RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14621
(248 letters)
>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 = 277 bits (710), Expect = 1e-93
Identities = 108/152 (71%), Positives = 132/152 (86%)
Query: 94 QLKGLNPTDVNVPVIGGHAGITIIPLISQATPSVSFPDDQLKALTGRIQEAGTEVVKAKA 153
+L GL+P VNVPVIGGH+G+TI+PL+SQ P +F ++++ALT RIQ G EVVKAKA
Sbjct: 159 ELLGLDPAKVNVPVIGGHSGVTILPLLSQCQPPFTFDQEEIEALTHRIQFGGDEVVKAKA 218
Query: 154 GAGSATLSMAYAGARFAFSLIQGLKGESNVIECAYVKSDVTEASYFSTPVHLGKNGIEKN 213
GAGSATLSMAYAGARFA SL++GLKGE VIECAYV+SDVTEA +F+TPV LGKNG+EKN
Sbjct: 219 GAGSATLSMAYAGARFANSLLRGLKGEKGVIECAYVESDVTEAPFFATPVELGKNGVEKN 278
Query: 214 LGLGKLSDFEKELVKAAVPELKKNIAKGEEFV 245
LGLGKL+D+EK+L++AA+PELKKNI KG +FV
Sbjct: 279 LGLGKLNDYEKKLLEAALPELKKNIEKGVDFV 310
Score = 116 bits (294), Expect = 3e-31
Identities = 42/62 (67%), Positives = 50/62 (80%)
Query: 35 KVMVAGASGGIGQPLSLLLKQSPLVDHLSLYDIVHTPGVAADLSHIESKAHVQAFNGADQ 94
KV V GA+GGIGQPLSLLLK +PLV L+LYDIV+TPGVAADLSHI + A V + G ++
Sbjct: 2 KVAVLGAAGGIGQPLSLLLKLNPLVSELALYDIVNTPGVAADLSHINTPAKVTGYLGPEE 61
Query: 95 LK 96
LK
Sbjct: 62 LK 63
>gnl|CDD|215058 PLN00106, PLN00106, malate dehydrogenase.
Length = 323
Score = 233 bits (596), Expect = 3e-76
Identities = 92/147 (62%), Positives = 125/147 (85%)
Query: 94 QLKGLNPTDVNVPVIGGHAGITIIPLISQATPSVSFPDDQLKALTGRIQEAGTEVVKAKA 153
+ KGL+P DV+VPV+GGHAGITI+PL+SQATP VSF D++++ALT RIQ GTEVV+AKA
Sbjct: 177 EKKGLDPADVDVPVVGGHAGITILPLLSQATPKVSFTDEEIEALTKRIQNGGTEVVEAKA 236
Query: 154 GAGSATLSMAYAGARFAFSLIQGLKGESNVIECAYVKSDVTEASYFSTPVHLGKNGIEKN 213
GAGSATLSMAYA ARFA + ++GL GE++V+EC+YV+S+VTE +F++ V LG+NG+E+
Sbjct: 237 GAGSATLSMAYAAARFADACLRGLNGEADVVECSYVQSEVTELPFFASKVRLGRNGVEEV 296
Query: 214 LGLGKLSDFEKELVKAAVPELKKNIAK 240
LGLG LS++E++ ++A PELK +I K
Sbjct: 297 LGLGPLSEYEQKGLEALKPELKASIEK 323
Score = 100 bits (252), Expect = 4e-25
Identities = 41/63 (65%), Positives = 48/63 (76%)
Query: 35 KVMVAGASGGIGQPLSLLLKQSPLVDHLSLYDIVHTPGVAADLSHIESKAHVQAFNGADQ 94
KV V GA+GGIGQPLSLL+K +PLV L LYDI +TPGVAAD+SHI + A V+ F G DQ
Sbjct: 20 KVAVLGAAGGIGQPLSLLMKMNPLVSELHLYDIANTPGVAADVSHINTPAQVRGFLGDDQ 79
Query: 95 LKG 97
L
Sbjct: 80 LGD 82
>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 = 231 bits (591), Expect = 1e-75
Identities = 109/155 (70%), Positives = 131/155 (84%), Gaps = 1/155 (0%)
Query: 94 QLKGLNPTDVNVPVIGGHAGITIIPLISQATPSVSFPDDQLKALTGRIQEAGTEVVKAKA 153
+LKG +P +VNVPVIGGH+G TIIPLISQ V F +DQL+AL RIQ AGTEVVKAKA
Sbjct: 158 ELKGKDPMEVNVPVIGGHSGETIIPLISQCPGKVLFTEDQLEALIHRIQNAGTEVVKAKA 217
Query: 154 GAGSATLSMAYAGARFAFSLIQGLKGESNVIECAYVKSD-VTEASYFSTPVHLGKNGIEK 212
GAGSATLSMA+AGARF SL++GLKGE V+ECAYV+SD VTEA++F+TP+ LGKNG+EK
Sbjct: 218 GAGSATLSMAFAGARFVLSLVRGLKGEEGVVECAYVESDGVTEATFFATPLLLGKNGVEK 277
Query: 213 NLGLGKLSDFEKELVKAAVPELKKNIAKGEEFVAK 247
LG+GKLS FE++++ A+PELKKNI KGEEFVA
Sbjct: 278 RLGIGKLSSFEEKMLNGALPELKKNIKKGEEFVAS 312
Score = 92.5 bits (230), Expect = 4e-22
Identities = 44/76 (57%), Positives = 50/76 (65%), Gaps = 1/76 (1%)
Query: 35 KVMVAGASGGIGQPLSLLLKQSPLVDHLSLYDIVHTPGVAADLSHIESKAHVQAFNGADQ 94
KV V GA+GGIGQPLSLLLK P V LSLYDI GVAADLSHI + A V+ F+G +
Sbjct: 1 KVAVLGAAGGIGQPLSLLLKLQPYVSELSLYDIAGAAGVAADLSHIPTAASVKGFSGEEG 60
Query: 95 LK-GLNPTDVNVPVIG 109
L+ L DV V G
Sbjct: 61 LENALKGADVVVIPAG 76
>gnl|CDD|235340 PRK05086, PRK05086, malate dehydrogenase; Provisional.
