RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 018265
(358 letters)
>gnl|CDD|215058 PLN00106, PLN00106, malate dehydrogenase.
Length = 323
Score = 644 bits (1663), Expect = 0.0
Identities = 245/323 (75%), Positives = 270/323 (83%)
Query: 29 ESSGLGRMDCRAKGGSPGFKVAVLGAAGGIGQPLAMLMKINPLVSVLHLYDVVNTPGVTA 88
CRAKGG+PGFKVAVLGAAGGIGQPL++LMK+NPLVS LHLYD+ NTPGV A
Sbjct: 1 SMEASSLRACRAKGGAPGFKVAVLGAAGGIGQPLSLLMKMNPLVSELHLYDIANTPGVAA 60
Query: 89 DISHMDTNAVVRGFLGQQQLEDALTGMDIVIIPAGVPRKPGMTRDDLFNINAGIVKTLCE 148
D+SH++T A VRGFLG QL DAL G D+VIIPAGVPRKPGMTRDDLFNINAGIVKTLCE
Sbjct: 61 DVSHINTPAQVRGFLGDDQLGDALKGADLVIIPAGVPRKPGMTRDDLFNINAGIVKTLCE 120
Query: 149 GIAKCCPKAIVNLISNPVNSTVPIAAEVFKKVGTYDPKRLLGVTMLDVVRANTFVAEVLG 208
+AK CP A+VN+ISNPVNSTVPIAAEV KK G YDPK+L GVT LDVVRANTFVAE G
Sbjct: 121 AVAKHCPNALVNIISNPVNSTVPIAAEVLKKAGVYDPKKLFGVTTLDVVRANTFVAEKKG 180
Query: 209 LDPREVDVPVVGGHAGVTILPLLSQVKPSCSLTPTEIDYLTDRIQNGGTEVVEAKTGAGS 268
LDP +VDVPVVGGHAG+TILPLLSQ P S T EI+ LT RIQNGGTEVVEAK GAGS
Sbjct: 181 LDPADVDVPVVGGHAGITILPLLSQATPKVSFTDEEIEALTKRIQNGGTEVVEAKAGAGS 240
Query: 269 ATLSMAYAAAKFADACLRGLRGDAGVIECAYVASTVTELPFFASKVRLGRAGIEEIYSLG 328
ATLSMAYAAA+FADACLRGL G+A V+EC+YV S VTELPFFASKVRLGR G+EE+ LG
Sbjct: 241 ATLSMAYAAARFADACLRGLNGEADVVECSYVQSEVTELPFFASKVRLGRNGVEEVLGLG 300
Query: 329 PLNEYERAGLEKAKKELAGSIQK 351
PL+EYE+ GLE K EL SI+K
Sbjct: 301 PLSEYEQKGLEALKPELKASIEK 323
>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 = 570 bits (1472), Expect = 0.0
Identities = 213/310 (68%), Positives = 254/310 (81%)
Query: 47 FKVAVLGAAGGIGQPLAMLMKINPLVSVLHLYDVVNTPGVTADISHMDTNAVVRGFLGQQ 106
KVAVLGAAGGIGQPL++L+K+NPLVS L LYD+VNTPGV AD+SH++T A V G+LG +
Sbjct: 1 VKVAVLGAAGGIGQPLSLLLKLNPLVSELALYDIVNTPGVAADLSHINTPAKVTGYLGPE 60
Query: 107 QLEDALTGMDIVIIPAGVPRKPGMTRDDLFNINAGIVKTLCEGIAKCCPKAIVNLISNPV 166
+L+ AL G D+V+IPAGVPRKPGMTRDDLFNINAGIV+ L +AK CPKA++ +ISNPV
Sbjct: 61 ELKKALKGADVVVIPAGVPRKPGMTRDDLFNINAGIVRDLATAVAKACPKALILIISNPV 120
Query: 167 NSTVPIAAEVFKKVGTYDPKRLLGVTMLDVVRANTFVAEVLGLDPREVDVPVVGGHAGVT 226
NSTVPIAAEV KK G YDPKRL GVT LDVVRANTFVAE+LGLDP +V+VPV+GGH+GVT
Sbjct: 121 NSTVPIAAEVLKKAGVYDPKRLFGVTTLDVVRANTFVAELLGLDPAKVNVPVIGGHSGVT 180
Query: 227 ILPLLSQVKPSCSLTPTEIDYLTDRIQNGGTEVVEAKTGAGSATLSMAYAAAKFADACLR 286
ILPLLSQ +P + EI+ LT RIQ GG EVV+AK GAGSATLSMAYA A+FA++ LR
Sbjct: 181 ILPLLSQCQPPFTFDQEEIEALTHRIQFGGDEVVKAKAGAGSATLSMAYAGARFANSLLR 240
Query: 287 GLRGDAGVIECAYVASTVTELPFFASKVRLGRAGIEEIYSLGPLNEYERAGLEKAKKELA 346
GL+G+ GVIECAYV S VTE PFFA+ V LG+ G+E+ LG LN+YE+ LE A EL
Sbjct: 241 GLKGEKGVIECAYVESDVTEAPFFATPVELGKNGVEKNLGLGKLNDYEKKLLEAALPELK 300
Query: 347 GSIQKGVSFV 356
+I+KGV FV
Sbjct: 301 KNIEKGVDFV 310
>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 = 431 bits (1110), Expect = e-152
Identities = 186/312 (59%), Positives = 235/312 (75%), Gaps = 1/312 (0%)
Query: 48 KVAVLGAAGGIGQPLAMLMKINPLVSVLHLYDVVNTPGVTADISHMDTNAVVRGFLGQQQ 107
KVAVLGAAGGIGQPL++L+K+ P VS L LYD+ GV AD+SH+ T A V+GF G++
Sbjct: 1 KVAVLGAAGGIGQPLSLLLKLQPYVSELSLYDIAGAAGVAADLSHIPTAASVKGFSGEEG 60
Query: 108 LEDALTGMDIVIIPAGVPRKPGMTRDDLFNINAGIVKTLCEGIAKCCPKAIVNLISNPVN 167
LE+AL G D+V+IPAGVPRKPGMTRDDLFN+NAGIVK L +A+ CPKA++ +I+NPVN
Sbjct: 61 LENALKGADVVVIPAGVPRKPGMTRDDLFNVNAGIVKDLVAAVAESCPKAMILVITNPVN 120
Query: 168 STVPIAAEVFKKVGTYDPKRLLGVTMLDVVRANTFVAEVLGLDPREVDVPVVGGHAGVTI 227
STVPIAAEV KK G YDP +L GVT LD+VRANTFVAE+ G DP EV+VPV+GGH+G TI
Sbjct: 121 STVPIAAEVLKKKGVYDPNKLFGVTTLDIVRANTFVAELKGKDPMEVNVPVIGGHSGETI 180
Query: 228 LPLLSQVKPSCSLTPTEIDYLTDRIQNGGTEVVEAKTGAGSATLSMAYAAAKFADACLRG 287
+PL+SQ T +++ L RIQN GTEVV+AK GAGSATLSMA+A A+F + +RG
Sbjct: 181 IPLISQCPGKVLFTEDQLEALIHRIQNAGTEVVKAKAGAGSATLSMAFAGARFVLSLVRG 240
Query: 288 LRGDAGVIECAYVAS-TVTELPFFASKVRLGRAGIEEIYSLGPLNEYERAGLEKAKKELA 346
L+G+ GV+ECAYV S VTE FFA+ + LG+ G+E+ +G L+ +E L A EL
Sbjct: 241 LKGEEGVVECAYVESDGVTEATFFATPLLLGKNGVEKRLGIGKLSSFEEKMLNGALPELK 300
Query: 347 GSIQKGVSFVRK 358
+I+KG FV
Sbjct: 301 KNIKKGEEFVAS 312
>gnl|CDD|235340 PRK05086, PRK05086, malate dehydrogenase; Provisional.
Length = 312
Score = 412 bits (1061), Expect = e-145
Identities = 178/313 (56%), Positives = 214/313 (68%), Gaps = 4/313 (1%)
Query: 48 KVAVLGAAGGIGQPLAMLMKIN-PLVSVLHLYDVVN-TPGVTADISHMDTNAVVRGFLGQ 105
KVAVLGAAGGIGQ LA+L+K P S L LYD+ TPGV D+SH+ T ++GF G+
Sbjct: 2 KVAVLGAAGGIGQALALLLKTQLPAGSELSLYDIAPVTPGVAVDLSHIPTAVKIKGFSGE 61
Query: 106 QQLEDALTGMDIVIIPAGVPRKPGMTRDDLFNINAGIVKTLCEGIAKCCPKAIVNLISNP 165
AL G D+V+I AGV RKPGM R DLFN+NAGIVK L E +AK CPKA + +I+NP
Sbjct: 62 D-PTPALEGADVVLISAGVARKPGMDRSDLFNVNAGIVKNLVEKVAKTCPKACIGIITNP 120
Query: 166 VNSTVPIAAEVFKKVGTYDPKRLLGVTMLDVVRANTFVAEVLGLDPREVDVPVVGGHAGV 225
VN+TV IAAEV KK G YD +L GVT LDV+R+ TFVAE+ G P EV+VPV+GGH+GV
Sbjct: 121 VNTTVAIAAEVLKKAGVYDKNKLFGVTTLDVIRSETFVAELKGKQPGEVEVPVIGGHSGV 180
Query: 226 TILPLLSQVKPSCSLTPTEIDYLTDRIQNGGTEVVEAKTGAGSATLSMAYAAAKFADACL 285
TILPLLSQV P S T E+ LT RIQN GTEVVEAK G GSATLSM AAA+F + +
Sbjct: 181 TILPLLSQV-PGVSFTEQEVADLTKRIQNAGTEVVEAKAGGGSATLSMGQAAARFGLSLV 239
Query: 286 RGLRGDAGVIECAYVASTVTELPFFASKVRLGRAGIEEIYSLGPLNEYERAGLEKAKKEL 345
R L+G+ GV+ECAYV FFA V LG+ G+EE +G L+ +E+ LE L
Sbjct: 240 RALQGEQGVVECAYVEGDGKYARFFAQPVLLGKNGVEERLPIGTLSAFEQNALEGMLDTL 299
Query: 346 AGSIQKGVSFVRK 358
I G FV K
Sbjct: 300 KKDIALGEEFVNK 312
>gnl|CDD|240360 PTZ00325, PTZ00325, malate dehydrogenase; Provisional.
