RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 025206
(256 letters)
>gnl|CDD|215058 PLN00106, PLN00106, malate dehydrogenase.
Length = 323
Score = 481 bits (1241), Expect = e-174
Identities = 181/239 (75%), Positives = 205/239 (85%)
Query: 18 ARGYSSESVPDRKVAVLGAAGGIGQPLALLMKLNPLVSRLALYDIANTPGVAADVGHINT 77
+ P KVAVLGAAGGIGQPL+LLMK+NPLVS L LYDIANTPGVAADV HINT
Sbjct: 8 RACRAKGGAPGFKVAVLGAAGGIGQPLSLLMKMNPLVSELHLYDIANTPGVAADVSHINT 67
Query: 78 RSEVAGYMGNDQLGQALEDSDVVIIPAGVPRKPGMTRDDLFNINAGIVKDLCSAIAKYCP 137
++V G++G+DQLG AL+ +D+VIIPAGVPRKPGMTRDDLFNINAGIVK LC A+AK+CP
Sbjct: 68 PAQVRGFLGDDQLGDALKGADLVIIPAGVPRKPGMTRDDLFNINAGIVKTLCEAVAKHCP 127
Query: 138 NAIVNMISNPVNSTVPIAAEVFKKAGTYNEKKLFGVTTLDVVRAKTFYAGKANVNVAEVN 197
NA+VN+ISNPVNSTVPIAAEV KKAG Y+ KKLFGVTTLDVVRA TF A K ++ A+V+
Sbjct: 128 NALVNIISNPVNSTVPIAAEVLKKAGVYDPKKLFGVTTLDVVRANTFVAEKKGLDPADVD 187
Query: 198 VPVVGGHAGITILPLFSQATPKANLADEDIKALTKRTQDGGTEVVEAKAGKGSATLSMA 256
VPVVGGHAGITILPL SQATPK + DE+I+ALTKR Q+GGTEVVEAKAG GSATLSMA
Sbjct: 188 VPVVGGHAGITILPLLSQATPKVSFTDEEIEALTKRIQNGGTEVVEAKAGAGSATLSMA 246
>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 = 435 bits (1121), Expect = e-156
Identities = 162/227 (71%), Positives = 191/227 (84%)
Query: 30 KVAVLGAAGGIGQPLALLMKLNPLVSRLALYDIANTPGVAADVGHINTRSEVAGYMGNDQ 89
KVAVLGAAGGIGQPL+LL+KLNPLVS LALYDI NTPGVAAD+ HINT ++V GY+G ++
Sbjct: 2 KVAVLGAAGGIGQPLSLLLKLNPLVSELALYDIVNTPGVAADLSHINTPAKVTGYLGPEE 61
Query: 90 LGQALEDSDVVIIPAGVPRKPGMTRDDLFNINAGIVKDLCSAIAKYCPNAIVNMISNPVN 149
L +AL+ +DVV+IPAGVPRKPGMTRDDLFNINAGIV+DL +A+AK CP A++ +ISNPVN
Sbjct: 62 LKKALKGADVVVIPAGVPRKPGMTRDDLFNINAGIVRDLATAVAKACPKALILIISNPVN 121
Query: 150 STVPIAAEVFKKAGTYNEKKLFGVTTLDVVRAKTFYAGKANVNVAEVNVPVVGGHAGITI 209
STVPIAAEV KKAG Y+ K+LFGVTTLDVVRA TF A ++ A+VNVPV+GGH+G+TI
Sbjct: 122 STVPIAAEVLKKAGVYDPKRLFGVTTLDVVRANTFVAELLGLDPAKVNVPVIGGHSGVTI 181
Query: 210 LPLFSQATPKANLADEDIKALTKRTQDGGTEVVEAKAGKGSATLSMA 256
LPL SQ P E+I+ALT R Q GG EVV+AKAG GSATLSMA
Sbjct: 182 LPLLSQCQPPFTFDQEEIEALTHRIQFGGDEVVKAKAGAGSATLSMA 228
>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 = 340 bits (874), Expect = e-118
Identities = 147/227 (64%), Positives = 177/227 (77%)
Query: 30 KVAVLGAAGGIGQPLALLMKLNPLVSRLALYDIANTPGVAADVGHINTRSEVAGYMGNDQ 89
KVAVLGAAGGIGQPL+LL+KL P VS L+LYDIA GVAAD+ HI T + V G+ G +
Sbjct: 1 KVAVLGAAGGIGQPLSLLLKLQPYVSELSLYDIAGAAGVAADLSHIPTAASVKGFSGEEG 60
Query: 90 LGQALEDSDVVIIPAGVPRKPGMTRDDLFNINAGIVKDLCSAIAKYCPNAIVNMISNPVN 149
L AL+ +DVV+IPAGVPRKPGMTRDDLFN+NAGIVKDL +A+A+ CP A++ +I+NPVN
Sbjct: 61 LENALKGADVVVIPAGVPRKPGMTRDDLFNVNAGIVKDLVAAVAESCPKAMILVITNPVN 120
Query: 150 STVPIAAEVFKKAGTYNEKKLFGVTTLDVVRAKTFYAGKANVNVAEVNVPVVGGHAGITI 209
STVPIAAEV KK G Y+ KLFGVTTLD+VRA TF A + EVNVPV+GGH+G TI
Sbjct: 121 STVPIAAEVLKKKGVYDPNKLFGVTTLDIVRANTFVAELKGKDPMEVNVPVIGGHSGETI 180
Query: 210 LPLFSQATPKANLADEDIKALTKRTQDGGTEVVEAKAGKGSATLSMA 256
+PL SQ K ++ ++AL R Q+ GTEVV+AKAG GSATLSMA
Sbjct: 181 IPLISQCPGKVLFTEDQLEALIHRIQNAGTEVVKAKAGAGSATLSMA 227
>gnl|CDD|235340 PRK05086, PRK05086, malate dehydrogenase; Provisional.
Length = 312
Score = 331 bits (851), Expect = e-115
Identities = 140/229 (61%), Positives = 169/229 (73%), Gaps = 4/229 (1%)
Query: 30 KVAVLGAAGGIGQPLALLMKLN-PLVSRLALYDIAN-TPGVAADVGHINTRSEVAGYMGN 87
KVAVLGAAGGIGQ LALL+K P S L+LYDIA TPGVA D+ HI T ++ G+ G
Sbjct: 2 KVAVLGAAGGIGQALALLLKTQLPAGSELSLYDIAPVTPGVAVDLSHIPTAVKIKGFSGE 61
Query: 88 DQLGQALEDSDVVIIPAGVPRKPGMTRDDLFNINAGIVKDLCSAIAKYCPNAIVNMISNP 147
D ALE +DVV+I AGV RKPGM R DLFN+NAGIVK+L +AK CP A + +I+NP
Sbjct: 62 D-PTPALEGADVVLISAGVARKPGMDRSDLFNVNAGIVKNLVEKVAKTCPKACIGIITNP 120
Query: 148 VNSTVPIAAEVFKKAGTYNEKKLFGVTTLDVVRAKTFYAGKANVNVAEVNVPVVGGHAGI 207
VN+TV IAAEV KKAG Y++ KLFGVTTLDV+R++TF A EV VPV+GGH+G+
Sbjct: 121 VNTTVAIAAEVLKKAGVYDKNKLFGVTTLDVIRSETFVAELKGKQPGEVEVPVIGGHSGV 180
Query: 208 TILPLFSQATPKANLADEDIKALTKRTQDGGTEVVEAKAGKGSATLSMA 256
TILPL SQ P + ++++ LTKR Q+ GTEVVEAKAG GSATLSM
Sbjct: 181 TILPLLSQV-PGVSFTEQEVADLTKRIQNAGTEVVEAKAGGGSATLSMG 228
>gnl|CDD|240360 PTZ00325, PTZ00325, malate dehydrogenase; Provisional.
Length = 321
Score = 303 bits (778), Expect = e-103
Identities = 144/227 (63%), Positives = 175/227 (77%), Gaps = 2/227 (0%)
Query: 30 KVAVLGAAGGIGQPLALLMKLNPLVSRLALYDIANTPGVAADVGHINTRSEVAGYMGNDQ 89
KVAVLGAAGGIGQPL+LL+K NP VS L+LYDI PGVAAD+ HI+T ++V GY +
Sbjct: 10 KVAVLGAAGGIGQPLSLLLKQNPHVSELSLYDIVGAPGVAADLSHIDTPAKVTGYADGEL 69
Query: 90 LGQALEDSDVVIIPAGVPRKPGMTRDDLFNINAGIVKDLCSAIAKYCPNAIVNMISNPVN 149
+AL +D+V+I AGVPRKPGMTRDDLFN NA IV+DL +A+A P AIV ++SNPVN
Sbjct: 70 WEKALRGADLVLICAGVPRKPGMTRDDLFNTNAPIVRDLVAAVASSAPKAIVGIVSNPVN 129
Query: 150 STVPIAAEVFKKAGTYNEKKLFGVTTLDVVRAKTFYAGKANVNVAEVNVPVVGGHAGITI 209
STVPIAAE KKAG Y+ +KLFGVTTLDVVRA+ F A +N +VNVPVVGGH+G+TI
Sbjct: 130 STVPIAAETLKKAGVYDPRKLFGVTTLDVVRARKFVAEALGMNPYDVNVPVVGGHSGVTI 189
Query: 210 LPLFSQATPKANLADEDIKALTKRTQDGGTEVVEAKAGKGSATLSMA 256
+PL SQ T + L +E ++ +T R Q GG EVV+AK G GSATLSMA
Sbjct: 190 VPLLSQ-TGLS-LPEEQVEQITHRVQVGGDEVVKAKEGAGSATLSMA 234
>gnl|CDD|223117 COG0039, Mdh, Malate/lactate dehydrogenases [Energy production and
conversion].
