RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 015172
(412 letters)
>gnl|CDD|215058 PLN00106, PLN00106, malate dehydrogenase.
Length = 323
Score = 616 bits (1592), Expect = 0.0
Identities = 237/322 (73%), Positives = 267/322 (82%), Gaps = 2/322 (0%)
Query: 79 SSEQRPQYALQPQASFKVAVLGAAGGIGQPLALLIKMSPLVSALHLYDVMNVKGVAADLS 138
+S R A FKVAVLGAAGGIGQPL+LL+KM+PLVS LHLYD+ N GVAAD+S
Sbjct: 4 ASSLRACRAKGGAPGFKVAVLGAAGGIGQPLSLLMKMNPLVSELHLYDIANTPGVAADVS 63
Query: 139 HCNTPSQVLDFTGPEELASALKGVNVVVIPAGVPRKPGMTRDDLFNINANIVKTLVEAVA 198
H NTP+QV F G ++L ALKG ++V+IPAGVPRKPGMTRDDLFNINA IVKTL EAVA
Sbjct: 64 HINTPAQVRGFLGDDQLGDALKGADLVIIPAGVPRKPGMTRDDLFNINAGIVKTLCEAVA 123
Query: 199 DNCPDAFIHIISNPVNSTVPIAAEVLKQKGVYDPKKLFGVTTLDVVRANTFVAQKKNLKL 258
+CP+A ++IISNPVNSTVPIAAEVLK+ GVYDPKKLFGVTTLDVVRANTFVA+KK L
Sbjct: 124 KHCPNALVNIISNPVNSTVPIAAEVLKKAGVYDPKKLFGVTTLDVVRANTFVAEKKGLDP 183
Query: 259 IDVDVPVVGGHAGITILPLLSKTMPSVSFTDEEVGDLTVRIQNAGTEVVEAKAGAGSATL 318
DVDVPVVGGHAGITILPLLS+ P VSFTDEE+ LT RIQN GTEVVEAKAGAGSATL
Sbjct: 184 ADVDVPVVGGHAGITILPLLSQATPKVSFTDEEIEALTKRIQNGGTEVVEAKAGAGSATL 243
Query: 319 SMAYAAARFVESSLRALDGDGDVYECVFVESNLTELPFFASRVKLGRNGVESLISSDLQG 378
SMAYAAARF ++ LR L+G+ DV EC +V+S +TELPFFAS+V+LGRNGVE L
Sbjct: 244 SMAYAAARFADACLRGLNGEADVVECSYVQSEVTELPFFASKVRLGRNGVE--EVLGLGP 301
Query: 379 LTEYEQKALEALKPELKASIEK 400
L+EYEQK LEALKPELKASIEK
Sbjct: 302 LSEYEQKGLEALKPELKASIEK 323
>gnl|CDD|133422 cd01337, MDH_glyoxysomal_mitochondrial, Glyoxysomal and
mitochondrial malate dehydrogenases. MDH is one of the
key enzymes in the citric acid cycle, facilitating both
the conversion of malate to oxaloacetate and
replenishing levels of oxalacetate by reductive
carboxylation of pyruvate. Members of this subfamily are
localized to the glycosome and mitochondria. MDHs are
part of the NAD(P)-binding Rossmann fold superfamily,
which includes a wide variety of protein families
including the NAD(P)-binding domains of alcohol
dehydrogenases, tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate dehydrogenases,
formate/glycerate dehydrogenases, siroheme synthases,
6-phosphogluconate dehydrogenases, aminoacid
dehydrogenases, repressor rex, and NAD-binding potassium
channel domains, among others.
Length = 310
Score = 541 bits (1397), Expect = 0.0
Identities = 212/312 (67%), Positives = 245/312 (78%), Gaps = 2/312 (0%)
Query: 94 FKVAVLGAAGGIGQPLALLIKMSPLVSALHLYDVMNVKGVAADLSHCNTPSQVLDFTGPE 153
KVAVLGAAGGIGQPL+LL+K++PLVS L LYD++N GVAADLSH NTP++V + GPE
Sbjct: 1 VKVAVLGAAGGIGQPLSLLLKLNPLVSELALYDIVNTPGVAADLSHINTPAKVTGYLGPE 60
Query: 154 ELASALKGVNVVVIPAGVPRKPGMTRDDLFNINANIVKTLVEAVADNCPDAFIHIISNPV 213
EL ALKG +VVVIPAGVPRKPGMTRDDLFNINA IV+ L AVA CP A I IISNPV
Sbjct: 61 ELKKALKGADVVVIPAGVPRKPGMTRDDLFNINAGIVRDLATAVAKACPKALILIISNPV 120
Query: 214 NSTVPIAAEVLKQKGVYDPKKLFGVTTLDVVRANTFVAQKKNLKLIDVDVPVVGGHAGIT 273
NSTVPIAAEVLK+ GVYDPK+LFGVTTLDVVRANTFVA+ L V+VPV+GGH+G+T
Sbjct: 121 NSTVPIAAEVLKKAGVYDPKRLFGVTTLDVVRANTFVAELLGLDPAKVNVPVIGGHSGVT 180
Query: 274 ILPLLSKTMPSVSFTDEEVGDLTVRIQNAGTEVVEAKAGAGSATLSMAYAAARFVESSLR 333
ILPLLS+ P +F EE+ LT RIQ G EVV+AKAGAGSATLSMAYA ARF S LR
Sbjct: 181 ILPLLSQCQPPFTFDQEEIEALTHRIQFGGDEVVKAKAGAGSATLSMAYAGARFANSLLR 240
Query: 334 ALDGDGDVYECVFVESNLTELPFFASRVKLGRNGVESLISSDLQGLTEYEQKALEALKPE 393
L G+ V EC +VES++TE PFFA+ V+LG+NGVE + L L +YE+K LEA PE
Sbjct: 241 GLKGEKGVIECAYVESDVTEAPFFATPVELGKNGVEKNLG--LGKLNDYEKKLLEAALPE 298
Query: 394 LKASIEKGVAFA 405
LK +IEKGV F
Sbjct: 299 LKKNIEKGVDFV 310
>gnl|CDD|235340 PRK05086, PRK05086, malate dehydrogenase; Provisional.
Length = 312
Score = 425 bits (1094), Expect = e-149
Identities = 188/315 (59%), Positives = 224/315 (71%), Gaps = 6/315 (1%)
Query: 95 KVAVLGAAGGIGQPLALLIKMS-PLVSALHLYDVMNVK-GVAADLSHCNTPSQVLDFTGP 152
KVAVLGAAGGIGQ LALL+K P S L LYD+ V GVA DLSH T ++ F+G
Sbjct: 2 KVAVLGAAGGIGQALALLLKTQLPAGSELSLYDIAPVTPGVAVDLSHIPTAVKIKGFSG- 60
Query: 153 EELASALKGVNVVVIPAGVPRKPGMTRDDLFNINANIVKTLVEAVADNCPDAFIHIISNP 212
E+ AL+G +VV+I AGV RKPGM R DLFN+NA IVK LVE VA CP A I II+NP
Sbjct: 61 EDPTPALEGADVVLISAGVARKPGMDRSDLFNVNAGIVKNLVEKVAKTCPKACIGIITNP 120
Query: 213 VNSTVPIAAEVLKQKGVYDPKKLFGVTTLDVVRANTFVAQKKNLKLIDVDVPVVGGHAGI 272
VN+TV IAAEVLK+ GVYD KLFGVTTLDV+R+ TFVA+ K + +V+VPV+GGH+G+
Sbjct: 121 VNTTVAIAAEVLKKAGVYDKNKLFGVTTLDVIRSETFVAELKGKQPGEVEVPVIGGHSGV 180
Query: 273 TILPLLSKTMPSVSFTDEEVGDLTVRIQNAGTEVVEAKAGAGSATLSMAYAAARFVESSL 332
TILPLLS+ +P VSFT++EV DLT RIQNAGTEVVEAKAG GSATLSM AAARF S +
Sbjct: 181 TILPLLSQ-VPGVSFTEQEVADLTKRIQNAGTEVVEAKAGGGSATLSMGQAAARFGLSLV 239
Query: 333 RALDGDGDVYECVFVESNLTELPFFASRVKLGRNGVESLISSDLQGLTEYEQKALEALKP 392
RAL G+ V EC +VE + FFA V LG+NGVE + + L+ +EQ ALE +
Sbjct: 240 RALQGEQGVVECAYVEGDGKYARFFAQPVLLGKNGVEERL--PIGTLSAFEQNALEGMLD 297
Query: 393 ELKASIEKGVAFAQK 407
LK I G F K
Sbjct: 298 TLKKDIALGEEFVNK 312
>gnl|CDD|130833 TIGR01772, MDH_euk_gproteo, malate dehydrogenase, NAD-dependent.
This model represents the NAD-dependent malate
dehydrogenase found in eukaryotes and certain gamma
proteobacteria. The enzyme is involved in the citric
acid cycle as well as the glyoxalate cycle. Several
isoforms exidt in eukaryotes. In S. cereviseae, for
example, there are cytoplasmic, mitochondrial and
peroxisomal forms. Although malate dehydrogenases have
in some cases been mistaken for lactate dehydrogenases
due to the similarity of these two substrates and the
apparent ease with which evolution can toggle these
activities, critical residues have been identified which
can discriminate between the two activities. At the time
of the creation of this model no hits above the trusted
cutoff contained critical residues typical of lactate
dehydrogenases [Energy metabolism, TCA cycle].
Length = 312
Score = 421 bits (1085), Expect = e-148
Identities = 196/314 (62%), Positives = 239/314 (76%), Gaps = 3/314 (0%)
Query: 95 KVAVLGAAGGIGQPLALLIKMSPLVSALHLYDVMNVKGVAADLSHCNTPSQVLDFTGPEE 154
KVAVLGAAGGIGQPL+LL+K+ P VS L LYD+ GVAADLSH T + V F+G E
Sbjct: 1 KVAVLGAAGGIGQPLSLLLKLQPYVSELSLYDIAGAAGVAADLSHIPTAASVKGFSGEEG 60
Query: 155 LASALKGVNVVVIPAGVPRKPGMTRDDLFNINANIVKTLVEAVADNCPDAFIHIISNPVN 214
L +ALKG +VVVIPAGVPRKPGMTRDDLFN+NA IVK LV AVA++CP A I +I+NPVN
Sbjct: 61 LENALKGADVVVIPAGVPRKPGMTRDDLFNVNAGIVKDLVAAVAESCPKAMILVITNPVN 120
Query: 215 STVPIAAEVLKQKGVYDPKKLFGVTTLDVVRANTFVAQKKNLKLIDVDVPVVGGHAGITI 274
STVPIAAEVLK+KGVYDP KLFGVTTLD+VRANTFVA+ K ++V+VPV+GGH+G TI
Sbjct: 121 STVPIAAEVLKKKGVYDPNKLFGVTTLDIVRANTFVAELKGKDPMEVNVPVIGGHSGETI 180
Query: 275 LPLLSKTMPSVSFTDEEVGDLTVRIQNAGTEVVEAKAGAGSATLSMAYAAARFVESSLRA 334
+PL+S+ V FT++++ L RIQNAGTEVV+AKAGAGSATLSMA+A ARFV S +R
Sbjct: 181 IPLISQCPGKVLFTEDQLEALIHRIQNAGTEVVKAKAGAGSATLSMAFAGARFVLSLVRG 240
Query: 335 LDGDGDVYECVFVESNL-TELPFFASRVKLGRNGVESLISSDLQGLTEYEQKALEALKPE 393
L G+ V EC +VES+ TE FFA+ + LG+NGVE + L+ +E+K L PE
Sbjct: 241 LKGEEGVVECAYVESDGVTEATFFATPLLLGKNGVEK--RLGIGKLSSFEEKMLNGALPE 298
Query: 394 LKASIEKGVAFAQK 407
LK +I+KG F
Sbjct: 299 LKKNIKKGEEFVAS 312
>gnl|CDD|240360 PTZ00325, PTZ00325, malate dehydrogenase; Provisional.
Length = 321
Score = 398 bits (1024), Expect = e-138
Identities = 189/318 (59%), Positives = 239/318 (75%), Gaps = 5/318 (1%)
Query: 93 SFKVAVLGAAGGIGQPLALLIKMSPLVSALHLYDVMNVKGVAADLSHCNTPSQVLDFTGP 152
FKVAVLGAAGGIGQPL+LL+K +P VS L LYD++ GVAADLSH +TP++V +
Sbjct: 8 MFKVAVLGAAGGIGQPLSLLLKQNPHVSELSLYDIVGAPGVAADLSHIDTPAKVTGYADG 67
Query: 153 EELASALKGVNVVVIPAGVPRKPGMTRDDLFNINANIVKTLVEAVADNCPDAFIHIISNP 212
E AL+G ++V+I AGVPRKPGMTRDDLFN NA IV+ LV AVA + P A + I+SNP
Sbjct: 68 ELWEKALRGADLVLICAGVPRKPGMTRDDLFNTNAPIVRDLVAAVASSAPKAIVGIVSNP 127
Query: 213 VNSTVPIAAEVLKQKGVYDPKKLFGVTTLDVVRANTFVAQKKNLKLIDVDVPVVGGHAGI 272
VNSTVPIAAE LK+ GVYDP+KLFGVTTLDVVRA FVA+ + DV+VPVVGGH+G+
Sbjct: 128 VNSTVPIAAETLKKAGVYDPRKLFGVTTLDVVRARKFVAEALGMNPYDVNVPVVGGHSGV 187
Query: 273 TILPLLSKTMPSVSFTDEEVGDLTVRIQNAGTEVVEAKAGAGSATLSMAYAAARFVESSL 332
TI+PLLS+T +S +E+V +T R+Q G EVV+AK GAGSATLSMAYAAA + S L
Sbjct: 188 TIVPLLSQT--GLSLPEEQVEQITHRVQVGGDEVVKAKEGAGSATLSMAYAAAEWSTSVL 245
Query: 333 RALDGDGDVYECVFVESNLT-ELPFFASRVKLGRNGVESLISSDLQGLTEYEQKALEALK 391
+AL GD + EC FVES++ E PFF+S V+LG+ GVE ++ + L YE++ LEA
Sbjct: 246 KALRGDKGIVECAFVESDMRPECPFFSSPVELGKEGVERVLP--IGPLNAYEEELLEAAV 303
Query: 392 PELKASIEKGVAFAQKQA 409
P+LK +IEKG+ FA+K+
Sbjct: 304 PDLKKNIEKGLEFARKKL 321
>gnl|CDD|223117 COG0039, Mdh, Malate/lactate dehydrogenases [Energy production and
conversion].