Length = 321
Score = 405 bits (1044), Expect = e-142
Identities = 189/313 (60%), Positives = 235/313 (75%), Gaps = 3/313 (0%)
Query: 47 FKVAVLGAAGGIGQPLAMLMKINPLVSVLHLYDVVNTPGVTADISHMDTNAVVRGFLGQQ 106
FKVAVLGAAGGIGQPL++L+K NP VS L LYD+V PGV AD+SH+DT A V G+ +
Sbjct: 9 FKVAVLGAAGGIGQPLSLLLKQNPHVSELSLYDIVGAPGVAADLSHIDTPAKVTGYADGE 68
Query: 107 QLEDALTGMDIVIIPAGVPRKPGMTRDDLFNINAGIVKTLCEGIAKCCPKAIVNLISNPV 166
E AL G D+V+I AGVPRKPGMTRDDLFN NA IV+ L +A PKAIV ++SNPV
Sbjct: 69 LWEKALRGADLVLICAGVPRKPGMTRDDLFNTNAPIVRDLVAAVASSAPKAIVGIVSNPV 128
Query: 167 NSTVPIAAEVFKKVGTYDPKRLLGVTMLDVVRANTFVAEVLGLDPREVDVPVVGGHAGVT 226
NSTVPIAAE KK G YDP++L GVT LDVVRA FVAE LG++P +V+VPVVGGH+GVT
Sbjct: 129 NSTVPIAAETLKKAGVYDPRKLFGVTTLDVVRARKFVAEALGMNPYDVNVPVVGGHSGVT 188
Query: 227 ILPLLSQVKPSCSLTPTEIDYLTDRIQNGGTEVVEAKTGAGSATLSMAYAAAKFADACLR 286
I+PLLSQ SL +++ +T R+Q GG EVV+AK GAGSATLSMAYAAA+++ + L+
Sbjct: 189 IVPLLSQT--GLSLPEEQVEQITHRVQVGGDEVVKAKEGAGSATLSMAYAAAEWSTSVLK 246
Query: 287 GLRGDAGVIECAYVASTVT-ELPFFASKVRLGRAGIEEIYSLGPLNEYERAGLEKAKKEL 345
LRGD G++ECA+V S + E PFF+S V LG+ G+E + +GPLN YE LE A +L
Sbjct: 247 ALRGDKGIVECAFVESDMRPECPFFSSPVELGKEGVERVLPIGPLNAYEEELLEAAVPDL 306
Query: 346 AGSIQKGVSFVRK 358
+I+KG+ F RK
Sbjct: 307 KKNIEKGLEFARK 319
>gnl|CDD|223117 COG0039, Mdh, Malate/lactate dehydrogenases [Energy production and
conversion].
Length = 313
Score = 250 bits (641), Expect = 2e-81
Identities = 116/321 (36%), Positives = 166/321 (51%), Gaps = 23/321 (7%)
Query: 48 KVAVLGAAGGIGQPLAMLMKINPLVSVLHLYDVVN--TPGVTADISHMDTNAVVRGFLGQ 105
KVAV+GA G +G LA L+ + L S L L D+ GV D+SH +
Sbjct: 2 KVAVIGA-GNVGSSLAFLLLLQGLGSELVLIDINEEKAEGVALDLSHAAAPLGSDVKITG 60
Query: 106 QQLEDALTGMDIVIIPAGVPRKPGMTRDDLFNINAGIVKTLCEGIAKCCPKAIVNLISNP 165
+ L G DIV+I AGVPRKPGMTR DL NA IVK + + IAK P AIV +++NP
Sbjct: 61 DGDYEDLKGADIVVITAGVPRKPGMTRLDLLEKNAKIVKDIAKAIAKYAPDAIVLVVTNP 120
Query: 166 VNSTVPIAAEVFKKVGTYDPKRLLG-VTMLDVVRANTFVAEVLGLDPREVDVPVVGGHAG 224
V+ IA + R++G T+LD R TF+AE LG+ P++V V+G H G
Sbjct: 121 VDILTYIAMKFSGF----PKNRVIGSGTVLDSARFRTFLAEKLGVSPKDVHAYVIGEH-G 175
Query: 225 VTILPLLSQV----KPSCSL----TPTEIDYLTDRIQNGGTEVVEAKTGAGSATLSMAYA 276
T++PL SQ KP L T +++ L +R++N G E++EAK A A
Sbjct: 176 DTMVPLWSQATVGGKPLEELLKEDTEEDLEELIERVRNAGAEIIEAKG--AGTYYGPAAA 233
Query: 277 AAKFADACLRGLRGDAGVIECAYV-ASTVTELPFFASKVRLGRAGIEEIYSLGPLNEYER 335
A+ +A LR + + Y+ E +F LG+ G+EEI L L++ E+
Sbjct: 234 LARMVEAILRDEK--RVLPVSVYLDGEYGVEDVYFGVPAVLGKNGVEEILEL-LLSDDEQ 290
Query: 336 AGLEKAKKELAGSIQKGVSFV 356
L+K+ +EL +I+ V
Sbjct: 291 EKLDKSAEELKKNIELVKELV 311
>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 = 186 bits (474), Expect = 2e-58
Identities = 81/177 (45%), Positives = 108/177 (61%), Gaps = 16/177 (9%)
Query: 192 TMLDVVRANTFVAEVLGLDPREVDVPVVGGHAG----------VTILPLLSQVKPSCSLT 241
T LD RA TF+AE G+DPR V+V V+G H+G VTI+PL+SQVK + T
Sbjct: 1 TTLDTARARTFLAEKFGVDPRSVNVYVIGEHSGTQFPDWSHAKVTIIPLISQVKENLKDT 60
Query: 242 PTEIDYLTDRIQNGGTEVVEAKTGAGSATLSMAYAAAKFADACLRGLRGD--AGVIECAY 299
E++ L +R+QN G EV+EAK AGS T SMAYAAA+ A A LRG G GV Y
Sbjct: 61 DWELEELIERVQNAGYEVIEAK--AGSTTYSMAYAAARIAKAILRGTGGVLSVGVYLDGY 118
Query: 300 VASTVTELPFFASKVRLGRAGIEEIYSLGPLNEYERAGLEKAKKELAGSIQKGVSFV 356
+ +F+ V LG+ G+E++ + PLN++ER LEK+ EL I+KG +FV
Sbjct: 119 YG--SPDDIYFSVPVVLGKDGVEKVVEILPLNDFEREKLEKSAAELKKEIEKGFAFV 173
>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 = 178 bits (453), Expect = 1e-55
Identities = 63/145 (43%), Positives = 80/145 (55%), Gaps = 6/145 (4%)
Query: 48 KVAVLGAAGGIGQPLAMLMKINPLVSVLHLYDVV--NTPGVTADISHMDTNAVVRGFLGQ 105
KVAV+GA GG+G LA + + L L L D+ GV D+SH T V G +G
Sbjct: 2 KVAVVGAGGGVGSSLAFALALQGLADELVLVDINKDKAEGVAMDLSHGSTFLSVPGIVGG 61
Query: 106 QQLEDALTGMDIVIIPAGVPRKPGMTRDDLFNINAGIVKTLCEGIAKCCPKAIVNLISNP 165
+AL D+V+I AGVPRKPGMTR DL N NAGI K + IAK P AIV ++SNP
Sbjct: 62 DD-YEALKDADVVVITAGVPRKPGMTRLDLLNRNAGIFKDIVPAIAKSAPDAIVLVVSNP 120
Query: 166 VNSTVPIAAEVFKKVGTYDPKRLLG 190
V+ IA +V G + +
Sbjct: 121 VDILTYIAWKVS---GLPPERVIGS 142
>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 = 164 bits (419), Expect = 2e-48
Identities = 102/319 (31%), Positives = 162/319 (50%), Gaps = 38/319 (11%)
Query: 49 VAVLGAAGGIGQPLAMLMKINPLVSVLHLYDVV-NTP-GVTADISHM----DTNAVVRGF 102
++++GA G +G LA L+ + L V+ L D+V P G DIS ++ V G
Sbjct: 1 ISIIGA-GNVGATLAQLLALKELGDVV-LLDIVEGLPQGKALDISQAAPILGSDTKVTGT 58
Query: 103 LGQQQLEDALTGMDIVIIPAGVPRKPGMTRDDLFNINAGIVKTLCEGIAKCCPKAIVNLI 162
+ + + D+V+I AG+PRKPGM+RDDL NA IVK + E I K P AIV ++
Sbjct: 59 NDYEDIAGS----DVVVITAGIPRKPGMSRDDLLGTNAKIVKEVAENIKKYAPNAIVIVV 114
Query: 163 SNPVNSTVPIAAEVFKKVGTYDPKRLLGV-TMLDVVRANTFVAEVLGLDPREVDVPVVGG 221
+NP++ V K + R++G+ +LD R F+AE LG+ ++V V+GG
Sbjct: 115 TNPLDVMT----YVAYKASGFPRNRVIGMAGVLDSARFRYFIAEELGVSVKDVQAMVLGG 170
Query: 222 HAGVTILPLLSQ-----VKPSCSLTPTEIDYLTDRIQNGGTEVVEAKTGAGSATLSMAYA 276
H G T++PL + + +T EID + +R +NGG E+V GSA + A A
Sbjct: 171 H-GDTMVPLPRYSTVGGIPLTELITKEEIDEIVERTRNGGAEIVNLL-KTGSAYYAPAAA 228
Query: 277 AAKFADACLRGLRGDAGVIECA------YVASTVTELPFFASKVRLGRAGIEEIYSLGPL 330
A+ +A L+ + V+ C+ Y + F V LG+ G+E+I L L
Sbjct: 229 IAEMVEAILKDKK---RVLPCSAYLEGEYGIKDI----FVGVPVVLGKNGVEKIIEL-DL 280
Query: 331 NEYERAGLEKAKKELAGSI 349
+ E+ +K+ + + I
Sbjct: 281 TDEEKEAFDKSVESVKELI 299
>gnl|CDD|180477 PRK06223, PRK06223, malate dehydrogenase; Reviewed.
Length = 307
Score = 161 bits (409), Expect = 7e-47
Identities = 112/324 (34%), Positives = 173/324 (53%), Gaps = 42/324 (12%)
Query: 48 KVAVLGAAGGIGQPLAMLMKINPLVSVLHLYDVV-NTP-GVTADISHMDTNAVVRGF--- 102
K++++GA G +G LA L+ + L V+ L+D+V P G DI+ A V GF
Sbjct: 4 KISIIGA-GNVGATLAHLLALKELGDVV-LFDIVEGVPQGKALDIAEA---APVEGFDTK 58
Query: 103 -LGQQQLEDALTGMDIVIIPAGVPRKPGMTRDDLFNINAGIVKTLCEGIAKCCPKAIVNL 161
G ED + G D+V+I AGVPRKPGM+RDDL INA I+K + EGI K P AIV +
Sbjct: 59 ITGTNDYED-IAGSDVVVITAGVPRKPGMSRDDLLGINAKIMKDVAEGIKKYAPDAIVIV 117
Query: 162 ISNPVNSTVPIAAEVFKKVGTYDPKRLLGV-TMLDVVRANTFVAEVLGLDPREVDVPVVG 220
++NPV++ +A K + R++G+ +LD R TF+AE L + ++V V+G
Sbjct: 118 VTNPVDAMTYVA----LKESGFPKNRVIGMAGVLDSARFRTFIAEELNVSVKDVTAFVLG 173
Query: 221 GHAGVTILPLLSQV----KPSCSLTPTE-IDYLTDRIQNGGTEVVEAKTGAGSATLSMAY 275
GH G +++PL+ P L E +D + +R + GG E+V GSA + A
Sbjct: 174 GH-GDSMVPLVRYSTVGGIPLEDLLSKEKLDEIVERTRKGGAEIVGLL-KTGSAYYAPAA 231
Query: 276 AAAKFADACLRGLRGDAG-VIEC-AY------VASTVTELPFFASKVRLGRAGIEEIYSL 327
+ A+ +A L+ D V+ C AY V +P V+LG+ G+E+I L
Sbjct: 232 SIAEMVEAILK----DKKRVLPCSAYLEGEYGVKDVYVGVP-----VKLGKNGVEKIIEL 282
Query: 328 GPLNEYERAGLEKAKKELAGSIQK 351
L++ E+A +K+ + + I+
Sbjct: 283 -ELDDEEKAAFDKSVEAVKKLIEA 305
>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 = 142 bits (360), Expect = 3e-40
Identities = 81/310 (26%), Positives = 124/310 (40%), Gaps = 65/310 (20%)
Query: 49 VAVLGAAGGIGQPLA--MLMKINPLVSVLHLYDVVN--TPGVTADISHMDTNAVVRGFLG 104
+AV+GA G +G LA + L L LYD+ GV D+
Sbjct: 1 IAVIGAGGNVGPALAFGLADGSVLLAIELVLYDIDEEKLKGVAMDLQDAVEPLADIKVSI 60
Query: 105 QQQLEDALTGMDIVIIPAGVPRKPGMTRDDLFNINAGIVKTLCEGIAKCCPKAIVNLISN 164
+A D+VII AGV RKPGM R DL N IVK + + I K P A + ++SN
Sbjct: 61 TDDPYEAFKDADVVIITAGVGRKPGMGRLDLLKRNVPIVKEIGDNIEKYSPDAWIIVVSN 120
Query: 165 PVNSTVPIAAEVFKKVGTYDPKRLLGVTMLDVVRANTFVAEVLGLDPREVDVPVVGGHAG 224
PV+ I + + ++++G+ LD +R +AE LG+DP +V V ++G H G
Sbjct: 121 PVD----IITYLVWRYSGLPKEKVIGLGTLDPIRFRRILAEKLGVDPDDVKVYILGEHGG 176
Query: 225 VTILPLLSQVKPSCSLTPTEIDYLTDRIQNGGTEVVEAKTGAGSATLSMAYAAAKFADAC 284
+ +P S V+ +A + A +
Sbjct: 177 -SQVPDWSTVR-------------------------------------IATSIADLIRSL 198
Query: 285 LRGLRGDAGVIECAYVAS---------TVTELPFFASKVRLGRAGIEEIYSLGPLNEYER 335
L D G I V + V +P +G+ G+EE + L ++E
Sbjct: 199 LN----DEGEILPVGVRNNGQIGIPDDVVVSVP-----CIVGKNGVEEPIEV-GLTDFEL 248
Query: 336 AGLEKAKKEL 345
L+K+ L
Sbjct: 249 EKLQKSADTL 258
>gnl|CDD|173409 PTZ00117, PTZ00117, malate dehydrogenase; Provisional.
