RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 018314
(358 letters)
>gnl|CDD|215058 PLN00106, PLN00106, malate dehydrogenase.
Length = 323
Score = 631 bits (1629), Expect = 0.0
Identities = 237/308 (76%), Positives = 267/308 (86%)
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 VPVVGGHAGITILPLFSQATPKANLADEDIKALTKRTQDGGTEVVEAKAGKGSATLSMAY 257
VPVVGGHAGITILPL SQATPK + DE+I+ALTKR Q+GGTEVVEAKAG GSATLSMAY
Sbjct: 188 VPVVGGHAGITILPLLSQATPKVSFTDEEIEALTKRIQNGGTEVVEAKAGAGSATLSMAY 247
Query: 258 AGAIFADACLKGLNGVPDVVECSFVQSTVTELPFFASKVRLGKNGVEEVLGLGPLSDFEQ 317
A A FADACL+GLNG DVVECS+VQS VTELPFFASKVRLG+NGVEEVLGLGPLS++EQ
Sbjct: 248 AAARFADACLRGLNGEADVVECSYVQSEVTELPFFASKVRLGRNGVEEVLGLGPLSEYEQ 307
Query: 318 EGLEKLNP 325
+GLE L P
Sbjct: 308 KGLEALKP 315
>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 = 546 bits (1409), Expect = 0.0
Identities = 202/296 (68%), Positives = 244/296 (82%)
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 LPLFSQATPKANLADEDIKALTKRTQDGGTEVVEAKAGKGSATLSMAYAGAIFADACLKG 269
LPL SQ P E+I+ALT R Q GG EVV+AKAG GSATLSMAYAGA FA++ L+G
Sbjct: 182 LPLLSQCQPPFTFDQEEIEALTHRIQFGGDEVVKAKAGAGSATLSMAYAGARFANSLLRG 241
Query: 270 LNGVPDVVECSFVQSTVTELPFFASKVRLGKNGVEEVLGLGPLSDFEQEGLEKLNP 325
L G V+EC++V+S VTE PFFA+ V LGKNGVE+ LGLG L+D+E++ LE P
Sbjct: 242 LKGEKGVIECAYVESDVTEAPFFATPVELGKNGVEKNLGLGKLNDYEKKLLEAALP 297
>gnl|CDD|235340 PRK05086, PRK05086, malate dehydrogenase; Provisional.
Length = 312
Score = 417 bits (1073), Expect = e-147
Identities = 172/301 (57%), Positives = 209/301 (69%), Gaps = 4/301 (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 TILPLFSQATPKANLADEDIKALTKRTQDGGTEVVEAKAGKGSATLSMAYAGAIFADACL 267
TILPL SQ P + ++++ LTKR Q+ GTEVVEAKAG GSATLSM A A F + +
Sbjct: 181 TILPLLSQV-PGVSFTEQEVADLTKRIQNAGTEVVEAKAGGGSATLSMGQAAARFGLSLV 239
Query: 268 KGLNGVPDVVECSFVQSTVTELPFFASKVRLGKNGVEEVLGLGPLSDFEQEGLEKLNPTF 327
+ L G VVEC++V+ FFA V LGKNGVEE L +G LS FEQ LE + T
Sbjct: 240 RALQGEQGVVECAYVEGDGKYARFFAQPVLLGKNGVEERLPIGTLSAFEQNALEGMLDTL 299
Query: 328 H 328
Sbjct: 300 K 300
>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 = 416 bits (1071), Expect = e-146
Identities = 182/298 (61%), Positives = 225/298 (75%), Gaps = 1/298 (0%)
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 LPLFSQATPKANLADEDIKALTKRTQDGGTEVVEAKAGKGSATLSMAYAGAIFADACLKG 269
+PL SQ K ++ ++AL R Q+ GTEVV+AKAG GSATLSMA+AGA F + ++G
Sbjct: 181 IPLISQCPGKVLFTEDQLEALIHRIQNAGTEVVKAKAGAGSATLSMAFAGARFVLSLVRG 240
Query: 270 LNGVPDVVECSFVQS-TVTELPFFASKVRLGKNGVEEVLGLGPLSDFEQEGLEKLNPT 326
L G VVEC++V+S VTE FFA+ + LGKNGVE+ LG+G LS FE++ L P
Sbjct: 241 LKGEEGVVECAYVESDGVTEATFFATPLLLGKNGVEKRLGIGKLSSFEEKMLNGALPE 298
>gnl|CDD|240360 PTZ00325, PTZ00325, malate dehydrogenase; Provisional.
Length = 321
Score = 382 bits (983), Expect = e-133
Identities = 178/294 (60%), Positives = 221/294 (75%), Gaps = 3/294 (1%)
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 LPLFSQATPKANLADEDIKALTKRTQDGGTEVVEAKAGKGSATLSMAYAGAIFADACLKG 269
+PL SQ T + L +E ++ +T R Q GG EVV+AK G GSATLSMAYA A ++ + LK
Sbjct: 190 VPLLSQ-TGLS-LPEEQVEQITHRVQVGGDEVVKAKEGAGSATLSMAYAAAEWSTSVLKA 247
Query: 270 LNGVPDVVECSFVQSTVT-ELPFFASKVRLGKNGVEEVLGLGPLSDFEQEGLEK 322
L G +VEC+FV+S + E PFF+S V LGK GVE VL +GPL+ +E+E LE
Sbjct: 248 LRGDKGIVECAFVESDMRPECPFFSSPVELGKEGVERVLPIGPLNAYEEELLEA 301
>gnl|CDD|223117 COG0039, Mdh, Malate/lactate dehydrogenases [Energy production and
conversion].