Length = 312
Score = 214 bits (546), Expect = 6e-69
Identities = 88/154 (57%), Positives = 113/154 (73%), Gaps = 1/154 (0%)
Query: 94 QLKGLNPTDVNVPVIGGHAGITIIPLISQATPSVSFPDDQLKALTGRIQEAGTEVVKAKA 153
+LKG P +V VPVIGGH+G+TI+PL+SQ P VSF + ++ LT RIQ AGTEVV+AKA
Sbjct: 160 ELKGKQPGEVEVPVIGGHSGVTILPLLSQV-PGVSFTEQEVADLTKRIQNAGTEVVEAKA 218
Query: 154 GAGSATLSMAYAGARFAFSLIQGLKGESNVIECAYVKSDVTEASYFSTPVHLGKNGIEKN 213
G GSATLSM A ARF SL++ L+GE V+ECAYV+ D A +F+ PV LGKNG+E+
Sbjct: 219 GGGSATLSMGQAAARFGLSLVRALQGEQGVVECAYVEGDGKYARFFAQPVLLGKNGVEER 278
Query: 214 LGLGKLSDFEKELVKAAVPELKKNIAKGEEFVAK 247
L +G LS FE+ ++ + LKK+IA GEEFV K
Sbjct: 279 LPIGTLSAFEQNALEGMLDTLKKDIALGEEFVNK 312
Score = 73.9 bits (182), Expect = 2e-15
Identities = 39/71 (54%), Positives = 45/71 (63%), Gaps = 2/71 (2%)
Query: 35 KVMVAGASGGIGQPLSLLLK-QSPLVDHLSLYDIVH-TPGVAADLSHIESKAHVQAFNGA 92
KV V GA+GGIGQ L+LLLK Q P LSLYDI TPGVA DLSHI + ++ F+G
Sbjct: 2 KVAVLGAAGGIGQALALLLKTQLPAGSELSLYDIAPVTPGVAVDLSHIPTAVKIKGFSGE 61
Query: 93 DQLKGLNPTDV 103
D L DV
Sbjct: 62 DPTPALEGADV 72
>gnl|CDD|240360 PTZ00325, PTZ00325, malate dehydrogenase; Provisional.
Length = 321
Score = 197 bits (504), Expect = 2e-62
Identities = 84/152 (55%), Positives = 120/152 (78%), Gaps = 3/152 (1%)
Query: 97 GLNPTDVNVPVIGGHAGITIIPLISQATPSVSFPDDQLKALTGRIQEAGTEVVKAKAGAG 156
G+NP DVNVPV+GGH+G+TI+PL+SQ +S P++Q++ +T R+Q G EVVKAK GAG
Sbjct: 170 GMNPYDVNVPVVGGHSGVTIVPLLSQT--GLSLPEEQVEQITHRVQVGGDEVVKAKEGAG 227
Query: 157 SATLSMAYAGARFAFSLIQGLKGESNVIECAYVKSDVT-EASYFSTPVHLGKNGIEKNLG 215
SATLSMAYA A ++ S+++ L+G+ ++ECA+V+SD+ E +FS+PV LGK G+E+ L
Sbjct: 228 SATLSMAYAAAEWSTSVLKALRGDKGIVECAFVESDMRPECPFFSSPVELGKEGVERVLP 287
Query: 216 LGKLSDFEKELVKAAVPELKKNIAKGEEFVAK 247
+G L+ +E+EL++AAVP+LKKNI KG EF K
Sbjct: 288 IGPLNAYEEELLEAAVPDLKKNIEKGLEFARK 319
Score = 87.4 bits (217), Expect = 3e-20
Identities = 39/56 (69%), Positives = 44/56 (78%)
Query: 34 AKVMVAGASGGIGQPLSLLLKQSPLVDHLSLYDIVHTPGVAADLSHIESKAHVQAF 89
KV V GA+GGIGQPLSLLLKQ+P V LSLYDIV PGVAADLSHI++ A V +
Sbjct: 9 FKVAVLGAAGGIGQPLSLLLKQNPHVSELSLYDIVGAPGVAADLSHIDTPAKVTGY 64
>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 = 164 bits (416), Expect = 4e-51
Identities = 71/164 (43%), Positives = 97/164 (59%), Gaps = 16/164 (9%)
Query: 94 QLKGLNPTDVNVPVIGGHAG----------ITIIPLISQATPSVSFPDDQLKALTGRIQE 143
+ G++P VNV VIG H+G +TIIPLISQ ++ D +L+ L R+Q
Sbjct: 14 EKFGVDPRSVNVYVIGEHSGTQFPDWSHAKVTIIPLISQVKENLKDTDWELEELIERVQN 73
Query: 144 AGTEVVKAKAGAGSATLSMAYAGARFAFSLIQGLKGESN--VIECAYVKSDVTEASYFST 201
AG EV++AK AGS T SMAYA AR A ++++G G + V Y S YFS
Sbjct: 74 AGYEVIEAK--AGSTTYSMAYAAARIAKAILRGTGGVLSVGVYLDGYYGSPDDI--YFSV 129
Query: 202 PVHLGKNGIEKNLGLGKLSDFEKELVKAAVPELKKNIAKGEEFV 245
PV LGK+G+EK + + L+DFE+E ++ + ELKK I KG FV
Sbjct: 130 PVVLGKDGVEKVVEILPLNDFEREKLEKSAAELKKEIEKGFAFV 173
>gnl|CDD|223117 COG0039, Mdh, Malate/lactate dehydrogenases [Energy production and
conversion].