Length = 319
Score = 127 bits (321), Expect = 5e-34
Identities = 95/308 (30%), Positives = 149/308 (48%), Gaps = 37/308 (12%)
Query: 48 KVAVLGAAGGIGQPLAMLMKINPLVSVLHLYDVV-NTP-GVTADISH-MDTNAVVRGFLG 104
K++++GA G IG +A+L+ L V+ LYDV+ P G D+ H LG
Sbjct: 7 KISMIGA-GQIGSTVALLILQKNLGDVV-LYDVIKGVPQGKALDLKHFSTLVGSNINILG 64
Query: 105 QQQLEDALTGMDIVIIPAGVPRKPGMTRDDLFNINAGIVKTLCEGIAKCCPKAIVNLISN 164
ED + D+V+I AGV RK MTR+DL IN I+K++ E + K CP A V ++N
Sbjct: 65 TNNYED-IKDSDVVVITAGVQRKEEMTREDLLTINGKIMKSVAESVKKYCPNAFVICVTN 123
Query: 165 PVNSTVPIAAEVFKKVGTYDPKRLLGVT-MLDVVRANTFVAEVLGLDPREVDVPVVGGHA 223
P++ +VF++ ++ G+ +LD R +AE LG+ P +V V+GGH
Sbjct: 124 PLD----CMVKVFQEKSGIPSNKICGMAGVLDSSRFRCNLAEKLGVSPGDVSAVVIGGH- 178
Query: 224 GVTILPL----------LSQVKPSCSLTPTEIDYLTDRIQNGGTEVVEAKTGAGSATLSM 273
G ++PL LS ++T EI+ + + +N G E+V+ GSA +
Sbjct: 179 GDLMVPLPRYCTVNGIPLSDFVKKGAITEKEINEIIKKTRNMGGEIVKL-LKKGSAFFAP 237
Query: 274 AYAAAKFADACLRGLRGDAGVIECA------YVASTVTELPFFASKVRLGRAGIEEIYSL 327
A A +A L+ + V+ C+ Y + F V +G GIE++ L
Sbjct: 238 AAAIVAMIEAYLKDEK---RVLVCSVYLNGQYNCKNL----FVGVPVVIGGKGIEKVIEL 290
Query: 328 GPLNEYER 335
LN E+
Sbjct: 291 -ELNAEEK 297
>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 = 124 bits (314), Expect = 3e-33
Identities = 90/309 (29%), Positives = 142/309 (45%), Gaps = 26/309 (8%)
Query: 49 VAVLGAAGGIGQPLAMLMKINPLVSVLHLYDVVN--TPGVTADISHMDTNAVVRGFLGQQ 106
+ ++GA G +G +A + L S L L DV G D+SH +
Sbjct: 1 ITIIGA-GNVGAAVAFALIAKGLASELVLVDVNEEKAKGDALDLSHASAFLATGTIVRGG 59
Query: 107 QLEDALTGMDIVIIPAGVPRKPGMTRDDLFNINAGIVKTLCEGIAKCCPKAIVNLISNPV 166
DA DIV+I AG PRKPG TR DL N NA I++++ + K P AI+ ++SNPV
Sbjct: 60 DYADA-ADADIVVITAGAPRKPGETRLDLINRNAPILRSVITNLKKYGPDAIILVVSNPV 118
Query: 167 NSTVPIAAEVFKKVGTYDPKRLLGV-TMLDVVRANTFVAEVLGLDPREVDVPVVGGHAGV 225
+ I V +K+ R++G T+LD R + +AE L +DP+ V V+G H G
Sbjct: 119 D----ILTYVAQKLSGLPKNRVIGSGTLLDSARFRSLLAEKLDVDPQSVHAYVLGEH-GD 173
Query: 226 TILPLLSQV----KPSCSLTPT---EIDYLTDRIQNGGTEVVEAKTGAGSATLSMAYAAA 278
+ + S P L P +++ + + ++ G E++ K G+ +A A A
Sbjct: 174 SQVVAWSTATVGGLPLEELAPFTKLDLEAIEEEVRTSGYEIIRLK---GATNYGIATAIA 230
Query: 279 KFADACLRGLRGDAGVIECAYVASTVTELP--FFASKVRLGRAGIEEIYSLGPLNEYERA 336
+ L R V+ + V + + +GR G+ I + PL E E A
Sbjct: 231 DIVKSILLDER---RVLPVSAVQEGQYGIEDVALSVPAVVGREGVVRILEI-PLTEDEEA 286
Query: 337 GLEKAKKEL 345
L+K+ + L
Sbjct: 287 KLQKSAEAL 295
>gnl|CDD|173376 PTZ00082, PTZ00082, L-lactate dehydrogenase; Provisional.
Length = 321
Score = 119 bits (300), Expect = 4e-31
Identities = 101/322 (31%), Positives = 168/322 (52%), Gaps = 42/322 (13%)
Query: 48 KVAVLGAAGGIGQPLAMLMKINPLVSVLHLYDVV-NTP-GVTADISHMDTNAVVR-GFLG 104
K++++G+ G IG +A L+ + L V+ L+D+V N P G DISH + A +G
Sbjct: 8 KISLIGS-GNIGGVMAYLIVLKNLGDVV-LFDIVKNIPQGKALDISHSNVIAGSNSKVIG 65
Query: 105 QQQLEDALTGMDIVIIPAGVPRKPGMT-----RDDLFNINAGIVKTLCEGIAKCCPKAIV 159
ED + G D+VI+ AG+ ++PG + RDDL +NA I+ + EGI K CP A V
Sbjct: 66 TNNYED-IAGSDVVIVTAGLTKRPGKSDKEWNRDDLLPLNAKIMDEVAEGIKKYCPNAFV 124
Query: 160 NLISNPVNSTVPIAAEVFKKVGTYDPKRLLGVT-MLDVVRANTFVAEVLGLDPREVDVPV 218
+I+NP++ V ++ ++ ++ G+ +LD R T++AE LG++PR+V V
Sbjct: 125 IVITNPLDVMV----KLLQEHSGLPKNKVCGMAGVLDSSRLRTYIAEKLGVNPRDVHASV 180
Query: 219 VGGHAGVTILPL----------LSQVKPSCSLTPTEIDYLTDRIQNGGTEVVEAKTGAGS 268
+G H G ++PL LS+ +T EID + +R +N G E+V+ G GS
Sbjct: 181 IGAH-GDKMVPLPRYVTVGGIPLSEFIKKGLITQEEIDEIVERTRNTGKEIVDL-LGTGS 238
Query: 269 ATLSMAYAAAKFADACLRGLRGDAGVIECA------YVASTVTELPFFASKVRLGRAGIE 322
A + A AA + A+A L+ + V+ C+ Y + + + +G G+E
Sbjct: 239 AYFAPAAAAIEMAEAYLKDKK---RVLPCSAYLEGQYGHKDI----YMGTPAVIGANGVE 291
Query: 323 EIYSLGPLNEYERAGLEKAKKE 344
+I L L E+ +++ KE
Sbjct: 292 KIIEL-DLTPEEQKKFDESIKE 312
>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 = 118 bits (296), Expect = 1e-30
Identities = 95/310 (30%), Positives = 157/310 (50%), Gaps = 30/310 (9%)
Query: 48 KVAVLGAAGGIGQPLAMLMKINPLVSVLHLYDVVNTP--GVTADISHMDTNAVVRGF--- 102
K++V+GA G +G A + L ++ L DVV G D M + V GF
Sbjct: 3 KISVIGA-GFVGATTAFRLAEKELADLV-LLDVVEGIPQGKALD---MYEASPVGGFDTK 57
Query: 103 -LGQQQLEDALTGMDIVIIPAGVPRKPGMTRDDLFNINAGIVKTLCEGIAKCCPKAIVNL 161
G D DIV+I AG+PRKPGM+R+DL ++NAGIV+ + I + P I+ +
Sbjct: 58 VTGTNNYADT-ANSDIVVITAGLPRKPGMSREDLLSMNAGIVREVTGRIMEHSPNPIIVV 116
Query: 162 ISNPVNSTVPIAAEVFKKVGTYDPKRLLGVT-MLDVVRANTFVAEVLGLDPREVDVPVVG 220
+SNP+++ +A + + +R++G +LD R TF+A LG+ ++V V+G
Sbjct: 117 VSNPLDAMTYVAWQ----KSGFPKERVIGQAGVLDSARFRTFIAMELGVSVQDVTACVLG 172
Query: 221 GHAGVTILPL-----LSQVKPSCSLTPTEIDYLTDRIQNGGTEVVEAKTGAGSATLSMAY 275
GH G ++PL ++ + + ++ I + +R + GG E+V GSA + A
Sbjct: 173 GH-GDAMVPLVRYSTVAGIPVADLISAERIAEIVERTRKGGGEIVNL-LKQGSAYYAPAA 230
Query: 276 AAAKFADACLRGLRGDAGVIEC-AYVASTV-TELPFFASKVRLGRAGIEEIYSLGPLNEY 333
+ + +A L+ + V+ C AY+ + + V LG+ G+E IY L L++
Sbjct: 231 SVVEMVEAILKDRK---RVLPCAAYLDGQYGIDGIYVGVPVILGKNGVEHIYEL-KLDQS 286
Query: 334 ERAGLEKAKK 343
E A L K+ K
Sbjct: 287 ELALLNKSAK 296
>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 = 105 bits (263), Expect = 6e-26
Identities = 85/335 (25%), Positives = 144/335 (42%), Gaps = 75/335 (22%)
Query: 48 KVAVLGAAGGIGQPLAMLMKINPLVSVLHL-----------------YDVVNTPGVTADI 90
KV+++GA+G +G A+L+ +V ++L YD + G+ A+I
Sbjct: 2 KVSIIGASGRVGSATALLLAKEDVVKEINLISRPKSLEKLKGLRLDIYDALAAAGIDAEI 61
Query: 91 SHMDTNAVVRGFLGQQQLEDALTGMDIVIIPAGVPRKPGMTRDDLFNINAGIVKTLCEGI 150
+ V G DIVII AGVPRK GM+R DL NA IVK + I
Sbjct: 62 KISSDLSDV-------------AGSDIVIITAGVPRKEGMSRLDLAKKNAKIVKKYAKQI 108
Query: 151 AKCCPKAIVNLISNPVNSTVPIAAEVFKKVGTYDPKRLLGV-TMLDVVRANTFVAEVLGL 209
A+ P + +++NPV+ A K +D R+ G+ T LD +R +A+ +
Sbjct: 109 AEFAPDTKILVVTNPVDVMTYKAL----KESGFDKNRVFGLGTHLDSLRFKVAIAKHFNV 164
Query: 210 DPREVDVPVVGGHAGVTILPLLSQVK----PSCSLTPTE---IDYLTDRIQNGGTEVVEA 262
EV ++G H G +++PL+S P + ++ + + ++N G ++
Sbjct: 165 HISEVHTRIIGEH-GDSMVPLISSTSIGGIPIKRFPEYKDFDVEKIVETVKNAGQNIISL 223
Query: 263 KTGA----GSATLSMAYAAAK----------FADACLRGLRGDAGVIECAYVASTVTELP 308
K G+ SA ++ A + + + G+R C V
Sbjct: 224 KGGSEYGPASAISNLVRTIANDERRILTVSTYLEGEIDGIRD-----VCIGVP------- 271
Query: 309 FFASKVRLGRAGIEEIYSLGPLNEYERAGLEKAKK 343
V+LG+ GIEEI + +++ ER K+ +
Sbjct: 272 -----VKLGKNGIEEIVPI-EMDDDEREAFRKSAE 300
>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 = 99.2 bits (248), Expect = 9e-24
