RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 023671
(279 letters)
>gnl|CDD|215058 PLN00106, PLN00106, malate dehydrogenase.
Length = 323
Score = 511 bits (1319), Expect = 0.0
Identities = 194/236 (82%), Positives = 207/236 (87%)
Query: 33 CRAKGGAAGFKVAILGAAGGIGQPLAMLMKINPLVSVLHLYDVVNTPGVTADISHMDTGA 92
CRAKGGA GFKVA+LGAAGGIGQPL++LMK+NPLVS LHLYD+ NTPGV AD+SH++T A
Sbjct: 10 CRAKGGAPGFKVAVLGAAGGIGQPLSLLMKMNPLVSELHLYDIANTPGVAADVSHINTPA 69
Query: 93 VVRGFLGQPQLENALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAKCCPNA 152
VRGFLG QL +AL G DLVIIPAGVPRKPGMTRDDLFNINAGIV+TLCE +AK CPNA
Sbjct: 70 QVRGFLGDDQLGDALKGADLVIIPAGVPRKPGMTRDDLFNINAGIVKTLCEAVAKHCPNA 129
Query: 153 TVNLISNPVNSTVPIAAEVFKKAGTYDPKKLLGVTMLDVVRANTFVAEVLGLDPRDVDVP 212
VN+ISNPVNSTVPIAAEV KKAG YDPKKL GVT LDVVRANTFVAE GLDP DVDVP
Sbjct: 130 LVNIISNPVNSTVPIAAEVLKKAGVYDPKKLFGVTTLDVVRANTFVAEKKGLDPADVDVP 189
Query: 213 VVGGHAGVTILPLLSQVKPPCSFTQEETEYLTNRIQNGGTEVVEAKAGAGSATLSM 268
VVGGHAG+TILPLLSQ P SFT EE E LT RIQNGGTEVVEAKAGAGSATLSM
Sbjct: 190 VVGGHAGITILPLLSQATPKVSFTDEEIEALTKRIQNGGTEVVEAKAGAGSATLSM 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 = 451 bits (1164), Expect = e-162
Identities = 168/227 (74%), Positives = 194/227 (85%)
Query: 42 FKVAILGAAGGIGQPLAMLMKINPLVSVLHLYDVVNTPGVTADISHMDTGAVVRGFLGQP 101
KVA+LGAAGGIGQPL++L+K+NPLVS L LYD+VNTPGV AD+SH++T A V G+LG
Sbjct: 1 VKVAVLGAAGGIGQPLSLLLKLNPLVSELALYDIVNTPGVAADLSHINTPAKVTGYLGPE 60
Query: 102 QLENALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAKCCPNATVNLISNPV 161
+L+ AL G D+V+IPAGVPRKPGMTRDDLFNINAGIVR L +AK CP A + +ISNPV
Sbjct: 61 ELKKALKGADVVVIPAGVPRKPGMTRDDLFNINAGIVRDLATAVAKACPKALILIISNPV 120
Query: 162 NSTVPIAAEVFKKAGTYDPKKLLGVTMLDVVRANTFVAEVLGLDPRDVDVPVVGGHAGVT 221
NSTVPIAAEV KKAG YDPK+L GVT LDVVRANTFVAE+LGLDP V+VPV+GGH+GVT
Sbjct: 121 NSTVPIAAEVLKKAGVYDPKRLFGVTTLDVVRANTFVAELLGLDPAKVNVPVIGGHSGVT 180
Query: 222 ILPLLSQVKPPCSFTQEETEYLTNRIQNGGTEVVEAKAGAGSATLSM 268
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 = 357 bits (918), Expect = e-124
Identities = 149/226 (65%), Positives = 181/226 (80%)
Query: 43 KVAILGAAGGIGQPLAMLMKINPLVSVLHLYDVVNTPGVTADISHMDTGAVVRGFLGQPQ 102
KVA+LGAAGGIGQPL++L+K+ P VS L LYD+ GV AD+SH+ T A V+GF G+
Sbjct: 1 KVAVLGAAGGIGQPLSLLLKLQPYVSELSLYDIAGAAGVAADLSHIPTAASVKGFSGEEG 60
Query: 103 LENALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAKCCPNATVNLISNPVN 162
LENAL G D+V+IPAGVPRKPGMTRDDLFN+NAGIV+ L +A+ CP A + +I+NPVN
Sbjct: 61 LENALKGADVVVIPAGVPRKPGMTRDDLFNVNAGIVKDLVAAVAESCPKAMILVITNPVN 120
Query: 163 STVPIAAEVFKKAGTYDPKKLLGVTMLDVVRANTFVAEVLGLDPRDVDVPVVGGHAGVTI 222
STVPIAAEV KK G YDP KL GVT LD+VRANTFVAE+ G DP +V+VPV+GGH+G TI
Sbjct: 121 STVPIAAEVLKKKGVYDPNKLFGVTTLDIVRANTFVAELKGKDPMEVNVPVIGGHSGETI 180
Query: 223 LPLLSQVKPPCSFTQEETEYLTNRIQNGGTEVVEAKAGAGSATLSM 268
+PL+SQ FT+++ E L +RIQN GTEVV+AKAGAGSATLSM
Sbjct: 181 IPLISQCPGKVLFTEDQLEALIHRIQNAGTEVVKAKAGAGSATLSM 226
>gnl|CDD|235340 PRK05086, PRK05086, malate dehydrogenase; Provisional.
Length = 312
Score = 341 bits (876), Expect = e-118
Identities = 144/228 (63%), Positives = 171/228 (75%), Gaps = 4/228 (1%)
Query: 43 KVAILGAAGGIGQPLAMLMKIN-PLVSVLHLYDVVN-TPGVTADISHMDTGAVVRGFLGQ 100
KVA+LGAAGGIGQ LA+L+K P S L LYD+ TPGV D+SH+ T ++GF G+
Sbjct: 2 KVAVLGAAGGIGQALALLLKTQLPAGSELSLYDIAPVTPGVAVDLSHIPTAVKIKGFSGE 61
Query: 101 PQLENALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAKCCPNATVNLISNP 160
AL G D+V+I AGV RKPGM R DLFN+NAGIV+ L E +AK CP A + +I+NP
Sbjct: 62 -DPTPALEGADVVLISAGVARKPGMDRSDLFNVNAGIVKNLVEKVAKTCPKACIGIITNP 120
Query: 161 VNSTVPIAAEVFKKAGTYDPKKLLGVTMLDVVRANTFVAEVLGLDPRDVDVPVVGGHAGV 220
VN+TV IAAEV KKAG YD KL GVT LDV+R+ TFVAE+ G P +V+VPV+GGH+GV
Sbjct: 121 VNTTVAIAAEVLKKAGVYDKNKLFGVTTLDVIRSETFVAELKGKQPGEVEVPVIGGHSGV 180
Query: 221 TILPLLSQVKPPCSFTQEETEYLTNRIQNGGTEVVEAKAGAGSATLSM 268
TILPLLSQV P SFT++E LT RIQN GTEVVEAKAG GSATLSM
Sbjct: 181 TILPLLSQV-PGVSFTEQEVADLTKRIQNAGTEVVEAKAGGGSATLSM 227
>gnl|CDD|240360 PTZ00325, PTZ00325, malate dehydrogenase; Provisional.