Length = 313
Score = 103 bits (259), Expect = 3e-26
Identities = 55/163 (33%), Positives = 82/163 (50%), Gaps = 15/163 (9%)
Query: 94 QLKGLNPTDVNVPVIGGHAGITIIPLISQATPS--------VSFPDDQLKALTGRIQEAG 145
+ G++P DV+ VIG H G T++PL SQAT ++ L+ L R++ AG
Sbjct: 157 EKLGVSPKDVHAYVIGEH-GDTMVPLWSQATVGGKPLEELLKEDTEEDLEELIERVRNAG 215
Query: 146 TEVVKAKAGAGSATLSMAYAGARFAFSLIQGLKGESNVIECAYVKSD-VTEASYFSTPVH 204
E+++AK A A AR ++++ K + Y+ + E YF P
Sbjct: 216 AEIIEAKGA--GTYYGPAAALARMVEAILRDEK--RVLPVSVYLDGEYGVEDVYFGVPAV 271
Query: 205 LGKNGIEKNLGLGKLSDFEKELVKAAVPELKKNIAKGEEFVAK 247
LGKNG+E+ L L LSD E+E + + ELKKNI +E V
Sbjct: 272 LGKNGVEEILEL-LLSDDEQEKLDKSAEELKKNIELVKELVLI 313
Score = 49.5 bits (119), Expect = 4e-07
Identities = 26/69 (37%), Positives = 30/69 (43%), Gaps = 7/69 (10%)
Query: 35 KVMVAGASGGIGQPLSLLLKQSPLVDHLSLYDIVH--TPGVAADLSHI----ESKAHVQA 88
KV V GA G +G L+ LL L L L DI GVA DLSH S +
Sbjct: 2 KVAVIGA-GNVGSSLAFLLLLQGLGSELVLIDINEEKAEGVALDLSHAAAPLGSDVKITG 60
Query: 89 FNGADQLKG 97
+ LKG
Sbjct: 61 DGDYEDLKG 69
>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 = 66.1 bits (162), Expect = 1e-13
Identities = 31/78 (39%), Positives = 36/78 (46%), Gaps = 3/78 (3%)
Query: 35 KVMVAGASGGIGQPLSLLLKQSPLVDHLSLYDIV--HTPGVAADLSHIESKAHVQAFNGA 92
KV V GA GG+G L+ L L D L L DI GVA DLSH + V G
Sbjct: 2 KVAVVGAGGGVGSSLAFALALQGLADELVLVDINKDKAEGVAMDLSHGSTFLSVPGIVGG 61
Query: 93 DQLKGLNPTDVNVPVIGG 110
D + L DV V + G
Sbjct: 62 DDYEALKDADV-VVITAG 78
>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 = 64.8 bits (159), Expect = 3e-12
Identities = 46/154 (29%), Positives = 73/154 (47%), Gaps = 21/154 (13%)
Query: 97 GLNPTDVNVPVIGGHAGITIIPLISQAT-----PSVSFPDDQLKALTGRIQEAGTEVVKA 151
G++ DV V+GGH G T++PL +T + +++ + R + G E+V
Sbjct: 157 GVSVKDVQAMVLGGH-GDTMVPLPRYSTVGGIPLTELITKEEIDEIVERTRNGGAEIVNL 215
Query: 152 KAGAGSATLSMAYAGARFAFSLIQGLKGESNVIECA------YVKSDVTEASYFSTPVHL 205
GSA + A A A ++ LK + V+ C+ Y D+ + PV L
Sbjct: 216 L-KTGSAYYAPAAAIAEMVEAI---LKDKKRVLPCSAYLEGEYGIKDI----FVGVPVVL 267
Query: 206 GKNGIEKNLGLGKLSDFEKELVKAAVPELKKNIA 239
GKNG+EK + L L+D EKE +V +K+ I
Sbjct: 268 GKNGVEKIIEL-DLTDEEKEAFDKSVESVKELID 300
>gnl|CDD|180477 PRK06223, PRK06223, malate dehydrogenase; Reviewed.
Length = 307
Score = 62.8 bits (154), Expect = 1e-11
Identities = 47/155 (30%), Positives = 74/155 (47%), Gaps = 21/155 (13%)
Query: 97 GLNPTDVNVPVIGGHAGITIIPLISQAT-----PSVSFPDDQLKALTGRIQEAGTEVVKA 151
++ DV V+GGH G +++PL+ +T ++L + R ++ G E+V
Sbjct: 161 NVSVKDVTAFVLGGH-GDSMVPLVRYSTVGGIPLEDLLSKEKLDEIVERTRKGGAEIVGL 219
Query: 152 KAGAGSATLSMAYAGARFAFSLIQGLKGESNVIEC-AYVK-----SDVTEASYFSTPVHL 205
GSA + A + A ++ LK + V+ C AY++ DV Y PV L
Sbjct: 220 L-KTGSAYYAPAASIAEMVEAI---LKDKKRVLPCSAYLEGEYGVKDV----YVGVPVKL 271
Query: 206 GKNGIEKNLGLGKLSDFEKELVKAAVPELKKNIAK 240
GKNG+EK + L +L D EK +V +KK I
Sbjct: 272 GKNGVEKIIEL-ELDDEEKAAFDKSVEAVKKLIEA 305
>gnl|CDD|173376 PTZ00082, PTZ00082, L-lactate dehydrogenase; Provisional.
