RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9933
(208 letters)
>gnl|CDD|133422 cd01337, MDH_glyoxysomal_mitochondrial, Glyoxysomal and
mitochondrial malate dehydrogenases. MDH is one of the
key enzymes in the citric acid cycle, facilitating both
the conversion of malate to oxaloacetate and
replenishing levels of oxalacetate by reductive
carboxylation of pyruvate. Members of this subfamily are
localized to the glycosome and mitochondria. MDHs are
part of the NAD(P)-binding Rossmann fold superfamily,
which includes a wide variety of protein families
including the NAD(P)-binding domains of alcohol
dehydrogenases, tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate dehydrogenases,
formate/glycerate dehydrogenases, siroheme synthases,
6-phosphogluconate dehydrogenases, aminoacid
dehydrogenases, repressor rex, and NAD-binding potassium
channel domains, among others.
Length = 310
Score = 299 bits (769), Expect = e-103
Identities = 133/232 (57%), Positives = 162/232 (69%), Gaps = 32/232 (13%)
Query: 1 MTRDDLFNTNASIVRDIIKAVAEVAPKALIGIISNPVNSTVPIAAEVLKKAGVFDPRRLF 60
MTRDDLFN NA IVRD+ AVA+ PKALI IISNPVNSTVPIAAEVLKKAGV+DP+RLF
Sbjct: 84 MTRDDLFNINAGIVRDLATAVAKACPKALILIISNPVNSTVPIAAEVLKKAGVYDPKRLF 143
Query: 61 GVTTLDIVRANTFVAEAKGLNPTDVNVPVIGGHAGITIIPLISQATPSVSFPDDQLKALT 120
GVTTLD+VRANTFVAE GL+P VNVPVIGGH+G+TI+PL+SQ P +F ++++ALT
Sbjct: 144 GVTTLDVVRANTFVAELLGLDPAKVNVPVIGGHSGVTILPLLSQCQPPFTFDQEEIEALT 203
Query: 121 GRIQEA----VSLKNGIEKNLGLGKLS----------------DFEKERQQFSPFIK--- 157
RIQ V K G G LS EK + + +++
Sbjct: 204 HRIQFGGDEVVKAKAG----AGSATLSMAYAGARFANSLLRGLKGEKGVIECA-YVESDV 258
Query: 158 TFASFFS-P---QKNGIEKNLGLGKLSDFEKELVKAAVPELKKNIAKGEEFV 205
T A FF+ P KNG+EKNLGLGKL+D+EK+L++AA+PELKKNI KG +FV
Sbjct: 259 TEAPFFATPVELGKNGVEKNLGLGKLNDYEKKLLEAALPELKKNIEKGVDFV 310
>gnl|CDD|215058 PLN00106, PLN00106, malate dehydrogenase.
Length = 323
Score = 263 bits (674), Expect = 1e-88
Identities = 123/225 (54%), Positives = 155/225 (68%), Gaps = 28/225 (12%)
Query: 1 MTRDDLFNTNASIVRDIIKAVAEVAPKALIGIISNPVNSTVPIAAEVLKKAGVFDPRRLF 60
MTRDDLFN NA IV+ + +AVA+ P AL+ IISNPVNSTVPIAAEVLKKAGV+DP++LF
Sbjct: 102 MTRDDLFNINAGIVKTLCEAVAKHCPNALVNIISNPVNSTVPIAAEVLKKAGVYDPKKLF 161
Query: 61 GVTTLDIVRANTFVAEAKGLNPTDVNVPVIGGHAGITIIPLISQATPSVSFPDDQLKALT 120
GVTTLD+VRANTFVAE KGL+P DV+VPV+GGHAGITI+PL+SQATP VSF D++++ALT
Sbjct: 162 GVTTLDVVRANTFVAEKKGLDPADVDVPVVGGHAGITILPLLSQATPKVSFTDEEIEALT 221
Query: 121 GRIQ----EAVSLKNG---------------IEKNL-GLGKLSD-----FEKERQQFSPF 155
RIQ E V K G + L GL +D + + PF
Sbjct: 222 KRIQNGGTEVVEAKAGAGSATLSMAYAAARFADACLRGLNGEADVVECSYVQSEVTELPF 281
Query: 156 IKTFASFFSPQKNGIEKNLGLGKLSDFEKELVKAAVPELKKNIAK 200
FAS +NG+E+ LGLG LS++E++ ++A PELK +I K
Sbjct: 282 ---FASKVRLGRNGVEEVLGLGPLSEYEQKGLEALKPELKASIEK 323
>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 = 252 bits (645), Expect = 2e-84
Identities = 126/230 (54%), Positives = 150/230 (65%), Gaps = 23/230 (10%)
Query: 1 MTRDDLFNTNASIVRDIIKAVAEVAPKALIGIISNPVNSTVPIAAEVLKKAGVFDPRRLF 60
MTRDDLFN NA IV+D++ AVAE PKA+I +I+NPVNSTVPIAAEVLKK GV+DP +LF
Sbjct: 83 MTRDDLFNVNAGIVKDLVAAVAESCPKAMILVITNPVNSTVPIAAEVLKKKGVYDPNKLF 142
Query: 61 GVTTLDIVRANTFVAEAKGLNPTDVNVPVIGGHAGITIIPLISQATPSVSFPDDQLKALT 120
GVTTLDIVRANTFVAE KG +P +VNVPVIGGH+G TIIPLISQ V F +DQL+AL
Sbjct: 143 GVTTLDIVRANTFVAELKGKDPMEVNVPVIGGHSGETIIPLISQCPGKVLFTEDQLEALI 202
Query: 121 GRIQEA----VSLKNG-------------------IEKNLGLGKLSDFEKERQQFSPFIK 157
RIQ A V K G + G + +
Sbjct: 203 HRIQNAGTEVVKAKAGAGSATLSMAFAGARFVLSLVRGLKGEEGVVECAYVESDGVTEAT 262
Query: 158 TFASFFSPQKNGIEKNLGLGKLSDFEKELVKAAVPELKKNIAKGEEFVAK 207
FA+ KNG+EK LG+GKLS FE++++ A+PELKKNI KGEEFVA
Sbjct: 263 FFATPLLLGKNGVEKRLGIGKLSSFEEKMLNGALPELKKNIKKGEEFVAS 312
>gnl|CDD|240360 PTZ00325, PTZ00325, malate dehydrogenase; Provisional.
