RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 018512
(354 letters)
>gnl|CDD|215058 PLN00106, PLN00106, malate dehydrogenase.
Length = 323
Score = 656 bits (1694), Expect = 0.0
Identities = 249/314 (79%), Positives = 271/314 (86%)
Query: 34 CRAKGGAAGFKVAILGAAGGIGQPLAMLMKINPLVSVLHLYDVVNTPGVTADISHMDTGA 93
CRAKGGA GFKVA+LGAAGGIGQPL++LMK+NPLVS LHLYD+ NTPGV AD+SH++T A
Sbjct: 10 CRAKGGAPGFKVAVLGAAGGIGQPLSLLMKMNPLVSELHLYDIANTPGVAADVSHINTPA 69
Query: 94 VVRGFLGQPQLENALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAKCCPNA 153
VRGFLG QL +AL G DLVIIPAGVPRKPGMTRDDLFNINAGIV+TLCE +AK CPNA
Sbjct: 70 QVRGFLGDDQLGDALKGADLVIIPAGVPRKPGMTRDDLFNINAGIVKTLCEAVAKHCPNA 129
Query: 154 TVNLISNPVNSTVPIAAEVFKKAGTYDPKKLLGVTMLDVVRANTFVAEVLGLDPRDVDVP 213
VN+ISNPVNSTVPIAAEV KKAG YDPKKL GVT LDVVRANTFVAE GLDP DVDVP
Sbjct: 130 LVNIISNPVNSTVPIAAEVLKKAGVYDPKKLFGVTTLDVVRANTFVAEKKGLDPADVDVP 189
Query: 214 VVGGHAGVTILPLLSQVKPPCSFTQEETEYLTNRIQNGGTEVVEAKAGAGSATLSMAYAA 273
VVGGHAG+TILPLLSQ P SFT EE E LT RIQNGGTEVVEAKAGAGSATLSMAYAA
Sbjct: 190 VVGGHAGITILPLLSQATPKVSFTDEEIEALTKRIQNGGTEVVEAKAGAGSATLSMAYAA 249
Query: 274 VKFADACLRGLRGDAGVVECAFVASQVTELPFFASKVRLGRQGAEEIFQLGPLNEYERIG 333
+FADACLRGL G+A VVEC++V S+VTELPFFASKVRLGR G EE+ LGPL+EYE+ G
Sbjct: 250 ARFADACLRGLNGEADVVECSYVQSEVTELPFFASKVRLGRNGVEEVLGLGPLSEYEQKG 309
Query: 334 LEKAKKELAGSIQK 347
LE K EL SI+K
Sbjct: 310 LEALKPELKASIEK 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 = 570 bits (1471), Expect = 0.0
Identities = 212/309 (68%), Positives = 253/309 (81%)
Query: 43 FKVAILGAAGGIGQPLAMLMKINPLVSVLHLYDVVNTPGVTADISHMDTGAVVRGFLGQP 102
KVA+LGAAGGIGQPL++L+K+NPLVS L LYD+VNTPGV AD+SH++T A V G+LG
Sbjct: 1 VKVAVLGAAGGIGQPLSLLLKLNPLVSELALYDIVNTPGVAADLSHINTPAKVTGYLGPE 60
Query: 103 QLENALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAKCCPNATVNLISNPV 162
+L+ AL G D+V+IPAGVPRKPGMTRDDLFNINAGIVR L +AK CP A + +ISNPV
Sbjct: 61 ELKKALKGADVVVIPAGVPRKPGMTRDDLFNINAGIVRDLATAVAKACPKALILIISNPV 120
Query: 163 NSTVPIAAEVFKKAGTYDPKKLLGVTMLDVVRANTFVAEVLGLDPRDVDVPVVGGHAGVT 222
NSTVPIAAEV KKAG YDPK+L GVT LDVVRANTFVAE+LGLDP V+VPV+GGH+GVT
Sbjct: 121 NSTVPIAAEVLKKAGVYDPKRLFGVTTLDVVRANTFVAELLGLDPAKVNVPVIGGHSGVT 180
Query: 223 ILPLLSQVKPPCSFTQEETEYLTNRIQNGGTEVVEAKAGAGSATLSMAYAAVKFADACLR 282
ILPLLSQ +PP +F QEE E LT+RIQ GG EVV+AKAGAGSATLSMAYA +FA++ LR
Sbjct: 181 ILPLLSQCQPPFTFDQEEIEALTHRIQFGGDEVVKAKAGAGSATLSMAYAGARFANSLLR 240
Query: 283 GLRGDAGVVECAFVASQVTELPFFASKVRLGRQGAEEIFQLGPLNEYERIGLEKAKKELA 342
GL+G+ GV+ECA+V S VTE PFFA+ V LG+ G E+ LG LN+YE+ LE A EL
Sbjct: 241 GLKGEKGVIECAYVESDVTEAPFFATPVELGKNGVEKNLGLGKLNDYEKKLLEAALPELK 300
Query: 343 GSIQKGISF 351
+I+KG+ F
Sbjct: 301 KNIEKGVDF 309
>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 = 428 bits (1103), Expect = e-151
Identities = 185/312 (59%), Positives = 233/312 (74%), Gaps = 1/312 (0%)
Query: 44 KVAILGAAGGIGQPLAMLMKINPLVSVLHLYDVVNTPGVTADISHMDTGAVVRGFLGQPQ 103
KVA+LGAAGGIGQPL++L+K+ P VS L LYD+ GV AD+SH+ T A V+GF G+
Sbjct: 1 KVAVLGAAGGIGQPLSLLLKLQPYVSELSLYDIAGAAGVAADLSHIPTAASVKGFSGEEG 60
Query: 104 LENALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAKCCPNATVNLISNPVN 163
LENAL G D+V+IPAGVPRKPGMTRDDLFN+NAGIV+ L +A+ CP A + +I+NPVN
Sbjct: 61 LENALKGADVVVIPAGVPRKPGMTRDDLFNVNAGIVKDLVAAVAESCPKAMILVITNPVN 120
Query: 164 STVPIAAEVFKKAGTYDPKKLLGVTMLDVVRANTFVAEVLGLDPRDVDVPVVGGHAGVTI 223
STVPIAAEV KK G YDP KL GVT LD+VRANTFVAE+ G DP +V+VPV+GGH+G TI
Sbjct: 121 STVPIAAEVLKKKGVYDPNKLFGVTTLDIVRANTFVAELKGKDPMEVNVPVIGGHSGETI 180
Query: 224 LPLLSQVKPPCSFTQEETEYLTNRIQNGGTEVVEAKAGAGSATLSMAYAAVKFADACLRG 283
+PL+SQ FT+++ E L +RIQN GTEVV+AKAGAGSATLSMA+A +F + +RG
Sbjct: 181 IPLISQCPGKVLFTEDQLEALIHRIQNAGTEVVKAKAGAGSATLSMAFAGARFVLSLVRG 240
Query: 284 LRGDAGVVECAFVASQ-VTELPFFASKVRLGRQGAEEIFQLGPLNEYERIGLEKAKKELA 342
L+G+ GVVECA+V S VTE FFA+ + LG+ G E+ +G L+ +E L A EL
Sbjct: 241 LKGEEGVVECAYVESDGVTEATFFATPLLLGKNGVEKRLGIGKLSSFEEKMLNGALPELK 300
Query: 343 GSIQKGISFSKK 354
+I+KG F
Sbjct: 301 KNIKKGEEFVAS 312
>gnl|CDD|235340 PRK05086, PRK05086, malate dehydrogenase; Provisional.
Length = 312
Score = 412 bits (1061), Expect = e-145
Identities = 176/313 (56%), Positives = 214/313 (68%), Gaps = 4/313 (1%)
Query: 44 KVAILGAAGGIGQPLAMLMKIN-PLVSVLHLYDVVN-TPGVTADISHMDTGAVVRGFLGQ 101
KVA+LGAAGGIGQ LA+L+K P S L LYD+ TPGV D+SH+ T ++GF G+
Sbjct: 2 KVAVLGAAGGIGQALALLLKTQLPAGSELSLYDIAPVTPGVAVDLSHIPTAVKIKGFSGE 61
Query: 102 PQLENALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAKCCPNATVNLISNP 161
AL G D+V+I AGV RKPGM R DLFN+NAGIV+ L E +AK CP A + +I+NP
Sbjct: 62 -DPTPALEGADVVLISAGVARKPGMDRSDLFNVNAGIVKNLVEKVAKTCPKACIGIITNP 120
Query: 162 VNSTVPIAAEVFKKAGTYDPKKLLGVTMLDVVRANTFVAEVLGLDPRDVDVPVVGGHAGV 221
VN+TV IAAEV KKAG YD KL GVT LDV+R+ TFVAE+ G P +V+VPV+GGH+GV
Sbjct: 121 VNTTVAIAAEVLKKAGVYDKNKLFGVTTLDVIRSETFVAELKGKQPGEVEVPVIGGHSGV 180
Query: 222 TILPLLSQVKPPCSFTQEETEYLTNRIQNGGTEVVEAKAGAGSATLSMAYAAVKFADACL 281
TILPLLSQV P SFT++E LT RIQN GTEVVEAKAG GSATLSM AA +F + +
Sbjct: 181 TILPLLSQV-PGVSFTEQEVADLTKRIQNAGTEVVEAKAGGGSATLSMGQAAARFGLSLV 239
Query: 282 RGLRGDAGVVECAFVASQVTELPFFASKVRLGRQGAEEIFQLGPLNEYERIGLEKAKKEL 341
R L+G+ GVVECA+V FFA V LG+ G EE +G L+ +E+ LE L
Sbjct: 240 RALQGEQGVVECAYVEGDGKYARFFAQPVLLGKNGVEERLPIGTLSAFEQNALEGMLDTL 299
Query: 342 AGSIQKGISFSKK 354
I G F K
Sbjct: 300 KKDIALGEEFVNK 312
>gnl|CDD|240360 PTZ00325, PTZ00325, malate dehydrogenase; Provisional.