Length = 321
Score = 58.2 bits (141), Expect = 6e-10
Identities = 47/160 (29%), Positives = 74/160 (46%), Gaps = 27/160 (16%)
Query: 92 ADQLKGLNPTDVNVPVIGGHAGITIIPLISQAT----PSVSF------PDDQLKALTGRI 141
A++L G+NP DV+ VIG H G ++PL T P F +++ + R
Sbjct: 166 AEKL-GVNPRDVHASVIGAH-GDKMVPLPRYVTVGGIPLSEFIKKGLITQEEIDEIVERT 223
Query: 142 QEAGTEVVKAKAGAGSATLSMAYAGARFAFSLIQGLKGESNVIECA------YVKSDVTE 195
+ G E+V G GSA + A A A + LK + V+ C+ Y D+
Sbjct: 224 RNTGKEIVDL-LGTGSAYFAPAAAAIEMAEAY---LKDKKRVLPCSAYLEGQYGHKDI-- 277
Query: 196 ASYFSTPVHLGKNGIEKNLGLGKLSDFEKELVKAAVPELK 235
Y TP +G NG+EK + L L+ E++ ++ E+K
Sbjct: 278 --YMGTPAVIGANGVEKIIEL-DLTPEEQKKFDESIKEVK 314
>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 = 51.1 bits (123), Expect = 1e-07
Identities = 37/157 (23%), Positives = 70/157 (44%), Gaps = 20/157 (12%)
Query: 92 ADQLKGLNPTDVNVPVIGGHAGITIIPLISQAT-------PSVSFPDDQLKALTGRIQEA 144
A++L ++P V+ V+G H G + + S AT F L+A+ ++ +
Sbjct: 153 AEKLD-VDPQSVHAYVLGEH-GDSQVVAWSTATVGGLPLEELAPFTKLDLEAIEEEVRTS 210
Query: 145 GTEVVKAKAGAGSATLSMAYAGARFAFSLIQGLKGE---SNVIECAYVKSDVTEASYFST 201
G E+++ K G+ +A A A S++ + S V E Y DV S
Sbjct: 211 GYEIIRLK---GATNYGIATAIADIVKSILLDERRVLPVSAVQEGQYGIEDV----ALSV 263
Query: 202 PVHLGKNGIEKNLGLGKLSDFEKELVKAAVPELKKNI 238
P +G+ G+ + L L++ E+ ++ + LK+ +
Sbjct: 264 PAVVGREGVVRIL-EIPLTEDEEAKLQKSAEALKEVL 299
>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 = 48.0 bits (115), Expect = 1e-06
Identities = 44/159 (27%), Positives = 75/159 (47%), Gaps = 24/159 (15%)
Query: 92 ADQLKGLNPTDVNVPVIGGHAGITIIPLISQAT----PSVSFP-------DDQLKALTGR 140
A++L G++P V+ +IG H G + +P+ S AT P + + D L+ +
Sbjct: 151 AEKL-GVDPQSVHAYIIGEH-GDSEVPVWSSATIGGVPLLDYLKAKGTETDLDLEEIEKE 208
Query: 141 IQEAGTEVVKAKAGAGSATLSMAYAGARFAFSLIQGLKGE---SNVIECAYVKSDVTEAS 197
+++A E++ K G+ + A AR +++ S ++ Y DV
Sbjct: 209 VRDAAYEIINRK---GATYYGIGMAVARIVEAILHDENRVLPVSAYLDGEYGIKDV---- 261
Query: 198 YFSTPVHLGKNGIEKNLGLGKLSDFEKELVKAAVPELKK 236
Y P LG+NG+E+ + L LSD EKE + + LKK
Sbjct: 262 YIGVPAVLGRNGVEEIIEL-PLSDEEKEAFQKSAETLKK 299
>gnl|CDD|173409 PTZ00117, PTZ00117, malate dehydrogenase; Provisional.
Length = 319
Score = 47.8 bits (114), Expect = 1e-06
Identities = 47/166 (28%), Positives = 79/166 (47%), Gaps = 29/166 (17%)
Query: 92 ADQLKGLNPTDVNVPVIGGHAGITIIPLISQAT----PSVSF------PDDQLKALTGRI 141
A++L G++P DV+ VIGGH G ++PL T P F + ++ + +
Sbjct: 160 AEKL-GVSPGDVSAVVIGGH-GDLMVPLPRYCTVNGIPLSDFVKKGAITEKEINEIIKKT 217
Query: 142 QEAGTEVVKAKAGAGSATLSMAYAGARFAFSLIQG-LKGESNVIECA------YVKSDVT 194
+ G E+VK GSA +A A ++I+ LK E V+ C+ Y ++
Sbjct: 218 RNMGGEIVKL-LKKGSAF----FAPAAAIVAMIEAYLKDEKRVLVCSVYLNGQYNCKNL- 271
Query: 195 EASYFSTPVHLGKNGIEKNLGLGKLSDFEKELVKAAVPELKKNIAK 240
+ PV +G GIEK + L +L+ EKEL ++ +++ K
Sbjct: 272 ---FVGVPVVIGGKGIEKVIEL-ELNAEEKELFDKSIESIQELTQK 313
>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 = 47.2 bits (112), Expect = 3e-06
Identities = 41/149 (27%), Positives = 67/149 (44%), Gaps = 13/149 (8%)
Query: 97 GLNPTDVNVPVIGGHAGITIIPLISQAT----PSVSF-PDDQLKALTGRIQEAGTEVVKA 151