Identities = 66/248 (26%), Positives = 115/248 (46%), Gaps = 26/248 (10%)
Query: 112 LTGMDIVIIPAGVPRKPGMTRDDLFNINAGIVKTLCEGIAKCCPKAIVNLISNPVNSTVP 171
D+V+I AG P+KPG TR +L N I+K++ + K I + +NPV+
Sbjct: 62 CKDADLVVITAGAPQKPGETRLELVGRNVRIMKSIVPEVVKSGFDGIFLVATNPVD---- 117
Query: 172 IAAEVFKKVGTYDPKRLLGV-TMLDVVRANTFVAEVLGLDPREVDVPVVGGH-------- 222
I V K+ + R++G T+LD R +AE LG+DP+ V ++G H
Sbjct: 118 ILTYVAWKLSGFPKNRVIGSGTVLDTARLRYLLAEKLGVDPQSVHAYIIGEHGDSEVPVW 177
Query: 223 --AGVTILPLLSQVKPSCSLTPTEIDYLTDRIQNGGTEVVEAKTGAGSATLSMAYAAAKF 280
A + +PLL +K + T +++ + +++ E++ K G+ + A A+
Sbjct: 178 SSATIGGVPLLDYLKAKGTETDLDLEEIEKEVRDAAYEIINRK---GATYYGIGMAVARI 234
Query: 281 ADACLRGLRGD---AGVIECAYVASTVTELPFFASKVRLGRAGIEEIYSLGPLNEYERAG 337
+A L + ++ Y V + LGR G+EEI L PL++ E+
Sbjct: 235 VEAILHDENRVLPVSAYLDGEYGIKDV----YIGVPAVLGRNGVEEIIEL-PLSDEEKEA 289
Query: 338 LEKAKKEL 345
+K+ + L
Sbjct: 290 FQKSAETL 297
>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 = 99.1 bits (248), Expect = 1e-23
Identities = 91/331 (27%), Positives = 140/331 (42%), Gaps = 53/331 (16%)
Query: 48 KVAVLGAAGGIGQPLAMLMKINPLVSVLHLYDVVNTPGVTA---DISHM--DTNAVVRGF 102
KV ++GA G +G A + + L L D+ N D+ + V+
Sbjct: 2 KVVIIGA-GHVGSSFAYSLVNQGIADELVLIDI-NEEKAEGEALDLEDALAFLPSPVKIK 59
Query: 103 LGQ-QQLEDALTGMDIVIIPAGVPRKPGMTRDDLFNINAGIVKTLCEGIAKCCPKAIVNL 161
G +DA DIV+I AG P+KPG TR DL NA I+K++ I I +
Sbjct: 60 AGDYSDCKDA----DIVVITAGAPQKPGETRLDLLEKNAKIMKSIVPKIKASGFDGIFLV 115
Query: 162 ISNPVNSTVPIAAEVFKKVGTYDPKRLLGV-TMLDVVRANTFVAEVLGLDPREVDVPVVG 220
SNPV+ + V +K+ R++G T LD R +AE L +DPR V V+G
Sbjct: 116 ASNPVD----VITYVVQKLSGLPKNRVIGTGTSLDTARLRRALAEKLNVDPRSVHAYVLG 171
Query: 221 GH-------------AGVTILPLLSQVKPSCSLTPTEIDYLTDRIQNGGTEVVEAKTGAG 267
H G +L LL + K L+ ++D + + ++ G E++ K G
Sbjct: 172 EHGDSQFVAWSTVTVGGKPLLDLLKEGK----LSELDLDEIEEDVRKAGYEIINGK---G 224
Query: 268 SATLSMAYAAAKFADACLRGLRGDAGVI-------ECAYVASTVTELPFFASKVRLGRAG 320
+ +A A A+ A L D I + Y V + +GR G
Sbjct: 225 ATYYGIATALARIVKAILN----DENAILPVSAYLDGEYGEKDV----YIGVPAIIGRNG 276
Query: 321 IEEIYSLGPLNEYERAGLEKAKKELAGSIQK 351
+EE+ L L E E+ EK+ + +I+K
Sbjct: 277 VEEVIEL-DLTEEEQEKFEKSADIIKENIKK 306
>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 = 83.7 bits (208), Expect = 3e-18
Identities = 89/330 (26%), Positives = 143/330 (43%), Gaps = 52/330 (15%)
Query: 48 KVAVLGAAGGIGQPLAMLMKINPLVSVLHLYDVVNTPGVTA---DISH-MDTNAVVRGFL 103
KVA++GA G +G A + + L S + L D+ N D++H VR +
Sbjct: 2 KVAIVGA-GFVGSTTAYALLLRGLASEIVLVDI-NKAKAEGEAMDLAHGTPFVKPVRIYA 59
Query: 104 GQ-QQLEDALTGMDIVIIPAGVPRKPGMTRDDLFNINAGIVKTLCEGIAKCCPKAIVNLI 162
G + A D+V+I AG +KPG TR DL N I K + I K P AI+ ++
Sbjct: 60 GDYADCKGA----DVVVITAGANQKPGETRLDLLKRNVAIFKEIIPQILKYAPDAILLVV 115
Query: 163 SNPVNSTVPIAAEVFKKVGTYDPKRLLGV-TMLDVVRANTFVAEVLGLDPREVDVPVVGG 221
+NPV+ + V K+ P R++G T+LD R + E LG+DPR V ++G
Sbjct: 116 TNPVD----VLTYVAYKLSGLPPNRVIGSGTVLDTARFRYLLGEHLGVDPRSVHAYIIGE 171
Query: 222 H-------------AGVTILPLLSQVKPSCSLTPTEIDYLTDRIQNGGTEVVEAKTGAGS 268
H GV + + + + ++N E++E K G+
Sbjct: 172 HGDSEVAVWSSANIGGVPLDEFCKLCGRPF--DEEVREEIFEEVRNAAYEIIERK---GA 226
Query: 269 ATLSMAYAAAKFADACLRGLRGD-------AGVIECAYVASTVT-ELPFFASKVRLGRAG 320
++ A A+ +A LR D + +++ Y V LP V GR+G
Sbjct: 227 TYYAIGLALARIVEAILR----DENSVLTVSSLLDGQYGIKDVALSLP---CIV--GRSG 277
Query: 321 IEEIYSLGPLNEYERAGLEKAKKELAGSIQ 350
+E + PL+E E L + + L +I+
Sbjct: 278 VERVLPP-PLSEEEEEALRASAEVLKEAIE 306
>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 = 77.8 bits (192), Expect = 4e-16
Identities = 74/253 (29%), Positives = 113/253 (44%), Gaps = 33/253 (13%)
Query: 48 KVAVLGAAGGIGQPLA-------MLMKINPLVSVLHLYDVVNT----PGVTADISHMDTN 96
+VAV GAAG IG L + K P+V LHL D+ GV ++ D
Sbjct: 5 RVAVTGAAGQIGYSLLFRIASGELFGKDQPVV--LHLLDIPPAMKALEGVAMEL--EDCA 60
Query: 97 -AVVRGFLGQQQLEDALTGMDIVIIPAGVPRKPGMTRDDLFNINAGIVKTLCEGIAKCCP 155
++ G + E+A +D ++ PRKPGM R DL + N I K + + K
Sbjct: 61 FPLLAGVVATTDPEEAFKDVDAALLVGAFPRKPGMERADLLSKNGKIFKEQGKALNKVAK 120
Query: 156 KAI-VNLISNPVNSTVPIAAEVFKKVGTYDPKRLLGVTMLDVVRANTFVAEVLGLDPREV 214
K + V ++ NP N+ IA++ + PK +T LD RA +A G+ +V
Sbjct: 121 KDVKVLVVGNPANTNALIASKNAPDI---PPKNFSAMTRLDHNRAKYQLAAKAGVPVSDV 177
Query: 215 -DVPVVGGHAGVTILPLLSQ----VKPSCSLTPTEIDYL----TDRIQNGGTEVVEAKTG 265
+V + G H+ T +P + +P + + +L +Q G V+EA+ G
Sbjct: 178 KNVIIWGNHSN-TQVPDFTHATVDGRPVKEVIKDD-KWLEGEFIPTVQQRGAAVIEAR-G 234
Query: 266 AGSATLSMAYAAA 278
A SA S A AA
Sbjct: 235 ASSA-ASAANAAI 246
>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 = 76.5 bits (189), Expect = 1e-15
Identities = 83/329 (25%), Positives = 130/329 (39%), Gaps = 37/329 (11%)
Query: 44 SPGFKVAVLGA-AGGIGQPLAMLMKINPLVSVLHLYDVVN--TPGVTADISHMDTNAVVR 100
P KV V+G G+ +++L K L L L DVV G D+ H
Sbjct: 1 KPRNKVTVVGVGQVGMACAISILAK--GLADELVLVDVVEDKLKGEAMDLQH------GS 52
Query: 101 GFLGQQQLE-----DALTGMDIVIIPAGVPRKPGMTRDDLFNINAGIVKTLCEGIAKCCP 155
FL ++E +VI+ AG + G +R DL N I K + + K P
Sbjct: 53 AFLKNPKIEADKDYSVTANSKVVIVTAGARQNEGESRLDLVQRNVDIFKGIIPKLVKYSP 112
Query: 156 KAIVNLISNPVNSTVPIAAEVFKKVGTYDPKRLLGV-TMLDVVRANTFVAEVLGLDPREV 214
AI+ ++SNPV+ I V K+ R++G LD R +AE LG+ P V
Sbjct: 113 NAILLVVSNPVD----IMTYVAWKLSGLPKHRVIGSGCNLDSARFRYLIAERLGVAPSSV 168
Query: 215 DVPVVGGH--------AGVTI--LPLLSQVK-PSCSLTPTEIDYLTDRIQNGGTEVVEAK 263
++G H +GV + + L P + + ++ + EV++ K
Sbjct: 169 HGWIIGEHGDSSVPVWSGVNVAGVRLQDLNPDIGTDKDPEKWKEVHKQVVDSAYEVIKLK 228
Query: 264 TGAGSATLSMAYAAAKFADACLRGLRGDAGVIECAYVASTVTELPFFASKVRLGRAGIEE 323
G + ++ + A DA LR V + + F + LG GI
Sbjct: 229 ---GYTSWAIGLSVADLVDAILRNTGRVHSVSTLVKGLHGIEDEVFLSLPCILGENGITH 285
Query: 324 IYSLGPLNEYERAGLEKAKKELAGSIQKG 352
+ PL E E+ L+K+ L +QK
Sbjct: 286 VIKQ-PLTEEEQEKLQKSADTLW-EVQKQ 312
>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 = 75.8 bits (187), Expect = 2e-15
Identities = 71/259 (27%), Positives = 104/259 (40%), Gaps = 42/259 (16%)
Query: 48 KVAVLGAAGGIGQPLA-------MLMKINPLVSVLHLYDVVNTPGVTADISHMDTNAV-- 98
V + GAAG IG L + P++ LHL D+ + ++ +
Sbjct: 2 HVLITGAAGQIGYNLLFLIASGELFGDDQPVI--LHLLDI------PPAMKALEGVVMEL 53
Query: 99 -------VRGFLGQQQLEDALTGMDIVIIPAGVPRKPGMTRDDLFNINAGIVKTLCEGIA 151
++G + E+A +D+ I+ PRKPGM R DL NA I K E +
Sbjct: 54 QDCAFPLLKGVVITTDPEEAFKDVDVAILVGAFPRKPGMERADLLRKNAKIFKEQGEALN 113
