RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 026051
(244 letters)
>gnl|CDD|215058 PLN00106, PLN00106, malate dehydrogenase.
Length = 323
Score = 492 bits (1269), Expect = e-178
Identities = 185/237 (78%), Positives = 202/237 (85%)
Query: 1 MDIVIIPAGVPRKPGMTRDDLFNINAGIVKTLCEGIAKCCPKAIVNLISNPVNSTVPIAA 60
D+VIIPAGVPRKPGMTRDDLFNINAGIVKTLCE +AK CP A+VN+ISNPVNSTVPIAA
Sbjct: 87 ADLVIIPAGVPRKPGMTRDDLFNINAGIVKTLCEAVAKHCPNALVNIISNPVNSTVPIAA 146
Query: 61 EVFKKVGTYDPKRLLGVTMLDVVRANTFVAEVLGLDPREVDVPVVGGHAGVTILPLLSQV 120
EV KK G YDPK+L GVT LDVVRANTFVAE GLDP +VDVPVVGGHAG+TILPLLSQ
Sbjct: 147 EVLKKAGVYDPKKLFGVTTLDVVRANTFVAEKKGLDPADVDVPVVGGHAGITILPLLSQA 206
Query: 121 KPSCSLTPTEIDYLTDRIQNGGTEVVEAKTGAGSATLSMAYAAAKFADACLRGLRGDAGV 180
P S T EI+ LT RIQNGGTEVVEAK GAGSATLSMAYAAA+FADACLRGL G+A V
Sbjct: 207 TPKVSFTDEEIEALTKRIQNGGTEVVEAKAGAGSATLSMAYAAARFADACLRGLNGEADV 266
Query: 181 IECAYVASTVTELPFFASKVRLGRAGIEEIYSLGPLNEYERAGLEKAKKELAGSIQK 237
+EC+YV S VTELPFFASKVRLGR G+EE+ LGPL+EYE+ GLE K EL SI+K
Sbjct: 267 VECSYVQSEVTELPFFASKVRLGRNGVEEVLGLGPLSEYEQKGLEALKPELKASIEK 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 = 443 bits (1141), Expect = e-159
Identities = 167/242 (69%), Positives = 196/242 (80%)
Query: 1 MDIVIIPAGVPRKPGMTRDDLFNINAGIVKTLCEGIAKCCPKAIVNLISNPVNSTVPIAA 60
D+V+IPAGVPRKPGMTRDDLFNINAGIV+ L +AK CPKA++ +ISNPVNSTVPIAA
Sbjct: 69 ADVVVIPAGVPRKPGMTRDDLFNINAGIVRDLATAVAKACPKALILIISNPVNSTVPIAA 128
Query: 61 EVFKKVGTYDPKRLLGVTMLDVVRANTFVAEVLGLDPREVDVPVVGGHAGVTILPLLSQV 120
EV KK G YDPKRL GVT LDVVRANTFVAE+LGLDP +V+VPV+GGH+GVTILPLLSQ
Sbjct: 129 EVLKKAGVYDPKRLFGVTTLDVVRANTFVAELLGLDPAKVNVPVIGGHSGVTILPLLSQC 188
Query: 121 KPSCSLTPTEIDYLTDRIQNGGTEVVEAKTGAGSATLSMAYAAAKFADACLRGLRGDAGV 180
+P + EI+ LT RIQ GG EVV+AK GAGSATLSMAYA A+FA++ LRGL+G+ GV
Sbjct: 189 QPPFTFDQEEIEALTHRIQFGGDEVVKAKAGAGSATLSMAYAGARFANSLLRGLKGEKGV 248
Query: 181 IECAYVASTVTELPFFASKVRLGRAGIEEIYSLGPLNEYERAGLEKAKKELAGSIQKGVS 240
IECAYV S VTE PFFA+ V LG+ G+E+ LG LN+YE+ LE A EL +I+KGV
Sbjct: 249 IECAYVESDVTEAPFFATPVELGKNGVEKNLGLGKLNDYEKKLLEAALPELKKNIEKGVD 308
Query: 241 FV 242
FV
Sbjct: 309 FV 310
>gnl|CDD|235340 PRK05086, PRK05086, malate dehydrogenase; Provisional.
Length = 312
Score = 344 bits (884), Expect = e-120
Identities = 141/243 (58%), Positives = 169/243 (69%), Gaps = 1/243 (0%)
Query: 2 DIVIIPAGVPRKPGMTRDDLFNINAGIVKTLCEGIAKCCPKAIVNLISNPVNSTVPIAAE 61
D+V+I AGV RKPGM R DLFN+NAGIVK L E +AK CPKA + +I+NPVN+TV IAAE
Sbjct: 71 DVVLISAGVARKPGMDRSDLFNVNAGIVKNLVEKVAKTCPKACIGIITNPVNTTVAIAAE 130
Query: 62 VFKKVGTYDPKRLLGVTMLDVVRANTFVAEVLGLDPREVDVPVVGGHAGVTILPLLSQVK 121
V KK G YD +L GVT LDV+R+ TFVAE+ G P EV+VPV+GGH+GVTILPLLSQV
Sbjct: 131 VLKKAGVYDKNKLFGVTTLDVIRSETFVAELKGKQPGEVEVPVIGGHSGVTILPLLSQV- 189
Query: 122 PSCSLTPTEIDYLTDRIQNGGTEVVEAKTGAGSATLSMAYAAAKFADACLRGLRGDAGVI 181
P S T E+ LT RIQN GTEVVEAK G GSATLSM AAA+F + +R L+G+ GV+
Sbjct: 190 PGVSFTEQEVADLTKRIQNAGTEVVEAKAGGGSATLSMGQAAARFGLSLVRALQGEQGVV 249
Query: 182 ECAYVASTVTELPFFASKVRLGRAGIEEIYSLGPLNEYERAGLEKAKKELAGSIQKGVSF 241
ECAYV FFA V LG+ G+EE +G L+ +E+ LE L I G F
Sbjct: 250 ECAYVEGDGKYARFFAQPVLLGKNGVEERLPIGTLSAFEQNALEGMLDTLKKDIALGEEF 309
Query: 242 VRK 244
V K
Sbjct: 310 VNK 312
>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 = 335 bits (862), Expect = e-117
Identities = 145/244 (59%), Positives = 183/244 (75%), Gaps = 1/244 (0%)
Query: 2 DIVIIPAGVPRKPGMTRDDLFNINAGIVKTLCEGIAKCCPKAIVNLISNPVNSTVPIAAE 61
D+V+IPAGVPRKPGMTRDDLFN+NAGIVK L +A+ CPKA++ +I+NPVNSTVPIAAE
Sbjct: 69 DVVVIPAGVPRKPGMTRDDLFNVNAGIVKDLVAAVAESCPKAMILVITNPVNSTVPIAAE 128
Query: 62 VFKKVGTYDPKRLLGVTMLDVVRANTFVAEVLGLDPREVDVPVVGGHAGVTILPLLSQVK 121
V KK G YDP +L GVT LD+VRANTFVAE+ G DP EV+VPV+GGH+G TI+PL+SQ
Sbjct: 129 VLKKKGVYDPNKLFGVTTLDIVRANTFVAELKGKDPMEVNVPVIGGHSGETIIPLISQCP 188
Query: 122 PSCSLTPTEIDYLTDRIQNGGTEVVEAKTGAGSATLSMAYAAAKFADACLRGLRGDAGVI 181
T +++ L RIQN GTEVV+AK GAGSATLSMA+A A+F + +RGL+G+ GV+
Sbjct: 189 GKVLFTEDQLEALIHRIQNAGTEVVKAKAGAGSATLSMAFAGARFVLSLVRGLKGEEGVV 248
Query: 182 ECAYVAS-TVTELPFFASKVRLGRAGIEEIYSLGPLNEYERAGLEKAKKELAGSIQKGVS 240
ECAYV S VTE FFA+ + LG+ G+E+ +G L+ +E L A EL +I+KG
Sbjct: 249 ECAYVESDGVTEATFFATPLLLGKNGVEKRLGIGKLSSFEEKMLNGALPELKKNIKKGEE 308
Query: 241 FVRK 244
FV
Sbjct: 309 FVAS 312
>gnl|CDD|240360 PTZ00325, PTZ00325, malate dehydrogenase; Provisional.