G++ DV V+GGH G ++PL+ +T P +++ + R ++ G E+V
Sbjct: 160 GVSVQDVTACVLGGH-GDAMVPLVRYSTVAGIPVADLISAERIAEIVERTRKGGGEIVNL 218
Query: 152 KAGAGSATLSMAYAGARFAFSLIQGLKGESNVIEC-AYVKSDV-TEASYFSTPVHLGKNG 209
GSA + A + ++ LK V+ C AY+ + Y PV LGKNG
Sbjct: 219 -LKQGSAYYAPAASVVEMVEAI---LKDRKRVLPCAAYLDGQYGIDGIYVGVPVILGKNG 274
Query: 210 IEKNLGLGKLSDFEKELVKAAVPELKKNI 238
+E L KL E L+ + + +N
Sbjct: 275 VEHIYEL-KLDQSELALLNKSAKIVDENC 302
>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 = 44.0 bits (105), Expect = 3e-05
Identities = 36/157 (22%), Positives = 68/157 (43%), Gaps = 22/157 (14%)
Query: 97 GLNPTDVNVPVIGGHAGITIIPLISQAT----------PSVSFPDDQLKALTGRIQEAGT 146
++P V+ V+G H G + S T + L + +++AG
Sbjct: 159 NVDPRSVHAYVLGEH-GDSQFVAWSTVTVGGKPLLDLLKEGKLSELDLDEIEEDVRKAGY 217
Query: 147 EVVKAKAGAGSATLSMAYAGARFAFSLIQGLKGE---SNVIECAYVKSDVTEASYFSTPV 203
E++ K G+ +A A AR +++ S ++ Y + DV Y P
Sbjct: 218 EIINGK---GATYYGIATALARIVKAILNDENAILPVSAYLDGEYGEKDV----YIGVPA 270
Query: 204 HLGKNGIEKNLGLGKLSDFEKELVKAAVPELKKNIAK 240
+G+NG+E+ + L L++ E+E + + +K+NI K
Sbjct: 271 IIGRNGVEEVIEL-DLTEEEQEKFEKSADIIKENIKK 306
>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 = 41.9 bits (99), Expect = 1e-04
Identities = 34/149 (22%), Positives = 57/149 (38%), Gaps = 47/149 (31%)
Query: 94 QLKGLNPTDVNVPVIGGHAGITIIPLISQATPSVSFPDDQLKALTGRIQEAGTEVVKAKA 153
+ G++P DV V ++G H G + +P S + S
Sbjct: 157 EKLGVDPDDVKVYILGEHGG-SQVPDWSTVRIATSI------------------------ 191
Query: 154 GAGSATLSMAYAGARFAFSLIQGLKGESNVIECAYVKSD----VTEASYFSTPVHLGKNG 209
A SL L E I V+++ + + S P +GKNG
Sbjct: 192 -------------ADLIRSL---LNDE-GEILPVGVRNNGQIGIPDDVVVSVPCIVGKNG 234
Query: 210 IEKNLGLGKLSDFEKELVKAAVPELKKNI 238
+E+ + +G L+DFE E ++ + LKK +
Sbjct: 235 VEEPIEVG-LTDFELEKLQKSADTLKKEL 262
Score = 36.1 bits (84), Expect = 0.009
Identities = 18/49 (36%), Positives = 20/49 (40%), Gaps = 4/49 (8%)
Query: 36 VMVAGASGGIGQPL--SLLLKQSPLVDHLSLYDIV--HTPGVAADLSHI 80
+ V GA G +G L L L L LYDI GVA DL
Sbjct: 1 IAVIGAGGNVGPALAFGLADGSVLLAIELVLYDIDEEKLKGVAMDLQDA 49
Score = 28.8 bits (65), Expect = 2.6
Identities = 14/37 (37%), Positives = 17/37 (45%), Gaps = 2/37 (5%)
Query: 2 VAGASGGIGQPL--SLLLKQSPLVDHLSLYDINNAKV 36
V GA G +G L L L L LYDI+ K+
Sbjct: 3 VIGAGGNVGPALAFGLADGSVLLAIELVLYDIDEEKL 39
>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 = 36.3 bits (85), Expect = 0.009
Identities = 37/161 (22%), Positives = 74/161 (45%), Gaps = 30/161 (18%)
Query: 97 GLNPTDVNVPVIGGHAGITIIPLISQAT------------PSVSFPDDQLKALTGRIQEA 144
G++P V+ +IG H G + + + S A F ++ + + ++ A
Sbjct: 158 GVDPRSVHAYIIGEH-GDSEVAVWSSANIGGVPLDEFCKLCGRPFDEEVREEIFEEVRNA 216
Query: 145 GTEVVKAKAGAGSATLSMAYAGARFAFSLIQGLKGE------SNVIECAYVKSDVTEASY 198
E+++ K G+ ++ A AR ++ L+ E S++++ Y DV
Sbjct: 217 AYEIIERK---GATYYAIGLALARIVEAI---LRDENSVLTVSSLLDGQYGIKDV----A 266
Query: 199 FSTPVHLGKNGIEKNLGLGKLSDFEKELVKAAVPELKKNIA 239
S P +G++G+E+ L LS+ E+E ++A+ LK+ I
Sbjct: 267 LSLPCIVGRSGVERVLPP-PLSEEEEEALRASAEVLKEAIE 306
>gnl|CDD|236372 PRK09072, PRK09072, short chain dehydrogenase; Provisional.