Length = 313
Score = 260 bits (667), Expect = 2e-85
Identities = 118/305 (38%), Positives = 162/305 (53%), Gaps = 21/305 (6%)
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----DEDIKALTKRTQDGGTEVVEAKAGKGSATLSMAYA 258
T++PL+SQAT P L +ED++ L +R ++ G E++EAK A A
Sbjct: 176 DTMVPLWSQATVGGKPLEELLKEDTEEDLEELIERVRNAGAEIIEAK--GAGTYYGPAAA 233
Query: 259 GAIFADACLKGLNGVPDVVECSFVQ-STVTELPFFASKVRLGKNGVEEVLGLGPLSDFEQ 317
A +A L+ V + ++ E +F LGKNGVEE+L L D EQ
Sbjct: 234 LARMVEAILRDEKRV--LPVSVYLDGEYGVEDVYFGVPAVLGKNGVEEILELLLSDD-EQ 290
Query: 318 EGLEK 322
E L+K
Sbjct: 291 EKLDK 295
>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 = 188 bits (479), Expect = 2e-59
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 = 182 bits (465), Expect = 3e-55
Identities = 109/318 (34%), Positives = 166/318 (52%), Gaps = 52/318 (16%)
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----PKANL-ADEDIKALTKRTQDGGTEVVEAKAGKGSATLSMAY 257
GH G +++PL +T P +L + E + + +RT+ GG E+V GSA + A
Sbjct: 174 GH-GDSMVPLVRYSTVGGIPLEDLLSKEKLDEIVERTRKGGAEIVGLL-KTGSAYYAPAA 231
Query: 258 AGAIFADA-------------CLKGLNGVPDVVECSFVQSTVTELPFFASKVRLGKNGVE 304
+ A +A L+G GV DV + V+LGKNGVE
Sbjct: 232 SIAEMVEAILKDKKRVLPCSAYLEGEYGVKDV--------------YVGVPVKLGKNGVE 277
Query: 305 EVLGLGPLSDFEQEGLEK 322
+++ L L D E+ +K
Sbjct: 278 KIIEL-ELDDEEKAAFDK 294
>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 = 171 bits (436), Expect = 1e-52
Identities = 69/161 (42%), Positives = 92/161 (57%), Gaps = 16/161 (9%)
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 DEDIKALTKRTQDGGTEVVEAKAGKGSATLSMAYAGAIFADACLKGLNGV--PDVVECSF 281
D +++ L +R Q+ G EV+EAKA GS T SMAYA A A A L+G GV V +
Sbjct: 61 DWELEELIERVQNAGYEVIEAKA--GSTTYSMAYAAARIAKAILRGTGGVLSVGVYLDGY 118
Query: 282 VQSTVTELPFFASKVRLGKNGVEEVLGLGPLSDFEQEGLEK 322
+ +F+ V LGK+GVE+V+ + PL+DFE+E LEK
Sbjct: 119 YG--SPDDIYFSVPVVLGKDGVEKVVEILPLNDFEREKLEK 157
>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 = 174 bits (444), Expect = 3e-52
Identities = 108/317 (34%), Positives = 161/317 (50%), Gaps = 52/317 (16%)
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-----PKANLADEDIKALTKRTQDGGTEVVEAKAGKGSATLSMAYA 258
H G T++PL +T + E+I + +RT++GG E+V GSA + A A
Sbjct: 171 H-GDTMVPLPRYSTVGGIPLTELITKEEIDEIVERTRNGGAEIVNLL-KTGSAYYAPAAA 228
Query: 259 GAIFADACLK-------------GLNGVPDVVECSFVQSTVTELPFFASKVRLGKNGVEE 305
A +A LK G G+ D+ F V LGKNGVE+
Sbjct: 229 IAEMVEAILKDKKRVLPCSAYLEGEYGIKDI--------------FVGVPVVLGKNGVEK 274
Query: 306 VLGLGPLSDFEQEGLEK 322
++ L L+D E+E +K
Sbjct: 275 IIEL-DLTDEEKEAFDK 290
>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 = 140 bits (355), Expect = 2e-39
Identities = 96/298 (32%), Positives = 139/298 (46%), Gaps = 51/298 (17%)
Query: 31 VAVLGAAGGIGQPLALLM--KLNPLVSRLALYDI--ANTPGVAADVGHINTRSEVAGYM- 85
+AV+GA G +G LA + L L LYDI GVA D+ +A
Sbjct: 1 IAVIGAGGNVGPALAFGLADGSVLLAIELVLYDIDEEKLKGVAMDLQDAV--EPLADIKV 58
Query: 86 -GNDQLGQALEDSDVVIIPAGVPRKPGMTRDDLFNINAGIVKDLCSAIAKYCPNAIVNMI 144
D +A +D+DVVII AGV RKPGM R DL N IVK++ I KY P+A + ++
Sbjct: 59 SITDDPYEAFKDADVVIITAGVGRKPGMGRLDLLKRNVPIVKEIGDNIEKYSPDAWIIVV 118
Query: 145 SNPVNSTVPIAAEVFKKAGTYNEKKLFGVTTLDVVRAKTFYAGKANVNVAEVNVPVVGGH 204
SNPV+ I + + ++K+ G+ TLD +R + A K V+ +V V ++G H
Sbjct: 119 SNPVD----IITYLVWRYSGLPKEKVIGLGTLDPIRFRRILAEKLGVDPDDVKVYILGEH 174
Query: 205 AGITILPLFSQATPKANLADEDIKALTKRTQDGGTEVVEAKAGKGSATLSMAYAGAIFAD 264
G + +P +S ++AD I++L D G + G
Sbjct: 175 GG-SQVPDWSTVRIATSIADL-IRSLLN---DEGEILP---------------VGVR--- 211
Query: 265 ACLKGLNGVPDVVECSFVQSTVTELPFFASKVRLGKNGVEEVLGLGPLSDFEQEGLEK 322
G G+PD V V +P +GKNGVEE + + L+DFE E L+K
Sbjct: 212 --NNGQIGIPDDV--------VVSVP-----CIVGKNGVEEPIEV-GLTDFELEKLQK 253
>gnl|CDD|173409 PTZ00117, PTZ00117, malate dehydrogenase; Provisional.