Length = 321
Score = 318 bits (818), Expect = e-110
Identities = 146/244 (59%), Positives = 184/244 (75%), Gaps = 3/244 (1%)
Query: 2 DIVIIPAGVPRKPGMTRDDLFNINAGIVKTLCEGIAKCCPKAIVNLISNPVNSTVPIAAE 61
D+V+I AGVPRKPGMTRDDLFN NA IV+ L +A PKAIV ++SNPVNSTVPIAAE
Sbjct: 78 DLVLICAGVPRKPGMTRDDLFNTNAPIVRDLVAAVASSAPKAIVGIVSNPVNSTVPIAAE 137
Query: 62 VFKKVGTYDPKRLLGVTMLDVVRANTFVAEVLGLDPREVDVPVVGGHAGVTILPLLSQVK 121
KK G YDP++L GVT LDVVRA FVAE LG++P +V+VPVVGGH+GVTI+PLLSQ
Sbjct: 138 TLKKAGVYDPRKLFGVTTLDVVRARKFVAEALGMNPYDVNVPVVGGHSGVTIVPLLSQT- 196
Query: 122 PSCSLTPTEIDYLTDRIQNGGTEVVEAKTGAGSATLSMAYAAAKFADACLRGLRGDAGVI 181
SL +++ +T R+Q GG EVV+AK GAGSATLSMAYAAA+++ + L+ LRGD G++
Sbjct: 197 -GLSLPEEQVEQITHRVQVGGDEVVKAKEGAGSATLSMAYAAAEWSTSVLKALRGDKGIV 255
Query: 182 ECAYVASTVT-ELPFFASKVRLGRAGIEEIYSLGPLNEYERAGLEKAKKELAGSIQKGVS 240
ECA+V S + E PFF+S V LG+ G+E + +GPLN YE LE A +L +I+KG+
Sbjct: 256 ECAFVESDMRPECPFFSSPVELGKEGVERVLPIGPLNAYEEELLEAAVPDLKKNIEKGLE 315
Query: 241 FVRK 244
F RK
Sbjct: 316 FARK 319
>gnl|CDD|223117 COG0039, Mdh, Malate/lactate dehydrogenases [Energy production and
conversion].
Length = 313
Score = 205 bits (523), Expect = 3e-65
Identities = 93/251 (37%), Positives = 135/251 (53%), Gaps = 20/251 (7%)
Query: 2 DIVIIPAGVPRKPGMTRDDLFNINAGIVKTLCEGIAKCCPKAIVNLISNPVNSTVPIAAE 61
DIV+I AGVPRKPGMTR DL NA IVK + + IAK P AIV +++NPV+ IA +
Sbjct: 71 DIVVITAGVPRKPGMTRLDLLEKNAKIVKDIAKAIAKYAPDAIVLVVTNPVDILTYIAMK 130
Query: 62 VFKKVGTYDPKRLLG-VTMLDVVRANTFVAEVLGLDPREVDVPVVGGHAGVTILPLLSQV 120
R++G T+LD R TF+AE LG+ P++V V+G H G T++PL SQ
Sbjct: 131 FSGF----PKNRVIGSGTVLDSARFRTFLAEKLGVSPKDVHAYVIGEH-GDTMVPLWSQA 185
Query: 121 ----KPSCSL----TPTEIDYLTDRIQNGGTEVVEAKTGAGSATLSMAYAAAKFADACLR 172
KP L T +++ L +R++N G E++EAK A A A+ +A LR
Sbjct: 186 TVGGKPLEELLKEDTEEDLEELIERVRNAGAEIIEAKG--AGTYYGPAAALARMVEAILR 243
Query: 173 GLRGDAGVIECAYV-ASTVTELPFFASKVRLGRAGIEEIYSLGPLNEYERAGLEKAKKEL 231
+ + Y+ E +F LG+ G+EEI L L++ E+ L+K+ +EL
Sbjct: 244 DEK--RVLPVSVYLDGEYGVEDVYFGVPAVLGKNGVEEILEL-LLSDDEQEKLDKSAEEL 300
Query: 232 AGSIQKGVSFV 242
+I+ V
Sbjct: 301 KKNIELVKELV 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 = 184 bits (468), Expect = 5e-59
Identities = 81/177 (45%), Positives = 108/177 (61%), Gaps = 16/177 (9%)
Query: 78 TMLDVVRANTFVAEVLGLDPREVDVPVVGGHAG----------VTILPLLSQVKPSCSLT 127
T LD RA TF+AE G+DPR V+V V+G H+G VTI+PL+SQVK + T
Sbjct: 1 TTLDTARARTFLAEKFGVDPRSVNVYVIGEHSGTQFPDWSHAKVTIIPLISQVKENLKDT 60
Query: 128 PTEIDYLTDRIQNGGTEVVEAKTGAGSATLSMAYAAAKFADACLRGLRGD--AGVIECAY 185
E++ L +R+QN G EV+EAK AGS T SMAYAAA+ A A LRG G GV Y
Sbjct: 61 DWELEELIERVQNAGYEVIEAK--AGSTTYSMAYAAARIAKAILRGTGGVLSVGVYLDGY 118
Query: 186 VASTVTELPFFASKVRLGRAGIEEIYSLGPLNEYERAGLEKAKKELAGSIQKGVSFV 242
+ +F+ V LG+ G+E++ + PLN++ER LEK+ EL I+KG +FV
Sbjct: 119 YG--SPDDIYFSVPVVLGKDGVEKVVEILPLNDFEREKLEKSAAELKKEIEKGFAFV 173
>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 = 144 bits (366), Expect = 5e-42
Identities = 83/246 (33%), Positives = 129/246 (52%), Gaps = 26/246 (10%)
Query: 2 DIVIIPAGVPRKPGMTRDDLFNINAGIVKTLCEGIAKCCPKAIVNLISNPVNSTVPIAAE 61
D+V+I AG+PRKPGM+RDDL NA IVK + E I K P AIV +++NP++
Sbjct: 68 DVVVITAGIPRKPGMSRDDLLGTNAKIVKEVAENIKKYAPNAIVIVVTNPLDVMT----Y 123
Query: 62 VFKKVGTYDPKRLLGV-TMLDVVRANTFVAEVLGLDPREVDVPVVGGHAGVTILPLLSQ- 119
V K + R++G+ +LD R F+AE LG+ ++V V+GGH G T++PL
Sbjct: 124 VAYKASGFPRNRVIGMAGVLDSARFRYFIAEELGVSVKDVQAMVLGGH-GDTMVPLPRYS 182
Query: 120 ----VKPSCSLTPTEIDYLTDRIQNGGTEVVEAKTGAGSATLSMAYAAAKFADACLRGLR 175
+ + +T EID + +R +NGG E+V GSA + A A A+ +A L+ +
Sbjct: 183 TVGGIPLTELITKEEIDEIVERTRNGGAEIVNLL-KTGSAYYAPAAAIAEMVEAILKDKK 241
Query: 176 GDAGVIECA------YVASTVTELPFFASKVRLGRAGIEEIYSLGPLNEYERAGLEKAKK 229
V+ C+ Y + F V LG+ G+E+I L L + E+ +K+ +
Sbjct: 242 ---RVLPCSAYLEGEYGIKDI----FVGVPVVLGKNGVEKIIEL-DLTDEEKEAFDKSVE 293
Query: 230 ELAGSI 235
+ I
Sbjct: 294 SVKELI 299
>gnl|CDD|180477 PRK06223, PRK06223, malate dehydrogenase; Reviewed.