Length = 263
Score = 36.1 bits (84), Expect = 0.011
Identities = 23/85 (27%), Positives = 34/85 (40%), Gaps = 19/85 (22%)
Query: 30 DINNAKVMVAGASGGIGQPLSLLL------------KQSPL---VDHLSLYDIVHTPGVA 74
D+ + +V++ GASGGIGQ L+ L L L V
Sbjct: 2 DLKDKRVLLTGASGGIGQALAEALAAAGARLLLVGRNAEKLEALAARLPYPGRHRW--VV 59
Query: 75 ADLSHIESKAHVQAFNGADQLKGLN 99
ADL+ + V A A ++ G+N
Sbjct: 60 ADLTSEAGREAVLAR--AREMGGIN 82
>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 = 32.8 bits (75), Expect = 0.14
Identities = 41/154 (26%), Positives = 74/154 (48%), Gaps = 26/154 (16%)
Query: 97 GLNPTDVNVPVIGGHAGITIIPLISQAT----PSVSFP---DDQLKALTGRIQEAGTEVV 149
++ ++V+ +IG H G +++PLIS + P FP D ++ + ++ AG ++
Sbjct: 163 NVHISEVHTRIIGEH-GDSMVPLISSTSIGGIPIKRFPEYKDFDVEKIVETVKNAGQNII 221
Query: 150 KAKAGA----GSATLSMAYAGA---RFAFSLIQGLKGESNVIECAYVKSDVTEASYFSTP 202
K G+ SA ++ A R ++ L+GE + I DV P
Sbjct: 222 SLKGGSEYGPASAISNLVRTIANDERRILTVSTYLEGEIDGIR------DVC----IGVP 271
Query: 203 VHLGKNGIEKNLGLGKLSDFEKELVKAAVPELKK 236
V LGKNGIE+ + + ++ D E+E + + +KK
Sbjct: 272 VKLGKNGIEEIVPI-EMDDDEREAFRKSAEIVKK 304
Score = 30.8 bits (70), Expect = 0.56
Identities = 12/30 (40%), Positives = 19/30 (63%)
Query: 35 KVMVAGASGGIGQPLSLLLKQSPLVDHLSL 64
KV + GASG +G +LLL + +V ++L
Sbjct: 2 KVSIIGASGRVGSATALLLAKEDVVKEINL 31
Score = 27.8 bits (62), Expect = 5.7
Identities = 10/27 (37%), Positives = 17/27 (62%)
Query: 2 VAGASGGIGQPLSLLLKQSPLVDHLSL 28
+ GASG +G +LLL + +V ++L
Sbjct: 5 IIGASGRVGSATALLLAKEDVVKEINL 31
>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 = 31.9 bits (73), Expect = 0.27
Identities = 38/162 (23%), Positives = 71/162 (43%), Gaps = 34/162 (20%)
Query: 97 GLNPTDVNVPVIGGHAGITIIPLISQATPSVS-FPDDQLKALTGR-----------IQEA 144
G++P +V V+G H G P+ S +++ P D+L+AL G+ + +A
Sbjct: 161 GVDPKNVTGYVLGEH-GSHAFPVWSLV--NIAGLPLDELEALFGKEPIDKDELLEEVVQA 217
Query: 145 GTEVVKAKAGAGSATLSMAYAGARFAFSLIQGLKGE-------SNVIECAYVKSDVTEAS 197
+V K G +A ++ + A LI+ + + ++ Y SDV
Sbjct: 218 AYDVFNRK-GWTNAGIAKS------ASRLIKAILLDERSILPVCTLLSGEYGLSDVA--- 267
Query: 198 YFSTPVHLGKNGIEKNLGLGKLSDFEKELVKAAVPELKKNIA 239
S P +G GIE+ L + L ++E E + + +++ I
Sbjct: 268 -LSLPTVIGAKGIERVLEI-PLDEWELEKLHKSAKAIRETIE 307
>gnl|CDD|180408 PRK06114, PRK06114, short chain dehydrogenase; Provisional.
Length = 254
Score = 31.3 bits (71), Expect = 0.42
Identities = 18/55 (32%), Positives = 31/55 (56%), Gaps = 2/55 (3%)
Query: 28 LYDINNAKVMVAGASGGIGQPLSLLLKQSPLVDHLSLYDIVHTPGVAADLSHIES 82
L+D++ V GA GIGQ +++ L Q+ ++L+D+ G+A HIE+
Sbjct: 3 LFDLDGQVAFVTGAGSGIGQRIAIGLAQAG--ADVALFDLRTDDGLAETAEHIEA 55
>gnl|CDD|235164 PRK03824, hypA, hydrogenase nickel incorporation protein;
Provisional.
Length = 135
Score = 30.1 bits (68), Expect = 0.47
Identities = 17/44 (38%), Positives = 25/44 (56%), Gaps = 5/44 (11%)
Query: 207 KNGIEK----NLGLGKLSDFEKELVKAAVPELKK-NIAKGEEFV 245
K G K + LG+L D +KE+V+ A+ EL K I +G E +
Sbjct: 20 KEGASKVKALKVVLGELQDVDKEIVEFALNELLKGTILEGAEII 63
>gnl|CDD|187549 cd05238, Gne_like_SDR_e, Escherichia coli Gne (a
nucleoside-diphosphate-sugar 4-epimerase)-like, extended
(e) SDRs. Nucleoside-diphosphate-sugar 4-epimerase has
the characteristic active site tetrad and NAD-binding
motif of the extended SDR, and is related to more
specifically defined epimerases such as UDP-glucose 4
epimerase (aka UDP-galactose-4-epimerase), which
catalyzes the NAD-dependent conversion of UDP-galactose
to UDP-glucose, the final step in Leloir galactose
synthesis. This subgroup includes Escherichia coli
055:H7 Gne, a UDP-GlcNAc 4-epimerase, essential for O55
antigen synthesis. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately 100
amino acids. Extended SDRs are a diverse collection of
proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 305
Score = 30.4 bits (69), Expect = 0.75
Identities = 19/69 (27%), Positives = 29/69 (42%), Gaps = 1/69 (1%)
Query: 35 KVMVAGASGGIGQPLSLLLKQSPLVDHLSLYDIVHTPGVAADLSHIESKAHVQAFNGADQ 94
KV++ GASG +GQ L+ L + L L D+V +P + + A A +
Sbjct: 2 KVLITGASGFVGQRLAERLLSDVPNERLILIDVV-SPKAPSGAPRVTQIAGDLAVPALIE 60
Query: 95 LKGLNPTDV 103
DV
Sbjct: 61 ALANGRPDV 69
>gnl|CDD|171820 PRK12936, PRK12936, 3-ketoacyl-(acyl-carrier-protein) reductase
NodG; Reviewed.
Length = 245
Score = 29.5 bits (66), Expect = 1.3
Identities = 14/33 (42%), Positives = 23/33 (69%), Gaps = 1/33 (3%)
Query: 28 LYDINNAKVMVAGASGGIGQPLSLLL-KQSPLV 59
++D++ K +V GASGGIG+ ++ LL Q +V
Sbjct: 1 MFDLSGRKALVTGASGGIGEEIARLLHAQGAIV 33
>gnl|CDD|239483 cd03389, PAP2_lipid_A_1_phosphatase, PAP2_like proteins, Lipid A
1-phosphatase subfamily. Lipid A 1-phosphatase, or LpxE
from Francisella novicida selectively dephosphorylates
lipid A at the 1-position. Lipid A is the
membrane-anchor component of lipopolysaccharides (LPS),
the major constituents of the outer membrane in many
gram-negative bacteria.