Length = 313
Score = 218 bits (557), Expect = 3e-70
Identities = 95/238 (39%), Positives = 131/238 (55%), Gaps = 17/238 (7%)
Query: 29 RKVAVLGAAGGIGQPLALLMKLNPLVSRLALYDIAN--TPGVAADVGHINTRSEVAGYMG 86
KVAV+GA G +G LA L+ L L S L L DI GVA D+ H +
Sbjct: 1 MKVAVIGA-GNVGSSLAFLLLLQGLGSELVLIDINEEKAEGVALDLSHAAAPLGSDVKIT 59
Query: 87 NDQLGQALEDSDVVIIPAGVPRKPGMTRDDLFNINAGIVKDLCSAIAKYCPNAIVNMISN 146
D + L+ +D+V+I AGVPRKPGMTR DL NA IVKD+ AIAKY P+AIV +++N
Sbjct: 60 GDGDYEDLKGADIVVITAGVPRKPGMTRLDLLEKNAKIVKDIAKAIAKYAPDAIVLVVTN 119
Query: 147 PVNSTVPIAAEVFKKAGTYNEKKLFGVTTLDVVRAKTFYAGKANVNVAEVNVPVVGGHAG 206
PV+ IA + +G + + T LD R +TF A K V+ +V+ V+G H G
Sbjct: 120 PVDILTYIAMKF---SGFPKNRVIGSGTVLDSARFRTFLAEKLGVSPKDVHAYVIGEH-G 175
Query: 207 ITILPLFSQAT----PKANLA----DEDIKALTKRTQDGGTEVVEAKAGKGSATLSMA 256
T++PL+SQAT P L +ED++ L +R ++ G E++EAK A
Sbjct: 176 DTMVPLWSQATVGGKPLEELLKEDTEEDLEELIERVRNAGAEIIEAK--GAGTYYGPA 231
>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 = 179 bits (456), Expect = 2e-57
Identities = 71/146 (48%), Positives = 90/146 (61%), Gaps = 6/146 (4%)
Query: 29 RKVAVLGAAGGIGQPLALLMKLNPLVSRLALYDIA--NTPGVAADVGHINTRSEVAGYMG 86
KVAV+GA GG+G LA + L L L L DI GVA D+ H +T V G +G
Sbjct: 1 VKVAVVGAGGGVGSSLAFALALQGLADELVLVDINKDKAEGVAMDLSHGSTFLSVPGIVG 60
Query: 87 NDQLGQALEDSDVVIIPAGVPRKPGMTRDDLFNINAGIVKDLCSAIAKYCPNAIVNMISN 146
D +AL+D+DVV+I AGVPRKPGMTR DL N NAGI KD+ AIAK P+AIV ++SN
Sbjct: 61 GDD-YEALKDADVVVITAGVPRKPGMTRLDLLNRNAGIFKDIVPAIAKSAPDAIVLVVSN 119
Query: 147 PVNSTVPIAAEVFKKAGTYNEKKLFG 172
PV+ IA +V +G E+ +
Sbjct: 120 PVDILTYIAWKV---SGLPPERVIGS 142
>gnl|CDD|180477 PRK06223, PRK06223, malate dehydrogenase; Reviewed.
Length = 307
Score = 155 bits (394), Expect = 5e-46
Identities = 86/234 (36%), Positives = 132/234 (56%), Gaps = 24/234 (10%)
Query: 30 KVAVLGAAGGIGQPLALLMKLNPLVSRLALYDIA-NTP-GVAADVGH----INTRSEVAG 83
K++++GA G +G LA L+ L L + L+DI P G A D+ +++ G
Sbjct: 4 KISIIGA-GNVGATLAHLLALKELGD-VVLFDIVEGVPQGKALDIAEAAPVEGFDTKITG 61
Query: 84 YMGNDQLGQALEDSDVVIIPAGVPRKPGMTRDDLFNINAGIVKDLCSAIAKYCPNAIVNM 143
ND + + SDVV+I AGVPRKPGM+RDDL INA I+KD+ I KY P+AIV +
Sbjct: 62 --TNDY--EDIAGSDVVVITAGVPRKPGMSRDDLLGINAKIMKDVAEGIKKYAPDAIVIV 117
Query: 144 ISNPVNSTVPIAAEVFKKAGTYNEKKLFGVTT-LDVVRAKTFYAGKANVNVAEVNVPVVG 202
++NPV++ +A K + + ++ G+ LD R +TF A + NV+V +V V+G
Sbjct: 118 VTNPVDAMTYVA----LKESGFPKNRVIGMAGVLDSARFRTFIAEELNVSVKDVTAFVLG 173
Query: 203 GHAGITILPLFSQAT-----PKANLADEDIKALTKRTQDGGTEVVEAKAGKGSA 251
GH G +++PL +T + L+ E + + +RT+ GG E+V GSA
Sbjct: 174 GH-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 = 147 bits (373), Expect = 6e-43
Identities = 84/233 (36%), Positives = 127/233 (54%), Gaps = 24/233 (10%)
Query: 31 VAVLGAAGGIGQPLALLMKLNPLVSRLALYDIA-NTP-GVAADVGH----INTRSEVAGY 84
++++GA G +G LA L+ L L + L DI P G A D+ + + ++V G
Sbjct: 1 ISIIGA-GNVGATLAQLLALKELGD-VVLLDIVEGLPQGKALDISQAAPILGSDTKVTG- 57
Query: 85 MGNDQLGQALEDSDVVIIPAGVPRKPGMTRDDLFNINAGIVKDLCSAIAKYCPNAIVNMI 144
ND + + SDVV+I AG+PRKPGM+RDDL NA IVK++ I KY PNAIV ++
Sbjct: 58 -TNDY--EDIAGSDVVVITAGIPRKPGMSRDDLLGTNAKIVKEVAENIKKYAPNAIVIVV 114
Query: 145 SNPVNSTVPIAAEVFKKAGTYNEKKLFGV-TTLDVVRAKTFYAGKANVNVAEVNVPVVGG 203
+NP++ V KA + ++ G+ LD R + F A + V+V +V V+GG
Sbjct: 115 TNPLDVMT----YVAYKASGFPRNRVIGMAGVLDSARFRYFIAEELGVSVKDVQAMVLGG 170
Query: 204 HAGITILPLFSQAT-----PKANLADEDIKALTKRTQDGGTEVVEAKAGKGSA 251
H G T++PL +T + E+I + +RT++GG 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 = 129 bits (326), Expect = 2e-36
Identities = 67/192 (34%), Positives = 97/192 (50%), Gaps = 9/192 (4%)
Query: 31 VAVLGAAGGIGQPLALLM--KLNPLVSRLALYDI--ANTPGVAADVGHINTRSEVAGYMG 86
+AV+GA G +G LA + L L LYDI GVA D+
Sbjct: 1 IAVIGAGGNVGPALAFGLADGSVLLAIELVLYDIDEEKLKGVAMDLQDAVEPLADIKVSI 60
Query: 87 NDQLGQALEDSDVVIIPAGVPRKPGMTRDDLFNINAGIVKDLCSAIAKYCPNAIVNMISN 146
D +A +D+DVVII AGV RKPGM R DL N IVK++ I KY P+A + ++SN
Sbjct: 61 TDDPYEAFKDADVVIITAGVGRKPGMGRLDLLKRNVPIVKEIGDNIEKYSPDAWIIVVSN 120
Query: 147 PVNSTVPIAAEVFKKAGTYNEKKLFGVTTLDVVRAKTFYAGKANVNVAEVNVPVVGGHAG 206
PV+ I + + ++K+ G+ TLD +R + A K V+ +V V ++G H G
Sbjct: 121 PVD----IITYLVWRYSGLPKEKVIGLGTLDPIRFRRILAEKLGVDPDDVKVYILGEHGG 176
Query: 207 ITILPLFSQATP 218
+ +P +S
Sbjct: 177 -SQVPDWSTVRI 187
>gnl|CDD|173409 PTZ00117, PTZ00117, malate dehydrogenase; Provisional.
Length = 319
Score = 120 bits (302), Expect = 2e-32
Identities = 78/240 (32%), Positives = 125/240 (52%), Gaps = 21/240 (8%)
Query: 30 KVAVLGAAGGIGQPLALLMKLNPLVSRLALYDIAN--TPGVAADVGHINTRSEVAGYMGN 87
K++++GA G IG +ALL+ L + LYD+ G A D+ H +T +
Sbjct: 7 KISMIGA-GQIGSTVALLILQKNL-GDVVLYDVIKGVPQGKALDLKHFSTLVGSNINILG 64
Query: 88 DQLGQALEDSDVVIIPAGVPRKPGMTRDDLFNINAGIVKDLCSAIAKYCPNAIVNMISNP 147
+ ++DSDVV+I AGV RK MTR+DL IN I+K + ++ KYCPNA V ++NP
Sbjct: 65 TNNYEDIKDSDVVVITAGVQRKEEMTREDLLTINGKIMKSVAESVKKYCPNAFVICVTNP 124
Query: 148 VNSTVPIAAEVFKKAGTYNEKKLFGVT-TLDVVRAKTFYAGKANVNVAEVNVPVVGGHAG 206
++ +VF++ K+ G+ LD R + A K V+ +V+ V+GGH G
Sbjct: 125 LD----CMVKVFQEKSGIPSNKICGMAGVLDSSRFRCNLAEKLGVSPGDVSAVVIGGH-G 179
Query: 207 ITILPL----------FSQATPKANLADEDIKALTKRTQDGGTEVVEAKAGKGSATLSMA 256
++PL S K + +++I + K+T++ G E+V+ KGSA + A
Sbjct: 180 DLMVPLPRYCTVNGIPLSDFVKKGAITEKEINEIIKKTRNMGGEIVKL-LKKGSAFFAPA 238
>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 = 108 bits (271), Expect = 6e-28
Identities = 75/243 (30%), Positives = 125/243 (51%), Gaps = 43/243 (17%)
Query: 30 KVAVLGAAGGIGQPLALLMKLNP------LVSR-----------LALYDIANTPGVAADV 72
KV+++GA+G +G ALL+ L+SR L +YD G+ A++
Sbjct: 2 KVSIIGASGRVGSATALLLAKEDVVKEINLISRPKSLEKLKGLRLDIYDALAAAGIDAEI 61
Query: 73 GHINTRSEVAGYMGNDQLGQALEDSDVVIIPAGVPRKPGMTRDDLFNINAGIVKDLCSAI 132
+ S+VAG SD+VII AGVPRK GM+R DL NA IVK I
Sbjct: 62 KISSDLSDVAG-------------SDIVIITAGVPRKEGMSRLDLAKKNAKIVKKYAKQI 108
Query: 133 AKYCPNAIVNMISNPVNSTVPIAAEVFKKAGTYNEKKLFGVTT-LDVVRAKTFYAGKANV 191
A++ P+ + +++NPV+ A K++G +++ ++FG+ T LD +R K A NV
Sbjct: 109 AEFAPDTKILVVTNPVDVMTYKA---LKESG-FDKNRVFGLGTHLDSLRFKVAIAKHFNV 164
Query: 192 NVAEVNVPVVGGHAGITILPLFSQAT----PKANLA---DEDIKALTKRTQDGGTEVVEA 244
+++EV+ ++G H G +++PL S + P D D++ + + ++ G ++
Sbjct: 165 HISEVHTRIIGEH-GDSMVPLISSTSIGGIPIKRFPEYKDFDVEKIVETVKNAGQNIISL 223
Query: 245 KAG 247
K G
Sbjct: 224 KGG 226
>gnl|CDD|173376 PTZ00082, PTZ00082, L-lactate dehydrogenase; Provisional.