Length = 313
Score = 249 bits (637), Expect = 5e-80
Identities = 118/321 (36%), Positives = 167/321 (52%), Gaps = 23/321 (7%)
Query: 95 KVAVLGAAGGIGQPLALLIKMSPLVSALHLYDVMN--VKGVAADLSHCNTPSQVLDFTGP 152
KVAV+GA G +G LA L+ + L S L L D+ +GVA DLSH P
Sbjct: 2 KVAVIGA-GNVGSSLAFLLLLQGLGSELVLIDINEEKAEGVALDLSHAAAPLGSDVKITG 60
Query: 153 EELASALKGVNVVVIPAGVPRKPGMTRDDLFNINANIVKTLVEAVADNCPDAFIHIISNP 212
+ LKG ++VVI AGVPRKPGMTR DL NA IVK + +A+A PDA + +++NP
Sbjct: 61 DGDYEDLKGADIVVITAGVPRKPGMTRLDLLEKNAKIVKDIAKAIAKYAPDAIVLVVTNP 120
Query: 213 VNSTVPIAAEVLKQKGVYDPKKLFGVTTLDVVRANTFVAQKKNLKLIDVDVPVVGGHAGI 272
V+ IA + G + + T LD R TF+A+K + DV V+G H G
Sbjct: 121 VDILTYIAMKFS---GFPKNRVIGSGTVLDSARFRTFLAEKLGVSPKDVHAYVIGEH-GD 176
Query: 273 TILPLLSKTMPS--------VSFTDEEVGDLTVRIQNAGTEVVEAKAGAGSATLSMAYAA 324
T++PL S+ T+E++ +L R++NAG E++EAK GAG A A
Sbjct: 177 TMVPLWSQATVGGKPLEELLKEDTEEDLEELIERVRNAGAEIIEAK-GAG-TYYGPAAAL 234
Query: 325 ARFVESSLRALDGDGDVYECVFVESNL-TELPFFASRVKLGRNGVESLISSDLQGLTEYE 383
AR VE+ LR D + V+++ E +F LG+NGVE ++ L++ E
Sbjct: 235 ARMVEAILR--DEKRVLPVSVYLDGEYGVEDVYFGVPAVLGKNGVEEILELL---LSDDE 289
Query: 384 QKALEALKPELKASIEKGVAF 404
Q+ L+ ELK +IE
Sbjct: 290 QEKLDKSAEELKKNIELVKEL 310
>gnl|CDD|200963 pfam00056, Ldh_1_N, lactate/malate dehydrogenase, NAD binding
domain. L-lactate dehydrogenases are metabolic enzymes
which catalyze the conversion of L-lactate to pyruvate,
the last step in anaerobic glycolysis.
L-2-hydroxyisocaproate dehydrogenases are also members
of the family. Malate dehydrogenases catalyze the
interconversion of malate to oxaloacetate. The enzyme
participates in the citric acid cycle. L-lactate
dehydrogenase is also found as a lens crystallin in bird
and crocodile eyes. N-terminus (this family) is a
Rossmann NAD-binding fold. C-terminus is an unusual
alpha+beta fold.
Length = 142
Score = 176 bits (448), Expect = 3e-54
Identities = 64/145 (44%), Positives = 85/145 (58%), Gaps = 6/145 (4%)
Query: 95 KVAVLGAAGGIGQPLALLIKMSPLVSALHLYDVM--NVKGVAADLSHCNTPSQVLDFTGP 152
KVAV+GA GG+G LA + + L L L D+ +GVA DLSH +T V G
Sbjct: 2 KVAVVGAGGGVGSSLAFALALQGLADELVLVDINKDKAEGVAMDLSHGSTFLSVPGIVGG 61
Query: 153 EELASALKGVNVVVIPAGVPRKPGMTRDDLFNINANIVKTLVEAVADNCPDAFIHIISNP 212
++ ALK +VVVI AGVPRKPGMTR DL N NA I K +V A+A + PDA + ++SNP
Sbjct: 62 DD-YEALKDADVVVITAGVPRKPGMTRLDLLNRNAGIFKDIVPAIAKSAPDAIVLVVSNP 120
Query: 213 VNSTVPIAAEVLKQKGVYDPKKLFG 237
V+ IA +V G+ + +
Sbjct: 121 VDILTYIAWKVS---GLPPERVIGS 142
>gnl|CDD|202437 pfam02866, Ldh_1_C, lactate/malate dehydrogenase, alpha/beta
C-terminal domain. L-lactate dehydrogenases are
metabolic enzymes which catalyze the conversion of
L-lactate to pyruvate, the last step in anaerobic
glycolysis. L-2-hydroxyisocaproate dehydrogenases are
also members of the family. Malate dehydrogenases
catalyze the interconversion of malate to oxaloacetate.
The enzyme participates in the citric acid cycle.
L-lactate dehydrogenase is also found as a lens
crystallin in bird and crocodile eyes.
Length = 173
Score = 155 bits (393), Expect = 9e-46
Identities = 73/179 (40%), Positives = 105/179 (58%), Gaps = 18/179 (10%)
Query: 239 TTLDVVRANTFVAQKKNLKLIDVDVPVVGGHAG----------ITILPLLSKTMPSVSFT 288
TTLD RA TF+A+K + V+V V+G H+G +TI+PL+S+ ++ T
Sbjct: 1 TTLDTARARTFLAEKFGVDPRSVNVYVIGEHSGTQFPDWSHAKVTIIPLISQVKENLKDT 60
Query: 289 DEEVGDLTVRIQNAGTEVVEAKAGAGSATLSMAYAAARFVESSLRALDGDG--DVYECVF 346
D E+ +L R+QNAG EV+EAK AGS T SMAYAAAR ++ LR G VY +
Sbjct: 61 DWELEELIERVQNAGYEVIEAK--AGSTTYSMAYAAARIAKAILRGTGGVLSVGVYLDGY 118
Query: 347 VESNLTELPFFASRVKLGRNGVESLISSDLQGLTEYEQKALEALKPELKASIEKGVAFA 405
S + +F+ V LG++GVE ++ ++ L ++E++ LE ELK IEKG AF
Sbjct: 119 YGSP--DDIYFSVPVVLGKDGVEKVV--EILPLNDFEREKLEKSAAELKKEIEKGFAFV 173
>gnl|CDD|133424 cd01339, LDH-like_MDH, L-lactate dehydrogenase-like malate
dehydrogenase proteins. Members of this subfamily have
an LDH-like structure and an MDH enzymatic activity.
Some members, like MJ0490 from Methanococcus jannaschii,
exhibit both MDH and LDH activities. Tetrameric MDHs,
including those from phototrophic bacteria, are more
similar to LDHs than to other MDHs. LDH catalyzes the
last step of glycolysis in which pyruvate is converted
to L-lactate. MDH is one of the key enzymes in the
citric acid cycle, facilitating both the conversion of
malate to oxaloacetate and replenishing levels of
oxalacetate by reductive carboxylation of pyruvate. The
LDH-like MDHs are part of the NAD(P)-binding Rossmann
fold superfamily, which includes a wide variety of
protein families including the NAD(P)-binding domains of
alcohol dehydrogenases, tyrosine-dependent
oxidoreductases, glyceraldehyde-3-phosphate
dehydrogenases, formate/glycerate dehydrogenases,
siroheme synthases, 6-phosphogluconate dehydrogenases,
aminoacid dehydrogenases, repressor rex, and NAD-binding
potassium channel domains, among others.
Length = 300
Score = 156 bits (396), Expect = 2e-44
Identities = 96/313 (30%), Positives = 158/313 (50%), Gaps = 44/313 (14%)
Query: 96 VAVLGAAGGIGQPLALLIKMSPLVSALHLYDVMN--VKGVAADLSHCNTPSQVLDF---- 149
++++GA G +G LA L+ + L + L D++ +G A D+S + +L
Sbjct: 1 ISIIGA-GNVGATLAQLLALKELGDVV-LLDIVEGLPQGKALDISQA---APILGSDTKV 55
Query: 150 TGPEELASALKGVNVVVIPAGVPRKPGMTRDDLFNINANIVKTLVEAVADNCPDAFIHII 209
TG + + G +VVVI AG+PRKPGM+RDDL NA IVK + E + P+A + ++
Sbjct: 56 TGTNDYE-DIAGSDVVVITAGIPRKPGMSRDDLLGTNAKIVKEVAENIKKYAPNAIVIVV 114
Query: 210 SNPVNSTVPIAAEVLKQKGVYDPKKLFGV-TTLDVVRANTFVAQKKNLKLIDVDVPVVGG 268
+NP++ +A + + ++ G+ LD R F+A++ + + DV V+GG
Sbjct: 115 TNPLDVMTYVAYKASG----FPRNRVIGMAGVLDSARFRYFIAEELGVSVKDVQAMVLGG 170
Query: 269 HAGITILPLLSKTMPSVS-------FTDEEVGDLTVRIQNAGTEVVEAKAGAGSATLSMA 321
H G T++PL + +V T EE+ ++ R +N G E+V GSA + A
Sbjct: 171 H-GDTMVPLPRYS--TVGGIPLTELITKEEIDEIVERTRNGGAEIVNLL-KTGSAYYAPA 226
Query: 322 YAAARFVESSLRALDGDGDVYEC-VFVE-----SNLTELPFFASRVKLGRNGVESLISSD 375
A A VE+ L+ V C ++E ++ F V LG+NGVE +I D
Sbjct: 227 AAIAEMVEAILK---DKKRVLPCSAYLEGEYGIKDI----FVGVPVVLGKNGVEKIIELD 279
Query: 376 LQGLTEYEQKALE 388
LT+ E++A +
Sbjct: 280 ---LTDEEKEAFD 289
>gnl|CDD|180477 PRK06223, PRK06223, malate dehydrogenase; Reviewed.
Length = 307
Score = 154 bits (392), Expect = 8e-44
Identities = 102/321 (31%), Positives = 167/321 (52%), Gaps = 58/321 (18%)
Query: 95 KVAVLGAAGGIGQPLALLIKMSPLVSALHLYDVMN--VKGVAADLSHCNTPSQVLDF--- 149
K++++GA G +G LA L+ + L + L+D++ +G A D++ + V F
Sbjct: 4 KISIIGA-GNVGATLAHLLALKELGD-VVLFDIVEGVPQGKALDIAEA---APVEGFDTK 58
Query: 150 -TGPEELASALKGVNVVVIPAGVPRKPGMTRDDLFNINANIVKTLVEAVADNCPDAFIHI 208
TG + + G +VVVI AGVPRKPGM+RDDL INA I+K + E + PDA + +
Sbjct: 59 ITGTNDYE-DIAGSDVVVITAGVPRKPGMSRDDLLGINAKIMKDVAEGIKKYAPDAIVIV 117
Query: 209 ISNPVNSTVPIAAEVLKQKGVYDPKKLFGVTT-LDVVRANTFVAQKKNLKLIDVDVPVVG 267
++NPV++ +A LK+ G + ++ G+ LD R TF+A++ N+ + DV V+G
Sbjct: 118 VTNPVDAMTYVA---LKESG-FPKNRVIGMAGVLDSARFRTFIAEELNVSVKDVTAFVLG 173
Query: 268 GHAGITILPLLSKTMPSVS-------FTDEEVGDLTVRIQNAGTEVVEAKAGAGSATLSM 320
GH G +++PL+ + +V + E++ ++ R + G E+V GSA +
Sbjct: 174 GH-GDSMVPLVRYS--TVGGIPLEDLLSKEKLDEIVERTRKGGAEIVGLL-KTGSAYYAP 229
Query: 321 AYAAARFVESSLR----------ALDGD---GDVYECVFVESNLTELPFFASRVKLGRNG 367
A + A VE+ L+ L+G+ DVY V P VKLG+NG
Sbjct: 230 AASIAEMVEAILKDKKRVLPCSAYLEGEYGVKDVYVGV---------P-----VKLGKNG 275
Query: 368 VESLISSDLQGLTEYEQKALE 388
VE +I + L + E+ A +
Sbjct: 276 VEKIIELE---LDDEEKAAFD 293
>gnl|CDD|133419 cd00650, LDH_MDH_like, NAD-dependent, lactate dehydrogenase-like,
2-hydroxycarboxylate dehydrogenase family. Members of
this family include ubiquitous enzymes like L-lactate
dehydrogenases (LDH), L-2-hydroxyisocaproate
dehydrogenases, and some malate dehydrogenases (MDH).
LDH catalyzes the last step of glycolysis in which
pyruvate is converted to L-lactate. MDH is one of the
key enzymes in the citric acid cycle, facilitating both
the conversion of malate to oxaloacetate and
replenishing levels of oxalacetate by reductive
carboxylation of pyruvate. The LDH/MDH-like proteins are
part of the NAD(P)-binding Rossmann fold superfamily,
which includes a wide variety of protein families
including the NAD(P)-binding domains of alcohol
dehydrogenases, tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate dehydrogenases,
formate/glycerate dehydrogenases, siroheme synthases,
6-phosphogluconate dehydrogenases, aminoacid
dehydrogenases, repressor rex, and NAD-binding potassium
channel domains, among others.
Length = 263
Score = 147 bits (372), Expect = 2e-41
Identities = 87/312 (27%), Positives = 139/312 (44%), Gaps = 57/312 (18%)
Query: 96 VAVLGAAGGIGQPLALLIKMSPLVSA--LHLYDVMN--VKGVAADLSHCNTPSQVLDFTG 151
+AV+GA G +G LA + ++ A L LYD+ +KGVA DL P + +
Sbjct: 1 IAVIGAGGNVGPALAFGLADGSVLLAIELVLYDIDEEKLKGVAMDLQDAVEPLADIKVSI 60
Query: 152 PEELASALKGVNVVVIPAGVPRKPGMTRDDLFNINANIVKTLVEAVADNCPDAFIHIISN 211
++ A K +VV+I AGV RKPGM R DL N IVK + + + PDA+I ++SN
Sbjct: 61 TDDPYEAFKDADVVIITAGVGRKPGMGRLDLLKRNVPIVKEIGDNIEKYSPDAWIIVVSN 120
Query: 212 PVNSTVPIAAEVLKQKGVYDPKKLFGVTTLDVVRANTFVAQKKNLKLIDVDVPVVGGHAG 271
PV+ I ++ + +K+ G+ TLD +R +A+K + DV V ++G H G
Sbjct: 121 PVD----IITYLVWRYSGLPKEKVIGLGTLDPIRFRRILAEKLGVDPDDVKVYILGEHGG 176
Query: 272 ITILPLLSKTMPSVSFTDEEVGDLTVRIQNAGTEVVEAKAGAGSATLSMAYAAARFVESS 331
+ +P S +A + A + S
Sbjct: 177 -SQVPDWSTV-------------------------------------RIATSIADLIRSL 198
Query: 332 LRALDGDGDVYECVFVESN----LTELPFFASRVKLGRNGVESLISSDLQGLTEYEQKAL 387
L +G++ V V +N + + + +G+NGVE I GLT++E + L
Sbjct: 199 LN---DEGEI-LPVGVRNNGQIGIPDDVVVSVPCIVGKNGVEEPIE---VGLTDFELEKL 251
Query: 388 EALKPELKASIE 399
+ LK +E
Sbjct: 252 QKSADTLKKELE 263
>gnl|CDD|173409 PTZ00117, PTZ00117, malate dehydrogenase; Provisional.
Length = 319
Score = 126 bits (319), Expect = 3e-33
Identities = 95/308 (30%), Positives = 154/308 (50%), Gaps = 33/308 (10%)
Query: 95 KVAVLGAAGGIGQPLALLIKMSPLVSALHLYDVMN--VKGVAADLSHCNTPSQV-LDFTG 151
K++++GA G IG +ALLI L + LYDV+ +G A DL H +T ++ G
Sbjct: 7 KISMIGA-GQIGSTVALLILQKNL-GDVVLYDVIKGVPQGKALDLKHFSTLVGSNINILG 64
Query: 152 PEELASALKGVNVVVIPAGVPRKPGMTRDDLFNINANIVKTLVEAVADNCPDAFIHIISN 211
+K +VVVI AGV RK MTR+DL IN I+K++ E+V CP+AF+ ++N
Sbjct: 65 TNNY-EDIKDSDVVVITAGVQRKEEMTREDLLTINGKIMKSVAESVKKYCPNAFVICVTN 123
Query: 212 PVNSTVPIAAEVLKQKGVYDPKKLFGVT-TLDVVRANTFVAQKKNLKLIDVDVPVVGGHA 270
P++ +V ++K K+ G+ LD R +A+K + DV V+GGH
Sbjct: 124 PLD----CMVKVFQEKSGIPSNKICGMAGVLDSSRFRCNLAEKLGVSPGDVSAVVIGGH- 178
Query: 271 GITILPL----------LSKTMPSVSFTDEEVGDLTVRIQNAGTEVVEAKAGAGSATLSM 320
G ++PL LS + + T++E+ ++ + +N G E+V+ GSA +
Sbjct: 179 GDLMVPLPRYCTVNGIPLSDFVKKGAITEKEINEIIKKTRNMGGEIVKL-LKKGSAFFAP 237
Query: 321 AYAAARFVESSLRALDGDGDVYEC-VFV--ESNLTELPFFASRVKLGRNGVESLISSDLQ 377
A A +E+ L+ V C V++ + N L F V +G G+E +I +
Sbjct: 238 AAAIVAMIEAYLKDEK---RVLVCSVYLNGQYNCKNL-FVGVPVVIGGKGIEKVIELE-- 291
Query: 378 GLTEYEQK 385
L E++
Sbjct: 292 -LNAEEKE 298
>gnl|CDD|133430 cd05294, LDH-like_MDH_nadp, A lactate dehydrogenases-like structure
with malate dehydrogenase enzymatic activity. The
LDH-like MDH proteins have a lactate
dehyhydrogenase-like (LDH-like) structure and malate
dehydrogenase (MDH) enzymatic activity. This subgroup is
composed of some archaeal LDH-like MDHs that prefer
NADP(H) rather than NAD(H) as a cofactor. One member,
MJ0490 from Methanococcus jannaschii, has been observed
to form dimers and tetramers during crystalization,
although it is believed to exist primarilly as a
tetramer in solution. In addition to its MDH activity,
MJ0490 also possesses
fructose-1,6-bisphosphate-activated LDH activity.
