RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 025075
(258 letters)
>gnl|CDD|215058 PLN00106, PLN00106, malate dehydrogenase.
Length = 323
Score = 508 bits (1311), Expect = 0.0
Identities = 198/247 (80%), Positives = 211/247 (85%), Gaps = 2/247 (0%)
Query: 1 MEENSCLRQAKCRAKGGAAGFKVAILGAAGGIGQPLAMLMKINPLVSVLHLYDVVNTPGV 60
E S LR CRAKGGA GFKVA+LGAAGGIGQPL++LMK+NPLVS LHLYD+ NTPGV
Sbjct: 1 SMEASSLRA--CRAKGGAPGFKVAVLGAAGGIGQPLSLLMKMNPLVSELHLYDIANTPGV 58
Query: 61 TADISHMDTGAVVRGFLGQPQLENALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTL 120
AD+SH++T A VRGFLG QL +AL G DLVIIPAGVPRKPGMTRDDLFNINAGIV+TL
Sbjct: 59 AADVSHINTPAQVRGFLGDDQLGDALKGADLVIIPAGVPRKPGMTRDDLFNINAGIVKTL 118
Query: 121 CEGIAKCCPNATVNLISNPVNSTVPIAAEVFKKAGTYDPKKLLGVTMLDVVRANTFVAEV 180
CE +AK CPNA VN+ISNPVNSTVPIAAEV KKAG YDPKKL GVT LDVVRANTFVAE
Sbjct: 119 CEAVAKHCPNALVNIISNPVNSTVPIAAEVLKKAGVYDPKKLFGVTTLDVVRANTFVAEK 178
Query: 181 LGLDPRDVDVPVVGGHAGVTILPLLSQVKPPCSFTQEETEYLTNRIQNGGTEVVEAKAGA 240
GLDP DVDVPVVGGHAG+TILPLLSQ P SFT EE E LT RIQNGGTEVVEAKAGA
Sbjct: 179 KGLDPADVDVPVVGGHAGITILPLLSQATPKVSFTDEEIEALTKRIQNGGTEVVEAKAGA 238
Query: 241 GSATLSM 247
GSATLSM
Sbjct: 239 GSATLSM 245
>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 = 449 bits (1157), Expect = e-161
Identities = 168/227 (74%), Positives = 194/227 (85%)
Query: 21 FKVAILGAAGGIGQPLAMLMKINPLVSVLHLYDVVNTPGVTADISHMDTGAVVRGFLGQP 80
KVA+LGAAGGIGQPL++L+K+NPLVS L LYD+VNTPGV AD+SH++T A V G+LG
Sbjct: 1 VKVAVLGAAGGIGQPLSLLLKLNPLVSELALYDIVNTPGVAADLSHINTPAKVTGYLGPE 60
Query: 81 QLENALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAKCCPNATVNLISNPV 140
+L+ AL G D+V+IPAGVPRKPGMTRDDLFNINAGIVR L +AK CP A + +ISNPV
Sbjct: 61 ELKKALKGADVVVIPAGVPRKPGMTRDDLFNINAGIVRDLATAVAKACPKALILIISNPV 120
Query: 141 NSTVPIAAEVFKKAGTYDPKKLLGVTMLDVVRANTFVAEVLGLDPRDVDVPVVGGHAGVT 200
NSTVPIAAEV KKAG YDPK+L GVT LDVVRANTFVAE+LGLDP V+VPV+GGH+GVT
Sbjct: 121 NSTVPIAAEVLKKAGVYDPKRLFGVTTLDVVRANTFVAELLGLDPAKVNVPVIGGHSGVT 180
Query: 201 ILPLLSQVKPPCSFTQEETEYLTNRIQNGGTEVVEAKAGAGSATLSM 247
ILPLLSQ +PP +F QEE E LT+RIQ GG EVV+AKAGAGSATLSM
Sbjct: 181 ILPLLSQCQPPFTFDQEEIEALTHRIQFGGDEVVKAKAGAGSATLSM 227
>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 = 354 bits (911), Expect = e-124
Identities = 149/226 (65%), Positives = 181/226 (80%)
Query: 22 KVAILGAAGGIGQPLAMLMKINPLVSVLHLYDVVNTPGVTADISHMDTGAVVRGFLGQPQ 81
KVA+LGAAGGIGQPL++L+K+ P VS L LYD+ GV AD+SH+ T A V+GF G+
Sbjct: 1 KVAVLGAAGGIGQPLSLLLKLQPYVSELSLYDIAGAAGVAADLSHIPTAASVKGFSGEEG 60
Query: 82 LENALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAKCCPNATVNLISNPVN 141
LENAL G D+V+IPAGVPRKPGMTRDDLFN+NAGIV+ L +A+ CP A + +I+NPVN
Sbjct: 61 LENALKGADVVVIPAGVPRKPGMTRDDLFNVNAGIVKDLVAAVAESCPKAMILVITNPVN 120
Query: 142 STVPIAAEVFKKAGTYDPKKLLGVTMLDVVRANTFVAEVLGLDPRDVDVPVVGGHAGVTI 201
STVPIAAEV KK G YDP KL GVT LD+VRANTFVAE+ G DP +V+VPV+GGH+G TI
Sbjct: 121 STVPIAAEVLKKKGVYDPNKLFGVTTLDIVRANTFVAELKGKDPMEVNVPVIGGHSGETI 180
Query: 202 LPLLSQVKPPCSFTQEETEYLTNRIQNGGTEVVEAKAGAGSATLSM 247
+PL+SQ FT+++ E L +RIQN GTEVV+AKAGAGSATLSM
Sbjct: 181 IPLISQCPGKVLFTEDQLEALIHRIQNAGTEVVKAKAGAGSATLSM 226
>gnl|CDD|235340 PRK05086, PRK05086, malate dehydrogenase; Provisional.
Length = 312
Score = 338 bits (868), Expect = e-117
Identities = 144/228 (63%), Positives = 171/228 (75%), Gaps = 4/228 (1%)
Query: 22 KVAILGAAGGIGQPLAMLMKIN-PLVSVLHLYDVVN-TPGVTADISHMDTGAVVRGFLGQ 79
KVA+LGAAGGIGQ LA+L+K P S L LYD+ TPGV D+SH+ T ++GF G+
Sbjct: 2 KVAVLGAAGGIGQALALLLKTQLPAGSELSLYDIAPVTPGVAVDLSHIPTAVKIKGFSGE 61
Query: 80 PQLENALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAKCCPNATVNLISNP 139
AL G D+V+I AGV RKPGM R DLFN+NAGIV+ L E +AK CP A + +I+NP
Sbjct: 62 -DPTPALEGADVVLISAGVARKPGMDRSDLFNVNAGIVKNLVEKVAKTCPKACIGIITNP 120
Query: 140 VNSTVPIAAEVFKKAGTYDPKKLLGVTMLDVVRANTFVAEVLGLDPRDVDVPVVGGHAGV 199
VN+TV IAAEV KKAG YD KL GVT LDV+R+ TFVAE+ G P +V+VPV+GGH+GV
Sbjct: 121 VNTTVAIAAEVLKKAGVYDKNKLFGVTTLDVIRSETFVAELKGKQPGEVEVPVIGGHSGV 180
Query: 200 TILPLLSQVKPPCSFTQEETEYLTNRIQNGGTEVVEAKAGAGSATLSM 247
TILPLLSQV P SFT++E LT RIQN GTEVVEAKAG GSATLSM
Sbjct: 181 TILPLLSQV-PGVSFTEQEVADLTKRIQNAGTEVVEAKAGGGSATLSM 227
>gnl|CDD|240360 PTZ00325, PTZ00325, malate dehydrogenase; Provisional.