Length = 321
Score = 108 bits (271), Expect = 7e-28
Identities = 82/249 (32%), Positives = 133/249 (53%), Gaps = 34/249 (13%)
Query: 25 SVPDRKVAVLGAAGGIGQPLALLMKLNPLVSRLALYDIA-NTP-GVAADVGHIN----TR 78
+ RK++++G+ G IG +A L+ L L + L+DI N P G A D+ H N +
Sbjct: 3 MIKRRKISLIGS-GNIGGVMAYLIVLKNL-GDVVLFDIVKNIPQGKALDISHSNVIAGSN 60
Query: 79 SEVAGYMGNDQLGQALEDSDVVIIPAGVPRKPGMT-----RDDLFNINAGIVKDLCSAIA 133
S+V G N+ + + SDVVI+ AG+ ++PG + RDDL +NA I+ ++ I
Sbjct: 61 SKVIG--TNNY--EDIAGSDVVIVTAGLTKRPGKSDKEWNRDDLLPLNAKIMDEVAEGIK 116
Query: 134 KYCPNAIVNMISNPVNSTVPIAAEVFKKAGTYNEKKLFGVT-TLDVVRAKTFYAGKANVN 192
KYCPNA V +I+NP++ V ++ ++ + K+ G+ LD R +T+ A K VN
Sbjct: 117 KYCPNAFVIVITNPLDVMV----KLLQEHSGLPKNKVCGMAGVLDSSRLRTYIAEKLGVN 172
Query: 193 VAEVNVPVVGGHAGITILPLFSQAT----------PKANLADEDIKALTKRTQDGGTEVV 242
+V+ V+G H G ++PL T K + E+I + +RT++ G E+V
Sbjct: 173 PRDVHASVIGAH-GDKMVPLPRYVTVGGIPLSEFIKKGLITQEEIDEIVERTRNTGKEIV 231
Query: 243 EAKAGKGSA 251
+ G GSA
Sbjct: 232 DL-LGTGSA 239
>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 = 107 bits (269), Expect = 1e-27
Identities = 71/235 (30%), Positives = 114/235 (48%), Gaps = 25/235 (10%)
Query: 31 VAVLGAAGGIGQPLALLMKLNPLVSRLALYDI--ANTPGVAADVGH----INTRSEVAGY 84
+ ++GA G +G +A + L S L L D+ G A D+ H + T + V G
Sbjct: 1 ITIIGA-GNVGAAVAFALIAKGLASELVLVDVNEEKAKGDALDLSHASAFLATGTIVRGG 59
Query: 85 MGNDQLGQALEDSDVVIIPAGVPRKPGMTRDDLFNINAGIVKDLCSAIAKYCPNAIVNMI 144
D D+D+V+I AG PRKPG TR DL N NA I++ + + + KY P+AI+ ++
Sbjct: 60 DYAD-----AADADIVVITAGAPRKPGETRLDLINRNAPILRSVITNLKKYGPDAIILVV 114
Query: 145 SNPVNSTVPIAAEVFKKAGTYNEKKLFGV-TTLDVVRAKTFYAGKANVNVAEVNVPVVGG 203
SNPV+ I V +K + ++ G T LD R ++ A K +V+ V+ V+G
Sbjct: 115 SNPVD----ILTYVAQKLSGLPKNRVIGSGTLLDSARFRSLLAEKLDVDPQSVHAYVLGE 170
Query: 204 HAGITILPLFSQAT-------PKANLADEDIKALTKRTQDGGTEVVEAKAGKGSA 251
H G + + +S AT A D++A+ + + G E++ K
Sbjct: 171 H-GDSQVVAWSTATVGGLPLEELAPFTKLDLEAIEEEVRTSGYEIIRLKGATNYG 224
>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 = 101 bits (254), Expect = 8e-27
Identities = 41/93 (44%), Positives = 53/93 (56%), Gaps = 12/93 (12%)
Query: 174 TTLDVVRAKTFYAGKANVNVAEVNVPVVGGHAG----------ITILPLFSQATPKANLA 223
TTLD RA+TF A K V+ VNV V+G H+G +TI+PL SQ
Sbjct: 1 TTLDTARARTFLAEKFGVDPRSVNVYVIGEHSGTQFPDWSHAKVTIIPLISQVKENLKDT 60
Query: 224 DEDIKALTKRTQDGGTEVVEAKAGKGSATLSMA 256
D +++ L +R Q+ G EV+EAKA GS T SMA
Sbjct: 61 DWELEELIERVQNAGYEVIEAKA--GSTTYSMA 91
>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 = 104 bits (262), Expect = 1e-26
Identities = 62/161 (38%), Positives = 101/161 (62%), Gaps = 10/161 (6%)
Query: 96 DSDVVIIPAGVPRKPGMTRDDLFNINAGIVKDLCSAIAKYCPNAIVNMISNPVNSTVPIA 155
+SD+V+I AG+PRKPGM+R+DL ++NAGIV+++ I ++ PN I+ ++SNP+++ +A
Sbjct: 69 NSDIVVITAGLPRKPGMSREDLLSMNAGIVREVTGRIMEHSPNPIIVVVSNPLDAMTYVA 128
Query: 156 AEVFKKAGTYNEKKLFGVTTLDVVRAKTFYAGKANVNVAEVNVPVVGGHAGITILPLFSQ 215
+ K+G E+ + LD R +TF A + V+V +V V+GGH G ++PL
Sbjct: 129 WQ---KSGFPKERVIGQAGVLDSARFRTFIAMELGVSVQDVTACVLGGH-GDAMVPLVRY 184
Query: 216 AT----PKANL-ADEDIKALTKRTQDGGTEVVEAKAGKGSA 251
+T P A+L + E I + +RT+ GG E+V +GSA
Sbjct: 185 STVAGIPVADLISAERIAEIVERTRKGGGEIVNL-LKQGSA 224
>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 = 90.6 bits (226), Expect = 2e-21
Identities = 68/244 (27%), Positives = 107/244 (43%), Gaps = 37/244 (15%)
Query: 29 RKVAVLGAAGGIGQPLALLMKLNPLVSRLALYDI--ANTPGVAADVGH----INTRSEVA 82
KVA++GA G +G A + L L S + L DI A G A D+ H + A
Sbjct: 1 MKVAIVGA-GFVGSTTAYALLLRGLASEIVLVDINKAKAEGEAMDLAHGTPFVKPVRIYA 59
Query: 83 G-YMGNDQLGQALEDSDVVIIPAGVPRKPGMTRDDLFNINAGIVKDLCSAIAKYCPNAIV 141
G Y + +DVV+I AG +KPG TR DL N I K++ I KY P+AI+
Sbjct: 60 GDY-------ADCKGADVVVITAGANQKPGETRLDLLKRNVAIFKEIIPQILKYAPDAIL 112
Query: 142 NMISNPVNSTVPIAAEVFKKAGTYNEKKLFGV-TTLDVVRAKTFYAGKANVNVAEVNVPV 200
+++NPV+ + V K ++ G T LD R + V+ V+ +
Sbjct: 113 LVVTNPVD----VLTYVAYKLSGLPPNRVIGSGTVLDTARFRYLLGEHLGVDPRSVHAYI 168
Query: 201 VGGHAGITILPLFSQAT------------PKANLADEDIKALTKRTQDGGTEVVEAKAGK 248
+G H G + + ++S A +E + + + ++ E++E K
Sbjct: 169 IGEH-GDSEVAVWSSANIGGVPLDEFCKLCGRPFDEEVREEIFEEVRNAAYEIIE---RK 224
Query: 249 GSAT 252
G AT
Sbjct: 225 G-AT 227
>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 = 88.7 bits (221), Expect = 1e-20
Identities = 61/230 (26%), Positives = 100/230 (43%), Gaps = 20/230 (8%)
Query: 29 RKVAVLGAAGGIGQPLALLMKLNPLVSRLALYDIANTPGVAADVGHINTRSEVAGYMGND 88
RKV ++GA G +G A + + L L DI N + +
Sbjct: 1 RKVVIIGA-GHVGSSFAYSLVNQGIADELVLIDI-NEEKAEGEALDLEDALAFLPSPVKI 58
Query: 89 QLG--QALEDSDVVIIPAGVPRKPGMTRDDLFNINAGIVKDLCSAIAKYCPNAIVNMISN 146
+ G +D+D+V+I AG P+KPG TR DL NA I+K + I + I + SN
Sbjct: 59 KAGDYSDCKDADIVVITAGAPQKPGETRLDLLEKNAKIMKSIVPKIKASGFDGIFLVASN 118
Query: 147 PVNSTVPIAAEVFKKAGTYNEKKLFGV-TTLDVVRAKTFYAGKANVNVAEVNVPVVGGHA 205
PV+ + V +K + ++ G T+LD R + A K NV+ V+ V+G H
Sbjct: 119 PVD----VITYVVQKLSGLPKNRVIGTGTSLDTARLRRALAEKLNVDPRSVHAYVLGEH- 173
Query: 206 GITILPLFSQAT----------PKANLADEDIKALTKRTQDGGTEVVEAK 245
G + +S T + L++ D+ + + + G E++ K
Sbjct: 174 GDSQFVAWSTVTVGGKPLLDLLKEGKLSELDLDEIEEDVRKAGYEIINGK 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 = 85.3 bits (212), Expect = 2e-19
Identities = 60/229 (26%), Positives = 100/229 (43%), Gaps = 32/229 (13%)
Query: 37 AGGIGQPLALLMKLNPLVSRLALYDIAN--TPGVAADVGH----INTRSEV--AGYMGND 88
AG +G A + + + L DI G A D+ H + T ++ Y
Sbjct: 4 AGNVGSSTAFALLNQGIADEIVLIDINKDKAEGEAMDLQHAASFLPTPKKIRSGDY---- 59
Query: 89 QLGQALEDSDVVIIPAGVPRKPGMTRDDLFNINAGIVKDLCSAIAKYCPNAIVNMISNPV 148
+D+D+V+I AG P+KPG TR +L N I+K + + K + I + +NPV
Sbjct: 60 ---SDCKDADLVVITAGAPQKPGETRLELVGRNVRIMKSIVPEVVKSGFDGIFLVATNPV 116
Query: 149 NSTVPIAAEVFKKAGTYNEKKLFGV-TTLDVVRAKTFYAGKANVNVAEVNVPVVGGHAGI 207