Length = 319
Score = 134 bits (339), Expect = 1e-36
Identities = 102/321 (31%), Positives = 160/321 (49%), Gaps = 31/321 (9%)
Query: 30 KVAVLGAAGGIGQPLALLMKLNPLVSRLALYDI-ANTP-GVAADVGHINTRSEVAGYMGN 87
K++++GA G IG +ALL+ L + LYD+ P 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
Query: 257 YAGAIFADACLKGLNGVPDVVECSFV---QSTVTELPFFASKVRLGKNGVEEVLGLGPLS 313
A +A LK V+ CS Q L F V +G G+E+V+ L L+
Sbjct: 239 AAIVAMIEAYLKDEK---RVLVCSVYLNGQYNCKNL-FVGVPVVIGGKGIEKVIEL-ELN 293
Query: 314 DFEQEGLEKLNPTFHIRKLFQ 334
E+E +K I++L Q
Sbjct: 294 AEEKELFDK--SIESIQELTQ 312
>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 = 127 bits (321), Expect = 4e-34
Identities = 87/310 (28%), Positives = 141/310 (45%), Gaps = 38/310 (12%)
Query: 31 VAVLGAAGGIGQPLALLMKLNPLVSRLALYDI--ANTPGVAADVGHINTRSEVAGYMGND 88
+ ++GA G +G +A + L S L L D+ G A D+ H A
Sbjct: 1 ITIIGA-GNVGAAVAFALIAKGLASELVLVDVNEEKAKGDALDLSH-------ASAFLAT 52
Query: 89 Q---LGQALED---SDVVIIPAGVPRKPGMTRDDLFNINAGIVKDLCSAIAKYCPNAIVN 142
G D +D+V+I AG PRKPG TR DL N NA I++ + + + KY P+AI+
Sbjct: 53 GTIVRGGDYADAADADIVVITAGAPRKPGETRLDLINRNAPILRSVITNLKKYGPDAIIL 112
Query: 143 MISNPVNSTVPIAAEVFKKAGTYNEKKLFGV-TTLDVVRAKTFYAGKANVNVAEVNVPVV 201
++SNPV+ I V +K + ++ G T LD R ++ A K +V+ V+ V+
Sbjct: 113 VVSNPVD----ILTYVAQKLSGLPKNRVIGSGTLLDSARFRSLLAEKLDVDPQSVHAYVL 168
Query: 202 GGHAGITILPLFSQAT-------PKANLADEDIKALTKRTQDGGTEVVEAKAGKGSATLS 254
G H G + + +S AT A D++A+ + + G E++ KG+
Sbjct: 169 GEH-GDSQVVAWSTATVGGLPLEELAPFTKLDLEAIEEEVRTSGYEIIR---LKGATNYG 224
Query: 255 MAYAGAIFADACLKGLNGVPDVVECSFVQSTVTELP--FFASKVRLGKNGVEEVLGLGPL 312
+A A A + L V+ S VQ + + +G+ GV +L PL
Sbjct: 225 IATAIADIVKSILLDERR---VLPVSAVQEGQYGIEDVALSVPAVVGREGVVRIL-EIPL 280
Query: 313 SDFEQEGLEK 322
++ E+ L+K
Sbjct: 281 TEDEEAKLQK 290
>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 = 125 bits (316), Expect = 1e-33
Identities = 102/307 (33%), Positives = 159/307 (51%), Gaps = 28/307 (9%)
Query: 29 RKVAVLGAAGGIGQPLALLMKLNPLVSRLALYDIANTP--GVAAD------VGHINTRSE 80
+K++V+GA G +G A + L + L L D+ G A D VG +T+
Sbjct: 2 KKISVIGA-GFVGATTAFRLAEKEL-ADLVLLDVVEGIPQGKALDMYEASPVGGFDTK-- 57
Query: 81 VAGYMGNDQLGQALEDSDVVIIPAGVPRKPGMTRDDLFNINAGIVKDLCSAIAKYCPNAI 140
V G N+ A +SD+V+I AG+PRKPGM+R+DL ++NAGIV+++ I ++ PN I
Sbjct: 58 VTG--TNNYADTA--NSDIVVITAGLPRKPGMSREDLLSMNAGIVREVTGRIMEHSPNPI 113
Query: 141 VNMISNPVNSTVPIAAEVFKKAGTYNEKKLFGVTTLDVVRAKTFYAGKANVNVAEVNVPV 200
+ ++SNP+++ +A + K+G E+ + LD R +TF A + V+V +V V
Sbjct: 114 IVVVSNPLDAMTYVAWQ---KSGFPKERVIGQAGVLDSARFRTFIAMELGVSVQDVTACV 170
Query: 201 VGGHAGITILPLFSQAT----PKANL-ADEDIKALTKRTQDGGTEVVEAKAGKGSATLSM 255
+GGH G ++PL +T P A+L + E I + +RT+ GG E+V +GSA +
Sbjct: 171 LGGH-GDAMVPLVRYSTVAGIPVADLISAERIAEIVERTRKGGGEIVNL-LKQGSAYYAP 228
Query: 256 AYAGAIFADACLKGLNGVPDVVECSFVQSTVTELPFFASKVRLGKNGVEEVLGLGPLSDF 315
A + +A LK V Q + + + V LGKNGVE + L L
Sbjct: 229 AASVVEMVEAILKDRKRVLPCAAYLDGQYGIDGI-YVGVPVILGKNGVEHIYEL-KLDQS 286
Query: 316 EQEGLEK 322
E L K
Sbjct: 287 ELALLNK 293
>gnl|CDD|173376 PTZ00082, PTZ00082, L-lactate dehydrogenase; Provisional.