Length = 321
Score = 312 bits (801), Expect = e-107
Identities = 150/227 (66%), Positives = 174/227 (76%), Gaps = 2/227 (0%)
Query: 21 FKVAILGAAGGIGQPLAMLMKINPLVSVLHLYDVVNTPGVTADISHMDTGAVVRGFLGQP 80
FKVA+LGAAGGIGQPL++L+K NP VS L LYD+V PGV AD+SH+DT A V G+
Sbjct: 9 FKVAVLGAAGGIGQPLSLLLKQNPHVSELSLYDIVGAPGVAADLSHIDTPAKVTGYADGE 68
Query: 81 QLENALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAKCCPNATVNLISNPV 140
E AL G DLV+I AGVPRKPGMTRDDLFN NA IVR L +A P A V ++SNPV
Sbjct: 69 LWEKALRGADLVLICAGVPRKPGMTRDDLFNTNAPIVRDLVAAVASSAPKAIVGIVSNPV 128
Query: 141 NSTVPIAAEVFKKAGTYDPKKLLGVTMLDVVRANTFVAEVLGLDPRDVDVPVVGGHAGVT 200
NSTVPIAAE KKAG YDP+KL GVT LDVVRA FVAE LG++P DV+VPVVGGH+GVT
Sbjct: 129 NSTVPIAAETLKKAGVYDPRKLFGVTTLDVVRARKFVAEALGMNPYDVNVPVVGGHSGVT 188
Query: 201 ILPLLSQVKPPCSFTQEETEYLTNRIQNGGTEVVEAKAGAGSATLSM 247
I+PLLSQ S +E+ E +T+R+Q GG EVV+AK GAGSATLSM
Sbjct: 189 IVPLLSQT--GLSLPEEQVEQITHRVQVGGDEVVKAKEGAGSATLSM 233
>gnl|CDD|223117 COG0039, Mdh, Malate/lactate dehydrogenases [Energy production and
conversion].
Length = 313
Score = 205 bits (525), Expect = 2e-65
Identities = 92/236 (38%), Positives = 127/236 (53%), Gaps = 17/236 (7%)
Query: 22 KVAILGAAGGIGQPLAMLMKINPLVSVLHLYDVVN--TPGVTADISHMDTGAVVRGFLGQ 79
KVA++GA G +G LA L+ + L S L L D+ GV D+SH +
Sbjct: 2 KVAVIGA-GNVGSSLAFLLLLQGLGSELVLIDINEEKAEGVALDLSHAAAPLGSDVKITG 60
Query: 80 PQLENALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAKCCPNATVNLISNP 139
L G D+V+I AGVPRKPGMTR DL NA IV+ + + IAK P+A V +++NP
Sbjct: 61 DGDYEDLKGADIVVITAGVPRKPGMTRLDLLEKNAKIVKDIAKAIAKYAPDAIVLVVTNP 120
Query: 140 VNSTVPIAAEVFKKAGTYDPKKLLGVTMLDVVRANTFVAEVLGLDPRDVDVPVVGGHAGV 199
V+ IA + +G + + T+LD R TF+AE LG+ P+DV V+G H G
Sbjct: 121 VDILTYIAMKF---SGFPKNRVIGSGTVLDSARFRTFLAEKLGVSPKDVHAYVIGEH-GD 176
Query: 200 TILPLLSQV----KPPCSF----TQEETEYLTNRIQNGGTEVVEAKAGAGSATLSM 247
T++PL SQ KP T+E+ E L R++N G E++EAK GAG
Sbjct: 177 TMVPLWSQATVGGKPLEELLKEDTEEDLEELIERVRNAGAEIIEAK-GAG-TYYGP 230
>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 = 171 bits (435), Expect = 3e-54
Identities = 60/145 (41%), Positives = 80/145 (55%), Gaps = 6/145 (4%)
Query: 22 KVAILGAAGGIGQPLAMLMKINPLVSVLHLYDVV--NTPGVTADISHMDTGAVVRGFLGQ 79
KVA++GA GG+G LA + + L L L D+ GV D+SH T V G +G
Sbjct: 2 KVAVVGAGGGVGSSLAFALALQGLADELVLVDINKDKAEGVAMDLSHGSTFLSVPGIVGG 61
Query: 80 PQLENALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAKCCPNATVNLISNP 139
AL D+V+I AGVPRKPGMTR DL N NAGI + + IAK P+A V ++SNP
Sbjct: 62 DD-YEALKDADVVVITAGVPRKPGMTRLDLLNRNAGIFKDIVPAIAKSAPDAIVLVVSNP 120
Query: 140 VNSTVPIAAEVFKKAGTYDPKKLLG 164
V+ IA +V +G + +
Sbjct: 121 VDILTYIAWKV---SGLPPERVIGS 142
>gnl|CDD|180477 PRK06223, PRK06223, malate dehydrogenase; Reviewed.
Length = 307
Score = 140 bits (356), Expect = 3e-40
Identities = 83/233 (35%), Positives = 130/233 (55%), Gaps = 22/233 (9%)
Query: 22 KVAILGAAGGIGQPLAMLMKINPLVSVLHLYDVV-NTP-GVTADISHMDTGAVVRGFLGQ 79
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: 80 PQLEN---ALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAKCCPNATVNLI 136
N + G D+V+I AGVPRKPGM+RDDL INA I++ + EGI K P+A V ++
Sbjct: 59 ITGTNDYEDIAGSDVVVITAGVPRKPGMSRDDLLGINAKIMKDVAEGIKKYAPDAIVIVV 118
Query: 137 SNPVNSTVPIAAEVFKKAGTYDPKKLLGV-TMLDVVRANTFVAEVLGLDPRDVDVPVVGG 195
+NPV++ +A K + +++G+ +LD R TF+AE L + +DV V+GG
Sbjct: 119 TNPVDAMTYVA----LKESGFPKNRVIGMAGVLDSARFRTFIAEELNVSVKDVTAFVLGG 174
Query: 196 HAGVTILPLLSQ-----VKPPCSFTQEETEYLTNRIQNGGTEVVEAKAGAGSA 243
H G +++PL+ + ++E+ + + R + GG E+V GSA
Sbjct: 175 H-GDSMVPLVRYSTVGGIPLEDLLSKEKLDEIVERTRKGGAEIVGLL-KTGSA 225
>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 = 139 bits (352), Expect = 8e-40
Identities = 83/233 (35%), Positives = 122/233 (52%), Gaps = 24/233 (10%)
Query: 23 VAILGAAGGIGQPLAMLMKINPLVSVLHLYDVV-NTP-GVTADISHM----DTGAVVRGF 76
++I+GA G +G LA L+ + L V+ L D+V P G DIS + V G
Sbjct: 1 ISIIGA-GNVGATLAQLLALKELGDVV-LLDIVEGLPQGKALDISQAAPILGSDTKVTGT 58
Query: 77 LGQPQLENALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAKCCPNATVNLI 136
+ + D+V+I AG+PRKPGM+RDDL NA IV+ + E I K PNA V ++
Sbjct: 59 NDYEDIAGS----DVVVITAGIPRKPGMSRDDLLGTNAKIVKEVAENIKKYAPNAIVIVV 114
Query: 137 SNPVNSTVPIAAEVFKKAGTYDPKKLLGV-TMLDVVRANTFVAEVLGLDPRDVDVPVVGG 195
+NP++ V KA + +++G+ +LD R F+AE LG+ +DV V+GG
Sbjct: 115 TNPLDVMT----YVAYKASGFPRNRVIGMAGVLDSARFRYFIAEELGVSVKDVQAMVLGG 170
Query: 196 HAGVTILPLLSQV----KPPCSF-TQEETEYLTNRIQNGGTEVVEAKAGAGSA 243
H G T++PL P T+EE + + R +NGG E+V GSA
Sbjct: 171 H-GDTMVPLPRYSTVGGIPLTELITKEEIDEIVERTRNGGAEIVNLL-KTGSA 221
>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 = 130 bits (328), Expect = 1e-36
Identities = 63/192 (32%), Positives = 93/192 (48%), Gaps = 9/192 (4%)
Query: 23 VAILGAAGGIGQPLA--MLMKINPLVSVLHLYDVVN--TPGVTADISHMDTGAVVRGFLG 78
+A++GA G +G LA + L L LYD+ GV D+
Sbjct: 1 IAVIGAGGNVGPALAFGLADGSVLLAIELVLYDIDEEKLKGVAMDLQDAVEPLADIKVSI 60
Query: 79 QPQLENALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAKCCPNATVNLISN 138
A D+VII AGV RKPGM R DL N IV+ + + I K P+A + ++SN
Sbjct: 61 TDDPYEAFKDADVVIITAGVGRKPGMGRLDLLKRNVPIVKEIGDNIEKYSPDAWIIVVSN 120
Query: 139 PVNSTVPIAAEVFKKAGTYDPKKLLGVTMLDVVRANTFVAEVLGLDPRDVDVPVVGGHAG 198
PV+ I + + +K++G+ LD +R +AE LG+DP DV V ++G H G
Sbjct: 121 PVD----IITYLVWRYSGLPKEKVIGLGTLDPIRFRRILAEKLGVDPDDVKVYILGEHGG 176
Query: 199 VTILPLLSQVKP 210
+ +P S V+
Sbjct: 177 -SQVPDWSTVRI 187
>gnl|CDD|173409 PTZ00117, PTZ00117, malate dehydrogenase; Provisional.