+ I V K + + ++ G T LD R + A K V+ V+ ++G H G
Sbjct: 117 D----ILTYVAWKLSGFPKNRVIGSGTVLDTARLRYLLAEKLGVDPQSVHAYIIGEH-GD 171
Query: 208 TILPLFSQAT-----------PKANLADEDIKALTKRTQDGGTEVVEAK 245
+ +P++S AT K D D++ + K +D E++ K
Sbjct: 172 SEVPVWSSATIGGVPLLDYLKAKGTETDLDLEEIEKEVRDAAYEIINRK 220
>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 = 81.2 bits (201), Expect = 6e-18
Identities = 80/246 (32%), Positives = 105/246 (42%), Gaps = 36/246 (14%)
Query: 30 KVAVLGAAGGIGQPLA-------LLMKLNPLVSRLALYDIANTPGVAADVGHINTRSE-- 80
+VAV GAAG IG L L K P+V L L DI V E
Sbjct: 5 RVAVTGAAGQIGYSLLFRIASGELFGKDQPVV--LHLLDIPPAMKALEGV-----AMELE 57
Query: 81 ------VAGYMGNDQLGQALEDSDVVIIPAGVPRKPGMTRDDLFNINAGIVKDLCSAIAK 134
+AG + +A +D D ++ PRKPGM R DL + N I K+ A+ K
Sbjct: 58 DCAFPLLAGVVATTDPEEAFKDVDAALLVGAFPRKPGMERADLLSKNGKIFKEQGKALNK 117
Query: 135 YC-PNAIVNMISNPVNSTVPIAAEVFKKAGTYNEKKLFGVTTLDVVRAKTFYAGKANVNV 193
+ V ++ NP N+ IA+ K A K +T LD RAK A KA V V
Sbjct: 118 VAKKDVKVLVVGNPANTNALIAS---KNAPDIPPKNFSAMTRLDHNRAKYQLAAKAGVPV 174
Query: 194 AEV-NVPVVGGHAGITILPLFSQATPKANLADEDIK-------ALTKRTQDGGTEVVEAK 245
++V NV + G H+ T +P F+ AT E IK Q G V+EA+
Sbjct: 175 SDVKNVIIWGNHSN-TQVPDFTHATVDGRPVKEVIKDDKWLEGEFIPTVQQRGAAVIEAR 233
Query: 246 AGKGSA 251
G SA
Sbjct: 234 -GASSA 238
>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 = 81.2 bits (201), Expect = 7e-18
Identities = 68/205 (33%), Positives = 88/205 (42%), Gaps = 28/205 (13%)
Query: 30 KVAVLGAAGGIGQPLA-------LLMKLNPLVSRLALYDIANTPGVAADVGHINTRSE-- 80
V + GAAG IG L L P++ L L DI P + A G E
Sbjct: 2 HVLITGAAGQIGYNLLFLIASGELFGDDQPVI--LHLLDI--PPAMKALEG---VVMELQ 54
Query: 81 ------VAGYMGNDQLGQALEDSDVVIIPAGVPRKPGMTRDDLFNINAGIVKDLCSAIAK 134
+ G + +A +D DV I+ PRKPGM R DL NA I K+ A+ K
Sbjct: 55 DCAFPLLKGVVITTDPEEAFKDVDVAILVGAFPRKPGMERADLLRKNAKIFKEQGEALNK 114
Query: 135 YC-PNAIVNMISNPVNSTVPIAAEVFKKAGTYNEKKLFGVTTLDVVRAKTFYAGKANVNV 193
P V ++ NP N+ IA K A K +T LD RAK A K V V
Sbjct: 115 VAKPTVKVLVVGNPANTNALIAL---KNAPNLPPKNFTALTRLDHNRAKAQVARKLGVRV 171
Query: 194 AEV-NVPVVGGHAGITILPLFSQAT 217
++V NV + G H+ T +P S A
Sbjct: 172 SDVKNVIIWGNHSN-TQVPDLSNAV 195
>gnl|CDD|178836 PRK00066, ldh, L-lactate dehydrogenase; Reviewed.
Length = 315
Score = 76.9 bits (190), Expect = 2e-16
Identities = 62/244 (25%), Positives = 97/244 (39%), Gaps = 48/244 (19%)
Query: 29 RKVAVLGAAGGIGQPLALLMKLNPLVSRLALYDIA--NTPGVAADVGHI-----NTRSEV 81
KV ++G G +G A + + L + DI G A D+ H T+
Sbjct: 7 NKVVLVGD-GAVGSSYAYALVNQGIADELVIIDINKEKAEGDAMDLSHAVPFTSPTKIYA 65
Query: 82 AGYMGNDQLGQALEDSDVVIIPAGVPRKPGMTRDDLFNINAGIVKDLCSAIAKYCPNAIV 141
Y +D+D+V+I AG P+KPG TR DL N I K + + + I
Sbjct: 66 GDY-------SDCKDADLVVITAGAPQKPGETRLDLVEKNLKIFKSIVGEVMASGFDGIF 118
Query: 142 NMISNPVNSTVPIAAEVFKKAGTYNEKKLFGV---------TTLDVVRAKTFYAGKANVN 192
+ SNPV+ TY KL G T+LD R + + K +V+
Sbjct: 119 LVASNPVDIL------------TYATWKLSGFPKERVIGSGTSLDSARFRYMLSEKLDVD 166
Query: 193 VAEVNVPVVGGHAGITILPLFSQAT-----------PKANLADEDIKALTKRTQDGGTEV 241
V+ ++G H G T P++S A +ED+ + + +D E+
Sbjct: 167 PRSVHAYIIGEH-GDTEFPVWSHANVAGVPLEEYLEENEQYDEEDLDEIFENVRDAAYEI 225
Query: 242 VEAK 245
+E K
Sbjct: 226 IEKK 229
>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 = 75.4 bits (186), Expect = 5e-16
Identities = 70/252 (27%), Positives = 103/252 (40%), Gaps = 42/252 (16%)
Query: 30 KVAVLGAAGGIG-QPLALLMKLNPLVSRLALYDIANTPGVAA----DVGH-------INT 77
K+ V+GA G +G L + L L S + L D+ GVA D H NT
Sbjct: 1 KLVVIGA-GHVGSAVLNYALALG-LFSEIVLIDV--NEGVAEGEALDFHHATALTYSTNT 56
Query: 78 RSEVAGYMGNDQLGQALEDSDVVIIPAGVPRKPGMT--RDDLFNINAGIVKDLCSAIAKY 135
+ Y D+D+++I AG PG T R DL NA I++++ I K
Sbjct: 57 KIRAGDY-------DDCADADIIVITAGPSIDPGNTDDRLDLAQTNAKIIREIMGNITKV 109
Query: 136 CPNAIVNMISNPVNSTVPIAAEVFKKAGTYNEKKLFGV-TTLDVVRAKTFYAGKANVNVA 194
A++ +I+NP++ V IAA F Y K+ G T LD R + A K V+
Sbjct: 110 TKEAVIILITNPLDIAVYIAATEFD----YPANKVIGTGTMLDTARLRRIVADKYGVDPK 165
Query: 195 EVNVPVVGGHAGITILPLFSQATPKANLADE----------DIKALTKRTQDGGTEVVEA 244
V V+G H G P++S DE D L + +V
Sbjct: 166 NVTGYVLGEH-GSHAFPVWSLVNIAGLPLDELEALFGKEPIDKDELLEEVVQAAYDVFNR 224
Query: 245 KAGKGSATLSMA 256
K G +A ++ +
Sbjct: 225 K-GWTNAGIAKS 235
>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 = 73.4 bits (181), Expect = 3e-15
Identities = 71/259 (27%), Positives = 105/259 (40%), Gaps = 49/259 (18%)
Query: 30 KVAVLGAAGGIGQPLALLMKLNPLVSR-----------LALYDIANTPGVAADVGHINTR 78
+V V GAAG I L P++++ L L DI V
Sbjct: 4 RVLVTGAAGQIAYSLL------PMIAKGDVFGPDQPVILHLLDIPPALKALEGV-----V 52
Query: 79 SE--------VAGYMGNDQLGQALEDSDVVIIPAGVPRKPGMTRDDLFNINAGIVKDLCS 130
E + + +A +D DV I+ +PRK GM R DL N I K+
Sbjct: 53 MELQDCAFPLLKSVVATTDPEEAFKDVDVAILVGAMPRKEGMERKDLLKANVKIFKEQGE 112
Query: 131 AIAKYC-PNAIVNMISNPVNSTVPIAAEVFKKAGTYNEKKLFGVTTLDVVRAKTFYAGKA 189
A+ KY N V ++ NP N+ I K A + ++ +T LD RAK+ A K
Sbjct: 113 ALDKYAKKNVKVLVVGNPANTNALILL---KYAPSIPKENFTALTRLDHNRAKSQIALKL 169
Query: 190 NVNVAEV-NVPVVGGHAGITILPLFSQATPKANLADEDIKALTK-----------RTQDG 237
V V++V NV + G H+ T P + AT + N + + K Q
Sbjct: 170 GVPVSDVKNVIIWGNHSS-TQYPDVNHATVELNGKGKPAREAVKDDAWLNGEFISTVQKR 228
Query: 238 GTEVVEAKAGKGSATLSMA 256
G V++A+ K S+ +S A
Sbjct: 229 GAAVIKAR--KLSSAMSAA 245
>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 = 71.1 bits (175), Expect = 2e-14
Identities = 71/247 (28%), Positives = 99/247 (40%), Gaps = 38/247 (15%)
Query: 30 KVAVLGAAGGIGQPLALLMKL---------NPLVSRLALYDIANT----PGVA---ADVG 73
+VAV GAAG IG +LL ++ P++ L L ++ GVA D
Sbjct: 4 RVAVTGAAGQIGY--SLLFRIASGEMFGPDQPVI--LQLLELPQALKALEGVAMELEDCA 59
Query: 74 HINTRSEVAGYMGNDQLGQALEDSDVVIIPAGVPRKPGMTRDDLFNINAGIVKDLCSAIA 133
V D A +D+D ++ PR PGM R DL N I A+
Sbjct: 60 FPLLAEIVIT----DDPNVAFKDADWALLVGAKPRGPGMERADLLKANGKIFTAQGKALN 115