Length = 186
Score = 28.8 bits (65), Expect = 1.7
Identities = 19/51 (37%), Positives = 26/51 (50%)
Query: 151 AKAGAGSATLSMAYAGARFAFSLIQGLKGESNVIECAYVKSDVTEASYFST 201
A AGA +A L++ + R+AF L+ L S VI A+ SDV S
Sbjct: 126 ATAGAAAAALALLFPRYRWAFILLALLIAFSRVIVGAHYPSDVIAGSLLGA 176
>gnl|CDD|225691 COG3149, PulM, Type II secretory pathway, component PulM
[Intracellular trafficking and secretion].
Length = 181
Score = 28.6 bits (64), Expect = 2.0
Identities = 10/29 (34%), Positives = 16/29 (55%)
Query: 133 QLKALTGRIQEAGTEVVKAKAGAGSATLS 161
+L+AL +Q+ +V +A A AT S
Sbjct: 72 ELRALLAYVQQQAPDVRALRAAAPQATPS 100
>gnl|CDD|178836 PRK00066, ldh, L-lactate dehydrogenase; Reviewed.
Length = 315
Score = 28.7 bits (65), Expect = 2.7
Identities = 17/60 (28%), Positives = 29/60 (48%), Gaps = 5/60 (8%)
Query: 181 SNVIECAYVKSDVTEASYFSTPVHLGKNGIEKNLGLGKLSDFEKELVKAAVPELKKNIAK 240
S +E Y + DV Y P + +NGI + + L L+D EK+ + LK+ + +
Sbjct: 258 SAYLEGQYGEEDV----YIGVPAVVNRNGIREIVEL-PLNDDEKQKFAHSADVLKEIMDE 312
>gnl|CDD|217267 pfam02882, THF_DHG_CYH_C, Tetrahydrofolate
dehydrogenase/cyclohydrolase, NAD(P)-binding domain.
Length = 160
Score = 27.8 bits (63), Expect = 4.0
Identities = 11/26 (42%), Positives = 16/26 (61%)
Query: 30 DINNAKVMVAGASGGIGQPLSLLLKQ 55
D+ V+V G S +G+PL+LLL
Sbjct: 33 DLAGKNVVVIGRSNIVGKPLALLLLN 58
>gnl|CDD|178212 PLN02602, PLN02602, lactate dehydrogenase.
Length = 350
Score = 28.2 bits (63), Expect = 4.2
Identities = 29/133 (21%), Positives = 57/133 (42%), Gaps = 20/133 (15%)
Query: 92 ADQLKGLNPTDVNVPVIGGH-------------AGITIIPLISQATPSVSFPDDQLKALT 138
AD L +N DV ++G H G+ ++ + + +++ + L+ +
Sbjct: 192 ADHL-DVNAQDVQAYIVGEHGDSSVALWSSVSVGGVPVLSFLEKQ--QIAYEKETLEEIH 248
Query: 139 GRIQEAGTEVVKAKAGAGSATLSMAYAGARFAFSLIQGLKGESNVIECAYVKSDVTEASY 198
+ ++ EV+K K G + ++ Y+ A SL++ + V A + E
Sbjct: 249 RAVVDSAYEVIKLK---GYTSWAIGYSVASLVRSLLRDQRRIHPVSVLAKGFHGIDEGDV 305
Query: 199 F-STPVHLGKNGI 210
F S P LG+NG+
Sbjct: 306 FLSLPAQLGRNGV 318
>gnl|CDD|238386 cd00757, ThiF_MoeB_HesA_family, ThiF_MoeB_HesA. Family of E1-like
enzymes involved in molybdopterin and thiamine
biosynthesis family. The common reaction mechanism
catalyzed by MoeB and ThiF, like other E1 enzymes,
begins with a nucleophilic attack of the C-terminal
carboxylate of MoaD and ThiS, respectively, on the
alpha-phosphate of an ATP molecule bound at the active
site of the activating enzymes, leading to the formation
of a high-energy acyladenylate intermediate and
subsequently to the formation of a thiocarboxylate at
the C termini of MoaD and ThiS. MoeB, as the MPT
synthase (MoaE/MoaD complex) sulfurase, is involved in
the biosynthesis of the molybdenum cofactor, a
derivative of the tricyclic pterin, molybdopterin (MPT).
ThiF catalyzes the adenylation of ThiS, as part of the
biosynthesis pathway of thiamin pyrophosphate (vitamin
B1). .
Length = 228
Score = 27.8 bits (63), Expect = 4.3
Identities = 28/87 (32%), Positives = 41/87 (47%), Gaps = 24/87 (27%)
Query: 31 INNAKVMVAGASGGIGQPLSLLLKQSPLVDHLSLYD------------IVHTPGVAADLS 78
+ NA+V+V GA GG+G P + L + V L L D I+HT AD+
Sbjct: 19 LKNARVLVVGA-GGLGSPAAEYLAAAG-VGKLGLVDDDVVELSNLQRQILHTE---ADVG 73
Query: 79 HIESKAHVQAFNGADQLKGLNPTDVNV 105
KA A++L+ +NP DV +
Sbjct: 74 Q--PKAEA----AAERLRAINP-DVEI 93
>gnl|CDD|184990 PRK15030, PRK15030, multidrug efflux system transporter AcrA;
Provisional.