Length = 319
Score = 115 bits (289), Expect = 2e-30
Identities = 78/239 (32%), Positives = 120/239 (50%), Gaps = 23/239 (9%)
Query: 22 KVAILGAAGGIGQPLAMLMKINPLVSVLHLYDVV-NTP-GVTADISH-MDTGAVVRGFLG 78
K++++GA G IG +A+L+ L V+ LYDV+ P G D+ H LG
Sbjct: 7 KISMIGA-GQIGSTVALLILQKNLGDVV-LYDVIKGVPQGKALDLKHFSTLVGSNINILG 64
Query: 79 QPQLENALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAKCCPNATVNLISN 138
E + D+V+I AGV RK MTR+DL IN I++++ E + K CPNA V ++N
Sbjct: 65 TNNYE-DIKDSDVVVITAGVQRKEEMTREDLLTINGKIMKSVAESVKKYCPNAFVICVTN 123
Query: 139 PVNSTVPIAAEVFKKAGTYDPKKLLGVT-MLDVVRANTFVAEVLGLDPRDVDVPVVGGHA 197
P++ +VF++ K+ G+ +LD R +AE LG+ P DV V+GGH
Sbjct: 124 PLD----CMVKVFQEKSGIPSNKICGMAGVLDSSRFRCNLAEKLGVSPGDVSAVVIGGH- 178
Query: 198 GVTILPLLSQVK----PPCSF------TQEETEYLTNRIQNGGTEVVEAKAGAGSATLS 246
G ++PL P F T++E + + +N G E+V+ GSA +
Sbjct: 179 GDLMVPLPRYCTVNGIPLSDFVKKGAITEKEINEIIKKTRNMGGEIVKL-LKKGSAFFA 236
>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 = 108 bits (273), Expect = 1e-29
Identities = 47/92 (51%), Positives = 56/92 (60%), Gaps = 12/92 (13%)
Query: 166 TMLDVVRANTFVAEVLGLDPRDVDVPVVGGHAG----------VTILPLLSQVKPPCSFT 215
T LD RA TF+AE G+DPR V+V V+G H+G VTI+PL+SQVK T
Sbjct: 1 TTLDTARARTFLAEKFGVDPRSVNVYVIGEHSGTQFPDWSHAKVTIIPLISQVKENLKDT 60
Query: 216 QEETEYLTNRIQNGGTEVVEAKAGAGSATLSM 247
E E L R+QN G EV+EAK AGS T SM
Sbjct: 61 DWELEELIERVQNAGYEVIEAK--AGSTTYSM 90
>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 = 109 bits (275), Expect = 1e-28
Identities = 72/235 (30%), Positives = 109/235 (46%), Gaps = 25/235 (10%)
Query: 23 VAILGAAGGIGQPLAMLMKINPLVSVLHLYDVVN--TPGVTADISHM----DTGAVVRGF 76
+ I+GA G +G +A + L S L L DV G D+SH TG +VRG
Sbjct: 1 ITIIGA-GNVGAAVAFALIAKGLASELVLVDVNEEKAKGDALDLSHASAFLATGTIVRG- 58
Query: 77 LGQPQLENALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAKCCPNATVNLI 136
D+V+I AG PRKPG TR DL N NA I+R++ + K P+A + ++
Sbjct: 59 ----GDYADAADADIVVITAGAPRKPGETRLDLINRNAPILRSVITNLKKYGPDAIILVV 114
Query: 137 SNPVNSTVPIAAEVFKKAGTYDPKKLLGV-TMLDVVRANTFVAEVLGLDPRDVDVPVVGG 195
SNPV+ I V +K +++G T+LD R + +AE L +DP+ V V+G
Sbjct: 115 SNPVD----ILTYVAQKLSGLPKNRVIGSGTLLDSARFRSLLAEKLDVDPQSVHAYVLGE 170
Query: 196 HAGVTILPLLSQVK-------PPCSFTQEETEYLTNRIQNGGTEVVEAKAGAGSA 243
H G + + S FT+ + E + ++ G E++ K
Sbjct: 171 H-GDSQVVAWSTATVGGLPLEELAPFTKLDLEAIEEEVRTSGYEIIRLKGATNYG 224
>gnl|CDD|173376 PTZ00082, PTZ00082, L-lactate dehydrogenase; Provisional.