Length = 321
Score = 314 bits (807), Expect = e-107
Identities = 150/227 (66%), Positives = 174/227 (76%), Gaps = 2/227 (0%)
Query: 42 FKVAILGAAGGIGQPLAMLMKINPLVSVLHLYDVVNTPGVTADISHMDTGAVVRGFLGQP 101
FKVA+LGAAGGIGQPL++L+K NP VS L LYD+V PGV AD+SH+DT A V G+
Sbjct: 9 FKVAVLGAAGGIGQPLSLLLKQNPHVSELSLYDIVGAPGVAADLSHIDTPAKVTGYADGE 68
Query: 102 QLENALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAKCCPNATVNLISNPV 161
E AL G DLV+I AGVPRKPGMTRDDLFN NA IVR L +A P A V ++SNPV
Sbjct: 69 LWEKALRGADLVLICAGVPRKPGMTRDDLFNTNAPIVRDLVAAVASSAPKAIVGIVSNPV 128
Query: 162 NSTVPIAAEVFKKAGTYDPKKLLGVTMLDVVRANTFVAEVLGLDPRDVDVPVVGGHAGVT 221
NSTVPIAAE KKAG YDP+KL GVT LDVVRA FVAE LG++P DV+VPVVGGH+GVT
Sbjct: 129 NSTVPIAAETLKKAGVYDPRKLFGVTTLDVVRARKFVAEALGMNPYDVNVPVVGGHSGVT 188
Query: 222 ILPLLSQVKPPCSFTQEETEYLTNRIQNGGTEVVEAKAGAGSATLSM 268
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 = 207 bits (530), Expect = 7e-66
Identities = 92/236 (38%), Positives = 127/236 (53%), Gaps = 17/236 (7%)
Query: 43 KVAILGAAGGIGQPLAMLMKINPLVSVLHLYDVVN--TPGVTADISHMDTGAVVRGFLGQ 100
KVA++GA G +G LA L+ + L S L L D+ GV D+SH +
Sbjct: 2 KVAVIGA-GNVGSSLAFLLLLQGLGSELVLIDINEEKAEGVALDLSHAAAPLGSDVKITG 60
Query: 101 PQLENALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAKCCPNATVNLISNP 160
L G D+V+I AGVPRKPGMTR DL NA IV+ + + IAK P+A V +++NP
Sbjct: 61 DGDYEDLKGADIVVITAGVPRKPGMTRLDLLEKNAKIVKDIAKAIAKYAPDAIVLVVTNP 120
Query: 161 VNSTVPIAAEVFKKAGTYDPKKLLGVTMLDVVRANTFVAEVLGLDPRDVDVPVVGGHAGV 220
V+ IA + +G + + T+LD R TF+AE LG+ P+DV V+G H G
Sbjct: 121 VDILTYIAMKF---SGFPKNRVIGSGTVLDSARFRTFLAEKLGVSPKDVHAYVIGEH-GD 176
Query: 221 TILPLLSQV----KPPCSF----TQEETEYLTNRIQNGGTEVVEAKAGAGSATLSM 268
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 = 172 bits (439), Expect = 1e-54
Identities = 60/145 (41%), Positives = 80/145 (55%), Gaps = 6/145 (4%)
Query: 43 KVAILGAAGGIGQPLAMLMKINPLVSVLHLYDVV--NTPGVTADISHMDTGAVVRGFLGQ 100
KVA++GA GG+G LA + + L L L D+ GV D+SH T V G +G
Sbjct: 2 KVAVVGAGGGVGSSLAFALALQGLADELVLVDINKDKAEGVAMDLSHGSTFLSVPGIVGG 61
Query: 101 PQLENALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAKCCPNATVNLISNP 160
AL D+V+I AGVPRKPGMTR DL N NAGI + + IAK P+A V ++SNP
Sbjct: 62 DD-YEALKDADVVVITAGVPRKPGMTRLDLLNRNAGIFKDIVPAIAKSAPDAIVLVVSNP 120
Query: 161 VNSTVPIAAEVFKKAGTYDPKKLLG 185
V+ IA +V +G + +
Sbjct: 121 VDILTYIAWKV---SGLPPERVIGS 142
>gnl|CDD|180477 PRK06223, PRK06223, malate dehydrogenase; Reviewed.
Length = 307
Score = 142 bits (360), Expect = 1e-40
Identities = 83/233 (35%), Positives = 130/233 (55%), Gaps = 22/233 (9%)
Query: 43 KVAILGAAGGIGQPLAMLMKINPLVSVLHLYDVV-NTP-GVTADISHMDTGAVVRGFLGQ 100
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: 101 PQLEN---ALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAKCCPNATVNLI 157
N + G D+V+I AGVPRKPGM+RDDL INA I++ + EGI K P+A V ++
Sbjct: 59 ITGTNDYEDIAGSDVVVITAGVPRKPGMSRDDLLGINAKIMKDVAEGIKKYAPDAIVIVV 118
Query: 158 SNPVNSTVPIAAEVFKKAGTYDPKKLLGV-TMLDVVRANTFVAEVLGLDPRDVDVPVVGG 216
+NPV++ +A K + +++G+ +LD R TF+AE L + +DV V+GG
Sbjct: 119 TNPVDAMTYVA----LKESGFPKNRVIGMAGVLDSARFRTFIAEELNVSVKDVTAFVLGG 174
Query: 217 HAGVTILPLLSQ-----VKPPCSFTQEETEYLTNRIQNGGTEVVEAKAGAGSA 264
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 = 141 bits (357), Expect = 3e-40
Identities = 83/233 (35%), Positives = 122/233 (52%), Gaps = 24/233 (10%)
Query: 44 VAILGAAGGIGQPLAMLMKINPLVSVLHLYDVV-NTP-GVTADISHM----DTGAVVRGF 97
++I+GA G +G LA L+ + L V+ L D+V P G DIS + V G
Sbjct: 1 ISIIGA-GNVGATLAQLLALKELGDVV-LLDIVEGLPQGKALDISQAAPILGSDTKVTGT 58
Query: 98 LGQPQLENALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAKCCPNATVNLI 157
+ + D+V+I AG+PRKPGM+RDDL NA IV+ + E I K PNA V ++
Sbjct: 59 NDYEDIAGS----DVVVITAGIPRKPGMSRDDLLGTNAKIVKEVAENIKKYAPNAIVIVV 114
Query: 158 SNPVNSTVPIAAEVFKKAGTYDPKKLLGV-TMLDVVRANTFVAEVLGLDPRDVDVPVVGG 216
+NP++ V KA + +++G+ +LD R F+AE LG+ +DV V+GG
Sbjct: 115 TNPLDVMT----YVAYKASGFPRNRVIGMAGVLDSARFRYFIAEELGVSVKDVQAMVLGG 170
Query: 217 HAGVTILPLLSQV----KPPCSF-TQEETEYLTNRIQNGGTEVVEAKAGAGSA 264
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 = 131 bits (331), Expect = 6e-37
Identities = 63/192 (32%), Positives = 93/192 (48%), Gaps = 9/192 (4%)
Query: 44 VAILGAAGGIGQPLA--MLMKINPLVSVLHLYDVVN--TPGVTADISHMDTGAVVRGFLG 99
+A++GA G +G LA + L L LYD+ GV D+
Sbjct: 1 IAVIGAGGNVGPALAFGLADGSVLLAIELVLYDIDEEKLKGVAMDLQDAVEPLADIKVSI 60
Query: 100 QPQLENALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAKCCPNATVNLISN 159
A D+VII AGV RKPGM R DL N IV+ + + I K P+A + ++SN
Sbjct: 61 TDDPYEAFKDADVVIITAGVGRKPGMGRLDLLKRNVPIVKEIGDNIEKYSPDAWIIVVSN 120
Query: 160 PVNSTVPIAAEVFKKAGTYDPKKLLGVTMLDVVRANTFVAEVLGLDPRDVDVPVVGGHAG 219
PV+ I + + +K++G+ LD +R +AE LG+DP DV V ++G H G
Sbjct: 121 PVD----IITYLVWRYSGLPKEKVIGLGTLDPIRFRRILAEKLGVDPDDVKVYILGEHGG 176
Query: 220 VTILPLLSQVKP 231
+ +P S V+
Sbjct: 177 -SQVPDWSTVRI 187
>gnl|CDD|173409 PTZ00117, PTZ00117, malate dehydrogenase; Provisional.