Length = 321
Score = 124 bits (312), Expect = 8e-33
Identities = 101/323 (31%), Positives = 167/323 (51%), Gaps = 42/323 (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 EAKAGKGSATLSMAYAGAIFADACLKGLNGVPDVVECSFV---QSTVTELPFFASKVRLG 299
+ G GSA + A A A+A LK V+ CS Q ++ + + +G
Sbjct: 232 DL-LGTGSAYFAPAAAAIEMAEAYLKDKK---RVLPCSAYLEGQYGHKDI-YMGTPAVIG 286
Query: 300 KNGVEEVLGLGPLSDFEQEGLEK 322
NGVE+++ L L+ EQ+ ++
Sbjct: 287 ANGVEKIIEL-DLTPEEQKKFDE 308
>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 = 117 bits (295), Expect = 2e-30
Identities = 98/340 (28%), Positives = 157/340 (46%), Gaps = 91/340 (26%)
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 KAGK--GSA------------------TLSMAYAGAI--FADACLKGLNGVPDVVECSFV 282
K G G A T+S G I D C+ GVP
Sbjct: 224 KGGSEYGPASAISNLVRTIANDERRILTVSTYLEGEIDGIRDVCI----GVP-------- 271
Query: 283 QSTVTELPFFASKVRLGKNGVEEVLGLGPLSDFEQEGLEK 322
V+LGKNG+EE++ + + D E+E K
Sbjct: 272 -------------VKLGKNGIEEIVPI-EMDDDEREAFRK 297
>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 = 109 bits (274), Expect = 3e-27
Identities = 88/320 (27%), Positives = 140/320 (43%), Gaps = 50/320 (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 GSATLSMAYAGAIFADACLKGLNGVPDVVECSFVQSTVTELPFFASKVRL------GKNG 302
G+ ++ A A +A L+ N V V S++ + + V L G++G
Sbjct: 225 GATYYAIGLALARIVEAILRDENSVLTV-------SSLLDGQYGIKDVALSLPCIVGRSG 277
Query: 303 VEEVLGLGPLSDFEQEGLEK 322
VE VL PLS+ E+E L
Sbjct: 278 VERVLPP-PLSEEEEEALRA 296
>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 = 105 bits (265), Expect = 4e-26
Identities = 84/309 (27%), Positives = 136/309 (44%), Gaps = 43/309 (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-----------PKANLADEDIKALTKRTQDGGTEVVEAKAGKGSATLSMA 256
+ +P++S AT K D D++ + K +D E++ KG+ +
Sbjct: 172 SEVPVWSSATIGGVPLLDYLKAKGTETDLDLEEIEKEVRDAAYEIIN---RKGATYYGIG 228
Query: 257 YAGAIFADACLKGLNGVPDV---VECSFVQSTVTELPFFASKVRLGKNGVEEVLGLGPLS 313
A A +A L N V V ++ + V + LG+NGVEE++ L PLS
Sbjct: 229 MAVARIVEAILHDENRVLPVSAYLDGEYGIKDV----YIGVPAVLGRNGVEEIIEL-PLS 283
Query: 314 DFEQEGLEK 322
D E+E +K
Sbjct: 284 DEEKEAFQK 292
>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 = 103 bits (260), Expect = 2e-25
Identities = 88/320 (27%), Positives = 134/320 (41%), Gaps = 51/320 (15%)
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----------PKANLADEDIKALTKRTQDGGTEVVEAKAGKGS----- 250
G + +S T + L++ D+ + + + G E++ GKG+
Sbjct: 174 GDSQFVAWSTVTVGGKPLLDLLKEGKLSELDLDEIEEDVRKAGYEIIN---GKGATYYGI 230
Query: 251 ATLSMAYAGAIFAD--------ACLKGLNGVPDVVECSFVQSTVTELPFFASKVRLGKNG 302
AT AI D A L G G DV + +G+NG
Sbjct: 231 ATALARIVKAILNDENAILPVSAYLDGEYGEKDV--------------YIGVPAIIGRNG 276
Query: 303 VEEVLGLGPLSDFEQEGLEK 322
VEEV+ L L++ EQE EK
Sbjct: 277 VEEVIEL-DLTEEEQEKFEK 295
>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 = 86.6 bits (215), Expect = 3e-19
Identities = 91/329 (27%), Positives = 131/329 (39%), Gaps = 68/329 (20%)
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---YAGAIFAD--------ACLKGLNGVPDVVECSFVQSTVTELPFFA 293
K G +A ++ + AI D L G G+ DV + TV
Sbjct: 225 K-GWTNAGIAKSASRLIKAILLDERSILPVCTLLSGEYGLSDV---ALSLPTV------- 273
Query: 294 SKVRLGKNGVEEVLGLGPLSDFEQEGLEK 322
+G G+E VL + PL ++E E L K
Sbjct: 274 ----IGAKGIERVLEI-PLDEWELEKLHK 297
>gnl|CDD|178836 PRK00066, ldh, L-lactate dehydrogenase; Reviewed.
Length = 315
Score = 86.1 bits (214), Expect = 5e-19
Identities = 83/332 (25%), Positives = 131/332 (39%), Gaps = 75/332 (22%)
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+ I TY KL G T+LD R + + K +V+
Sbjct: 119 LVASNPVD----IL--------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 VEAKAGKGSATLSMAYA---GAIFAD--------ACLKGLNGVPDVVECSFVQSTVTELP 290
+E K G ++MA A AI + A L+G G DV
Sbjct: 226 IEKK-GATYYGIAMALARITKAILNNENAVLPVSAYLEGQYGEEDV-------------- 270
Query: 291 FFASKVRLGKNGVEEVLGLGPLSDFEQEGLEK 322
+ + +NG+ E++ L PL+D E++
Sbjct: 271 YIGVPAVVNRNGIREIVEL-PLNDDEKQKFAH 301
>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 = 84.7 bits (210), Expect = 2e-18
Identities = 103/325 (31%), Positives = 134/325 (41%), Gaps = 50/325 (15%)
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 AGKGSATLSMAYAGAIFADACLKGLNGVP--DVVECSFVQST-----VTELPFFASKVRL 298
G SA S A A D + G P D V V S + E F+ V
Sbjct: 234 -GASSA-ASAANAA---IDHVRDWVTGTPEGDWVSMG-VYSDGNPYGIPEGIIFSFPVTC 287
Query: 299 GKNG-VEEVLGLGPLSDFEQEGLEK 322
+G E V GL PL DF + L+
Sbjct: 288 KGDGEWEIVEGL-PLDDFVRGKLDA 311
>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 = 83.1 bits (206), Expect = 6e-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|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 = 80.0 bits (198), Expect = 7e-17
Identities = 87/328 (26%), Positives = 136/328 (41%), Gaps = 66/328 (20%)
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-------------AGITILPLFSQATPKANLADEDIKALTKRTQDGGTEVVEAKAG 247
+G H AG+ + L + E K + K+ D EV+
Sbjct: 173 IGEHGDSSVPVWSGVNVAGVRLQDLNPDIGTDKD--PEKWKEVHKQVVDSAYEVI---KL 227
Query: 248 KGSATLSMAYAGAIFADA-------------CLKGLNGVPDVVECSFVQSTVTELPFFAS 294
KG + ++ + A DA +KGL+G+ D V S LP
Sbjct: 228 KGYTSWAIGLSVADLVDAILRNTGRVHSVSTLVKGLHGIEDEVFLS--------LP---- 275
Query: 295 KVRLGKNGVEEVLGLGPLSDFEQEGLEK 322
LG+NG+ V+ PL++ EQE L+K
Sbjct: 276 -CILGENGITHVIKQ-PLTEEEQEKLQK 301
>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 = 77.7 bits (192), Expect = 5e-16
Identities = 73/261 (27%), Positives = 108/261 (41%), Gaps = 49/261 (18%)
Query: 30 KVAVLGAAGGIGQPLALLMKLNPLVSR-----------LALYDIANTPGVAADVGHINTR 78
+V V GAAG I +LL P++++ L L DI V
Sbjct: 4 RVLVTGAAGQIA--YSLL----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 GTEVVEAKAGKGSATLSMAYA 258
G V++A+ K S+ +S A A
Sbjct: 229 GAAVIKAR--KLSSAMSAAKA 247
>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 = 77.2 bits (191), Expect = 6e-16
Identities = 93/333 (27%), Positives = 129/333 (38%), Gaps = 68/333 (20%)
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 KAGKGSATLSMAYA--------------GAIFADA-CLKGLNGVPDVVECSFVQSTVTEL 289
+ G SA S A A G F+ A G G+P+ + SF
Sbjct: 232 R-GASSAA-SAANAAIDHMRDWVLGTPEGDWFSMAVPSDGSYGIPEGLIFSF-------- 281
Query: 290 PFFASKVRLGKNGVEEVLGLGPLSDFEQEGLEK 322
P VR G E V GL + DF +E ++
Sbjct: 282 P-----VRSKGGGYEIVEGL-EIDDFAREKIDA 308
>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 = 72.2 bits (177), Expect = 3e-14
Identities = 72/257 (28%), Positives = 103/257 (40%), Gaps = 41/257 (15%)
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 VEAKAGKGSATLSMAYA 258
+ A+ K S+ LS A A
Sbjct: 230 IRAR--KLSSALSAAKA 244
>gnl|CDD|235468 PRK05442, PRK05442, malate dehydrogenase; Provisional.