Length = 307
Score = 139 bits (353), Expect = 5e-40
Identities = 85/252 (33%), Positives = 134/252 (53%), Gaps = 34/252 (13%)
Query: 2 DIVIIPAGVPRKPGMTRDDLFNINAGIVKTLCEGIAKCCPKAIVNLISNPVNSTVPIAAE 61
D+V+I AGVPRKPGM+RDDL INA I+K + EGI K P AIV +++NPV++ +A
Sbjct: 72 DVVVITAGVPRKPGMSRDDLLGINAKIMKDVAEGIKKYAPDAIVIVVTNPVDAMTYVA-- 129
Query: 62 VFKKVGTYDPKRLLGV-TMLDVVRANTFVAEVLGLDPREVDVPVVGGHAGVTILPLLSQV 120
K + R++G+ +LD R TF+AE L + ++V V+GGH G +++PL+
Sbjct: 130 --LKESGFPKNRVIGMAGVLDSARFRTFIAEELNVSVKDVTAFVLGGH-GDSMVPLVRYS 186
Query: 121 ----KPSCSLTPTE-IDYLTDRIQNGGTEVVEAKTGAGSATLSMAYAAAKFADACLRG-- 173
P L E +D + +R + GG E+V GSA + A + A+ +A L+
Sbjct: 187 TVGGIPLEDLLSKEKLDEIVERTRKGGAEIVGLL-KTGSAYYAPAASIAEMVEAILKDKK 245
Query: 174 --------LRGDAGVIECAYVASTVTELPFFASKVRLGRAGIEEIYSLGPLNEYERAGLE 225
L G+ G V +P V+LG+ G+E+I L L++ E+A +
Sbjct: 246 RVLPCSAYLEGEYG------VKDVYVGVP-----VKLGKNGVEKIIEL-ELDDEEKAAFD 293
Query: 226 KAKKELAGSIQK 237
K+ + + I+
Sbjct: 294 KSVEAVKKLIEA 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 = 114 bits (287), Expect = 9e-31
Identities = 62/234 (26%), Positives = 99/234 (42%), Gaps = 51/234 (21%)
Query: 2 DIVIIPAGVPRKPGMTRDDLFNINAGIVKTLCEGIAKCCPKAIVNLISNPVNSTVPIAAE 61
D+VII AGV RKPGM R DL N IVK + + I K P A + ++SNPV+ I
Sbjct: 72 DVVIITAGVGRKPGMGRLDLLKRNVPIVKEIGDNIEKYSPDAWIIVVSNPVD----IITY 127
Query: 62 VFKKVGTYDPKRLLGVTMLDVVRANTFVAEVLGLDPREVDVPVVGGHAGVTILPLLSQVK 121
+ + ++++G+ LD +R +AE LG+DP +V V ++G H G + +P S V+
Sbjct: 128 LVWRYSGLPKEKVIGLGTLDPIRFRRILAEKLGVDPDDVKVYILGEHGG-SQVPDWSTVR 186
Query: 122 PSCSLTPTEIDYLTDRIQNGGTEVVEAKTGAGSATLSMAYAAAKFADACLRGLRGDAGVI 181
+A + A + L D G I
Sbjct: 187 -------------------------------------IATSIADLIRSLLN----DEGEI 205
Query: 182 ECAYV----ASTVTELPFFASKVRLGRAGIEEIYSLGPLNEYERAGLEKAKKEL 231
V + + + +G+ G+EE + L ++E L+K+ L
Sbjct: 206 LPVGVRNNGQIGIPDDVVVSVPCIVGKNGVEEPIEV-GLTDFELEKLQKSADTL 258
>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 = 109 bits (276), Expect = 1e-30
Identities = 37/76 (48%), Positives = 46/76 (60%), Gaps = 3/76 (3%)
Query: 1 MDIVIIPAGVPRKPGMTRDDLFNINAGIVKTLCEGIAKCCPKAIVNLISNPVNSTVPIAA 60
D+V+I AGVPRKPGMTR DL N NAGI K + IAK P AIV ++SNPV+ IA
Sbjct: 70 ADVVVITAGVPRKPGMTRLDLLNRNAGIFKDIVPAIAKSAPDAIVLVVSNPVDILTYIAW 129
Query: 61 EVFKKVGTYDPKRLLG 76
+V G + +
Sbjct: 130 KVS---GLPPERVIGS 142
>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 = 113 bits (283), Expect = 6e-30
Identities = 75/236 (31%), Positives = 129/236 (54%), Gaps = 18/236 (7%)
Query: 2 DIVIIPAGVPRKPGMTRDDLFNINAGIVKTLCEGIAKCCPKAIVNLISNPVNSTVPIAAE 61
DIV+I AG+PRKPGM+R+DL ++NAGIV+ + I + P I+ ++SNP+++ +A +
Sbjct: 71 DIVVITAGLPRKPGMSREDLLSMNAGIVREVTGRIMEHSPNPIIVVVSNPLDAMTYVAWQ 130
Query: 62 VFKKVGTYDPKRLLGVT-MLDVVRANTFVAEVLGLDPREVDVPVVGGHAGVTILPL---- 116
+ +R++G +LD R TF+A LG+ ++V V+GGH G ++PL
Sbjct: 131 ----KSGFPKERVIGQAGVLDSARFRTFIAMELGVSVQDVTACVLGGH-GDAMVPLVRYS 185
Query: 117 -LSQVKPSCSLTPTEIDYLTDRIQNGGTEVVEAKTGAGSATLSMAYAAAKFADACLRGLR 175
++ + + ++ I + +R + GG E+V GSA + A + + +A L+ +
Sbjct: 186 TVAGIPVADLISAERIAEIVERTRKGGGEIVNL-LKQGSAYYAPAASVVEMVEAILKDRK 244
Query: 176 GDAGVIEC-AYVASTV-TELPFFASKVRLGRAGIEEIYSLGPLNEYERAGLEKAKK 229
V+ C AY+ + + V LG+ G+E IY L L++ E A L K+ K
Sbjct: 245 ---RVLPCAAYLDGQYGIDGIYVGVPVILGKNGVEHIYEL-KLDQSELALLNKSAK 296
>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 = 112 bits (283), Expect = 7e-30
Identities = 73/240 (30%), Positives = 117/240 (48%), Gaps = 22/240 (9%)
Query: 2 DIVIIPAGVPRKPGMTRDDLFNINAGIVKTLCEGIAKCCPKAIVNLISNPVNSTVPIAAE 61
DIV+I AG PRKPG TR DL N NA I++++ + K P AI+ ++SNPV+ I
Sbjct: 68 DIVVITAGAPRKPGETRLDLINRNAPILRSVITNLKKYGPDAIILVVSNPVD----ILTY 123
Query: 62 VFKKVGTYDPKRLLGV-TMLDVVRANTFVAEVLGLDPREVDVPVVGGHAGVTILPLLSQV 120
V +K+ R++G T+LD R + +AE L +DP+ V V+G H G + + S
Sbjct: 124 VAQKLSGLPKNRVIGSGTLLDSARFRSLLAEKLDVDPQSVHAYVLGEH-GDSQVVAWSTA 182
Query: 121 ----KPSCSLTPT---EIDYLTDRIQNGGTEVVEAKTGAGSATLSMAYAAAKFADACLRG 173
P L P +++ + + ++ G E++ K G+ +A A A + L
Sbjct: 183 TVGGLPLEELAPFTKLDLEAIEEEVRTSGYEIIRLK---GATNYGIATAIADIVKSILLD 239
Query: 174 LRGDAGVIECAYVASTVTELP--FFASKVRLGRAGIEEIYSLGPLNEYERAGLEKAKKEL 231
R V+ + V + + +GR G+ I + PL E E A L+K+ + L
Sbjct: 240 ER---RVLPVSAVQEGQYGIEDVALSVPAVVGREGVVRILEI-PLTEDEEAKLQKSAEAL 295
>gnl|CDD|173409 PTZ00117, PTZ00117, malate dehydrogenase; Provisional.
