RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17689
(216 letters)
>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 = 338 bits (869), Expect = e-118
Identities = 131/196 (66%), Positives = 169/196 (86%)
Query: 21 YALSEGSRIVIVTAGVRQREGESRLSLVERNVNIFKGIIPNIVKYSPQCTLLIVSNPVDI 80
Y+++ S++VIVTAG RQ EGESRL LV+RNV+IFKGIIP +VKYSP LL+VSNPVDI
Sbjct: 66 YSVTANSKVVIVTAGARQNEGESRLDLVQRNVDIFKGIIPKLVKYSPNAILLVVSNPVDI 125
Query: 81 LTYVSWKLSGFPKNRVIGSGTNLDSMRFRVLLAQKLGLSPESVYGFIIGEHGDSSVPVWS 140
+TYV+WKLSG PK+RVIGSG NLDS RFR L+A++LG++P SV+G+IIGEHGDSSVPVWS
Sbjct: 126 MTYVAWKLSGLPKHRVIGSGCNLDSARFRYLIAERLGVAPSSVHGWIIGEHGDSSVPVWS 185
Query: 141 GVNVAGVNLREVNPAIGTEGDTEEFGKLHTDVVNSAYEIIRLKGYTSWAIGLSIASLTYT 200
GVNVAGV L+++NP IGT+ D E++ ++H VV+SAYE+I+LKGYTSWAIGLS+A L
Sbjct: 186 GVNVAGVRLQDLNPDIGTDKDPEKWKEVHKQVVDSAYEVIKLKGYTSWAIGLSVADLVDA 245
Query: 201 LLNNTNKIHAISTLIQ 216
+L NT ++H++STL++
Sbjct: 246 ILRNTGRVHSVSTLVK 261
>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 = 277 bits (712), Expect = 1e-94
Identities = 96/197 (48%), Positives = 136/197 (69%), Gaps = 1/197 (0%)
Query: 20 NYALSEGSRIVIVTAGVRQREGESRLSLVERNVNIFKGIIPNIVKYSPQCTLLIVSNPVD 79
+Y+ + + +V++TAG Q+ GE+RL LV RNV I K I+P +VK L+ +NPVD
Sbjct: 58 DYSDCKDADLVVITAGAPQKPGETRLELVGRNVRIMKSIVPEVVKSGFDGIFLVATNPVD 117
Query: 80 ILTYVSWKLSGFPKNRVIGSGTNLDSMRFRVLLAQKLGLSPESVYGFIIGEHGDSSVPVW 139
ILTYV+WKLSGFPKNRVIGSGT LD+ R R LLA+KLG+ P+SV+ +IIGEHGDS VPVW
Sbjct: 118 ILTYVAWKLSGFPKNRVIGSGTVLDTARLRYLLAEKLGVDPQSVHAYIIGEHGDSEVPVW 177
Query: 140 SGVNVAGVNLREVNPAIGTEGDTEEFGKLHTDVVNSAYEIIRLKGYTSWAIGLSIASLTY 199
S + GV L + A GTE D + ++ +V ++AYEII KG T + IG+++A +
Sbjct: 178 SSATIGGVPLLDYLKAKGTETD-LDLEEIEKEVRDAAYEIINRKGATYYGIGMAVARIVE 236
Query: 200 TLLNNTNKIHAISTLIQ 216
+L++ N++ +S +
Sbjct: 237 AILHDENRVLPVSAYLD 253
>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 = 277 bits (711), Expect = 3e-94
Identities = 101/195 (51%), Positives = 137/195 (70%)
Query: 21 YALSEGSRIVIVTAGVRQREGESRLSLVERNVNIFKGIIPNIVKYSPQCTLLIVSNPVDI 80
YA +G+ +V++TAG Q+ GE+RL L++RNV IFK IIP I+KY+P LL+V+NPVD+
Sbjct: 62 YADCKGADVVVITAGANQKPGETRLDLLKRNVAIFKEIIPQILKYAPDAILLVVTNPVDV 121
Query: 81 LTYVSWKLSGFPKNRVIGSGTNLDSMRFRVLLAQKLGLSPESVYGFIIGEHGDSSVPVWS 140
LTYV++KLSG P NRVIGSGT LD+ RFR LL + LG+ P SV+ +IIGEHGDS V VWS
Sbjct: 122 LTYVAYKLSGLPPNRVIGSGTVLDTARFRYLLGEHLGVDPRSVHAYIIGEHGDSEVAVWS 181
Query: 141 GVNVAGVNLREVNPAIGTEGDTEEFGKLHTDVVNSAYEIIRLKGYTSWAIGLSIASLTYT 200
N+ GV L E G D E ++ +V N+AYEII KG T +AIGL++A +
Sbjct: 182 SANIGGVPLDEFCKLCGRPFDEEVREEIFEEVRNAAYEIIERKGATYYAIGLALARIVEA 241
Query: 201 LLNNTNKIHAISTLI 215
+L + N + +S+L+
Sbjct: 242 ILRDENSVLTVSSLL 256
>gnl|CDD|178212 PLN02602, PLN02602, lactate dehydrogenase.
Length = 350
Score = 276 bits (708), Expect = 2e-93
Identities = 112/204 (54%), Positives = 146/204 (71%)
Query: 13 VNVLTRLNYALSEGSRIVIVTAGVRQREGESRLSLVERNVNIFKGIIPNIVKYSPQCTLL 72
+L +YA++ GS + IVTAG RQ GESRL+L++RNV +F+ IIP + KYSP LL
Sbjct: 92 TKILASTDYAVTAGSDLCIVTAGARQIPGESRLNLLQRNVALFRKIIPELAKYSPDTILL 151
Query: 73 IVSNPVDILTYVSWKLSGFPKNRVIGSGTNLDSMRFRVLLAQKLGLSPESVYGFIIGEHG 132
IVSNPVD+LTYV+WKLSGFP NRVIGSGTNLDS RFR L+A L ++ + V +I+GEHG
Sbjct: 152 IVSNPVDVLTYVAWKLSGFPANRVIGSGTNLDSSRFRFLIADHLDVNAQDVQAYIVGEHG 211
Query: 133 DSSVPVWSGVNVAGVNLREVNPAIGTEGDTEEFGKLHTDVVNSAYEIIRLKGYTSWAIGL 192
DSSV +WS V+V GV + + E ++H VV+SAYE+I+LKGYTSWAIG
Sbjct: 212 DSSVALWSSVSVGGVPVLSFLEKQQIAYEKETLEEIHRAVVDSAYEVIKLKGYTSWAIGY 271
Query: 193 SIASLTYTLLNNTNKIHAISTLIQ 216
S+ASL +LL + +IH +S L +
Sbjct: 272 SVASLVRSLLRDQRRIHPVSVLAK 295
>gnl|CDD|178836 PRK00066, ldh, L-lactate dehydrogenase; Reviewed.