Length = 321
Score = 240 bits (614), Expect = 1e-79
Identities = 122/233 (52%), Positives = 159/233 (68%), Gaps = 31/233 (13%)
Query: 1 MTRDDLFNTNASIVRDIIKAVAEVAPKALIGIISNPVNSTVPIAAEVLKKAGVFDPRRLF 60
MTRDDLFNTNA IVRD++ AVA APKA++GI+SNPVNSTVPIAAE LKKAGV+DPR+LF
Sbjct: 92 MTRDDLFNTNAPIVRDLVAAVASSAPKAIVGIVSNPVNSTVPIAAETLKKAGVYDPRKLF 151
Query: 61 GVTTLDIVRANTFVAEAKGLNPTDVNVPVIGGHAGITIIPLISQATPSVSFPDDQLKALT 120
GVTTLD+VRA FVAEA G+NP DVNVPV+GGH+G+TI+PL+SQ +S P++Q++ +T
Sbjct: 152 GVTTLDVVRARKFVAEALGMNPYDVNVPVVGGHSGVTIVPLLSQT--GLSLPEEQVEQIT 209
Query: 121 GRIQ----EAVSLKNG------------------IEKNL----GLGKLSDFEKERQQFSP 154
R+Q E V K G + K L G+ + + E + + P
Sbjct: 210 HRVQVGGDEVVKAKEGAGSATLSMAYAAAEWSTSVLKALRGDKGIVECAFVESDMRPECP 269
Query: 155 FIKTFASFFSPQKNGIEKNLGLGKLSDFEKELVKAAVPELKKNIAKGEEFVAK 207
F F+S K G+E+ L +G L+ +E+EL++AAVP+LKKNI KG EF K
Sbjct: 270 F---FSSPVELGKEGVERVLPIGPLNAYEEELLEAAVPDLKKNIEKGLEFARK 319
>gnl|CDD|235340 PRK05086, PRK05086, malate dehydrogenase; Provisional.
Length = 312
Score = 235 bits (602), Expect = 7e-78
Identities = 107/237 (45%), Positives = 146/237 (61%), Gaps = 39/237 (16%)
Query: 1 MTRDDLFNTNASIVRDIIKAVAEVAPKALIGIISNPVNSTVPIAAEVLKKAGVFDPRRLF 60
M R DLFN NA IV+++++ VA+ PKA IGII+NPVN+TV IAAEVLKKAGV+D +LF
Sbjct: 85 MDRSDLFNVNAGIVKNLVEKVAKTCPKACIGIITNPVNTTVAIAAEVLKKAGVYDKNKLF 144
Query: 61 GVTTLDIVRANTFVAEAKGLNPTDVNVPVIGGHAGITIIPLISQATPSVSFPDDQLKALT 120
GVTTLD++R+ TFVAE KG P +V VPVIGGH+G+TI+PL+SQ P VSF + ++ LT
Sbjct: 145 GVTTLDVIRSETFVAELKGKQPGEVEVPVIGGHSGVTILPLLSQV-PGVSFTEQEVADLT 203
Query: 121 GRIQEA--------------------------VSLKNGIEKNLGLGKLSDFEKERQQFSP 154
RIQ A +SL ++ G+ + + E + +
Sbjct: 204 KRIQNAGTEVVEAKAGGGSATLSMGQAAARFGLSLVRALQGEQGVVECAYVEGDGK---- 259
Query: 155 FIKTFASFFSPQ----KNGIEKNLGLGKLSDFEKELVKAAVPELKKNIAKGEEFVAK 207
+A FF+ KNG+E+ L +G LS FE+ ++ + LKK+IA GEEFV K
Sbjct: 260 ----YARFFAQPVLLGKNGVEERLPIGTLSAFEQNALEGMLDTLKKDIALGEEFVNK 312
>gnl|CDD|223117 COG0039, Mdh, Malate/lactate dehydrogenases [Energy production and
conversion].
Length = 313
Score = 123 bits (312), Expect = 2e-34
Identities = 53/135 (39%), Positives = 75/135 (55%), Gaps = 14/135 (10%)
Query: 1 MTRDDLFNTNASIVRDIIKAVAEVAPKALIGIISNPVNSTVPIAAEVLKKAGVFDPRRLF 60
MTR DL NA IV+DI KA+A+ AP A++ +++NPV+ IA + F R+
Sbjct: 85 MTRLDLLEKNAKIVKDIAKAIAKYAPDAIVLVVTNPVDILTYIAMKFSG----FPKNRVI 140
Query: 61 G-VTTLDIVRANTFVAEAKGLNPTDVNVPVIGGHAGITIIPLISQATPS--------VSF 111
G T LD R TF+AE G++P DV+ VIG H G T++PL SQAT
Sbjct: 141 GSGTVLDSARFRTFLAEKLGVSPKDVHAYVIGEH-GDTMVPLWSQATVGGKPLEELLKED 199
Query: 112 PDDQLKALTGRIQEA 126
++ L+ L R++ A
Sbjct: 200 TEEDLEELIERVRNA 214
>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 = 110 bits (278), Expect = 6e-31
Identities = 58/174 (33%), Positives = 80/174 (45%), Gaps = 32/174 (18%)
Query: 63 TTLDIVRANTFVAEAKGLNPTDVNVPVIGGHAG----------ITIIPLISQATPSVSFP 112
TTLD RA TF+AE G++P VNV VIG H+G +TIIPLISQ ++
Sbjct: 1 TTLDTARARTFLAEKFGVDPRSVNVYVIGEHSGTQFPDWSHAKVTIIPLISQVKENLKDT 60
Query: 113 DDQLKALTGRIQEA----VSLKNGIEKNLGLGK-LSDFEK-----ERQQFSPF------- 155
D +L+ L R+Q A + K G + + K S
Sbjct: 61 DWELEELIERVQNAGYEVIEAKAG-STTYSMAYAAARIAKAILRGTGGVLSVGVYLDGYY 119
Query: 156 -IKTFASFFSP---QKNGIEKNLGLGKLSDFEKELVKAAVPELKKNIAKGEEFV 205
F P K+G+EK + + L+DFE+E ++ + ELKK I KG FV
Sbjct: 120 GSPDDIYFSVPVVLGKDGVEKVVEILPLNDFEREKLEKSAAELKKEIEKGFAFV 173
>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 = 91.6 bits (228), Expect = 1e-22
Identities = 34/110 (30%), Positives = 57/110 (51%), Gaps = 5/110 (4%)
Query: 1 MTRDDLFNTNASIVRDIIKAVAEVAPKALIGIISNPVNSTVPIAAEVLKKAGVFDPRRLF 60
M R DL N IV++I + + +P A I ++SNPV+ I ++ + ++
Sbjct: 86 MGRLDLLKRNVPIVKEIGDNIEKYSPDAWIIVVSNPVD----IITYLVWRYSGLPKEKVI 141
Query: 61 GVTTLDIVRANTFVAEAKGLNPTDVNVPVIGGHAGITIIPLISQATPSVS 110
G+ TLD +R +AE G++P DV V ++G H G + +P S + S
Sbjct: 142 GLGTLDPIRFRRILAEKLGVDPDDVKVYILGEHGG-SQVPDWSTVRIATS 190
>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 = 85.6 bits (213), Expect = 4e-20
Identities = 39/107 (36%), Positives = 64/107 (59%), Gaps = 6/107 (5%)
Query: 1 MTRDDLFNTNASIVRDIIKAVAEVAPKALIGIISNPVNSTVPIAAEVLKKAGVFDPRRLF 60
M+RDDL TNA IV+++ + + + AP A++ +++NP++ +A K +G F R+
Sbjct: 82 MSRDDLLGTNAKIVKEVAENIKKYAPNAIVIVVTNPLDVMTYVA---YKASG-FPRNRVI 137
Query: 61 GV-TTLDIVRANTFVAEAKGLNPTDVNVPVIGGHAGITIIPLISQAT 106
G+ LD R F+AE G++ DV V+GGH G T++PL +T
Sbjct: 138 GMAGVLDSARFRYFIAEELGVSVKDVQAMVLGGH-GDTMVPLPRYST 183
Score = 26.7 bits (60), Expect = 9.0
Identities = 14/33 (42%), Positives = 20/33 (60%), Gaps = 1/33 (3%)
Query: 167 KNGIEKNLGLGKLSDFEKELVKAAVPELKKNIA 199
KNG+EK + L L+D EKE +V +K+ I
Sbjct: 269 KNGVEKIIEL-DLTDEEKEAFDKSVESVKELID 300
>gnl|CDD|180477 PRK06223, PRK06223, malate dehydrogenase; Reviewed.