Members of this subgroup have a higher sequence
similarity to LDHs than to other MDHs. LDH catalyzes the
last step of glycolysis in which pyruvate is converted
to L-lactate. MDH is one of the key enzymes in the
citric acid cycle, facilitating both the conversion of
malate to oxaloacetate and replenishing levels of
oxalacetate by reductive carboxylation of pyruvate. The
LDH-like MDHs are part of the NAD(P)-binding Rossmann
fold superfamily, which includes a wide variety of
protein families including the NAD(P)- binding domains
of alcohol dehydrogenases, tyrosine-dependent
oxidoreductases, glyceraldehyde-3-phosphate
dehydrogenases, formate/glycerate dehydrogenases,
siroheme synthases, 6-phosphogluconate dehydrogenase,
aminoacid dehydrogenases, repressor rex, and NAD-binding
potassium channel domains, among others.
Length = 309
Score = 114 bits (286), Expect = 1e-28
Identities = 89/321 (27%), Positives = 149/321 (46%), Gaps = 74/321 (23%)
Query: 95 KVAVLGAAGGIGQPLALLIKMSPLVSALHL-----------------YDVMNVKGVAADL 137
KV+++GA+G +G ALL+ +V ++L YD + G+ A++
Sbjct: 2 KVSIIGASGRVGSATALLLAKEDVVKEINLISRPKSLEKLKGLRLDIYDALAAAGIDAEI 61
Query: 138 SHCNTPSQVLDFTGPEELASALKGVNVVVIPAGVPRKPGMTRDDLFNINANIVKTLVEAV 197
+ S V G ++V+I AGVPRK GM+R DL NA IVK + +
Sbjct: 62 KISSDLSDVA-------------GSDIVIITAGVPRKEGMSRLDLAKKNAKIVKKYAKQI 108
Query: 198 ADNCPDAFIHIISNPVNSTVPIAAEVLKQKGVYDPKKLFGVTT-LDVVRANTFVAQKKNL 256
A+ PD I +++NPV+ A LK+ G +D ++FG+ T LD +R +A+ N+
Sbjct: 109 AEFAPDTKILVVTNPVDVMTYKA---LKESG-FDKNRVFGLGTHLDSLRFKVAIAKHFNV 164
Query: 257 KLIDVDVPVVGGHAGITILPLLSKT----MPSVSFT---DEEVGDLTVRIQNAGTEVVEA 309
+ +V ++G H G +++PL+S T +P F D +V + ++NAG ++
Sbjct: 165 HISEVHTRIIGEH-GDSMVPLISSTSIGGIPIKRFPEYKDFDVEKIVETVKNAGQNIISL 223
Query: 310 KAGAGSATLSMAYAAARFVESSLR--------------ALDGDGDVYECVFVESNLTELP 355
K G + A A + V + +DG DV C+ V
Sbjct: 224 K---GGSEYGPASAISNLVRTIANDERRILTVSTYLEGEIDGIRDV--CIGVP------- 271
Query: 356 FFASRVKLGRNGVESLISSDL 376
VKLG+NG+E ++ ++
Sbjct: 272 -----VKLGKNGIEEIVPIEM 287
>gnl|CDD|173376 PTZ00082, PTZ00082, L-lactate dehydrogenase; Provisional.
Length = 321
Score = 112 bits (282), Expect = 4e-28
Identities = 92/320 (28%), Positives = 153/320 (47%), Gaps = 44/320 (13%)
Query: 95 KVAVLGAAGGIGQPLALLIKMSPLVSALHLYDVMN--VKGVAADLSHCNTPSQV-LDFTG 151
K++++G+ G IG +A LI + L + L+D++ +G A D+SH N + G
Sbjct: 8 KISLIGS-GNIGGVMAYLIVLKNLGDVV-LFDIVKNIPQGKALDISHSNVIAGSNSKVIG 65
Query: 152 PEELASALKGVNVVVIPAGVPRKPGMT-----RDDLFNINANIVKTLVEAVADNCPDAFI 206
+ G +VV++ AG+ ++PG + RDDL +NA I+ + E + CP+AF+
Sbjct: 66 TNNYED-IAGSDVVIVTAGLTKRPGKSDKEWNRDDLLPLNAKIMDEVAEGIKKYCPNAFV 124
Query: 207 HIISNPVNSTVPIAAEVLKQKGVYDPKKLFGVT-TLDVVRANTFVAQKKNLKLIDVDVPV 265
+I+NP++ V ++L++ K+ G+ LD R T++A+K + DV V
Sbjct: 125 IVITNPLDVMV----KLLQEHSGLPKNKVCGMAGVLDSSRLRTYIAEKLGVNPRDVHASV 180
Query: 266 VGGHAGITILPLLSKT----MPSVSF------TDEEVGDLTVRIQNAGTEVVEAKAGAGS 315
+G H G ++PL +P F T EE+ ++ R +N G E+V+ G GS
Sbjct: 181 IGAH-GDKMVPLPRYVTVGGIPLSEFIKKGLITQEEIDEIVERTRNTGKEIVDL-LGTGS 238
Query: 316 ATLSMAYAAARFVESSLRALDGDGDVYECVFVESNLTELP------FFASRVKLGRNGVE 369
A + A AA E+ L+ + V S E + + +G NGVE
Sbjct: 239 AYFAPAAAAIEMAEAYLKDK-------KRVLPCSAYLEGQYGHKDIYMGTPAVIGANGVE 291
Query: 370 SLISSDLQGLTEYEQKALEA 389
+I D LT EQK +
Sbjct: 292 KIIELD---LTPEEQKKFDE 308
>gnl|CDD|133418 cd00300, LDH_like, L-lactate dehydrogenase-like enzymes. Members
of this subfamily are tetrameric NAD-dependent
2-hydroxycarboxylate dehydrogenases including LDHs,
L-2-hydroxyisocaproate dehydrogenases (L-HicDH), and
LDH-like malate dehydrogenases (MDH). Dehydrogenases
catalyze the conversion of carbonyl compounds to
alcohols or amino acids. LDHs catalyze the last step of
glycolysis in which pyruvate is converted to L-lactate.
Vertebrate LDHs are non-allosteric, but some bacterial
LDHs are activated by an allosteric effector such as
fructose-1,6-bisphosphate. L-HicDH catalyzes the
conversion of a variety of 2-oxo carboxylic acids with
medium-sized aliphatic or aromatic side chains. MDH is
one of the key enzymes in the citric acid cycle,
facilitating both the conversion of malate to
oxaloacetate and replenishing levels of oxalacetate by
reductive carboxylation of pyruvate. The LDH-like
subfamily is part of the NAD(P)-binding Rossmann fold
superfamily, which includes a wide variety of protein
families including the NAD(P)-binding domains of alcohol
dehydrogenases, tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate dehydrogenases,
formate/glycerate dehydrogenases, siroheme synthases,
6-phosphogluconate dehydrogenases, aminoacid
dehydrogenases, repressor rex, and NAD-binding potassium
channel domains, among others.
Length = 300
Score = 108 bits (271), Expect = 1e-26
Identities = 84/306 (27%), Positives = 131/306 (42%), Gaps = 28/306 (9%)
Query: 96 VAVLGAAGGIGQPLALLIKMSPLVSALHLYDVMN--VKGVAADLSHCNTPSQVLDFTGPE 153
+ ++GA G +G +A + L S L L DV KG A DLSH +
Sbjct: 1 ITIIGA-GNVGAAVAFALIAKGLASELVLVDVNEEKAKGDALDLSHASAFLATGTIVRGG 59
Query: 154 ELASALKGVNVVVIPAGVPRKPGMTRDDLFNINANIVKTLVEAVADNCPDAFIHIISNPV 213
+ A ++VVI AG PRKPG TR DL N NA I+++++ + PDA I ++SNPV
Sbjct: 60 DYA-DAADADIVVITAGAPRKPGETRLDLINRNAPILRSVITNLKKYGPDAIILVVSNPV 118
Query: 214 NSTVPIAAEVLKQKGVYDPKKLFGV-TTLDVVRANTFVAQKKNLKLIDVDVPVVGGHAGI 272
+ I V ++ ++ G T LD R + +A+K ++ V V+G H G
Sbjct: 119 D----ILTYVAQKLSGLPKNRVIGSGTLLDSARFRSLLAEKLDVDPQSVHAYVLGEH-GD 173
Query: 273 TILPLLSKTM-------PSVSFTDEEVGDLTVRIQNAGTEVVEAKAGAGSATLSMAYAAA 325
+ + S FT ++ + ++ +G E++ K G+ +A A A
Sbjct: 174 SQVVAWSTATVGGLPLEELAPFTKLDLEAIEEEVRTSGYEIIRLK---GATNYGIATAIA 230
Query: 326 RFVESSLRALDGDGDVYEC-VFVESNLTELPFFAS-RVKLGRNGVESLISSDLQGLTEYE 383
V+S L V E S +GR GV ++ LTE E
Sbjct: 231 DIVKSILLDERR---VLPVSAVQEGQYGIEDVALSVPAVVGREGVVRILEIP---LTEDE 284
Query: 384 QKALEA 389
+ L+
Sbjct: 285 EAKLQK 290
>gnl|CDD|233562 TIGR01763, MalateDH_bact, malate dehydrogenase, NAD-dependent.
This enzyme converts malate into oxaloacetate in the
citric acid cycle. The critical residues which
discriminate malate dehydrogenase from lactate
dehydrogenase have been characterized , and have been
used to set the cutoffs for this model. Sequences
showing [aflimv][ap]R[rk]pgM[st] and [ltv][ilm]gGhgd
were kept above trusted, while those in which the
capitalized residues in the patterns were found to be Q,
E and E were kept below the noise cutoff. Some sequences
in the grey zone have been annotated as malate
dehydrogenases, but none have been characterized.
Phylogenetically, a clade of sequences from eukaryotes
such as Toxoplasma and Plasmodium which include a
characterized lactate dehydrogenase and show abiguous
critical residue patterns appears to be more closely
related to these bacterial sequences than other
eukaryotic sequences. These are relatively long branch
and have been excluded from the model. All other
sequences falling below trusted appear to be
phylogenetically outside of the clade including the
trusted hits. The annotation of Botryococcus braunii as
lactate dehydrogenase appears top be in error. This was
initially annotated as MDH by Swiss-Prot and then
changed. The rationale for either of these annotations
is not traceable [Energy metabolism, TCA cycle].
Length = 305
Score = 104 bits (260), Expect = 3e-25
Identities = 87/326 (26%), Positives = 148/326 (45%), Gaps = 50/326 (15%)
Query: 95 KVAVLGAAGGIGQPLALLIKMSPLVSALHLYDVMNV-KGVAADLSHCNTPSQVLD--FTG 151
K++V+GA G +G A + L + L V + +G A D+ +P D TG
Sbjct: 3 KISVIGA-GFVGATTAFRLAEKELADLVLLDVVEGIPQGKALDMYEA-SPVGGFDTKVTG 60
Query: 152 PEELASALKGVNVVVIPAGVPRKPGMTRDDLFNINANIVKTLVEAVADNCPDAFIHIISN 211
A ++VVI AG+PRKPGM+R+DL ++NA IV+ + + ++ P+ I ++SN
Sbjct: 61 TNNYADT-ANSDIVVITAGLPRKPGMSREDLLSMNAGIVREVTGRIMEHSPNPIIVVVSN 119
Query: 212 PVNSTVPIAAE--------VLKQKGVYDPKKLFGVTTLDVVRANTFVAQKKNLKLIDVDV 263
P+++ +A + V+ Q GV LD R TF+A + + + DV
Sbjct: 120 PLDAMTYVAWQKSGFPKERVIGQAGV-----------LDSARFRTFIAMELGVSVQDVTA 168
Query: 264 PVVGGHAGITILPLLSKT----MPSVSF-TDEEVGDLTVRIQNAGTEVVEAKAGAGSATL 318
V+GGH G ++PL+ + +P + E + ++ R + G E+V GSA
Sbjct: 169 CVLGGH-GDAMVPLVRYSTVAGIPVADLISAERIAEIVERTRKGGGEIVNL-LKQGSAYY 226
Query: 319 SMAYAAARFVESSLRALDGDGDVYECVFVESNLT-----ELPFFASRVKLGRNGVESLIS 373
+ A + VE+ L+ D + + L + + V LG+NGVE +
Sbjct: 227 APAASVVEMVEAILK------DRKRVLPCAAYLDGQYGIDGIYVGVPVILGKNGVEHIYE 280
Query: 374 SDLQGLTEYE----QKALEALKPELK 395
L + E K+ + + K
Sbjct: 281 LK---LDQSELALLNKSAKIVDENCK 303
>gnl|CDD|133427 cd05291, HicDH_like, L-2-hydroxyisocapronate dehydrogenases and
some bacterial L-lactate dehydrogenases.
L-2-hydroxyisocapronate dehydrogenase (HicDH) catalyzes
the conversion of a variety of 2-oxo carboxylic acids
with medium-sized aliphatic or aromatic side chains.
This subfamily is composed of HicDHs and some bacterial
L-lactate dehydrogenases (LDH). LDHs catalyze the last
step of glycolysis in which pyruvate is converted to
L-lactate. Bacterial LDHs can be non-allosteric or may
be activated by an allosteric effector such as
fructose-1,6-bisphosphate. Members of this subfamily
with known structures such as the HicDH of Lactobacillus
confusus, the non-allosteric LDH of Lactobacillus
pentosus, and the allosteric LDH of Bacillus
stearothermophilus, show that they exist as
homotetramers. The HicDH-like subfamily is part of the
NAD(P)-binding Rossmann fold superfamily, which includes
a wide variety of protein families including the
NAD(P)-binding domains of alcohol dehydrogenases,
tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate dehydrogenases,
formate/glycerate dehydrogenases, siroheme synthases,
6-phosphogluconate dehydrogenases, aminoacid
dehydrogenases, repressor rex, and NAD-binding potassium
channel domains, among others.