Length = 397
Score = 28.1 bits (62), Expect = 4.4
Identities = 19/50 (38%), Positives = 27/50 (54%), Gaps = 3/50 (6%)
Query: 142 QEAGTEVVKAKAGAGSATLSMAYAGARFAFSLIQGLKGESNVIECAYVKS 191
Q+A V AKA +A +++AY S I G G+SNV E A V++
Sbjct: 151 QQANAAVTAAKAAVETARINLAYTKVT---SPISGRIGKSNVTEGALVQN 197
>gnl|CDD|212497 cd11731, Lin1944_like_SDR_c, Lin1944 and related proteins,
classical (c) SDRs. Lin1944 protein from Listeria
Innocua is a classical SDR, it contains a glycine-rich
motif similar to the canonical motif of the SDR
NAD(P)-binding site. However, the typical SDR active
site residues are absent in this subgroup of proteins
of undetermined function. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold
(alpha/beta folding pattern with a central beta-sheet),
an NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRs are
approximately 350 residues. Sequence identity between
different SDR enzymes are typically in the 15-30%
range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes catalyze a
wide range of activities including the metabolism of
steroids, cofactors, carbohydrates, lipids, aromatic
compounds, and amino acids, and act in redox sensing.
Classical SDRs have an TGXXX[AG]XG cofactor binding
motif and a YXXXK active site motif, with the Tyr
residue of the active site motif serving as a critical
catalytic residue (Tyr-151, human prostaglandin
dehydrogenase (PGDH) numbering). In addition to the Tyr
and Lys, there is often an upstream Ser (Ser-138, PGDH
numbering) and/or an Asn (Asn-107, PGDH numbering)
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. Extended SDRs have additional
elements in the C-terminal region, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Some atypical SDRs have lost catalytic activity and/or
have an unusual NAD(P)-binding motif and missing or
unusual active site residues. Reactions catalyzed
within the SDR family include isomerization,
decarboxylation, epimerization, C=N bond reduction,
dehydratase activity, dehalogenation, Enoyl-CoA
reduction, and carbonyl-alcohol oxidoreduction.
Length = 198
Score = 27.9 bits (63), Expect = 4.5
Identities = 10/51 (19%), Positives = 22/51 (43%), Gaps = 11/51 (21%)
Query: 36 VMVAGASGGIGQPLSLLLKQSPLVDHLSLYDIV----HTPGVAADLSHIES 82
++V GA+G IG ++ LL ++++ + D++ S
Sbjct: 1 IIVIGATGTIGLAVAQLLSAHG-------HEVITAGRSSGDYQVDITDEAS 44
>gnl|CDD|181335 PRK08264, PRK08264, short chain dehydrogenase; Validated.
Length = 238
Score = 27.9 bits (63), Expect = 4.8
Identities = 9/21 (42%), Positives = 12/21 (57%)
Query: 29 YDINNAKVMVAGASGGIGQPL 49
DI V+V GA+ GIG+
Sbjct: 2 MDIKGKVVLVTGANRGIGRAF 22
>gnl|CDD|223268 COG0190, FolD, 5,10-methylene-tetrahydrofolate
dehydrogenase/Methenyl tetrahydrofolate cyclohydrolase
[Coenzyme metabolism].
Length = 283
Score = 27.9 bits (63), Expect = 4.8
Identities = 11/27 (40%), Positives = 16/27 (59%)
Query: 29 YDINNAKVMVAGASGGIGQPLSLLLKQ 55
D+ V+V G S +G+PL+LLL
Sbjct: 152 IDLRGKNVVVVGRSNIVGKPLALLLLN 178
>gnl|CDD|213839 TIGR03629, arch_S13P, archaeal ribosomal protein S13P. This model
describes exclusively the archaeal ribosomal protein
S13P. It excludes the homologous eukaryotic 40S
ribosomal protein S18 and bacterial 30S ribosomal
protein S13 [Protein synthesis, Ribosomal proteins:
synthesis and modification].
Length = 144
Score = 26.9 bits (60), Expect = 6.0
Identities = 11/30 (36%), Positives = 16/30 (53%)
Query: 209 GIEKNLGLGKLSDFEKELVKAAVPELKKNI 238
G++ N LG L D E E ++ AV + I
Sbjct: 42 GVDPNAKLGYLDDEEIEKLEEAVENYEYGI 71
>gnl|CDD|223139 COG0061, nadF, NAD kinase [Coenzyme metabolism].
Length = 281
Score = 27.7 bits (62), Expect = 6.5
Identities = 13/33 (39%), Positives = 20/33 (60%), Gaps = 1/33 (3%)
Query: 213 NLG-LGKLSDFEKELVKAAVPELKKNIAKGEEF 244
NLG LG L+DFE + ++ A+ L + + EE
Sbjct: 86 NLGHLGFLTDFEPDELEKALDALLEGEYRIEER 118
>gnl|CDD|137559 PRK09859, PRK09859, multidrug efflux system protein MdtE;
Provisional.
Length = 385
Score = 27.4 bits (60), Expect = 7.3
Identities = 18/57 (31%), Positives = 30/57 (52%), Gaps = 3/57 (5%)
Query: 140 RIQEAGTEVVKAKAGAGSATLSMAYAGARFAFSLIQGLKGESNVIECAYVKSDVTEA 196
++ EA V AKA AT+++ YA S I G+ G+S+V A V ++ ++
Sbjct: 145 QLNEAEANVTVAKAAVEQATINLQYANVT---SPITGVSGKSSVTVGALVTANQADS 198
>gnl|CDD|183685 PRK12690, flgF, flagellar basal body rod protein FlgF; Reviewed.
Length = 238
Score = 27.0 bits (60), Expect = 8.7
Identities = 14/31 (45%), Positives = 18/31 (58%), Gaps = 2/31 (6%)
Query: 146 TEVVKAKAGAGSATLSMAYAGARFAFSLIQG 176
+E VK+ +G A+LSMA A R L QG
Sbjct: 42 SEYVKS-LDSGEASLSMARASGR-QTDLEQG 70
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
0.314 0.133 0.367
Gapped
Lambda K H
0.267 0.0608 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,536,164
Number of extensions: 1194271
Number of successful extensions: 1209
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1182
Number of HSP's successfully gapped: 85
Length of query: 248
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 154
Effective length of database: 6,768,326
Effective search space: 1042322204
Effective search space used: 1042322204
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 58 (26.4 bits)