Length = 319
Score = 116 bits (292), Expect = 1e-30
Identities = 78/239 (32%), Positives = 120/239 (50%), Gaps = 23/239 (9%)
Query: 43 KVAILGAAGGIGQPLAMLMKINPLVSVLHLYDVV-NTP-GVTADISH-MDTGAVVRGFLG 99
K++++GA G IG +A+L+ L V+ LYDV+ P G D+ H LG
Sbjct: 7 KISMIGA-GQIGSTVALLILQKNLGDVV-LYDVIKGVPQGKALDLKHFSTLVGSNINILG 64
Query: 100 QPQLENALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAKCCPNATVNLISN 159
E + D+V+I AGV RK MTR+DL IN I++++ E + K CPNA V ++N
Sbjct: 65 TNNYE-DIKDSDVVVITAGVQRKEEMTREDLLTINGKIMKSVAESVKKYCPNAFVICVTN 123
Query: 160 PVNSTVPIAAEVFKKAGTYDPKKLLGVT-MLDVVRANTFVAEVLGLDPRDVDVPVVGGHA 218
P++ +VF++ K+ G+ +LD R +AE LG+ P DV V+GGH
Sbjct: 124 PLD----CMVKVFQEKSGIPSNKICGMAGVLDSSRFRCNLAEKLGVSPGDVSAVVIGGH- 178
Query: 219 GVTILPLLSQVK----PPCSF------TQEETEYLTNRIQNGGTEVVEAKAGAGSATLS 267
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 = 109 bits (275), Expect = 1e-29
Identities = 47/92 (51%), Positives = 56/92 (60%), Gaps = 12/92 (13%)
Query: 187 TMLDVVRANTFVAEVLGLDPRDVDVPVVGGHAG----------VTILPLLSQVKPPCSFT 236
T LD RA TF+AE G+DPR V+V V+G H+G VTI+PL+SQVK T
Sbjct: 1 TTLDTARARTFLAEKFGVDPRSVNVYVIGEHSGTQFPDWSHAKVTIIPLISQVKENLKDT 60
Query: 237 QEETEYLTNRIQNGGTEVVEAKAGAGSATLSM 268
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 = 110 bits (278), Expect = 9e-29
Identities = 72/235 (30%), Positives = 109/235 (46%), Gaps = 25/235 (10%)
Query: 44 VAILGAAGGIGQPLAMLMKINPLVSVLHLYDVVN--TPGVTADISHM----DTGAVVRGF 97
+ I+GA G +G +A + L S L L DV G D+SH TG +VRG
Sbjct: 1 ITIIGA-GNVGAAVAFALIAKGLASELVLVDVNEEKAKGDALDLSHASAFLATGTIVRG- 58
Query: 98 LGQPQLENALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAKCCPNATVNLI 157
D+V+I AG PRKPG TR DL N NA I+R++ + K P+A + ++
Sbjct: 59 ----GDYADAADADIVVITAGAPRKPGETRLDLINRNAPILRSVITNLKKYGPDAIILVV 114
Query: 158 SNPVNSTVPIAAEVFKKAGTYDPKKLLGV-TMLDVVRANTFVAEVLGLDPRDVDVPVVGG 216
SNPV+ I V +K +++G T+LD R + +AE L +DP+ V V+G
Sbjct: 115 SNPVD----ILTYVAQKLSGLPKNRVIGSGTLLDSARFRSLLAEKLDVDPQSVHAYVLGE 170
Query: 217 HAGVTILPLLSQVK-------PPCSFTQEETEYLTNRIQNGGTEVVEAKAGAGSA 264
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 = 109 bits (273), Expect = 7e-28
Identities = 86/241 (35%), Positives = 133/241 (55%), Gaps = 28/241 (11%)
Query: 43 KVAILGAAGGIGQPLAMLMKINPLVSVLHLYDVV-NTP-GVTADISHMDTGAVVR-GFLG 99
K++++G+ G IG +A L+ + L V+ L+D+V N P G DISH + A +G
Sbjct: 8 KISLIGS-GNIGGVMAYLIVLKNLGDVV-LFDIVKNIPQGKALDISHSNVIAGSNSKVIG 65
Query: 100 QPQLENALTGMDLVIIPAGVPRKPGMT-----RDDLFNINAGIVRTLCEGIAKCCPNATV 154
E+ + G D+VI+ AG+ ++PG + RDDL +NA I+ + EGI K CPNA V
Sbjct: 66 TNNYED-IAGSDVVIVTAGLTKRPGKSDKEWNRDDLLPLNAKIMDEVAEGIKKYCPNAFV 124
Query: 155 NLISNPVNSTVPIAAEVFKKAGTYDPKKLLGVT-MLDVVRANTFVAEVLGLDPRDVDVPV 213
+I+NP++ V ++ ++ K+ G+ +LD R T++AE LG++PRDV V
Sbjct: 125 IVITNPLDVMV----KLLQEHSGLPKNKVCGMAGVLDSSRLRTYIAEKLGVNPRDVHASV 180
Query: 214 VGGHAGVTILPLLSQVK----PPCSF------TQEETEYLTNRIQNGGTEVVEAKAGAGS 263
+G H G ++PL V P F TQEE + + R +N G E+V+ G GS
Sbjct: 181 IGAH-GDKMVPLPRYVTVGGIPLSEFIKKGLITQEEIDEIVERTRNTGKEIVDL-LGTGS 238
Query: 264 A 264
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 = 98.6 bits (246), Expect = 4e-24
Identities = 66/243 (27%), Positives = 115/243 (47%), Gaps = 43/243 (17%)
Query: 43 KVAILGAAGGIGQPLAMLMKINPLVSVLHL-----------------YDVVNTPGVTADI 85
KV+I+GA+G +G A+L+ +V ++L YD + G+ A+I
Sbjct: 2 KVSIIGASGRVGSATALLLAKEDVVKEINLISRPKSLEKLKGLRLDIYDALAAAGIDAEI 61
Query: 86 SHMDTGAVVRGFLGQPQLENALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGI 145
+ V G D+VII AGVPRK GM+R DL NA IV+ + I
Sbjct: 62 KISSDLSDV-------------AGSDIVIITAGVPRKEGMSRLDLAKKNAKIVKKYAKQI 108
Query: 146 AKCCPNATVNLISNPVNSTVPIAAEVFKKAGTYDPKKLLGV-TMLDVVRANTFVAEVLGL 204
A+ P+ + +++NPV+ A K++G +D ++ G+ T LD +R +A+ +
Sbjct: 109 AEFAPDTKILVVTNPVDVMTYKA---LKESG-FDKNRVFGLGTHLDSLRFKVAIAKHFNV 164
Query: 205 DPRDVDVPVVGGHAGVTILPLLSQ-------VKPPCSFTQEETEYLTNRIQNGGTEVVEA 257
+V ++G H G +++PL+S +K + + E + ++N G ++