Length = 319
Score = 106 bits (266), Expect = 3e-27
Identities = 73/237 (30%), Positives = 116/237 (48%), Gaps = 31/237 (13%)
Query: 2 DIVIIPAGVPRKPGMTRDDLFNINAGIVKTLCEGIAKCCPKAIVNLISNPVNSTVPIAAE 61
D+V+I AGV RK MTR+DL IN I+K++ E + K CP A V ++NP++ +
Sbjct: 75 DVVVITAGVQRKEEMTREDLLTINGKIMKSVAESVKKYCPNAFVICVTNPLD----CMVK 130
Query: 62 VFKKVGTYDPKRLLGVT-MLDVVRANTFVAEVLGLDPREVDVPVVGGHAGVTILPL---- 116
VF++ ++ G+ +LD R +AE LG+ P +V V+GGH G ++PL
Sbjct: 131 VFQEKSGIPSNKICGMAGVLDSSRFRCNLAEKLGVSPGDVSAVVIGGH-GDLMVPLPRYC 189
Query: 117 ------LSQVKPSCSLTPTEIDYLTDRIQNGGTEVVEAKTGAGSATLSMAYAAAKFADAC 170
LS ++T EI+ + + +N G E+V+ GSA + A A +A
Sbjct: 190 TVNGIPLSDFVKKGAITEKEINEIIKKTRNMGGEIVKL-LKKGSAFFAPAAAIVAMIEAY 248
Query: 171 LRGLRGDAGVIECA------YVASTVTELPFFASKVRLGRAGIEEIYSLGPLNEYER 221
L+ + V+ C+ Y + F V +G GIE++ L LN E+
Sbjct: 249 LKDEK---RVLVCSVYLNGQYNCKNL----FVGVPVVIGGKGIEKVIEL-ELNAEEK 297
>gnl|CDD|173376 PTZ00082, PTZ00082, L-lactate dehydrogenase; Provisional.
Length = 321
Score = 102 bits (256), Expect = 8e-26
Identities = 77/251 (30%), Positives = 130/251 (51%), Gaps = 36/251 (14%)
Query: 2 DIVIIPAGVPRKPGMT-----RDDLFNINAGIVKTLCEGIAKCCPKAIVNLISNPVNSTV 56
D+VI+ AG+ ++PG + RDDL +NA I+ + EGI K CP A V +I+NP++ V
Sbjct: 76 DVVIVTAGLTKRPGKSDKEWNRDDLLPLNAKIMDEVAEGIKKYCPNAFVIVITNPLDVMV 135
Query: 57 PIAAEVFKKVGTYDPKRLLGVT-MLDVVRANTFVAEVLGLDPREVDVPVVGGHAGVTILP 115
++ ++ ++ G+ +LD R T++AE LG++PR+V V+G H G ++P
Sbjct: 136 ----KLLQEHSGLPKNKVCGMAGVLDSSRLRTYIAEKLGVNPRDVHASVIGAH-GDKMVP 190
Query: 116 L----------LSQVKPSCSLTPTEIDYLTDRIQNGGTEVVEAKTGAGSATLSMAYAAAK 165
L LS+ +T EID + +R +N G E+V+ G GSA + A AA +
Sbjct: 191 LPRYVTVGGIPLSEFIKKGLITQEEIDEIVERTRNTGKEIVDL-LGTGSAYFAPAAAAIE 249
Query: 166 FADACLRGLRGDAGVIECA------YVASTVTELPFFASKVRLGRAGIEEIYSLGPLNEY 219
A+A L+ + V+ C+ Y + + + +G G+E+I L L
Sbjct: 250 MAEAYLKDKK---RVLPCSAYLEGQYGHKDI----YMGTPAVIGANGVEKIIEL-DLTPE 301
Query: 220 ERAGLEKAKKE 230
E+ +++ KE
Sbjct: 302 EQKKFDESIKE 312
>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 = 96.9 bits (242), Expect = 6e-24
Identities = 66/245 (26%), Positives = 115/245 (46%), Gaps = 26/245 (10%)
Query: 1 MDIVIIPAGVPRKPGMTRDDLFNINAGIVKTLCEGIAKCCPKAIVNLISNPVNSTVPIAA 60
D+V+I AG P+KPG TR +L N I+K++ + K I + +NPV+ I
Sbjct: 65 ADLVVITAGAPQKPGETRLELVGRNVRIMKSIVPEVVKSGFDGIFLVATNPVD----ILT 120
Query: 61 EVFKKVGTYDPKRLLGV-TMLDVVRANTFVAEVLGLDPREVDVPVVGGH----------A 109
V K+ + R++G T+LD R +AE LG+DP+ V ++G H A
Sbjct: 121 YVAWKLSGFPKNRVIGSGTVLDTARLRYLLAEKLGVDPQSVHAYIIGEHGDSEVPVWSSA 180
Query: 110 GVTILPLLSQVKPSCSLTPTEIDYLTDRIQNGGTEVVEAKTGAGSATLSMAYAAAKFADA 169
+ +PLL +K + T +++ + +++ E++ K G+ + A A+ +A
Sbjct: 181 TIGGVPLLDYLKAKGTETDLDLEEIEKEVRDAAYEIINRK---GATYYGIGMAVARIVEA 237
Query: 170 CLRGLRGD---AGVIECAYVASTVTELPFFASKVRLGRAGIEEIYSLGPLNEYERAGLEK 226
L + ++ Y V + LGR G+EEI L PL++ E+ +K
Sbjct: 238 ILHDENRVLPVSAYLDGEYGIKDV----YIGVPAVLGRNGVEEIIEL-PLSDEEKEAFQK 292
Query: 227 AKKEL 231
+ + L
Sbjct: 293 SAETL 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 = 96.0 bits (240), Expect = 1e-23