Length = 307
Score = 84.0 bits (209), Expect = 2e-19
Identities = 39/132 (29%), Positives = 69/132 (52%), Gaps = 11/132 (8%)
Query: 1 MTRDDLFNTNASIVRDIIKAVAEVAPKALIGIISNPVNSTVPIAAEVLKKAGVFDPRRLF 60
M+RDDL NA I++D+ + + + AP A++ +++NPV++ V K F R+
Sbjct: 86 MSRDDLLGINAKIMKDVAEGIKKYAPDAIVIVVTNPVDAMT----YVALKESGFPKNRVI 141
Query: 61 GVTT-LDIVRANTFVAEAKGLNPTDVNVPVIGGHAGITIIPLISQAT-----PSVSFPDD 114
G+ LD R TF+AE ++ DV V+GGH G +++PL+ +T +
Sbjct: 142 GMAGVLDSARFRTFIAEELNVSVKDVTAFVLGGH-GDSMVPLVRYSTVGGIPLEDLLSKE 200
Query: 115 QLKALTGRIQEA 126
+L + R ++
Sbjct: 201 KLDEIVERTRKG 212
>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 = 78.4 bits (194), Expect = 1e-18
Identities = 25/61 (40%), Positives = 38/61 (62%), Gaps = 3/61 (4%)
Query: 1 MTRDDLFNTNASIVRDIIKAVAEVAPKALIGIISNPVNSTVPIAAEVLKKAGVFDPRRLF 60
MTR DL N NA I +DI+ A+A+ AP A++ ++SNPV+ IA +V +G+ R +
Sbjct: 85 MTRLDLLNRNAGIFKDIVPAIAKSAPDAIVLVVSNPVDILTYIAWKV---SGLPPERVIG 141
Query: 61 G 61
Sbjct: 142 S 142
>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 = 72.1 bits (177), Expect = 4e-15
Identities = 49/146 (33%), Positives = 78/146 (53%), Gaps = 17/146 (11%)
Query: 1 MTRDDLFNTNASIVRDIIKAVAEVAPKALIGIISNPVNSTVPIAAEVLKKAGVFDPRRLF 60
M+R DL NA IV+ K +AE AP I +++NPV+ A LK++G FD R+F
Sbjct: 88 MSRLDLAKKNAKIVKKYAKQIAEFAPDTKILVVTNPVDVMTYKA---LKESG-FDKNRVF 143
Query: 61 GVTT-LDIVRANTFVAEAKGLNPTDVNVPVIGGHAGITIIPLISQAT----PSVSFP--- 112
G+ T LD +R +A+ ++ ++V+ +IG H G +++PLIS + P FP
Sbjct: 144 GLGTHLDSLRFKVAIAKHFNVHISEVHTRIIGEH-GDSMVPLISSTSIGGIPIKRFPEYK 202
Query: 113 ----DDQLKALTGRIQEAVSLKNGIE 134
+ ++ + Q +SLK G E
Sbjct: 203 DFDVEKIVETVKNAGQNIISLKGGSE 228
>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 = 67.2 bits (164), Expect = 2e-13
Identities = 38/109 (34%), Positives = 64/109 (58%), Gaps = 6/109 (5%)
Query: 1 MTRDDLFNTNASIVRDIIKAVAEVAPKALIGIISNPVNSTVPIAAEVLKKAGVFDPRRLF 60
M+R+DL + NA IVR++ + E +P +I ++SNP+++ +A + K+G F R+
Sbjct: 85 MSREDLLSMNAGIVREVTGRIMEHSPNPIIVVVSNPLDAMTYVAWQ---KSG-FPKERVI 140
Query: 61 GVT-TLDIVRANTFVAEAKGLNPTDVNVPVIGGHAGITIIPLISQATPS 108
G LD R TF+A G++ DV V+GGH G ++PL+ +T +
Sbjct: 141 GQAGVLDSARFRTFIAMELGVSVQDVTACVLGGH-GDAMVPLVRYSTVA 188
>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 = 67.3 bits (165), Expect = 2e-13
Identities = 38/119 (31%), Positives = 56/119 (47%), Gaps = 10/119 (8%)
Query: 1 MTRDDLFNTNASIVRDIIKAVAEVAPKALIGIISNPVNSTVPIAAEVLKKAGVFDPRRLF 60
TR DL N NA I+R +I + + P A+I ++SNPV+ I V +K R+
Sbjct: 82 ETRLDLINRNAPILRSVITNLKKYGPDAIILVVSNPVD----ILTYVAQKLSGLPKNRVI 137
Query: 61 GV-TTLDIVRANTFVAEAKGLNPTDVNVPVIGGHAGITIIPLISQAT----PSVSFPDD 114
G T LD R + +AE ++P V+ V+G H G + + S AT P
Sbjct: 138 GSGTLLDSARFRSLLAEKLDVDPQSVHAYVLGEH-GDSQVVAWSTATVGGLPLEELAPF 195
>gnl|CDD|173376 PTZ00082, PTZ00082, L-lactate dehydrogenase; Provisional.