Length = 306
Score = 99.8 bits (250), Expect = 9e-24
Identities = 99/338 (29%), Positives = 146/338 (43%), Gaps = 65/338 (19%)
Query: 95 KVAVLGAAGGIGQPLALLIKMSPLVSALHLYDVMN---VKGVAADLSHC--NTPSQVLDF 149
KV ++GA G +G A + + L L D+ N +G A DL PS V
Sbjct: 2 KVVIIGA-GHVGSSFAYSLVNQGIADELVLIDI-NEEKAEGEALDLEDALAFLPSPVKIK 59
Query: 150 TGPEELASALKGVNVVVIPAGVPRKPGMTRDDLFNINANIVKTLVEAVADNCPDAFIHII 209
G S K ++VVI AG P+KPG TR DL NA I+K++V + + D +
Sbjct: 60 AG---DYSDCKDADIVVITAGAPQKPGETRLDLLEKNAKIMKSIVPKIKASGFDGIFLVA 116
Query: 210 SNPVNSTVPIAAEVLKQKGVYDPKKLFGV-TTLDVVRANTFVAQKKNLKLIDVDVPVVGG 268
SNPV+ I V K G ++ G T+LD R +A+K N+ V V+G
Sbjct: 117 SNPVDV---ITYVVQKLSG-LPKNRVIGTGTSLDTARLRRALAEKLNVDPRSVHAYVLGE 172
Query: 269 H-------------AGITILPLLSKTMPSVSFTDEEVGDLTVRIQNAGTEVVEAKAGAGS 315
H G +L LL ++ ++ ++ ++ AG E++ K G+
Sbjct: 173 HGDSQFVAWSTVTVGGKPLLDLL----KEGKLSELDLDEIEEDVRKAGYEIINGK---GA 225
Query: 316 ATLSMAYAAARFVESSLR----------ALDGD---GDVYECVFVESNLTELPFFASRVK 362
+A A AR V++ L LDG+ DVY +P
Sbjct: 226 TYYGIATALARIVKAILNDENAILPVSAYLDGEYGEKDVY---------IGVP-----AI 271
Query: 363 LGRNGVESLISSDLQGLTEYEQKALEALKPELKASIEK 400
+GRNGVE +I D LTE EQ+ E +K +I+K
Sbjct: 272 IGRNGVEEVIELD---LTEEEQEKFEKSADIIKENIKK 306
>gnl|CDD|233566 TIGR01771, L-LDH-NAD, L-lactate dehydrogenase. This model
represents the NAD-dependent L-lactate dehydrogenases
from bacteria and eukaryotes. This enzyme function as as
the final step in anaerobic glycolysis. Although lactate
dehydrogenases have in some cases been mistaken for
malate dehydrogenases due to the similarity of these two
substrates and the apparent ease with which evolution
can toggle these activities, critical residues have been
identified which can discriminate between the two
activities. At the time of the creation of this model no
hits above the trusted cutoff contained critical
residues typical of malate dehydrogenases [Energy
metabolism, Anaerobic, Energy metabolism,
Glycolysis/gluconeogenesis].
Length = 299
Score = 97.7 bits (244), Expect = 7e-23
Identities = 77/310 (24%), Positives = 124/310 (40%), Gaps = 45/310 (14%)
Query: 102 AGGIGQPLALLIKMSPLVSALHLYDVMN--VKGVAADLSH----CNTPSQVLDFTGPEEL 155
AG +G A + + + L D+ +G A DL H TP ++
Sbjct: 4 AGNVGSSTAFALLNQGIADEIVLIDINKDKAEGEAMDLQHAASFLPTPKKIRSGD----- 58
Query: 156 ASALKGVNVVVIPAGVPRKPGMTRDDLFNINANIVKTLVEAVADNCPDAFIHIISNPVNS 215
S K ++VVI AG P+KPG TR +L N I+K++V V + D + +NPV+
Sbjct: 59 YSDCKDADLVVITAGAPQKPGETRLELVGRNVRIMKSIVPEVVKSGFDGIFLVATNPVD- 117
Query: 216 TVPIAAEV-LKQKGVYDPKKLFGV-TTLDVVRANTFVAQKKNLKLIDVDVPVVGGH---- 269
I V K G + ++ G T LD R +A+K + V ++G H
Sbjct: 118 ---ILTYVAWKLSG-FPKNRVIGSGTVLDTARLRYLLAEKLGVDPQSVHAYIIGEHGDSE 173
Query: 270 ---------AGITILPLLSKTMPSVSFTDEEVGDLTVRIQNAGTEVVEAKAGAGSATLSM 320
G+ +L L EE+ +A E++ K G+ +
Sbjct: 174 VPVWSSATIGGVPLLDYLKAKGTETDLDLEEIEKEVR---DAAYEIINRK---GATYYGI 227
Query: 321 AYAAARFVESSLRALDGDGDVYEC-VFVESNLTELPFFASR-VKLGRNGVESLISSDLQG 378
A AR VE+ L + V +++ + LGRNGVE +I
Sbjct: 228 GMAVARIVEAILHDENR---VLPVSAYLDGEYGIKDVYIGVPAVLGRNGVEEIIELP--- 281
Query: 379 LTEYEQKALE 388
L++ E++A +
Sbjct: 282 LSDEEKEAFQ 291
>gnl|CDD|133420 cd00704, MDH, Malate dehydrogenase. Malate dehydrogenase (MDH) is
one of the key enzymes in the citric acid cycle,
facilitating both the conversion of malate to
oxaloacetate and replenishing levels of oxalacetate by
reductive carboxylation of pyruvate. MDHs belong to the
NAD-dependent, lactate dehydrogenase (LDH)-like,
2-hydroxycarboxylate dehydrogenase family, which also
includes the GH4 family of glycoside hydrolases. They
are part of the NAD(P)-binding Rossmann fold
superfamily, which includes a wide variety of protein
families including the NAD(P)-binding domains of alcohol
dehydrogenases, tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate dehydrogenases,
formate/glycerate dehydrogenases, siroheme synthases,
6-phosphogluconate dehydrogenases, aminoacid
dehydrogenases, repressor rex, and NAD-binding potassium
channel domains, among others.
Length = 323
Score = 92.3 bits (230), Expect = 7e-21
Identities = 84/256 (32%), Positives = 116/256 (45%), Gaps = 36/256 (14%)
Query: 95 KVAVLGAAGGIGQPLALLI-------KMSPLVSALHLYDV----MNVKGVAADLSHCNTP 143
V + GAAG IG L LI P++ LHL D+ ++GV +L C P
Sbjct: 2 HVLITGAAGQIGYNLLFLIASGELFGDDQPVI--LHLLDIPPAMKALEGVVMELQDCAFP 59
Query: 144 --SQVLDFTGPEELASALKGVNVVVIPAGVPRKPGMTRDDLFNINANIVKTLVEAVADNC 201
V+ T PEE A K V+V ++ PRKPGM R DL NA I K EA+
Sbjct: 60 LLKGVVITTDPEE---AFKDVDVAILVGAFPRKPGMERADLLRKNAKIFKEQGEALNKVA 116
Query: 202 -PDAFIHIISNPVNSTVPIAAEVLKQKGVYDPKKLFGVTTLDVVRANTFVAQKKNLKLID 260
P + ++ NP N+ A LK PK +T LD RA VA+K +++ D
Sbjct: 117 KPTVKVLVVGNPANTN---ALIALKNAPNLPPKNFTALTRLDHNRAKAQVARKLGVRVSD 173
Query: 261 V-DVPVVGGHAGITILPLLS--------KTMPSVSFTDEEV--GDLTVRIQNAGTEVVEA 309
V +V + G H+ T +P LS T + DEE + +Q G +++
Sbjct: 174 VKNVIIWGNHSN-TQVPDLSNAVVYGPGGTEWVLDLLDEEWLNDEFVKTVQKRGAAIIKK 232
Query: 310 KAGAGSATLSMAYAAA 325
+ GA SA S A A A
Sbjct: 233 R-GASSA-ASAAKAIA 246
>gnl|CDD|130820 TIGR01759, MalateDH-SF1, malate dehydrogenase. This model
represents a family of malate dehydrogenases in bacteria
and eukaryotes which utilize either NAD or NADP
depending on the species and context. MDH interconverts
malate and oxaloacetate and is a part of the citric acid
cycle as well as the C4 cycle in certain photosynthetic
organisms.
Length = 323
Score = 85.1 bits (211), Expect = 2e-18
Identities = 84/254 (33%), Positives = 118/254 (46%), Gaps = 35/254 (13%)
Query: 95 KVAVLGAAGGIGQPLALLI-------KMSPLVSALHLYDV---MNV-KGVAADLSHCNTP 143
+VAV GAAG IG L I K P+V LHL D+ M +GVA +L C P
Sbjct: 5 RVAVTGAAGQIGYSLLFRIASGELFGKDQPVV--LHLLDIPPAMKALEGVAMELEDCAFP 62
Query: 144 --SQVLDFTGPEELASALKGVNVVVIPAGVPRKPGMTRDDLFNINANIVKTLVEAVADNC 201
+ V+ T PEE A K V+ ++ PRKPGM R DL + N I K +A+
Sbjct: 63 LLAGVVATTDPEE---AFKDVDAALLVGAFPRKPGMERADLLSKNGKIFKEQGKALNKVA 119
Query: 202 -PDAFIHIISNPVNSTVPIAAEVLKQKGVYDPKKLF-GVTTLDVVRANTFVAQKKNLKLI 259
D + ++ NP N+ IA++ P K F +T LD RA +A K + +
Sbjct: 120 KKDVKVLVVGNPANTNALIASKNAPDI----PPKNFSAMTRLDHNRAKYQLAAKAGVPVS 175
Query: 260 DV-DVPVVGGHAGITILPLLS----KTMPSVSFTDEE---VGDLTVRIQNAGTEVVEAKA 311
DV +V + G H+ T +P + P ++ G+ +Q G V+EA+
Sbjct: 176 DVKNVIIWGNHSN-TQVPDFTHATVDGRPVKEVIKDDKWLEGEFIPTVQQRGAAVIEAR- 233
Query: 312 GAGSATLSMAYAAA 325
GA SA S A AA
Sbjct: 234 GASSA-ASAANAAI 246
>gnl|CDD|133428 cd05292, LDH_2, A subgroup of L-lactate dehydrogenases. L-lactate
dehydrogenases (LDH) are tetrameric enzymes catalyzing
the last step of glycolysis in which pyruvate is
converted to L-lactate. This subgroup is composed
predominantly of bacterial LDHs and a few fungal LDHs.
Bacterial LDHs may be non-allosteric or may be activated
by an allosteric effector such as
fructose-1,6-bisphosphate. LDHs are part of the
NAD(P)-binding Rossmann fold superfamily, which includes
a wide variety of protein families including the
NAD(P)-binding domains of alcohol dehydrogenases,
tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate dehydrogenases,
formate/glycerate dehydrogenases, siroheme synthases,
6-phosphogluconate dehydrogenases, aminoacid
dehydrogenases, repressor rex, and NAD-binding potassium
channel domains, among others.
Length = 308
Score = 84.5 bits (210), Expect = 3e-18
Identities = 92/334 (27%), Positives = 146/334 (43%), Gaps = 58/334 (17%)
Query: 95 KVAVLGAAGGIGQPLALLIKMSPLVSALHLYDVMN--VKGVAADLSHCNTPSQVLDFTGP 152
KVA++GA G +G A + + L S + L D+ +G A DL+H TP F P
Sbjct: 2 KVAIVGA-GFVGSTTAYALLLRGLASEIVLVDINKAKAEGEAMDLAH-GTP-----FVKP 54
Query: 153 EEL----ASALKGVNVVVIPAGVPRKPGMTRDDLFNINANIVKTLVEAVADNCPDAFIHI 208
+ + KG +VVVI AG +KPG TR DL N I K ++ + PDA + +
Sbjct: 55 VRIYAGDYADCKGADVVVITAGANQKPGETRLDLLKRNVAIFKEIIPQILKYAPDAILLV 114
Query: 209 ISNPVNSTVPIAAEVLKQKGVYDPKKLFGV-TTLDVVRANTFVAQKKNLKLIDVDVPVVG 267
++NPV+ + V + P ++ G T LD R + + + V ++G
Sbjct: 115 VTNPVD----VLTYVAYKLSGLPPNRVIGSGTVLDTARFRYLLGEHLGVDPRSVHAYIIG 170
Query: 268 GHAGITILPLLSKTM------------PSVSFTDEEVGDLTVRIQNAGTEVVEAKAGAGS 315
H G + + + S F +E ++ ++NA E++E K G+
Sbjct: 171 EH-GDSEVAVWSSANIGGVPLDEFCKLCGRPFDEEVREEIFEEVRNAAYEIIERK---GA 226
Query: 316 ATLSMAYAAARFVESSLR----------ALDGDGDVYECVFVESNLTELPFFASRVKLGR 365
++ A AR VE+ LR LDG + + LP +GR
Sbjct: 227 TYYAIGLALARIVEAILRDENSVLTVSSLLDGQYGIKDVAL------SLP-----CIVGR 275
Query: 366 NGVESLISSDLQGLTEYEQKALEALKPELKASIE 399
+GVE ++ L+E E++AL A LK +IE
Sbjct: 276 SGVERVLPPP---LSEEEEEALRASAEVLKEAIE 306
>gnl|CDD|178836 PRK00066, ldh, L-lactate dehydrogenase; Reviewed.
Length = 315
Score = 76.5 bits (189), Expect = 2e-15
Identities = 69/264 (26%), Positives = 115/264 (43%), Gaps = 47/264 (17%)
Query: 95 KVAVLGAAGGIGQPLALLIKMSPLVSALHLYDVMNVK--GVAADLSHCNTPSQVLDFTGP 152
KV ++G G +G A + + L + D+ K G A DLSH + FT P
Sbjct: 8 KVVLVGD-GAVGSSYAYALVNQGIADELVIIDINKEKAEGDAMDLSHA------VPFTSP 60
Query: 153 EELASA----LKGVNVVVIPAGVPRKPGMTRDDLFNINANIVKTLVEAVADNCPDAFIHI 208
++ + K ++VVI AG P+KPG TR DL N I K++V V + D +
Sbjct: 61 TKIYAGDYSDCKDADLVVITAGAPQKPGETRLDLVEKNLKIFKSIVGEVMASGFDGIFLV 120
Query: 209 ISNPVNSTVPIAAEVLKQKGVYDPKKLFGV---------TTLDVVRANTFVAQKKNLKLI 259
SNPV ++L Y KL G T+LD R +++K ++
Sbjct: 121 ASNPV--------DIL----TYATWKLSGFPKERVIGSGTSLDSARFRYMLSEKLDVDPR 168
Query: 260 DVDVPVVGGH----------AGITILPLLSKTMPSVSFTDEEVGDLTVRIQNAGTEVVEA 309
V ++G H A + +PL + + +E++ ++ +++A E++E
Sbjct: 169 SVHAYIIGEHGDTEFPVWSHANVAGVPLEEYLEENEQYDEEDLDEIFENVRDAAYEIIEK 228
Query: 310 KAGAGSATLSMAYAAARFVESSLR 333
K G+ +A A AR ++ L
Sbjct: 229 K---GATYYGIAMALARITKAILN 249
>gnl|CDD|133423 cd01338, MDH_choloroplast_like, Chloroplast-like malate
dehydrogenases. MDH is one of the key enzymes in the
citric acid cycle, facilitating both the conversion of
malate to oxaloacetate and replenishing levels of
oxalacetate by reductive carboxylation of pyruvate.
Members of this subfamily are bacterial MDHs, and plant
MDHs localized to the choloroplasts. MDHs are part of
the NAD(P)-binding Rossmann fold superfamily, which
includes a wide variety of protein families including
the NAD(P)-binding domains of alcohol dehydrogenases,
tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate dehydrogenases,
formate/glycerate dehydrogenases, siroheme synthases,
6-phosphogluconate dehydrogenases, aminoacid
dehydrogenases, repressor rex, and NAD-binding potassium
channel domains, among others.