Identities = 75/258 (29%), Positives = 114/258 (44%), Gaps = 41/258 (15%)
Query: 1 MDIVIIPAGVPRKPGMTRDDLFNINAGIVKTLCEGIAKCCPKAIVNLISNPVNSTVPIAA 60
DIV+I AG P+KPG TR DL NA I+K++ I I + SNPV+ +
Sbjct: 69 ADIVVITAGAPQKPGETRLDLLEKNAKIMKSIVPKIKASGFDGIFLVASNPVD----VIT 124
Query: 61 EVFKKVGTYDPKRLLGV-TMLDVVRANTFVAEVLGLDPREVDVPVVGGH----------- 108
V +K+ R++G T LD R +AE L +DPR V V+G H
Sbjct: 125 YVVQKLSGLPKNRVIGTGTSLDTARLRRALAEKLNVDPRSVHAYVLGEHGDSQFVAWSTV 184
Query: 109 --AGVTILPLLSQVKPSCSLTPTEIDYLTDRIQNGGTEVVEAKTGAGSATLSMAYAAAKF 166
G +L LL + K L+ ++D + + ++ G E++ K G+ +A A A+
Sbjct: 185 TVGGKPLLDLLKEGK----LSELDLDEIEEDVRKAGYEIINGK---GATYYGIATALARI 237
Query: 167 ADACLRGLRGDAGVI-------ECAYVASTVTELPFFASKVRLGRAGIEEIYSLGPLNEY 219
A L D I + Y V + +GR G+EE+ L L E
Sbjct: 238 VKAILN----DENAILPVSAYLDGEYGEKDV----YIGVPAIIGRNGVEEVIEL-DLTEE 288
Query: 220 ERAGLEKAKKELAGSIQK 237
E+ EK+ + +I+K
Sbjct: 289 EQEKFEKSADIIKENIKK 306
>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 = 92.9 bits (231), Expect = 3e-22
Identities = 68/250 (27%), Positives = 113/250 (45%), Gaps = 45/250 (18%)
Query: 2 DIVIIPAGVPRKPGMTRDDLFNINAGIVKTLCEGIAKCCPKAIVNLISNPVNSTVPIAAE 61
DIVII AGVPRK GM+R DL NA IVK + IA+ P + +++NPV+ A
Sbjct: 74 DIVIITAGVPRKEGMSRLDLAKKNAKIVKKYAKQIAEFAPDTKILVVTNPVDVMTYKAL- 132
Query: 62 VFKKVGTYDPKRLLGV-TMLDVVRANTFVAEVLGLDPREVDVPVVGGHAGVTILPLLSQV 120
K +D R+ G+ T LD +R +A+ + EV ++G H G +++PL+S
Sbjct: 133 ---KESGFDKNRVFGLGTHLDSLRFKVAIAKHFNVHISEVHTRIIGEH-GDSMVPLISST 188
Query: 121 K----PSCSLTPTE---IDYLTDRIQNGGTEVVEAKTGA----GSATLSMAYAAAK---- 165
P + ++ + + ++N G ++ K G+ SA ++ A
Sbjct: 189 SIGGIPIKRFPEYKDFDVEKIVETVKNAGQNIISLKGGSEYGPASAISNLVRTIANDERR 248
Query: 166 ------FADACLRGLRGDAGVIECAYVASTVTELPFFASKVRLGRAGIEEIYSLGPLNEY 219
+ + + G+R C V V+LG+ GIEEI + +++
Sbjct: 249 ILTVSTYLEGEIDGIRD-----VCIGVP------------VKLGKNGIEEIVPI-EMDDD 290
Query: 220 ERAGLEKAKK 229
ER K+ +
Sbjct: 291 EREAFRKSAE 300
>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 = 77.9 bits (193), Expect = 5e-17
Identities = 70/257 (27%), Positives = 113/257 (43%), Gaps = 41/257 (15%)
Query: 2 DIVIIPAGVPRKPGMTRDDLFNINAGIVKTLCEGIAKCCPKAIVNLISNPVNSTVPIAAE 61
D+V+I AG +KPG TR DL N I K + I K P AI+ +++NPV+ +
Sbjct: 69 DVVVITAGANQKPGETRLDLLKRNVAIFKEIIPQILKYAPDAILLVVTNPVD----VLTY 124
Query: 62 VFKKVGTYDPKRLLGV-TMLDVVRANTFVAEVLGLDPREVDVPVVGGH------------ 108
V K+ P R++G T+LD R + E LG+DPR V ++G H
Sbjct: 125 VAYKLSGLPPNRVIGSGTVLDTARFRYLLGEHLGVDPRSVHAYIIGEHGDSEVAVWSSAN 184
Query: 109 -AGVTILPLLSQVKPSCSLTPTEIDYLTDRIQNGGTEVVEAKTGAGSATLSMAYAAAKFA 167
GV + + + + ++N E++E K G+ ++ A A+
Sbjct: 185 IGGVPLDEFCKLCGRPF--DEEVREEIFEEVRNAAYEIIERK---GATYYAIGLALARIV 239
Query: 168 DACLRGLRGD-------AGVIECAYVASTVT-ELPFFASKVRLGRAGIEEIYSLGPLNEY 219
+A LR D + +++ Y V LP V GR+G+E + PL+E
Sbjct: 240 EAILR----DENSVLTVSSLLDGQYGIKDVALSLP---CIV--GRSGVERVLPP-PLSEE 289
Query: 220 ERAGLEKAKKELAGSIQ 236
E L + + L +I+
Sbjct: 290 EEEALRASAEVLKEAIE 306
>gnl|CDD|178836 PRK00066, ldh, L-lactate dehydrogenase; Reviewed.