Length = 321
Score = 405 bits (1042), Expect = e-142
Identities = 192/313 (61%), Positives = 234/313 (74%), Gaps = 3/313 (0%)
Query: 43 FKVAILGAAGGIGQPLAMLMKINPLVSVLHLYDVVNTPGVTADISHMDTGAVVRGFLGQP 102
FKVA+LGAAGGIGQPL++L+K NP VS L LYD+V PGV AD+SH+DT A V G+
Sbjct: 9 FKVAVLGAAGGIGQPLSLLLKQNPHVSELSLYDIVGAPGVAADLSHIDTPAKVTGYADGE 68
Query: 103 QLENALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAKCCPNATVNLISNPV 162
E AL G DLV+I AGVPRKPGMTRDDLFN NA IVR L +A P A V ++SNPV
Sbjct: 69 LWEKALRGADLVLICAGVPRKPGMTRDDLFNTNAPIVRDLVAAVASSAPKAIVGIVSNPV 128
Query: 163 NSTVPIAAEVFKKAGTYDPKKLLGVTMLDVVRANTFVAEVLGLDPRDVDVPVVGGHAGVT 222
NSTVPIAAE KKAG YDP+KL GVT LDVVRA FVAE LG++P DV+VPVVGGH+GVT
Sbjct: 129 NSTVPIAAETLKKAGVYDPRKLFGVTTLDVVRARKFVAEALGMNPYDVNVPVVGGHSGVT 188
Query: 223 ILPLLSQVKPPCSFTQEETEYLTNRIQNGGTEVVEAKAGAGSATLSMAYAAVKFADACLR 282
I+PLLSQ S +E+ E +T+R+Q GG EVV+AK GAGSATLSMAYAA +++ + L+
Sbjct: 189 IVPLLSQT--GLSLPEEQVEQITHRVQVGGDEVVKAKEGAGSATLSMAYAAAEWSTSVLK 246
Query: 283 GLRGDAGVVECAFVASQVT-ELPFFASKVRLGRQGAEEIFQLGPLNEYERIGLEKAKKEL 341
LRGD G+VECAFV S + E PFF+S V LG++G E + +GPLN YE LE A +L
Sbjct: 247 ALRGDKGIVECAFVESDMRPECPFFSSPVELGKEGVERVLPIGPLNAYEEELLEAAVPDL 306
Query: 342 AGSIQKGISFSKK 354
+I+KG+ F++K
Sbjct: 307 KKNIEKGLEFARK 319
>gnl|CDD|223117 COG0039, Mdh, Malate/lactate dehydrogenases [Energy production and
conversion].
Length = 313
Score = 247 bits (632), Expect = 4e-80
Identities = 113/319 (35%), Positives = 166/319 (52%), Gaps = 21/319 (6%)
Query: 44 KVAILGAAGGIGQPLAMLMKINPLVSVLHLYDVVN--TPGVTADISHMDTGAVVRGFLGQ 101
KVA++GA G +G LA L+ + L S L L D+ GV D+SH +
Sbjct: 2 KVAVIGA-GNVGSSLAFLLLLQGLGSELVLIDINEEKAEGVALDLSHAAAPLGSDVKITG 60
Query: 102 PQLENALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAKCCPNATVNLISNP 161
L G D+V+I AGVPRKPGMTR DL NA IV+ + + IAK P+A V +++NP
Sbjct: 61 DGDYEDLKGADIVVITAGVPRKPGMTRLDLLEKNAKIVKDIAKAIAKYAPDAIVLVVTNP 120
Query: 162 VNSTVPIAAEVFKKAGTYDPKKLLGVTMLDVVRANTFVAEVLGLDPRDVDVPVVGGHAGV 221
V+ IA + +G + + T+LD R TF+AE LG+ P+DV V+G H G
Sbjct: 121 VDILTYIAMKF---SGFPKNRVIGSGTVLDSARFRTFLAEKLGVSPKDVHAYVIGEH-GD 176
Query: 222 TILPLLSQV----KPPCSF----TQEETEYLTNRIQNGGTEVVEAKAGAGSATLSMAYAA 273
T++PL SQ KP T+E+ E L R++N G E++EAK GAG A A
Sbjct: 177 TMVPLWSQATVGGKPLEELLKEDTEEDLEELIERVRNAGAEIIEAK-GAG-TYYGPAAAL 234
Query: 274 VKFADACLRGLRGDAGVVECAFVASQ-VTELPFFASKVRLGRQGAEEIFQLGPLNEYERI 332
+ +A LR + + ++ + E +F LG+ G EEI +L L++ E+
Sbjct: 235 ARMVEAILRDEK--RVLPVSVYLDGEYGVEDVYFGVPAVLGKNGVEEILEL-LLSDDEQE 291
Query: 333 GLEKAKKELAGSIQKGISF 351
L+K+ +EL +I+
Sbjct: 292 KLDKSAEELKKNIELVKEL 310
>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 = 185 bits (471), Expect = 5e-58
Identities = 79/176 (44%), Positives = 103/176 (58%), Gaps = 16/176 (9%)
Query: 188 TMLDVVRANTFVAEVLGLDPRDVDVPVVGGHAG----------VTILPLLSQVKPPCSFT 237
T LD RA TF+AE G+DPR V+V V+G H+G VTI+PL+SQVK T
Sbjct: 1 TTLDTARARTFLAEKFGVDPRSVNVYVIGEHSGTQFPDWSHAKVTIIPLISQVKENLKDT 60
Query: 238 QEETEYLTNRIQNGGTEVVEAKAGAGSATLSMAYAAVKFADACLRGLRGD--AGVVECAF 295
E E L R+QN G EV+EAK AGS T SMAYAA + A A LRG G GV +
Sbjct: 61 DWELEELIERVQNAGYEVIEAK--AGSTTYSMAYAAARIAKAILRGTGGVLSVGVYLDGY 118
Query: 296 VASQVTELPFFASKVRLGRQGAEEIFQLGPLNEYERIGLEKAKKELAGSIQKGISF 351
+ +F+ V LG+ G E++ ++ PLN++ER LEK+ EL I+KG +F
Sbjct: 119 Y--GSPDDIYFSVPVVLGKDGVEKVVEILPLNDFEREKLEKSAAELKKEIEKGFAF 172
>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 = 174 bits (444), Expect = 3e-54
Identities = 60/145 (41%), Positives = 80/145 (55%), Gaps = 6/145 (4%)
Query: 44 KVAILGAAGGIGQPLAMLMKINPLVSVLHLYDVV--NTPGVTADISHMDTGAVVRGFLGQ 101
KVA++GA GG+G LA + + L L L D+ GV D+SH T V G +G
Sbjct: 2 KVAVVGAGGGVGSSLAFALALQGLADELVLVDINKDKAEGVAMDLSHGSTFLSVPGIVGG 61
Query: 102 PQLENALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAKCCPNATVNLISNP 161
AL D+V+I AGVPRKPGMTR DL N NAGI + + IAK P+A V ++SNP
Sbjct: 62 DD-YEALKDADVVVITAGVPRKPGMTRLDLLNRNAGIFKDIVPAIAKSAPDAIVLVVSNP 120
Query: 162 VNSTVPIAAEVFKKAGTYDPKKLLG 186
V+ IA +V +G + +
Sbjct: 121 VDILTYIAWKV---SGLPPERVIGS 142
>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 = 161 bits (409), Expect = 5e-47
Identities = 102/323 (31%), Positives = 158/323 (48%), Gaps = 46/323 (14%)
Query: 45 VAILGAAGGIGQPLAMLMKINPLVSVLHLYDVV-NTP-GVTADISHM----DTGAVVRGF 98
++I+GA G +G LA L+ + L V+ L D+V P G DIS + V G
Sbjct: 1 ISIIGA-GNVGATLAQLLALKELGDVV-LLDIVEGLPQGKALDISQAAPILGSDTKVTGT 58
Query: 99 LGQPQLENALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAKCCPNATVNLI 158
+ + D+V+I AG+PRKPGM+RDDL NA IV+ + E I K PNA V ++
Sbjct: 59 NDYEDIAGS----DVVVITAGIPRKPGMSRDDLLGTNAKIVKEVAENIKKYAPNAIVIVV 114
Query: 159 SNPVNSTVPIAAEVFKKAGTYDPKKLLGV-TMLDVVRANTFVAEVLGLDPRDVDVPVVGG 217
+NP++ V KA + +++G+ +LD R F+AE LG+ +DV V+GG
Sbjct: 115 TNPLDVMT----YVAYKASGFPRNRVIGMAGVLDSARFRYFIAEELGVSVKDVQAMVLGG 170
Query: 218 HAGVTILPLLSQV----KPPCSF-TQEETEYLTNRIQNGGTEVVEAKAGAGSATLSMAYA 272
H G T++PL P T+EE + + R +NGG E+V GSA + A A
Sbjct: 171 H-GDTMVPLPRYSTVGGIPLTELITKEEIDEIVERTRNGGAEIVNLL-KTGSAYYAPAAA 228
Query: 273 AVKFADACLRG----------LRGDAGVVECAFVASQVTELPFFASKVRLGRQGAEEIFQ 322
+ +A L+ L G+ G+ + +P V LG+ G E+I +
Sbjct: 229 IAEMVEAILKDKKRVLPCSAYLEGEYGIKDIFV------GVP-----VVLGKNGVEKIIE 277
Query: 323 LGPLNEYERIGLEKAKKELAGSI 345
L L + E+ +K+ + + I
Sbjct: 278 L-DLTDEEKEAFDKSVESVKELI 299
>gnl|CDD|180477 PRK06223, PRK06223, malate dehydrogenase; Reviewed.