Length = 322
Score = 73.4 bits (181), Expect = 2e-14
Identities = 68/261 (26%), Positives = 105/261 (40%), Gaps = 49/261 (18%)
Query: 95 KVAVLGAAGGIGQPL-------ALLIKMSPLVSALHLYDVMN----VKGVAADLSHCNTP 143
+VAV GAAG IG L + P+ L L ++ ++GVA +L C P
Sbjct: 4 RVAVTGAAGQIGYSLLFRIASGEMFGPDQPV--ILQLLELPQALKALEGVAMELEDCAFP 61
Query: 144 --SQVLDFTGPEELASALKGVNVVVIPAGVPRKPGMTRDDLFNINANIVKTLVEAVADNC 201
++++ P A K + ++ PR PGM R DL N I +A+ D
Sbjct: 62 LLAEIVITDDPNV---AFKDADWALLVGAKPRGPGMERADLLKANGKIFTAQGKALNDVA 118
Query: 202 -PDAFIHIISNPVNSTVPIAAEVLKQKGVYDPKKLFGVTTLDVVRANTFVAQKKNLKLID 260
D + ++ NP N+ IA K P +T LD RA + +A+K + + D
Sbjct: 119 SRDVKVLVVGNPCNTNALIAM---KNAPDIPPDNFTAMTRLDHNRAKSQLAKKAGVPVTD 175
Query: 261 V-DVPVVGGHAGITILPLLSKTM-PSVSFT------------DEE--VGDLTVRIQNAGT 304
V ++ + G H S T P + D + +Q G
Sbjct: 176 VKNMVIWGNH---------SPTQYPDFTNATIGGKPAAEVINDRAWLEDEFIPTVQKRGA 226
Query: 305 EVVEAKAGAGSATLSMAYAAA 325
+++A+ GA SA S A AA
Sbjct: 227 AIIKAR-GASSAA-SAANAAI 245
>gnl|CDD|130819 TIGR01758, MDH_euk_cyt, malate dehydrogenase, NAD-dependent. This
model represents the NAD-dependent cytosolic malate
dehydrogenase from eukaryotes. The enzyme from pig has
been studied by X-ray crystallography.
Length = 324
Score = 72.6 bits (178), Expect = 4e-14
Identities = 73/254 (28%), Positives = 108/254 (42%), Gaps = 33/254 (12%)
Query: 95 KVAVLGAAGGIGQPLALLIKMSPLVSA-----LHLYDVMNVK----GVAADLSHCNTPSQ 145
+V V GAAG IG L +I ++ LHL D+ GV +L C P
Sbjct: 1 RVVVTGAAGQIGYALLPMIARGRMLGKDQPIILHLLDIPPAMKVLEGVVMELMDCAFP-- 58
Query: 146 VLDFTGP-EELASALKGVNVVVIPAGVPRKPGMTRDDLFNINANIVKTLVEAVADNC-PD 203
+LD P + A A V+V ++ PRK GM R DL + N I K A+ D
Sbjct: 59 LLDGVVPTHDPAVAFTDVDVAILVGAFPRKEGMERRDLLSKNVKIFKEQGRALDKLAKKD 118
Query: 204 AFIHIISNPVNSTVPIAAEVLKQKGVYDPKKLF-GVTTLDVVRANTFVAQKKNLKLIDV- 261
+ ++ NP N+ A VL P K F +T LD RA VA++ + + DV
Sbjct: 119 CKVLVVGNPANTN----ALVLSNYAPSIPPKNFSALTRLDHNRALAQVAERAGVPVSDVK 174
Query: 262 DVPVVGGHAGITILPLLSKTMPSVSFTDEEV-----------GDLTVRIQNAGTEVVEAK 310
+V + G H+ T P ++ + + V G+ +Q G ++ A+
Sbjct: 175 NVIIWGNHSS-TQYPDVNHATVTKGGKQKPVREAIKDDAYLDGEFITTVQQRGAAIIRAR 233
Query: 311 AGAGSATLSMAYAA 324
S+ LS A AA
Sbjct: 234 --KLSSALSAAKAA 245
>gnl|CDD|133421 cd01336, MDH_cytoplasmic_cytosolic, Cytoplasmic and cytosolic
Malate dehydrogenases. MDH is one of the key enzymes in
the citric acid cycle, facilitating both the conversion
of malate to oxaloacetate and replenishing levels of
oxalacetate by reductive carboxylation of pyruvate.
Members of this subfamily are eukaryotic MDHs localized
to the cytoplasm and cytosol. MDHs are part of the
NAD(P)-binding Rossmann fold superfamily, which includes
a wide variety of protein families including the
NAD(P)-binding domains of alcohol dehydrogenases,
tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate dehydrogenases,
formate/glycerate dehydrogenases, siroheme synthases,
6-phosphogluconate dehydrogenases, aminoacid
dehydrogenases, repressor rex, and NAD-binding potassium
channel domains, among others.
Length = 325
Score = 70.3 bits (173), Expect = 2e-13
Identities = 76/259 (29%), Positives = 114/259 (44%), Gaps = 43/259 (16%)
Query: 95 KVAVLGAAGGIGQPLALLI-------KMSPLVSALHLYDV---MNV-KGVAADLSHCNTP 143
+V V GAAG I L +I P++ LHL D+ + +GV +L C P
Sbjct: 4 RVLVTGAAGQIAYSLLPMIAKGDVFGPDQPVI--LHLLDIPPALKALEGVVMELQDCAFP 61
Query: 144 --SQVLDFTGPEELASALKGVNVVVIPAGVPRKPGMTRDDLFNINANIVKTLVEA---VA 198
V+ T PEE A K V+V ++ +PRK GM R DL N I K EA A
Sbjct: 62 LLKSVVATTDPEE---AFKDVDVAILVGAMPRKEGMERKDLLKANVKIFKEQGEALDKYA 118
Query: 199 DNCPDAFIHIISNPVNSTVPIAAEVLKQKGVYDPKKLF-GVTTLDVVRANTFVAQKKNLK 257
+ + ++ NP N+ I + + PK+ F +T LD RA + +A K +
Sbjct: 119 K--KNVKVLVVGNPANTNALILLK--YAPSI--PKENFTALTRLDHNRAKSQIALKLGVP 172
Query: 258 LIDV-DVPVVGGHAGITILP--------LLSKTMPSVSFTDEEV---GDLTVRIQNAGTE 305
+ DV +V + G H+ T P L K P+ ++ G+ +Q G
Sbjct: 173 VSDVKNVIIWGNHSS-TQYPDVNHATVELNGKGKPAREAVKDDAWLNGEFISTVQKRGAA 231
Query: 306 VVEAKAGAGSATLSMAYAA 324
V++A+ SA +S A A
Sbjct: 232 VIKAR-KLSSA-MSAAKAI 248
>gnl|CDD|235468 PRK05442, PRK05442, malate dehydrogenase; Provisional.
Length = 326
Score = 67.9 bits (167), Expect = 1e-12
Identities = 70/266 (26%), Positives = 105/266 (39%), Gaps = 61/266 (22%)
Query: 95 KVAVLGAAGGIG----------------QPLAL-LIKMSPLVSALHLYDVMNVKGVAADL 137
+VAV GAAG IG QP+ L L+++ P + AL +GV +L
Sbjct: 6 RVAVTGAAGQIGYSLLFRIASGDMLGKDQPVILQLLEIPPALKAL--------EGVVMEL 57
Query: 138 SHCNTP--SQVLDFTGPEELASALKGVNVVVIPAGVPRKPGMTRDDLFNINANIVKTLVE 195
C P + V+ P A K +V ++ PR PGM R DL N I +
Sbjct: 58 DDCAFPLLAGVVITDDPNV---AFKDADVALLVGARPRGPGMERKDLLEANGAIFTAQGK 114
Query: 196 AVADNC-PDAFIHIISNPVNSTVPIAAEVLKQKGVYDPKKLFGVTTLDVVRANTFVAQKK 254
A+ + D + ++ NP N+ IA + + + +T LD RA + +A K
Sbjct: 115 ALNEVAARDVKVLVVGNPANTNALIAMK--NAPDL-PAENFTAMTRLDHNRALSQLAAKA 171
Query: 255 NLKLIDV-DVPVVGGHAGITILPLLSKTM-PSVSFT------------DEE--VGDLTVR 298
+ + D+ + V G H S T P D+
Sbjct: 172 GVPVADIKKMTVWGNH---------SATQYPDFRHATIDGKPAAEVINDQAWLEDTFIPT 222
Query: 299 IQNAGTEVVEAKAGAGSATLSMAYAA 324
+Q G ++EA+ GA SA S A AA
Sbjct: 223 VQKRGAAIIEAR-GASSAA-SAANAA 246
>gnl|CDD|133429 cd05293, LDH_1, A subgroup of L-lactate dehydrogenases. L-lactate
dehydrogenases (LDH) are tetrameric enzymes catalyzing
the last step of glycolysis in which pyruvate is
converted to L-lactate. This subgroup is composed of
eukaryotic LDHs. Vertebrate LDHs are non-allosteric.
This is in contrast to some bacterial LDHs that are
activated by an allosteric effector such as
fructose-1,6-bisphosphate. LDHs are part of the
NAD(P)-binding Rossmann fold superfamily, which includes
a wide variety of protein families including the
NAD(P)-binding domains of alcohol dehydrogenases,
tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate dehydrogenases,
formate/glycerate dehydrogenases, siroheme synthases,
6-phosphogluconate dehydrogenases, aminoacid
dehydrogenases, repressor rex, and NAD-binding potassium
channel domains, among others.
Length = 312
Score = 66.1 bits (162), Expect = 4e-12
Identities = 80/333 (24%), Positives = 133/333 (39%), Gaps = 70/333 (21%)
Query: 93 SFKVAVLGAAGGIGQPLALLIKMSPLVSALHLYDVMN--VKGVAADLSH----CNTPSQV 146
KV V+G G +G A+ I L L L DV+ +KG A DL H P
Sbjct: 3 RNKVTVVGV-GQVGMACAISILAKGLADELVLVDVVEDKLKGEAMDLQHGSAFLKNPKIE 61
Query: 147 LDFTGPEELASALKGVNVVVIPAGVPRKPGMTRDDLFNINANIVKTLVEAVADNCPDAFI 206
D S VV++ AG + G +R DL N +I K ++ + P+A +
Sbjct: 62 ADKDY-----SVTANSKVVIVTAGARQNEGESRLDLVQRNVDIFKGIIPKLVKYSPNAIL 116
Query: 207 HIISNPVNSTVPIAAEVL-----KQKGVYDPK-KLFGV-TTLDVVRANTFVAQKKNLKLI 259
++SNPV +++ K G+ PK ++ G LD R +A++ +
Sbjct: 117 LVVSNPV--------DIMTYVAWKLSGL--PKHRVIGSGCNLDSARFRYLIAERLGVAPS 166
Query: 260 DVDVPVVGGH-------------AGITILPLLSKTMPSVSFTDEEVGDLTVRIQNAGTEV 306
V ++G H AG+ + L E+ ++ ++ ++ EV
Sbjct: 167 SVHGWIIGEHGDSSVPVWSGVNVAGVRLQDLNPD--IGTDKDPEKWKEVHKQVVDSAYEV 224
Query: 307 VEAKAGAGSATLSMAYAAARFVESSLRAL----------DGDGDVYECVFVESNLTELPF 356
++ K G + ++ + A V++ LR G + + VF+ LP
Sbjct: 225 IKLK---GYTSWAIGLSVADLVDAILRNTGRVHSVSTLVKGLHGIEDEVFL-----SLP- 275
Query: 357 FASRVKLGRNGVESLISSDLQGLTEYEQKALEA 389
LG NG+ +I Q LTE EQ+ L+
Sbjct: 276 ----CILGENGITHVIK---QPLTEEEQEKLQK 301
>gnl|CDD|177744 PLN00135, PLN00135, malate dehydrogenase.
Length = 309
Score = 64.8 bits (158), Expect = 1e-11
Identities = 63/241 (26%), Positives = 108/241 (44%), Gaps = 33/241 (13%)
Query: 100 GAAGGIGQPLAL-LIKMSPLVSALHLYDVMNVKGVAADLSHCNTP--SQVLDFTGPEELA 156
G G QP+ L ++ + P AL GV +L P V+ T E
Sbjct: 5 GVMLGPDQPVILHMLDIPPAAEAL--------NGVKMELIDAAFPLLKGVVATTDVVE-- 54
Query: 157 SALKGVNVVVIPAGVPRKPGMTRDDLFNINANIVKTLVEAVADNC-PDAFIHIISNPVNS 215
A KGVN+ V+ G PRK GM R D+ + N +I K+ A+ + PD + +++NP N+
Sbjct: 55 -ACKGVNIAVMVGGFPRKEGMERKDVMSKNVSIYKSQASALEKHAAPDCKVLVVANPANT 113
Query: 216 TVPIAAEVLKQKGVYDPKK-LFGVTTLDVVRANTFVAQKKNLKLIDVDVPVVGGHAGITI 274
A +LK+ P+K + +T LD RA ++++ + + DV ++ G+ T
Sbjct: 114 N----ALILKEFAPSIPEKNITCLTRLDHNRALGQISERLGVPVSDVKNVIIWGNHSSTQ 169
Query: 275 LPLLSKTMPSVSFTDEEV-----------GDLTVRIQNAGTEVVEAKAGAGSATLSMAYA 323
P ++ ++ V G+ +Q G +++A+ S+ LS A +
Sbjct: 170 YPDVNHATVKTPSGEKPVRELVADDAWLNGEFITTVQQRGAAIIKAR--KLSSALSAASS 227
Query: 324 A 324
A
Sbjct: 228 A 228
>gnl|CDD|178212 PLN02602, PLN02602, lactate dehydrogenase.
Length = 350
Score = 62.9 bits (153), Expect = 8e-11
Identities = 75/309 (24%), Positives = 129/309 (41%), Gaps = 29/309 (9%)
Query: 95 KVAVLGAAGGIGQPLALLIKMSPLVSALHLYDVM--NVKGVAADLSHCNTPSQVLDFTGP 152
KV+V+G G +G +A I L L L DV ++G DL H
Sbjct: 39 KVSVVGV-GNVGMAIAQTILTQDLADELALVDVNPDKLRGEMLDLQHAAAFLPRTKILAS 97
Query: 153 EELASALKGVNVVVIPAGVPRKPGMTRDDLFNINANIVKTLVEAVADNCPDAFIHIISNP 212
+ + G ++ ++ AG + PG +R +L N + + ++ +A PD + I+SNP
Sbjct: 98 TDY-AVTAGSDLCIVTAGARQIPGESRLNLLQRNVALFRKIIPELAKYSPDTILLIVSNP 156
Query: 213 VNSTVPIAAEVLKQKGVYDPKKLFGVTTLDVVRANTFVAQKKNLKLIDVDVPVVGGH--- 269
V+ +A K G + + T LD R +A ++ DV +VG H
Sbjct: 157 VDVLTYVA---WKLSGFPANRVIGSGTNLDSSRFRFLIADHLDVNAQDVQAYIVGEHGDS 213
Query: 270 ----------AGITILPLLSKTMPSVSFTDEEVGDLTVRIQNAGTEVVEAKAGAGSATLS 319
G+ +L L K +++ E + ++ + ++ EV++ K G + +
Sbjct: 214 SVALWSSVSVGGVPVLSFLEKQ--QIAYEKETLEEIHRAVVDSAYEVIKLK---GYTSWA 268
Query: 320 MAYAAARFVESSLRALDGDGDVYECVFVESNLTELPFFAS-RVKLGRNGVESLISSDLQG 378
+ Y+ A V S LR V + E F S +LGRNGV +++
Sbjct: 269 IGYSVASLVRSLLRDQRRIHPVSVLAKGFHGIDEGDVFLSLPAQLGRNGVLGVVNVH--- 325
Query: 379 LTEYEQKAL 387
LT+ E + L
Sbjct: 326 LTDEEAERL 334
>gnl|CDD|130817 TIGR01756, LDH_protist, lactate dehydrogenase. This model
represents a family of protist lactate dehydrogenases
which have aparrently evolved from a recent protist
malate dehydrogenase ancestor. Lactate dehydrogenase
converts the hydroxyl at C-2 of lactate to a carbonyl in
the product, pyruvate. The preference of this enzyme for
NAD or NADP has not been determined. A critical residue
in malate dehydrogenase, arginine-91 (T. vaginalis
numbering) has been mutated to a leucine, eliminating
the positive charge which complemeted the carboxylate in
malate which is absent in lactate. Several other more
subtle changes are proposed to make the active site
smaller to accomadate the less bulky lactate molecule.