Length = 321
Score = 107 bits (269), Expect = 1e-27
Identities = 86/241 (35%), Positives = 133/241 (55%), Gaps = 28/241 (11%)
Query: 22 KVAILGAAGGIGQPLAMLMKINPLVSVLHLYDVV-NTP-GVTADISHMDTGAVVR-GFLG 78
K++++G+ G IG +A L+ + L V+ L+D+V N P G DISH + A +G
Sbjct: 8 KISLIGS-GNIGGVMAYLIVLKNLGDVV-LFDIVKNIPQGKALDISHSNVIAGSNSKVIG 65
Query: 79 QPQLENALTGMDLVIIPAGVPRKPGMT-----RDDLFNINAGIVRTLCEGIAKCCPNATV 133
E+ + G D+VI+ AG+ ++PG + RDDL +NA I+ + EGI K CPNA V
Sbjct: 66 TNNYED-IAGSDVVIVTAGLTKRPGKSDKEWNRDDLLPLNAKIMDEVAEGIKKYCPNAFV 124
Query: 134 NLISNPVNSTVPIAAEVFKKAGTYDPKKLLGVT-MLDVVRANTFVAEVLGLDPRDVDVPV 192
+I+NP++ V ++ ++ K+ G+ +LD R T++AE LG++PRDV V
Sbjct: 125 IVITNPLDVMV----KLLQEHSGLPKNKVCGMAGVLDSSRLRTYIAEKLGVNPRDVHASV 180
Query: 193 VGGHAGVTILPLLSQVK----PPCSF------TQEETEYLTNRIQNGGTEVVEAKAGAGS 242
+G H G ++PL V P F TQEE + + R +N G E+V+ G GS
Sbjct: 181 IGAH-GDKMVPLPRYVTVGGIPLSEFIKKGLITQEEIDEIVERTRNTGKEIVDL-LGTGS 238
Query: 243 A 243
A
Sbjct: 239 A 239
>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 = 97.5 bits (243), Expect = 6e-24
Identities = 66/243 (27%), Positives = 115/243 (47%), Gaps = 43/243 (17%)
Query: 22 KVAILGAAGGIGQPLAMLMKINPLVSVLHL-----------------YDVVNTPGVTADI 64
KV+I+GA+G +G A+L+ +V ++L YD + G+ A+I
Sbjct: 2 KVSIIGASGRVGSATALLLAKEDVVKEINLISRPKSLEKLKGLRLDIYDALAAAGIDAEI 61
Query: 65 SHMDTGAVVRGFLGQPQLENALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGI 124
+ V G D+VII AGVPRK GM+R DL NA IV+ + I
Sbjct: 62 KISSDLSDV-------------AGSDIVIITAGVPRKEGMSRLDLAKKNAKIVKKYAKQI 108
Query: 125 AKCCPNATVNLISNPVNSTVPIAAEVFKKAGTYDPKKLLGV-TMLDVVRANTFVAEVLGL 183
A+ P+ + +++NPV+ A K++G +D ++ G+ T LD +R +A+ +
Sbjct: 109 AEFAPDTKILVVTNPVDVMTYKA---LKESG-FDKNRVFGLGTHLDSLRFKVAIAKHFNV 164
Query: 184 DPRDVDVPVVGGHAGVTILPLLSQ-------VKPPCSFTQEETEYLTNRIQNGGTEVVEA 236
+V ++G H G +++PL+S +K + + E + ++N G ++
Sbjct: 165 HISEVHTRIIGEH-GDSMVPLISSTSIGGIPIKRFPEYKDFDVEKIVETVKNAGQNIISL 223
Query: 237 KAG 239
K G
Sbjct: 224 KGG 226
>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 = 89.9 bits (223), Expect = 3e-21
Identities = 69/237 (29%), Positives = 115/237 (48%), Gaps = 30/237 (12%)
Query: 22 KVAILGAAGGIGQPLAMLMKINPLVSVLHLYDVVNTPGVTADISHMDTGAVVRGF----L 77
K++++GA G +G A + L ++ L DVV + + V GF
Sbjct: 3 KISVIGA-GFVGATTAFRLAEKELADLV-LLDVVEGIPQGKALDMYEASPV-GGFDTKVT 59
Query: 78 GQPQLENALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAKCCPNATVNLIS 137
G + D+V+I AG+PRKPGM+R+DL ++NAGIVR + I + PN + ++S
Sbjct: 60 GTNNYADT-ANSDIVVITAGLPRKPGMSREDLLSMNAGIVREVTGRIMEHSPNPIIVVVS 118
Query: 138 NPVNSTVPIAAEVFKKAGTYDPKKLLGVT-MLDVVRANTFVAEVLGLDPRDVDVPVVGGH 196
NP+++ +A + + ++++G +LD R TF+A LG+ +DV V+GGH
Sbjct: 119 NPLDAMTYVAWQK----SGFPKERVIGQAGVLDSARFRTFIAMELGVSVQDVTACVLGGH 174
Query: 197 AGVTILPL----------LSQVKPPCSFTQEETEYLTNRIQNGGTEVVEAKAGAGSA 243
G ++PL ++ + E + R + GG E+V GSA
Sbjct: 175 -GDAMVPLVRYSTVAGIPVADLISA-----ERIAEIVERTRKGGGEIVNL-LKQGSA 224
>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 = 81.4 bits (202), Expect = 4e-18
Identities = 47/160 (29%), Positives = 77/160 (48%), Gaps = 16/160 (10%)
Query: 89 MDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAKCCPNATVNLISNPVNSTVPIAA 148
D+V+I AG P+KPG TR DL NA I++++ I + + SNPV+ +
Sbjct: 69 ADIVVITAGAPQKPGETRLDLLEKNAKIMKSIVPKIKASGFDGIFLVASNPVD----VIT 124
Query: 149 EVFKKAGTYDPKKLLGV-TMLDVVRANTFVAEVLGLDPRDVDVPVVGGH--------AGV 199
V +K +++G T LD R +AE L +DPR V V+G H + V
Sbjct: 125 YVVQKLSGLPKNRVIGTGTSLDTARLRRALAEKLNVDPRSVHAYVLGEHGDSQFVAWSTV 184
Query: 200 TIL--PLLSQVKPPCSFTQEETEYLTNRIQNGGTEVVEAK 237
T+ PLL +K ++ + + + ++ G E++ K
Sbjct: 185 TVGGKPLLDLLKEGK-LSELDLDEIEEDVRKAGYEIINGK 223
>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 = 80.3 bits (199), Expect = 9e-18
Identities = 45/163 (27%), Positives = 78/163 (47%), Gaps = 15/163 (9%)
Query: 86 LTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAKCCPNATVNLISNPVNSTVP 145
DLV+I AG P+KPG TR +L N I++++ + K + + +NPV+
Sbjct: 62 CKDADLVVITAGAPQKPGETRLELVGRNVRIMKSIVPEVVKSGFDGIFLVATNPVD---- 117
Query: 146 IAAEVFKKAGTYDPKKLLGV-TMLDVVRANTFVAEVLGLDPRDVDVPVVGGH-------- 196
I V K + +++G T+LD R +AE LG+DP+ V ++G H
Sbjct: 118 ILTYVAWKLSGFPKNRVIGSGTVLDTARLRYLLAEKLGVDPQSVHAYIIGEHGDSEVPVW 177
Query: 197 --AGVTILPLLSQVKPPCSFTQEETEYLTNRIQNGGTEVVEAK 237
A + +PLL +K + T + E + +++ E++ K
Sbjct: 178 SSATIGGVPLLDYLKAKGTETDLDLEEIEKEVRDAAYEIINRK 220
>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 = 79.6 bits (197), Expect = 2e-17
Identities = 68/258 (26%), Positives = 102/258 (39%), Gaps = 48/258 (18%)
Query: 22 KVAILGAAGGIGQPLA-------MLMKINPLVSVLHLYDVVNTPGVTADISHMDTGAV-- 72
V I GAAG IG L + P++ LHL D+ + ++ +
Sbjct: 2 HVLITGAAGQIGYNLLFLIASGELFGDDQPVI--LHLLDI------PPAMKALEGVVMEL 53
Query: 73 -------VRGFLGQPQLENALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIA 125
++G + E A +D+ I+ PRKPGM R DL NA I + E +
Sbjct: 54 QDCAFPLLKGVVITTDPEEAFKDVDVAILVGAFPRKPGMERADLLRKNAKIFKEQGEALN 113
Query: 126 KCC-PNATVNLISNPVNSTVPIAAEVFKKAGTYDPKKLLGVTMLDVVRANTFVAEVLGLD 184
K P V ++ NP N+ IA K A PK +T LD RA VA LG+
Sbjct: 114 KVAKPTVKVLVVGNPANTNALIAL---KNAPNLPPKNFTALTRLDHNRAKAQVARKLGVR 170
Query: 185 PRDV-DVPVVGGHAGVTILPLLSQ-------------VKPPCSFTQEETEYLTNRIQNGG 230
DV +V + G H+ T +P LS + +E +Q G
Sbjct: 171 VSDVKNVIIWGNHSN-TQVPDLSNAVVYGPGGTEWVLDLLDEEWLNDE---FVKTVQKRG 226
Query: 231 TEVVEAK--AGAGSATLS 246
+++ + + A SA +
Sbjct: 227 AAIIKKRGASSAASAAKA 244
>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 = 74.4 bits (184), Expect = 1e-15
Identities = 58/181 (32%), Positives = 88/181 (48%), Gaps = 16/181 (8%)
Query: 22 KVAILGAAGGIGQPLAMLMKINPLVSVLHLYDVVNTPGVTA---DISH-MDTGAVVRGFL 77
KVAI+GA G +G A + + L S + L D+ N D++H VR +
Sbjct: 2 KVAIVGA-GFVGSTTAYALLLRGLASEIVLVDI-NKAKAEGEAMDLAHGTPFVKPVRIYA 59
Query: 78 GQPQ-LENALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAKCCPNATVNLI 136
G + A D+V+I AG +KPG TR DL N I + + I K P+A + ++
Sbjct: 60 GDYADCKGA----DVVVITAGANQKPGETRLDLLKRNVAIFKEIIPQILKYAPDAILLVV 115
