +G A IVKE
Sbjct: 8 QGKIIIVTGGSSGIGLA---IVKE 28
>gnl|CDD|161732 TIGR00147, TIGR00147, lipid kinase, YegS/Rv2252/BmrU family. The
E. coli member of this family, YegS has been purified
and shown to have phosphatidylglycerol kinase activity.
The member from M. tuberculosis, Rv2252, has
diacylglycerol kinase activity. BmrU from B. subtilis
is in an operon with multidrug efflux transporter Bmr,
but is uncharacterized [Unknown function, Enzymes of
unknown specificity].
Length = 293
Score = 27.9 bits (62), Expect = 8.0
Identities = 8/51 (15%), Positives = 20/51 (39%)
Query: 6 IILVTGGTGLVGKAIEKIVKEEEKRDDETWIFVSSKEADLSNLESTQQLFS 56
I+ T G K + +++ + E + V+ ++ D + + F
Sbjct: 7 ILNPTAGKSNDNKPLREVIMLLREEGMEIHVRVTWEKGDAARYVEEARKFG 57
>gnl|CDD|219687 pfam07993, NAD_binding_4, Male sterility protein. This family
represents the C-terminal region of the male sterility
protein in a number of arabidopsis and drosophila. A
sequence-related jojoba acyl CoA reductase is also
included.
Length = 245
Score = 27.6 bits (62), Expect = 8.4
Identities = 37/187 (19%), Positives = 58/187 (31%), Gaps = 64/187 (34%)
Query: 9 VTGGTGLVGKAI-EKIVK-----------------------EEEKRDDETW--IFVSSK- 41
+TG TG +GK + EK+++ +E + + +
Sbjct: 1 LTGATGFLGKVLLEKLLRSTPEVKIYCLVRAKDGESALERLRQELLKYGLFDRLKALERI 60
Query: 42 ---EADLS--NL----ESTQQLFSKYKPTHVIHLAAMVGGLFHNMSHNLDFFRVNMKIND 92
DLS NL E Q+L + +IH AA V N R
Sbjct: 61 IPVAGDLSEPNLGLSDEDFQELAE--EVDVIIHNAATV-----NFVEPYSDLR-----AT 108
Query: 93 NVLDTSY-----KQGVKK--------VVSCLSTCIFPDKTTYPIDETMVHNGPPHPSNFG 139
NVL T KQ K V+ + +K ++ G G
Sbjct: 109 NVLGTREVLRLAKQMKKLPFHHVSTAYVNGERGGLLEEKPYKLDEDEPALLGGLP---NG 165
Query: 140 YSHAKRM 146
Y+ +K +
Sbjct: 166 YTQSKWL 172
>gnl|CDD|235546 PRK05653, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Validated.
Length = 246
Score = 27.8 bits (63), Expect = 8.4
Identities = 8/16 (50%), Positives = 11/16 (68%)
Query: 5 KIILVTGGTGLVGKAI 20
K LVTG + +G+AI
Sbjct: 6 KTALVTGASRGIGRAI 21
>gnl|CDD|215310 PLN02572, PLN02572, UDP-sulfoquinovose synthase.
Length = 442
Score = 27.8 bits (62), Expect = 9.0
Identities = 11/38 (28%), Positives = 16/38 (42%), Gaps = 5/38 (13%)
Query: 35 WIFVSSKEADLSNL-----ESTQQLFSKYKPTHVIHLA 67
W VS KE +L E + F ++P V+H
Sbjct: 107 WKEVSGKEIELYVGDICDFEFLSEAFKSFEPDAVVHFG 144
>gnl|CDD|214395 CHL00204, ycf1, Ycf1; Provisional.
Length = 1832
Score = 28.1 bits (63), Expect = 9.1
Identities = 17/57 (29%), Positives = 30/57 (52%)
Query: 3 EEKIILVTGGTGLVGKAIEKIVKEEEKRDDETWIFVSSKEADLSNLESTQQLFSKYK 59
E+KI +T T + IEKI KE++K + I + D +ES+++++ K
Sbjct: 1024 EKKIKDLTDRTKTIRNQIEKITKEKKKITNTINISPNKTSYDSKIIESSKKIWQILK 1080
>gnl|CDD|183298 PRK11752, PRK11752, putative S-transferase; Provisional.
Length = 264
Score = 27.6 bits (62), Expect = 9.5
Identities = 14/38 (36%), Positives = 17/38 (44%), Gaps = 15/38 (39%)
Query: 116 PDKTTYPIDE-TMVHNGPPHPSNFGYSHAKRMLDVLNK 152
P+K Y I+ TM AKR LDVL+K
Sbjct: 169 PEKIEYAINRFTM--------------EAKRQLDVLDK 192
>gnl|CDD|236145 PRK08063, PRK08063, enoyl-(acyl carrier protein) reductase;
Provisional.
Length = 250
Score = 27.8 bits (62), Expect = 9.5
Identities = 16/54 (29%), Positives = 25/54 (46%), Gaps = 2/54 (3%)
Query: 1 MAEEKIILVTGGTGLVGKAIEKIVKEEEKRDDETWIFVSSKEADLSNLESTQQL 54
+ K+ LVTG + +GKAI + EE D + S++A E + L
Sbjct: 1 VFSGKVALVTGSSRGIGKAIALRLAEEGY--DIAVNYARSRKAAEETAEEIEAL 52
>gnl|CDD|180462 PRK06198, PRK06198, short chain dehydrogenase; Provisional.
Length = 260
Score = 27.7 bits (62), Expect = 9.9
Identities = 11/25 (44%), Positives = 15/25 (60%)
Query: 3 EEKIILVTGGTGLVGKAIEKIVKEE 27
+ K+ LVTGGT +G AI + E
Sbjct: 5 DGKVALVTGGTQGLGAAIARAFAER 29
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.320 0.137 0.406
Gapped
Lambda K H
0.267 0.0806 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 18,612,079
Number of extensions: 1808228
Number of successful extensions: 2219
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2156
Number of HSP's successfully gapped: 141
Length of query: 358
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 260
Effective length of database: 6,590,910
Effective search space: 1713636600
Effective search space used: 1713636600
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 60 (26.7 bits)