Length = 321
Score = 67.4 bits (165), Expect = 2e-13
Identities = 34/105 (32%), Positives = 58/105 (55%), Gaps = 6/105 (5%)
Query: 3 RDDLFNTNASIVRDIIKAVAEVAPKALIGIISNPVNSTVPIAAEVLKKAGVFDPRRLFGV 62
RDDL NA I+ ++ + + + P A + +I+NP++ V ++L++ ++ G+
Sbjct: 97 RDDLLPLNAKIMDEVAEGIKKYCPNAFVIVITNPLDVMV----KLLQEHSGLPKNKVCGM 152
Query: 63 T-TLDIVRANTFVAEAKGLNPTDVNVPVIGGHAGITIIPLISQAT 106
LD R T++AE G+NP DV+ VIG H G ++PL T
Sbjct: 153 AGVLDSSRLRTYIAEKLGVNPRDVHASVIGAH-GDKMVPLPRYVT 196
>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 = 62.2 bits (152), Expect = 9e-12
Identities = 33/106 (31%), Positives = 51/106 (48%), Gaps = 6/106 (5%)
Query: 2 TRDDLFNTNASIVRDIIKAVAEVAPKALIGIISNPVNSTVPIAAEVLKKAGVFDPRRLFG 61
TR +L N I++ I+ V + + + +NPV+ I V K F R+ G
Sbjct: 81 TRLELVGRNVRIMKSIVPEVVKSGFDGIFLVATNPVD----ILTYVAWKLSGFPKNRVIG 136
Query: 62 V-TTLDIVRANTFVAEAKGLNPTDVNVPVIGGHAGITIIPLISQAT 106
T LD R +AE G++P V+ +IG H G + +P+ S AT
Sbjct: 137 SGTVLDTARLRYLLAEKLGVDPQSVHAYIIGEH-GDSEVPVWSSAT 181
>gnl|CDD|173409 PTZ00117, PTZ00117, malate dehydrogenase; Provisional.
Length = 319
Score = 61.7 bits (150), Expect = 2e-11
Identities = 32/107 (29%), Positives = 56/107 (52%), Gaps = 6/107 (5%)
Query: 1 MTRDDLFNTNASIVRDIIKAVAEVAPKALIGIISNPVNSTVPIAAEVLKKAGVFDPRRLF 60
MTR+DL N I++ + ++V + P A + ++NP++ +V ++ ++
Sbjct: 89 MTREDLLTINGKIMKSVAESVKKYCPNAFVICVTNPLD----CMVKVFQEKSGIPSNKIC 144
Query: 61 GVT-TLDIVRANTFVAEAKGLNPTDVNVPVIGGHAGITIIPLISQAT 106
G+ LD R +AE G++P DV+ VIGGH G ++PL T
Sbjct: 145 GMAGVLDSSRFRCNLAEKLGVSPGDVSAVVIGGH-GDLMVPLPRYCT 190
>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 = 60.6 bits (148), Expect = 4e-11
Identities = 30/106 (28%), Positives = 48/106 (45%), Gaps = 6/106 (5%)
Query: 2 TRDDLFNTNASIVRDIIKAVAEVAPKALIGIISNPVNSTVPIAAEVLKKAGVFDPRRLFG 61
TR DL NA I++ I+ + + + SNPV+ + V++K R+ G
Sbjct: 85 TRLDLLEKNAKIMKSIVPKIKASGFDGIFLVASNPVD----VITYVVQKLSGLPKNRVIG 140
Query: 62 V-TTLDIVRANTFVAEAKGLNPTDVNVPVIGGHAGITIIPLISQAT 106
T+LD R +AE ++P V+ V+G H G + S T
Sbjct: 141 TGTSLDTARLRRALAEKLNVDPRSVHAYVLGEH-GDSQFVAWSTVT 185
>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 = 60.0 bits (146), Expect = 7e-11
Identities = 41/122 (33%), Positives = 67/122 (54%), Gaps = 9/122 (7%)
Query: 3 RDDLFNTNASIVRDIIKAVAEVAPKALIGIISNPVNSTVPIAAEVLKKAGVFDPRRLFGV 62
R DL TNA I+R+I+ + +V +A+I +I+NP++ V IAA + ++ G
Sbjct: 88 RLDLAQTNAKIIREIMGNITKVTKEAVIILITNPLDIAVYIAATEFD----YPANKVIGT 143
Query: 63 -TTLDIVRANTFVAEAKGLNPTDVNVPVIGGHAGITIIPLISQATPSVS-FPDDQLKALT 120
T LD R VA+ G++P +V V+G H G P+ S +++ P D+L+AL
Sbjct: 144 GTMLDTARLRRIVADKYGVDPKNVTGYVLGEH-GSHAFPVWSLV--NIAGLPLDELEALF 200
Query: 121 GR 122
G+
Sbjct: 201 GK 202
>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 = 59.4 bits (145), Expect = 9e-11
Identities = 33/106 (31%), Positives = 54/106 (50%), Gaps = 6/106 (5%)
Query: 2 TRDDLFNTNASIVRDIIKAVAEVAPKALIGIISNPVNSTVPIAAEVLKKAGVFDPRRLFG 61
TR DL N +I ++II + + AP A++ +++NPV+ + V K P R+ G
Sbjct: 84 TRLDLLKRNVAIFKEIIPQILKYAPDAILLVVTNPVD----VLTYVAYKLSGLPPNRVIG 139
Query: 62 V-TTLDIVRANTFVAEAKGLNPTDVNVPVIGGHAGITIIPLISQAT 106
T LD R + E G++P V+ +IG H G + + + S A
Sbjct: 140 SGTVLDTARFRYLLGEHLGVDPRSVHAYIIGEH-GDSEVAVWSSAN 184
>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 = 55.3 bits (134), Expect = 3e-09
Identities = 29/93 (31%), Positives = 45/93 (48%), Gaps = 5/93 (5%)
Query: 2 TRDDLFNTNASIVRDIIKAVAEVAPKALIGIISNPVNSTVPIAAEVLKKAGVFDPRRLFG 61
+R DL N I + II + + +P A++ ++SNPV+ I V K R+ G
Sbjct: 88 SRLDLVQRNVDIFKGIIPKLVKYSPNAILLVVSNPVD----IMTYVAWKLSGLPKHRVIG 143
Query: 62 V-TTLDIVRANTFVAEAKGLNPTDVNVPVIGGH 93
LD R +AE G+ P+ V+ +IG H
Sbjct: 144 SGCNLDSARFRYLIAERLGVAPSSVHGWIIGEH 176
>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 = 52.3 bits (126), Expect = 3e-08
Identities = 37/108 (34%), Positives = 54/108 (50%), Gaps = 6/108 (5%)
Query: 1 MTRDDLFNTNASIVRDIIKAVAEVA-PKALIGIISNPVNSTVPIAAEVLKKAGVFDPRRL 59
M R DL NA I ++ +A+ +VA P + ++ NP N+ A LK A P+
Sbjct: 92 MERADLLRKNAKIFKEQGEALNKVAKPTVKVLVVGNPANTN---ALIALKNAPNLPPKNF 148
Query: 60 FGVTTLDIVRANTFVAEAKGLNPTDV-NVPVIGGHAGITIIPLISQAT 106
+T LD RA VA G+ +DV NV + G H+ T +P +S A
Sbjct: 149 TALTRLDHNRAKAQVARKLGVRVSDVKNVIIWGNHSN-TQVPDLSNAV 195
>gnl|CDD|178212 PLN02602, PLN02602, lactate dehydrogenase.