Length = 307
Score = 158 bits (402), Expect = 6e-46
Identities = 102/325 (31%), Positives = 169/325 (52%), Gaps = 44/325 (13%)
Query: 44 KVAILGAAGGIGQPLAMLMKINPLVSVLHLYDVV-NTP-GVTADISHMDTGAVVRGFLGQ 101
K++I+GA G +G LA L+ + L V+ L+D+V P G DI+ A V GF +
Sbjct: 4 KISIIGA-GNVGATLAHLLALKELGDVV-LFDIVEGVPQGKALDIAEA---APVEGFDTK 58
Query: 102 PQLEN---ALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAKCCPNATVNLI 158
N + G D+V+I AGVPRKPGM+RDDL INA I++ + EGI K P+A V ++
Sbjct: 59 ITGTNDYEDIAGSDVVVITAGVPRKPGMSRDDLLGINAKIMKDVAEGIKKYAPDAIVIVV 118
Query: 159 SNPVNSTVPIAAEVFKKAGTYDPKKLLGV-TMLDVVRANTFVAEVLGLDPRDVDVPVVGG 217
+NPV++ +A K + +++G+ +LD R TF+AE L + +DV V+GG
Sbjct: 119 TNPVDAMTYVA----LKESGFPKNRVIGMAGVLDSARFRTFIAEELNVSVKDVTAFVLGG 174
Query: 218 HAGVTILPLLSQ-----VKPPCSFTQEETEYLTNRIQNGGTEVVEAKAGAGSATLSMAYA 272
H G +++PL+ + ++E+ + + R + GG E+V GSA + A +
Sbjct: 175 H-GDSMVPLVRYSTVGGIPLEDLLSKEKLDEIVERTRKGGAEIVGLL-KTGSAYYAPAAS 232
Query: 273 AVKFADACLRG----------LRGDAGVVECAFVASQVTELPFFASKVRLGRQGAEEIFQ 322
+ +A L+ L G+ GV + +P V+LG+ G E+I +
Sbjct: 233 IAEMVEAILKDKKRVLPCSAYLEGEYGVKDVYV------GVP-----VKLGKNGVEKIIE 281
Query: 323 LGPLNEYERIGLEKAKKELAGSIQK 347
L L++ E+ +K+ + + I+
Sbjct: 282 L-ELDDEEKAAFDKSVEAVKKLIEA 305
>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 = 131 bits (332), Expect = 3e-36
Identities = 63/192 (32%), Positives = 93/192 (48%), Gaps = 9/192 (4%)
Query: 45 VAILGAAGGIGQPLA--MLMKINPLVSVLHLYDVVN--TPGVTADISHMDTGAVVRGFLG 100
+A++GA G +G LA + L L LYD+ GV D+
Sbjct: 1 IAVIGAGGNVGPALAFGLADGSVLLAIELVLYDIDEEKLKGVAMDLQDAVEPLADIKVSI 60
Query: 101 QPQLENALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAKCCPNATVNLISN 160
A D+VII AGV RKPGM R DL N IV+ + + I K P+A + ++SN
Sbjct: 61 TDDPYEAFKDADVVIITAGVGRKPGMGRLDLLKRNVPIVKEIGDNIEKYSPDAWIIVVSN 120
Query: 161 PVNSTVPIAAEVFKKAGTYDPKKLLGVTMLDVVRANTFVAEVLGLDPRDVDVPVVGGHAG 220
PV+ I + + +K++G+ LD +R +AE LG+DP DV V ++G H G
Sbjct: 121 PVD----IITYLVWRYSGLPKEKVIGLGTLDPIRFRRILAEKLGVDPDDVKVYILGEHGG 176
Query: 221 VTILPLLSQVKP 232
+ +P S V+
Sbjct: 177 -SQVPDWSTVRI 187
>gnl|CDD|173409 PTZ00117, PTZ00117, malate dehydrogenase; Provisional.
Length = 319
Score = 127 bits (320), Expect = 6e-34
Identities = 95/305 (31%), Positives = 149/305 (48%), Gaps = 31/305 (10%)
Query: 44 KVAILGAAGGIGQPLAMLMKINPLVSVLHLYDVV-NTP-GVTADISH-MDTGAVVRGFLG 100
K++++GA G IG +A+L+ L V+ LYDV+ P G D+ H LG
Sbjct: 7 KISMIGA-GQIGSTVALLILQKNLGDVV-LYDVIKGVPQGKALDLKHFSTLVGSNINILG 64
Query: 101 QPQLENALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAKCCPNATVNLISN 160
E + D+V+I AGV RK MTR+DL IN I++++ E + K CPNA V ++N
Sbjct: 65 TNNYE-DIKDSDVVVITAGVQRKEEMTREDLLTINGKIMKSVAESVKKYCPNAFVICVTN 123
Query: 161 PVNSTVPIAAEVFKKAGTYDPKKLLGVT-MLDVVRANTFVAEVLGLDPRDVDVPVVGGHA 219
P++ +VF++ K+ G+ +LD R +AE LG+ P DV V+GGH
Sbjct: 124 PLD----CMVKVFQEKSGIPSNKICGMAGVLDSSRFRCNLAEKLGVSPGDVSAVVIGGH- 178
Query: 220 GVTILPLLSQVK----PPCSF------TQEETEYLTNRIQNGGTEVVEAKAGAGSATLSM 269
G ++PL P F T++E + + +N G E+V+ GSA +
Sbjct: 179 GDLMVPLPRYCTVNGIPLSDFVKKGAITEKEINEIIKKTRNMGGEIVKL-LKKGSAFFAP 237
Query: 270 AYAAVKFADACLRGLRGDAGVVECAFVAS---QVTELPFFASKVRLGRQGAEEIFQLGPL 326
A A V +A L+ + V+ C+ + L F V +G +G E++ +L L
Sbjct: 238 AAAIVAMIEAYLKDEK---RVLVCSVYLNGQYNCKNL-FVGVPVVIGGKGIEKVIEL-EL 292
Query: 327 NEYER 331
N E+
Sbjct: 293 NAEEK 297
>gnl|CDD|173376 PTZ00082, PTZ00082, L-lactate dehydrogenase; Provisional.
Length = 321
Score = 121 bits (306), Expect = 7e-32
Identities = 105/319 (32%), Positives = 172/319 (53%), Gaps = 36/319 (11%)
Query: 44 KVAILGAAGGIGQPLAMLMKINPLVSVLHLYDVV-NTP-GVTADISHMDTGAVVR-GFLG 100
K++++G+ G IG +A L+ + L V+ L+D+V N P G DISH + A +G
Sbjct: 8 KISLIGS-GNIGGVMAYLIVLKNLGDVV-LFDIVKNIPQGKALDISHSNVIAGSNSKVIG 65
Query: 101 QPQLENALTGMDLVIIPAGVPRKPGMT-----RDDLFNINAGIVRTLCEGIAKCCPNATV 155
E+ + G D+VI+ AG+ ++PG + RDDL +NA I+ + EGI K CPNA V
Sbjct: 66 TNNYED-IAGSDVVIVTAGLTKRPGKSDKEWNRDDLLPLNAKIMDEVAEGIKKYCPNAFV 124
Query: 156 NLISNPVNSTVPIAAEVFKKAGTYDPKKLLGVT-MLDVVRANTFVAEVLGLDPRDVDVPV 214
+I+NP++ V ++ ++ K+ G+ +LD R T++AE LG++PRDV V
Sbjct: 125 IVITNPLDVMV----KLLQEHSGLPKNKVCGMAGVLDSSRLRTYIAEKLGVNPRDVHASV 180
Query: 215 VGGHAGVTILPLLSQVK----PPCSF------TQEETEYLTNRIQNGGTEVVEAKAGAGS 264
+G H G ++PL V P F TQEE + + R +N G E+V+ G GS
Sbjct: 181 IGAH-GDKMVPLPRYVTVGGIPLSEFIKKGLITQEEIDEIVERTRNTGKEIVDL-LGTGS 238
Query: 265 ATLSMAYAAVKFADACLRGLRGDAGVVEC-AFVASQ--VTELPFFASKVRLGRQGAEEIF 321
A + A AA++ A+A L+ + V+ C A++ Q ++ + + +G G E+I
Sbjct: 239 AYFAPAAAAIEMAEAYLKDKK---RVLPCSAYLEGQYGHKDI-YMGTPAVIGANGVEKII 294
Query: 322 QLGPLNEYERIGLEKAKKE 340
+L L E+ +++ KE
Sbjct: 295 EL-DLTPEEQKKFDESIKE 312
>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 = 120 bits (303), Expect = 1e-31
Identities = 89/318 (27%), Positives = 140/318 (44%), Gaps = 44/318 (13%)
Query: 45 VAILGAAGGIGQPLAMLMKINPLVSVLHLYDVVN--TPGVTADISHM----DTGAVVRGF 98
+ I+GA G +G +A + L S L L DV G D+SH TG +VRG
Sbjct: 1 ITIIGA-GNVGAAVAFALIAKGLASELVLVDVNEEKAKGDALDLSHASAFLATGTIVRG- 58
Query: 99 LGQPQLENALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAKCCPNATVNLI 158
D+V+I AG PRKPG TR DL N NA I+R++ + K P+A + ++
Sbjct: 59 ----GDYADAADADIVVITAGAPRKPGETRLDLINRNAPILRSVITNLKKYGPDAIILVV 114
Query: 159 SNPVNSTVPIAAEVFKKAGTYDPKKLLGV-TMLDVVRANTFVAEVLGLDPRDVDVPVVGG 217
SNPV+ I V +K +++G T+LD R + +AE L +DP+ V V+G
Sbjct: 115 SNPVD----ILTYVAQKLSGLPKNRVIGSGTLLDSARFRSLLAEKLDVDPQSVHAYVLGE 170
Query: 218 HAGVTILPLLSQVK-------PPCSFTQEETEYLTNRIQNGGTEVVEAKAGA----GSAT 266
H G + + S FT+ + E + ++ G E++ K +A
Sbjct: 171 H-GDSQVVAWSTATVGGLPLEELAPFTKLDLEAIEEEVRTSGYEIIRLKGATNYGIATAI 229
Query: 267 LSMAYAAVKFADACL---RGLRGDAGVVECAFVASQVTELPFFASKVRLGRQGAEEIFQL 323
+ + + L G G+ + A +P +GR+G I ++
Sbjct: 230 ADIVKSILLDERRVLPVSAVQEGQYGIEDVAL------SVP-----AVVGREGVVRILEI 278
Query: 324 GPLNEYERIGLEKAKKEL 341
PL E E L+K+ + L
Sbjct: 279 -PLTEDEEAKLQKSAEAL 295
>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 = 109 bits (274), Expect = 2e-27