Query: 137 SNPVNSTVPIAAEVFKKAGTYDPKKLLGV-TMLDVVRANTFVAEVLGLDPRDVDVPVVGG 195
+NPV+ + V K P +++G T+LD R + E LG+DPR V ++G
Sbjct: 116 TNPVD----VLTYVAYKLSGLPPNRVIGSGTVLDTARFRYLLGEHLGVDPRSVHAYIIGE 171
Query: 196 H 196
H
Sbjct: 172 H 172
>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 = 72.7 bits (179), Expect = 6e-15
Identities = 68/242 (28%), Positives = 105/242 (43%), Gaps = 28/242 (11%)
Query: 22 KVAILGAAGGIGQPLA-------MLMKINPLVSVLHLYDVVNT----PGVTADISHMDTG 70
+VA+ GAAG IG L + K P+V LHL D+ GV ++ D
Sbjct: 5 RVAVTGAAGQIGYSLLFRIASGELFGKDQPVV--LHLLDIPPAMKALEGVAMEL--EDCA 60
Query: 71 -AVVRGFLGQPQLENALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAKCC- 128
++ G + E A +D ++ PRKPGM R DL + N I + + + K
Sbjct: 61 FPLLAGVVATTDPEEAFKDVDAALLVGAFPRKPGMERADLLSKNGKIFKEQGKALNKVAK 120
Query: 129 PNATVNLISNPVNSTVPIAAEVFKKAGTYDPKKLLGVTMLDVVRANTFVAEVLGLDPRDV 188
+ V ++ NP N+ IA+ K A PK +T LD RA +A G+ DV
Sbjct: 121 KDVKVLVVGNPANTNALIAS---KNAPDIPPKNFSAMTRLDHNRAKYQLAAKAGVPVSDV 177
Query: 189 DVPVVGGHAGVTILPLLSQVK---PPCSFTQEETEYLTN----RIQNGGTEVVEAKAGAG 241
++ G+ T +P + P ++ ++L +Q G V+EA+ GA
Sbjct: 178 KNVIIWGNHSNTQVPDFTHATVDGRPVKEVIKDDKWLEGEFIPTVQQRGAAVIEAR-GAS 236
Query: 242 SA 243
SA
Sbjct: 237 SA 238
>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 = 72.4 bits (178), Expect = 8e-15
Identities = 47/127 (37%), Positives = 64/127 (50%), Gaps = 8/127 (6%)
Query: 85 ALTGMDLVIIPAGVPRKPGMT--RDDLFNINAGIVRTLCEGIAKCCPNATVNLISNPVNS 142
D+++I AG PG T R DL NA I+R + I K A + LI+NP++
Sbjct: 65 DCADADIIVITAGPSIDPGNTDDRLDLAQTNAKIIREIMGNITKVTKEAVIILITNPLDI 124
Query: 143 TVPIAAEVFKKAGTYDPKKLLGV-TMLDVVRANTFVAEVLGLDPRDVDVPVVGGHAGVTI 201
V IAA F Y K++G TMLD R VA+ G+DP++V V+G H G
Sbjct: 125 AVYIAATEFD----YPANKVIGTGTMLDTARLRRIVADKYGVDPKNVTGYVLGEH-GSHA 179
Query: 202 LPLLSQV 208
P+ S V
Sbjct: 180 FPVWSLV 186
>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 = 65.3 bits (159), Expect = 2e-12
Identities = 62/239 (25%), Positives = 96/239 (40%), Gaps = 29/239 (12%)
Query: 22 KVAILGAAGGIGQPLA-------MLMKINPLVSVLHLYDVVNTPGVTADISH--MDTG-A 71
+V + GAAG IG L ML K P++ LHL D+ V + MD
Sbjct: 1 RVVVTGAAGQIGYALLPMIARGRMLGKDQPII--LHLLDIPPAMKVLEGVVMELMDCAFP 58
Query: 72 VVRGFLGQPQLENALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAK-CCPN 130
++ G + A T +D+ I+ PRK GM R DL + N I + + K +
Sbjct: 59 LLDGVVPTHDPAVAFTDVDVAILVGAFPRKEGMERRDLLSKNVKIFKEQGRALDKLAKKD 118
Query: 131 ATVNLISNPVNSTVPIAAEVFKKAGTYDPKKLLGVTMLDVVRANTFVAEVLGLDPRDV-D 189
V ++ NP N+ + + A + PK +T LD RA VAE G+ DV +
Sbjct: 119 CKVLVVGNPANTNALVLSNY---APSIPPKNFSALTRLDHNRALAQVAERAGVPVSDVKN 175
Query: 190 VPVVGGHAGVTILPLLSQVKPPCSFTQEETEYLTNR-----------IQNGGTEVVEAK 237
V + G H+ T P ++ Q+ +Q G ++ A+
Sbjct: 176 VIIWGNHSS-TQYPDVNHATVTKGGKQKPVREAIKDDAYLDGEFITTVQQRGAAIIRAR 233
>gnl|CDD|178836 PRK00066, ldh, L-lactate dehydrogenase; Reviewed.
Length = 315
Score = 64.5 bits (158), Expect = 4e-12
Identities = 45/164 (27%), Positives = 77/164 (46%), Gaps = 16/164 (9%)
Query: 88 GMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAKCCPNATVNLISNPVNSTVPIA 147
DLV+I AG P+KPG TR DL N I +++ + + + SNPV+ I
Sbjct: 73 DADLVVITAGAPQKPGETRLDLVEKNLKIFKSIVGEVMASGFDGIFLVASNPVD----IL 128
Query: 148 AEVFKKAGTYDPKKLLGV-TMLDVVRANTFVAEVLGLDPRDVDVPVVGGH---------- 196
K + ++++G T LD R ++E L +DPR V ++G H
Sbjct: 129 TYATWKLSGFPKERVIGSGTSLDSARFRYMLSEKLDVDPRSVHAYIIGEHGDTEFPVWSH 188
Query: 197 AGVTILPLLSQVKPPCSFTQEETEYLTNRIQNGGTEVVEAKAGA 240
A V +PL ++ + +E+ + + +++ E++E K GA
Sbjct: 189 ANVAGVPLEEYLEENEQYDEEDLDEIFENVRDAAYEIIEKK-GA 231
>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 = 61.9 bits (151), Expect = 3e-11
Identities = 50/187 (26%), Positives = 79/187 (42%), Gaps = 17/187 (9%)
Query: 22 KVAILGAAGGIGQPLA-------MLMKINPLVSVLHLYDVVNTPGVTADIS-HMDTGA-- 71
+V + GAAG I L + P++ LHL D+ + + A
Sbjct: 4 RVLVTGAAGQIAYSLLPMIAKGDVFGPDQPVI--LHLLDIPPALKALEGVVMELQDCAFP 61
Query: 72 VVRGFLGQPQLENALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAKCC-PN 130
+++ + E A +D+ I+ +PRK GM R DL N I + E + K N
Sbjct: 62 LLKSVVATTDPEEAFKDVDVAILVGAMPRKEGMERKDLLKANVKIFKEQGEALDKYAKKN 121
Query: 131 ATVNLISNPVNSTVPIAAEVFKKAGTYDPKKLLGVTMLDVVRANTFVAEVLGLDPRDV-D 189
V ++ NP N+ I K A + + +T LD RA + +A LG+ DV +
Sbjct: 122 VKVLVVGNPANTNALILL---KYAPSIPKENFTALTRLDHNRAKSQIALKLGVPVSDVKN 178
Query: 190 VPVVGGH 196
V + G H
Sbjct: 179 VIIWGNH 185
>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 = 60.7 bits (148), Expect = 8e-11
Identities = 57/200 (28%), Positives = 89/200 (44%), Gaps = 22/200 (11%)
Query: 20 GFKVAILGA-AGGIGQPLAMLMKINPLVSVLHLYDVVN--TPGVTADISHMDTGAVVRGF 76
KV ++G G+ +++L K L L L DVV G D+ H G+ F
Sbjct: 3 RNKVTVVGVGQVGMACAISILAK--GLADELVLVDVVEDKLKGEAMDLQH---GSA---F 54
Query: 77 LGQPQLE-----NALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAKCCPNA 131
L P++E + +VI+ AG + G +R DL N I + + + K PNA
Sbjct: 55 LKNPKIEADKDYSVTANSKVVIVTAGARQNEGESRLDLVQRNVDIFKGIIPKLVKYSPNA 114
Query: 132 TVNLISNPVNSTVPIAAEVFKKAGTYDPKKLLGV-TMLDVVRANTFVAEVLGLDPRDVDV 190
+ ++SNPV+ I V K +++G LD R +AE LG+ P V
Sbjct: 115 ILLVVSNPVD----IMTYVAWKLSGLPKHRVIGSGCNLDSARFRYLIAERLGVAPSSVHG 170
Query: 191 PVVGGHAGVTILPLLSQVKP 210
++G H G + +P+ S V
Sbjct: 171 WIIGEH-GDSSVPVWSGVNV 189
>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 = 1e-10
Identities = 37/135 (27%), Positives = 59/135 (43%), Gaps = 4/135 (2%)
Query: 75 GFLGQPQLENALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAKCC-PNATV 133
G + +LE A +D + A VP KPG R DL N I + E +++ P V
Sbjct: 47 GTIVTTKLEEAFKDIDCAFLVASVPLKPGEVRADLLTKNTPIFKATGEALSEYAKPTVKV 106
Query: 134 NLISNPVNSTVPIAAEVFKKAGTYDPKKLLGVTMLDVVRANTFVAEVLGLDPRDVDVPVV 193
+I NPVN+ +A A + + MLD RA + +A L + + VV
Sbjct: 107 LVIGNPVNTNCLVA---MLHAPKLSAENFSSLCMLDHNRAVSRIASKLKVPVDHIYHVVV 163
Query: 194 GGHAGVTILPLLSQV 208
G+ +++ L+
Sbjct: 164 WGNHAESMVADLTHA 178
>gnl|CDD|178212 PLN02602, PLN02602, lactate dehydrogenase.