Sbjct: 165 HISEVHTRIIGEH-GDSMVPLISSTSIGGIPIKRFPEYKDFDVEKIVETVKNAGQNIISL 223
Query: 258 KAG 260
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 = 91.5 bits (227), Expect = 2e-21
Identities = 69/237 (29%), Positives = 115/237 (48%), Gaps = 30/237 (12%)
Query: 43 KVAILGAAGGIGQPLAMLMKINPLVSVLHLYDVVNTPGVTADISHMDTGAVVRGF----L 98
K++++GA G +G A + L ++ L DVV + + V GF
Sbjct: 3 KISVIGA-GFVGATTAFRLAEKELADLV-LLDVVEGIPQGKALDMYEASPV-GGFDTKVT 59
Query: 99 GQPQLENALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAKCCPNATVNLIS 158
G + D+V+I AG+PRKPGM+R+DL ++NAGIVR + I + PN + ++S
Sbjct: 60 GTNNYADT-ANSDIVVITAGLPRKPGMSREDLLSMNAGIVREVTGRIMEHSPNPIIVVVS 118
Query: 159 NPVNSTVPIAAEVFKKAGTYDPKKLLGVT-MLDVVRANTFVAEVLGLDPRDVDVPVVGGH 217
NP+++ +A + + ++++G +LD R TF+A LG+ +DV V+GGH
Sbjct: 119 NPLDAMTYVAWQK----SGFPKERVIGQAGVLDSARFRTFIAMELGVSVQDVTACVLGGH 174
Query: 218 AGVTILPL----------LSQVKPPCSFTQEETEYLTNRIQNGGTEVVEAKAGAGSA 264
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 = 81.7 bits (203), Expect = 4e-18
Identities = 47/160 (29%), Positives = 77/160 (48%), Gaps = 16/160 (10%)
Query: 110 MDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAKCCPNATVNLISNPVNSTVPIAA 169
D+V+I AG P+KPG TR DL NA I++++ I + + SNPV+ +
Sbjct: 69 ADIVVITAGAPQKPGETRLDLLEKNAKIMKSIVPKIKASGFDGIFLVASNPVD----VIT 124
Query: 170 EVFKKAGTYDPKKLLGV-TMLDVVRANTFVAEVLGLDPRDVDVPVVGGH--------AGV 220
V +K +++G T LD R +AE L +DPR V V+G H + V
Sbjct: 125 YVVQKLSGLPKNRVIGTGTSLDTARLRRALAEKLNVDPRSVHAYVLGEHGDSQFVAWSTV 184
Query: 221 TIL--PLLSQVKPPCSFTQEETEYLTNRIQNGGTEVVEAK 258
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 = 81.1 bits (201), Expect = 8e-18
Identities = 45/164 (27%), Positives = 76/164 (46%), Gaps = 17/164 (10%)
Query: 107 LTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAKCCPNATVNLISNPVNSTVP 166
DLV+I AG P+KPG TR +L N I++++ + K + + +NPV+
Sbjct: 62 CKDADLVVITAGAPQKPGETRLELVGRNVRIMKSIVPEVVKSGFDGIFLVATNPVD---- 117
Query: 167 IAAEVFKKAGTYDPKKLLGV-TMLDVVRANTFVAEVLGLDPRDVDVPVVGGHAGVTILPL 225
I V K + +++G T+LD R +AE LG+DP+ V ++G H G + +P+
Sbjct: 118 ILTYVAWKLSGFPKNRVIGSGTVLDTARLRYLLAEKLGVDPQSVHAYIIGEH-GDSEVPV 176
Query: 226 LSQVK----PPCSF---TQEETEYLTNRI----QNGGTEVVEAK 258
S P + ET+ I ++ E++ K
Sbjct: 177 WSSATIGGVPLLDYLKAKGTETDLDLEEIEKEVRDAAYEIINRK 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 = 80.4 bits (199), Expect = 2e-17
Identities = 68/258 (26%), Positives = 102/258 (39%), Gaps = 48/258 (18%)
Query: 43 KVAILGAAGGIGQPLA-------MLMKINPLVSVLHLYDVVNTPGVTADISHMDTGAV-- 93
V I GAAG IG L + P++ LHL D+ + ++ +
Sbjct: 2 HVLITGAAGQIGYNLLFLIASGELFGDDQPVI--LHLLDI------PPAMKALEGVVMEL 53
Query: 94 -------VRGFLGQPQLENALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIA 146
++G + E A +D+ I+ PRKPGM R DL NA I + E +
Sbjct: 54 QDCAFPLLKGVVITTDPEEAFKDVDVAILVGAFPRKPGMERADLLRKNAKIFKEQGEALN 113
Query: 147 KCC-PNATVNLISNPVNSTVPIAAEVFKKAGTYDPKKLLGVTMLDVVRANTFVAEVLGLD 205
K P V ++ NP N+ IA K A PK +T LD RA VA LG+
Sbjct: 114 KVAKPTVKVLVVGNPANTNALIAL---KNAPNLPPKNFTALTRLDHNRAKAQVARKLGVR 170
Query: 206 PRDV-DVPVVGGHAGVTILPLLSQ-------------VKPPCSFTQEETEYLTNRIQNGG 251
DV +V + G H+ T +P LS + +E +Q G
Sbjct: 171 VSDVKNVIIWGNHSN-TQVPDLSNAVVYGPGGTEWVLDLLDEEWLNDE---FVKTVQKRG 226
Query: 252 TEVVEAK--AGAGSATLS 267
+++ + + 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 = 75.2 bits (186), Expect = 1e-15
Identities = 58/181 (32%), Positives = 88/181 (48%), Gaps = 16/181 (8%)
Query: 43 KVAILGAAGGIGQPLAMLMKINPLVSVLHLYDVVNTPGVTA---DISH-MDTGAVVRGFL 98
KVAI+GA G +G A + + L S + L D+ N D++H VR +
Sbjct: 2 KVAIVGA-GFVGSTTAYALLLRGLASEIVLVDI-NKAKAEGEAMDLAHGTPFVKPVRIYA 59
Query: 99 GQPQ-LENALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAKCCPNATVNLI 157
G + A D+V+I AG +KPG TR DL N I + + I K P+A + ++
Sbjct: 60 GDYADCKGA----DVVVITAGANQKPGETRLDLLKRNVAIFKEIIPQILKYAPDAILLVV 115
Query: 158 SNPVNSTVPIAAEVFKKAGTYDPKKLLGV-TMLDVVRANTFVAEVLGLDPRDVDVPVVGG 216