Length = 315
Score = 249 bits (639), Expect = 2e-83
Identities = 91/197 (46%), Positives = 132/197 (67%), Gaps = 1/197 (0%)
Query: 20 NYALSEGSRIVIVTAGVRQREGESRLSLVERNVNIFKGIIPNIVKYSPQCTLLIVSNPVD 79
+Y+ + + +V++TAG Q+ GE+RL LVE+N+ IFK I+ ++ L+ SNPVD
Sbjct: 67 DYSDCKDADLVVITAGAPQKPGETRLDLVEKNLKIFKSIVGEVMASGFDGIFLVASNPVD 126
Query: 80 ILTYVSWKLSGFPKNRVIGSGTNLDSMRFRVLLAQKLGLSPESVYGFIIGEHGDSSVPVW 139
ILTY +WKLSGFPK RVIGSGT+LDS RFR +L++KL + P SV+ +IIGEHGD+ PVW
Sbjct: 127 ILTYATWKLSGFPKERVIGSGTSLDSARFRYMLSEKLDVDPRSVHAYIIGEHGDTEFPVW 186
Query: 140 SGVNVAGVNLREVNPAIGTEGDTEEFGKLHTDVVNSAYEIIRLKGYTSWAIGLSIASLTY 199
S NVAGV L E + E+ ++ +V ++AYEII KG T + I +++A +T
Sbjct: 187 SHANVAGVPLEEYLEENEQYDE-EDLDEIFENVRDAAYEIIEKKGATYYGIAMALARITK 245
Query: 200 TLLNNTNKIHAISTLIQ 216
+LNN N + +S ++
Sbjct: 246 AILNNENAVLPVSAYLE 262
>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 = 246 bits (631), Expect = 2e-82
Identities = 90/197 (45%), Positives = 129/197 (65%), Gaps = 5/197 (2%)
Query: 20 NYALSEGSRIVIVTAGVRQREGESRLSLVERNVNIFKGIIPNIVKYSPQCTLLIVSNPVD 79
+YA + + IV++TAG ++ GE+RL L+ RN I + +I N+ KY P +L+VSNPVD
Sbjct: 60 DYADAADADIVVITAGAPRKPGETRLDLINRNAPILRSVITNLKKYGPDAIILVVSNPVD 119
Query: 80 ILTYVSWKLSGFPKNRVIGSGTNLDSMRFRVLLAQKLGLSPESVYGFIIGEHGDSSVPVW 139
ILTYV+ KLSG PKNRVIGSGT LDS RFR LLA+KL + P+SV+ +++GEHGDS V W
Sbjct: 120 ILTYVAQKLSGLPKNRVIGSGTLLDSARFRSLLAEKLDVDPQSVHAYVLGEHGDSQVVAW 179
Query: 140 SGVNVAGVNLREVNPAIGTEGDTEEFGKLHTDVVNSAYEIIRLKGYTSWAIGLSIASLTY 199
S V G+ L E+ P + + +V S YEIIRLKG T++ I +IA +
Sbjct: 180 STATVGGLPLEELAP-----FTKLDLEAIEEEVRTSGYEIIRLKGATNYGIATAIADIVK 234
Query: 200 TLLNNTNKIHAISTLIQ 216
++L + ++ +S + +
Sbjct: 235 SILLDERRVLPVSAVQE 251
>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 = 223 bits (572), Expect = 3e-73
Identities = 80/186 (43%), Positives = 113/186 (60%), Gaps = 2/186 (1%)
Query: 29 IVIVTAGVRQREGESRLSLVERNVNIFKGIIPNIVKYSPQCTLLIVSNPVDILTYVSWKL 88
IV++TAG Q+ GE+RL L+E+N I K I+P I L+ SNPVD++TYV KL
Sbjct: 71 IVVITAGAPQKPGETRLDLLEKNAKIMKSIVPKIKASGFDGIFLVASNPVDVITYVVQKL 130
Query: 89 SGFPKNRVIGSGTNLDSMRFRVLLAQKLGLSPESVYGFIIGEHGDSSVPVWSGVNVAGVN 148
SG PKNRVIG+GT+LD+ R R LA+KL + P SV+ +++GEHGDS WS V V G
Sbjct: 131 SGLPKNRVIGTGTSLDTARLRRALAEKLNVDPRSVHAYVLGEHGDSQFVAWSTVTVGGKP 190
Query: 149 LREVNPAIGTEGDTEEFGKLHTDVVNSAYEIIRLKGYTSWAIGLSIASLTYTLLNNTNKI 208
L ++ G + + ++ DV + YEII KG T + I ++A + +LN+ N I
Sbjct: 191 LLDL-LKEGKLSE-LDLDEIEEDVRKAGYEIINGKGATYYGIATALARIVKAILNDENAI 248
Query: 209 HAISTL 214
+S
Sbjct: 249 LPVSAY 254
>gnl|CDD|223117 COG0039, Mdh, Malate/lactate dehydrogenases [Energy production and
conversion].
Length = 313
Score = 217 bits (555), Expect = 1e-70
Identities = 91/215 (42%), Positives = 131/215 (60%), Gaps = 8/215 (3%)
Query: 6 DHSSF---KGVNVLTRLNYALSEGSRIVIVTAGVRQREGESRLSLVERNVNIFKGIIPNI 62
H++ V + +Y +G+ IV++TAGV ++ G +RL L+E+N I K I I
Sbjct: 46 SHAAAPLGSDVKITGDGDYEDLKGADIVVITAGVPRKPGMTRLDLLEKNAKIVKDIAKAI 105
Query: 63 VKYSPQCTLLIVSNPVDILTYVSWKLSGFPKNRVIGSGTNLDSMRFRVLLAQKLGLSPES 122
KY+P +L+V+NPVDILTY++ K SGFPKNRVIGSGT LDS RFR LA+KLG+SP+
Sbjct: 106 AKYAPDAIVLVVTNPVDILTYIAMKFSGFPKNRVIGSGTVLDSARFRTFLAEKLGVSPKD 165
Query: 123 VYGFIIGEHGDSSVPVWSGVNVAGVNLREVNPAIGTEGDTEEFGKLHTDVVNSAYEIIRL 182
V+ ++IGEHGD+ VP+WS V G L E+ TE D EE + V N+ EII
Sbjct: 166 VHAYVIGEHGDTMVPLWSQATVGGKPLEELLKED-TEEDLEELIE---RVRNAGAEIIEA 221
Query: 183 KGY-TSWAIGLSIASLTYTLLNNTNKIHAISTLIQ 216
KG T + ++A + +L + ++ +S +
Sbjct: 222 KGAGTYYGPAAALARMVEAILRDEKRVLPVSVYLD 256
>gnl|CDD|180477 PRK06223, PRK06223, malate dehydrogenase; Reviewed.