Query: 134 KYC-PNAIVNMISNPVNSTVPIAAEVFKKAGTYNEKKLFGVTTLDVVRAKTFYAGKANVN 192
+ V ++ NP N+ IA K A +T LD RAK+ A KA V
Sbjct: 116 DVASRDVKVLVVGNPCNTNALIAM---KNAPDIPPDNFTAMTRLDHNRAKSQLAKKAGVP 172
Query: 193 VAEV-NVPVVGGHAGITILPLFSQATPKANLADEDI-------KALTKRTQDGGTEVVEA 244
V +V N+ + G H+ T P F+ AT A E I Q G +++A
Sbjct: 173 VTDVKNMVIWGNHSP-TQYPDFTNATIGGKPAAEVINDRAWLEDEFIPTVQKRGAAIIKA 231
Query: 245 KAGKGSA 251
+ G SA
Sbjct: 232 R-GASSA 237
>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 = 67.9 bits (166), Expect = 3e-13
Identities = 71/255 (27%), Positives = 102/255 (40%), Gaps = 41/255 (16%)
Query: 30 KVAVLGAAGGIGQPLA-------LLMKLNPLVSRLALYDIANTPGVAADVGHINTRSEV- 81
+V V GAAG IG L +L K P++ L L DI V V E+
Sbjct: 1 RVVVTGAAGQIGYALLPMIARGRMLGKDQPII--LHLLDIPPAMKVLEGV-----VMELM 53
Query: 82 -------AGYMGNDQLGQALEDSDVVIIPAGVPRKPGMTRDDLFNINAGIVKDLCSAIAK 134
G + A D DV I+ PRK GM R DL + N I K+ A+ K
Sbjct: 54 DCAFPLLDGVVPTHDPAVAFTDVDVAILVGAFPRKEGMERRDLLSKNVKIFKEQGRALDK 113
Query: 135 YC-PNAIVNMISNPVNSTVPIAAEVFKKAGTYNEKKLFGVTTLDVVRAKTFYAGKANVNV 193
+ V ++ NP N+ + + A + K +T LD RA A +A V V
Sbjct: 114 LAKKDCKVLVVGNPANTNALVLSNY---APSIPPKNFSALTRLDHNRALAQVAERAGVPV 170
Query: 194 AEV-NVPVVGGHAGITILPLFSQATPKANLADEDIKALTKR-----------TQDGGTEV 241
++V NV + G H+ T P + AT + ++ K Q G +
Sbjct: 171 SDVKNVIIWGNHSS-TQYPDVNHATVTKGGKQKPVREAIKDDAYLDGEFITTVQQRGAAI 229
Query: 242 VEAKAGKGSATLSMA 256
+ A+ K S+ LS A
Sbjct: 230 IRAR--KLSSALSAA 242
>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 = 67.6 bits (165), Expect = 3e-13
Identities = 41/138 (29%), Positives = 63/138 (45%), Gaps = 4/138 (2%)
Query: 81 VAGYMGNDQLGQALEDSDVVIIPAGVPRKPGMTRDDLFNINAGIVKDLCSAIAKYC-PNA 139
+AG + +L +A +D D + A VP KPG R DL N I K A+++Y P
Sbjct: 45 LAGTIVTTKLEEAFKDIDCAFLVASVPLKPGEVRADLLTKNTPIFKATGEALSEYAKPTV 104
Query: 140 IVNMISNPVNSTVPIAAEVFKKAGTYNEKKLFGVTTLDVVRAKTFYAGKANVNVAEVNVP 199
V +I NPVN+ +A A + + + LD RA + A K V V +
Sbjct: 105 KVLVIGNPVNTNCLVA---MLHAPKLSAENFSSLCMLDHNRAVSRIASKLKVPVDHIYHV 161
Query: 200 VVGGHAGITILPLFSQAT 217
VV G+ +++ + A
Sbjct: 162 VVWGNHAESMVADLTHAE 179
>gnl|CDD|235468 PRK05442, PRK05442, malate dehydrogenase; Provisional.
Length = 326
Score = 65.6 bits (161), Expect = 2e-12
Identities = 78/250 (31%), Positives = 106/250 (42%), Gaps = 44/250 (17%)
Query: 30 KVAVLGAAGGIGQPL-------ALLMKLNPLVSRLALYDIANTPGVAADVGHINTRSE-- 80
+VAV GAAG IG L +L K P+ L L +I P + A G E
Sbjct: 6 RVAVTGAAGQIGYSLLFRIASGDMLGKDQPV--ILQLLEI--PPALKALEG---VVMELD 58
Query: 81 ------VAGYMGNDQLGQALEDSDVVIIPAGVPRKPGMTRDDLFNINAGIVKDLCSAIAK 134
+AG + D A +D+DV ++ PR PGM R DL N I A+ +
Sbjct: 59 DCAFPLLAGVVITDDPNVAFKDADVALLVGARPRGPGMERKDLLEANGAIFTAQGKALNE 118
Query: 135 YC-PNAIVNMISNPVNSTVPIAAEVFKKAGTYNEKKLFGVTTLDVVRAKTFYAGKANVNV 193
+ V ++ NP N+ IA K A + +T LD RA + A KA V V
Sbjct: 119 VAARDVKVLVVGNPANTNALIAM---KNAPDLPAENFTAMTRLDHNRALSQLAAKAGVPV 175
Query: 194 AEV-NVPVVGGHAGITILPLFSQAT----PKAN-------LADEDIKALTKRTQDGGTEV 241
A++ + V G H+ T P F AT P A L D I + KR G +
Sbjct: 176 ADIKKMTVWGNHSA-TQYPDFRHATIDGKPAAEVINDQAWLEDTFIPTVQKR----GAAI 230
Query: 242 VEAKAGKGSA 251
+EA+ G SA
Sbjct: 231 IEAR-GASSA 239
>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 = 62.6 bits (153), Expect = 2e-11
Identities = 52/184 (28%), Positives = 82/184 (44%), Gaps = 21/184 (11%)
Query: 30 KVAVLGA-AGGIGQPLALLMKLNPLVSRLALYDIAN--TPGVAADVGHINTRSEVAGYMG 86
KV V+G G+ +++L K L L L D+ G A D+ H + ++
Sbjct: 5 KVTVVGVGQVGMACAISILAK--GLADELVLVDVVEDKLKGEAMDLQH------GSAFLK 56
Query: 87 N-----DQLGQALEDSDVVIIPAGVPRKPGMTRDDLFNINAGIVKDLCSAIAKYCPNAIV 141
N D+ +S VVI+ AG + G +R DL N I K + + KY PNAI+
Sbjct: 57 NPKIEADKDYSVTANSKVVIVTAGARQNEGESRLDLVQRNVDIFKGIIPKLVKYSPNAIL 116
Query: 142 NMISNPVNSTVPIAAEVFKKAGTYNEKKLFGV-TTLDVVRAKTFYAGKANVNVAEVNVPV 200
++SNPV+ I V K + ++ G LD R + A + V + V+ +
Sbjct: 117 LVVSNPVD----IMTYVAWKLSGLPKHRVIGSGCNLDSARFRYLIAERLGVAPSSVHGWI 172
Query: 201 VGGH 204
+G H
Sbjct: 173 IGEH 176
>gnl|CDD|177744 PLN00135, PLN00135, malate dehydrogenase.
Length = 309
Score = 59.8 bits (145), Expect = 2e-10
Identities = 51/178 (28%), Positives = 85/178 (47%), Gaps = 19/178 (10%)
Query: 92 QALEDSDVVIIPAGVPRKPGMTRDDLFNINAGIVKDLCSAIAKYC-PNAIVNMISNPVNS 150
+A + ++ ++ G PRK GM R D+ + N I K SA+ K+ P+ V +++NP N+
Sbjct: 54 EACKGVNIAVMVGGFPRKEGMERKDVMSKNVSIYKSQASALEKHAAPDCKVLVVANPANT 113
Query: 151 TVPIAAEVFKKAGTYNEKKLFGVTTLDVVRAKTFYAGKANVNVAEV-NVPVVGGHAGITI 209
I E A + EK + +T LD RA + + V V++V NV + G H+ T
Sbjct: 114 NALILKEF---APSIPEKNITCLTRLDHNRALGQISERLGVPVSDVKNVIIWGNHSS-TQ 169
Query: 210 LPLFSQATPKANLADEDIKALT-----------KRTQDGGTEVVEAKAGKGSATLSMA 256
P + AT K ++ ++ L Q G +++A+ K S+ LS A
Sbjct: 170 YPDVNHATVKTPSGEKPVRELVADDAWLNGEFITTVQQRGAAIIKAR--KLSSALSAA 225
>gnl|CDD|178212 PLN02602, PLN02602, lactate dehydrogenase.
Length = 350
Score = 57.9 bits (140), Expect = 1e-09
Identities = 56/201 (27%), Positives = 92/201 (45%), Gaps = 17/201 (8%)
Query: 22 SSESVPDR---KVAVLGAAGGIGQPLALLMKLNPLVSRLALYDIA--NTPGVAADVGH-- 74
SS P R KV+V+G G +G +A + L LAL D+ G D+ H
Sbjct: 28 SSPPSPTRRHTKVSVVGV-GNVGMAIAQTILTQDLADELALVDVNPDKLRGEMLDLQHAA 86
Query: 75 -INTRSEVAGYMGNDQLGQALEDSDVVIIPAGVPRKPGMTRDDLFNINAGIVKDLCSAIA 133
R+++ SD+ I+ AG + PG +R +L N + + + +A
Sbjct: 87 AFLPRTKILA----STDYAVTAGSDLCIVTAGARQIPGESRLNLLQRNVALFRKIIPELA 142
Query: 134 KYCPNAIVNMISNPVNSTVPIAAEVFKKAGTYNEKKLFGVTTLDVVRAKTFYAGKANVNV 193
KY P+ I+ ++SNPV+ +A +K +G + + T LD R + A +VN
Sbjct: 143 KYSPDTILLIVSNPVDVLTYVA---WKLSGFPANRVIGSGTNLDSSRFRFLIADHLDVNA 199
Query: 194 AEVNVPVVGGHAGITILPLFS 214
+V +VG H G + + L+S
Sbjct: 200 QDVQAYIVGEH-GDSSVALWS 219
>gnl|CDD|215060 PLN00112, PLN00112, malate dehydrogenase (NADP); Provisional.