+NPV+ + V K P +++G T+LD R + E LG+DPR V ++G
Sbjct: 116 TNPVD----VLTYVAYKLSGLPPNRVIGSGTVLDTARFRYLLGEHLGVDPRSVHAYIIGE 171
Query: 217 H 217
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 = 73.1 bits (180), Expect = 6e-15
Identities = 68/242 (28%), Positives = 105/242 (43%), Gaps = 28/242 (11%)
Query: 43 KVAILGAAGGIGQPLA-------MLMKINPLVSVLHLYDVVNT----PGVTADISHMDTG 91
+VA+ GAAG IG L + K P+V LHL D+ GV ++ D
Sbjct: 5 RVAVTGAAGQIGYSLLFRIASGELFGKDQPVV--LHLLDIPPAMKALEGVAMEL--EDCA 60
Query: 92 -AVVRGFLGQPQLENALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAKCC- 149
++ G + E A +D ++ PRKPGM R DL + N I + + + K
Sbjct: 61 FPLLAGVVATTDPEEAFKDVDAALLVGAFPRKPGMERADLLSKNGKIFKEQGKALNKVAK 120
Query: 150 PNATVNLISNPVNSTVPIAAEVFKKAGTYDPKKLLGVTMLDVVRANTFVAEVLGLDPRDV 209
+ V ++ NP N+ IA+ K A PK +T LD RA +A G+ DV
Sbjct: 121 KDVKVLVVGNPANTNALIAS---KNAPDIPPKNFSAMTRLDHNRAKYQLAAKAGVPVSDV 177
Query: 210 DVPVVGGHAGVTILPLLSQVK---PPCSFTQEETEYLTN----RIQNGGTEVVEAKAGAG 262
++ G+ T +P + P ++ ++L +Q G V+EA+ GA
Sbjct: 178 KNVIIWGNHSNTQVPDFTHATVDGRPVKEVIKDDKWLEGEFIPTVQQRGAAVIEAR-GAS 236
Query: 263 SA 264
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 = 72.7 bits (179), Expect = 8e-15
Identities = 47/127 (37%), Positives = 64/127 (50%), Gaps = 8/127 (6%)
Query: 106 ALTGMDLVIIPAGVPRKPGMT--RDDLFNINAGIVRTLCEGIAKCCPNATVNLISNPVNS 163
D+++I AG PG T R DL NA I+R + I K A + LI+NP++
Sbjct: 65 DCADADIIVITAGPSIDPGNTDDRLDLAQTNAKIIREIMGNITKVTKEAVIILITNPLDI 124
Query: 164 TVPIAAEVFKKAGTYDPKKLLGV-TMLDVVRANTFVAEVLGLDPRDVDVPVVGGHAGVTI 222
V IAA F Y K++G TMLD R VA+ G+DP++V V+G H G
Sbjct: 125 AVYIAATEFD----YPANKVIGTGTMLDTARLRRIVADKYGVDPKNVTGYVLGEH-GSHA 179
Query: 223 LPLLSQV 229
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 = 65.6 bits (160), Expect = 2e-12
Identities = 62/239 (25%), Positives = 96/239 (40%), Gaps = 29/239 (12%)
Query: 43 KVAILGAAGGIGQPLA-------MLMKINPLVSVLHLYDVVNTPGVTADISH--MDTG-A 92
+V + GAAG IG L ML K P++ LHL D+ V + MD
Sbjct: 1 RVVVTGAAGQIGYALLPMIARGRMLGKDQPII--LHLLDIPPAMKVLEGVVMELMDCAFP 58
Query: 93 VVRGFLGQPQLENALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAK-CCPN 151
++ G + A T +D+ I+ PRK GM R DL + N I + + K +
Sbjct: 59 LLDGVVPTHDPAVAFTDVDVAILVGAFPRKEGMERRDLLSKNVKIFKEQGRALDKLAKKD 118
Query: 152 ATVNLISNPVNSTVPIAAEVFKKAGTYDPKKLLGVTMLDVVRANTFVAEVLGLDPRDV-D 210
V ++ NP N+ + + A + PK +T LD RA VAE G+ DV +
Sbjct: 119 CKVLVVGNPANTNALVLSNY---APSIPPKNFSALTRLDHNRALAQVAERAGVPVSDVKN 175
Query: 211 VPVVGGHAGVTILPLLSQVKPPCSFTQEETEYLTNR-----------IQNGGTEVVEAK 258
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 = 64.9 bits (159), Expect = 4e-12
Identities = 45/164 (27%), Positives = 77/164 (46%), Gaps = 16/164 (9%)
Query: 109 GMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAKCCPNATVNLISNPVNSTVPIA 168
DLV+I AG P+KPG TR DL N I +++ + + + SNPV+ I
Sbjct: 73 DADLVVITAGAPQKPGETRLDLVEKNLKIFKSIVGEVMASGFDGIFLVASNPVD----IL 128
Query: 169 AEVFKKAGTYDPKKLLGV-TMLDVVRANTFVAEVLGLDPRDVDVPVVGGH---------- 217
K + ++++G T LD R ++E L +DPR V ++G H
Sbjct: 129 TYATWKLSGFPKERVIGSGTSLDSARFRYMLSEKLDVDPRSVHAYIIGEHGDTEFPVWSH 188
Query: 218 AGVTILPLLSQVKPPCSFTQEETEYLTNRIQNGGTEVVEAKAGA 261
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 = 62.3 bits (152), Expect = 3e-11
Identities = 50/187 (26%), Positives = 79/187 (42%), Gaps = 17/187 (9%)
Query: 43 KVAILGAAGGIGQPLA-------MLMKINPLVSVLHLYDVVNTPGVTADIS-HMDTGA-- 92
+V + GAAG I L + P++ LHL D+ + + A
Sbjct: 4 RVLVTGAAGQIAYSLLPMIAKGDVFGPDQPVI--LHLLDIPPALKALEGVVMELQDCAFP 61
Query: 93 VVRGFLGQPQLENALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAKCC-PN 151
+++ + E A +D+ I+ +PRK GM R DL N I + E + K N
Sbjct: 62 LLKSVVATTDPEEAFKDVDVAILVGAMPRKEGMERKDLLKANVKIFKEQGEALDKYAKKN 121
Query: 152 ATVNLISNPVNSTVPIAAEVFKKAGTYDPKKLLGVTMLDVVRANTFVAEVLGLDPRDV-D 210
V ++ NP N+ I K A + + +T LD RA + +A LG+ DV +
Sbjct: 122 VKVLVVGNPANTNALILL---KYAPSIPKENFTALTRLDHNRAKSQIALKLGVPVSDVKN 178