Length = 307
Score = 188 bits (480), Expect = 2e-59
Identities = 70/199 (35%), Positives = 108/199 (54%), Gaps = 9/199 (4%)
Query: 20 NYALSEGSRIVIVTAGVRQREGESRLSLVERNVNIFKGIIPNIVKYSPQCTLLIVSNPVD 79
+Y GS +V++TAGV ++ G SR L+ N I K + I KY+P +++V+NPVD
Sbjct: 64 DYEDIAGSDVVVITAGVPRKPGMSRDDLLGINAKIMKDVAEGIKKYAPDAIVIVVTNPVD 123
Query: 80 ILTYVSWKLSGFPKNRVIGSGTNLDSMRFRVLLAQKLGLSPESVYGFIIGEHGDSSVPVW 139
+TYV+ K SGFPKNRVIG LDS RFR +A++L +S + V F++G HGDS VP+
Sbjct: 124 AMTYVALKESGFPKNRVIGMAGVLDSARFRTFIAEELNVSVKDVTAFVLGGHGDSMVPLV 183
Query: 140 SGVNVAGVNLREVNPAIGTEGDTEEFGKLHTDVVNSAYEIIRL--KGYTSWAIGLSIASL 197
V G+ L ++ E+ ++ EI+ L G +A SIA +
Sbjct: 184 RYSTVGGIPLEDLLSK-------EKLDEIVERTRKGGAEIVGLLKTGSAYYAPAASIAEM 236
Query: 198 TYTLLNNTNKIHAISTLIQ 216
+L + ++ S ++
Sbjct: 237 VEAILKDKKRVLPCSAYLE 255
>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 = 178 bits (454), Expect = 1e-55
Identities = 69/199 (34%), Positives = 112/199 (56%), Gaps = 9/199 (4%)
Query: 20 NYALSEGSRIVIVTAGVRQREGESRLSLVERNVNIFKGIIPNIVKYSPQCTLLIVSNPVD 79
+Y GS +V++TAG+ ++ G SR L+ N I K + NI KY+P +++V+NP+D
Sbjct: 60 DYEDIAGSDVVVITAGIPRKPGMSRDDLLGTNAKIVKEVAENIKKYAPNAIVIVVTNPLD 119
Query: 80 ILTYVSWKLSGFPKNRVIGSGTNLDSMRFRVLLAQKLGLSPESVYGFIIGEHGDSSVPVW 139
++TYV++K SGFP+NRVIG LDS RFR +A++LG+S + V ++G HGD+ VP+
Sbjct: 120 VMTYVAYKASGFPRNRVIGMAGVLDSARFRYFIAEELGVSVKDVQAMVLGGHGDTMVPLP 179
Query: 140 SGVNVAGVNLREVNPAIGTEGDTEEFGKLHTDVVNSAYEIIRLKGYTS--WAIGLSIASL 197
V G+ L E+ EE ++ N EI+ L S +A +IA +
Sbjct: 180 RYSTVGGIPLTELITK-------EEIDEIVERTRNGGAEIVNLLKTGSAYYAPAAAIAEM 232
Query: 198 TYTLLNNTNKIHAISTLIQ 216
+L + ++ S ++
Sbjct: 233 VEAILKDKKRVLPCSAYLE 251
>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 = 166 bits (422), Expect = 1e-50
Identities = 68/198 (34%), Positives = 116/198 (58%), Gaps = 6/198 (3%)
Query: 20 NYALSEGSRIVIVTAG--VRQREGESRLSLVERNVNIFKGIIPNIVKYSPQCTLLIVSNP 77
+Y + I+++TAG + + RL L + N I + I+ NI K + + +++++NP
Sbjct: 62 DYDDCADADIIVITAGPSIDPGNTDDRLDLAQTNAKIIREIMGNITKVTKEAVIILITNP 121
Query: 78 VDILTYVSWKLSGFPKNRVIGSGTNLDSMRFRVLLAQKLGLSPESVYGFIIGEHGDSSVP 137
+DI Y++ +P N+VIG+GT LD+ R R ++A K G+ P++V G+++GEHG + P
Sbjct: 122 LDIAVYIAATEFDYPANKVIGTGTMLDTARLRRIVADKYGVDPKNVTGYVLGEHGSHAFP 181
Query: 138 VWSGVNVAGVNLREVNPAIGTEG-DTEEFGKLHTDVVNSAYEIIRLKGYTSWAIGLSIAS 196
VWS VN+AG+ L E+ G E D +E + +VV +AY++ KG+T+ I S +
Sbjct: 182 VWSLVNIAGLPLDELEALFGKEPIDKDELLE---EVVQAAYDVFNRKGWTNAGIAKSASR 238
Query: 197 LTYTLLNNTNKIHAISTL 214
L +L + I + TL
Sbjct: 239 LIKAILLDERSILPVCTL 256
>gnl|CDD|133419 cd00650, LDH_MDH_like, NAD-dependent, lactate dehydrogenase-like,
2-hydroxycarboxylate dehydrogenase family. Members of
this family include ubiquitous enzymes like L-lactate
dehydrogenases (LDH), L-2-hydroxyisocaproate
dehydrogenases, and some malate dehydrogenases (MDH).
LDH catalyzes the last step of glycolysis in which
pyruvate is converted to L-lactate. MDH is one of the
key enzymes in the citric acid cycle, facilitating both
the conversion of malate to oxaloacetate and
replenishing levels of oxalacetate by reductive
carboxylation of pyruvate. The LDH/MDH-like proteins are
part of the NAD(P)-binding Rossmann fold superfamily,
which includes a wide variety of protein families
including the NAD(P)-binding domains of alcohol
dehydrogenases, tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate dehydrogenases,
formate/glycerate dehydrogenases, siroheme synthases,
6-phosphogluconate dehydrogenases, aminoacid
dehydrogenases, repressor rex, and NAD-binding potassium
channel domains, among others.