Length = 313
Score = 60.3 bits (146), Expect = 4e-10
Identities = 48/190 (25%), Positives = 85/190 (44%), Gaps = 13/190 (6%)
Query: 122 LHLYDV---MN-VKGVAADLSHCNTP--SQVLDFTGPEELASALKGVNVVVIPAGVPRKP 175
LHL ++ +N ++ +A +L C P + + T EE A K ++ + A VP KP
Sbjct: 18 LHLLEIPPALNRLEALAMELEDCAFPNLAGTIVTTKLEE---AFKDIDCAFLVASVPLKP 74
Query: 176 GMTRDDLFNINANIVKTLVEAVADNC-PDAFIHIISNPVNSTVPIAAEVLKQKGVYDPKK 234
G R DL N I K EA+++ P + +I NPVN+ +A +L + +
Sbjct: 75 GEVRADLLTKNTPIFKATGEALSEYAKPTVKVLVIGNPVNTNCLVA--MLHAPKL-SAEN 131
Query: 235 LFGVTTLDVVRANTFVAQKKNLKLIDVDVPVVGGHAGITILPLLSKTMPSVSFTDEEVGD 294
+ LD RA + +A K + + + VV G+ +++ L+ + + ++V D
Sbjct: 132 FSSLCMLDHNRAVSRIASKLKVPVDHIYHVVVWGNHAESMVADLTHAEFTKNGKHQKVFD 191
Query: 295 LTVRIQNAGT 304
R
Sbjct: 192 ELCRDYPEPD 201
>gnl|CDD|133426 cd05290, LDH_3, A subgroup of L-lactate dehydrogenases. L-lactate
dehydrogenases (LDH) are tetrameric enzymes catalyzing
the last step of glycolysis in which pyruvate is
converted to L-lactate. This subgroup is composed of
some bacterial LDHs from firmicutes,
gammaproteobacteria, and actinobacteria. Vertebrate LDHs
are non-allosteric, but some bacterial LDHs are
activated by an allosteric effector such as
fructose-1,6-bisphosphate. LDHs are part of the
NAD(P)-binding Rossmann fold superfamily, which includes
a wide variety of protein families including the
NAD(P)-binding domains of alcohol dehydrogenases,
tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate dehydrogenases,
formate/glycerate dehydrogenases, siroheme synthases,
6-phosphogluconate dehydrogenase, aminoacid
dehydrogenases, repressor rex, and NAD-binding potassium
channel domains, among others.
Length = 307
Score = 57.7 bits (140), Expect = 3e-09
Identities = 62/251 (24%), Positives = 96/251 (38%), Gaps = 31/251 (12%)
Query: 95 KVAVLGAAGGIGQPLALLIKMSPLVSALHLYDVMNVK--GVAADLSHCNTPSQVLDFTGP 152
K+ V+GA G +G + L S + L DV G A D H + +
Sbjct: 1 KLVVIGA-GHVGSAVLNYALALGLFSEIVLIDVNEGVAEGEALDFHHATALTYSTNTKIR 59
Query: 153 EELASALKGVNVVVIPAGVPRKPGMT--RDDLFNINANIVKTLVEAVADNCPDAFIHIIS 210
+++VI AG PG T R DL NA I++ ++ + +A I +I+
Sbjct: 60 AGDYDDCADADIIVITAGPSIDPGNTDDRLDLAQTNAKIIREIMGNITKVTKEAVIILIT 119
Query: 211 NPVNSTVPIAAEVLKQKGVYDPKKLFGV-TTLDVVRANTFVAQKKNLKLIDVDVPVVGGH 269
NP++ V IAA + Y K+ G T LD R VA K + +V V+G H
Sbjct: 120 NPLDIAVYIAA----TEFDYPANKVIGTGTMLDTARLRRIVADKYGVDPKNVTGYVLGEH 175
Query: 270 AGITILPLLSKT----MPSVSFTD---------EEVGDLTVRIQNAGTEVVEAK----AG 312
G P+ S +P +E+ + + A +V K AG
Sbjct: 176 -GSHAFPVWSLVNIAGLPLDELEALFGKEPIDKDELLE---EVVQAAYDVFNRKGWTNAG 231
Query: 313 AGSATLSMAYA 323
+ + A
Sbjct: 232 IAKSASRLIKA 242
>gnl|CDD|215060 PLN00112, PLN00112, malate dehydrogenase (NADP); Provisional.
Length = 444
Score = 43.3 bits (102), Expect = 2e-04
Identities = 52/182 (28%), Positives = 69/182 (37%), Gaps = 40/182 (21%)
Query: 95 KVAVLGAAGGIG----------------QPLAL-LIKMSPLVSALHLYDVMNVKGVAADL 137
VAV GAAG I QP+AL L+ AL +GVA +L
Sbjct: 102 NVAVSGAAGMISNHLLFKLASGEVFGPDQPIALKLLGSERSKQAL--------EGVAMEL 153
Query: 138 SHCNTP--SQVLDFTGPEELASALKGVNVVVIPAGVPRKPGMTRDDLFNINANIV----K 191
P +V P E+ + ++ PR PGM R DL +IN I K
Sbjct: 154 EDSLYPLLREVSIGIDPYEV---FQDAEWALLIGAKPRGPGMERADLLDINGQIFAEQGK 210
Query: 192 TLVEAVADNCPDAFIHIISNPVNSTVPIAAEVLKQKGVYDPKKLFGVTTLDVVRANTFVA 251
L E + N + ++ NP N+ I LK K +T LD RA +A
Sbjct: 211 ALNEVASRNVK---VIVVGNPCNTNALIC---LKNAPNIPAKNFHALTRLDENRAKCQLA 264
Query: 252 QK 253
K
Sbjct: 265 LK 266
>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 = 40.8 bits (96), Expect = 8e-04
Identities = 26/120 (21%), Positives = 52/120 (43%), Gaps = 4/120 (3%)
Query: 97 AVLGAAGGIGQPLA-LLIKMSPLVSALHLYDVMNVKGVAADLSHCNTPSQVL-DFTGPEE 154
V G G +G+ + LL++ L + ++D+ + D S + + D T ++
Sbjct: 1 LVTGGGGFLGRHIVRLLLREGEL-QEVRVFDLRFSPELLEDFSKLQVITYIEGDVTDKQD 59
Query: 155 LASALKGVNVVVIPAGVPRKPGM-TRDDLFNINANIVKTLVEAVADNCPDAFIHIISNPV 213
L AL+G +VV+ A + G RD + +N + +++A ++ S V
Sbjct: 60 LRRALQGSDVVIHTAAIIDVFGKAYRDTIMKVNVKGTQNVLDACVKAGVRVLVYTSSMEV 119
>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 = 38.2 bits (89), Expect = 0.002
Identities = 29/116 (25%), Positives = 48/116 (41%), Gaps = 14/116 (12%)
Query: 96 VAVLGAAGGIGQPLAL-LIKMSPLVSALHLYDVMNVKGVAADLSHCNTPS--QVLDFTGP 152
+ +LGA G IG+ LA L++ V+ L V+ P D
Sbjct: 1 ILILGATGFIGRALARELLEQGHEVTLL-------VRNTKRLSKEDQEPVAVVEGDLRDL 53
Query: 153 EELASALKGVNVVVIPAGVPRKPGMTRDDLFNINANIVKTLVEAVADNCPDAFIHI 208
+ L+ A++GV+VV+ AG PR + + + ++EA + FI I
Sbjct: 54 DSLSDAVQGVDVVIHLAGAPRDTRDFCEV----DVEGTRNVLEAAKEAGVKHFIFI 105
>gnl|CDD|223528 COG0451, WcaG, Nucleoside-diphosphate-sugar epimerases [Cell
envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 314
Score = 39.2 bits (91), Expect = 0.003
Identities = 29/123 (23%), Positives = 44/123 (35%), Gaps = 9/123 (7%)
Query: 95 KVAVLGAAGGIGQPLALLIKMSPLVSALHLYDVMNVKGVAADLSHCNTPSQVLDFTGPEE 154
++ V G AG IG L L++A H ++ D VLD T +
Sbjct: 2 RILVTGGAGFIGSHLVER-----LLAAGHDVRGLDRLRDGLDPLLSGVEFVVLDLTDRDL 56
Query: 155 LASALKGVNVVVI----PAGVPRKPGMTRDDLFNINANIVKTLVEAVADNCPDAFIHIIS 210
+ KGV VI + VP + ++N + L+EA F+ S
Sbjct: 57 VDELAKGVPDAVIHLAAQSSVPDSNASDPAEFLDVNVDGTLNLLEAARAAGVKRFVFASS 116
Query: 211 NPV 213
V
Sbjct: 117 VSV 119
>gnl|CDD|130818 TIGR01757, Malate-DH_plant, malate dehydrogenase, NADP-dependent.
This model represents the NADP-dependent malate
dehydrogenase found in plants, mosses and green algae
and localized to the chloroplast. Malate dehydrogenase
converts oxaloacetate into malate, a critical step in
the C4 cycle which allows circumvention of the effects
of photorespiration. Malate is subsequenctly transported
from the chloroplast to the cytoplasm (and then to the
bundle sheath cells in C4 plants). The plant and moss
enzymes are light regulated via cysteine disulfide
bonds. The enzyme from Sorghum has been crystallized.
Length = 387
Score = 38.0 bits (88), Expect = 0.007
Identities = 54/201 (26%), Positives = 78/201 (38%), Gaps = 24/201 (11%)
Query: 91 QASFKVAVLGAAGGIGQPLALLIKMSPLVS-----ALHLYDVMNVK----GVAADLSHCN 141
+ + VAV GAAG I L ++ + AL L K GVA +L
Sbjct: 42 KKTVNVAVSGAAGMISNHLLFMLASGEVFGQDQPIALKLLGSERSKEALEGVAMELEDSL 101
Query: 142 TP--SQVLDFTGPEELASALKGVNVVVIPAGVPRKPGMTRDDLFNINANIV----KTLVE 195
P +V P E+ + + ++ PR PGM R DL +IN I K L
Sbjct: 102 YPLLREVSIGIDPYEV---FEDADWALLIGAKPRGPGMERADLLDINGQIFADQGKALNA 158
Query: 196 AVADNCPDAFIHIISNPVNSTVPIAAEVLKQKGVYDPKKLFGVTTLDVVRANTFVAQKKN 255
+ NC + ++ NP N+ IA +K K +T LD RA +A K
Sbjct: 159 VASKNCK---VLVVGNPCNTNALIA---MKNAPNIPRKNFHALTRLDENRAKCQLALKSG 212
Query: 256 LKLIDVDVPVVGGHAGITILP 276
V + G+ T +P
Sbjct: 213 KFYTSVSNVTIWGNHSTTQVP 233
>gnl|CDD|187579 cd05271, NDUFA9_like_SDR_a, NADH dehydrogenase (ubiquinone) 1 alpha
subcomplex, subunit 9, 39 kDa, (NDUFA9) -like, atypical
(a) SDRs. This subgroup of extended SDR-like proteins
are atypical SDRs. They have a glycine-rich
NAD(P)-binding motif similar to the typical SDRs,
GXXGXXG, and have the YXXXK active site motif (though
not the other residues of the SDR tetrad). Members
identified include NDUFA9 (mitochondrial) and putative
nucleoside-diphosphate-sugar epimerase. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Atypical SDRs include
biliverdin IX beta reductase (BVR-B,aka flavin
reductase), NMRa (a negative transcriptional regulator
of various fungi), progesterone 5-beta-reductase like
proteins, phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. In addition to the
Rossmann fold core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 273
Score = 37.2 bits (87), Expect = 0.010
Identities = 28/119 (23%), Positives = 44/119 (36%), Gaps = 12/119 (10%)
Query: 95 KVAVLGAAGGIGQPL-ALLIKMSPLVSALHLYDVMNVKGVAADLSHCNTPSQVL----DF 149
V V GA G IG+ + L K V + + A L QVL D
Sbjct: 2 VVTVFGATGFIGRYVVNRLAKRGSQVIVPY-----RCEAYARRLLVMGDLGQVLFVEFDL 56
Query: 150 TGPEELASALKGVNVVVIPAGVPRKPGMTRDDLFNINANIVKTLVEAVADNCPDAFIHI 208
E + AL+G +VV+ G + +++ + L +A + + IHI
Sbjct: 57 RDDESIRKALEGSDVVINLVGRLYETK--NFSFEDVHVEGPERLAKAAKEAGVERLIHI 113
>gnl|CDD|234595 PRK00048, PRK00048, dihydrodipicolinate reductase; Provisional.
Length = 257
Score = 36.3 bits (85), Expect = 0.018
Identities = 27/87 (31%), Positives = 38/87 (43%), Gaps = 15/87 (17%)
Query: 95 KVAVLGAAGGIGQPLALLIKMSP---LVSAL----HLYDVMNVKGVA--ADLSHCNTPSQ 145
KVAV GA+G +G+ L ++ + LV+A+ GVA DL +
Sbjct: 3 KVAVAGASGRMGRELIEAVEAAEDLELVAAVDRPGSPLVGQGALGVAITDDLEAVLADAD 62
Query: 146 VL-DFTGPE---ELASAL--KGVNVVV 166
VL DFT PE E G +V+
Sbjct: 63 VLIDFTTPEATLENLEFALEHGKPLVI 89
>gnl|CDD|187569 cd05259, PCBER_SDR_a, phenylcoumaran benzylic ether reductase
(PCBER) like, atypical (a) SDRs. PCBER and
pinoresinol-lariciresinol reductases are NADPH-dependent
aromatic alcohol reductases, and are atypical members of
the SDR family. Other proteins in this subgroup are
identified as eugenol synthase. These proteins contain
an N-terminus characteristic of NAD(P)-binding proteins
and a small C-terminal domain presumed to be involved in
substrate binding, but they do not have the conserved
active site Tyr residue typically found in SDRs.
Numerous other members have unknown functions. The
glycine rich NADP-binding motif in this subgroup is of 2
forms: GXGXXG and G[GA]XGXXG; it tends to be atypical
compared with the forms generally seen in classical or
extended SDRs. The usual SDR active site tetrad is not
present, but a critical active site Lys at the usual SDR
position has been identified in various members, though
other charged and polar residues are found at this
position in this subgroup. Atypical SDR-related proteins
retain the Rossmann fold of the SDRs, but have limited
sequence identity and generally lack the catalytic
properties of the archetypical members. Atypical SDRs
include biliverdin IX beta reductase (BVR-B,aka flavin
reductase), NMRa (a negative transcriptional regulator
of various fungi), progesterone 5-beta-reductase like
proteins, phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. In addition to the
Rossmann fold core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 282
Score = 34.6 bits (80), Expect = 0.065
Identities = 25/80 (31%), Positives = 37/80 (46%), Gaps = 16/80 (20%)
Query: 95 KVAVLGAAGGIGQPLALLIKMSPLVSALHLYDVMNVKGVA---ADLSHCNTPSQV----L 147
K+A+ GA G +G P+VSAL V + + S+ PS V +
Sbjct: 1 KIAIAGATGTLG---------GPIVSALLASPGFTVTVLTRPSSTSSNEFQPSGVKVVPV 51
Query: 148 DFTGPEELASALKGVNVVVI 167
D+ E L +ALKGV+ V+
Sbjct: 52 DYASHESLVAALKGVDAVIS 71
>gnl|CDD|222146 pfam13460, NAD_binding_10, NADH(P)-binding.