Query: 211 VPVVGGH 217
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 = 61.5 bits (150), Expect = 7e-11
Identities = 57/200 (28%), Positives = 89/200 (44%), Gaps = 22/200 (11%)
Query: 41 GFKVAILGA-AGGIGQPLAMLMKINPLVSVLHLYDVVN--TPGVTADISHMDTGAVVRGF 97
KV ++G G+ +++L K L L L DVV G D+ H G+ F
Sbjct: 3 RNKVTVVGVGQVGMACAISILAK--GLADELVLVDVVEDKLKGEAMDLQH---GSA---F 54
Query: 98 LGQPQLE-----NALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAKCCPNA 152
L P++E + +VI+ AG + G +R DL N I + + + K PNA
Sbjct: 55 LKNPKIEADKDYSVTANSKVVIVTAGARQNEGESRLDLVQRNVDIFKGIIPKLVKYSPNA 114
Query: 153 TVNLISNPVNSTVPIAAEVFKKAGTYDPKKLLGV-TMLDVVRANTFVAEVLGLDPRDVDV 211
+ ++SNPV+ I V K +++G LD R +AE LG+ P V
Sbjct: 115 ILLVVSNPVD----IMTYVAWKLSGLPKHRVIGSGCNLDSARFRYLIAERLGVAPSSVHG 170
Query: 212 PVVGGHAGVTILPLLSQVKP 231
++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 = 2e-10
Identities = 37/135 (27%), Positives = 59/135 (43%), Gaps = 4/135 (2%)
Query: 96 GFLGQPQLENALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAKCC-PNATV 154
G + +LE A +D + A VP KPG R DL N I + E +++ P V
Sbjct: 47 GTIVTTKLEEAFKDIDCAFLVASVPLKPGEVRADLLTKNTPIFKATGEALSEYAKPTVKV 106
Query: 155 NLISNPVNSTVPIAAEVFKKAGTYDPKKLLGVTMLDVVRANTFVAEVLGLDPRDVDVPVV 214
+I NPVN+ +A A + + MLD RA + +A L + + VV
Sbjct: 107 LVIGNPVNTNCLVA---MLHAPKLSAENFSSLCMLDHNRAVSRIASKLKVPVDHIYHVVV 163
Query: 215 GGHAGVTILPLLSQV 229
G+ +++ L+
Sbjct: 164 WGNHAESMVADLTHA 178
>gnl|CDD|178212 PLN02602, PLN02602, lactate dehydrogenase.
Length = 350
Score = 57.5 bits (139), Expect = 2e-09
Identities = 62/238 (26%), Positives = 108/238 (45%), Gaps = 34/238 (14%)
Query: 43 KVAILGAAGGIGQPLAMLMKINPLVSVLHLYDVV--NTPGVTADISHMDTGAVVRGFLGQ 100
KV+++G G +G +A + L L L DV G D+ H FL +
Sbjct: 39 KVSVVGV-GNVGMAIAQTILTQDLADELALVDVNPDKLRGEMLDLQH------AAAFLPR 91
Query: 101 PQL----ENALT-GMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAKCCPNATVN 155
++ + A+T G DL I+ AG + PG +R +L N + R + +AK P+ +
Sbjct: 92 TKILASTDYAVTAGSDLCIVTAGARQIPGESRLNLLQRNVALFRKIIPELAKYSPDTILL 151
Query: 156 LISNPVNSTVPIAAEVFKKAGTYDPKKLLGV-TMLDVVRANTFVAEVLGLDPRDVDVPVV 214
++SNPV+ +A +K +G + +++G T LD R +A+ L ++ +DV +V
Sbjct: 152 IVSNPVDVLTYVA---WKLSG-FPANRVIGSGTNLDSSRFRFLIADHLDVNAQDVQAYIV 207
Query: 215 GGH-------------AGVTILPLLSQVKPPCSFTQEETEYLTNRIQNGGTEVVEAKA 259
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 = 52.9 bits (127), Expect = 5e-08
Identities = 46/175 (26%), Positives = 83/175 (47%), Gaps = 17/175 (9%)
Query: 48 GAAGGIGQPLAM-LMKINPLVSVLHLYDVVNTPGVTADISHMDTG-AVVRGFLGQPQLEN 105
G G QP+ + ++ I P L+ GV ++ +D +++G + +
Sbjct: 5 GVMLGPDQPVILHMLDIPPAAEALN--------GVKMEL--IDAAFPLLKGVVATTDVVE 54
Query: 106 ALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAKCC-PNATVNLISNPVNST 164
A G+++ ++ G PRK GM R D+ + N I ++ + K P+ V +++NP N+
Sbjct: 55 ACKGVNIAVMVGGFPRKEGMERKDVMSKNVSIYKSQASALEKHAAPDCKVLVVANPANTN 114
Query: 165 VPIAAEVFKKAGTYDPKKLLGVTMLDVVRANTFVAEVLGLDPRDV-DVPVVGGHA 218
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: 43 KVAILGAAGGIGQPL-------AMLMKINPLVSVLHLYDVVNT----PGVTADISHMDTG 91
+VA+ GAAG IG L M P++ L L ++ GV ++ +
Sbjct: 4 RVAVTGAAGQIGYSLLFRIASGEMFGPDQPVI--LQLLELPQALKALEGVAMEL---EDC 58
Query: 92 A--VVRGFLGQPQLENALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAK-C 148
A ++ + A D ++ PR PGM R DL N I + +
Sbjct: 59 AFPLLAEIVITDDPNVAFKDADWALLVGAKPRGPGMERADLLKANGKIFTAQGKALNDVA 118
Query: 149 CPNATVNLISNPVNSTVPIAAEVFKKAGTYDPKKLLGVTMLDVVRANTFVAEVLGLDPRD 208
+ V ++ NP N+ IA K A P +T LD RA + +A+ G+ D
Sbjct: 119 SRDVKVLVVGNPCNTNALIAM---KNAPDIPPDNFTAMTRLDHNRAKSQLAKKAGVPVTD 175
Query: 209 VDVPVVGGHAGVTILPLLSQVK---PPCSFTQEETEYLTN----RIQNGGTEVVEAKAGA 261
V V+ G+ T P + P + + +L + +Q G +++A+ GA
Sbjct: 176 VKNMVIWGNHSPTQYPDFTNATIGGKPAAEVINDRAWLEDEFIPTVQKRGAAIIKAR-GA 234
Query: 262 GSA 264
SA
Sbjct: 235 SSA 237
>gnl|CDD|235468 PRK05442, PRK05442, malate dehydrogenase; Provisional.