Length = 263
Score = 147 bits (374), Expect = 4e-44
Identities = 66/125 (52%), Positives = 89/125 (71%), Gaps = 1/125 (0%)
Query: 21 YALSEGSRIVIVTAGVRQREGESRLSLVERNVNIFKGIIPNIVKYSPQCTLLIVSNPVDI 80
Y + + +VI+TAGV ++ G RL L++RNV I K I NI KYSP +++VSNPVDI
Sbjct: 65 YEAFKDADVVIITAGVGRKPGMGRLDLLKRNVPIVKEIGDNIEKYSPDAWIIVVSNPVDI 124
Query: 81 LTYVSWKLSGFPKNRVIGSGTNLDSMRFRVLLAQKLGLSPESVYGFIIGEHGDSSVPVWS 140
+TY+ W+ SG PK +VIG GT LD +RFR +LA+KLG+ P+ V +I+GEHG S VP WS
Sbjct: 125 ITYLVWRYSGLPKEKVIGLGT-LDPIRFRRILAEKLGVDPDDVKVYILGEHGGSQVPDWS 183
Query: 141 GVNVA 145
V +A
Sbjct: 184 TVRIA 188
>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 = 146 bits (371), Expect = 3e-43
Identities = 75/191 (39%), Positives = 116/191 (60%), Gaps = 5/191 (2%)
Query: 26 GSRIVIVTAGVRQREGESRLSLVERNVNIFKGIIPNIVKYSPQCTLLIVSNPVDILTYVS 85
GS IVI+TAGV ++EG SRL L ++N I K I +++P +L+V+NPVD++TY +
Sbjct: 72 GSDIVIITAGVPRKEGMSRLDLAKKNAKIVKKYAKQIAEFAPDTKILVVTNPVDVMTYKA 131
Query: 86 WKLSGFPKNRVIGSGTNLDSMRFRVLLAQKLGLSPESVYGFIIGEHGDSSVPVWSGVNVA 145
K SGF KNRV G GT+LDS+RF+V +A+ + V+ IIGEHGDS VP+ S ++
Sbjct: 132 LKESGFDKNRVFGLGTHLDSLRFKVAIAKHFNVHISEVHTRIIGEHGDSMVPLISSTSIG 191
Query: 146 GVNLREVNPAIGTEGDTEEFGKLHTDVVNSAYEIIRLKGYTSWAIGLSIASLTYTLLNNT 205
G+ ++ E + K+ V N+ II LKG + + +I++L T+ N+
Sbjct: 192 GIPIKRF-----PEYKDFDVEKIVETVKNAGQNIISLKGGSEYGPASAISNLVRTIANDE 246
Query: 206 NKIHAISTLIQ 216
+I +ST ++
Sbjct: 247 RRILTVSTYLE 257
>gnl|CDD|173376 PTZ00082, PTZ00082, L-lactate dehydrogenase; Provisional.
Length = 321
Score = 130 bits (328), Expect = 1e-36
Identities = 67/214 (31%), Positives = 109/214 (50%), Gaps = 11/214 (5%)
Query: 11 KGVNVLTRLNYALSEGSRIVIVTAGVRQREGES-----RLSLVERNVNIFKGIIPNIVKY 65
V+ NY GS +VIVTAG+ +R G+S R L+ N I + I KY
Sbjct: 59 SNSKVIGTNNYEDIAGSDVVIVTAGLTKRPGKSDKEWNRDDLLPLNAKIMDEVAEGIKKY 118
Query: 66 SPQCTLLIVSNPVDILTYVSWKLSGFPKNRVIGSGTNLDSMRFRVLLAQKLGLSPESVYG 125
P +++++NP+D++ + + SG PKN+V G LDS R R +A+KLG++P V+
Sbjct: 119 CPNAFVIVITNPLDVMVKLLQEHSGLPKNKVCGMAGVLDSSRLRTYIAEKLGVNPRDVHA 178
Query: 126 FIIGEHGDSSVPVWSGVNVAGVNLRE-VNPAIGTEGDTEEFGKLHTDVVNSAYEIIRLKG 184
+IG HGD VP+ V V G+ L E + + T+ + +E + T N+ EI+ L G
Sbjct: 179 SVIGAHGDKMVPLPRYVTVGGIPLSEFIKKGLITQEEIDEIVE-RT--RNTGKEIVDLLG 235
Query: 185 YTS--WAIGLSIASLTYTLLNNTNKIHAISTLIQ 216
S +A + + L + ++ S ++
Sbjct: 236 TGSAYFAPAAAAIEMAEAYLKDKKRVLPCSAYLE 269
>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 = 129 bits (325), Expect = 2e-36
Identities = 57/136 (41%), Positives = 88/136 (64%)
Query: 20 NYALSEGSRIVIVTAGVRQREGESRLSLVERNVNIFKGIIPNIVKYSPQCTLLIVSNPVD 79
NYA + S IV++TAG+ ++ G SR L+ N I + + I+++SP +++VSNP+D
Sbjct: 63 NYADTANSDIVVITAGLPRKPGMSREDLLSMNAGIVREVTGRIMEHSPNPIIVVVSNPLD 122
Query: 80 ILTYVSWKLSGFPKNRVIGSGTNLDSMRFRVLLAQKLGLSPESVYGFIIGEHGDSSVPVW 139
+TYV+W+ SGFPK RVIG LDS RFR +A +LG+S + V ++G HGD+ VP+
Sbjct: 123 AMTYVAWQKSGFPKERVIGQAGVLDSARFRTFIAMELGVSVQDVTACVLGGHGDAMVPLV 182
Query: 140 SGVNVAGVNLREVNPA 155
VAG+ + ++ A
Sbjct: 183 RYSTVAGIPVADLISA 198
>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 = 122 bits (308), Expect = 1e-35
Identities = 41/79 (51%), Positives = 57/79 (72%)
Query: 21 YALSEGSRIVIVTAGVRQREGESRLSLVERNVNIFKGIIPNIVKYSPQCTLLIVSNPVDI 80
Y + + +V++TAGV ++ G +RL L+ RN IFK I+P I K +P +L+VSNPVDI
Sbjct: 64 YEALKDADVVVITAGVPRKPGMTRLDLLNRNAGIFKDIVPAIAKSAPDAIVLVVSNPVDI 123
Query: 81 LTYVSWKLSGFPKNRVIGS 99
LTY++WK+SG P RVIGS
Sbjct: 124 LTYIAWKVSGLPPERVIGS 142
>gnl|CDD|173409 PTZ00117, PTZ00117, malate dehydrogenase; Provisional.