Identities = 89/313 (28%), Positives = 152/313 (48%), Gaps = 36/313 (11%)
Query: 44 KVAILGAAGGIGQPLAMLMKINPLVSVLHLYDVVNTPGVTADISHMDTGAVVRGF----L 99
K++++GA G +G A + L ++ L DVV + + V GF
Sbjct: 3 KISVIGA-GFVGATTAFRLAEKELADLV-LLDVVEGIPQGKALDMYEASPV-GGFDTKVT 59
Query: 100 GQPQLENALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAKCCPNATVNLIS 159
G + D+V+I AG+PRKPGM+R+DL ++NAGIVR + I + PN + ++S
Sbjct: 60 GTNNYADT-ANSDIVVITAGLPRKPGMSREDLLSMNAGIVREVTGRIMEHSPNPIIVVVS 118
Query: 160 NPVNSTVPIAAEVFKKAGTYDPKKLLGVT-MLDVVRANTFVAEVLGLDPRDVDVPVVGGH 218
NP+++ +A + + ++++G +LD R TF+A LG+ +DV V+GGH
Sbjct: 119 NPLDAMTYVAWQK----SGFPKERVIGQAGVLDSARFRTFIAMELGVSVQDVTACVLGGH 174
Query: 219 AGVTILPL----------LSQVKPPCSFTQEETEYLTNRIQNGGTEVVEAKAGAGSATLS 268
G ++PL ++ + E + R + GG E+V GSA +
Sbjct: 175 -GDAMVPLVRYSTVAGIPVADLISA-----ERIAEIVERTRKGGGEIVNL-LKQGSAYYA 227
Query: 269 MAYAAVKFADACLRGLRGDAGVVEC-AFVASQV-TELPFFASKVRLGRQGAEEIFQLGPL 326
A + V+ +A L+ + V+ C A++ Q + + V LG+ G E I++L L
Sbjct: 228 PAASVVEMVEAILKDRK---RVLPCAAYLDGQYGIDGIYVGVPVILGKNGVEHIYEL-KL 283
Query: 327 NEYERIGLEKAKK 339
++ E L K+ K
Sbjct: 284 DQSELALLNKSAK 296
>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 = 98.6 bits (246), Expect = 1e-23
Identities = 66/243 (27%), Positives = 115/243 (47%), Gaps = 43/243 (17%)
Query: 44 KVAILGAAGGIGQPLAMLMKINPLVSVLHL-----------------YDVVNTPGVTADI 86
KV+I+GA+G +G A+L+ +V ++L YD + G+ A+I
Sbjct: 2 KVSIIGASGRVGSATALLLAKEDVVKEINLISRPKSLEKLKGLRLDIYDALAAAGIDAEI 61
Query: 87 SHMDTGAVVRGFLGQPQLENALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGI 146
+ V G D+VII AGVPRK GM+R DL NA IV+ + I
Sbjct: 62 KISSDLSDV-------------AGSDIVIITAGVPRKEGMSRLDLAKKNAKIVKKYAKQI 108
Query: 147 AKCCPNATVNLISNPVNSTVPIAAEVFKKAGTYDPKKLLGV-TMLDVVRANTFVAEVLGL 205
A+ P+ + +++NPV+ A K++G +D ++ G+ T LD +R +A+ +
Sbjct: 109 AEFAPDTKILVVTNPVDVMTYKA---LKESG-FDKNRVFGLGTHLDSLRFKVAIAKHFNV 164
Query: 206 DPRDVDVPVVGGHAGVTILPLLSQ-------VKPPCSFTQEETEYLTNRIQNGGTEVVEA 258
+V ++G H G +++PL+S +K + + E + ++N G ++
Sbjct: 165 HISEVHTRIIGEH-GDSMVPLISSTSIGGIPIKRFPEYKDFDVEKIVETVKNAGQNIISL 223
Query: 259 KAG 261
K G
Sbjct: 224 KGG 226
>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 = 95.0 bits (237), Expect = 2e-22
Identities = 64/248 (25%), Positives = 111/248 (44%), Gaps = 26/248 (10%)
Query: 108 LTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAKCCPNATVNLISNPVNSTVP 167
DLV+I AG P+KPG TR +L N I++++ + K + + +NPV+
Sbjct: 62 CKDADLVVITAGAPQKPGETRLELVGRNVRIMKSIVPEVVKSGFDGIFLVATNPVD---- 117
Query: 168 IAAEVFKKAGTYDPKKLLGV-TMLDVVRANTFVAEVLGLDPRDVDVPVVGGHAGVTILPL 226
I V K + +++G T+LD R +AE LG+DP+ V ++G H G + +P+
Sbjct: 118 ILTYVAWKLSGFPKNRVIGSGTVLDTARLRYLLAEKLGVDPQSVHAYIIGEH-GDSEVPV 176
Query: 227 LSQVK----PPCSF---TQEETEYLTNRI----QNGGTEVVEAKAGAGSATLSMAYAAVK 275
S P + ET+ I ++ E++ K G+ + A +
Sbjct: 177 WSSATIGGVPLLDYLKAKGTETDLDLEEIEKEVRDAAYEIINRK---GATYYGIGMAVAR 233
Query: 276 FADACLRGLRGDAGVVEC-AFVASQVTELPFFASKVR-LGRQGAEEIFQLGPLNEYERIG 333
+A L V+ A++ + + LGR G EEI +L PL++ E+
Sbjct: 234 IVEAILHDEN---RVLPVSAYLDGEYGIKDVYIGVPAVLGRNGVEEIIEL-PLSDEEKEA 289
Query: 334 LEKAKKEL 341
+K+ + L
Sbjct: 290 FQKSAETL 297
>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 = 90.6 bits (226), Expect = 1e-20
Identities = 67/261 (25%), Positives = 110/261 (42%), Gaps = 47/261 (18%)
Query: 111 MDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAKCCPNATVNLISNPVNSTVPIAA 170
D+V+I AG P+KPG TR DL NA I++++ I + + SNPV+ +
Sbjct: 69 ADIVVITAGAPQKPGETRLDLLEKNAKIMKSIVPKIKASGFDGIFLVASNPVD----VIT 124
Query: 171 EVFKKAGTYDPKKLLGV-TMLDVVRANTFVAEVLGLDPRDVDVPVVGGH----------- 218
V +K +++G T LD R +AE L +DPR V V+G H
Sbjct: 125 YVVQKLSGLPKNRVIGTGTSLDTARLRRALAEKLNVDPRSVHAYVLGEHGDSQFVAWSTV 184
Query: 219 --AGVTILPLLSQVKPPCSFTQEETEYLTNRIQNGGTEVVEAKAGAGSATLSMAYAAVKF 276
G +L LL + K ++ + + + ++ G E++ K G+ +A A +
Sbjct: 185 TVGGKPLLDLLKEGK----LSELDLDEIEEDVRKAGYEIINGK---GATYYGIATALARI 237
Query: 277 ADACLRG----------LRGDAGVVECAFVASQVTELPFFASKVRLGRQGAEEIFQLGPL 326
A L L G+ G + + +GR G EE+ +L L
Sbjct: 238 VKAILNDENAILPVSAYLDGEYGEKDV-----------YIGVPAIIGRNGVEEVIEL-DL 285
Query: 327 NEYERIGLEKAKKELAGSIQK 347
E E+ EK+ + +I+K
Sbjct: 286 TEEEQEKFEKSADIIKENIKK 306
>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 = 83.1 bits (206), Expect = 6e-18
Identities = 72/262 (27%), Positives = 104/262 (39%), Gaps = 48/262 (18%)
Query: 44 KVAILGAAGGIGQPLA-------MLMKINPLVSVLHLYDVVNTPGVTADISHMDTGAV-- 94
V I GAAG IG L + P++ LHL D+ + ++ +
Sbjct: 2 HVLITGAAGQIGYNLLFLIASGELFGDDQPVI--LHLLDI------PPAMKALEGVVMEL 53
Query: 95 -------VRGFLGQPQLENALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIA 147
++G + E A +D+ I+ PRKPGM R DL NA I + E +
Sbjct: 54 QDCAFPLLKGVVITTDPEEAFKDVDVAILVGAFPRKPGMERADLLRKNAKIFKEQGEALN 113
Query: 148 KCC-PNATVNLISNPVNSTVPIAAEVFKKAGTYDPKKLLGVTMLDVVRANTFVAEVLGLD 206
K P V ++ NP N+ IA K A PK +T LD RA VA LG+
Sbjct: 114 KVAKPTVKVLVVGNPANTNALIAL---KNAPNLPPKNFTALTRLDHNRAKAQVARKLGVR 170
Query: 207 PRDV-DVPVVGGHAGVTILPLLSQ-------------VKPPCSFTQEETEYLTNRIQNGG 252
DV +V + G H+ T +P LS + +E +Q G
Sbjct: 171 VSDVKNVIIWGNHSN-TQVPDLSNAVVYGPGGTEWVLDLLDEEWLNDE---FVKTVQKRG 226
Query: 253 TEVVEAKAGAGSATLSMAYAAV 274
+++ + GA SA S A A
Sbjct: 227 AAIIKKR-GASSA-ASAAKAIA 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 = 82.2 bits (204), Expect = 9e-18
Identities = 92/330 (27%), Positives = 142/330 (43%), Gaps = 52/330 (15%)
Query: 44 KVAILGAAGGIGQPLAMLMKINPLVSVLHLYDVVNTPGVTA---DISH-MDTGAVVRGFL 99
KVAI+GA G +G A + + L S + L D+ N D++H VR +
Sbjct: 2 KVAIVGA-GFVGSTTAYALLLRGLASEIVLVDI-NKAKAEGEAMDLAHGTPFVKPVRIYA 59
Query: 100 GQPQ-LENALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAKCCPNATVNLI 158
G + A D+V+I AG +KPG TR DL N I + + I K P+A + ++
Sbjct: 60 GDYADCKGA----DVVVITAGANQKPGETRLDLLKRNVAIFKEIIPQILKYAPDAILLVV 115
Query: 159 SNPVNSTVPIAAEVFKKAGTYDPKKLLGV-TMLDVVRANTFVAEVLGLDPRDVDVPVVGG 217
+NPV+ + V K P +++G T+LD R + E LG+DPR V ++G
Sbjct: 116 TNPVD----VLTYVAYKLSGLPPNRVIGSGTVLDTARFRYLLGEHLGVDPRSVHAYIIGE 171