Length = 350
Score = 47.8 bits (114), Expect = 1e-06
Identities = 31/103 (30%), Positives = 51/103 (49%), Gaps = 6/103 (5%)
Query: 2 TRDDLFNTNASIVRDIIKAVAEVAPKALIGIISNPVNSTVPIAAEVLKKAGVFDPRRLFG 61
+R +L N ++ R II +A+ +P ++ I+SNPV+ + V K F R+ G
Sbjct: 122 SRLNLLQRNVALFRKIIPELAKYSPDTILLIVSNPVD----VLTYVAWKLSGFPANRVIG 177
Query: 62 V-TTLDIVRANTFVAEAKGLNPTDVNVPVIGGHAGITIIPLIS 103
T LD R +A+ +N DV ++G H G + + L S
Sbjct: 178 SGTNLDSSRFRFLIADHLDVNAQDVQAYIVGEH-GDSSVALWS 219
>gnl|CDD|178836 PRK00066, ldh, L-lactate dehydrogenase; Reviewed.
Length = 315
Score = 44.9 bits (107), Expect = 9e-06
Identities = 32/107 (29%), Positives = 46/107 (42%), Gaps = 6/107 (5%)
Query: 1 MTRDDLFNTNASIVRDIIKAVAEVAPKALIGIISNPVNSTVPIAAEVLKKAGVFDPRRLF 60
TR DL N I + I+ V + + SNPV+ I K F R+
Sbjct: 89 ETRLDLVEKNLKIFKSIVGEVMASGFDGIFLVASNPVD----ILTYATWKLSGFPKERVI 144
Query: 61 GV-TTLDIVRANTFVAEAKGLNPTDVNVPVIGGHAGITIIPLISQAT 106
G T+LD R ++E ++P V+ +IG H G T P+ S A
Sbjct: 145 GSGTSLDSARFRYMLSEKLDVDPRSVHAYIIGEH-GDTEFPVWSHAN 190
>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 = 43.9 bits (104), Expect = 2e-05
Identities = 33/108 (30%), Positives = 53/108 (49%), Gaps = 6/108 (5%)
Query: 1 MTRDDLFNTNASIVRDIIKAVAEVA-PKALIGIISNPVNSTVPIAAEVLKKAGVFDPRRL 59
M R DL + N I ++ KA+ +VA + ++ NP N+ IA++ P+
Sbjct: 95 MERADLLSKNGKIFKEQGKALNKVAKKDVKVLVVGNPANTNALIASKNAPD---IPPKNF 151
Query: 60 FGVTTLDIVRANTFVAEAKGLNPTDV-NVPVIGGHAGITIIPLISQAT 106
+T LD RA +A G+ +DV NV + G H+ T +P + AT
Sbjct: 152 SAMTRLDHNRAKYQLAAKAGVPVSDVKNVIIWGNHSN-TQVPDFTHAT 198
>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 = 43.7 bits (103), Expect = 2e-05
Identities = 36/109 (33%), Positives = 55/109 (50%), Gaps = 8/109 (7%)
Query: 1 MTRDDLFNTNASIVRDIIKAVAEVAPKAL-IGIISNPVNSTVPIAAEVLKKAGVFDPRRL 59
M R DL + N I ++ +A+ ++A K + ++ NP N+ A VL P +
Sbjct: 91 MERRDLLSKNVKIFKEQGRALDKLAKKDCKVLVVGNPANTN----ALVLSNYAPSIPPKN 146
Query: 60 F-GVTTLDIVRANTFVAEAKGLNPTDV-NVPVIGGHAGITIIPLISQAT 106
F +T LD RA VAE G+ +DV NV + G H+ T P ++ AT
Sbjct: 147 FSALTRLDHNRALAQVAERAGVPVSDVKNVIIWGNHSS-TQYPDVNHAT 194
>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 = 43.3 bits (103), Expect = 3e-05
Identities = 35/108 (32%), Positives = 50/108 (46%), Gaps = 6/108 (5%)
Query: 1 MTRDDLFNTNASIVRDIIKAVAEVA-PKALIGIISNPVNSTVPIAAEVLKKAGVFDPRRL 59
M R DL N I KA+ +VA + ++ NP N+ IA K A P
Sbjct: 94 MERADLLKANGKIFTAQGKALNDVASRDVKVLVVGNPCNTNALIAM---KNAPDIPPDNF 150
Query: 60 FGVTTLDIVRANTFVAEAKGLNPTDV-NVPVIGGHAGITIIPLISQAT 106
+T LD RA + +A+ G+ TDV N+ + G H+ T P + AT
Sbjct: 151 TAMTRLDHNRAKSQLAKKAGVPVTDVKNMVIWGNHSP-TQYPDFTNAT 197
>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 = 42.2 bits (100), Expect = 8e-05
Identities = 33/108 (30%), Positives = 52/108 (48%), Gaps = 6/108 (5%)
Query: 1 MTRDDLFNTNASIVRDIIKAVAEVAPKAL-IGIISNPVNSTVPIAAEVLKKAGVFDPRRL 59
M R DL N I ++ +A+ + A K + + ++ NP N+ I LK A
Sbjct: 94 MERKDLLKANVKIFKEQGEALDKYAKKNVKVLVVGNPANTNALIL---LKYAPSIPKENF 150
Query: 60 FGVTTLDIVRANTFVAEAKGLNPTDV-NVPVIGGHAGITIIPLISQAT 106
+T LD RA + +A G+ +DV NV + G H+ T P ++ AT
Sbjct: 151 TALTRLDHNRAKSQIALKLGVPVSDVKNVIIWGNHSS-TQYPDVNHAT 197
>gnl|CDD|235468 PRK05442, PRK05442, malate dehydrogenase; Provisional.