Length = 326
Score = 69.8 bits (172), Expect = 2e-13
Identities = 77/250 (30%), Positives = 107/250 (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----PKANL-ADED------IKALTKRTQDGGTEV 241
A++ + V G H+ T P F AT P A + D+ I + KR G +
Sbjct: 176 ADIKKMTVWGNHSA-TQYPDFRHATIDGKPAAEVINDQAWLEDTFIPTVQKR----GAAI 230
Query: 242 VEAKAGKGSA 251
+EA+ G SA
Sbjct: 231 IEAR-GASSA 239
>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 = 68.0 bits (166), Expect = 8e-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|178212 PLN02602, PLN02602, lactate dehydrogenase.
Length = 350
Score = 65.6 bits (160), Expect = 7e-12
Identities = 80/323 (24%), Positives = 137/323 (42%), Gaps = 36/323 (11%)
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 AEVNVPVVGGH-------------AGITILPLFSQATPKANLADEDIKALTKRTQDGGTE 240
+V +VG H G+ +L + + E ++ + + D E
Sbjct: 200 QDVQAYIVGEHGDSSVALWSSVSVGGVPVLSFLEKQ--QIAYEKETLEEIHRAVVDSAYE 257
Query: 241 VVEAKAGKGSATLSMAYAGAIFADACLKGLNGVPDVVECSFVQSTVTELPFFAS-KVRLG 299
V++ KG + ++ Y+ A + L+ + V + + E F S +LG
Sbjct: 258 VIKL---KGYTSWAIGYSVASLVRSLLRDQRRIHPVSVLAKGFHGIDEGDVFLSLPAQLG 314
Query: 300 KNGVEEVLGLGPLSDFEQEGLEK 322
+NGV V+ + L+D E E L K
Sbjct: 315 RNGVLGVVNV-HLTDEEAERLRK 336
>gnl|CDD|177744 PLN00135, PLN00135, malate dehydrogenase.
Length = 309
Score = 62.5 bits (152), Expect = 6e-11
Identities = 51/180 (28%), Positives = 86/180 (47%), Gaps = 19/180 (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-----------KRTQDGGTEVVEAKAGKGSATLSMAYA 258
P + AT K ++ ++ L Q G +++A+ K S+ LS A +
Sbjct: 170 YPDVNHATVKTPSGEKPVRELVADDAWLNGEFITTVQQRGAAIIKAR--KLSSALSAASS 227
>gnl|CDD|215060 PLN00112, PLN00112, malate dehydrogenase (NADP); Provisional.
Length = 444
Score = 49.8 bits (119), 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 = 48.8 bits (116), Expect = 2e-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 = 37.2 bits (87), Expect = 0.009
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 = 36.8 bits (86), Expect = 0.013
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|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 = 34.9 bits (81), Expect = 0.016
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|223936 COG1004, Ugd, Predicted UDP-glucose 6-dehydrogenase [Cell envelope
biogenesis, outer membrane].
Length = 414
Score = 36.4 bits (85), Expect = 0.019
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|202102 pfam02056, Glyco_hydro_4, Family 4 glycosyl hydrolase.
Length = 183
Score = 35.1 bits (81), Expect = 0.028
Identities = 32/147 (21%), Positives = 46/147 (31%), 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 -YMGNDQLGQALEDSDVVIIPAGVPRKPGMTRDD-----------LFNINA--------- 122
+ +AL D+D VI V P D+ +
Sbjct: 60 KFEKTTDRKEALTDADFVINAIRVGLLPARELDEKIPLRHGVVGTIQETVGPGGIFRGLR 119
Query: 123 --GIVKDLCSAIAKYCPNAIVNMISNP 147
+ D+ I + CP+A V +NP
Sbjct: 120 TIPVFFDIAKDIEELCPDAWVLNYTNP 146
>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 = 0.037
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|223366 COG0289, DapB, Dihydrodipicolinate reductase [Amino acid transport
and metabolism].
Length = 266
Score = 33.0 bits (76), Expect = 0.16
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|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 = 0.21
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|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 = 32.3 bits (74), Expect = 0.31
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|180408 PRK06114, PRK06114, short chain dehydrogenase; Provisional.
Length = 254
Score = 32.1 bits (73), Expect = 0.31
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|107197 PHA02515, PHA02515, hypothetical protein; Provisional.
Length = 508
Score = 32.1 bits (72), Expect = 0.47
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|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 = 30.2 bits (69), Expect = 0.67
Identities = 22/79 (27%), Positives = 38/79 (48%), Gaps = 3/79 (3%)
Query: 30 KVAVLGAAGGIGQPLALLMKLNPLVSRLALYDIANTPGVAADVGHINTRSEVAGYMGNDQ 89
KVA++GA G +GQ L L+ +P + +AL + + G + + +
Sbjct: 1 KVAIVGATGYVGQELLRLLAEHPPLELVALVASSRSAGKKVAFAYPILEGGKDLLLEDVD 60
Query: 90 LGQALEDSDVVII--PAGV 106
+ L+D D+V + PAGV
Sbjct: 61 P-EDLKDVDIVFLALPAGV 78
>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 = 30.0 bits (68), Expect = 1.8
Identities = 18/76 (23%), Positives = 32/76 (42%), Gaps = 8/76 (10%)
Query: 30 KVAVLGAAGGIGQPLALLMKLNPLVSRLALYDIANT-PGVAADVGHINTRSEV--AGYMG 86
K+A+ GA G +G P+ ++ L++ T P + + +V Y
Sbjct: 1 KIAIAGATGTLGGPI-----VSALLASPGFTVTVLTRPSSTSSNEFQPSGVKVVPVDYAS 55
Query: 87 NDQLGQALEDSDVVII 102
++ L AL+ D VI
Sbjct: 56 HESLVAALKGVDAVIS 71
>gnl|CDD|182639 PRK10675, PRK10675, UDP-galactose-4-epimerase; Provisional.