Length = 444
Score = 48.7 bits (116), Expect = 1e-06
Identities = 47/155 (30%), Positives = 67/155 (43%), Gaps = 7/155 (4%)
Query: 95 EDSDVVIIPAGVPRKPGMTRDDLFNINAGIVKDLCSAI-AKYCPNAIVNMISNPVNSTVP 153
+D++ ++ PR PGM R DL +IN I + A+ N V ++ NP N+
Sbjct: 175 QDAEWALLIGAKPRGPGMERADLLDINGQIFAEQGKALNEVASRNVKVIVVGNPCNTNAL 234
Query: 154 IAAEVFKKAGTYNEKKLFGVTTLDVVRAKTFYAGKANVNVAEV-NVPVVGGHAGITILPL 212
I K A K +T LD RAK A KA V +V NV + G H+ T +P
Sbjct: 235 IC---LKNAPNIPAKNFHALTRLDENRAKCQLALKAGVFYDKVSNVTIWGNHS-TTQVPD 290
Query: 213 FSQATPKANLADEDIKALTKRTQDGGTEVVEAKAG 247
F A E I K ++ T V+ + G
Sbjct: 291 FLNAKINGLPVKEVITD-HKWLEEEFTPKVQKRGG 324
>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 = 47.3 bits (112), Expect = 3e-06
Identities = 52/158 (32%), Positives = 70/158 (44%), Gaps = 7/158 (4%)
Query: 92 QALEDSDVVIIPAGVPRKPGMTRDDLFNINAGIVKDLCSAIAKYCP-NAIVNMISNPVNS 150
+ ED+D ++ PR PGM R DL +IN I D A+ N V ++ NP N+
Sbjct: 116 EVFEDADWALLIGAKPRGPGMERADLLDINGQIFADQGKALNAVASKNCKVLVVGNPCNT 175
Query: 151 TVPIAAEVFKKAGTYNEKKLFGVTTLDVVRAKTFYAGKANVNVAEV-NVPVVGGHAGITI 209
IA K A K +T LD RAK A K+ V NV + G H+ T
Sbjct: 176 NALIA---MKNAPNIPRKNFHALTRLDENRAKCQLALKSGKFYTSVSNVTIWGNHS-TTQ 231
Query: 210 LPLFSQATPKANLADEDIKALTKRTQDGGTEVVEAKAG 247
+P F A A E IK TK ++ T V+ + G
Sbjct: 232 VPDFVNAKIGGRPAKEVIKD-TKWLEEEFTPTVQKRGG 268
>gnl|CDD|224403 COG1486, CelF, Alpha-galactosidases/6-phospho-beta-glucosidases,
family 4 of glycosyl hydrolases [Carbohydrate transport
and metabolism].
Length = 442
Score = 36.1 bits (84), Expect = 0.013
Identities = 33/149 (22%), Positives = 51/149 (34%), Gaps = 34/149 (22%)
Query: 30 KVAVLGAAGGIGQPLALLMKLNPL----VSRLALYDIANTPGVAADVGHINTR------S 79
K+ ++G G P LL L V LALYDI + + + +
Sbjct: 5 KIVIIGG-GSTYTPKLLLGDLARTEELPVRELALYDI--DEERLKIIAILAKKLVEEAGA 61
Query: 80 EVAGYMGNDQLGQALEDSDVVIIPA------------GVPRKPGMTRDDLFNI------- 120
V D +ALE +D VI +P K G+ +
Sbjct: 62 PVKVEATTD-RREALEGADFVITQIRVGGLEAREKDERIPLKHGLYGQETNGPGGIFYGL 120
Query: 121 -NAGIVKDLCSAIAKYCPNAIVNMISNPV 148
++ D+ + K CPNA + +NP
Sbjct: 121 RTIPVILDIAKDMEKVCPNAWMLNYTNPA 149
>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 = 36.0 bits (84), Expect = 0.015
Identities = 29/128 (22%), Positives = 47/128 (36%), Gaps = 43/128 (33%)
Query: 55 SRLALYDIANTPGVAADVGHINTRSEVAGYMGNDQLG------------QALEDSDVVII 102
S +AL DI D + T +A + ++LG +AL+ +D VI
Sbjct: 30 STIALMDI--------DEERLETVEILAKKI-VEELGAPLKIEATTDRREALDGADFVIN 80
Query: 103 ---PAG---------VPRKPG------MTRD--DLFNINAGI--VKDLCSAIAKYCPNAI 140
G +P K G T +F I + D+ I + CP+A
Sbjct: 81 TIQVGGHEYTETDFEIPEKYGYYQTVGDTSGPGGIFRALRTIPVLLDIARDIEELCPDAW 140
Query: 141 VNMISNPV 148
+ +NP+
Sbjct: 141 LLNYANPM 148
>gnl|CDD|223936 COG1004, Ugd, Predicted UDP-glucose 6-dehydrogenase [Cell envelope
biogenesis, outer membrane].
Length = 414
Score = 35.3 bits (82), Expect = 0.026
Identities = 22/83 (26%), Positives = 34/83 (40%), Gaps = 12/83 (14%)
Query: 93 ALEDSDVVIIPAGVPRKPGMTRDDLFNINAGIVKDLCSAIAKYCPNAIVNMISNPVNSTV 152
A++D+DVV I G P + + V+ + I + V ++ + STV
Sbjct: 73 AVKDADVVFIAVGTPPDE------DGSADLSYVEAVAKDIGEILDGKAV-VV---IKSTV 122
Query: 153 PI--AAEVFKKAGTYNEKKLFGV 173
P+ EV K N K F V
Sbjct: 123 PVGTTEEVRAKIREENSGKDFEV 145
>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 = 35.0 bits (81), Expect = 0.027
Identities = 24/93 (25%), Positives = 45/93 (48%), Gaps = 4/93 (4%)
Query: 32 AVLGAAGGIGQPLA-LLMKLNPLVSRLALYDIANTPGVAADVGHINTRSEVAGYMGN-DQ 89
V G G +G+ + LL++ L + ++D+ +P + D + + + G + +
Sbjct: 1 LVTGGGGFLGRHIVRLLLREGEL-QEVRVFDLRFSPELLEDFSKLQVITYIEGDVTDKQD 59
Query: 90 LGQALEDSDVVIIPAGVPRKPGM-TRDDLFNIN 121
L +AL+ SDVVI A + G RD + +N
Sbjct: 60 LRRALQGSDVVIHTAAIIDVFGKAYRDTIMKVN 92
>gnl|CDD|216304 pfam01113, DapB_N, Dihydrodipicolinate reductase, N-terminus.
Dihydrodipicolinate reductase (DapB) reduces the
alpha,beta-unsaturated cyclic imine,
dihydro-dipicolinate. This reaction is the second
committed step in the biosynthesis of L-lysine and its
precursor meso-diaminopimelate, which are critical for
both protein and cell wall biosynthesis. The N-terminal
domain of DapB binds the dinucleotide NADPH.
Length = 122
Score = 33.8 bits (78), Expect = 0.028
Identities = 22/72 (30%), Positives = 35/72 (48%), Gaps = 3/72 (4%)
Query: 30 KVAVLGAAGGIGQPLALLMKLNPLVSRLALYDIANTPGVAADVGHINTRSEVAGYMGNDQ 89
KVAV+GA+G +G+ L + P +A D + + +D G + V D
Sbjct: 2 KVAVVGASGRMGRELIKAILEAPDFELVAAVDRPGSSLLGSDAGELAGPLGVP---VTDD 58
Query: 90 LGQALEDSDVVI 101
L + L D+DV+I
Sbjct: 59 LEEVLADADVLI 70
>gnl|CDD|202102 pfam02056, Glyco_hydro_4, Family 4 glycosyl hydrolase.
Length = 183
Score = 33.9 bits (78), Expect = 0.041
Identities = 34/147 (23%), Positives = 48/147 (32%), Gaps = 30/147 (20%)
Query: 30 KVAVLGAAGGIGQPLALLMKLNPL----VSRLALYDIANTPGVAADVGHINTRSEVAG-- 83
K+ ++G G P LL L+ LALYDI A E
Sbjct: 1 KIVIIGG-GSTITPKNLLGDLDHTEELPGRELALYDIDEERLDAIQTACKKLVDEAGPDI 59
Query: 84 -YMGNDQLGQALEDSDVVIIPAGVPRKPGMTRDDLFNINAGIVK---------------- 126
+ +AL D+D VI V P D+ + G+V
Sbjct: 60 KFEKTTDRKEALTDADFVINAIRVGLLPARELDEKIPLRHGVVGTIQETVGPGGIFRGLR 119
Query: 127 ------DLCSAIAKYCPNAIVNMISNP 147
D+ I + CP+A V +NP
Sbjct: 120 TIPVFFDIAKDIEELCPDAWVLNYTNP 146
>gnl|CDD|133431 cd05295, MDH_like, Malate dehydrogenase-like. These MDH-like
proteins are related to other groups in the MDH family
but do not have conserved substrate and cofactor binding
residues. 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
subgroup are uncharacterized MDH-like proteins from
animals. 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 = 452
Score = 33.1 bits (76), Expect = 0.13
Identities = 32/131 (24%), Positives = 47/131 (35%), Gaps = 7/131 (5%)
Query: 89 QLGQALEDSDVVIIPAGVPRKPGMTRDDLFNINAGIVKDLCSAIAKYCPNAIVNMIS--- 145
L A +D+ V+++ K G + I + I K V +I
Sbjct: 192 DLDVAFKDAHVIVLLDDFLIKEGEDLEGCIRSRVAICQLYGPLIEKNA-KEDVKVIVAGR 250
Query: 146 NPVNSTVPIAAEVFKKAGTYNEKKLFGVTTLDVVRAKTFYAGKANVNVAEVNVPVVGGHA 205
+N I K A + K + V L RAK A K NVN A + +V G+
Sbjct: 251 TFLNLKTSILI---KYAPSIPRKNIIAVARLQENRAKALLARKLNVNSAGIKDVIVWGNI 307
Query: 206 GITILPLFSQA 216
G S+A
Sbjct: 308 GGNTYIDLSKA 318
>gnl|CDD|223366 COG0289, DapB, Dihydrodipicolinate reductase [Amino acid transport
and metabolism].
Length = 266
Score = 32.2 bits (74), Expect = 0.22
Identities = 22/80 (27%), Positives = 36/80 (45%), Gaps = 4/80 (5%)
Query: 30 KVAVLGAAGGIGQPLALLMKLNPLVSRLALYDIANTPGVAADVGHINTRSEVAGYMGNDQ 89
KVAV GA+G +G+ L + P + +A +D + + +D G + + G D
Sbjct: 4 KVAVAGASGRMGRTLIRAVLEAPDLELVAAFDRPGSLSLGSDAGELAGLGLL-GVPVTDD 62
Query: 90 LGQALEDSDVVI---IPAGV 106
L D+DV+I P
Sbjct: 63 LLLVKADADVLIDFTTPEAT 82
>gnl|CDD|180408 PRK06114, PRK06114, short chain dehydrogenase; Provisional.
Length = 254
Score = 31.3 bits (71), Expect = 0.40
Identities = 16/50 (32%), Positives = 24/50 (48%), Gaps = 2/50 (4%)
Query: 28 DRKVAVLGAAGGIGQPLALLMKLNPLVSRLALYDIANTPGVAADVGHINT 77
+ V GA GIGQ +A + L + +AL+D+ G+A HI
Sbjct: 8 GQVAFVTGAGSGIGQRIA--IGLAQAGADVALFDLRTDDGLAETAEHIEA 55
>gnl|CDD|187540 cd05229, SDR_a3, atypical (a) SDRs, subgroup 3. These atypical SDR
family members of unknown function have a glycine-rich
NAD(P)-binding motif consensus that is very similar to
the extended SDRs, GXXGXXG. Generally, this group has
poor conservation of the active site tetrad, However,
individual sequences do contain matches to the YXXXK
active site motif, and generally Tyr or Asn in place of
the upstream Ser found in most SDRs. 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. Atypical SDRs include
biliverdin IX beta reductase (BVR-B,aka flavin
reductase), NMRa (a negative transcriptional regulator
of various fungi), progesterone 5-beta-reductase like
proteins, phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. 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. In addition to the
Rossmann fold core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids, 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.