Length = 326
Score = 44.0 bits (105), Expect = 4e-05
Identities = 64/244 (26%), Positives = 102/244 (41%), Gaps = 32/244 (13%)
Query: 43 KVAILGAAGGIGQPL-------AMLMKINPLVSVLHLYDVVNTPGVTA---DISHMDTGA 92
+VA+ GAAG IG L ML K P++ L L ++ P + A + +D A
Sbjct: 6 RVAVTGAAGQIGYSLLFRIASGDMLGKDQPVI--LQLLEI--PPALKALEGVVMELDDCA 61
Query: 93 --VVRGFLGQPQLENALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRTLCEGIAKCC- 149
++ G + A D+ ++ PR PGM R DL N I + + +
Sbjct: 62 FPLLAGVVITDDPNVAFKDADVALLVGARPRGPGMERKDLLEANGAIFTAQGKALNEVAA 121
Query: 150 PNATVNLISNPVNSTVPIAAEVFKKAGTYDPKKLLGVTMLDVVRANTFVAEVLGLDPRDV 209
+ V ++ NP N+ IA K A + +T LD RA + +A G+ D+
Sbjct: 122 RDVKVLVVGNPANTNALIAM---KNAPDLPAENFTAMTRLDHNRALSQLAAKAGVPVADI 178
Query: 210 -DVPVVGGHAGVTILPLLSQV----KPPCSFTQEETEYLTN----RIQNGGTEVVEAKAG 260
+ V G H+ T P KP ++ +L + +Q G ++EA+ G
Sbjct: 179 KKMTVWGNHSA-TQYPDFRHATIDGKPAAEVINDQ-AWLEDTFIPTVQKRGAAIIEAR-G 235
Query: 261 AGSA 264
A SA
Sbjct: 236 ASSA 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: 120 PRKPGMTRDDLFNINAGIV----RTLCEGIAKCCPNATVNLISNPVNSTVPIAAEVFKKA 175
PR PGM R DL +IN I + L E +A N V ++ NP N+ I K A
Sbjct: 187 PRGPGMERADLLDINGQIFAEQGKALNE-VAS--RNVKVIVVGNPCNTNALIC---LKNA 240
Query: 176 GTYDPKKLLGVTMLDVVRA 194
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 = 35.8 bits (83), Expect = 0.018
Identities = 23/93 (24%), Positives = 42/93 (45%), Gaps = 4/93 (4%)
Query: 45 AILGAAGGIGQPLA-MLMKINPLVSVLHLYDVVNTPGVTADISHMDTGAVVRG-FLGQPQ 102
+ G G +G+ + +L++ L V ++D+ +P + D S + + G +
Sbjct: 1 LVTGGGGFLGRHIVRLLLREGELQEV-RVFDLRFSPELLEDFSKLQVITYIEGDVTDKQD 59
Query: 103 LENALTGMDLVIIPAGVPRKPGM-TRDDLFNIN 134
L AL G D+VI A + G RD + +N
Sbjct: 60 LRRALQGSDVVIHTAAIIDVFGKAYRDTIMKVN 92
>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 = 0.044
Identities = 53/219 (24%), Positives = 73/219 (33%), Gaps = 68/219 (31%)
Query: 41 GFKVAILGAAGGIGQP--LAMLMKINPLVSV--LHLYDV---------------VNTPGV 81
FK+ I+G G P L + + V L LYD+ V G
Sbjct: 3 KFKIVIIGG-GSTYTPKLLLGDLARTEELPVRELALYDIDEERLKIIAILAKKLVEEAGA 61
Query: 82 TADIS-HMDTGAVVRGFLGQPQLENALTGMDLVIIPA------------GVPRKPGMTRD 128
+ D AL G D VI +P K G+
Sbjct: 62 PVKVEATTD-------------RREALEGADFVITQIRVGGLEAREKDERIPLKHGLYGQ 108
Query: 129 DLFNINAGIVRTL---------CEGIAKCCPNATVNLISNPVNSTVPIAAEVFKKAGTYD 179
+ N GI L + + K CPNA + +NP AA V +
Sbjct: 109 E-TNGPGGIFYGLRTIPVILDIAKDMEKVCPNAWMLNYTNP-------AAIVTEAVRRLY 160
Query: 180 PK-KLLGVTMLDVVRANTF-VAEVLGLDPR-DVDVPVVG 215
PK K++G+ +AEVLGL+PR D+ V G
Sbjct: 161 PKIKIVGLC--HGPIGIAMELAEVLGLEPREDLRYRVAG 197
>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: 111 DLVIIPAGVPRKPGMTRDDLFNINAGIV----RTLCEGIAKCCPNATVNLISNPVNSTVP 166
D ++ PR PGM R DL +IN I + L +K C V ++ NP N+
Sbjct: 122 DWALLIGAKPRGPGMERADLLDINGQIFADQGKALNAVASKNC---KVLVVGNPCNTNAL 178
Query: 167 IAAEVFKKAGTYDPKKLLGVTMLDVVRA 194
IA K A K +T LD RA
Sbjct: 179 IA---MKNAPNIPRKNFHALTRLDENRA 203
>gnl|CDD|172654 PRK14166, PRK14166, bifunctional 5,10-methylene-tetrahydrofolate
dehydrogenase/ 5,10-methylene-tetrahydrofolate
cyclohydrolase; Provisional.
Length = 282
Score = 33.5 bits (76), Expect = 0.092
Identities = 26/102 (25%), Positives = 42/102 (41%), Gaps = 29/102 (28%)
Query: 41 GFKVAILGAAGGIGQPLA-MLMKINPLVSVLHLYDVVNTPGVTADISHMDTGAVVRGFLG 99
G I+GA+ +G+P+A ML+ VSV H+ T D+S A
Sbjct: 157 GKDAVIIGASNIVGRPMATMLLNAGATVSVCHIK--------TKDLSLYTRQA------- 201
Query: 100 QPQLENALTGMDLVIIPAGVPR--KPGMTRDDLFNINAGIVR 139
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 = 0.17
Identities = 14/38 (36%), Positives = 20/38 (52%), Gaps = 4/38 (10%)
Query: 91 GAVVR----GFLGQPQLENALTGMDLVIIPAGVPRKPG 124
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: 43 KVAILGAAGGIGQPLAMLMKINPLVSVLHLYDVVNTPGVTADISHMDTGAVVRGFLGQPQ 102
KVAI+GA G +GQ L L+ +P + ++ L + G ++ L +
Sbjct: 1 KVAIVGATGYVGQELLRLLAEHPPLELVALVASSRSAGKKVAFAYPILEGGKDLLL-EDV 59
Query: 103 LENALTGMDLVII--PAGV 119
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 = 0.33
Identities = 34/149 (22%), Positives = 44/149 (29%), Gaps = 58/149 (38%)
Query: 103 LENALTGMDLVIIPAGVPRKPGMTRDDLFNINA---------------GIVRTL------ 141
AL G D VI V D F I GI R L
Sbjct: 68 RREALDGADFVINTIQVGGHEYTETD--FEIPEKYGYYQTVGDTSGPGGIFRALRTIPVL 125
Query: 142 ---CEGIAKCCPNATVNLISNPV-------NSTVPIAA-----EVFKKAGTYDPKKLLGV 186
I + CP+A + +NP+ N PI V GT +
Sbjct: 126 LDIARDIEELCPDAWLLNYANPMAELTWALNRYTPIKTVGLCHGVQ---GTAE------- 175
Query: 187 TMLDVVRANTFVAEVLGLDPRDVDVPVVG 215
+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 = 30.9 bits (70), Expect = 0.56
Identities = 23/100 (23%), Positives = 39/100 (39%), Gaps = 29/100 (29%)
Query: 41 GFKVAILGAAGGIGQPLA-MLMKINPLVSVLHLYDVVNTPGVTADISHMDTGAVVRGFLG 99
G I+G + +G+P+A ML+ N VSV H++ T D+ A
Sbjct: 164 GKNAVIVGHSNVVGKPMAAMLLNRNATVSVCHVF--------TDDLKKYTLDA------- 208
Query: 100 QPQLENALTGMDLVIIPAGVPR--KPGMTRDDLFNINAGI 137
D++++ GV K M ++ + GI
Sbjct: 209 -----------DILVVATGVKHLIKADMVKEGAVIFDVGI 237
>gnl|CDD|179337 PRK01810, PRK01810, DNA polymerase IV; Validated.