Length = 338
Score = 30.2 bits (68), Expect = 1.8
Identities = 17/51 (33%), Positives = 25/51 (49%), Gaps = 3/51 (5%)
Query: 221 NLADEDIKALTKRTQDGGTEVVEAKAGKGSATLSMAYAGAIFADACLKGLN 271
+LAD + A+ K G + AG GS+ L + A F+ AC K +N
Sbjct: 238 DLADGHVAAMEKLANKPGVHIYNLGAGVGSSVLDVVNA---FSKACGKPVN 285
>gnl|CDD|181139 PRK07832, PRK07832, short chain dehydrogenase; Provisional.
Length = 272
Score = 30.0 bits (68), Expect = 1.9
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|223980 COG1052, LdhA, Lactate dehydrogenase and related dehydrogenases
[Energy production and conversion / Coenzyme metabolism
/ General function prediction only].
Length = 324
Score = 29.9 bits (68), Expect = 1.9
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|223959 COG1028, FabG, Dehydrogenases with different specificities (related
to short-chain alcohol dehydrogenases) [Secondary
metabolites biosynthesis, transport, and catabolism /
General function prediction only].
Length = 251
Score = 29.4 bits (66), Expect = 2.3
Identities = 26/143 (18%), Positives = 45/143 (31%), Gaps = 29/143 (20%)
Query: 28 DRKVAVLGAAGGIGQPLALLM-----------------KLNPLVSRLALYDIANTPGVAA 70
+ V GA+ GIG+ +A + L + + VAA
Sbjct: 5 GKVALVTGASSGIGRAIARALAREGARVVVAARRSEEEAAEALAAAIKEAGGGRAAAVAA 64
Query: 71 DVGHINTRSEVAGYMGNDQLGQALEDSDVVIIPAGVPRKPG----MTRDDL---FNINAG 123
DV + V + + D+++ AG+ +T +D ++N
Sbjct: 65 DVS--DDEESVEALV--AAAEEEFGRIDILVNNAGIAGPDAPLEELTEEDWDRVIDVNLL 120
Query: 124 IVKDLCSAIAKYC-PNAIVNMIS 145
L A IVN+ S
Sbjct: 121 GAFLLTRAALPLMKKQRIVNISS 143
>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 = 29.7 bits (67), Expect = 2.3
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|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 = 29.5 bits (66), Expect = 2.3
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|236372 PRK09072, PRK09072, short chain dehydrogenase; Provisional.
Length = 263
Score = 29.5 bits (67), Expect = 2.5
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|214856 smart00852, MoCF_biosynth, Probable molybdopterin binding domain.
This domain is found a variety of proteins involved in
biosynthesis of molybdopterin cofactor. The domain is
presumed to bind molybdopterin. The structure of this
domain is known, and it forms an alpha/beta structure.
In the known structure of Gephyrin this domain mediates
trimerisation.
Length = 138
Score = 28.3 bits (64), Expect = 2.8
Identities = 21/87 (24%), Positives = 34/87 (39%), Gaps = 16/87 (18%)
Query: 88 DQLGQALEDSDVVIIPAGVPRKPGMTRDDLFNINAGIVKDLCSAIAKYCPNAIVN--MIS 145
+ L +AL ++DVVI G G DDL + A+A+ ++ +
Sbjct: 51 EALREALAEADVVITTGGT----GPGPDDL-------TPE---ALAELGGRELLGHGVAM 96
Query: 146 NPVNSTVPIAAEVFKKAGTYNEKKLFG 172
P P+A G +K +FG
Sbjct: 97 RPGGPPGPLANLSGTAPGVRGKKPVFG 123
>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 = 28.8 bits (65), Expect = 3.0
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|171820 PRK12936, PRK12936, 3-ketoacyl-(acyl-carrier-protein) reductase
NodG; Reviewed.
Length = 245
Score = 29.1 bits (65), Expect = 3.1
Identities = 30/102 (29%), Positives = 47/102 (46%), Gaps = 24/102 (23%)
Query: 29 RKVAVLGAAGGIGQPLALLMKLNPLVSRLALYDIANTPGVAADVG--------HINTRSE 80
RK V GA+GGIG+ +A L+ + L + +AA++G +++ R E
Sbjct: 7 RKALVTGASGGIGEEIARLLHAQGAIVGLHGTRVEKLEALAAELGERVKIFPANLSDRDE 66
Query: 81 VAGYMGNDQLGQA----LEDSDVVIIPAGVPRKPGMTRDDLF 118
V LGQ LE D+++ AG+ T+D LF
Sbjct: 67 VKA------LGQKAEADLEGVDILVNNAGI------TKDGLF 96
>gnl|CDD|234351 TIGR03773, anch_rpt_wall, putative ABC transporter-associated
repeat protein. Members of this protein family occur in
genomes that contain a three-gene ABC transporter operon
associated with the presence of domain TIGR03769. That
domain occurs as a single-copy insert in the
substrate-binding protein, and occurs in two or more
copies in members of this protein family. Members of
this family typically are encoded adjacent to the said
transporter operon and may serve as a substrate
receptor.
Length = 513
Score = 29.5 bits (66), Expect = 3.2
Identities = 23/112 (20%), Positives = 36/112 (32%), Gaps = 16/112 (14%)
Query: 158 VFKKAGTYNEKKLFGVTTLDVVRAKTFYAGKANVNVAEVNVPVVGGHAGITILPLFSQAT 217
F K GTY L V ++ T GK + + V + + + S +T
Sbjct: 406 AFSKPGTY---------KLQVTQSATTTNGKKASDTTTLTFAVGDNNDPVGAVGPLSAST 456
Query: 218 PKANLADE---DIKALTKRTQDGGTEVVE----AKAGKGSATLSMAYAGAIF 262
P ++ A + + A G G L+M GA F
Sbjct: 457 PTDGAPGGKGCELAAKGAEGSGKKADKGKTGLLANTGLGLMALAMLLIGAGF 508
>gnl|CDD|181185 PRK07979, PRK07979, acetolactate synthase 3 catalytic subunit;
Validated.