Length = 319
Score = 124 bits (312), Expect = 3e-34
Identities = 69/204 (33%), Positives = 107/204 (52%), Gaps = 6/204 (2%)
Query: 13 VNVLTRLNYALSEGSRIVIVTAGVRQREGESRLSLVERNVNIFKGIIPNIVKYSPQCTLL 72
+N+L NY + S +V++TAGV+++E +R L+ N I K + ++ KY P ++
Sbjct: 60 INILGTNNYEDIKDSDVVVITAGVQRKEEMTREDLLTINGKIMKSVAESVKKYCPNAFVI 119
Query: 73 IVSNPVDILTYVSWKLSGFPKNRVIGSGTNLDSMRFRVLLAQKLGLSPESVYGFIIGEHG 132
V+NP+D + V + SG P N++ G LDS RFR LA+KLG+SP V +IG HG
Sbjct: 120 CVTNPLDCMVKVFQEKSGIPSNKICGMAGVLDSSRFRCNLAEKLGVSPGDVSAVVIGGHG 179
Query: 133 DSSVPVWSGVNVAGVNLRE-VNPAIGTEGDTEEFGKLHTDVVNSAYEIIRL--KGYTSWA 189
D VP+ V G+ L + V TE + E K T N EI++L KG +A
Sbjct: 180 DLMVPLPRYCTVNGIPLSDFVKKGAITEKEINEIIK-KTR--NMGGEIVKLLKKGSAFFA 236
Query: 190 IGLSIASLTYTLLNNTNKIHAIST 213
+I ++ L + ++ S
Sbjct: 237 PAAAIVAMIEAYLKDEKRVLVCSV 260
>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 = 82.0 bits (203), Expect = 1e-19
Identities = 35/115 (30%), Positives = 57/115 (49%), Gaps = 4/115 (3%)
Query: 101 TNLDSMRFRVLLAQKLGLSPESVYGFIIGEHGDSSVPVWSGVNVAGVNLRE-VNPAIGTE 159
T LD+ R R LA+K G+ P SV ++IGEH + P WS V + L V + +
Sbjct: 1 TTLDTARARTFLAEKFGVDPRSVNVYVIGEHSGTQFPDWSHAKVTIIPLISQVKENL--K 58
Query: 160 GDTEEFGKLHTDVVNSAYEIIRLK-GYTSWAIGLSIASLTYTLLNNTNKIHAIST 213
E +L V N+ YE+I K G T++++ + A + +L T + ++
Sbjct: 59 DTDWELEELIERVQNAGYEVIEAKAGSTTYSMAYAAARIAKAILRGTGGVLSVGV 113
>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 = 66.0 bits (162), Expect = 6e-13
Identities = 42/132 (31%), Positives = 66/132 (50%), Gaps = 7/132 (5%)
Query: 19 LNYALSEGSRIVIVTAGVRQREGESRLSLVERNVNIFKGIIPNIVKYSPQCTLLIVSNPV 78
L AL +G+ +V++ AGV ++ G +R L N I + + + K P+ +LI+SNPV
Sbjct: 62 LKKAL-KGADVVVIPAGVPRKPGMTRDDLFNINAGIVRDLATAVAKACPKALILIISNPV 120
Query: 79 D----ILTYVSWKLSGFPKNRVIGSGTNLDSMRFRVLLAQKLGLSPESVYGFIIGEH-GD 133
+ I V K + R+ G T LD +R +A+ LGL P V +IG H G
Sbjct: 121 NSTVPIAAEVLKKAGVYDPKRLFGV-TTLDVVRANTFVAELLGLDPAKVNVPVIGGHSGV 179
Query: 134 SSVPVWSGVNVA 145
+ +P+ S
Sbjct: 180 TILPLLSQCQPP 191
>gnl|CDD|240360 PTZ00325, PTZ00325, malate dehydrogenase; Provisional.
Length = 321
Score = 59.7 bits (145), Expect = 1e-10
Identities = 34/125 (27%), Positives = 63/125 (50%), Gaps = 6/125 (4%)
Query: 22 ALSEGSRIVIVTAGVRQREGESRLSLVERNVNIFKGIIPNIVKYSPQCTLLIVSNPVDIL 81
G+ +V++ AGV ++ G +R L N I + ++ + +P+ + IVSNPV+
Sbjct: 72 KALRGADLVLICAGVPRKPGMTRDDLFNTNAPIVRDLVAAVASSAPKAIVGIVSNPVNST 131
Query: 82 TYVSW----KLSGFPKNRVIGSGTNLDSMRFRVLLAQKLGLSPESVYGFIIGEHGDSS-V 136
++ K + ++ G T LD +R R +A+ LG++P V ++G H + V
Sbjct: 132 VPIAAETLKKAGVYDPRKLFGV-TTLDVVRARKFVAEALGMNPYDVNVPVVGGHSGVTIV 190
Query: 137 PVWSG 141
P+ S
Sbjct: 191 PLLSQ 195
>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 = 57.3 bits (139), Expect = 7e-10
Identities = 51/190 (26%), Positives = 80/190 (42%), Gaps = 20/190 (10%)
Query: 1 VLTTNDHSSFKGVNVLTRLNYALSEGSRIVIVTAGVRQREGESRLSLVERNVNIFKGIIP 60
V+TT+ +FK V+V I+ ++ G R L+ +N IFK
Sbjct: 65 VITTDPEEAFKDVDV--------------AILVGAFPRKPGMERADLLRKNAKIFKEQGE 110
Query: 61 NIVKY-SPQCTLLIVSNPVDILTYVSWKLSGFPKNRVIGSGTNLDSMRFRVLLAQKLGLS 119
+ K P +L+V NP + ++ K + + + T LD R + +A+KLG+
Sbjct: 111 ALNKVAKPTVKVLVVGNPANTNALIALKNAPNLPPKNFTALTRLDHNRAKAQVARKLGVR 170
Query: 120 PESVYGFII-GEHGDSSVPVWSGVNVAGVNLRE-VNPAIGTEGDTEEFGKLHTDVVNSAY 177
V II G H ++ VP S V G E V + E +EF K V
Sbjct: 171 VSDVKNVIIWGNHSNTQVPDLSNAVVYGPGGTEWVLDLLDEEWLNDEFVK---TVQKRGA 227
Query: 178 EIIRLKGYTS 187
II+ +G +S
Sbjct: 228 AIIKKRGASS 237
>gnl|CDD|215058 PLN00106, PLN00106, malate dehydrogenase.