Length = 350
Score = 57.5 bits (139), Expect = 1e-09
Identities = 62/238 (26%), Positives = 108/238 (45%), Gaps = 34/238 (14%)
Query: 22 KVAILGAAGGIGQPLAMLMKINPLVSVLHLYDVV--NTPGVTADISHMDTGAVVRGFLGQ 79
KV+++G G +G +A + L L L DV G D+ H FL +
Sbjct: 39 KVSVVGV-GNVGMAIAQTILTQDLADELALVDVNPDKLRGEMLDLQH------AAAFLPR 91
Query: 80 PQL----ENALT-GMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAKCCPNATVN 134
++ + A+T G DL I+ AG + PG +R +L N + R + +AK P+ +
Sbjct: 92 TKILASTDYAVTAGSDLCIVTAGARQIPGESRLNLLQRNVALFRKIIPELAKYSPDTILL 151
Query: 135 LISNPVNSTVPIAAEVFKKAGTYDPKKLLGV-TMLDVVRANTFVAEVLGLDPRDVDVPVV 193
++SNPV+ +A +K +G + +++G T LD R +A+ L ++ +DV +V
Sbjct: 152 IVSNPVDVLTYVA---WKLSG-FPANRVIGSGTNLDSSRFRFLIADHLDVNAQDVQAYIV 207
Query: 194 GGH-------------AGVTILPLLSQVKPPCSFTQEETEYLTNRIQNGGTEVVEAKA 238
G H GV +L L K ++ +E E + + + EV++ K
Sbjct: 208 GEHGDSSVALWSSVSVGGVPVLSFLE--KQQIAYEKETLEEIHRAVVDSAYEVIKLKG 263
>gnl|CDD|177744 PLN00135, PLN00135, malate dehydrogenase.
Length = 309
Score = 52.5 bits (126), Expect = 5e-08
Identities = 46/175 (26%), Positives = 83/175 (47%), Gaps = 17/175 (9%)
Query: 27 GAAGGIGQPLAM-LMKINPLVSVLHLYDVVNTPGVTADISHMDTG-AVVRGFLGQPQLEN 84
G G QP+ + ++ I P L+ GV ++ +D +++G + +
Sbjct: 5 GVMLGPDQPVILHMLDIPPAAEALN--------GVKMEL--IDAAFPLLKGVVATTDVVE 54
Query: 85 ALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAKCC-PNATVNLISNPVNST 143
A G+++ ++ G PRK GM R D+ + N I ++ + K P+ V +++NP N+
Sbjct: 55 ACKGVNIAVMVGGFPRKEGMERKDVMSKNVSIYKSQASALEKHAAPDCKVLVVANPANTN 114
Query: 144 VPIAAEVFKKAGTYDPKKLLGVTMLDVVRANTFVAEVLGLDPRDV-DVPVVGGHA 197
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 = 50.7 bits (122), Expect = 2e-07
Identities = 59/243 (24%), Positives = 96/243 (39%), Gaps = 30/243 (12%)
Query: 22 KVAILGAAGGIGQPL-------AMLMKINPLVSVLHLYDVVNT----PGVTADISHMDTG 70
+VA+ GAAG IG L M P++ L L ++ GV ++ +
Sbjct: 4 RVAVTGAAGQIGYSLLFRIASGEMFGPDQPVI--LQLLELPQALKALEGVAMEL---EDC 58
Query: 71 A--VVRGFLGQPQLENALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAK-C 127
A ++ + A D ++ PR PGM R DL N I + +
Sbjct: 59 AFPLLAEIVITDDPNVAFKDADWALLVGAKPRGPGMERADLLKANGKIFTAQGKALNDVA 118
Query: 128 CPNATVNLISNPVNSTVPIAAEVFKKAGTYDPKKLLGVTMLDVVRANTFVAEVLGLDPRD 187
+ V ++ NP N+ IA K A P +T LD RA + +A+ G+ D
Sbjct: 119 SRDVKVLVVGNPCNTNALIAM---KNAPDIPPDNFTAMTRLDHNRAKSQLAKKAGVPVTD 175
Query: 188 VDVPVVGGHAGVTILPLLSQVK---PPCSFTQEETEYLTN----RIQNGGTEVVEAKAGA 240
V V+ G+ T P + P + + +L + +Q G +++A+ GA
Sbjct: 176 VKNMVIWGNHSPTQYPDFTNATIGGKPAAEVINDRAWLEDEFIPTVQKRGAAIIKAR-GA 234
Query: 241 GSA 243
SA
Sbjct: 235 SSA 237
>gnl|CDD|235468 PRK05442, PRK05442, malate dehydrogenase; Provisional.
Length = 326
Score = 43.6 bits (104), Expect = 4e-05
Identities = 63/243 (25%), Positives = 100/243 (41%), Gaps = 30/243 (12%)
Query: 22 KVAILGAAGGIGQPL-------AMLMKINPLVSVLHLYDVVNTPGVTA---DISHMDTGA 71
+VA+ GAAG IG L ML K P++ L L ++ P + A + +D A
Sbjct: 6 RVAVTGAAGQIGYSLLFRIASGDMLGKDQPVI--LQLLEI--PPALKALEGVVMELDDCA 61
Query: 72 --VVRGFLGQPQLENALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAKCC- 128
++ G + A D+ ++ PR PGM R DL N I + + +
Sbjct: 62 FPLLAGVVITDDPNVAFKDADVALLVGARPRGPGMERKDLLEANGAIFTAQGKALNEVAA 121
Query: 129 PNATVNLISNPVNSTVPIAAEVFKKAGTYDPKKLLGVTMLDVVRANTFVAEVLGLDPRDV 188
+ V ++ NP N+ IA K A + +T LD RA + +A G+ D+
Sbjct: 122 RDVKVLVVGNPANTNALIAM---KNAPDLPAENFTAMTRLDHNRALSQLAAKAGVPVADI 178
Query: 189 DVPVVGGHAGVTILPLLSQV----KPPCSFTQEETEYLTN----RIQNGGTEVVEAKAGA 240
V G+ T P KP ++ +L + +Q G ++EA+ GA
Sbjct: 179 KKMTVWGNHSATQYPDFRHATIDGKPAAEVINDQ-AWLEDTFIPTVQKRGAAIIEAR-GA 236
Query: 241 GSA 243
SA
Sbjct: 237 SSA 239
>gnl|CDD|215060 PLN00112, PLN00112, malate dehydrogenase (NADP); Provisional.