Length = 302
Score = 30.8 bits (70), Expect = 0.69
Identities = 20/86 (23%), Positives = 31/86 (36%), Gaps = 22/86 (25%)
Query: 30 KVAVLGAAGGIGQPLALLMK--------LNPLVSRLALYDIANTPGVAADVGHINTRSEV 81
VLGA+G IG+ +A ++ ++ S+LA VAAD
Sbjct: 1 TAHVLGASGPIGREVARELRRRGWDVRLVSRSGSKLAWLPGVEI--VAADA--------- 49
Query: 82 AGYMGNDQLGQALEDSDVVIIPAGVP 107
M + A +DV+ A
Sbjct: 50 ---MDASSVIAAARGADVIYHCANPA 72
>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 = 29.0 bits (66), Expect = 0.98
Identities = 18/76 (23%), Positives = 34/76 (44%), Gaps = 1/76 (1%)
Query: 30 KVAVLGAAGGIGQPLALLMKLNPLVSRLALYDIANTPGVAADVGHINTRSEVAGYMGNDQ 89
KVA++GA G +GQ L L+ +P + +AL + + G + + +
Sbjct: 1 KVAIVGATGYVGQELLRLLAEHPPLELVALVASSRSAGKKVAFAYPILEGGKDLLLEDVD 60
Query: 90 LGQALEDSDVVIIPAG 105
+ L+D D+V +
Sbjct: 61 P-EDLKDVDIVFLALP 75
>gnl|CDD|133174 cd05042, PTKc_Aatyk, Catalytic domain of the Protein Tyrosine
Kinases, Apoptosis-associated tyrosine kinases. Protein
Tyrosine Kinase (PTK) family; Apoptosis-associated
tyrosine kinase (Aatyk) subfamily; catalytic (c) domain.
The Aatyk subfamily is also referred to as the lemur
tyrosine kinase (Lmtk) subfamily. It consists of Aatyk1
(Lmtk1), Aatyk2 (Lmtk2, Brek), Aatyk3 (Lmtk3), and
similar proteins. The PTKc family is part of a larger
superfamily that includes the catalytic domains of other
kinases such as protein serine/threonine kinases, RIO
kinases, and phosphoinositide 3-kinase (PI3K). PTKs
catalyze the transfer of the gamma-phosphoryl group from
ATP to tyrosine (tyr) residues in protein substrates.
Aatyk proteins are mostly receptor tyr kinases (RTKs)
containing a transmembrane segment and a long C-terminal
cytoplasmic tail with a catalytic domain. Aatyk1 does
not contain a transmembrane segment and is a cytoplasmic
(or nonreceptor) kinase. Aatyk proteins are classified
as tyr kinases based on overall sequence similarity and
the phylogenetic tree. However, analysis of catalytic
residues suggests that Aatyk proteins may be
multispecific kinases, functioning also as
serine/threonine kinases. They are involved in neural
differentiation, nerve growth factor (NGF) signaling,
apoptosis, and spermatogenesis.
Length = 269
Score = 30.2 bits (68), Expect = 1.0
Identities = 12/32 (37%), Positives = 18/32 (56%), Gaps = 1/32 (3%)
Query: 206 GITILPLFSQAT-PKANLADEDIKALTKRTQD 236
G+T+ LF+ A P +L+DE + R QD
Sbjct: 196 GVTMWELFTAADQPYPDLSDEQVLKQVVREQD 227
>gnl|CDD|107197 PHA02515, PHA02515, hypothetical protein; Provisional.
Length = 508
Score = 29.4 bits (65), Expect = 2.0
Identities = 25/80 (31%), Positives = 34/80 (42%), Gaps = 2/80 (2%)
Query: 32 AVLGAAGGIGQPLALLMKLNPLVSRLALYDIANTPGVAADVGHINTRSEVAGYMGNDQLG 91
AV+G A I A +N +V LA D+ G+AADV + +GND G
Sbjct: 362 AVVGNANNINAVAANEGNVNTVVDNLA--DVQTVAGIAADVSTVAENEAAVAALGNDLTG 419
Query: 92 QALEDSDVVIIPAGVPRKPG 111
Q + + PA P P
Sbjct: 420 QPMVIDYGDLSPASNPAAPA 439
>gnl|CDD|187569 cd05259, PCBER_SDR_a, phenylcoumaran benzylic ether reductase
(PCBER) like, atypical (a) SDRs. PCBER and
pinoresinol-lariciresinol reductases are NADPH-dependent
aromatic alcohol reductases, and are atypical members of
the SDR family. Other proteins in this subgroup are
identified as eugenol synthase. These proteins contain
an N-terminus characteristic of NAD(P)-binding proteins
and a small C-terminal domain presumed to be involved in
substrate binding, but they do not have the conserved
active site Tyr residue typically found in SDRs.
Numerous other members have unknown functions. The
glycine rich NADP-binding motif in this subgroup is of 2
forms: GXGXXG and G[GA]XGXXG; it tends to be atypical
compared with the forms generally seen in classical or
extended SDRs. The usual SDR active site tetrad is not
present, but a critical active site Lys at the usual SDR
position has been identified in various members, though
other charged and polar residues are found at this
position in this subgroup. Atypical SDR-related proteins
retain the Rossmann fold of the SDRs, but have limited
sequence identity and generally lack the catalytic
properties of the archetypical members. Atypical SDRs
include biliverdin IX beta reductase (BVR-B,aka flavin
reductase), NMRa (a negative transcriptional regulator
of various fungi), progesterone 5-beta-reductase like
proteins, phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. 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. In addition to the
Rossmann fold core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids, 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.
Length = 282
Score = 29.2 bits (66), Expect = 2.1
Identities = 19/75 (25%), Positives = 30/75 (40%), Gaps = 6/75 (8%)
Query: 30 KVAVLGAAGGIGQPL--ALLMKLNPLVSRLALYDIANTPGVAADVGHINTRSEVAGYMGN 87
K+A+ GA G +G P+ ALL V+ L ++ + Y +
Sbjct: 1 KIAIAGATGTLGGPIVSALLASPGFTVTVLTRPSSTSSNEFQP----SGVKVVPVDYASH 56
Query: 88 DQLGQALEDSDVVII 102
+ L AL+ D VI
Sbjct: 57 ESLVAALKGVDAVIS 71
>gnl|CDD|181139 PRK07832, PRK07832, short chain dehydrogenase; Provisional.
Length = 272
Score = 28.5 bits (64), Expect = 3.0
Identities = 15/50 (30%), Positives = 22/50 (44%), Gaps = 3/50 (6%)
Query: 29 RKVAVLGAAGGIGQPLALLMKLNPLVSRLALYDIANTPGVAADVGHINTR 78
++ V GAA GIG+ AL + + L L D + G+A V
Sbjct: 1 KRCFVTGAASGIGRATALRLAAQG--AELFLTDR-DADGLAQTVADARAL 47
>gnl|CDD|236372 PRK09072, PRK09072, short chain dehydrogenase; Provisional.
Length = 263
Score = 28.4 bits (64), Expect = 3.1
Identities = 26/95 (27%), Positives = 37/95 (38%), Gaps = 23/95 (24%)
Query: 27 PDRKVAVLGAAGGIGQPLALLM---------------KLNPLVSRLALYDIANTPGVAAD 71
D++V + GA+GGIGQ LA + KL L +RL V AD
Sbjct: 4 KDKRVLLTGASGGIGQALAEALAAAGARLLLVGRNAEKLEALAARLPYPGRHRW--VVAD 61
Query: 72 VGHINTRSEVAGYMGNDQLGQALEDSDVVIIPAGV 106
+ R V + + +V+I AGV
Sbjct: 62 LTSEAGREAV------LARAREMGGINVLINNAGV 90
>gnl|CDD|223980 COG1052, LdhA, Lactate dehydrogenase and related dehydrogenases
[Energy production and conversion / Coenzyme metabolism
/ General function prediction only].
Length = 324
Score = 28.4 bits (64), Expect = 3.3
Identities = 18/87 (20%), Positives = 36/87 (41%), Gaps = 14/87 (16%)
Query: 16 AGARGYSSESVPDRKVAVLGAAGGIGQPLALLMKLNPLVSRLALYDIANTPGVAADVGHI 75
G + + + ++G G IGQ A+ +L ++ YD + P ++G
Sbjct: 134 GGPDPLLGFDLRGKTLGIIGL-GRIGQ--AVARRLKGFGMKVLYYDRSPNPEAEKELG-- 188
Query: 76 NTRSEVAGYMGNDQLGQALEDSDVVII 102
A Y+ L + L +SD++ +
Sbjct: 189 ------ARYV---DLDELLAESDIISL 206
>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 = 28.5 bits (64), Expect = 3.4
Identities = 23/79 (29%), Positives = 37/79 (46%), Gaps = 6/79 (7%)
Query: 30 KVAVLGAAGGIGQPLALLMKLNPLVSRLALYDIANTPGVAADVGHINTRSEVAGYMGNDQ 89
KV + GA+G +GQ LA + + RL L D+ +P + + +AG +
Sbjct: 2 KVLITGASGFVGQRLAERLLSDVPNERLILIDVV-SPKAPSGAPRVTQ---IAGDLAVPA 57
Query: 90 LGQALED--SDVVIIPAGV 106
L +AL + DVV A +
Sbjct: 58 LIEALANGRPDVVFHLAAI 76
>gnl|CDD|181185 PRK07979, PRK07979, acetolactate synthase 3 catalytic subunit;
Validated.
Length = 574
Score = 28.7 bits (64), Expect = 3.4
Identities = 13/33 (39%), Positives = 17/33 (51%), Gaps = 7/33 (21%)
Query: 132 IAKYCPNAIV-------NMISNPVNSTVPIAAE 157
+AKYCPNA V IS V + +PI +
Sbjct: 291 LAKYCPNATVLHIDIDPTSISKTVTADIPIVGD 323
>gnl|CDD|227770 COG5483, COG5483, Uncharacterized conserved protein [Function
unknown].