Length = 323
Score = 55.0 bits (133), Expect = 5e-09
Identities = 35/111 (31%), Positives = 56/111 (50%), Gaps = 5/111 (4%)
Query: 25 EGSRIVIVTAGVRQREGESRLSLVERNVNIFKGIIPNIVKYSPQCTLLIVSNPVD----I 80
+G+ +VI+ AGV ++ G +R L N I K + + K+ P + I+SNPV+ I
Sbjct: 85 KGADLVIIPAGVPRKPGMTRDDLFNINAGIVKTLCEAVAKHCPNALVNIISNPVNSTVPI 144
Query: 81 LTYVSWKLSGFPKNRVIGSGTNLDSMRFRVLLAQKLGLSPESVYGFIIGEH 131
V K + ++ G T LD +R +A+K GL P V ++G H
Sbjct: 145 AAEVLKKAGVYDPKKLFGV-TTLDVVRANTFVAEKKGLDPADVDVPVVGGH 194
>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 = 54.3 bits (131), Expect = 8e-09
Identities = 35/124 (28%), Positives = 64/124 (51%), Gaps = 6/124 (4%)
Query: 25 EGSRIVIVTAGVRQREGESRLSLVERNVNIFKGIIPNIVKYSPQCTLLIVSNPVD----I 80
+G+ +V++ AGV ++ G +R L N I K ++ + + P+ +L+++NPV+ I
Sbjct: 66 KGADVVVIPAGVPRKPGMTRDDLFNVNAGIVKDLVAAVAESCPKAMILVITNPVNSTVPI 125
Query: 81 LTYVSWKLSGFPKNRVIGSGTNLDSMRFRVLLAQKLGLSPESVYGFIIGEH-GDSSVPVW 139
V K + N++ G T LD +R +A+ G P V +IG H G++ +P+
Sbjct: 126 AAEVLKKKGVYDPNKLFGV-TTLDIVRANTFVAELKGKDPMEVNVPVIGGHSGETIIPLI 184
Query: 140 SGVN 143
S
Sbjct: 185 SQCP 188
>gnl|CDD|235340 PRK05086, PRK05086, malate dehydrogenase; Provisional.
Length = 312
Score = 51.9 bits (125), Expect = 4e-08
Identities = 42/132 (31%), Positives = 68/132 (51%), Gaps = 8/132 (6%)
Query: 25 EGSRIVIVTAGVRQREGESRLSLVERNVNIFKGIIPNIVKYSPQCTLLIVSNPVD----I 80
EG+ +V+++AGV ++ G R L N I K ++ + K P+ + I++NPV+ I
Sbjct: 68 EGADVVLISAGVARKPGMDRSDLFNVNAGIVKNLVEKVAKTCPKACIGIITNPVNTTVAI 127
Query: 81 LTYVSWKLSGFPKNRVIGSGTNLDSMRFRVLLAQKLGLSPESVYGFIIGEH-GDSSVPVW 139
V K + KN++ G T LD +R +A+ G P V +IG H G + +P+
Sbjct: 128 AAEVLKKAGVYDKNKLFGV-TTLDVIRSETFVAELKGKQPGEVEVPVIGGHSGVTILPLL 186
Query: 140 SGVNVAGVNLRE 151
S V GV+ E
Sbjct: 187 S--QVPGVSFTE 196
>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 = 50.4 bits (121), Expect = 1e-07
Identities = 51/195 (26%), Positives = 79/195 (40%), Gaps = 29/195 (14%)
Query: 1 VLTTNDHSSFKGVNVLTRLNYALSEGSRIVIVTAGVRQREGESRLSLVERNVNIFKGIIP 60
V TT+ +FK V + AL G+ ++ G R L+ +N IFK
Sbjct: 68 VATTDPEEAFKDV------DAALLVGAF--------PRKPGMERADLLSKNGKIFKEQGK 113
Query: 61 NIVKY-SPQCTLLIVSNPVD----ILTYVSWKLSGFPKNRVIGSGTNLDSMRFRVLLAQK 115
+ K +L+V NP + I + + + PKN + T LD R + LA K
Sbjct: 114 ALNKVAKKDVKVLVVGNPANTNALIASKNAPDIP--PKN--FSAMTRLDHNRAKYQLAAK 169
Query: 116 LGLSPESVYGFII-GEHGDSSVPVWSGVNVAGVNLREVNPAIGTEGDTEEFGKLHTDVVN 174
G+ V II G H ++ VP ++ V G ++EV D G+ V
Sbjct: 170 AGVPVSDVKNVIIWGNHSNTQVPDFTHATVDGRPVKEVIKD-----DKWLEGEFIPTVQQ 224
Query: 175 SAYEIIRLKGYTSWA 189
+I +G +S A
Sbjct: 225 RGAAVIEARGASSAA 239
>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 = 50.2 bits (120), Expect = 2e-07
Identities = 46/190 (24%), Positives = 72/190 (37%), Gaps = 19/190 (10%)
Query: 1 VLTTNDHSSFKGVNVLTRLNYALSEGSRIVIVTAGVRQREGESRLSLVERNVNIFKGIIP 60
V T + +F V+V I+ ++EG R L+ +NV IFK
Sbjct: 64 VPTHDPAVAFTDVDV--------------AILVGAFPRKEGMERRDLLSKNVKIFKEQGR 109
Query: 61 NIVKY-SPQCTLLIVSNPVDILTYVSWKLSGFPKNRVIGSGTNLDSMRFRVLLAQKLGLS 119
+ K C +L+V NP + V + + + T LD R +A++ G+
Sbjct: 110 ALDKLAKKDCKVLVVGNPANTNALVLSNYAPSIPPKNFSALTRLDHNRALAQVAERAGVP 169
Query: 120 PESVYGFII-GEHGDSSVP-VWSGVNVAGVNLREVNPAIGTEGDTEEFGKLHTDVVNSAY 177
V II G H + P V G + V AI + + G+ T V
Sbjct: 170 VSDVKNVIIWGNHSSTQYPDVNHATVTKGGKQKPVREAIKDDAYLD--GEFITTVQQRGA 227
Query: 178 EIIRLKGYTS 187
IIR + +S
Sbjct: 228 AIIRARKLSS 237
>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 = 49.9 bits (119), Expect = 2e-07
Identities = 44/196 (22%), Positives = 81/196 (41%), Gaps = 28/196 (14%)
Query: 1 VLTTNDHSSFKGVNVLTRLNYALSEGSRIVIVTAGVRQREGESRLSLVERNVNIFKGIIP 60