Length = 326
Score = 39.8 bits (94), Expect = 5e-04
Identities = 33/108 (30%), Positives = 47/108 (43%), Gaps = 6/108 (5%)
Query: 1 MTRDDLFNTNASIVRDIIKAVAEVAPK-ALIGIISNPVNSTVPIAAEVLKKAGVFDPRRL 59
M R DL N +I KA+ EVA + + ++ NP N+ IA K A
Sbjct: 96 MERKDLLEANGAIFTAQGKALNEVAARDVKVLVVGNPANTNALIAM---KNAPDLPAENF 152
Query: 60 FGVTTLDIVRANTFVAEAKGLNPTDV-NVPVIGGHAGITIIPLISQAT 106
+T LD RA + +A G+ D+ + V G H+ T P AT
Sbjct: 153 TAMTRLDHNRALSQLAAKAGVPVADIKKMTVWGNHSA-TQYPDFRHAT 199
>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 = 38.7 bits (90), Expect = 0.001
Identities = 24/105 (22%), Positives = 45/105 (42%), Gaps = 4/105 (3%)
Query: 3 RDDLFNTNASIVRDIIKAVAEVA-PKALIGIISNPVNSTVPIAAEVLKKAGVFDPRRLFG 61
R DL N I + +A++E A P + +I NPVN+ +A + A
Sbjct: 78 RADLLTKNTPIFKATGEALSEYAKPTVKVLVIGNPVNTNCLVA---MLHAPKLSAENFSS 134
Query: 62 VTTLDIVRANTFVAEAKGLNPTDVNVPVIGGHAGITIIPLISQAT 106
+ LD RA + +A + + V+ G+ +++ ++ A
Sbjct: 135 LCMLDHNRAVSRIASKLKVPVDHIYHVVVWGNHAESMVADLTHAE 179
>gnl|CDD|215060 PLN00112, PLN00112, malate dehydrogenase (NADP); Provisional.
Length = 444
Score = 35.6 bits (82), Expect = 0.013
Identities = 30/96 (31%), Positives = 43/96 (44%), Gaps = 5/96 (5%)
Query: 1 MTRDDLFNTNASIVRDIIKAVAEVA-PKALIGIISNPVNSTVPIAAEVLKKAGVFDPRRL 59
M R DL + N I + KA+ EVA + ++ NP N+ I LK A +
Sbjct: 192 MERADLLDINGQIFAEQGKALNEVASRNVKVIVVGNPCNTNALIC---LKNAPNIPAKNF 248
Query: 60 FGVTTLDIVRANTFVAEAKGLNPTDV-NVPVIGGHA 94
+T LD RA +A G+ V NV + G H+
Sbjct: 249 HALTRLDENRAKCQLALKAGVFYDKVSNVTIWGNHS 284
>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 = 34.6 bits (79), Expect = 0.032
Identities = 32/101 (31%), Positives = 45/101 (44%), Gaps = 4/101 (3%)
Query: 1 MTRDDLFNTNASIVRDIIKAVAEVAPKAL-IGIISNPVNSTVPIAAEVLKKAGVFDPRRL 59
M R DL + N I D KA+ VA K + ++ NP N+ IA +K A +
Sbjct: 136 MERADLLDINGQIFADQGKALNAVASKNCKVLVVGNPCNTNALIA---MKNAPNIPRKNF 192
Query: 60 FGVTTLDIVRANTFVAEAKGLNPTDVNVPVIGGHAGITIIP 100
+T LD RA +A G T V+ I G+ T +P
Sbjct: 193 HALTRLDENRAKCQLALKSGKFYTSVSNVTIWGNHSTTQVP 233
>gnl|CDD|233224 TIGR00993, 3a0901s04IAP86, chloroplast protein import component
Toc86/159, G and M domains. The long precursor of the
86K protein originally described is proposed to have
three domains. The N-terminal A-domain is acidic,
repetitive, weakly conserved, readily removed by
proteolysis during chloroplast isolation, and not
required for protein translocation. The other domains
are designated G (GTPase) and M (membrane anchor); this
family includes most of the G domain and all of M
[Transport and binding proteins, Amino acids, peptides
and amines].
Length = 763
Score = 32.2 bits (73), Expect = 0.16
Identities = 29/94 (30%), Positives = 46/94 (48%), Gaps = 3/94 (3%)
Query: 43 IAAEVLKKAGVFDPRRLFGVTTLDIVRANTFVAEAKGLNPTD--VNVPVIGGHAGITIIP 100
IAA+VL + G+ R+ G +LD +A EA+G +P D +N+ V+ G +G+
Sbjct: 75 IAAQVLYRLGLLAGRQGGGAFSLDAAKAMAEQLEAEGQDPLDFSLNILVL-GKSGVGKSA 133
Query: 101 LISQATPSVSFPDDQLKALTGRIQEAVSLKNGIE 134
I+ V F D T +QE L G++
Sbjct: 134 TINSIFGEVKFSTDAFGMGTTSVQEIEGLVQGVK 167
>gnl|CDD|177744 PLN00135, PLN00135, malate dehydrogenase.
Length = 309
Score = 32.1 bits (73), Expect = 0.19
Identities = 34/124 (27%), Positives = 60/124 (48%), Gaps = 8/124 (6%)
Query: 1 MTRDDLFNTNASIVRDIIKAVAE-VAPKALIGIISNPVNSTVPIAAEVLKKAGVFDPRR- 58
M R D+ + N SI + A+ + AP + +++NP N+ A +LK+ P +
Sbjct: 74 MERKDVMSKNVSIYKSQASALEKHAAPDCKVLVVANPANTN----ALILKEFAPSIPEKN 129
Query: 59 LFGVTTLDIVRANTFVAEAKGLNPTDV-NVPVIGGHAGITIIPLISQATPSVSFPDDQLK 117
+ +T LD RA ++E G+ +DV NV + G H+ T P ++ AT + ++
Sbjct: 130 ITCLTRLDHNRALGQISERLGVPVSDVKNVIIWGNHSS-TQYPDVNHATVKTPSGEKPVR 188
Query: 118 ALTG 121
L
Sbjct: 189 ELVA 192
>gnl|CDD|235164 PRK03824, hypA, hydrogenase nickel incorporation protein;
Provisional.
Length = 135
Score = 31.2 bits (71), Expect = 0.19
Identities = 18/45 (40%), Positives = 26/45 (57%), Gaps = 5/45 (11%)
Query: 166 QKNGIEK----NLGLGKLSDFEKELVKAAVPELKK-NIAKGEEFV 205
QK G K + LG+L D +KE+V+ A+ EL K I +G E +
Sbjct: 19 QKEGASKVKALKVVLGELQDVDKEIVEFALNELLKGTILEGAEII 63
>gnl|CDD|129130 TIGR00019, prfA, peptide chain release factor 1. This model
describes peptide chain release factor 1 (PrfA, RF-1),
and excludes the related peptide chain release factor 2
(PrfB, RF-2). RF-1 helps recognize and terminate
translation at UAA and UAG stop codons. The
mitochondrial release factors are prfA-like, although
not included above the trusted cutoff for this model.
RF-1 does not have a translational frameshift [Protein
synthesis, Translation factors].