Length = 289
Score = 28.0 bits (62), Expect = 4.6
Identities = 15/59 (25%), Positives = 22/59 (37%), Gaps = 6/59 (10%)
Query: 62 IANTPGVAADVGHINTRSEVAGYMGNDQLGQALEDSDVVI--IPAGVPRKPGMTRDDLF 118
I N+ V DV + + L LE+S++ IP + G R DL
Sbjct: 167 IQNSIDVLVDVRKNPFSMKF--DFTKNSLKNYLENSEIRYLHIPELGIK--GEKRKDLR 221
>gnl|CDD|187548 cd05237, UDP_invert_4-6DH_SDR_e, UDP-Glcnac (UDP-linked
N-acetylglucosamine) inverting 4,6-dehydratase,
extended (e) SDRs. UDP-Glcnac inverting
4,6-dehydratase was identified in Helicobacter pylori
as the hexameric flaA1 gene product (FlaA1). FlaA1 is
hexameric, possesses UDP-GlcNAc-inverting
4,6-dehydratase activity, and catalyzes the first step
in the creation of a pseudaminic acid derivative in
protein glycosylation. Although this subgroup has the
NADP-binding motif characteristic of extended SDRs, its
members tend to have a Met substituted for the active
site Tyr found in most SDR families. 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 = 287
Score = 27.6 bits (62), Expect = 5.9
Identities = 11/39 (28%), Positives = 18/39 (46%), Gaps = 3/39 (7%)
Query: 28 DRKVAVLGAAGGIGQPLAL-LMKLNPLVSRLALYDIANT 65
+ + V G AG IG L ++K P +L ++D
Sbjct: 2 GKTILVTGGAGSIGSELVRQILKFGP--KKLIVFDRDEN 38
>gnl|CDD|240642 cd12165, 2-Hacid_dh_6, Putative D-isomer specific 2-hydroxyacid
dehydrogenases. 2-Hydroxyacid dehydrogenases catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 314
Score = 27.6 bits (62), Expect = 7.3
Identities = 19/85 (22%), Positives = 30/85 (35%), Gaps = 14/85 (16%)
Query: 18 ARGYSSESVPDRKVAVLGAAGGIGQPLALLMKLNPLVSRLALYDIANTPGVAADVGHINT 77
S+ + + V +LG G IG+ +A L+K A V
Sbjct: 127 GEEPESKELRGKTVGILGY-GHIGREIARLLK-------------AFGMRVIGVSRSPKE 172
Query: 78 RSEVAGYMGNDQLGQALEDSDVVII 102
L +ALE +DVV++
Sbjct: 173 DEGADFVGTLSDLDEALEQADVVVV 197
>gnl|CDD|171820 PRK12936, PRK12936, 3-ketoacyl-(acyl-carrier-protein) reductase
NodG; Reviewed.
Length = 245
Score = 27.2 bits (60), Expect = 7.7
Identities = 27/98 (27%), Positives = 45/98 (45%), Gaps = 16/98 (16%)
Query: 29 RKVAVLGAAGGIGQPLALLMKLNPLVSRLALYDIANTPGVAADVG--------HINTRSE 80
RK V GA+GGIG+ +A L+ + L + +AA++G +++ R E
Sbjct: 7 RKALVTGASGGIGEEIARLLHAQGAIVGLHGTRVEKLEALAAELGERVKIFPANLSDRDE 66
Query: 81 VAGYMGNDQLGQALEDSDVVIIPAGVPRKPGMTRDDLF 118
V + LE D+++ AG+ T+D LF
Sbjct: 67 VKAL--GQKAEADLEGVDILVNNAGI------TKDGLF 96
>gnl|CDD|133443 cd01065, NAD_bind_Shikimate_DH, NAD(P) binding domain of Shikimate
dehydrogenase. Shikimate dehydrogenase (DH) is an amino
acid DH family member. Shikimate pathway links
metabolism of carbohydrates to de novo biosynthesis of
aromatic amino acids, quinones and folate. It is
essential in plants, bacteria, and fungi but absent in
mammals, thus making enzymes involved in this pathway
ideal targets for broad spectrum antibiotics and
herbicides. Shikimate DH catalyzes the reduction of
3-hydroshikimate to shikimate using the cofactor NADH.
Amino acid DH-like NAD(P)-binding domains are members of
the Rossmann fold superfamily and include glutamate,
leucine, and phenylalanine DHs, methylene
tetrahydrofolate DH, methylene-tetrahydromethanopterin
DH, methylene-tetrahydropholate 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 DHs, amino acid DHs, repressor rex,
NAD-binding potassium channel domain, CoA-binding, and
ornithine cyclodeaminase-like domains. These domains
have an alpha-beta-alpha configuration. NAD binding
involves numerous hydrogen and van der Waals contacts.
Length = 155
Score = 26.9 bits (60), Expect = 8.2
Identities = 21/110 (19%), Positives = 43/110 (39%), Gaps = 14/110 (12%)
Query: 25 SVPDRKVAVLGAAGGIGQPLAL-LMKLNPLVSRLALY--DIANTPGVAADVGHINTRSEV 81
+ +KV +LG AGG + +A L +L +++ + + +A
Sbjct: 16 ELKGKKVLILG-AGGAARAVAYALAELG--AAKIVIVNRTLEKAKALAE---RFGELGIA 69
Query: 82 AGYMGNDQLGQALEDSDVVI--IPAGVPRKPGMTRDDLFNINAGIVKDLC 129
Y+ L + L ++D++I P G+ + G+V D+
Sbjct: 70 IAYL---DLEELLAEADLIINTTPVGMKPGDELPLPPSLLKPGGVVYDVV 116
>gnl|CDD|234595 PRK00048, PRK00048, dihydrodipicolinate reductase; Provisional.
Length = 257
Score = 27.0 bits (61), Expect = 8.5
Identities = 21/85 (24%), Positives = 28/85 (32%), Gaps = 22/85 (25%)
Query: 30 KVAVLGAAGGIGQPLALLMKLNPLVSRLALYDIANTPG---VAADV--GHINTRSEVAGY 84
KVAV GA+G +G+ + + VAA G G
Sbjct: 3 KVAVAGASGRMGR----------ELIEA----VEAAEDLELVAAVDRPGSPLVGQGALGV 48
Query: 85 MGNDQLGQALEDSDVVI---IPAGV 106
D L L D+DV+I P
Sbjct: 49 AITDDLEAVLADADVLIDFTTPEAT 73
>gnl|CDD|176157 cd08468, PBP2_Pa0477, The C-terminal substrate biniding domain of
an uncharacterized LysR-like transcriptional regulator
Pa0477 related to DntR, contains the type 2 periplasmic
binding fold. LysR-type transcriptional regulator
Pa0477 is related to DntR, which controls genes encoding
enzymes for oxidative degradation of the nitro-aromatic
compound 2,4-dinitrotoluene. The transcription of the
genes encoding enzymes involved in such degradation is
regulated and expression of these enzymes is enhanced by
inducers, which are either an intermediate in the
metabolic pathway or compounds to be degraded. The
topology of this substrate-binding domain is most
similar to that of the type 2 periplasmic binding
proteins (PBP2), which are responsible for the uptake of
a variety of substrates such as phosphate, sulfate,
polysaccharides, lysine/arginine/ornithine, and
histidine. The PBP2 bind their ligand in the cleft
between these domains in a manner resembling a Venus
flytrap. After binding their specific ligand with high
affinity, they can interact with a cognate membrane
transport complex comprised of two integral membrane
domains and two cytoplasmically located ATPase domains.
This interaction triggers the ligand translocation
across the cytoplasmic membrane energized by ATP
hydrolysis.
Length = 202
Score = 27.0 bits (60), Expect = 8.7
Identities = 22/80 (27%), Positives = 30/80 (37%), Gaps = 10/80 (12%)
Query: 44 LALLMKLNPLVSRLALYDIANTPGVAADVGHINTRSEVAGYMGNDQLGQAL-------ED 96
+A L +L P V ++ P A G I+ GY +D L ED
Sbjct: 19 MARLEELAPSVRLNLVHAEQKLPLDALLAGEIDF---ALGYSHDDGAEPRLIEERDWWED 75
Query: 97 SDVVIIPAGVPRKPGMTRDD 116
+ VVI PR +T D
Sbjct: 76 TYVVIASRDHPRLSRLTLDA 95
>gnl|CDD|99993 cd03823, GT1_ExpE7_like, This family is most closely related to the
GT1 family of glycosyltransferases. ExpE7 in
Sinorhizobium meliloti has been shown to be involved in
the biosynthesis of galactoglucans (exopolysaccharide
II).
Length = 359
Score = 27.2 bits (61), Expect = 9.1
Identities = 6/29 (20%), Positives = 14/29 (48%)
Query: 75 INTRSEVAGYMGNDQLGQALEDSDVVIIP 103
+ R E G +++ + DV+++P
Sbjct: 241 GDPRVEFLGAYPQEEIDDFYAEIDVLVVP 269
>gnl|CDD|215267 PLN02485, PLN02485, oxidoreductase.
Length = 329
Score = 27.0 bits (60), Expect = 9.5
Identities = 17/53 (32%), Positives = 22/53 (41%), Gaps = 8/53 (15%)
Query: 185 YAGKANVNVAEVNVPVVGGHAGITILPLFSQATPKANLADEDIKALTKRTQDG 237
Y G +N+N N G H +L L +Q D+DI AL R G
Sbjct: 191 YPGVSNLNGPPENDIGCGAHTDYGLLTLVNQ--------DDDITALQVRNLSG 235
>gnl|CDD|217666 pfam03665, UPF0172, Uncharacterized protein family (UPF0172). In
Chlamydomonas reinhardtii the protein TLA1 (truncated
light-harvesting chlorophyll antenna size) apparently
regulates genes that define the chlorophyll-a antenna
size in the photosynthetic apparatus. This family was
formerly known as UPF0172.
Length = 195
Score = 26.9 bits (60), Expect = 9.9
Identities = 10/60 (16%), Positives = 22/60 (36%), Gaps = 6/60 (10%)
Query: 124 IVKDLCSAIAKYCPNAIVNMISN------PVNSTVPIAAEVFKKAGTYNEKKLFGVTTLD 177
+ K + IA+ NA++ ++ N P + + + KK + + D
Sbjct: 95 VAKKIADKIAENFNNAVLLLVDNEKLESDPRVPALQVYEKDGKKGWRWKKADKSLEAVED 154
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
0.315 0.132 0.367
Gapped
Lambda K H
0.267 0.0829 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,819,587
Number of extensions: 1252449
Number of successful extensions: 1220
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1157
Number of HSP's successfully gapped: 124
Length of query: 256
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 161
Effective length of database: 6,723,972
Effective search space: 1082559492
Effective search space used: 1082559492
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: 42 (22.0 bits)
S2: 58 (25.9 bits)