Query: 152 KCC-PKAIVNLISNPVNSTVPIAAEVFKKVGTYDPKRLLGVTMLDVVRANTFVAEVLGLD 210
K P V ++ NP N+ IA K PK +T LD RA VA LG+
Sbjct: 114 KVAKPTVKVLVVGNPANTNALIAL---KNAPNLPPKNFTALTRLDHNRAKAQVARKLGVR 170
Query: 211 PREV-DVPVVGGHAGVTILPLLSQVK----PSCSLTPTEIDY------LTDRIQNGGTEV 259
+V +V + G H+ T +P LS +D +Q G +
Sbjct: 171 VSDVKNVIIWGNHSN-TQVPDLSNAVVYGPGGTEWVLDLLDEEWLNDEFVKTVQKRGAAI 229
Query: 260 VEAKTGAGSATLSMAYAAA 278
++ + GA SA S A A A
Sbjct: 230 IKKR-GASSA-ASAAKAIA 246
>gnl|CDD|133426 cd05290, LDH_3, A subgroup of L-lactate dehydrogenases. L-lactate
dehydrogenases (LDH) are tetrameric enzymes catalyzing
the last step of glycolysis in which pyruvate is
converted to L-lactate. This subgroup is composed of
some bacterial LDHs from firmicutes,
gammaproteobacteria, and actinobacteria. Vertebrate LDHs
are non-allosteric, but some bacterial LDHs are
activated by an allosteric effector such as
fructose-1,6-bisphosphate. LDHs are part of the
NAD(P)-binding Rossmann fold superfamily, which includes
a wide variety of protein families including the
NAD(P)-binding domains of alcohol dehydrogenases,
tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate dehydrogenases,
formate/glycerate dehydrogenases, siroheme synthases,
6-phosphogluconate dehydrogenase, aminoacid
dehydrogenases, repressor rex, and NAD-binding potassium
channel domains, among others.
Length = 307
Score = 75.4 bits (186), Expect = 2e-15
Identities = 49/144 (34%), Positives = 71/144 (49%), Gaps = 12/144 (8%)
Query: 110 DALTGMDIVIIPAGVPRKPGMT--RDDLFNINAGIVKTLCEGIAKCCPKAIVNLISNPVN 167
D DI++I AG PG T R DL NA I++ + I K +A++ LI+NP++
Sbjct: 64 DDCADADIIVITAGPSIDPGNTDDRLDLAQTNAKIIREIMGNITKVTKEAVIILITNPLD 123
Query: 168 STVPIAAEVFKKVGTYDPKRLLGV-TMLDVVRANTFVAEVLGLDPREVDVPVVGGHAGVT 226
V IAA F Y +++G TMLD R VA+ G+DP+ V V+G H G
Sbjct: 124 IAVYIAATEFD----YPANKVIGTGTMLDTARLRRIVADKYGVDPKNVTGYVLGEH-GSH 178
Query: 227 ILPLLSQVKPSCSLTPTEIDYLTD 250
P+ S V ++ +D L
Sbjct: 179 AFPVWSLV----NIAGLPLDELEA 198
>gnl|CDD|178836 PRK00066, ldh, L-lactate dehydrogenase; Reviewed.
Length = 315
Score = 73.4 bits (181), Expect = 1e-14
Identities = 65/253 (25%), Positives = 105/253 (41%), Gaps = 40/253 (15%)
Query: 114 GMDIVIIPAGVPRKPGMTRDDLFNINAGIVKTLCEGIAKCCPKAIVNLISNPVNSTVPIA 173
D+V+I AG P+KPG TR DL N I K++ + I + SNPV+ I
Sbjct: 73 DADLVVITAGAPQKPGETRLDLVEKNLKIFKSIVGEVMASGFDGIFLVASNPVD----IL 128
Query: 174 AEVFKKVGTYDPKRLLGV-TMLDVVRANTFVAEVLGLDPREVDVPVVGGH---------- 222
K+ + +R++G T LD R ++E L +DPR V ++G H
Sbjct: 129 TYATWKLSGFPKERVIGSGTSLDSARFRYMLSEKLDVDPRSVHAYIIGEHGDTEFPVWSH 188
Query: 223 AGVTILPLLSQVKPSCSLTPTEIDYLTDRIQNGGTEVVEAKTGAGSATLSMAYAAAKFAD 282
A V +PL ++ + ++D + + +++ E++E K G+ +A A A+
Sbjct: 189 ANVAGVPLEEYLEENEQYDEEDLDEIFENVRDAAYEIIEKK---GATYYGIAMALARITK 245
Query: 283 ACLRG----------LRGDAGVIECAYVASTVTELPFFASKVRLGRAGIEEIYSLGPLNE 332
A L L G G + + + R GI EI L PLN+
Sbjct: 246 AILNNENAVLPVSAYLEGQYGEEDV-----------YIGVPAVVNRNGIREIVEL-PLND 293
Query: 333 YERAGLEKAKKEL 345
E+ + L
Sbjct: 294 DEKQKFAHSADVL 306
>gnl|CDD|178212 PLN02602, PLN02602, lactate dehydrogenase.
Length = 350
Score = 70.2 bits (172), Expect = 2e-13
Identities = 80/326 (24%), Positives = 139/326 (42%), Gaps = 39/326 (11%)
Query: 48 KVAVLGAAGGIGQPLAMLMKINPLVSVLHLYDVV--NTPGVTADISHMDTNAVVRGFLGQ 105
KV+V+G G +G +A + L L L DV G D+ H FL +
Sbjct: 39 KVSVVGV-GNVGMAIAQTILTQDLADELALVDVNPDKLRGEMLDLQH------AAAFLPR 91
Query: 106 QQL----EDALT-GMDIVIIPAGVPRKPGMTRDDLFNINAGIVKTLCEGIAKCCPKAIVN 160
++ + A+T G D+ I+ AG + PG +R +L N + + + +AK P I+
Sbjct: 92 TKILASTDYAVTAGSDLCIVTAGARQIPGESRLNLLQRNVALFRKIIPELAKYSPDTILL 151
Query: 161 LISNPVNSTVPIAAEVFKKVGTYDPKRLLGV-TMLDVVRANTFVAEVLGLDPREVDVPVV 219
++SNPV+ + V K+ + R++G T LD R +A+ L ++ ++V +V
Sbjct: 152 IVSNPVD----VLTYVAWKLSGFPANRVIGSGTNLDSSRFRFLIADHLDVNAQDVQAYIV 207
Query: 220 GGH-------------AGVTILPLLSQVKPSCSLTPTEIDYLTDRIQNGGTEVVEAKTGA 266
G H GV +L L K + ++ + + + EV++ K
Sbjct: 208 GEHGDSSVALWSSVSVGGVPVLSFLE--KQQIAYEKETLEEIHRAVVDSAYEVIKLK--- 262
Query: 267 GSATLSMAYAAAKFADACLRGLRGDAGVIECAYVASTVTELPFFAS-KVRLGRAGIEEIY 325
G + ++ Y+ A + LR R V A + E F S +LGR G+ +
Sbjct: 263 GYTSWAIGYSVASLVRSLLRDQRRIHPVSVLAKGFHGIDEGDVFLSLPAQLGRNGVLGVV 322
Query: 326 SLGPLNEYERAGLEKAKKELAGSIQK 351
++ L + E L K+ K L +
Sbjct: 323 NV-HLTDEEAERLRKSAKTLWEVQSQ 347
>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 = 64.1 bits (156), Expect = 2e-11
Identities = 72/258 (27%), Positives = 106/258 (41%), Gaps = 37/258 (14%)
Query: 48 KVAVLGAAGGIGQPLA-------MLMKINPLVSVLHLYDVVNTPGVTADISH--MDTN-A 97
+V V GAAG IG L ML K P++ LHL D+ V + MD
Sbjct: 1 RVVVTGAAGQIGYALLPMIARGRMLGKDQPII--LHLLDIPPAMKVLEGVVMELMDCAFP 58
Query: 98 VVRGFLGQQQLEDALTGMDIVIIPAGVPRKPGMTRDDLFNINAGIVKTLCEGIAKCCPKA 157
++ G + A T +D+ I+ PRK GM R DL + N I K + K K
Sbjct: 59 LLDGVVPTHDPAVAFTDVDVAILVGAFPRKEGMERRDLLSKNVKIFKEQGRALDKLAKKD 118
Query: 158 I-VNLISNPVNSTVPIAAEVFKKVGTYDPKRLLGVTMLDVVRANTFVAEVLGLDPREV-D 215
V ++ NP N+ + + + PK +T LD RA VAE G+ +V +
Sbjct: 119 CKVLVVGNPANTNALVLSNYAPSI---PPKNFSALTRLDHNRALAQVAERAGVPVSDVKN 175
Query: 216 VPVVGGHAGVTILPLLSQ--VKPSCSLTPTEIDYLTDR----------IQNGGTEVVEAK 263
V + G H+ T P ++ V P + + D +Q G ++ A+
Sbjct: 176 VIIWGNHSS-TQYPDVNHATVTKGGKQKPVR-EAIKDDAYLDGEFITTVQQRGAAIIRAR 233
Query: 264 TGAGSATLSMAYAAAKFA 281
LS A +AAK A
Sbjct: 234 ------KLSSALSAAKAA 245
>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 = 63.0 bits (153), Expect = 4e-11
Identities = 40/137 (29%), Positives = 61/137 (44%), Gaps = 8/137 (5%)
Query: 101 GFLGQQQLEDALTGMDIVIIPAGVPRKPGMTRDDLFNINAGIVKTLCEGI---AKCCPKA 157
G + +LE+A +D + A VP KPG R DL N I K E + AK K
Sbjct: 47 GTIVTTKLEEAFKDIDCAFLVASVPLKPGEVRADLLTKNTPIFKATGEALSEYAKPTVKV 106
Query: 158 IVNLISNPVNSTVPIAAEVFKKVGTYDPKRLLGVTMLDVVRANTFVAEVLGLDPREVDVP 217
+V I NPVN+ +A K+ + + MLD RA + +A L + +
Sbjct: 107 LV--IGNPVNTNCLVAMLHAPKL---SAENFSSLCMLDHNRAVSRIASKLKVPVDHIYHV 161
Query: 218 VVGGHAGVTILPLLSQV 234
VV G+ +++ L+
Sbjct: 162 VVWGNHAESMVADLTHA 178
>gnl|CDD|133421 cd01336, MDH_cytoplasmic_cytosolic, Cytoplasmic and cytosolic
Malate dehydrogenases. MDH is one of the key enzymes in
the citric acid cycle, facilitating both the conversion
of malate to oxaloacetate and replenishing levels of
oxalacetate by reductive carboxylation of pyruvate.