Length = 360
Score = 30.8 bits (70), Expect = 0.47
Identities = 23/91 (25%), Positives = 45/91 (49%), Gaps = 2/91 (2%)
Query: 114 DQLKALTGRIQEAVSLKNGIEKNLGLGKLSDFEKERQQFSPFIKTFASFFSPQKNGIEKN 173
++L++L R +E +L + E KL KE Q + + + Q++ I++
Sbjct: 7 EKLESLLERYEELEALLSDPEVISDQDKLRKLSKEYSQLEEIVDCYREYQQAQED-IKEA 65
Query: 174 LGLGKLSDFE-KELVKAAVPELKKNIAKGEE 203
+ + SD E +E+ K + EL++ I + EE
Sbjct: 66 KEILEESDPEMREMAKEELEELEEKIEELEE 96
>gnl|CDD|200462 cd11323, AmyAc_AGS, Alpha amylase catalytic domain found in Alpha
1,3-glucan synthase (also called uridine
diphosphoglucose-1,3-alpha-glucan glucosyltransferase
and 1,3-alpha-D-glucan synthase). Alpha 1,3-glucan
synthase (AGS, EC 2.4.1.183) is an enzyme that catalyzes
the reversible chemical reaction of UDP-glucose and
[alpha-D-glucosyl-(1-3)]n to form UDP and
[alpha-D-glucosyl-(1-3)]n+1. AGS is a component of
fungal cell walls. The cell wall of filamentous fungi is
composed of 10-15% chitin and 10-35% alpha-1,3-glucan.
AGS is triggered in fungi as a response to cell wall
stress and elongates the glucan chains in cell wall
synthesis. This group includes proteins from Ascomycetes
and Basidomycetes. The Alpha-amylase family comprises
the largest family of glycoside hydrolases (GH), with
the majority of enzymes acting on starch, glycogen, and
related oligo- and polysaccharides. These proteins
catalyze the transformation of alpha-1,4 and alpha-1,6
glucosidic linkages with retention of the anomeric
center. The protein is described as having 3 domains: A,
B, C. A is a (beta/alpha) 8-barrel; B is a loop between
the beta 3 strand and alpha 3 helix of A; C is the
C-terminal extension characterized by a Greek key. The
majority of the enzymes have an active site cleft found
between domains A and B where a triad of catalytic
residues (Asp, Glu and Asp) performs catalysis. Other
members of this family have lost the catalytic activity
as in the case of the human 4F2hc, or only have 2
residues that serve as the catalytic nucleophile and the
acid/base, such as Thermus A4 beta-galactosidase with 2
Glu residues (GH42) and human alpha-galactosidase with 2
Asp residues (GH31). The family members are quite
extensive and include: alpha amylase,
maltosyltransferase, cyclodextrin glycotransferase,
maltogenic amylase, neopullulanase, isoamylase,
1,4-alpha-D-glucan maltotetrahydrolase,
4-alpha-glucotransferase, oligo-1,6-glucosidase,
amylosucrase, sucrose phosphorylase, and amylomaltase.
Length = 569
Score = 30.7 bits (70), Expect = 0.47
Identities = 9/18 (50%), Positives = 13/18 (72%)
Query: 52 GVFDPRRLFGVTTLDIVR 69
G FDPR ++GV+ D+ R
Sbjct: 438 GKFDPRHMYGVSNQDVFR 455
>gnl|CDD|148445 pfam06838, Alum_res, Aluminium resistance protein. This family
represents the aluminium resistance protein, which
confers resistance to aluminium in bacteria. Structural
characterisation has shown proteins in this family bind
a pyridoxal-5'-phosphate cofactor, and that they belongs
to the PLP dependent aminotransferase superfamily.
Crystal packing analysis suggests that in solution, a
tetramer may be the stable oligomeric form. This is in
contrast to most other aminotransferases which form
dimers (information from TOPSAN).
Length = 405
Score = 30.0 bits (68), Expect = 0.89
Identities = 28/90 (31%), Positives = 40/90 (44%), Gaps = 20/90 (22%)
Query: 60 FGVTTLDIVRANTFVAEAKGLNPTDVNVPVIGGHAGITIIPLISQATPSVSFPDDQLKAL 119
G TL+ V A F AEA + P V+ G HA I+ A V P D+L +
Sbjct: 55 IGRDTLERVYARVFGAEAALVRPQFVS----GTHA-------IATALFGVLRPGDELLYI 103
Query: 120 TGR----IQEAVSLKNGIEKNLGLGKLSDF 145
TG+ ++E + ++ G G L DF
Sbjct: 104 TGKPYDTLEEVIGIRGE-----GQGSLKDF 128
>gnl|CDD|223294 COG0216, PrfA, Protein chain release factor A [Translation,
ribosomal structure and biogenesis].
Length = 363
Score = 29.5 bits (67), Expect = 1.1
Identities = 21/98 (21%), Positives = 45/98 (45%), Gaps = 15/98 (15%)
Query: 114 DQLKALTGRIQEAVSLKNGIEKNLGLGKL-SDFE------KERQQFSPFIKTFASFFSPQ 166
++L++L R +E +E L ++ SD + KE + P ++ + + Q
Sbjct: 7 EKLESLLERYEE-------LEALLSDPEVISDPDEYRKLSKEYAELEPIVEKYREYKKAQ 59
Query: 167 KNGIEKNLGLGKLSDFE-KELVKAAVPELKKNIAKGEE 203
++ + L + D E +E+ + + EL+ I + EE
Sbjct: 60 EDLEDAKEMLAEEKDPEMREMAEEEIKELEAKIEELEE 97
>gnl|CDD|233976 TIGR02687, TIGR02687, TIGR02687 family protein. Members of this
family are uncharacterized proteins sporadically
distributed in bacteria and archaea, about 880 amino
acids in length. This protein is repeatedly found
upstream of another uncharacterized protein of about 470
amino acids in length, modeled by TIGR02688.
Length = 844
Score = 29.0 bits (65), Expect = 2.0
Identities = 12/47 (25%), Positives = 18/47 (38%), Gaps = 1/47 (2%)
Query: 142 LSDFEKERQQFSPFIKTFASFFSPQKNGIEKNLGLGKLSDFEKELVK 188
LS+ E + + + FF K ++ L D EKEL
Sbjct: 99 LSELEIDGLELRDHFQAREKFFG-AKERVQALKKLVTKDDREKELDL 144
>gnl|CDD|233002 TIGR00510, lipA, lipoate synthase. This enzyme is an iron-sulfur
protein. It is localized to mitochondria in yeast and
Arabidopsis. It generates lipoic acid, a thiol
antioxidant that is linked to a specific Lys as
prosthetic group for the pyruvate and
alpha-ketoglutarate dehydrogenase complexes and the
glycine-cleavage system. The family shows strong
sequence conservation [Biosynthesis of cofactors,
prosthetic groups, and carriers, Lipoate].