Length = 315
Score = 72.2 bits (178), Expect = 7e-15
Identities = 65/252 (25%), Positives = 105/252 (41%), Gaps = 40/252 (15%)
Query: 1 MDIVIIPAGVPRKPGMTRDDLFNINAGIVKTLCEGIAKCCPKAIVNLISNPVNSTVPIAA 60
D+V+I AG P+KPG TR DL N I K++ + I + SNPV+ I
Sbjct: 74 ADLVVITAGAPQKPGETRLDLVEKNLKIFKSIVGEVMASGFDGIFLVASNPVD----ILT 129
Query: 61 EVFKKVGTYDPKRLLGV-TMLDVVRANTFVAEVLGLDPREVDVPVVGGH----------A 109
K+ + +R++G T LD R ++E L +DPR V ++G H A
Sbjct: 130 YATWKLSGFPKERVIGSGTSLDSARFRYMLSEKLDVDPRSVHAYIIGEHGDTEFPVWSHA 189
Query: 110 GVTILPLLSQVKPSCSLTPTEIDYLTDRIQNGGTEVVEAKTGAGSATLSMAYAAAKFADA 169
V +PL ++ + ++D + + +++ E++E K G+ +A A A+ A
Sbjct: 190 NVAGVPLEEYLEENEQYDEEDLDEIFENVRDAAYEIIEKK---GATYYGIAMALARITKA 246
Query: 170 CLRG----------LRGDAGVIECAYVASTVTELPFFASKVRLGRAGIEEIYSLGPLNEY 219
L L G G + + + R GI EI L PLN+
Sbjct: 247 ILNNENAVLPVSAYLEGQYGEEDV-----------YIGVPAVVNRNGIREIVEL-PLNDD 294
Query: 220 ERAGLEKAKKEL 231
E+ + L
Sbjct: 295 EKQKFAHSADVL 306
>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 = 72.0 bits (177), Expect = 8e-15
Identities = 48/138 (34%), Positives = 70/138 (50%), Gaps = 12/138 (8%)
Query: 2 DIVIIPAGVPRKPGMT--RDDLFNINAGIVKTLCEGIAKCCPKAIVNLISNPVNSTVPIA 59
DI++I AG PG T R DL NA I++ + I K +A++ LI+NP++ V IA
Sbjct: 70 DIIVITAGPSIDPGNTDDRLDLAQTNAKIIREIMGNITKVTKEAVIILITNPLDIAVYIA 129
Query: 60 AEVFKKVGTYDPKRLLGV-TMLDVVRANTFVAEVLGLDPREVDVPVVGGHAGVTILPLLS 118
A F Y +++G TMLD R VA+ G+DP+ V V+G H G P+ S
Sbjct: 130 ATEFD----YPANKVIGTGTMLDTARLRRIVADKYGVDPKNVTGYVLGEH-GSHAFPVWS 184
Query: 119 QVKPSCSLTPTEIDYLTD 136
V ++ +D L
Sbjct: 185 LV----NIAGLPLDELEA 198
>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 = 71.5 bits (176), Expect = 1e-14
Identities = 63/249 (25%), Positives = 102/249 (40%), Gaps = 21/249 (8%)
Query: 2 DIVIIPAGVPRKPGMTRDDLFNINAGIVKTLCEGIAKCCPKAIVNLISNPVNSTVPIAAE 61
+VI+ AG + G +R DL N I K + + K P AI+ ++SNPV+ I
Sbjct: 73 KVVIVTAGARQNEGESRLDLVQRNVDIFKGIIPKLVKYSPNAILLVVSNPVD----IMTY 128
Query: 62 VFKKVGTYDPKRLLGV-TMLDVVRANTFVAEVLGLDPREVDVPVVGGH--------AGVT 112
V K+ R++G LD R +AE LG+ P V ++G H +GV
Sbjct: 129 VAWKLSGLPKHRVIGSGCNLDSARFRYLIAERLGVAPSSVHGWIIGEHGDSSVPVWSGVN 188
Query: 113 I--LPLLSQVK-PSCSLTPTEIDYLTDRIQNGGTEVVEAKTGAGSATLSMAYAAAKFADA 169
+ + L P + + ++ + EV++ K G + ++ + A DA
Sbjct: 189 VAGVRLQDLNPDIGTDKDPEKWKEVHKQVVDSAYEVIKLK---GYTSWAIGLSVADLVDA 245
Query: 170 CLRGLRGDAGVIECAYVASTVTELPFFASKVRLGRAGIEEIYSLGPLNEYERAGLEKAKK 229
LR V + + F + LG GI + PL E E+ L+K+
Sbjct: 246 ILRNTGRVHSVSTLVKGLHGIEDEVFLSLPCILGENGITHVIKQ-PLTEEEQEKLQKSAD 304
Query: 230 ELAGSIQKG 238
L +QK
Sbjct: 305 TLW-EVQKQ 312
>gnl|CDD|178212 PLN02602, PLN02602, lactate dehydrogenase.
Length = 350
Score = 67.9 bits (166), Expect = 2e-13
Identities = 60/251 (23%), Positives = 108/251 (43%), Gaps = 25/251 (9%)
Query: 2 DIVIIPAGVPRKPGMTRDDLFNINAGIVKTLCEGIAKCCPKAIVNLISNPVNSTVPIAAE 61
D+ I+ AG + PG +R +L N + + + +AK P I+ ++SNPV+ +
Sbjct: 107 DLCIVTAGARQIPGESRLNLLQRNVALFRKIIPELAKYSPDTILLIVSNPVD----VLTY 162
Query: 62 VFKKVGTYDPKRLLGV-TMLDVVRANTFVAEVLGLDPREVDVPVVGGH------------ 108
V K+ + R++G T LD R +A+ L ++ ++V +VG H
Sbjct: 163 VAWKLSGFPANRVIGSGTNLDSSRFRFLIADHLDVNAQDVQAYIVGEHGDSSVALWSSVS 222
Query: 109 -AGVTILPLLSQVKPSCSLTPTEIDYLTDRIQNGGTEVVEAKTGAGSATLSMAYAAAKFA 167
GV +L L K + ++ + + + EV++ K G + ++ Y+ A
Sbjct: 223 VGGVPVLSFLE--KQQIAYEKETLEEIHRAVVDSAYEVIKLK---GYTSWAIGYSVASLV 277
Query: 168 DACLRGLRGDAGVIECAYVASTVTELPFFAS-KVRLGRAGIEEIYSLGPLNEYERAGLEK 226
+ LR R V A + E F S +LGR G+ + ++ L + E L K
Sbjct: 278 RSLLRDQRRIHPVSVLAKGFHGIDEGDVFLSLPAQLGRNGVLGVVNV-HLTDEEAERLRK 336
Query: 227 AKKELAGSIQK 237
+ K L +
Sbjct: 337 SAKTLWEVQSQ 347
>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 = 65.0 bits (159), Expect = 2e-12
Identities = 55/175 (31%), Positives = 74/175 (42%), Gaps = 18/175 (10%)
Query: 2 DIVIIPAGVPRKPGMTRDDLFNINAGIVKTLCEGIAKCC-PKAIVNLISNPVNSTVPIAA 60
D+ I+ PRKPGM R DL NA I K E + K P V ++ NP N+ IA
Sbjct: 78 DVAILVGAFPRKPGMERADLLRKNAKIFKEQGEALNKVAKPTVKVLVVGNPANTNALIAL 137
Query: 61 EVFKKVGTYDPKRLLGVTMLDVVRANTFVAEVLGLDPREV-DVPVVGGHAGVTILPLLSQ 119
K PK +T LD RA VA LG+ +V +V + G H+ T +P LS
Sbjct: 138 ---KNAPNLPPKNFTALTRLDHNRAKAQVARKLGVRVSDVKNVIIWGNHSN-TQVPDLSN 193
Query: 120 VK----PSCSLTPTEIDY------LTDRIQNGGTEVVEAKTGAGSATLSMAYAAA 164
+D +Q G +++ + GA SA S A A A
Sbjct: 194 AVVYGPGGTEWVLDLLDEEWLNDEFVKTVQKRGAAIIKKR-GASSA-ASAAKAIA 246
>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 = 63.1 bits (154), Expect = 9e-12
Identities = 49/172 (28%), Positives = 77/172 (44%), Gaps = 15/172 (8%)
Query: 2 DIVIIPAGVPRKPGMTRDDLFNINAGIVKTLCEGIAKCCPKAI-VNLISNPVNSTVPIAA 60
D ++ PRKPGM R DL + N I K + + K K + V ++ NP N+ IA+
Sbjct: 81 DAALLVGAFPRKPGMERADLLSKNGKIFKEQGKALNKVAKKDVKVLVVGNPANTNALIAS 140