Length = 407
Score = 29.6 bits (67), Expect = 1.7
Identities = 11/25 (44%), Positives = 16/25 (64%)
Query: 168 AAEVFKKAGTYDPKKLLGVTMLDVV 192
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 = 2.5
Identities = 16/35 (45%), Positives = 21/35 (60%), Gaps = 1/35 (2%)
Query: 40 AGFKVAILGAAGGIGQPLAMLM-KINPLVSVLHLY 73
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 = 28.4 bits (64), Expect = 3.8
Identities = 19/74 (25%), Positives = 33/74 (44%), Gaps = 3/74 (4%)
Query: 43 KVAILGAAGGIGQPLA-MLMKINPLVSVLHLYDVVNTPGVTADISHMDTGAVVRGFLGQP 101
V + GA G IG L L++ V L +Y+ N+ G+ + H D + G +
Sbjct: 1 NVLVTGADGFIGSHLTERLLREGHEVRALDIYNSFNSWGLLDNAVH-DRFHFISGDVRDA 59
Query: 102 -QLENALTGMDLVI 114
++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 = 27.9 bits (63), Expect = 4.0
Identities = 14/35 (40%), Positives = 22/35 (62%), Gaps = 1/35 (2%)
Query: 40 AGFKVAILGAAGGIGQPLA-MLMKINPLVSVLHLY 73
AG KV ++G + +G+PLA +L+ N V+V H
Sbjct: 43 AGKKVVVVGRSNIVGKPLAALLLNRNATVTVCHSK 77
>gnl|CDD|202102 pfam02056, Glyco_hydro_4, Family 4 glycosyl hydrolase.
Length = 183
Score = 27.7 bits (62), Expect = 5.9
Identities = 42/196 (21%), Positives = 65/196 (33%), Gaps = 47/196 (23%)
Query: 43 KVAILGAAGGIGQPLAMLMKINPL----VSVLHLYDVVNTPGVTADISH------MDTGA 92
K+ I+G G P +L ++ L LYD+ D +D
Sbjct: 1 KIVIIGG-GSTITPKNLLGDLDHTEELPGRELALYDI---DEERLDAIQTACKKLVDEAG 56
Query: 93 VVRGFLGQPQLENALTGMDLVIIPAGVPRKPGMTRDDLFNINAGIVRT------------ 140
F + ALT D VI V P D+ + G+V T
Sbjct: 57 PDIKFEKTTDRKEALTDADFVINAIRVGLLPARELDEKIPLRHGVVGTIQETVGPGGIFR 116
Query: 141 ----------LCEGIAKCCPNATVNLISNPVNSTVPIA--AEVFKKAGTYDPKKLLGVTM 188
+ + I + CP+A V +N T P A E + Y K +G+
Sbjct: 117 GLRTIPVFFDIAKDIEELCPDAWV------LNYTNPAAMVTEAVYR--RYPNIKAVGLCH 168
Query: 189 LDVVRANTFVAEVLGL 204
+ +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 = 27.7 bits (62), Expect = 6.2
Identities = 12/32 (37%), Positives = 16/32 (50%), Gaps = 3/32 (9%)
Query: 161 VNSTVPIAAEVFKKAGTYDPKKLLGVTMLDVV 192
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 = 7.1
Identities = 13/38 (34%), Positives = 17/38 (44%), Gaps = 2/38 (5%)
Query: 35 AKGGAAGFKVAILGAAGGI--GQPLAMLMKINPLVSVL 70
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 = 7.6
Identities = 25/79 (31%), Positives = 35/79 (44%), Gaps = 6/79 (7%)
Query: 43 KVAILGAAGGIGQPLAMLMKINPLVSVLHLYDVVNTPGVTADISHMDTGAVVRGFLGQPQ 102
KV I GA+G +GQ LA + + L L DVV +P + + + G L P
Sbjct: 2 KVLITGASGFVGQRLAERLLSDVPNERLILIDVV-SPKAPSGAPRVTQ---IAGDLAVPA 57
Query: 103 LENALT--GMDLVIIPAGV 119
L AL D+V A +
Sbjct: 58 LIEALANGRPDVVFHLAAI 76
>gnl|CDD|222146 pfam13460, NAD_binding_10, NADH(P)-binding.
Length = 182
Score = 26.9 bits (60), Expect = 9.1
Identities = 15/79 (18%), Positives = 25/79 (31%), Gaps = 7/79 (8%)
Query: 44 VAILGAAGGIGQPLAMLMKINPLVSVLHLYDVVNTPGVTADISHMDTGAVVRGFLGQPQL 103
+A++GA G G+ L + + + P V + L
Sbjct: 1 IAVIGATGKTGRRLVKELLARG----HQVTALSRNPSKAPA---PGVTPVQKDLFDLADL 53
Query: 104 ENALTGMDLVIIPAGVPRK 122
AL G+D V+ G
Sbjct: 54 AEALAGVDAVVDAFGARPD 72
>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 = 9.2
Identities = 10/31 (32%), Positives = 17/31 (54%)
Query: 43 KVAILGAAGGIGQPLAMLMKINPLVSVLHLY 73
+VA+LGA G +GQ L+ +P + +
Sbjct: 2 RVAVLGATGLVGQKFVKLLAKHPYFELAKVV 32
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 0.395
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: 14,204,165
Number of extensions: 1388312
Number of successful extensions: 1580
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1530
Number of HSP's successfully gapped: 87
Length of query: 279
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 183
Effective length of database: 6,679,618
Effective search space: 1222370094
Effective search space used: 1222370094
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)