Length = 574
Score = 29.4 bits (66), Expect = 3.3
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|234595 PRK00048, PRK00048, dihydrodipicolinate reductase; Provisional.
Length = 257
Score = 28.6 bits (65), Expect = 4.2
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|211353 cd07263, Glo_EDI_BRP_like_16, This conserved domain belongs to a
superfamily including the bleomycin resistance protein,
glyoxalase I, and type I ring-cleaving dioxygenases.
This protein family belongs to a conserved domain
superfamily that is found in a variety of structurally
related metalloproteins, including the bleomycin
resistance protein, glyoxalase I, and type I
ring-cleaving dioxygenases. A bound metal ion is
required for protein activities for the members of this
superfamily. A variety of metal ions have been found in
the catalytic centers of these proteins including
Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein
superfamily contains members with or without domain
swapping.
Length = 120
Score = 27.5 bits (62), Expect = 5.0
Identities = 25/112 (22%), Positives = 36/112 (32%), Gaps = 29/112 (25%)
Query: 177 DVVRAKTFYAGKANVNVAEVNVPVVG----------GHAGITIL------------PLFS 214
D +A FY K V E +VP+ G G +++ L
Sbjct: 8 DQDKALAFYTEKLGFEVRE-DVPMGGGFRWVTVAPPGSPETSLVLAPPANPAAMASGLQP 66
Query: 215 QATPKANLADEDIKALTKRTQDGGTEVVEAKAGKGSATLSMAYAGAIFADAC 266
TP L +DI A + + G E E T+ A+F D
Sbjct: 67 GGTPGLVLVTDDIDATYEELKARGVEFTEEPREMPYGTV------AVFRDPD 112
>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 = 28.4 bits (64), Expect = 5.2
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|133448 cd01080, NAD_bind_m-THF_DH_Cyclohyd, NADP binding domain of
methylene-tetrahydrofolate dehydrogenase/cyclohydrolase.
NADP binding domain of the Methylene-Tetrahydrofolate
Dehydrogenase/cyclohydrolase (m-THF DH/cyclohydrolase)
bifunctional enzyme. Tetrahydrofolate is a versatile
carrier of activated one-carbon units. The major
one-carbon folate donors are N-5 methyltetrahydrofolate,
N5,N10-m-THF, and N10-formayltetrahydrofolate. The
oxidation of metabolic intermediate m-THF to m-THF
requires the enzyme m-THF DH. In addition, most DHs also
have an associated cyclohydrolase activity which
catalyzes its hydrolysis to N10-formyltetrahydrofolate.
m-THF DH is typically found as part of a multifunctional
protein in eukaryotes. NADP-dependent m-THF DH in
mammals, birds and yeast are components of a
trifunctional enzyme with DH, cyclohydrolase, and
synthetase activities. Certain eukaryotic cells also
contain homodimeric bifunctional DH/cyclodrolase form.
In bacteria, monofucntional DH, as well as bifunctional
m-THF m-THF DHm-THF DHDH/cyclodrolase are found. In
addition, yeast (S. cerevisiae) also express an
monofunctional DH. This family contains the bifunctional
DH/cyclohydrolase. M-THF DH, like other amino acid
DH-like NAD(P)-binding domains, is a member of the
Rossmann fold superfamily which includes glutamate,
leucine, and phenylalanine DHs, m-THF DH,
methylene-tetrahydromethanopterin DH, m-THF
DH/cyclohydrolase, Shikimate DH-like proteins, malate
oxidoreductases, and glutamyl tRNA reductase. Amino acid
DHs catalyze the deamination of amino acids to keto
acids with NAD(P)+ as a cofactor. The NAD(P)-binding
Rossmann fold superfamily includes a wide variety of
protein families including NAD(P)- binding domains of
alcohol DHs, tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate DH, lactate/malate DHs,
formate/glycerate DHs, siroheme synthases,
6-phosphogluconate DH, amino acid DHs, repressor rex,
NAD-binding potassium channel domain, CoA-binding, and
ornithine cyclodeaminase-like domains.
Length = 168
Score = 27.9 bits (63), Expect = 5.8
Identities = 26/107 (24%), Positives = 42/107 (39%), Gaps = 29/107 (27%)
Query: 21 YSSESVPDRKVAVLGAAGGIGQPLA-LLMKLNPLVSRLALYDIANTPGVAADVGHINTRS 79
+ +KV V+G + +G+PLA LL+ N V+ V H T+
Sbjct: 37 RYGIDLAGKKVVVVGRSNIVGKPLAALLLNRNATVT----------------VCHSKTK- 79
Query: 80 EVAGYMGNDQLGQALEDSDVVIIPAGVPR--KPGMTRDDLFNINAGI 124
L + + +D+VI+ G P K M + I+ GI
Sbjct: 80 ---------NLKEHTKQADIVIVAVGKPGLVKGDMVKPGAVVIDVGI 117
>gnl|CDD|187537 cd05226, SDR_e_a, Extended (e) and atypical (a) SDRs. Extended or
atypical short-chain dehydrogenases/reductases (SDRs,
aka tyrosine-dependent oxidoreductases) 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. 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. 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 = 176
Score = 27.8 bits (62), Expect = 5.9
Identities = 25/100 (25%), Positives = 38/100 (38%), Gaps = 12/100 (12%)
Query: 31 VAVLGAAGGIGQPLA--LLMKLNP--LVSRLALYDIANTPGVAADVGHINTRSEVAGYMG 86
+ +LGA G IG+ LA LL + + L+ R V + R
Sbjct: 1 ILILGATGFIGRALARELLEQGHEVTLLVRNTKRLS-KEDQEPVAVVEGDLRDL------ 53
Query: 87 NDQLGQALEDSDVVIIPAGVPRKPGMTRDDLFNINAGIVK 126
D L A++ DVVI AG PR + +++
Sbjct: 54 -DSLSDAVQGVDVVIHLAGAPRDTRDFCEVDVEGTRNVLE 92
>gnl|CDD|222146 pfam13460, NAD_binding_10, NADH(P)-binding.