Length = 444
Score = 39.4 bits (92), Expect = 0.001
Identities = 28/79 (35%), Positives = 35/79 (44%), Gaps = 10/79 (12%)
Query: 99 PRKPGMTRDDLFNINAGIV----RTLCEGIAKCCPNATVNLISNPVNSTVPIAAEVFKKA 154
PR PGM R DL +IN I + L E +A N V ++ NP N+ I K A
Sbjct: 187 PRGPGMERADLLDINGQIFAEQGKALNE-VAS--RNVKVIVVGNPCNTNALIC---LKNA 240
Query: 155 GTYDPKKLLGVTMLDVVRA 173
K +T LD RA
Sbjct: 241 PNIPAKNFHALTRLDENRA 259
>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 = 35.4 bits (82), Expect = 0.017
Identities = 23/93 (24%), Positives = 42/93 (45%), Gaps = 4/93 (4%)
Query: 24 AILGAAGGIGQPLA-MLMKINPLVSVLHLYDVVNTPGVTADISHMDTGAVVRG-FLGQPQ 81
+ G G +G+ + +L++ L V ++D+ +P + D S + + G +
Sbjct: 1 LVTGGGGFLGRHIVRLLLREGELQEV-RVFDLRFSPELLEDFSKLQVITYIEGDVTDKQD 59
Query: 82 LENALTGMDLVIIPAGVPRKPGM-TRDDLFNIN 113
L AL G D+VI A + G RD + +N
Sbjct: 60 LRRALQGSDVVIHTAAIIDVFGKAYRDTIMKVN 92
>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 = 34.6 bits (79), Expect = 0.044
Identities = 29/88 (32%), Positives = 38/88 (43%), Gaps = 10/88 (11%)
Query: 90 DLVIIPAGVPRKPGMTRDDLFNINAGIV----RTLCEGIAKCCPNATVNLISNPVNSTVP 145
D ++ PR PGM R DL +IN I + L +K C V ++ NP N+
Sbjct: 122 DWALLIGAKPRGPGMERADLLDINGQIFADQGKALNAVASKNC---KVLVVGNPCNTNAL 178
Query: 146 IAAEVFKKAGTYDPKKLLGVTMLDVVRA 173
IA K A K +T LD RA
Sbjct: 179 IA---MKNAPNIPRKNFHALTRLDENRA 203
>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 = 0.047
Identities = 53/219 (24%), Positives = 73/219 (33%), Gaps = 68/219 (31%)
Query: 20 GFKVAILGAAGGIGQP--LAMLMKINPLVSV--LHLYDV---------------VNTPGV 60
FK+ I+G G P L + + V L LYD+ V G
Sbjct: 3 KFKIVIIGG-GSTYTPKLLLGDLARTEELPVRELALYDIDEERLKIIAILAKKLVEEAGA 61
Query: 61 TADIS-HMDTGAVVRGFLGQPQLENALTGMDLVIIPA------------GVPRKPGMTRD 107
+ D AL G D VI +P K G+
Sbjct: 62 PVKVEATTD-------------RREALEGADFVITQIRVGGLEAREKDERIPLKHGLYGQ 108
Query: 108 DLFNINAGIVRTL---------CEGIAKCCPNATVNLISNPVNSTVPIAAEVFKKAGTYD 158
+ N GI L + + K CPNA + +NP AA V +
Sbjct: 109 E-TNGPGGIFYGLRTIPVILDIAKDMEKVCPNAWMLNYTNP-------AAIVTEAVRRLY 160
Query: 159 PK-KLLGVTMLDVVRANTF-VAEVLGLDPR-DVDVPVVG 194
PK K++G+ +AEVLGL+PR D+ V G
Sbjct: 161 PKIKIVGLC--HGPIGIAMELAEVLGLEPREDLRYRVAG 197
>gnl|CDD|172654 PRK14166, PRK14166, bifunctional 5,10-methylene-tetrahydrofolate
dehydrogenase/ 5,10-methylene-tetrahydrofolate
cyclohydrolase; Provisional.
Length = 282
Score = 33.1 bits (75), Expect = 0.11
Identities = 26/102 (25%), Positives = 42/102 (41%), Gaps = 29/102 (28%)
Query: 20 GFKVAILGAAGGIGQPLA-MLMKINPLVSVLHLYDVVNTPGVTADISHMDTGAVVRGFLG 78
G I+GA+ +G+P+A ML+ VSV H+ T D+S A
Sbjct: 157 GKDAVIIGASNIVGRPMATMLLNAGATVSVCHIK--------TKDLSLYTRQA------- 201
Query: 79 QPQLENALTGMDLVIIPAGVPR--KPGMTRDDLFNINAGIVR 118
DL+I+ AG + M ++ + ++ GI R
Sbjct: 202 -----------DLIIVAAGCVNLLRSDMVKEGVIVVDVGINR 232
>gnl|CDD|178031 PLN02409, PLN02409, serine--glyoxylate aminotransaminase.
Length = 401
Score = 32.8 bits (75), Expect = 0.16
Identities = 14/38 (36%), Positives = 20/38 (52%), Gaps = 4/38 (10%)
Query: 70 GAVVR----GFLGQPQLENALTGMDLVIIPAGVPRKPG 103
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 = 0.22
Identities = 22/79 (27%), Positives = 36/79 (45%), Gaps = 3/79 (3%)
Query: 22 KVAILGAAGGIGQPLAMLMKINPLVSVLHLYDVVNTPGVTADISHMDTGAVVRGFLGQPQ 81
KVAI+GA G +GQ L L+ +P + ++ L + G ++ L +
Sbjct: 1 KVAIVGATGYVGQELLRLLAEHPPLELVALVASSRSAGKKVAFAYPILEGGKDLLL-EDV 59
Query: 82 LENALTGMDLVII--PAGV 98
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 = 31.8 bits (73), Expect = 0.33
Identities = 34/149 (22%), Positives = 44/149 (29%), Gaps = 58/149 (38%)
Query: 82 LENALTGMDLVIIPAGVPRKPGMTRDDLFNINA---------------GIVRTL------ 120
AL G D VI V D F I GI R L
Sbjct: 68 RREALDGADFVINTIQVGGHEYTETD--FEIPEKYGYYQTVGDTSGPGGIFRALRTIPVL 125
Query: 121 ---CEGIAKCCPNATVNLISNPV-------NSTVPIAA-----EVFKKAGTYDPKKLLGV 165
I + CP+A + +NP+ N PI V GT +
Sbjct: 126 LDIARDIEELCPDAWLLNYANPMAELTWALNRYTPIKTVGLCHGVQ---GTAE------- 175
Query: 166 TMLDVVRANTFVAEVLGLDPRDVDVPVVG 194
+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 = 30.5 bits (69), Expect = 0.70
Identities = 23/100 (23%), Positives = 39/100 (39%), Gaps = 29/100 (29%)
Query: 20 GFKVAILGAAGGIGQPLA-MLMKINPLVSVLHLYDVVNTPGVTADISHMDTGAVVRGFLG 78
G I+G + +G+P+A ML+ N VSV H++ T D+ A
Sbjct: 164 GKNAVIVGHSNVVGKPMAAMLLNRNATVSVCHVF--------TDDLKKYTLDA------- 208
Query: 79 QPQLENALTGMDLVIIPAGVPR--KPGMTRDDLFNINAGI 116
D++++ GV K M ++ + GI
Sbjct: 209 -----------DILVVATGVKHLIKADMVKEGAVIFDVGI 237
>gnl|CDD|179337 PRK01810, PRK01810, DNA polymerase IV; Validated.