Length = 182
Score = 33.8 bits (78), Expect = 0.078
Identities = 21/81 (25%), Positives = 29/81 (35%), Gaps = 11/81 (13%)
Query: 96 VAVLGAAGGIGQPLA--LLIKMSPLVSALHLYDVMNVKGVAADLSHCNTPSQVLDFTGPE 153
+AV+GA G G+ L LL + + + N A D
Sbjct: 1 IAVIGATGKTGRRLVKELLARGHQVTALSR-----NPSKAPAP----GVTPVQKDLFDLA 51
Query: 154 ELASALKGVNVVVIPAGVPRK 174
+LA AL GV+ VV G
Sbjct: 52 DLAEALAGVDAVVDAFGARPD 72
>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 = 33.5 bits (77), Expect = 0.16
Identities = 25/105 (23%), Positives = 40/105 (38%), Gaps = 7/105 (6%)
Query: 96 VAVLGAAGGIGQPLALLIKMSPLVSALHLYDVMNVKGVAADLSHCNTPSQVLDFTGPE-E 154
+ V GAAGG+G+ LA + SP V D ++ S LD P
Sbjct: 1 ILVTGAAGGLGRLLARRLAASPRV---IGVDGLDR--RRPPGSPPKVEYVRLDIRDPAAA 55
Query: 155 LASALKGVNVVVIPAGVPRKPGMTRDDLFNINANIVKTLVEAVAD 199
+ + VV A + P + IN + + +++A A
Sbjct: 56 DVFREREADAVVHLAFI-LDPPRDGAERHRINVDGTQNVLDACAA 99
>gnl|CDD|187636 cd08931, SDR_c9, classical (c) SDR, subgroup 9. This subgroup has
the canonical active site tetrad and NAD-binding motif
of the classical SDRs. SDRs are a functionally diverse
family of oxidoreductases that have a single domain with
a structurally conserved Rossmann fold (alpha/beta
folding pattern with a central beta-sheet), an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRs are approximately
350 residues. Sequence identity between different SDR
enzymes are typically in the 15-30% range, but the
enzymes share the Rossmann fold NAD-binding motif and
characteristic NAD-binding and catalytic sequence
patterns. These enzymes catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase (15-PGDH) numbering). In addition to the
Tyr and Lys, there is often an upstream Ser (Ser-138,
15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH
numbering) contributing to the active site; while
substrate binding is in the C-terminal region, which
determines specificity. The standard reaction mechanism
is a 4-pro-S hydride transfer and proton relay involving
the conserved Tyr and Lys, a water molecule stabilized
by Asn, and nicotinamide. Extended SDRs have additional
elements in the C-terminal region, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Some atypical SDRs have lost catalytic activity and/or
have an unusual NAD(P)-binding motif and missing or
unusual active site residues. Reactions catalyzed within
the SDR family include isomerization, decarboxylation,
epimerization, C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 227
Score = 33.2 bits (76), Expect = 0.16
Identities = 29/92 (31%), Positives = 39/92 (42%), Gaps = 10/92 (10%)
Query: 98 VLGAAGGIGQPLALLIKMSPLVSALHLYDVMNVKGVAADLSHCNTPSQVLDFTGPEELAS 157
+ GAA GIG+ ALL + L+ D + +AA+L N + LD T A+
Sbjct: 5 ITGAASGIGRETALLFARNGWFVGLYDIDEDGLAALAAELGAENVVAGALDVTDRAAWAA 64
Query: 158 ALKGVNVVVIPAGVPRKPGMTRDDLFNINANI 189
AL A G D LFN NA +
Sbjct: 65 AL---------ADFAAATGGRLDALFN-NAGV 86
>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 = 32.6 bits (75), Expect = 0.26
Identities = 21/72 (29%), Positives = 32/72 (44%), Gaps = 6/72 (8%)
Query: 97 AVLGAAGGIGQPLA-LLIKMSPLVSALHLYDVMNVKGVAADLSHCNTPSQVLDFTGPEEL 155
V GA G +G + LL+ V AL + K AAD + D+ PE L
Sbjct: 2 LVTGATGKLGTAVVELLLAKVASVVALVR-NPEKAKAFAAD----GVEVRQGDYDDPETL 56
Query: 156 ASALKGVNVVVI 167
A +GV+ +++
Sbjct: 57 ERAFEGVDRLLL 68
>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 = 32.2 bits (74), Expect = 0.35
Identities = 26/77 (33%), Positives = 37/77 (48%), Gaps = 6/77 (7%)
Query: 95 KVAVLGAAGGIGQPLA-LLIKMSPLVSALHLYDVMNVKGVAADLSHCNTPSQVLDFTGPE 153
KV V+GA G +G+ + L+ V AL V + A L V D T E
Sbjct: 1 KVLVVGATGKVGRHVVRELLDRGYQVRAL----VRDPSQ-AEKLEAAGAEVVVGDLTDAE 55
Query: 154 ELASALKGVNVVVIPAG 170
LA+AL+G++ V+ AG
Sbjct: 56 SLAAALEGIDAVISAAG 72
>gnl|CDD|171820 PRK12936, PRK12936, 3-ketoacyl-(acyl-carrier-protein) reductase
NodG; Reviewed.
Length = 245
Score = 31.8 bits (72), Expect = 0.47
Identities = 29/95 (30%), Positives = 48/95 (50%), Gaps = 12/95 (12%)
Query: 95 KVAVLGAAGGIGQPLALLIKMSPLVSALHLYDVMNVKGVAADLSHCNT--PSQVLDFTGP 152
K V GA+GGIG+ +A L+ + LH V ++ +AA+L P+ + D
Sbjct: 8 KALVTGASGGIGEEIARLLHAQGAIVGLHGTRVEKLEALAAELGERVKIFPANLSDRDEV 67
Query: 153 EELA----SALKGVNVVVIPAGVPRKPGMTRDDLF 183
+ L + L+GV+++V AG+ T+D LF
Sbjct: 68 KALGQKAEADLEGVDILVNNAGI------TKDGLF 96
>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 = 32.1 bits (73), Expect = 0.53
Identities = 27/122 (22%), Positives = 48/122 (39%), Gaps = 6/122 (4%)
Query: 98 VLGAAGGIGQPLA-LLIKMSPLVSALHLYDVMNVKGVAADLSHCNTPSQVLDFTGP---- 152
V G G +GQ + LL++ + + + D + + V D G
Sbjct: 4 VTGGGGFLGQHIIRLLLERKEELKEIRVLDKAFGPELIEHFEKSQGKTYVTDIEGDIKDL 63
Query: 153 EELASALKGVNVVVIPAGVPRKPGMT-RDDLFNINANIVKTLVEAVADNCPDAFIHIISN 211
L A +GV+VV+ A + G ++L +N N + ++EA N ++ S
Sbjct: 64 SFLFRACQGVSVVIHTAAIVDVFGPPNYEELEEVNVNGTQAVLEACVQNNVKRLVYTSSI 123
Query: 212 PV 213
V
Sbjct: 124 EV 125
>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 = 31.1 bits (71), Expect = 0.75
Identities = 25/121 (20%), Positives = 38/121 (31%), Gaps = 17/121 (14%)
Query: 96 VAVLGAAGGIGQPLALLIKMSPLVSAL--HLYDVMNV-KGVAADLSHCNTPSQV-LDFTG 151
+ V G G IG S LV L Y+V+ + + ++ + D T
Sbjct: 1 ILVTGGTGFIG---------SHLVRRLLQEGYEVIVLGRRRRSESLNTGRIRFHEGDLTD 51
Query: 152 PEELASALKGV--NVVVIPAG-VPRKPGMTRD-DLFNINANIVKTLVEAVADNCPDAFIH 207
P+ L L V + V+ A D N L+EA F+
Sbjct: 52 PDALERLLAEVQPDAVIHLAAQSGVGASFEDPADFIRANVLGTLRLLEAARRAGVKRFVF 111
Query: 208 I 208
Sbjct: 112 A 112
>gnl|CDD|187540 cd05229, SDR_a3, atypical (a) SDRs, subgroup 3. These atypical SDR
family members of unknown function have a glycine-rich
NAD(P)-binding motif consensus that is very similar to
the extended SDRs, GXXGXXG. Generally, this group has
poor conservation of the active site tetrad, However,
individual sequences do contain matches to the YXXXK
active site motif, and generally Tyr or Asn in place of
the upstream Ser found in most SDRs. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Atypical SDRs include
biliverdin IX beta reductase (BVR-B,aka flavin
reductase), NMRa (a negative transcriptional regulator
of various fungi), progesterone 5-beta-reductase like
proteins, phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. In addition to the
Rossmann fold core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 302
Score = 31.1 bits (71), Expect = 1.0
Identities = 20/84 (23%), Positives = 32/84 (38%), Gaps = 18/84 (21%)
Query: 95 KVAVLGAAGGIGQPLA-LLIKMSPLVSALH-----LYDVMNVKGVAADLSHCNTPSQVLD 148
VLGA+G IG+ +A L + V + L + V+ VAAD
Sbjct: 1 TAHVLGASGPIGREVARELRRRGWDVRLVSRSGSKLAWLPGVEIVAADA----------- 49
Query: 149 FTGPEELASALKGVNVVVIPAGVP 172
+ +A +G +V+ A
Sbjct: 50 -MDASSVIAAARGADVIYHCANPA 72
>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 = 30.8 bits (70), Expect = 1.1
Identities = 18/75 (24%), Positives = 29/75 (38%), Gaps = 7/75 (9%)
Query: 95 KVAVLGAAGGIGQPLALLIKMSPLVSALHLYDVMNVKGVA--ADLSHCNTPSQVLDFTGP 152
KV + GA+G +GQ LA L+S + ++ + V+ A D P
Sbjct: 2 KVLITGASGFVGQRLA-----ERLLSDVPNERLILIDVVSPKAPSGAPRVTQIAGDLAVP 56
Query: 153 EELASALKGVNVVVI 167
+ + G VV
Sbjct: 57 ALIEALANGRPDVVF 71
>gnl|CDD|216304 pfam01113, DapB_N, Dihydrodipicolinate reductase, N-terminus.
Dihydrodipicolinate reductase (DapB) reduces the
alpha,beta-unsaturated cyclic imine,
dihydro-dipicolinate. This reaction is the second
committed step in the biosynthesis of L-lysine and its
precursor meso-diaminopimelate, which are critical for
both protein and cell wall biosynthesis. The N-terminal
domain of DapB binds the dinucleotide NADPH.
Length = 122
Score = 29.1 bits (66), Expect = 1.5
Identities = 24/93 (25%), Positives = 38/93 (40%), Gaps = 21/93 (22%)
Query: 95 KVAVLGAAGGIGQPLALLIKMSP---LVSALH----------LYDVMNVKGVAADLSHCN 141
KVAV+GA+G +G+ L I +P LV+A+ ++ GV
Sbjct: 2 KVAVVGASGRMGRELIKAILEAPDFELVAAVDRPGSSLLGSDAGELAGPLGVPVTDDLEE 61
Query: 142 TPSQ---VLDFTGPE---ELASAL--KGVNVVV 166
+ ++DFT PE E G +V+
Sbjct: 62 VLADADVLIDFTTPEATLENLELALKHGKPLVI 94
>gnl|CDD|182885 PRK10991, fucI, L-fucose isomerase; Provisional.
Length = 588
Score = 30.7 bits (70), Expect = 1.6
Identities = 11/29 (37%), Positives = 16/29 (55%), Gaps = 2/29 (6%)
Query: 317 TLSMAYAAARFVESSLRALDGDGDVYECV 345
T++MA A A + +LR G+ ECV
Sbjct: 28 TMNMAKATAALITENLR--HACGEPVECV 54
>gnl|CDD|236016 PRK07424, PRK07424, bifunctional sterol desaturase/short chain
dehydrogenase; Validated.
Length = 406
Score = 30.4 bits (69), Expect = 1.9
Identities = 24/80 (30%), Positives = 40/80 (50%), Gaps = 7/80 (8%)
Query: 95 KVAVLGAAGGIGQPL-ALLIKMSPLVSALHLYDVMNVKGVAADLSHCNTPSQVLDF-TGP 152
VAV GA+G +GQ L L + V AL N + +++ + P + L + G
Sbjct: 180 TVAVTGASGTLGQALLKELHQQGAKVVAL----TSNSDKITLEINGEDLPVKTLHWQVGQ 235
Query: 153 E-ELASALKGVNVVVIPAGV 171
E LA L+ V++++I G+
Sbjct: 236 EAALAELLEKVDILIINHGI 255
>gnl|CDD|224180 COG1260, INO1, Myo-inositol-1-phosphate synthase [Lipid
metabolism].
Length = 362
Score = 30.4 bits (69), Expect = 2.0
Identities = 24/97 (24%), Positives = 39/97 (40%), Gaps = 2/97 (2%)
Query: 231 DPKKLFGVTTLDVVRANTFVAQKKNLKLIDVDVPVVGGHAGITILPLLSKTMPSVS-FTD 289
D +K G + ++A V K + V V G L++ + + ++
Sbjct: 60 DARK-VGKDLSEAIKAPPNVTSKIAPDVPKTGVKVRRGPTLDGEGLHLAEYIERIQEESE 118
Query: 290 EEVGDLTVRIQNAGTEVVEAKAGAGSATLSMAYAAAR 326
E D+ V + A TEV+ GS + S YAAA
Sbjct: 119 AEAVDVVVVLNVAKTEVLVNYLPVGSESASYFYAAAA 155
>gnl|CDD|239618 cd03556, L-fucose_isomerase, L-fucose isomerase (FucIase); FucIase
converts L-fucose, an aldohexose, to its ketose form,
which prepares it for aldol cleavage (similar to the
isomerization of glucose during glycolysis). L-fucose
(or 6-deoxy-L-galactose) is found in blood group
determinants as well as in various oligo- and
polysaccharides, and glycosides in mammals, bacteria and
plants.
Length = 584
Score = 30.2 bits (68), Expect = 2.2
Identities = 18/58 (31%), Positives = 31/58 (53%), Gaps = 3/58 (5%)
Query: 317 TLSMAYAAARFVESSLRALDGDGDVYECVFVESNLTELP-FFASRVKLGRNGVESLIS 373
T++MA AAA+ +E +L+ DG+ ECV ++ + + A K R V + I+
Sbjct: 24 TMNMAKAAAKLIEENLK--YADGEPVECVIADTTIGRVAEAAACAEKFTRENVGATIT 79
>gnl|CDD|223366 COG0289, DapB, Dihydrodipicolinate reductase [Amino acid transport
and metabolism].
Length = 266
Score = 29.5 bits (67), Expect = 2.5
Identities = 41/155 (26%), Positives = 57/155 (36%), Gaps = 46/155 (29%)
Query: 95 KVAVLGAAGGIGQPLALLIKMSPLV----------SALHLYDVMNVKG-------VAADL 137
KVAV GA+G +G+ L + +P + S D + G V DL
Sbjct: 4 KVAVAGASGRMGRTLIRAVLEAPDLELVAAFDRPGSLSLGSDAGELAGLGLLGVPVTDDL 63
Query: 138 SHCNTPSQVL-DFTGPE----ELASALK-GVNVVVIPAGVPRKPGMTRDDL--------- 182
+ VL DFT PE L AL+ G +V+ G G T + L
Sbjct: 64 LLVKADADVLIDFTTPEATLENLEFALEHGKPLVI---GT---TGFTEEQLEKLREAAEK 117
Query: 183 --------FNINANIVKTLVEAVADNCPDAFIHII 209
F++ N++ L E A D I II
Sbjct: 118 VPVVIAPNFSLGVNLLFKLAEQAAKVLDDYDIEII 152
>gnl|CDD|236372 PRK09072, PRK09072, short chain dehydrogenase; Provisional.