Query: 218 H-------------AGVTILPLLSQVKPPCSFTQEETEYLTNRIQNGGTEVVEAKAGA-- 262
H GV + P F +E E + ++N E++E K GA
Sbjct: 172 HGDSEVAVWSSANIGGVPLDEFCKLCGRP--FDEEVREEIFEEVRNAAYEIIERK-GATY 228
Query: 263 ---GSATLSMAYAAVKFADACL---RGLRGDAGVVECAFVASQVTELPFFASKVRLGRQG 316
G A + A ++ ++ L L G G+ + A LP V GR G
Sbjct: 229 YAIGLALARIVEAILRDENSVLTVSSLLDGQYGIKDVAL------SLP---CIV--GRSG 277
Query: 317 AEEIFQLGPLNEYERIGLEKAKKELAGSIQ 346
E + PL+E E L + + L +I+
Sbjct: 278 VERVLPP-PLSEEEEEALRASAEVLKEAIE 306
>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 = 77.4 bits (191), Expect = 5e-16
Identities = 90/324 (27%), Positives = 137/324 (42%), Gaps = 38/324 (11%)
Query: 44 KVAILGAAGGIGQPLA-------MLMKINPLVSVLHLYDVVNT----PGVTADISHMDTG 92
+VA+ GAAG IG L + K P+V LHL D+ GV ++ D
Sbjct: 5 RVAVTGAAGQIGYSLLFRIASGELFGKDQPVV--LHLLDIPPAMKALEGVAMEL--EDCA 60
Query: 93 -AVVRGFLGQPQLENALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAKCC- 150
++ G + E A +D ++ PRKPGM R DL + N I + + + K
Sbjct: 61 FPLLAGVVATTDPEEAFKDVDAALLVGAFPRKPGMERADLLSKNGKIFKEQGKALNKVAK 120
Query: 151 PNATVNLISNPVNSTVPIAAEVFKKAGTYDPKKLLGVTMLDVVRANTFVAEVLGLDPRDV 210
+ V ++ NP N+ IA+ K A PK +T LD RA +A G+ DV
Sbjct: 121 KDVKVLVVGNPANTNALIAS---KNAPDIPPKNFSAMTRLDHNRAKYQLAAKAGVPVSDV 177
Query: 211 -DVPVVGGHAGVTILPLLSQVK---PPCSFTQEETEYLTN----RIQNGGTEVVEAKAGA 262
+V + G H+ T +P + P ++ ++L +Q G V+EA+ GA
Sbjct: 178 KNVIIWGNHSN-TQVPDFTHATVDGRPVKEVIKDDKWLEGEFIPTVQQRGAAVIEAR-GA 235
Query: 263 GSATLSMAYAAVKFADACLRGLRGDAGVVECAFVASQ-----VTELPFFASKVRLGRQGA 317
SA S A AA+ + G G V S + E F+ V G
Sbjct: 236 SSA-ASAANAAIDHVRDWVTGTP--EGDWVSMGVYSDGNPYGIPEGIIFSFPVTCKGDGE 292
Query: 318 EEIFQLGPLNEYERIGLEKAKKEL 341
EI + PL+++ R L+ + EL
Sbjct: 293 WEIVEGLPLDDFVRGKLDATEDEL 316
>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 = 73.9 bits (182), Expect = 6e-15
Identities = 57/193 (29%), Positives = 82/193 (42%), Gaps = 31/193 (16%)
Query: 107 ALTGMDLVIIPAGVPRKPGMT--RDDLFNINAGIVRTLCEGIAKCCPNATVNLISNPVNS 164
D+++I AG PG T R DL NA I+R + I K A + LI+NP++
Sbjct: 65 DCADADIIVITAGPSIDPGNTDDRLDLAQTNAKIIREIMGNITKVTKEAVIILITNPLDI 124
Query: 165 TVPIAAEVFKKAGTYDPKKLLGV-TMLDVVRANTFVAEVLGLDPRDVDVPVVGGHAGVTI 223
V IAA F Y K++G TMLD R VA+ G+DP++V V+G H G
Sbjct: 125 AVYIAATEFD----YPANKVIGTGTMLDTARLRRIVADKYGVDPKNVTGYVLGEH-GSHA 179
Query: 224 LPLLSQV---------------KPPCSFTQEETEYLTNRIQNGGTEVVEAKAGAGSATLS 268
P+ S V K P + L + +V K G +A ++
Sbjct: 180 FPVWSLVNIAGLPLDELEALFGKEPID-----KDELLEEVVQAAYDVFNRK-GWTNAGIA 233
Query: 269 MAYAAVKFADACL 281
+A + A L
Sbjct: 234 K--SASRLIKAIL 244
>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 = 70.7 bits (174), Expect = 9e-14
Identities = 82/337 (24%), Positives = 135/337 (40%), Gaps = 57/337 (16%)
Query: 42 GFKVAILGA-AGGIGQPLAMLMKINPLVSVLHLYDVVN--TPGVTADISHMDTGAVVRGF 98
KV ++G G+ +++L K L L L DVV G D+ H G+ F
Sbjct: 3 RNKVTVVGVGQVGMACAISILAK--GLADELVLVDVVEDKLKGEAMDLQH---GSA---F 54
Query: 99 LGQPQLE-----NALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAKCCPNA 153
L P++E + +VI+ AG + G +R DL N I + + + K PNA
Sbjct: 55 LKNPKIEADKDYSVTANSKVVIVTAGARQNEGESRLDLVQRNVDIFKGIIPKLVKYSPNA 114
Query: 154 TVNLISNPVNSTVPIAAEVFKKAGTYDPKKLLGV-TMLDVVRANTFVAEVLGLDPRDVDV 212
+ ++SNPV+ I V K +++G LD R +AE LG+ P V
Sbjct: 115 ILLVVSNPVD----IMTYVAWKLSGLPKHRVIGSGCNLDSARFRYLIAERLGVAPSSVHG 170
Query: 213 PVVGGH--------AGVTI--LPLLSQVKPPCSFTQEETEY-LTNRIQNGGTEVVEAKAG 261
++G H +GV + + L + E + ++ + EV++ K
Sbjct: 171 WIIGEHGDSSVPVWSGVNVAGVRLQDLNPDIGTDKDPEKWKEVHKQVVDSAYEVIKLK-- 228
Query: 262 AGSATLSMAYAAVKFADACLRGLR----------GDAGVVECAFVASQVTELPFFASKVR 311
G + ++ + DA LR G G+ + F++ LP
Sbjct: 229 -GYTSWAIGLSVADLVDAILRNTGRVHSVSTLVKGLHGIEDEVFLS-----LP-----CI 277
Query: 312 LGRQGAEEIFQLGPLNEYERIGLEKAKKELAGSIQKG 348
LG G + + PL E E+ L+K+ L +QK
Sbjct: 278 LGENGITHVIKQ-PLTEEEQEKLQKSADTLW-EVQKQ 312
>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 = 70.3 bits (172), Expect = 2e-13
Identities = 69/254 (27%), Positives = 104/254 (40%), Gaps = 31/254 (12%)
Query: 44 KVAILGAAGGIGQPLA-------MLMKINPLVSVLHLYDVVNTPGVTADISH--MDTG-A 93
+V + GAAG IG L ML K P++ LHL D+ V + MD
Sbjct: 1 RVVVTGAAGQIGYALLPMIARGRMLGKDQPII--LHLLDIPPAMKVLEGVVMELMDCAFP 58
Query: 94 VVRGFLGQPQLENALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAK-CCPN 152
++ G + A T +D+ I+ PRK GM R DL + N I + + K +
Sbjct: 59 LLDGVVPTHDPAVAFTDVDVAILVGAFPRKEGMERRDLLSKNVKIFKEQGRALDKLAKKD 118
Query: 153 ATVNLISNPVNSTVPIAAEVFKKAGTYDPKKLLGVTMLDVVRANTFVAEVLGLDPRDV-D 211
V ++ NP N+ + + A + PK +T LD RA VAE G+ DV +
Sbjct: 119 CKVLVVGNPANTNALVLSNY---APSIPPKNFSALTRLDHNRALAQVAERAGVPVSDVKN 175
Query: 212 VPVVGGHAGVTILPLLSQVKPPCSFTQEETEYLTNR-----------IQNGGTEVVEAKA 260
V + G H+ T P ++ Q+ +Q G ++ A+
Sbjct: 176 VIIWGNHSS-TQYPDVNHATVTKGGKQKPVREAIKDDAYLDGEFITTVQQRGAAIIRAR- 233
Query: 261 GAGSATLSMAYAAV 274
S+ LS A AAV
Sbjct: 234 -KLSSALSAAKAAV 246
>gnl|CDD|178836 PRK00066, ldh, L-lactate dehydrogenase; Reviewed.
Length = 315
Score = 68.0 bits (167), Expect = 7e-13
Identities = 64/251 (25%), Positives = 107/251 (42%), Gaps = 36/251 (14%)
Query: 110 GMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAKCCPNATVNLISNPVNSTVPIA 169
DLV+I AG P+KPG TR DL N I +++ + + + SNPV+ I
Sbjct: 73 DADLVVITAGAPQKPGETRLDLVEKNLKIFKSIVGEVMASGFDGIFLVASNPVD----IL 128
Query: 170 AEVFKKAGTYDPKKLLGV-TMLDVVRANTFVAEVLGLDPRDVDVPVVGGH---------- 218
K + ++++G T LD R ++E L +DPR V ++G H
Sbjct: 129 TYATWKLSGFPKERVIGSGTSLDSARFRYMLSEKLDVDPRSVHAYIIGEHGDTEFPVWSH 188
Query: 219 AGVTILPLLSQVKPPCSFTQEETEYLTNRIQNGGTEVVEAKAGAGSATLSMAYAAVKFA- 277
A V +PL ++ + +E+ + + +++ E++E K GA ++MA A + A
Sbjct: 189 ANVAGVPLEEYLEENEQYDEEDLDEIFENVRDAAYEIIEKK-GATYYGIAMALARITKAI 247
Query: 278 ----DACL---RGLRGDAGVVECAFVASQVTELPFFASKVRLGRQGAEEIFQLGPLNEYE 330
+A L L G G + + + R G EI +L PLN+ E
Sbjct: 248 LNNENAVLPVSAYLEGQYGEEDV-----------YIGVPAVVNRNGIREIVEL-PLNDDE 295
Query: 331 RIGLEKAKKEL 341
+ + L
Sbjct: 296 KQKFAHSADVL 306
>gnl|CDD|178212 PLN02602, PLN02602, lactate dehydrogenase.