Query: 61 EVFKKVGTYDPKRLLGVTMLDVVRANTFVAEVLGLDPREVDVPVVGGHAGVTILPLLSQ- 119
+ + PK +T LD RA +A G+ +V ++ G+ T +P +
Sbjct: 141 KNAPDI---PPKNFSAMTRLDHNRAKYQLAAKAGVPVSDVKNVIIWGNHSNTQVPDFTHA 197
Query: 120 ---VKPSCSLTPTEIDYL----TDRIQNGGTEVVEAKTGAGSATLSMAYAAA 164
+P + + +L +Q G V+EA+ GA SA S A AA
Sbjct: 198 TVDGRPVKEVIKDD-KWLEGEFIPTVQQRGAAVIEAR-GASSA-ASAANAAI 246
>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 = 53.3 bits (128), Expect = 2e-08
Identities = 36/123 (29%), Positives = 54/123 (43%), Gaps = 8/123 (6%)
Query: 1 MDIVIIPAGVPRKPGMTRDDLFNINAGIVKTLCEGI---AKCCPKAIVNLISNPVNSTVP 57
+D + A VP KPG R DL N I K E + AK K +V I NPVN+
Sbjct: 61 IDCAFLVASVPLKPGEVRADLLTKNTPIFKATGEALSEYAKPTVKVLV--IGNPVNTNCL 118
Query: 58 IAAEVFKKVGTYDPKRLLGVTMLDVVRANTFVAEVLGLDPREVDVPVVGGHAGVTILPLL 117
+A K+ + + MLD RA + +A L + + VV G+ +++ L
Sbjct: 119 VAMLHAPKL---SAENFSSLCMLDHNRAVSRIASKLKVPVDHIYHVVVWGNHAESMVADL 175
Query: 118 SQV 120
+
Sbjct: 176 THA 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 = 51.5 bits (124), Expect = 9e-08
Identities = 48/179 (26%), Positives = 76/179 (42%), Gaps = 25/179 (13%)
Query: 1 MDIVIIPAGVPRKPGMTRDDLFNINAGIVKTLCEGIAKCCPKAI-VNLISNPVNSTVPIA 59
+D+ I+ +PRK GM R DL N I K E + K K + V ++ NP N+ I
Sbjct: 79 VDVAILVGAMPRKEGMERKDLLKANVKIFKEQGEALDKYAKKNVKVLVVGNPANTNALIL 138
Query: 60 AEVFKKVGTYDPKR-LLGVTMLDVVRANTFVAEVLGLDPREV-DVPVVGGHAGVTILPLL 117
+ + PK +T LD RA + +A LG+ +V +V + G H+ T P +
Sbjct: 139 LKYAPSI----PKENFTALTRLDHNRAKSQIALKLGVPVSDVKNVIIWGNHSS-TQYPDV 193
Query: 118 SQVKPSCSLTPTEI-------DYLTD----RIQNGGTEVVEAKTGAGSATLSMAYAAAK 165
+ + +L +Q G V++A+ LS A +AAK
Sbjct: 194 NHATVELNGKGKPAREAVKDDAWLNGEFISTVQKRGAAVIKAR------KLSSAMSAAK 246
>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 = 51.0 bits (122), Expect = 1e-07
Identities = 49/181 (27%), Positives = 75/181 (41%), Gaps = 25/181 (13%)
Query: 1 MDIVIIPAGVPRKPGMTRDDLFNINAGIVKTLCEGIAKCCPKAI-VNLISNPVNSTVPIA 59
+D+ I+ PRK GM R DL + N I K + K K V ++ NP N+ +
Sbjct: 76 VDVAILVGAFPRKEGMERRDLLSKNVKIFKEQGRALDKLAKKDCKVLVVGNPANTNALVL 135
Query: 60 AEVFKKVGTYDPKRLLGVTMLDVVRANTFVAEVLGLDPREV-DVPVVGGHAGVTILPLLS 118
+ + PK +T LD RA VAE G+ +V +V + G H+ T P ++
Sbjct: 136 SNYAPSI---PPKNFSALTRLDHNRALAQVAERAGVPVSDVKNVIIWGNHSS-TQYPDVN 191
Query: 119 Q--VKPSCSLTPTEIDYLTDR----------IQNGGTEVVEAKTGAGSATLSMAYAAAKF 166
V P + + D +Q G ++ A+ LS A +AAK
Sbjct: 192 HATVTKGGKQKPVR-EAIKDDAYLDGEFITTVQQRGAAIIRAR------KLSSALSAAKA 244
Query: 167 A 167
A
Sbjct: 245 A 245
>gnl|CDD|133423 cd01338, MDH_choloroplast_like, Chloroplast-like malate
dehydrogenases. MDH is one of the key enzymes in the
citric acid cycle, facilitating both the conversion of
malate to oxaloacetate and replenishing levels of
oxalacetate by reductive carboxylation of pyruvate.
Members of this subfamily are bacterial MDHs, and plant
MDHs localized to the choloroplasts. MDHs are part of
the NAD(P)-binding Rossmann fold superfamily, which
includes a wide variety of protein families including
the NAD(P)-binding domains of alcohol dehydrogenases,
tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate dehydrogenases,
formate/glycerate dehydrogenases, siroheme synthases,
6-phosphogluconate dehydrogenases, aminoacid
dehydrogenases, repressor rex, and NAD-binding potassium
channel domains, among others.
Length = 322
Score = 48.0 bits (115), Expect = 2e-06
Identities = 43/171 (25%), Positives = 66/171 (38%), Gaps = 13/171 (7%)
Query: 2 DIVIIPAGVPRKPGMTRDDLFNINAGIVKTLCEGIAK-CCPKAIVNLISNPVNSTVPIAA 60
D ++ PR PGM R DL N I + + V ++ NP N+ IA
Sbjct: 80 DWALLVGAKPRGPGMERADLLKANGKIFTAQGKALNDVASRDVKVLVVGNPCNTNALIAM 139
Query: 61 EVFKKVGTYDPKRLLGVTMLDVVRANTFVAEVLGLDPREVDVPVVGGHAGVTILPLLSQV 120
+ + P +T LD RA + +A+ G+ +V V+ G+ T P +
Sbjct: 140 KNAPDI---PPDNFTAMTRLDHNRAKSQLAKKAGVPVTDVKNMVIWGNHSPTQYPDFTNA 196
Query: 121 KPSCSLTPTEI-------DYLTDRIQNGGTEVVEAKTGAGSATLSMAYAAA 164
I D +Q G +++A+ GA SA S A AA
Sbjct: 197 TIGGKPAAEVINDRAWLEDEFIPTVQKRGAAIIKAR-GASSAA-SAANAAI 245
>gnl|CDD|235468 PRK05442, PRK05442, malate dehydrogenase; Provisional.
Length = 326
Score = 45.6 bits (109), Expect = 8e-06
Identities = 44/164 (26%), Positives = 71/164 (43%), Gaps = 17/164 (10%)
Query: 10 VPRKPGMTRDDLFNINAGIVKTLCEGIAKCCPKAI-VNLISNPVNSTVPIAAEVFKKVGT 68
PR PGM R DL N I + + + + + V ++ NP N+ IA + +
Sbjct: 90 RPRGPGMERKDLLEANGAIFTAQGKALNEVAARDVKVLVVGNPANTNALIAMKNAPDL-- 147
Query: 69 YDPKRLLGVTMLDVVRANTFVAEVLGLDPREV-DVPVVGGHAGVTILPLLSQV----KPS 123
+ +T LD RA + +A G+ ++ + V G H+ T P KP+
Sbjct: 148 -PAENFTAMTRLDHNRALSQLAAKAGVPVADIKKMTVWGNHSA-TQYPDFRHATIDGKPA 205
Query: 124 CSLTPTEIDYLTD----RIQNGGTEVVEAKTGAGSATLSMAYAA 163
+ + +L D +Q G ++EA+ GA SA S A AA
Sbjct: 206 AEVINDQ-AWLEDTFIPTVQKRGAAIIEAR-GASSAA-SAANAA 246
>gnl|CDD|177744 PLN00135, PLN00135, malate dehydrogenase.