Length = 263
Score = 29.5 bits (67), Expect = 3.1
Identities = 26/90 (28%), Positives = 37/90 (41%), Gaps = 19/90 (21%)
Query: 95 KVAVLGAAGGIGQPLALLI------------KMSPLVS-ALHLYDVMNVKGVAADLSHCN 141
+V + GA+GGIGQ LA + L + A L + V ADL+
Sbjct: 7 RVLLTGASGGIGQALAEALAAAGARLLLVGRNAEKLEALAARLPYPGRHRWVVADLTSEA 66
Query: 142 TPSQVLDFTGPEELASALKGVNVVVIPAGV 171
VL A + G+NV++ AGV
Sbjct: 67 GREAVLAR------AREMGGINVLINNAGV 90
>gnl|CDD|217030 pfam02432, Fimbrial_K88, Fimbrial, major and minor subunit.
Fimbriae (also know as pili) are polar filaments found
on the bacterial surface, allowing colonisation of the
host. This family consists of the minor and major
fimbrial subunits.
Length = 238
Score = 28.9 bits (65), Expect = 3.8
Identities = 17/79 (21%), Positives = 31/79 (39%), Gaps = 6/79 (7%)
Query: 283 PSVSFTDEEVGDLTVRIQNAGTEVV------EAKAGAGSATLSMAYAAARFVESSLRALD 336
P +SF E +T+ + GT V E+ G+ + ++ A S
Sbjct: 71 PQISFKSYEGFSVTLSTTSPGTARVTLPVKGESGTVIGTLSFNLQAAGVLSTGSDGDIGG 130
Query: 337 GDGDVYECVFVESNLTELP 355
G G ++E + ++ LP
Sbjct: 131 GAGSIFEGGVLPLGMSGLP 149
>gnl|CDD|217556 pfam03435, Saccharop_dh, Saccharopine dehydrogenase. This family
comprised of three structural domains that can not be
separated in the linear sequence. In some organisms this
enzyme is found as a bifunctional polypeptide with
lysine ketoglutarate reductase. The saccharopine
dehydrogenase can also function as a saccharopine
reductase.
Length = 380
Score = 29.2 bits (66), Expect = 4.0
Identities = 18/78 (23%), Positives = 34/78 (43%), Gaps = 14/78 (17%)
Query: 96 VAVLGAAGGIGQPLALLIKMSPLVSALHLYDVM-------NVKGVAADLSHCNTPSQVLD 148
V ++GA GG+GQ +A PL++ ++ + +AA + +D
Sbjct: 1 VLIIGA-GGVGQGVA------PLLARHGDLEITVADRSLEKAQALAAPKLGLRFIAIAVD 53
Query: 149 FTGPEELASALKGVNVVV 166
E L + LK ++V+
Sbjct: 54 ADNYEALVALLKEGDLVI 71
>gnl|CDD|184944 PRK14982, PRK14982, acyl-ACP reductase; Provisional.
Length = 340
Score = 29.2 bits (66), Expect = 4.1
Identities = 28/123 (22%), Positives = 44/123 (35%), Gaps = 37/123 (30%)
Query: 84 PQYALQPQASFKVAVLGAAGGIG-----------------------QPLALLI------K 114
P+ + + VAV+GA G IG + L L K
Sbjct: 147 PRLGIDLSKA-TVAVVGATGDIGSAVCRWLDAKTGVAELLLVARQQERLQELQAELGGGK 205
Query: 115 MSPLVSALHLYDV------MNVKGVAADLSHCNTPSQVLDFTGPEELASALKGVNVVVIP 168
+ L AL D+ M KGV D P ++D P+ L + ++G + V+
Sbjct: 206 ILSLEEALPEADIVVWVASMP-KGVEIDPETLKKPCLMIDGGYPKNLDTKVQGPGIHVLK 264
Query: 169 AGV 171
G+
Sbjct: 265 GGI 267
>gnl|CDD|238915 cd01940, Fructoselysine_kinase_like, Fructoselysine kinase-like.
Fructoselysine is a fructoseamine formed by glycation, a
non-enzymatic reaction of glucose with a primary amine
followed by an Amadori rearrangement, resulting in a
protein that is modified at the amino terminus and at
the lysine side chains. Fructoseamines are typically
metabolized by fructoseamine-3-kinase, especially in
higher eukaryotes. In E. coli, fructoselysine kinase has
been shown in vitro to catalyze the phosphorylation of
fructoselysine. It is proposed that fructoselysine is
released from glycated proteins during human digestion
and is partly metabolized by bacteria in the hind gut
using a protein such as fructoselysine kinase. This
family is found only in bacterial sequences, and its
oligomeric state is currently unknown.
Length = 264
Score = 28.9 bits (65), Expect = 4.6
Identities = 16/61 (26%), Positives = 25/61 (40%), Gaps = 8/61 (13%)
Query: 287 FTDEEVGDLTVRIQNAGTEVVEAKAGAGSATLSMAYAAARFVESSLRALD-----GDGDV 341
+DEEV + G ++V G A +AY A F + R ++ G GD
Sbjct: 171 LSDEEVKAKLKEAVSRGAKLVIVTRGEDGA---IAYDGAVFYSVAPRPVEVVDTLGAGDS 227
Query: 342 Y 342
+
Sbjct: 228 F 228
>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 = 28.9 bits (65), Expect = 4.9
Identities = 20/72 (27%), Positives = 30/72 (41%), Gaps = 5/72 (6%)
Query: 96 VAVLGAAGGIGQPLA-LLIKMSPLVSALHLYDVMNVKGVAADLSHCNTPSQVLDFTGPEE 154
V V GA G +G L L++ V AL V + + +A D PE
Sbjct: 1 VLVTGATGYVGGRLVPRLLQEGHQVRAL----VRSPEKLADRPWSERVTVVRGDLEDPES 56
Query: 155 LASALKGVNVVV 166
L +AL+G++
Sbjct: 57 LRAALEGIDTAY 68
>gnl|CDD|129147 TIGR00036, dapB, dihydrodipicolinate reductase. [Amino acid
biosynthesis, Aspartate family].
Length = 266
Score = 28.5 bits (64), Expect = 5.5
Identities = 32/95 (33%), Positives = 41/95 (43%), Gaps = 23/95 (24%)
Query: 95 KVAVLGAAGGIGQPLALLIKMSP---LVSALHLY-------DVMNVKGVA-------ADL 137
KVAV GAAG +G+ L + LV+A + D + G+ DL
Sbjct: 3 KVAVAGAAGRMGRELIKAALAAEGLQLVAAFERHGSSLQGTDAGELAGIGKVGVPVTDDL 62
Query: 138 SHCNTPSQVL-DFTGPE----ELASALK-GVNVVV 166
T VL DFT PE L AL+ GV +VV
Sbjct: 63 EAVETDPDVLIDFTTPEGVLNHLKFALEHGVRLVV 97
>gnl|CDD|187555 cd05244, BVR-B_like_SDR_a, biliverdin IX beta reductase (BVR-B, aka
flavin reductase)-like proteins; atypical (a) SDRs.
Human BVR-B catalyzes pyridine nucleotide-dependent
production of bilirubin-IX beta during fetal
development; in the adult BVR-B has flavin and ferric
reductase activities. Human BVR-B catalyzes the
reduction of FMN, FAD, and riboflavin. Recognition of
flavin occurs mostly by hydrophobic interactions,
accounting for the broad substrate specificity. Atypical
SDRs are distinct from classical SDRs. BVR-B does not
share the key catalytic triad, or conserved tyrosine
typical of SDRs. The glycine-rich NADP-binding motif of
BVR-B is GXXGXXG, which is similar but not identical to
the pattern seen in extended SDRs. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Atypical SDRs include
biliverdin IX beta reductase (BVR-B,aka flavin
reductase), NMRa (a negative transcriptional regulator
of various fungi), progesterone 5-beta-reductase like
proteins, phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. In addition to the
Rossmann fold core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 207
Score = 28.4 bits (64), Expect = 5.6
Identities = 21/96 (21%), Positives = 35/96 (36%), Gaps = 27/96 (28%)
Query: 95 KVAVLGAAGGIGQPL---AL--------LIKMSPLVSALHLYDVMNVKGVAADLSHCNTP 143
K+A++GA G G + AL L++ + A H +K V D+
Sbjct: 1 KIAIIGATGRTGSAIVREALARGHEVTALVRDPAKLPAEH----EKLKVVQGDVLD---- 52
Query: 144 SQVLDFTGPEELASALKGVNVVVIPAGVPRKPGMTR 179
E++ AL+G + V+ G T
Sbjct: 53 --------LEDVKEALEGQDAVISALGTRNDLSPTT 80
>gnl|CDD|236210 PRK08267, PRK08267, short chain dehydrogenase; Provisional.
Length = 260
Score = 28.4 bits (64), Expect = 5.9
Identities = 24/91 (26%), Positives = 35/91 (38%), Gaps = 26/91 (28%)
Query: 100 GAAGGIGQPLALLIKMSPLVSALH-------LYDV--MNVKGVAADLSHCNTPSQVLDFT 150
GAA GIG+ ALL YD+ + +AA+L N + LD T
Sbjct: 8 GAASGIGRATALL---------FAAEGWRVGAYDINEAGLAALAAELGAGNAWTGALDVT 58
Query: 151 GPEELASALK--------GVNVVVIPAGVPR 173
+AL ++V+ AG+ R
Sbjct: 59 DRAAWDAALADFAAATGGRLDVLFNNAGILR 89
>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 = 28.4 bits (64), Expect = 6.3
Identities = 32/134 (23%), Positives = 53/134 (39%), Gaps = 17/134 (12%)
Query: 96 VAVLGAAGGIGQPLALLI-KMSPLVSALHLYDVMNVK--GVAADLSHCNTPSQVLDFTGP 152
+ V G AG IG L I K P L ++D K + +L ++ G
Sbjct: 5 ILVTGGAGSIGSELVRQILKFGP--KKLIVFDRDENKLHELVRELRSRFPHDKLRFIIGD 62
Query: 153 ------EELASALKGVNVVVIPAGVPRKPGMTRDDLFNINANIVKT--LVEAVADNCPDA 204
A +G ++V A + P M + I N++ T +++A +N +
Sbjct: 63 VRDKERLRRAFKERGPDIVFHAAALKHVPSMEDNPEEAIKTNVLGTKNVIDAAIENGVEK 122
Query: 205 FIHIIS----NPVN 214
F+ I + NPVN
Sbjct: 123 FVCISTDKAVNPVN 136
>gnl|CDD|233220 TIGR00978, asd_EA, aspartate-semialdehyde dehydrogenase
(non-peptidoglycan organisms). Two closely related
families of aspartate-semialdehyde dehydrogenase are
found. They differ by a deep split in phylogenetic and
percent identity trees and in gap patterns. Separate
models are built for the two types in order to exclude
the USG-1 protein, found in several species, which is
specifically related to the Bacillus subtilis type of
aspartate-semialdehyde dehydrogenase. Members of this
type are found primarily in organisms that lack
peptidoglycan [Amino acid biosynthesis, Aspartate
family].
Length = 341
Score = 28.2 bits (63), Expect = 7.6
Identities = 29/131 (22%), Positives = 52/131 (39%), Gaps = 23/131 (17%)
Query: 95 KVAVLGAAGGIGQPLALLIKMSPLVSALHLYDVMNVKGVAADLSHCNTPSQVLDFTGPEE 154
+VAVLGA G +GQ L+ P +++ V VA+ S + + + P +
Sbjct: 2 RVAVLGATGLVGQKFVKLLAKHP------YFELAKV--VASPRSAGKRYGEAVKWIEPGD 53
Query: 155 LASALKGVNVVVIPAGVPRKPGMTRDD--LFNINANIVKTLVEAVADNCPDAFIHIISNP 212
+ ++ + +V +P D +F+ + V VE +A + SN
Sbjct: 54 MPEYVRDLPIVEP------EPIAEDDVDIVFSALPSEVAEEVEP---KLAEAGKPVFSNA 104
Query: 213 VN----STVPI 219
N VP+
Sbjct: 105 SNHRMDPDVPL 115
>gnl|CDD|227543 COG5218, YCG1, Chromosome condensation complex Condensin, subunit G
[Chromatin structure and dynamics / Cell division and
chromosome partitioning].
Length = 885
Score = 28.4 bits (63), Expect = 7.9
Identities = 16/87 (18%), Positives = 33/87 (37%), Gaps = 18/87 (20%)
Query: 118 LVSALHLYDVMNVKGVAADLSHCNTPSQVLDFTGPEELASALKGVNVVVIPAGVPRKPGM 177
L+ + + + V A LSH Q L +T +LA+ + G
Sbjct: 697 LLILCSVLEDL--PEVDAMLSHKVIIQQSLYWTDNSKLAN----------------QTGS 738
Query: 178 TRDDLFNINANIVKTLVEAVADNCPDA 204
T DL +N ++ + ++ ++ +
Sbjct: 739 TGSDLLFLNQIMICVRLNSIFESLDNV 765
>gnl|CDD|180723 PRK06841, PRK06841, short chain dehydrogenase; Provisional.
Length = 255
Score = 28.1 bits (63), Expect = 8.6
Identities = 27/86 (31%), Positives = 40/86 (46%), Gaps = 11/86 (12%)
Query: 95 KVAVL-GAAGGIGQPLA-LLIKMSPLVSALHLYDVMNVKGVAADLSHCNTPSQVLDFTGP 152
KVAV+ G A GIG +A L V+ L + +V VAA L N V D +
Sbjct: 16 KVAVVTGGASGIGHAIAELFAAKGARVALLDRSE--DVAEVAAQLLGGNAKGLVCDVSDS 73
Query: 153 EELASALKGV-------NVVVIPAGV 171
+ + +A+ V +++V AGV
Sbjct: 74 QSVEAAVAAVISAFGRIDILVNSAGV 99
>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 = 28.0 bits (63), Expect = 9.1
Identities = 15/54 (27%), Positives = 20/54 (37%), Gaps = 6/54 (11%)
Query: 154 ELASALKGVNVVVIPAGVPRKPGMTRDDLFNINANIVKTLVEAVADNCPDAFIH 207
L LK VI G R LF ++ + EA+ D PD I+
Sbjct: 14 ALVRLLKERGYEVIGTGRSRAS------LFKLDLTDPDAVEEAIRDYKPDVIIN 61
>gnl|CDD|223096 COG0017, AsnS, Aspartyl/asparaginyl-tRNA synthetases [Translation,
ribosomal structure and biogenesis].
Length = 435
Score = 27.9 bits (63), Expect = 9.9
Identities = 13/69 (18%), Positives = 29/69 (42%), Gaps = 11/69 (15%)
Query: 176 GMTRDDLFNINANIVKTLVEAVADNCPDAFIHI------ISNPVNSTVPI-----AAEVL 224
+D+ ++ ++K L + V + C D + + P ++ P A E+L
Sbjct: 232 FADLNDVMDLAEELIKYLFKKVLEECADELEFLGRDNSELKRPESAPFPRITYKEAIEIL 291
Query: 225 KQKGVYDPK 233
++KG +
Sbjct: 292 EEKGFEKVE 300
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
0.315 0.130 0.357
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: 20,267,712
Number of extensions: 1977449
Number of successful extensions: 2476
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2395
Number of HSP's successfully gapped: 102
Length of query: 412
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 313
Effective length of database: 6,546,556
Effective search space: 2049072028
Effective search space used: 2049072028
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 60 (26.7 bits)