Length = 350
Score = 67.5 bits (165), Expect = 2e-12
Identities = 82/326 (25%), Positives = 140/326 (42%), Gaps = 39/326 (11%)
Query: 44 KVAILGAAGGIGQPLAMLMKINPLVSVLHLYDVV--NTPGVTADISHMDTGAVVRGFLGQ 101
KV+++G G +G +A + L L L DV G D+ H FL +
Sbjct: 39 KVSVVGV-GNVGMAIAQTILTQDLADELALVDVNPDKLRGEMLDLQH------AAAFLPR 91
Query: 102 PQL----ENALT-GMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAKCCPNATVN 156
++ + A+T G DL I+ AG + PG +R +L N + R + +AK P+ +
Sbjct: 92 TKILASTDYAVTAGSDLCIVTAGARQIPGESRLNLLQRNVALFRKIIPELAKYSPDTILL 151
Query: 157 LISNPVNSTVPIAAEVFKKAGTYDPKKLLGV-TMLDVVRANTFVAEVLGLDPRDVDVPVV 215
++SNPV+ +A +K +G + +++G T LD R +A+ L ++ +DV +V
Sbjct: 152 IVSNPVDVLTYVA---WKLSG-FPANRVIGSGTNLDSSRFRFLIADHLDVNAQDVQAYIV 207
Query: 216 GGH-------------AGVTILPLLSQVKPPCSFTQEETEYLTNRIQNGGTEVVEAKAGA 262
G H GV +L L K ++ +E E + + + EV++ K
Sbjct: 208 GEHGDSSVALWSSVSVGGVPVLSFLE--KQQIAYEKETLEEIHRAVVDSAYEVIKLK--- 262
Query: 263 GSATLSMAYAAVKFADACLRGLRGDAGVVECAFVASQVTELPFFAS-KVRLGRQGAEEIF 321
G + ++ Y+ + LR R V A + E F S +LGR G +
Sbjct: 263 GYTSWAIGYSVASLVRSLLRDQRRIHPVSVLAKGFHGIDEGDVFLSLPAQLGRNGVLGVV 322
Query: 322 QLGPLNEYERIGLEKAKKELAGSIQK 347
+ L + E L K+ K L +
Sbjct: 323 NV-HLTDEEAERLRKSAKTLWEVQSQ 347
>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 = 64.2 bits (157), Expect = 2e-11
Identities = 64/255 (25%), Positives = 105/255 (41%), Gaps = 33/255 (12%)
Query: 44 KVAILGAAGGIGQPLA-------MLMKINPLVSVLHLYDVVNTPGVTADIS-HMDTGA-- 93
+V + GAAG I L + P++ LHL D+ + + A
Sbjct: 4 RVLVTGAAGQIAYSLLPMIAKGDVFGPDQPVI--LHLLDIPPALKALEGVVMELQDCAFP 61
Query: 94 VVRGFLGQPQLENALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAKCC-PN 152
+++ + E A +D+ I+ +PRK GM R DL N I + E + K N
Sbjct: 62 LLKSVVATTDPEEAFKDVDVAILVGAMPRKEGMERKDLLKANVKIFKEQGEALDKYAKKN 121
Query: 153 ATVNLISNPVNSTVPIAAEVFKKAGTYDPKKLLGVTMLDVVRANTFVAEVLGLDPRDV-D 211
V ++ NP N+ I K A + + +T LD RA + +A LG+ DV +
Sbjct: 122 VKVLVVGNPANTNALILL---KYAPSIPKENFTALTRLDHNRAKSQIALKLGVPVSDVKN 178
Query: 212 VPVVGGHAGVTILPLLSQ--------VKPPCSFTQEETEYLTN----RIQNGGTEVVEAK 259
V + G H+ T P ++ KP +++ +L +Q G V++A+
Sbjct: 179 VIIWGNHSS-TQYPDVNHATVELNGKGKPAREAVKDD-AWLNGEFISTVQKRGAAVIKAR 236
Query: 260 AGAGSATLSMAYAAV 274
SA +S A A
Sbjct: 237 -KLSSA-MSAAKAIC 249
>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 = 3e-10
Identities = 37/135 (27%), Positives = 59/135 (43%), Gaps = 4/135 (2%)
Query: 97 GFLGQPQLENALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAKCC-PNATV 155
G + +LE A +D + A VP KPG R DL N I + E +++ P V
Sbjct: 47 GTIVTTKLEEAFKDIDCAFLVASVPLKPGEVRADLLTKNTPIFKATGEALSEYAKPTVKV 106
Query: 156 NLISNPVNSTVPIAAEVFKKAGTYDPKKLLGVTMLDVVRANTFVAEVLGLDPRDVDVPVV 215
+I NPVN+ +A A + + MLD RA + +A L + + VV
Sbjct: 107 LVIGNPVNTNCLVA---MLHAPKLSAENFSSLCMLDHNRAVSRIASKLKVPVDHIYHVVV 163
Query: 216 GGHAGVTILPLLSQV 230
G+ +++ L+
Sbjct: 164 WGNHAESMVADLTHA 178
>gnl|CDD|177744 PLN00135, PLN00135, malate dehydrogenase.
Length = 309
Score = 53.2 bits (128), Expect = 6e-08
Identities = 46/175 (26%), Positives = 83/175 (47%), Gaps = 17/175 (9%)
Query: 49 GAAGGIGQPLAM-LMKINPLVSVLHLYDVVNTPGVTADISHMDTG-AVVRGFLGQPQLEN 106
G G QP+ + ++ I P L+ GV ++ +D +++G + +
Sbjct: 5 GVMLGPDQPVILHMLDIPPAAEALN--------GVKMEL--IDAAFPLLKGVVATTDVVE 54
Query: 107 ALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAKCC-PNATVNLISNPVNST 165
A G+++ ++ G PRK GM R D+ + N I ++ + K P+ V +++NP N+
Sbjct: 55 ACKGVNIAVMVGGFPRKEGMERKDVMSKNVSIYKSQASALEKHAAPDCKVLVVANPANTN 114
Query: 166 VPIAAEVFKKAGTYDPKKLLGVTMLDVVRANTFVAEVLGLDPRDV-DVPVVGGHA 219
I E A + K + +T LD RA ++E LG+ DV +V + G H+
Sbjct: 115 ALILKEF---APSIPEKNITCLTRLDHNRALGQISERLGVPVSDVKNVIIWGNHS 166
>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 = 53.0 bits (128), Expect = 8e-08
Identities = 63/252 (25%), Positives = 101/252 (40%), Gaps = 31/252 (12%)
Query: 44 KVAILGAAGGIGQPL-------AMLMKINPLVSVLHLYDVVNT----PGVTADISHMDTG 92
+VA+ GAAG IG L M P++ L L ++ GV ++ +
Sbjct: 4 RVAVTGAAGQIGYSLLFRIASGEMFGPDQPVI--LQLLELPQALKALEGVAMEL---EDC 58
Query: 93 A--VVRGFLGQPQLENALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAK-C 149
A ++ + A D ++ PR PGM R DL N I + +
Sbjct: 59 AFPLLAEIVITDDPNVAFKDADWALLVGAKPRGPGMERADLLKANGKIFTAQGKALNDVA 118
Query: 150 CPNATVNLISNPVNSTVPIAAEVFKKAGTYDPKKLLGVTMLDVVRANTFVAEVLGLDPRD 209
+ V ++ NP N+ IA K A P +T LD RA + +A+ G+ D
Sbjct: 119 SRDVKVLVVGNPCNTNALIAM---KNAPDIPPDNFTAMTRLDHNRAKSQLAKKAGVPVTD 175
Query: 210 VDVPVVGGHAGVTILPLLSQVK---PPCSFTQEETEYLTN----RIQNGGTEVVEAKAGA 262
V V+ G+ T P + P + + +L + +Q G +++A+ GA
Sbjct: 176 VKNMVIWGNHSPTQYPDFTNATIGGKPAAEVINDRAWLEDEFIPTVQKRGAAIIKAR-GA 234
Query: 263 GSATLSMAYAAV 274
SA S A AA+
Sbjct: 235 SSAA-SAANAAI 245
>gnl|CDD|235468 PRK05442, PRK05442, malate dehydrogenase; Provisional.
Length = 326
Score = 46.3 bits (111), Expect = 1e-05
Identities = 68/253 (26%), Positives = 107/253 (42%), Gaps = 33/253 (13%)
Query: 44 KVAILGAAGGIGQPL-------AMLMKINPLVSVLHLYDVVNTPGVTA---DISHMDTGA 93
+VA+ GAAG IG L ML K P++ L L ++ P + A + +D A
Sbjct: 6 RVAVTGAAGQIGYSLLFRIASGDMLGKDQPVI--LQLLEI--PPALKALEGVVMELDDCA 61
Query: 94 --VVRGFLGQPQLENALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAKCC- 150
++ G + A D+ ++ PR PGM R DL N I + + +
Sbjct: 62 FPLLAGVVITDDPNVAFKDADVALLVGARPRGPGMERKDLLEANGAIFTAQGKALNEVAA 121
Query: 151 PNATVNLISNPVNSTVPIAAEVFKKAGTYDPKKLLGVTMLDVVRANTFVAEVLGLDPRDV 210
+ V ++ NP N+ IA K A + +T LD RA + +A G+ D+
Sbjct: 122 RDVKVLVVGNPANTNALIAM---KNAPDLPAENFTAMTRLDHNRALSQLAAKAGVPVADI 178
Query: 211 -DVPVVGGHAGVTILPLLSQV----KPPCSFTQEETEYLTN----RIQNGGTEVVEAKAG 261
+ V G H+ T P KP ++ +L + +Q G ++EA+ G
Sbjct: 179 KKMTVWGNHSA-TQYPDFRHATIDGKPAAEVINDQ-AWLEDTFIPTVQKRGAAIIEAR-G 235
Query: 262 AGSATLSMAYAAV 274
A SA S A AA+
Sbjct: 236 ASSAA-SAANAAI 247
>gnl|CDD|215060 PLN00112, PLN00112, malate dehydrogenase (NADP); Provisional.