Members of this subfamily are eukaryotic MDHs localized
to the cytoplasm and cytosol. MDHs are part of the
NAD(P)-binding Rossmann fold superfamily, which includes
a wide variety of protein families including the
NAD(P)-binding domains of alcohol dehydrogenases,
tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate dehydrogenases,
formate/glycerate dehydrogenases, siroheme synthases,
6-phosphogluconate dehydrogenases, aminoacid
dehydrogenases, repressor rex, and NAD-binding potassium
channel domains, among others.
Length = 325
Score = 62.6 bits (153), Expect = 6e-11
Identities = 67/260 (25%), Positives = 107/260 (41%), Gaps = 45/260 (17%)
Query: 48 KVAVLGAAGGIGQPLA-------MLMKINPLVSVLHLYDVVNTP------GVTADISHMD 94
+V V GAAG I L + P++ LHL D+ P GV ++ D
Sbjct: 4 RVLVTGAAGQIAYSLLPMIAKGDVFGPDQPVI--LHLLDI--PPALKALEGVVMEL--QD 57
Query: 95 TN-AVVRGFLGQQQLEDALTGMDIVIIPAGVPRKPGMTRDDLFNINAGIVKTLCEGIAKC 153
+++ + E+A +D+ I+ +PRK GM R DL N I K E + K
Sbjct: 58 CAFPLLKSVVATTDPEEAFKDVDVAILVGAMPRKEGMERKDLLKANVKIFKEQGEALDKY 117
Query: 154 CPKAI-VNLISNPVNSTVPIAAEVFKKVGTYDPKR-LLGVTMLDVVRANTFVAEVLGLDP 211
K + V ++ NP N+ I + + PK +T LD RA + +A LG+
Sbjct: 118 AKKNVKVLVVGNPANTNALILLKYAPSI----PKENFTALTRLDHNRAKSQIALKLGVPV 173
Query: 212 REV-DVPVVGGHAGVTILPLLSQVKPSCSLTPTEI-------DYLTD----RIQNGGTEV 259
+V +V + G H+ T P ++ + +L +Q G V
Sbjct: 174 SDVKNVIIWGNHSS-TQYPDVNHATVELNGKGKPAREAVKDDAWLNGEFISTVQKRGAAV 232
Query: 260 VEAKTGAGSATLSMAYAAAK 279
++A+ LS A +AAK
Sbjct: 233 IKAR------KLSSAMSAAK 246
>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 = 53.7 bits (130), Expect = 4e-08
Identities = 61/252 (24%), Positives = 95/252 (37%), Gaps = 31/252 (12%)
Query: 48 KVAVLGAAGGIGQPL-------AMLMKINPLVSVLHLYDVVNT----PGVTADISHMDTN 96
+VAV GAAG IG L M P++ L L ++ GV ++ +
Sbjct: 4 RVAVTGAAGQIGYSLLFRIASGEMFGPDQPVI--LQLLELPQALKALEGVAMEL---EDC 58
Query: 97 A--VVRGFLGQQQLEDALTGMDIVIIPAGVPRKPGMTRDDLFNINAGIVKTLCEGIAK-C 153
A ++ + A D ++ PR PGM R DL N I + +
Sbjct: 59 AFPLLAEIVITDDPNVAFKDADWALLVGAKPRGPGMERADLLKANGKIFTAQGKALNDVA 118
Query: 154 CPKAIVNLISNPVNSTVPIAAEVFKKVGTYDPKRLLGVTMLDVVRANTFVAEVLGLDPRE 213
V ++ NP N+ IA + + P +T LD RA + +A+ G+ +
Sbjct: 119 SRDVKVLVVGNPCNTNALIAMKNAPDI---PPDNFTAMTRLDHNRAKSQLAKKAGVPVTD 175
Query: 214 VDVPVVGGHAGVTILPLLSQVKPSCSLTPTEI-------DYLTDRIQNGGTEVVEAKTGA 266
V V+ G+ T P + I D +Q G +++A+ GA
Sbjct: 176 VKNMVIWGNHSPTQYPDFTNATIGGKPAAEVINDRAWLEDEFIPTVQKRGAAIIKAR-GA 234
Query: 267 GSATLSMAYAAA 278
SA S A AA
Sbjct: 235 SSAA-SAANAAI 245
>gnl|CDD|177744 PLN00135, PLN00135, malate dehydrogenase.
Length = 309
Score = 51.3 bits (123), Expect = 3e-07
Identities = 36/127 (28%), Positives = 63/127 (49%), Gaps = 5/127 (3%)
Query: 99 VRGFLGQQQLEDALTGMDIVIIPAGVPRKPGMTRDDLFNINAGIVKTLCEGIAKCC-PKA 157
++G + + +A G++I ++ G PRK GM R D+ + N I K+ + K P
Sbjct: 43 LKGVVATTDVVEACKGVNIAVMVGGFPRKEGMERKDVMSKNVSIYKSQASALEKHAAPDC 102
Query: 158 IVNLISNPVNSTVPIAAEVFKKVGTYDPKRLLGVTMLDVVRANTFVAEVLGLDPREV-DV 216
V +++NP N+ I E + K + +T LD RA ++E LG+ +V +V
Sbjct: 103 KVLVVANPANTNALILKEFAPSI---PEKNITCLTRLDHNRALGQISERLGVPVSDVKNV 159
Query: 217 PVVGGHA 223
+ G H+
Sbjct: 160 IIWGNHS 166
>gnl|CDD|235468 PRK05442, PRK05442, malate dehydrogenase; Provisional.
Length = 326
Score = 50.2 bits (121), Expect = 7e-07
Identities = 67/258 (25%), Positives = 104/258 (40%), Gaps = 45/258 (17%)
Query: 48 KVAVLGAAGGIGQPL-------AMLMKINPLVSVLHLYDVVNTPGVTADISHMDTNAVV- 99
+VAV GAAG IG L ML K P++ L L ++ P + A VV
Sbjct: 6 RVAVTGAAGQIGYSLLFRIASGDMLGKDQPVI--LQLLEI--PPALKA------LEGVVM 55
Query: 100 ----------RGFLGQQQLEDALTGMDIVIIPAGVPRKPGMTRDDLFNINAGIVKTLCEG 149
G + A D+ ++ PR PGM R DL N I +
Sbjct: 56 ELDDCAFPLLAGVVITDDPNVAFKDADVALLVGARPRGPGMERKDLLEANGAIFTAQGKA 115
Query: 150 IAKCCPKAI-VNLISNPVNSTVPIAAEVFKKVGTYDPKRLLGVTMLDVVRANTFVAEVLG 208
+ + + + V ++ NP N+ IA + + + +T LD RA + +A G
Sbjct: 116 LNEVAARDVKVLVVGNPANTNALIAMKNAPDL---PAENFTAMTRLDHNRALSQLAAKAG 172
Query: 209 LDPREV-DVPVVGGHAGVTILPLLSQV----KPSCSLTPTEIDYLTD----RIQNGGTEV 259
+ ++ + V G H+ T P KP+ + + +L D +Q G +
Sbjct: 173 VPVADIKKMTVWGNHSA-TQYPDFRHATIDGKPAAEVINDQ-AWLEDTFIPTVQKRGAAI 230
Query: 260 VEAKTGAGSATLSMAYAA 277
+EA+ GA SA S A AA
Sbjct: 231 IEAR-GASSAA-SAANAA 246
>gnl|CDD|215060 PLN00112, PLN00112, malate dehydrogenase (NADP); Provisional.
Length = 444
Score = 36.7 bits (85), Expect = 0.015
Identities = 28/79 (35%), Positives = 34/79 (43%), Gaps = 10/79 (12%)
Query: 125 PRKPGMTRDDLFNINAGIV----KTLCEGIAKCCPKAIVNLISNPVNSTVPIAAEVFKKV 180
PR PGM R DL +IN I K L E ++ K IV + NP N+ I K
Sbjct: 187 PRGPGMERADLLDINGQIFAEQGKALNEVASRNV-KVIV--VGNPCNTNALIC---LKNA 240
Query: 181 GTYDPKRLLGVTMLDVVRA 199
K +T LD RA
Sbjct: 241 PNIPAKNFHALTRLDENRA 259
>gnl|CDD|224403 COG1486, CelF, Alpha-galactosidases/6-phospho-beta-glucosidases,
family 4 of glycosyl hydrolases [Carbohydrate transport
and metabolism].
Length = 442
Score = 36.1 bits (84), Expect = 0.023
Identities = 51/219 (23%), Positives = 75/219 (34%), Gaps = 66/219 (30%)
Query: 45 PGFKVAVLGAAGGIGQP--LAMLMKINPLVSV--LHLYDV---------------VNTPG 85
FK+ ++G G P L + + V L LYD+ V G
Sbjct: 2 KKFKIVIIGG-GSTYTPKLLLGDLARTEELPVRELALYDIDEERLKIIAILAKKLVEEAG 60
Query: 86 VTADISHMDTNAVVRGFLGQQQLEDALTGMDIVIIPA------------GVPRKPGMTRD 133
+ T+ +AL G D VI +P K G+
Sbjct: 61 APVKV-EATTD-----------RREALEGADFVITQIRVGGLEAREKDERIPLKHGLYGQ 108
Query: 134 DLFNINAGIVKTL---------CEGIAKCCPKAIVNLISNPVNSTVPIAAEVFKKVGTYD 184
+ N GI L + + K CP A + +NP AA V + V
Sbjct: 109 E-TNGPGGIFYGLRTIPVILDIAKDMEKVCPNAWMLNYTNP-------AAIVTEAVRRLY 160
Query: 185 PK-RLLGVTMLDVVRANTF-VAEVLGLDPRE-VDVPVVG 220
PK +++G+ +AEVLGL+PRE + V G
Sbjct: 161 PKIKIVGLC--HGPIGIAMELAEVLGLEPREDLRYRVAG 197
>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 = 35.4 bits (82), Expect = 0.034
Identities = 25/93 (26%), Positives = 43/93 (46%), Gaps = 4/93 (4%)
Query: 50 AVLGAAGGIGQPLA-MLMKINPLVSVLHLYDVVNTPGVTADISHMDTNAVVRG-FLGQQQ 107
V G G +G+ + +L++ L V ++D+ +P + D S + + G +Q
Sbjct: 1 LVTGGGGFLGRHIVRLLLREGELQEV-RVFDLRFSPELLEDFSKLQVITYIEGDVTDKQD 59
Query: 108 LEDALTGMDIVIIPAGVPRKPGM-TRDDLFNIN 139
L AL G D+VI A + G RD + +N
Sbjct: 60 LRRALQGSDVVIHTAAIIDVFGKAYRDTIMKVN 92
>gnl|CDD|172654 PRK14166, PRK14166, bifunctional 5,10-methylene-tetrahydrofolate
dehydrogenase/ 5,10-methylene-tetrahydrofolate
cyclohydrolase; Provisional.