++TT +FK ++ + A V + GE R L+ +N IFK
Sbjct: 49 IVTTKLEEAFKDID--------------CAFLVASVPLKPGEVRADLLTKNTPIFKATGE 94
Query: 61 NIVKYS-PQCTLLIVSNPVDILTYVSW----KLSGFPKNRVIGSGTNLDSMRFRVLLAQK 115
+ +Y+ P +L++ NPV+ V+ KLS +N S LD R +A K
Sbjct: 95 ALSEYAKPTVKVLVIGNPVNTNCLVAMLHAPKLS--AEN--FSSLCMLDHNRAVSRIASK 150
Query: 116 LGLSPESVYGFII-GEHGDSSVPVWSGVNVA-GVNLREVNPAIGTEGDTEEFGKLHTDVV 173
L + + +Y ++ G H +S V + ++V + + +
Sbjct: 151 LKVPVDHIYHVVVWGNHAESMVADLTHAEFTKNGKHQKVFDELCRD---YPEPDFFEVIA 207
Query: 174 NSAYEIIRLKGYTSWA 189
A++I+ ++G+TS A
Sbjct: 208 QRAWKILEMRGFTSAA 223
>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 = 46.1 bits (110), Expect = 4e-06
Identities = 47/152 (30%), Positives = 65/152 (42%), Gaps = 21/152 (13%)
Query: 1 VLTTNDHSSFKGVNVLTRLNYALSEGSRIVIVTAGVRQREGESRLSLVERNVNIFKGIIP 60
V TT+ +FK V+V ++V A R +EG R L++ NV IFK
Sbjct: 67 VATTDPEEAFKDVDV-------------AILVGAMPR-KEGMERKDLLKANVKIFKEQGE 112
Query: 61 NIVKY-SPQCTLLIVSNPVDILTYVSWKL-SGFPKNRVIGSGTNLDSMRFRVLLAQKLGL 118
+ KY +L+V NP + + K PK + T LD R + +A KLG+
Sbjct: 113 ALDKYAKKNVKVLVVGNPANTNALILLKYAPSIPK-ENFTALTRLDHNRAKSQIALKLGV 171
Query: 119 SPESVYGFII-GEHGDSSVPVWSGVNVAGVNL 149
V II G H + P VN A V L
Sbjct: 172 PVSDVKNVIIWGNHSSTQYP---DVNHATVEL 200
>gnl|CDD|177744 PLN00135, PLN00135, malate dehydrogenase.
Length = 309
Score = 42.1 bits (99), Expect = 8e-05
Identities = 40/144 (27%), Positives = 65/144 (45%), Gaps = 26/144 (18%)
Query: 1 VLTTNDHSSFKGVNVLTRLNYALSEGSRIVIVTAGVRQREGESRLSLVERNVNIFKGIIP 60
V TT+ + KGVN I ++ G ++EG R ++ +NV+I+K
Sbjct: 47 VATTDVVEACKGVN--------------IAVMVGGFPRKEGMERKDVMSKNVSIYKSQAS 92
Query: 61 NIVKY-SPQCTLLIVSNPVDILTYVSWKLSGFP-----KNRVIGSGTNLDSMRFRVLLAQ 114
+ K+ +P C +L+V+NP + + L F KN I T LD R +++
Sbjct: 93 ALEKHAAPDCKVLVVANPANTNALI---LKEFAPSIPEKN--ITCLTRLDHNRALGQISE 147
Query: 115 KLGLSPESVYGFII-GEHGDSSVP 137
+LG+ V II G H + P
Sbjct: 148 RLGVPVSDVKNVIIWGNHSSTQYP 171
>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 = 34.5 bits (80), Expect = 0.026
Identities = 37/155 (23%), Positives = 64/155 (41%), Gaps = 18/155 (11%)
Query: 1 VLTTNDHSSFKGVNVLTRLNYALSEGSRIVIVTAGVRQREGESRLSLVERNVNIFKGIIP 60
V+T + + +FK + +AL G++ R G R L++ N IF
Sbjct: 67 VITDDPNVAFKDAD------WALLVGAK-------PRGP-GMERADLLKANGKIFTAQGK 112
Query: 61 NIVKY-SPQCTLLIVSNPVDILTYVSWKLS-GFPKNRVIGSGTNLDSMRFRVLLAQKLGL 118
+ S +L+V NP + ++ K + P + + T LD R + LA+K G+
Sbjct: 113 ALNDVASRDVKVLVVGNPCNTNALIAMKNAPDIPPDN-FTAMTRLDHNRAKSQLAKKAGV 171
Query: 119 SPESVYGFII-GEHGDSSVPVWSGVNVAGVNLREV 152
V +I G H + P ++ + G EV
Sbjct: 172 PVTDVKNMVIWGNHSPTQYPDFTNATIGGKPAAEV 206
>gnl|CDD|224403 COG1486, CelF, Alpha-galactosidases/6-phospho-beta-glucosidases,
family 4 of glycosyl hydrolases [Carbohydrate transport
and metabolism].
Length = 442
Score = 32.2 bits (74), Expect = 0.15
Identities = 19/71 (26%), Positives = 33/71 (46%), Gaps = 4/71 (5%)
Query: 50 RNVNIFKGIIPNIVKYSPQCTLLIVSNPVDILTYVSWKLSGFPKNRVIGSGTNLDSMRFR 109
R + + I ++ K P +L +NP I+T +L +PK +++G +
Sbjct: 121 RTIPVILDIAKDMEKVCPNAWMLNYTNPAAIVTEAVRRL--YPKIKIVGLCHGPIGIAME 178
Query: 110 VLLAQKLGLSP 120
LA+ LGL P
Sbjct: 179 --LAEVLGLEP 187
>gnl|CDD|202102 pfam02056, Glyco_hydro_4, Family 4 glycosyl hydrolase.
Length = 183
Score = 30.8 bits (70), Expect = 0.29
Identities = 11/49 (22%), Positives = 24/49 (48%), Gaps = 2/49 (4%)
Query: 50 RNVNIFKGIIPNIVKYSPQCTLLIVSNPVDILTYVSWKLSGFPKNRVIG 98
R + +F I +I + P +L +NP ++T ++ +P + +G
Sbjct: 119 RTIPVFFDIAKDIEELCPDAWVLNYTNPAAMVTEAVYRR--YPNIKAVG 165
>gnl|CDD|234452 TIGR04063, stp3, PEP-CTERM/exosortase A-associated
glycosyltransferase, Daro_2409 family.