Length = 444
Score = 39.4 bits (92), Expect = 0.002
Identities = 28/79 (35%), Positives = 35/79 (44%), Gaps = 10/79 (12%)
Query: 121 PRKPGMTRDDLFNINAGIV----RTLCEGIAKCCPNATVNLISNPVNSTVPIAAEVFKKA 176
PR PGM R DL +IN I + L E +A N V ++ NP N+ I K A
Sbjct: 187 PRGPGMERADLLDINGQIFAEQGKALNE-VAS--RNVKVIVVGNPCNTNALIC---LKNA 240
Query: 177 GTYDPKKLLGVTMLDVVRA 195
K +T LD RA
Sbjct: 241 PNIPAKNFHALTRLDENRA 259
>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 = 36.9 bits (85), Expect = 0.015
Identities = 52/179 (29%), Positives = 73/179 (40%), Gaps = 22/179 (12%)
Query: 112 DLVIIPAGVPRKPGMTRDDLFNINAGIV----RTLCEGIAKCCPNATVNLISNPVNSTVP 167
D ++ PR PGM R DL +IN I + L +K C V ++ NP N+
Sbjct: 122 DWALLIGAKPRGPGMERADLLDINGQIFADQGKALNAVASKNC---KVLVVGNPCNTNAL 178
Query: 168 IAAEVFKKAGTYDPKKLLGVTMLDVVRANTFVAEVLGLDPRDVDVPVVGGHAGVTILPLL 227
IA K A K +T LD RA +A G V + G+ T +P
Sbjct: 179 IA---MKNAPNIPRKNFHALTRLDENRAKCQLALKSGKFYTSVSNVTIWGNHSTTQVPDF 235
Query: 228 SQVK---PPCSFTQEETEYL----TNRIQNGGTEVVEAKAGAGSATLSMAYAAVKFADA 279
K P ++T++L T +Q G +++ K G SA A AV ADA
Sbjct: 236 VNAKIGGRPAKEVIKDTKWLEEEFTPTVQKRGGALIK-KWGRSSA----ASTAVSIADA 289
>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 = 36.2 bits (84), Expect = 0.021
Identities = 23/93 (24%), Positives = 42/93 (45%), Gaps = 4/93 (4%)
Query: 46 AILGAAGGIGQPLA-MLMKINPLVSVLHLYDVVNTPGVTADISHMDTGAVVRG-FLGQPQ 103
+ G G +G+ + +L++ L V ++D+ +P + D S + + G +
Sbjct: 1 LVTGGGGFLGRHIVRLLLREGELQEV-RVFDLRFSPELLEDFSKLQVITYIEGDVTDKQD 59
Query: 104 LENALTGMDLVIIPAGVPRKPGM-TRDDLFNIN 135
L AL G D+VI A + G RD + +N
Sbjct: 60 LRRALQGSDVVIHTAAIIDVFGKAYRDTIMKVN 92
>gnl|CDD|172654 PRK14166, PRK14166, bifunctional 5,10-methylene-tetrahydrofolate
dehydrogenase/ 5,10-methylene-tetrahydrofolate
cyclohydrolase; Provisional.
Length = 282
Score = 34.2 bits (78), Expect = 0.077
Identities = 26/102 (25%), Positives = 42/102 (41%), Gaps = 29/102 (28%)
Query: 42 GFKVAILGAAGGIGQPLA-MLMKINPLVSVLHLYDVVNTPGVTADISHMDTGAVVRGFLG 100
G I+GA+ +G+P+A ML+ VSV H+ T D+S A
Sbjct: 157 GKDAVIIGASNIVGRPMATMLLNAGATVSVCHIK--------TKDLSLYTRQA------- 201
Query: 101 QPQLENALTGMDLVIIPAGVPR--KPGMTRDDLFNINAGIVR 140
DL+I+ AG + M ++ + ++ GI R
Sbjct: 202 -----------DLIIVAAGCVNLLRSDMVKEGVIVVDVGINR 232
>gnl|CDD|224403 COG1486, CelF, Alpha-galactosidases/6-phospho-beta-glucosidases,
family 4 of glycosyl hydrolases [Carbohydrate transport
and metabolism].
Length = 442
Score = 34.5 bits (80), Expect = 0.079
Identities = 53/219 (24%), Positives = 73/219 (33%), Gaps = 68/219 (31%)
Query: 42 GFKVAILGAAGGIGQP--LAMLMKINPLVSV--LHLYDV---------------VNTPGV 82
FK+ I+G G P L + + V L LYD+ V G
Sbjct: 3 KFKIVIIGG-GSTYTPKLLLGDLARTEELPVRELALYDIDEERLKIIAILAKKLVEEAGA 61
Query: 83 TADIS-HMDTGAVVRGFLGQPQLENALTGMDLVIIPA------------GVPRKPGMTRD 129
+ D AL G D VI +P K G+
Sbjct: 62 PVKVEATTD-------------RREALEGADFVITQIRVGGLEAREKDERIPLKHGLYGQ 108
Query: 130 DLFNINAGIVRTL---------CEGIAKCCPNATVNLISNPVNSTVPIAAEVFKKAGTYD 180
+ N GI L + + K CPNA + +NP AA V +
Sbjct: 109 E-TNGPGGIFYGLRTIPVILDIAKDMEKVCPNAWMLNYTNP-------AAIVTEAVRRLY 160
Query: 181 PK-KLLGVTMLDVVRANTF-VAEVLGLDPR-DVDVPVVG 216
PK K++G+ +AEVLGL+PR D+ V G
Sbjct: 161 PKIKIVGLC--HGPIGIAMELAEVLGLEPREDLRYRVAG 197
>gnl|CDD|178031 PLN02409, PLN02409, serine--glyoxylate aminotransaminase.
Length = 401
Score = 33.2 bits (76), Expect = 0.20
Identities = 14/38 (36%), Positives = 20/38 (52%), Gaps = 4/38 (10%)
Query: 92 GAVVR----GFLGQPQLENALTGMDLVIIPAGVPRKPG 125
G V R G + + QL AL G+++V+ G P K G
Sbjct: 343 GKVFRIGHLGNVNELQLLGALAGVEMVLKDVGYPVKLG 380
>gnl|CDD|201603 pfam01118, Semialdhyde_dh, Semialdehyde dehydrogenase, NAD binding
domain. This Pfam entry contains the following members:
N-acetyl-glutamine semialdehyde dehydrogenase (AgrC)
Aspartate-semialdehyde dehydrogenase.
Length = 121
Score = 31.0 bits (71), Expect = 0.33
Identities = 22/79 (27%), Positives = 36/79 (45%), Gaps = 3/79 (3%)
Query: 44 KVAILGAAGGIGQPLAMLMKINPLVSVLHLYDVVNTPGVTADISHMDTGAVVRGFLGQPQ 103
KVAI+GA G +GQ L L+ +P + ++ L + G ++ L +
Sbjct: 1 KVAIVGATGYVGQELLRLLAEHPPLELVALVASSRSAGKKVAFAYPILEGGKDLLL-EDV 59
Query: 104 LENALTGMDLVII--PAGV 120
L +D+V + PAGV
Sbjct: 60 DPEDLKDVDIVFLALPAGV 78
>gnl|CDD|133433 cd05297, GH4_alpha_glucosidase_galactosidase, Glycoside Hydrolases
Family 4; Alpha-glucosidases and alpha-galactosidases.
Glucosidases cleave glycosidic bonds to release glucose
from oligosaccharides. Alpha-glucosidases and
alpha-galactosidases release alpha-D-glucose and
alpha-D-galactose, respectively, via the hydrolysis of
alpha-glycopyranoside bonds. Some bacteria
simultaneously translocate and phosphorylate
disaccharides via the phosphoenolpyruvate-dependent
phosphotransferase system (PEP-PTS). After
translocation, these phospho-disaccharides may be
hydrolyzed by the GH4 glycoside hydrolases such as the
alpha-glucosidases. Other organsisms (such as archaea
and Thermotoga maritima) lack the PEP-PTS system, but
have several enzymes normally associated with the
PEP-PTS operon. Alpha-glucosidases and
alpha-galactosidases 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 = 423
Score = 32.2 bits (74), Expect = 0.45
Identities = 34/149 (22%), Positives = 44/149 (29%), Gaps = 58/149 (38%)
Query: 104 LENALTGMDLVIIPAGVPRKPGMTRDDLFNINA---------------GIVRTL------ 142
AL G D VI V D F I GI R L
Sbjct: 68 RREALDGADFVINTIQVGGHEYTETD--FEIPEKYGYYQTVGDTSGPGGIFRALRTIPVL 125
Query: 143 ---CEGIAKCCPNATVNLISNPV-------NSTVPIAA-----EVFKKAGTYDPKKLLGV 187
I + CP+A + +NP+ N PI V GT +
Sbjct: 126 LDIARDIEELCPDAWLLNYANPMAELTWALNRYTPIKTVGLCHGVQ---GTAE------- 175
Query: 188 TMLDVVRANTFVAEVLGLDPRDVDVPVVG 216
+A++LG P +VD V G
Sbjct: 176 ----------QLAKLLGEPPEEVDYQVAG 194
>gnl|CDD|184553 PRK14176, PRK14176, bifunctional 5,10-methylene-tetrahydrofolate
dehydrogenase/ 5,10-methylene-tetrahydrofolate
cyclohydrolase; Provisional.
Length = 287
Score = 31.7 bits (72), Expect = 0.53
Identities = 23/100 (23%), Positives = 39/100 (39%), Gaps = 29/100 (29%)
Query: 42 GFKVAILGAAGGIGQPLA-MLMKINPLVSVLHLYDVVNTPGVTADISHMDTGAVVRGFLG 100
G I+G + +G+P+A ML+ N VSV H++ T D+ A
Sbjct: 164 GKNAVIVGHSNVVGKPMAAMLLNRNATVSVCHVF--------TDDLKKYTLDA------- 208
Query: 101 QPQLENALTGMDLVIIPAGVPR--KPGMTRDDLFNINAGI 138
D++++ GV K M ++ + GI
Sbjct: 209 -----------DILVVATGVKHLIKADMVKEGAVIFDVGI 237
>gnl|CDD|216117 pfam00782, DSPc, Dual specificity phosphatase, catalytic domain.
Ser/Thr and Tyr protein phosphatases. The enzyme's
tertiary fold is highly similar to that of
tyrosine-specific phosphatases, except for a
"recognition" region.