Length = 282
Score = 35.0 bits (80), Expect = 0.046
Identities = 23/100 (23%), Positives = 41/100 (41%), Gaps = 29/100 (29%)
Query: 46 GFKVAVLGAAGGIGQPLA-MLMKINPLVSVLHLYDVVNTPGVTADISHMDTNAVVRGFLG 104
G ++GA+ +G+P+A ML+ VSV H+ T D+S A
Sbjct: 157 GKDAVIIGASNIVGRPMATMLLNAGATVSVCHIK--------TKDLSLYTRQA------- 201
Query: 105 QQQLEDALTGMDIVIIPAGVPR--KPGMTRDDLFNINAGI 142
D++I+ AG + M ++ + ++ GI
Sbjct: 202 -----------DLIIVAAGCVNLLRSDMVKEGVIVVDVGI 230
>gnl|CDD|184553 PRK14176, PRK14176, bifunctional 5,10-methylene-tetrahydrofolate
dehydrogenase/ 5,10-methylene-tetrahydrofolate
cyclohydrolase; Provisional.
Length = 287
Score = 33.2 bits (76), Expect = 0.16
Identities = 24/102 (23%), Positives = 41/102 (40%), Gaps = 29/102 (28%)
Query: 46 GFKVAVLGAAGGIGQPLA-MLMKINPLVSVLHLYDVVNTPGVTADISHMDTNAVVRGFLG 104
G ++G + +G+P+A ML+ N VSV H++ T D+ +A
Sbjct: 164 GKNAVIVGHSNVVGKPMAAMLLNRNATVSVCHVF--------TDDLKKYTLDA------- 208
Query: 105 QQQLEDALTGMDIVIIPAGVPR--KPGMTRDDLFNINAGIVK 144
DI+++ GV K M ++ + GI K
Sbjct: 209 -----------DILVVATGVKHLIKADMVKEGAVIFDVGITK 239
>gnl|CDD|201603 pfam01118, Semialdhyde_dh, Semialdehyde dehydrogenase, NAD binding
domain. This Pfam entry contains the following members:
N-acetyl-glutamine semialdehyde dehydrogenase (AgrC)
Aspartate-semialdehyde dehydrogenase.
Length = 121
Score = 31.0 bits (71), Expect = 0.31
Identities = 22/79 (27%), Positives = 37/79 (46%), Gaps = 3/79 (3%)
Query: 48 KVAVLGAAGGIGQPLAMLMKINPLVSVLHLYDVVNTPGVTADISHMDTNAVVRGFLGQQQ 107
KVA++GA G +GQ L L+ +P + ++ L + G ++ L +
Sbjct: 1 KVAIVGATGYVGQELLRLLAEHPPLELVALVASSRSAGKKVAFAYPILEGGKDLLL-EDV 59
Query: 108 LEDALTGMDIVII--PAGV 124
+ L +DIV + PAGV
Sbjct: 60 DPEDLKDVDIVFLALPAGV 78
>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 = 32.3 bits (73), Expect = 0.35
Identities = 21/55 (38%), Positives = 27/55 (49%), Gaps = 7/55 (12%)
Query: 125 PRKPGMTRDDLFNINAGIV----KTLCEGIAKCCPKAIVNLISNPVNSTVPIAAE 175
PR PGM R DL +IN I K L +K C V ++ NP N+ IA +
Sbjct: 131 PRGPGMERADLLDINGQIFADQGKALNAVASKNCK---VLVVGNPCNTNALIAMK 182
>gnl|CDD|133433 cd05297, GH4_alpha_glucosidase_galactosidase, Glycoside Hydrolases
Family 4; Alpha-glucosidases and alpha-galactosidases.
Glucosidases cleave glycosidic bonds to release glucose
from oligosaccharides. Alpha-glucosidases and
alpha-galactosidases release alpha-D-glucose and
alpha-D-galactose, respectively, via the hydrolysis of
alpha-glycopyranoside bonds. Some bacteria
simultaneously translocate and phosphorylate
disaccharides via the phosphoenolpyruvate-dependent
phosphotransferase system (PEP-PTS). After
translocation, these phospho-disaccharides may be
hydrolyzed by the GH4 glycoside hydrolases such as the
alpha-glucosidases. Other organsisms (such as archaea
and Thermotoga maritima) lack the PEP-PTS system, but
have several enzymes normally associated with the
PEP-PTS operon. Alpha-glucosidases and
alpha-galactosidases are part of the NAD(P)-binding
Rossmann fold superfamily, which includes a wide variety
of protein families including the NAD(P)-binding domains
of alcohol dehydrogenases, tyrosine-dependent
oxidoreductases, glyceraldehyde-3-phosphate
dehydrogenases, formate/glycerate dehydrogenases,
siroheme synthases, 6-phosphogluconate dehydrogenases,
aminoacid dehydrogenases, repressor rex, and NAD-binding
potassium channel domains, among others.
Length = 423
Score = 32.2 bits (74), Expect = 0.46
Identities = 34/149 (22%), Positives = 44/149 (29%), Gaps = 58/149 (38%)
Query: 108 LEDALTGMDIVIIPAGVPRKPGMTRDDLFNINA---------------GIVKTL------ 146
+AL G D VI V D F I GI + L
Sbjct: 68 RREALDGADFVINTIQVGGHEYTETD--FEIPEKYGYYQTVGDTSGPGGIFRALRTIPVL 125
Query: 147 ---CEGIAKCCPKAIVNLISNPV-------NSTVPIAA-----EVFKKVGTYDPKRLLGV 191
I + CP A + +NP+ N PI V GT +
Sbjct: 126 LDIARDIEELCPDAWLLNYANPMAELTWALNRYTPIKTVGLCHGVQ---GTAE------- 175
Query: 192 TMLDVVRANTFVAEVLGLDPREVDVPVVG 220
+A++LG P EVD V G
Sbjct: 176 ----------QLAKLLGEPPEEVDYQVAG 194
>gnl|CDD|182031 PRK09694, PRK09694, helicase Cas3; Provisional.
Length = 878
Score = 31.7 bits (72), Expect = 0.62
Identities = 15/53 (28%), Positives = 25/53 (47%), Gaps = 5/53 (9%)
Query: 241 TPTEIDYLTDRI-QNGGTEVVEAKTGAGSATLSMAYA----AAKFADACLRGL 288
P ++ L D + G ++EA TG+G ++AYA AD+ + L
Sbjct: 286 QPRQLQTLVDALPLQPGLTIIEAPTGSGKTEAALAYAWRLIDQGLADSIIFAL 338
>gnl|CDD|129954 TIGR00876, tal_mycobact, transaldolase, mycobacterial type. This
model describes one of three related but easily
separable famiiles of known and putative transaldolases.
This family and the family typified by E. coli TalA and
TalB both contain experimentally verified examples
[Energy metabolism, Pentose phosphate pathway].
Length = 350
Score = 31.2 bits (70), Expect = 0.76
Identities = 21/70 (30%), Positives = 34/70 (48%), Gaps = 1/70 (1%)
Query: 243 TEIDYLTDRIQNGGTEVVEAKTGAGSATLSMAYAAAKFADA-CLRGLRGDAGVIECAYVA 301
EID L D+I + ++A+ G +A L+ A F D+ C R ++ DA ++ A
Sbjct: 199 KEIDKLLDKIGSRQALELQAQAGIANARLAYATYREVFEDSDCYRQIKQDAAKLQRPLFA 258
Query: 302 STVTELPFFA 311
ST + A
Sbjct: 259 STGVKNNDLA 268
>gnl|CDD|236016 PRK07424, PRK07424, bifunctional sterol desaturase/short chain
dehydrogenase; Validated.
Length = 406
Score = 30.8 bits (70), Expect = 1.2
Identities = 27/87 (31%), Positives = 41/87 (47%), Gaps = 17/87 (19%)
Query: 46 GFKVAVLGAAGGIGQPLAMLMKINPLVSVLHLYD--VV----NTPGVTADISHMDTNA-V 98
G VAV GA+G +GQ L+ LH VV N+ +T +I+ D
Sbjct: 178 GKTVAVTGASGTLGQ---------ALLKELHQQGAKVVALTSNSDKITLEINGEDLPVKT 228
Query: 99 VRGFLGQQ-QLEDALTGMDIVIIPAGV 124
+ +GQ+ L + L +DI+II G+
Sbjct: 229 LHWQVGQEAALAELLEKVDILIINHGI 255
>gnl|CDD|222146 pfam13460, NAD_binding_10, NADH(P)-binding.
Length = 182
Score = 30.0 bits (68), Expect = 1.3
Identities = 16/79 (20%), Positives = 26/79 (32%), Gaps = 7/79 (8%)
Query: 49 VAVLGAAGGIGQPLAMLMKINPLVSVLHLYDVVNTPGVTADISHMDTNAVVRGFLGQQQL 108
+AV+GA G G+ L + + + P V + L
Sbjct: 1 IAVIGATGKTGRRLVKELLARG----HQVTALSRNPSKAPA---PGVTPVQKDLFDLADL 53
Query: 109 EDALTGMDIVIIPAGVPRK 127
+AL G+D V+ G
Sbjct: 54 AEALAGVDAVVDAFGARPD 72
>gnl|CDD|171820 PRK12936, PRK12936, 3-ketoacyl-(acyl-carrier-protein) reductase
NodG; Reviewed.
Length = 245
Score = 30.3 bits (68), Expect = 1.3
Identities = 28/99 (28%), Positives = 46/99 (46%), Gaps = 16/99 (16%)
Query: 46 GFKVAVLGAAGGIGQPLAMLMKINPLVSVLHLYDVVNTPGVTADI--------SHMDTNA 97
G K V GA+GGIG+ +A L+ + LH V + A++ +++
Sbjct: 6 GRKALVTGASGGIGEEIARLLHAQGAIVGLHGTRVEKLEALAAELGERVKIFPANLSDRD 65
Query: 98 VVRGFLGQQQLEDALTGMDIVIIPAGVPRKPGMTRDDLF 136
V+ Q+ E L G+DI++ AG+ T+D LF
Sbjct: 66 EVKAL--GQKAEADLEGVDILVNNAGI------TKDGLF 96
>gnl|CDD|216783 pfam01915, Glyco_hydro_3_C, Glycosyl hydrolase family 3 C-terminal
domain. This domain is involved in catalysis and may be
involved in binding beta-glucan. This domain is found
associated with pfam00933.
Length = 221
Score = 30.0 bits (68), Expect = 1.4
Identities = 18/85 (21%), Positives = 30/85 (35%), Gaps = 6/85 (7%)
Query: 205 EVLGLDPREVDVPVVGGHAGVTILPLL---SQVKPSCSLTPTEIDYLTDRIQNGGTEVV- 260
+L L ++ + V+G +A P T +D + R N V
Sbjct: 9 NLLPLSKKKRKIAVIGPNADDPPNGGGGWSGTGNP--PYLVTPLDGIRARAGNATVVVYG 66
Query: 261 EAKTGAGSATLSMAYAAAKFADACL 285
+ ++ A AAAK AD +
Sbjct: 67 GSNLEDDDTGIAEAVAAAKDADVAI 91
>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 = 29.4 bits (67), Expect = 1.5
Identities = 27/100 (27%), Positives = 39/100 (39%), Gaps = 29/100 (29%)
Query: 46 GFKVAVLGAAGGIGQPLA-MLMKINPLVSVLHLYDVVNTPGVTADISHMDTNAVVRGFLG 104
G KV V+G + +G+PLA +L+ N V+V H T ++ A
Sbjct: 44 GKKVVVVGRSNIVGKPLAALLLNRNATVTVCHSK--------TKNLKEHTKQA------- 88
Query: 105 QQQLEDALTGMDIVIIPAGVPR--KPGMTRDDLFNINAGI 142
DIVI+ G P K M + I+ GI
Sbjct: 89 -----------DIVIVAVGKPGLVKGDMVKPGAVVIDVGI 117
>gnl|CDD|189960 pfam01371, Trp_repressor, Trp repressor protein. This protein
binds to tryptophan and represses transcription of the
Trp operon.