Length = 407
Score = 30.0 bits (68), Expect = 1.4
Identities = 11/25 (44%), Positives = 16/25 (64%)
Query: 147 AAEVFKKAGTYDPKKLLGVTMLDVV 171
A+ +FK+ DP +LLGVT D+
Sbjct: 321 ASRLFKQHWNGDPVRLLGVTATDLE 345
>gnl|CDD|172679 PRK14191, PRK14191, bifunctional 5,10-methylene-tetrahydrofolate
dehydrogenase/ 5,10-methylene-tetrahydrofolate
cyclohydrolase; Provisional.
Length = 285
Score = 29.0 bits (65), Expect = 2.6
Identities = 16/35 (45%), Positives = 21/35 (60%), Gaps = 1/35 (2%)
Query: 19 AGFKVAILGAAGGIGQPLAMLM-KINPLVSVLHLY 52
G V I+GA+ +G+PLAMLM VSV H+
Sbjct: 156 KGKDVVIIGASNIVGKPLAMLMLNAGASVSVCHIL 190
>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 = 3.1
Identities = 19/74 (25%), Positives = 33/74 (44%), Gaps = 3/74 (4%)
Query: 22 KVAILGAAGGIGQPLA-MLMKINPLVSVLHLYDVVNTPGVTADISHMDTGAVVRGFLGQP 80
V + GA G IG L L++ V L +Y+ N+ G+ + H D + G +
Sbjct: 1 NVLVTGADGFIGSHLTERLLREGHEVRALDIYNSFNSWGLLDNAVH-DRFHFISGDVRDA 59
Query: 81 -QLENALTGMDLVI 93
++E + D+V
Sbjct: 60 SEVEYLVKKCDVVF 73
>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 = 27.5 bits (62), Expect = 4.6
Identities = 14/35 (40%), Positives = 22/35 (62%), Gaps = 1/35 (2%)
Query: 19 AGFKVAILGAAGGIGQPLA-MLMKINPLVSVLHLY 52
AG KV ++G + +G+PLA +L+ N V+V H
Sbjct: 43 AGKKVVVVGRSNIVGKPLAALLLNRNATVTVCHSK 77
>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 = 4.6
Identities = 12/32 (37%), Positives = 16/32 (50%), Gaps = 3/32 (9%)
Query: 140 VNSTVPIAAEVFKKAGTYDPKKLLGVTMLDVV 171
N I + VFKK +D + L +T DVV
Sbjct: 130 SNQFAEIKSSVFKK---FDKESLFQITCADVV 158
>gnl|CDD|224103 COG1182, AcpD, Acyl carrier protein phosphodiesterase [Lipid
metabolism].
Length = 202
Score = 27.2 bits (61), Expect = 6.6
Identities = 13/38 (34%), Positives = 17/38 (44%), Gaps = 2/38 (5%)
Query: 14 AKGGAAGFKVAILGAAGGI--GQPLAMLMKINPLVSVL 49
G G KV IL + GGI P +M L ++L
Sbjct: 127 PVGLLTGKKVLILTSRGGIYSEGPASMDHGEPYLRTIL 164
>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 = 6.7
Identities = 25/79 (31%), Positives = 35/79 (44%), Gaps = 6/79 (7%)
Query: 22 KVAILGAAGGIGQPLAMLMKINPLVSVLHLYDVVNTPGVTADISHMDTGAVVRGFLGQPQ 81
KV I GA+G +GQ LA + + L L DVV +P + + + G L P
Sbjct: 2 KVLITGASGFVGQRLAERLLSDVPNERLILIDVV-SPKAPSGAPRVTQ---IAGDLAVPA 57
Query: 82 LENALT--GMDLVIIPAGV 98
L AL D+V A +
Sbjct: 58 LIEALANGRPDVVFHLAAI 76
>gnl|CDD|202102 pfam02056, Glyco_hydro_4, Family 4 glycosyl hydrolase.
Length = 183
Score = 27.0 bits (60), Expect = 8.2
Identities = 42/196 (21%), Positives = 65/196 (33%), Gaps = 47/196 (23%)
Query: 22 KVAILGAAGGIGQPLAMLMKINPL----VSVLHLYDVVNTPGVTADISH------MDTGA 71
K+ I+G G P +L ++ L LYD+ D +D
Sbjct: 1 KIVIIGG-GSTITPKNLLGDLDHTEELPGRELALYDI---DEERLDAIQTACKKLVDEAG 56
Query: 72 VVRGFLGQPQLENALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRT------------ 119
F + ALT D VI V P D+ + G+V T
Sbjct: 57 PDIKFEKTTDRKEALTDADFVINAIRVGLLPARELDEKIPLRHGVVGTIQETVGPGGIFR 116
Query: 120 ----------LCEGIAKCCPNATVNLISNPVNSTVPIA--AEVFKKAGTYDPKKLLGVTM 167
+ + I + CP+A V +N T P A E + Y K +G+
Sbjct: 117 GLRTIPVFFDIAKDIEELCPDAWV------LNYTNPAAMVTEAVYR--RYPNIKAVGLCH 168
Query: 168 LDVVRANTFVAEVLGL 183
+ +A++LGL
Sbjct: 169 S-PIGIEERLAKILGL 183
>gnl|CDD|236016 PRK07424, PRK07424, bifunctional sterol desaturase/short chain
dehydrogenase; Validated.
Length = 406
Score = 27.3 bits (61), Expect = 8.3
Identities = 25/87 (28%), Positives = 39/87 (44%), Gaps = 17/87 (19%)
Query: 20 GFKVAILGAAGGIGQPLAMLMKINPLVSVLHLYD--VV----NTPGVTADISHMDTGA-V 72
G VA+ GA+G +GQ L+ LH VV N+ +T +I+ D
Sbjct: 178 GKTVAVTGASGTLGQ---------ALLKELHQQGAKVVALTSNSDKITLEINGEDLPVKT 228
Query: 73 VRGFLGQP-QLENALTGMDLVIIPAGV 98
+ +GQ L L +D++II G+
Sbjct: 229 LHWQVGQEAALAELLEKVDILIINHGI 255
>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 = 27.4 bits (61), Expect = 8.6
Identities = 10/31 (32%), Positives = 17/31 (54%)
Query: 22 KVAILGAAGGIGQPLAMLMKINPLVSVLHLY 52
+VA+LGA G +GQ L+ +P + +
Sbjct: 2 RVAVLGATGLVGQKFVKLLAKHPYFELAKVV 32
>gnl|CDD|222146 pfam13460, NAD_binding_10, NADH(P)-binding.
Length = 182
Score = 26.9 bits (60), Expect = 9.5
Identities = 15/79 (18%), Positives = 25/79 (31%), Gaps = 7/79 (8%)
Query: 23 VAILGAAGGIGQPLAMLMKINPLVSVLHLYDVVNTPGVTADISHMDTGAVVRGFLGQPQL 82
+A++GA G G+ L + + + P V + L
Sbjct: 1 IAVIGATGKTGRRLVKELLARG----HQVTALSRNPSKAPA---PGVTPVQKDLFDLADL 53
Query: 83 ENALTGMDLVIIPAGVPRK 101
AL G+D V+ G
Sbjct: 54 AEALAGVDAVVDAFGARPD 72
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 0.397
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: 13,168,708
Number of extensions: 1286027
Number of successful extensions: 1509
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1459
Number of HSP's successfully gapped: 89
Length of query: 258
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 163
Effective length of database: 6,723,972
Effective search space: 1096007436
Effective search space used: 1096007436
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: 58 (26.1 bits)