Length = 182
Score = 28.0 bits (63), Expect = 6.2
Identities = 18/80 (22%), Positives = 31/80 (38%), Gaps = 9/80 (11%)
Query: 31 VAVLGAAGGIGQPLALLMKLNPLVSR-LALYDIANTPGVAADVGHINTRSEVAGYMGNDQ 89
+AV+GA G G+ L L++R + ++ P A G + ++
Sbjct: 1 IAVIGATGKTGRRLVKE-----LLARGHQVTALSRNPSKAPAPGVTPVQKDLFDLAD--- 52
Query: 90 LGQALEDSDVVIIPAGVPRK 109
L +AL D V+ G
Sbjct: 53 LAEALAGVDAVVDAFGARPD 72
>gnl|CDD|187584 cd05323, ADH_SDR_c_like, insect type alcohol dehydrogenase
(ADH)-like, classical (c) SDRs. This subgroup contains
insect type ADH, and 15-hydroxyprostaglandin
dehydrogenase (15-PGDH) type I; these proteins are
classical SDRs. ADH catalyzes the NAD+-dependent
oxidation of alcohols to aldehydes/ketones. This
subgroup is distinct from the zinc-dependent alcohol
dehydrogenases of the medium chain
dehydrogenase/reductase family, and evolved in fruit
flies to allow the digestion of fermenting fruit.
15-PGDH catalyzes the NAD-dependent interconversion of
(5Z,13E)-(15S)-11alpha,
15-dihydroxy-9-oxoprost-13-enoate and
(5Z,13E)-11alpha-hydroxy-9,15-dioxoprost-13-enoate, and
has a typical SDR glycine-rich NAD-binding motif, which
is not fully present in ADH. 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
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-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 = 244
Score = 28.0 bits (63), Expect = 6.6
Identities = 20/54 (37%), Positives = 31/54 (57%), Gaps = 5/54 (9%)
Query: 30 KVAVL-GAAGGIGQPLA-LLMKLNPLVSRLALYDIANTPGVAADVGHINTRSEV 81
KVA++ G A GIG A LL+K +++A+ D PG AA++ IN + +
Sbjct: 1 KVAIITGGASGIGLATAKLLLKKG---AKVAILDRNENPGAAAELQAINPKVKA 51
>gnl|CDD|107330 cd06335, PBP1_ABC_ligand_binding_like_2, Type I periplasmic
ligand-binding domain of uncharacterized ABC (ATPase
Binding Cassette)-type active transport systems that
are predicted to be involved in transport of amino
acids, peptides, or inorganic ions. This subgroup
includes the type I periplasmic ligand-binding domain
of uncharacterized ABC (ATPase Binding Cassette)-type
active transport systems that are predicted to be
involved in transport of amino acids, peptides, or
inorganic ions. Members of this group are
sequence-similar to members of the family of ABC-type
hydrophobic amino acid transporters, such as
leucine-isoleucine-valine-binding protein (LIVBP);
however their ligand specificity has not been
determined experimentally.
Length = 347
Score = 28.4 bits (64), Expect = 6.7
Identities = 14/46 (30%), Positives = 23/46 (50%), Gaps = 4/46 (8%)
Query: 36 AAGGI-GQPLALLMK---LNPLVSRLALYDIANTPGVAADVGHINT 77
AAGG+ G+ L L+ + NP ++A V A +G ++T
Sbjct: 32 AAGGVLGRKLELVERDDRGNPARGLQNAQELAADEKVVAVLGGLHT 77
>gnl|CDD|215344 PLN02640, PLN02640, glucose-6-phosphate 1-dehydrogenase.
Length = 573
Score = 28.4 bits (63), Expect = 7.1
Identities = 12/26 (46%), Positives = 15/26 (57%)
Query: 235 QDGGTEVVEAKAGKGSATLSMAYAGA 260
QDG + E A KG +TLS+ GA
Sbjct: 71 QDGENHLTEEHAEKGESTLSITVVGA 96
>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 = 28.0 bits (63), Expect = 7.6
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|237633 PRK14168, PRK14168, bifunctional 5,10-methylene-tetrahydrofolate
dehydrogenase/ 5,10-methylene-tetrahydrofolate
cyclohydrolase; Provisional.
Length = 297
Score = 27.9 bits (62), Expect = 9.5
Identities = 26/95 (27%), Positives = 43/95 (45%), Gaps = 28/95 (29%)
Query: 30 KVAVLGAAGGIGQPLALLMKLNPLVSRLALYDIANTPGVAADVGHINTRSEVAGYMGNDQ 89
+V V+G + +G+P+A +M PG A V ++TRS+
Sbjct: 163 EVVVVGRSNIVGKPIANMM-------------TQKGPGANATVTIVHTRSK--------N 201
Query: 90 LGQALEDSDVVIIPAGVPR-------KPGMTRDDL 117
L + + +D++I+ AGVP KPG T D+
Sbjct: 202 LARHCQRADILIVAAGVPNLVKPEWIKPGATVIDV 236
>gnl|CDD|227770 COG5483, COG5483, Uncharacterized conserved protein [Function
unknown].
Length = 289
Score = 27.6 bits (61), Expect = 9.6
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|172654 PRK14166, PRK14166, bifunctional 5,10-methylene-tetrahydrofolate
dehydrogenase/ 5,10-methylene-tetrahydrofolate
cyclohydrolase; Provisional.
Length = 282
Score = 27.7 bits (61), Expect = 9.7
Identities = 20/96 (20%), Positives = 42/96 (43%), Gaps = 27/96 (28%)
Query: 31 VAVLGAAGGIGQPLALLMKLNPLVSRLALYDIANTPGVAADVGHINTRSEVAGYMGNDQL 90
++GA+ +G+P+A ++ LN G V HI T+ +++ Y
Sbjct: 160 AVIIGASNIVGRPMATML-LN--------------AGATVSVCHIKTK-DLSLYTRQ--- 200
Query: 91 GQALEDSDVVIIPAGVPR--KPGMTRDDLFNINAGI 124
+D++I+ AG + M ++ + ++ GI
Sbjct: 201 ------ADLIIVAAGCVNLLRSDMVKEGVIVVDVGI 230
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.319 0.135 0.395
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: 18,044,746
Number of extensions: 1777994
Number of successful extensions: 1961
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1885
Number of HSP's successfully gapped: 116
Length of query: 358
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 260
Effective length of database: 6,590,910
Effective search space: 1713636600
Effective search space used: 1713636600
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 60 (26.7 bits)