Length = 131
Score = 29.6 bits (67), Expect = 1.1
Identities = 15/45 (33%), Positives = 23/45 (51%), Gaps = 1/45 (2%)
Query: 228 SQVKPPCSFTQEETEYLTNRIQNGGTEVVEAKAGAG-SATLSMAY 271
+ + E E++ + IQ GG +V +AG SATL +AY
Sbjct: 48 NHETNISKYLPEAVEFIDDAIQKGGKVLVHCQAGISRSATLIIAY 92
>gnl|CDD|172679 PRK14191, PRK14191, bifunctional 5,10-methylene-tetrahydrofolate
dehydrogenase/ 5,10-methylene-tetrahydrofolate
cyclohydrolase; Provisional.
Length = 285
Score = 29.3 bits (66), Expect = 2.6
Identities = 16/35 (45%), Positives = 21/35 (60%), Gaps = 1/35 (2%)
Query: 41 AGFKVAILGAAGGIGQPLAMLM-KINPLVSVLHLY 74
G V I+GA+ +G+PLAMLM VSV H+
Sbjct: 156 KGKDVVIIGASNIVGKPLAMLMLNAGASVSVCHIL 190
>gnl|CDD|179337 PRK01810, PRK01810, DNA polymerase IV; Validated.
Length = 407
Score = 29.6 bits (67), Expect = 2.6
Identities = 11/25 (44%), Positives = 16/25 (64%)
Query: 169 AAEVFKKAGTYDPKKLLGVTMLDVV 193
A+ +FK+ DP +LLGVT D+
Sbjct: 321 ASRLFKQHWNGDPVRLLGVTATDLE 345
>gnl|CDD|133448 cd01080, NAD_bind_m-THF_DH_Cyclohyd, NADP binding domain of
methylene-tetrahydrofolate
dehydrogenase/cyclohydrolase. NADP binding domain of
the Methylene-Tetrahydrofolate
Dehydrogenase/cyclohydrolase (m-THF DH/cyclohydrolase)
bifunctional enzyme. Tetrahydrofolate is a versatile
carrier of activated one-carbon units. The major
one-carbon folate donors are N-5
methyltetrahydrofolate, N5,N10-m-THF, and
N10-formayltetrahydrofolate. The oxidation of metabolic
intermediate m-THF to m-THF requires the enzyme m-THF
DH. In addition, most DHs also have an associated
cyclohydrolase activity which catalyzes its hydrolysis
to N10-formyltetrahydrofolate. m-THF DH is typically
found as part of a multifunctional protein in
eukaryotes. NADP-dependent m-THF DH in mammals, birds
and yeast are components of a trifunctional enzyme with
DH, cyclohydrolase, and synthetase activities. Certain
eukaryotic cells also contain homodimeric bifunctional
DH/cyclodrolase form. In bacteria, monofucntional DH,
as well as bifunctional m-THF m-THF DHm-THF
DHDH/cyclodrolase are found. In addition, yeast (S.
cerevisiae) also express an monofunctional DH. This
family contains the bifunctional DH/cyclohydrolase.
M-THF DH, like other amino acid DH-like NAD(P)-binding
domains, is a member of the Rossmann fold superfamily
which includes glutamate, leucine, and phenylalanine
DHs, m-THF DH, methylene-tetrahydromethanopterin DH,
m-THF DH/cyclohydrolase, Shikimate DH-like proteins,
malate oxidoreductases, and glutamyl tRNA reductase.
Amino acid DHs catalyze the deamination of amino acids
to keto acids with NAD(P)+ as a cofactor. The
NAD(P)-binding Rossmann fold superfamily includes a
wide variety of protein families including NAD(P)-
binding domains of alcohol DHs, tyrosine-dependent
oxidoreductases, glyceraldehyde-3-phosphate DH,
lactate/malate DHs, formate/glycerate DHs, siroheme
synthases, 6-phosphogluconate DH, amino acid DHs,
repressor rex, NAD-binding potassium channel domain,
CoA-binding, and ornithine cyclodeaminase-like domains.
Length = 168
Score = 28.3 bits (64), Expect = 3.7
Identities = 19/49 (38%), Positives = 27/49 (55%), Gaps = 4/49 (8%)
Query: 41 AGFKVAILGAAGGIGQPLA-MLMKINPLVSVLHLYDVVNTPGVT--ADI 86
AG KV ++G + +G+PLA +L+ N V+V H N T ADI
Sbjct: 43 AGKKVVVVGRSNIVGKPLAALLLNRNATVTVCHSK-TKNLKEHTKQADI 90
>gnl|CDD|216783 pfam01915, Glyco_hydro_3_C, Glycosyl hydrolase family 3 C-terminal
domain. This domain is involved in catalysis and may be
involved in binding beta-glucan. This domain is found
associated with pfam00933.
Length = 221
Score = 28.8 bits (65), Expect = 3.8
Identities = 16/88 (18%), Positives = 26/88 (29%), Gaps = 12/88 (13%)
Query: 201 EVLGLDPRDVDVPVVGGHAGVTILPLLSQVKPPCSFTQEETEY------LTNRIQNGGTE 254
+L L + + V+G +A S T + R N
Sbjct: 9 NLLPLSKKKRKIAVIGPNADDPPNGGGG-----WSGTGNPPYLVTPLDGIRARAGNATVV 63
Query: 255 VV-EAKAGAGSATLSMAYAAVKFADACL 281
V + ++ A AA K AD +
Sbjct: 64 VYGGSNLEDDDTGIAEAVAAAKDADVAI 91
>gnl|CDD|187567 cd05257, Arna_like_SDR_e, Arna decarboxylase_like, extended (e)
SDRs. Decarboxylase domain of ArnA. ArnA, is an enzyme
involved in the modification of outer membrane protein
lipid A of gram-negative bacteria. It is a bifunctional
enzyme that catalyzes the NAD-dependent decarboxylation
of UDP-glucuronic acid and
N-10-formyltetrahydrofolate-dependent formylation of
UDP-4-amino-4-deoxy-l-arabinose; its NAD-dependent
decaboxylating activity is in the C-terminal 360
residues. This subgroup belongs to the extended SDR
family, however the NAD binding motif is not a perfect
match and the upstream Asn of the canonical active site
tetrad is not conserved. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately 100
amino acids. Extended SDRs are a diverse collection of
proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 316
Score = 28.8 bits (65), Expect = 4.8
Identities = 19/74 (25%), Positives = 33/74 (44%), Gaps = 3/74 (4%)
Query: 44 KVAILGAAGGIGQPLA-MLMKINPLVSVLHLYDVVNTPGVTADISHMDTGAVVRGFLGQP 102
V + GA G IG L L++ V L +Y+ N+ G+ + H D + G +
Sbjct: 1 NVLVTGADGFIGSHLTERLLREGHEVRALDIYNSFNSWGLLDNAVH-DRFHFISGDVRDA 59
Query: 103 -QLENALTGMDLVI 115
++E + D+V
Sbjct: 60 SEVEYLVKKCDVVF 73
>gnl|CDD|202102 pfam02056, Glyco_hydro_4, Family 4 glycosyl hydrolase.
Length = 183
Score = 27.7 bits (62), Expect = 7.8
Identities = 42/196 (21%), Positives = 65/196 (33%), Gaps = 47/196 (23%)
Query: 44 KVAILGAAGGIGQPLAMLMKINPL----VSVLHLYDVVNTPGVTADISH------MDTGA 93
K+ I+G G P +L ++ L LYD+ D +D
Sbjct: 1 KIVIIGG-GSTITPKNLLGDLDHTEELPGRELALYDI---DEERLDAIQTACKKLVDEAG 56
Query: 94 VVRGFLGQPQLENALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRT------------ 141
F + ALT D VI V P D+ + G+V T
Sbjct: 57 PDIKFEKTTDRKEALTDADFVINAIRVGLLPARELDEKIPLRHGVVGTIQETVGPGGIFR 116
Query: 142 ----------LCEGIAKCCPNATVNLISNPVNSTVPIA--AEVFKKAGTYDPKKLLGVTM 189
+ + I + CP+A V +N T P A E + Y K +G+
Sbjct: 117 GLRTIPVFFDIAKDIEELCPDAWV------LNYTNPAAMVTEAVYR--RYPNIKAVGLCH 168
Query: 190 LDVVRANTFVAEVLGL 205
+ +A++LGL
Sbjct: 169 S-PIGIEERLAKILGL 183
>gnl|CDD|218565 pfam05346, DUF747, Eukaryotic membrane protein family. This family
is a family of eukaryotic membrane proteins. It was
previously annotated as including a putative receptor
for human cytomegalovirus gH but this has has since been
disputed. Analysis of the mouse Tapt1 protein
(transmembrane anterior posterior transformation 1) has
shown it to be involved in patterning of the vertebrate
axial skeleton.
Length = 320
Score = 28.1 bits (63), Expect = 8.2
Identities = 12/32 (37%), Positives = 16/32 (50%), Gaps = 3/32 (9%)
Query: 162 VNSTVPIAAEVFKKAGTYDPKKLLGVTMLDVV 193
N I + VFKK +D + L +T DVV
Sbjct: 130 SNQFAEIKSSVFKK---FDKESLFQITCADVV 158
>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 = 27.7 bits (62), Expect = 9.3
Identities = 25/79 (31%), Positives = 35/79 (44%), Gaps = 6/79 (7%)
Query: 44 KVAILGAAGGIGQPLAMLMKINPLVSVLHLYDVVNTPGVTADISHMDTGAVVRGFLGQPQ 103
KV I GA+G +GQ LA + + L L DVV +P + + + G L P
Sbjct: 2 KVLITGASGFVGQRLAERLLSDVPNERLILIDVV-SPKAPSGAPRVTQ---IAGDLAVPA 57
Query: 104 LENALT--GMDLVIIPAGV 120
L AL D+V A +
Sbjct: 58 LIEALANGRPDVVFHLAAI 76
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
0.319 0.136 0.392
Gapped
Lambda K H
0.267 0.0728 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 18,062,000
Number of extensions: 1784283
Number of successful extensions: 1911
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1850
Number of HSP's successfully gapped: 83
Length of query: 354
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 256
Effective length of database: 6,590,910
Effective search space: 1687272960
Effective search space used: 1687272960
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 59 (26.5 bits)