PEP-CTERM/exosortase is a protein-sorting system
associated with exopolysaccharide production. Members of
this protein family are group 1 glycosyltransferases
(see pfam00534) in which the overwhelming majority occur
in species with the EpsH1 form of exosortase (see
TIGR03109), and usually co-clustered with the
exosortase. A typical member is Daro_2409 from
Dechloromonas aromatica RCB.
Length = 397
Score = 30.3 bits (69), Expect = 0.78
Identities = 15/44 (34%), Positives = 19/44 (43%), Gaps = 6/44 (13%)
Query: 90 GFPKNR--VIGSGTNLDSMRFRV----LLAQKLGLSPESVYGFI 127
G P + VI + +LD LA +LGL V GFI
Sbjct: 176 GIPAEKITVIPNAVDLDLFGLPAPRDPALAAELGLEGAPVIGFI 219
>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 = 29.8 bits (68), Expect = 1.1
Identities = 26/104 (25%), Positives = 38/104 (36%), Gaps = 32/104 (30%)
Query: 50 RNVNIFKGIIPNIVKYSPQCTLLIVSNPVDILTYVSWKLSGFPKNRVIG-----SGTNLD 104
R + + I +I + P LL +NP+ LT W L+ + + +G GT
Sbjct: 120 RTIPVLLDIARDIEELCPDAWLLNYANPMAELT---WALNRYTPIKTVGLCHGVQGT--- 173
Query: 105 SMRFRVLLAQKLGLSPESVYGFIIGEHGDSSVPVWSGVNVAGVN 148
LA+ LG PE V VAG+N
Sbjct: 174 ----AEQLAKLLGEPPEEVD-----------------YQVAGIN 196
>gnl|CDD|148055 pfam06222, Phage_TAC, Phage tail assembly chaperone.
Length = 126
Score = 28.6 bits (64), Expect = 1.3
Identities = 13/46 (28%), Positives = 15/46 (32%), Gaps = 15/46 (32%)
Query: 131 HGDSSVPVWSGVNVAGVNLRE------------VNPAIGTEGDTEE 164
H VP W GV V LRE + A G D +
Sbjct: 17 HKTVPVPEWEGVKVV---LREPSGEAWLFWQEILREAAGVGEDDDT 59
>gnl|CDD|115202 pfam06530, Phage_antitermQ, Phage antitermination protein Q.
This family consists of several phage antitermination
protein Q and related bacterial sequences.
Antiterminator proteins control gene expression by
recognising control signals near the promoter and
preventing transcriptional termination which would
otherwise occur at sites that may be a long way
downstream.
Length = 126
Score = 28.6 bits (64), Expect = 1.4
Identities = 16/39 (41%), Positives = 22/39 (56%), Gaps = 3/39 (7%)
Query: 55 FKGIIPNIVKYSPQCT---LLIVSNPVDILTYVSWKLSG 90
FK ++P VK P C+ +I+S VD L Y+ KL G
Sbjct: 31 FKSLLPGRVKTRPMCSDDDGMIISQCVDSLMYIDPKLFG 69
>gnl|CDD|185035 PRK15076, PRK15076, alpha-galactosidase; Provisional.
Length = 431
Score = 28.3 bits (64), Expect = 3.1
Identities = 11/49 (22%), Positives = 23/49 (46%), Gaps = 3/49 (6%)
Query: 50 RNVNIFKGIIPNIVKYSPQCTLLIVSNPVDILTYVSWKLSGFPKNRVIG 98
R + + I ++ + P LL NP+ + T W ++ +P + +G
Sbjct: 122 RTIPVLLDICEDMEEVCPDALLLNYVNPMAMNT---WAMNRYPGIKTVG 167
>gnl|CDD|220341 pfam09684, Tail_P2_I, Phage tail protein (Tail_P2_I). These
sequences represent the family of phage P2 protein I and
related tail proteins from a number of temperate phage
of Gram-negative bacteria.
Length = 139
Score = 26.5 bits (59), Expect = 6.3
Identities = 11/29 (37%), Positives = 15/29 (51%), Gaps = 1/29 (3%)
Query: 171 DVVNSAYEIIRLKGYTSWAIGLSIASLTY 199
V+ A EI R KG T A+ + +L Y
Sbjct: 63 AVIKEAIEIHRHKG-TPGAVRRVLEALGY 90
>gnl|CDD|237732 PRK14498, PRK14498, putative molybdopterin biosynthesis protein
MoeA/LysR substrate binding-domain-containing protein;
Provisional.
Length = 633
Score = 27.1 bits (61), Expect = 8.8
Identities = 20/64 (31%), Positives = 28/64 (43%), Gaps = 12/64 (18%)
Query: 94 NRVIGSGTNLDSMRFRVLLAQ---KLGLSPESVYGFIIGEHGDSSV--PVWSGVNVAGVN 148
NR GSGT R+LL +L + PE + G+ E +V V G AG+
Sbjct: 528 NRQRGSGT-------RILLDYHLKELAIDPERINGYDREEKTHMAVAAAVAQGRADAGLG 580
Query: 149 LREV 152
+R
Sbjct: 581 IRAA 584
>gnl|CDD|133434 cd05298, GH4_GlvA_pagL_like, Glycoside Hydrolases Family 4; GlvA-
and pagL-like glycosidases. Bacillus subtilis GlvA and
Clostridium acetobutylicum pagL are
6-phospho-alpha-glucosidase, catalyzing the hydrolysis
of alpha-glucopyranoside bonds to release glucose from
oligosaccharides. The substrate specificities of other
members of this subgroup are unknown. 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, which
include 6-phospho-beta-glucosidases,
6-phospho-alpha-glucosidases,
alpha-glucosidases/alpha-glucuronidases (only from
Thermotoga), and alpha-galactosidases. Members of this
subfamily 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 = 437
Score = 26.8 bits (60), Expect = 9.0
Identities = 15/40 (37%), Positives = 22/40 (55%), Gaps = 2/40 (5%)
Query: 58 IIPNIVKYSPQCTLLIVSNPVDILTYVSWKLSGFPKNRVI 97
+I +I KYSP +L SNP I+ +L FP R++
Sbjct: 126 LIDDIEKYSPDAWILNYSNPAAIVAEALRRL--FPNARIL 163
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
0.317 0.135 0.387
Gapped
Lambda K H
0.267 0.0669 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,899,687
Number of extensions: 1037228
Number of successful extensions: 954
Number of sequences better than 10.0: 1
Number of HSP's gapped: 927
Number of HSP's successfully gapped: 47
Length of query: 216
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 123
Effective length of database: 6,812,680
Effective search space: 837959640
Effective search space used: 837959640
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 57 (25.9 bits)