Length = 88
Score = 28.4 bits (64), Expect = 1.7
Identities = 11/41 (26%), Positives = 18/41 (43%), Gaps = 8/41 (19%)
Query: 240 LTPTEIDYLTDRIQ------NGGT--EVVEAKTGAGSATLS 272
LTP E + L R++ G + + GA AT++
Sbjct: 27 LTPDEREALAQRLRIAKELLRGELSQREIAQELGASIATIT 67
>gnl|CDD|179337 PRK01810, PRK01810, DNA polymerase IV; Validated.
Length = 407
Score = 30.0 bits (68), Expect = 1.9
Identities = 12/25 (48%), Positives = 16/25 (64%)
Query: 173 AAEVFKKVGTYDPKRLLGVTMLDVV 197
A+ +FK+ DP RLLGVT D+
Sbjct: 321 ASRLFKQHWNGDPVRLLGVTATDLE 345
>gnl|CDD|172669 PRK14181, PRK14181, bifunctional 5,10-methylene-tetrahydrofolate
dehydrogenase/ 5,10-methylene-tetrahydrofolate
cyclohydrolase; Provisional.
Length = 287
Score = 29.4 bits (66), Expect = 2.6
Identities = 25/82 (30%), Positives = 35/82 (42%), Gaps = 25/82 (30%)
Query: 46 GFKVAVLGAAGGIGQPL-AMLMKINPLVSVLHLYDVVNTPGVTADISHMDTNAVVRGFLG 104
G VA++G + +G+PL A+LM+ H DTNA V
Sbjct: 153 GRHVAIVGRSNIVGKPLAALLMQ-----------------------KHPDTNATVTLLHS 189
Query: 105 Q-QQLEDALTGMDIVIIPAGVP 125
Q + L + L DI+I GVP
Sbjct: 190 QSENLTEILKTADIIIAAIGVP 211
>gnl|CDD|178267 PLN02661, PLN02661, Putative thiazole synthesis.
Length = 357
Score = 29.4 bits (66), Expect = 2.6
Identities = 17/33 (51%), Positives = 20/33 (60%), Gaps = 2/33 (6%)
Query: 247 YLTDRIQNGGTEVVEAKTGAGSATLSMAYAAAK 279
Y+TD I T+VV GAGSA LS AY +K
Sbjct: 83 YMTDMITYADTDVV--IVGAGSAGLSCAYELSK 113
>gnl|CDD|117458 pfam08891, YfcL, YfcL protein. This family of proteins are
functionally uncharacterized. THey are related to the
short YfcL protein from E. coli.
Length = 85
Score = 27.6 bits (62), Expect = 2.8
Identities = 12/41 (29%), Positives = 19/41 (46%)
Query: 314 VRLGRAGIEEIYSLGPLNEYERAGLEKAKKELAGSIQKGVS 354
+ + + E L L + LEKAK EL+ + Q V+
Sbjct: 36 LAVAQLEEEGETDLEALKQKMEQSLEKAKGELSPADQALVN 76
>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 = 28.8 bits (65), Expect = 3.8
Identities = 16/80 (20%), Positives = 29/80 (36%), Gaps = 10/80 (12%)
Query: 48 KVAVLGAAGGIGQPLAMLMKINPLVSVLHLYDVVN-TPGVTADISHMDTNAVVRGFLGQ- 105
VLGA+G IG+ +A L +V+ + A + ++ +V
Sbjct: 1 TAHVLGASGPIGREVARE-----LRRRGWDVRLVSRSGSKLAWLPGVE---IVAADAMDA 52
Query: 106 QQLEDALTGMDIVIIPAGVP 125
+ A G D++ A
Sbjct: 53 SSVIAAARGADVIYHCANPA 72
>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 = 28.8 bits (65), Expect = 4.4
Identities = 21/80 (26%), Positives = 31/80 (38%), Gaps = 16/80 (20%)
Query: 48 KVAVLGAAGGIGQPLAMLMKINPLVSVLHLYD-----VVNTPGVTADISHMDTNAVVR-- 100
K+A+ GA G +G P+VS L V+ P T+ + V
Sbjct: 1 KIAIAGATGTLG---------GPIVSALLASPGFTVTVLTRPSSTSSNEFQPSGVKVVPV 51
Query: 101 GFLGQQQLEDALTGMDIVII 120
+ + L AL G+D VI
Sbjct: 52 DYASHESLVAALKGVDAVIS 71
>gnl|CDD|172679 PRK14191, PRK14191, bifunctional 5,10-methylene-tetrahydrofolate
dehydrogenase/ 5,10-methylene-tetrahydrofolate
cyclohydrolase; Provisional.
Length = 285
Score = 28.6 bits (64), Expect = 4.8
Identities = 20/53 (37%), Positives = 27/53 (50%), Gaps = 9/53 (16%)
Query: 46 GFKVAVLGAAGGIGQPLAMLM-KINPLVSVLHLYDVVNTPGVTADISHMDTNA 97
G V ++GA+ +G+PLAMLM VSV H+ T D+S NA
Sbjct: 157 GKDVVIIGASNIVGKPLAMLMLNAGASVSVCHIL--------TKDLSFYTQNA 201
>gnl|CDD|233220 TIGR00978, asd_EA, aspartate-semialdehyde dehydrogenase
(non-peptidoglycan organisms). Two closely related
families of aspartate-semialdehyde dehydrogenase are
found. They differ by a deep split in phylogenetic and
percent identity trees and in gap patterns. Separate
models are built for the two types in order to exclude
the USG-1 protein, found in several species, which is
specifically related to the Bacillus subtilis type of
aspartate-semialdehyde dehydrogenase. Members of this
type are found primarily in organisms that lack
peptidoglycan [Amino acid biosynthesis, Aspartate
family].
Length = 341
Score = 28.6 bits (64), Expect = 5.0
Identities = 11/31 (35%), Positives = 17/31 (54%)
Query: 48 KVAVLGAAGGIGQPLAMLMKINPLVSVLHLY 78
+VAVLGA G +GQ L+ +P + +
Sbjct: 2 RVAVLGATGLVGQKFVKLLAKHPYFELAKVV 32
>gnl|CDD|178031 PLN02409, PLN02409, serine--glyoxylate aminotransaminase.
Length = 401
Score = 28.6 bits (64), Expect = 5.4
Identities = 13/40 (32%), Positives = 20/40 (50%), Gaps = 7/40 (17%)
Query: 90 ISHMDTNAVVRGFLGQQQLEDALTGMDIVIIPAGVPRKPG 129
I H+ G + + QL AL G+++V+ G P K G
Sbjct: 348 IGHL-------GNVNELQLLGALAGVEMVLKDVGYPVKLG 380
>gnl|CDD|237633 PRK14168, PRK14168, bifunctional 5,10-methylene-tetrahydrofolate
dehydrogenase/ 5,10-methylene-tetrahydrofolate
cyclohydrolase; Provisional.
Length = 297
Score = 28.3 bits (63), Expect = 7.1
Identities = 28/112 (25%), Positives = 46/112 (41%), Gaps = 28/112 (25%)
Query: 31 SGLGRMDCRAKGGSPGFKVAVLGAAGGIGQPLAMLMKINPLVSVLHLYDVVNTPGVTADI 90
+G+ M R+ + G +V V+G + +G+P+A +M PG A +
Sbjct: 146 AGIQEMLVRSGVETSGAEVVVVGRSNIVGKPIANMM-------------TQKGPGANATV 192
Query: 91 SHMDTNAVVRGFLGQQQLEDALTGMDIVIIPAGVPR-------KPGMTRDDL 135
+ + T + L DI+I+ AGVP KPG T D+
Sbjct: 193 TIVHT--------RSKNLARHCQRADILIVAAGVPNLVKPEWIKPGATVIDV 236
>gnl|CDD|222360 pfam13749, HATPase_c_4, ATP-dependent DNA helicase recG
C-terminal. This domain may well interact selectively
and non-covalently with ATP, adenosine 5'-triphosphate,
a universally important coenzyme and enzyme regulator.
Length = 88
Score = 26.3 bits (59), Expect = 7.6
Identities = 9/36 (25%), Positives = 13/36 (36%), Gaps = 6/36 (16%)
Query: 9 NQRIARIAAHLHPPTLQIEGESSGLGRM--DCRAKG 42
N +A + L IE SG+ R+ G
Sbjct: 40 NPLLADLFRRLGL----IEERGSGIPRILDAMEEAG 71
>gnl|CDD|184555 PRK14183, PRK14183, bifunctional 5,10-methylene-tetrahydrofolate
dehydrogenase/ 5,10-methylene-tetrahydrofolate
cyclohydrolase; Provisional.
Length = 281
Score = 27.9 bits (62), Expect = 9.0
Identities = 27/102 (26%), Positives = 42/102 (41%), Gaps = 27/102 (26%)
Query: 46 GFKVAVLGAAGGIGQPLAMLMKINPLVSVLHLYDVVNTPGVTADISHMDTNAVVRGFLGQ 105
G V V+GA+ +G+P+A L+ +N T DI H+ T
Sbjct: 157 GKDVCVVGASNIVGKPMAALL--------------LNA-NATVDICHIFT---------- 191
Query: 106 QQLEDALTGMDIVIIPAGVPR--KPGMTRDDLFNINAGIVKT 145
+ L+ DIVI+ G P M ++ I+ GI +T
Sbjct: 192 KDLKAHTKKADIVIVGVGKPNLITEDMVKEGAIVIDIGINRT 233
>gnl|CDD|187647 cd08943, R1PA_ADH_SDR_c, rhamnulose-1-phosphate aldolase/alcohol
dehydrogenase, classical (c) SDRs. This family has
bifunctional proteins with an N-terminal aldolase and a
C-terminal classical SDR domain. One member is
identified as a rhamnulose-1-phosphate aldolase/alcohol
dehydrogenase. The SDR domain has a canonical SDR
glycine-rich NAD(P) binding motif and a match to the
characteristic active site triad. However, it lacks an
upstream active site Asn typical of SDRs. 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 = 250
Score = 27.7 bits (62), Expect = 9.8
Identities = 25/91 (27%), Positives = 37/91 (40%), Gaps = 19/91 (20%)
Query: 48 KVA-VLGAAGGIGQPLA----------MLMKINPLVSVLHLYDVVNTP---GVTADISHM 93
KVA V G A GIG +A ++ I+P ++ P GV D++
Sbjct: 2 KVALVTGGASGIGLAIAKRLAAEGAAVVVADIDPEIAEKVAEAAQGGPRALGVQCDVT-- 59
Query: 94 DTNAVVRGFLGQQQLEDALTGMDIVIIPAGV 124
V F +Q G+DIV+ AG+
Sbjct: 60 SEAQVQSAF---EQAVLEFGGLDIVVSNAGI 87
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
0.318 0.136 0.393
Gapped
Lambda K H
0.267 0.0830 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 18,558,235
Number of extensions: 1860124
Number of successful extensions: 2205
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2136
Number of HSP's successfully gapped: 91
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 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 60 (26.7 bits)