Length = 309
Score = 43.6 bits (103), Expect = 3e-05
Identities = 33/110 (30%), Positives = 54/110 (49%), Gaps = 5/110 (4%)
Query: 2 DIVIIPAGVPRKPGMTRDDLFNINAGIVKTLCEGIAKCC-PKAIVNLISNPVNSTVPIAA 60
+I ++ G PRK GM R D+ + N I K+ + K P V +++NP N+ I
Sbjct: 60 NIAVMVGGFPRKEGMERKDVMSKNVSIYKSQASALEKHAAPDCKVLVVANPANTNALILK 119
Query: 61 EVFKKVGTYDPKRLLGVTMLDVVRANTFVAEVLGLDPREV-DVPVVGGHA 109
E + K + +T LD RA ++E LG+ +V +V + G H+
Sbjct: 120 EFAPSI---PEKNITCLTRLDHNRALGQISERLGVPVSDVKNVIIWGNHS 166
>gnl|CDD|215060 PLN00112, PLN00112, malate dehydrogenase (NADP); Provisional.
Length = 444
Score = 36.3 bits (84), Expect = 0.009
Identities = 28/79 (35%), Positives = 34/79 (43%), Gaps = 10/79 (12%)
Query: 11 PRKPGMTRDDLFNINAGIV----KTLCEGIAKCCPKAIVNLISNPVNSTVPIAAEVFKKV 66
PR PGM R DL +IN I K L E ++ K IV + NP N+ I K
Sbjct: 187 PRGPGMERADLLDINGQIFAEQGKALNEVASRNV-KVIV--VGNPCNTNALIC---LKNA 240
Query: 67 GTYDPKRLLGVTMLDVVRA 85
K +T LD RA
Sbjct: 241 PNIPAKNFHALTRLDENRA 259
>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 = 0.22
Identities = 21/55 (38%), Positives = 27/55 (49%), Gaps = 7/55 (12%)
Query: 11 PRKPGMTRDDLFNINAGIV----KTLCEGIAKCCPKAIVNLISNPVNSTVPIAAE 61
PR PGM R DL +IN I K L +K C V ++ NP N+ IA +
Sbjct: 131 PRGPGMERADLLDINGQIFADQGKALNAVASKNCK---VLVVGNPCNTNALIAMK 182
>gnl|CDD|182031 PRK09694, PRK09694, helicase Cas3; Provisional.
Length = 878
Score = 32.5 bits (74), Expect = 0.24
Identities = 15/53 (28%), Positives = 25/53 (47%), Gaps = 5/53 (9%)
Query: 127 TPTEIDYLTDRI-QNGGTEVVEAKTGAGSATLSMAYA----AAKFADACLRGL 174
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 = 30.9 bits (69), Expect = 0.56
Identities = 21/70 (30%), Positives = 34/70 (48%), Gaps = 1/70 (1%)
Query: 129 TEIDYLTDRIQNGGTEVVEAKTGAGSATLSMAYAAAKFADA-CLRGLRGDAGVIECAYVA 187
EID L D+I + ++A+ G +A L+ A F D+ C R ++ DA ++ A
Sbjct: 199 KEIDKLLDKIGSRQALELQAQAGIANARLAYATYREVFEDSDCYRQIKQDAAKLQRPLFA 258
Query: 188 STVTELPFFA 197
ST + A
Sbjct: 259 STGVKNNDLA 268
>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 = 0.91
Identities = 18/85 (21%), Positives = 30/85 (35%), Gaps = 6/85 (7%)
Query: 91 EVLGLDPREVDVPVVGGHAGVTILPLL---SQVKPSCSLTPTEIDYLTDRIQNGGTEVV- 146
+L L ++ + V+G +A P T +D + R N V
Sbjct: 9 NLLPLSKKKRKIAVIGPNADDPPNGGGGWSGTGNP--PYLVTPLDGIRARAGNATVVVYG 66
Query: 147 EAKTGAGSATLSMAYAAAKFADACL 171
+ ++ A AAAK AD +
Sbjct: 67 GSNLEDDDTGIAEAVAAAKDADVAI 91
>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 = 0.99
Identities = 11/41 (26%), Positives = 18/41 (43%), Gaps = 8/41 (19%)
Query: 126 LTPTEIDYLTDRIQ------NGGT--EVVEAKTGAGSATLS 158
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 = 1.2
Identities = 12/25 (48%), Positives = 16/25 (64%)
Query: 59 AAEVFKKVGTYDPKRLLGVTMLDVV 83
A+ +FK+ DP RLLGVT D+
Sbjct: 321 ASRLFKQHWNGDPVRLLGVTATDLE 345
>gnl|CDD|178267 PLN02661, PLN02661, Putative thiazole synthesis.
Length = 357
Score = 29.8 bits (67), Expect = 1.3
Identities = 17/33 (51%), Positives = 20/33 (60%), Gaps = 2/33 (6%)
Query: 133 YLTDRIQNGGTEVVEAKTGAGSATLSMAYAAAK 165
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 = 27.9 bits (63), Expect = 1.5
Identities = 12/41 (29%), Positives = 19/41 (46%)
Query: 200 VRLGRAGIEEIYSLGPLNEYERAGLEKAKKELAGSIQKGVS 240
+ + + E L L + LEKAK EL+ + Q V+
Sbjct: 36 LAVAQLEEEGETDLEALKQKMEQSLEKAKGELSPADQALVN 76
>gnl|CDD|226893 COG4496, COG4496, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 100
Score = 26.7 bits (59), Expect = 5.3
Identities = 15/39 (38%), Positives = 20/39 (51%), Gaps = 7/39 (17%)
Query: 127 TPTEIDYLTDRIQ------NGGT-EVVEAKTGAGSATLS 158
T EI L R+Q G T +E +TGA +AT+S
Sbjct: 36 TINEIQSLAQRLQVAKMLKEGRTYRDIEDETGASTATIS 74
>gnl|CDD|224124 COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense
mechanisms].
Length = 733
Score = 27.8 bits (62), Expect = 6.9
Identities = 20/69 (28%), Positives = 27/69 (39%), Gaps = 21/69 (30%)
Query: 145 VVEAKTGAGSATLSMAYAAAKFADACLRGLRGDAGVIECAYVASTVTELPFFASKVRLGR 204
V+EA TG G S+ A A + + + VI YV LPF R
Sbjct: 218 VLEAPTGYGKTEASLILALALLDEKI----KLKSRVI---YV------LPF--------R 256
Query: 205 AGIEEIYSL 213
IE++Y
Sbjct: 257 TIIEDMYRR 265
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 0.137 0.393
Gapped
Lambda K H
0.267 0.0786 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,609,527
Number of extensions: 1219347
Number of successful extensions: 1339
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1289
Number of HSP's successfully gapped: 57
Length of query: 244
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 150
Effective length of database: 6,768,326
Effective search space: 1015248900
Effective search space used: 1015248900
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: 58 (26.0 bits)