Length = 302
Score = 28.7 bits (64), Expect = 2.2
Identities = 11/32 (34%), Positives = 17/32 (53%)
Query: 3 RDDLFNTNASIVRDIIKAVAEVAPKALIGIIS 34
RDDL + AS + + I+A+ E P I +
Sbjct: 118 RDDLEDGGASHLAECIEAIREKLPNIKIETLV 149
>gnl|CDD|223968 COG1038, PycA, Pyruvate carboxylase [Energy production and
conversion].
Length = 1149
Score = 28.1 bits (63), Expect = 3.8
Identities = 20/69 (28%), Positives = 30/69 (43%), Gaps = 15/69 (21%)
Query: 62 VTTLDIVRANTFVAEAKGLNPTDVNVP-----VIGGHAGITIIPLISQATPSVSF-PDDQ 115
+T +DIV+A +A L+ ++ +P G+A I I+ P F PD
Sbjct: 309 ITGIDIVKAQIHIAAGATLHTPELGLPQQKDIRTHGYA---IQCRITTEDPENGFIPD-- 363
Query: 116 LKALTGRIQ 124
TGRI
Sbjct: 364 ----TGRIT 368
>gnl|CDD|226585 COG4100, COG4100, Cystathionine beta-lyase family protein involved
in aluminum resistance [Inorganic ion transport and
metabolism].
Length = 416
Score = 27.8 bits (62), Expect = 4.2
Identities = 26/86 (30%), Positives = 37/86 (43%), Gaps = 12/86 (13%)
Query: 60 FGVTTLDIVRANTFVAEAKGLNPTDVNVPVIGGHAGITIIPLISQATPSVSFPDDQLKAL 119
G TL+ V A F AEA + P ++ G HA I+ A + P D+L +
Sbjct: 65 LGRDTLERVYAQVFGAEAALVRPQIIS----GTHA-------IACALFGILRPGDELLYI 113
Query: 120 TGRIQEAVSLKNGIEKNLGLGKLSDF 145
TG + + G+ G G L DF
Sbjct: 114 TGSPYDTLEEVIGLRGE-GQGSLKDF 138
>gnl|CDD|235319 PRK04914, PRK04914, ATP-dependent helicase HepA; Validated.
Length = 956
Score = 27.9 bits (63), Expect = 5.2
Identities = 10/50 (20%), Positives = 19/50 (38%), Gaps = 9/50 (18%)
Query: 158 TFASFFSPQKNGIEKNLGLGKLSDFEKELVKAAVPELKKNIAKGEEFVAK 207
F S + Q + + ++ +LVKA ++ K + K E
Sbjct: 847 EFESL-NRQLSAVNRHTA--------SKLVKAVQQDIHKLLQKAEAQAEA 887
>gnl|CDD|131341 TIGR02288, PaaN_2, phenylacetic acid degradation protein paaN.
This enzyme is proposed to act in the ring-opening step
of phenylacetic acid degradation which follows ligation
of the acid with coenzyme A (by PaaF) and hydroxylation
by a multicomponent non-heme iron hydroxylase complex
(PaaGHIJK). Gene symbols have been standardized in. This
enzyme is related to aldehyde dehydrogenases and has a
domain which is a member of the pfam00171 family. This
family includes sequences from Burkholderia, Bordetella,
Streptomyces. Other PaaN enzymes are represented by a
separate model, TIGR02278.
Length = 551
Score = 27.5 bits (61), Expect = 5.3
Identities = 18/59 (30%), Positives = 26/59 (44%), Gaps = 5/59 (8%)
Query: 36 PVNSTVPIAAEVLKKAGVFDPRRLFGVTTLDIVRANTFVAEAKGLNPTDVNVPVIGGHA 94
P+ TV +A EVL +AG FDP + TL A+ +P + G +A
Sbjct: 235 PLALTVQVAREVLGEAG-FDP----NLVTLAAFDPGHEAAQRLATDPAVRIIDFTGSNA 288
>gnl|CDD|176258 cd08298, CAD2, Cinnamyl alcohol dehydrogenases (CAD). These
alcohol dehydrogenases are related to the cinnamyl
alcohol dehydrogenases (CAD), members of the medium
chain dehydrogenase/reductase family.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. Cinnamyl alcohol dehydrogenases
(CAD) reduce cinnamaldehydes to cinnamyl alcohols in the
last step of monolignal metabolism in plant cells walls.
CAD binds 2 zinc ions and is NADPH- dependent. CAD
family members are also found in non-plant species, e.g.
in yeast where they have an aldehyde reductase activity.
The medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 329
Score = 27.5 bits (62), Expect = 5.3
Identities = 19/65 (29%), Positives = 26/65 (40%), Gaps = 14/65 (21%)
Query: 22 AEVAPKALIG-IISNPVNSTVPIAAEVLKKAGV-------------FDPRRLFGVTTLDI 67
++ P+ L II PV + VP A +KK G FD L+G T+
Sbjct: 219 DDLPPEPLDAAIIFAPVGALVPAALRAVKKGGRVVLAGIHMSDIPAFDYELLWGEKTIRS 278
Query: 68 VRANT 72
V T
Sbjct: 279 VANLT 283
>gnl|CDD|183576 PRK12534, PRK12534, RNA polymerase sigma factor; Provisional.
Length = 187
Score = 26.9 bits (59), Expect = 5.7
Identities = 14/41 (34%), Positives = 20/41 (48%)
Query: 47 VLKKAGVFDPRRLFGVTTLDIVRANTFVAEAKGLNPTDVNV 87
+ KAG FDP R G+T L ++ N + + P NV
Sbjct: 63 IWHKAGQFDPSRARGLTWLAMIARNKAIDHLRANAPQRRNV 103
>gnl|CDD|223397 COG0320, LipA, Lipoate synthase [Coenzyme metabolism].
Length = 306
Score = 27.2 bits (61), Expect = 6.1
Identities = 15/51 (29%), Positives = 26/51 (50%), Gaps = 1/51 (1%)
Query: 2 TRDDLFNTNASIVRDIIKAVAEVAPKALIGIISNPVNSTVPIAAEVLKKAG 52
RDDL + A + I+A+ E+ P+ I +++ P A E++ AG
Sbjct: 123 DRDDLPDGGAQHFAECIRAIRELNPQTTIEVLT-PDFRGNDDALEIVADAG 172
>gnl|CDD|201390 pfam00682, HMGL-like, HMGL-like. This family contains a diverse
set of enzymes. These include various aldolases and a
region of pyruvate carboxylase.
Length = 236
Score = 26.9 bits (60), Expect = 7.5
Identities = 14/40 (35%), Positives = 20/40 (50%)
Query: 15 RDIIKAVAEVAPKALIGIISNPVNSTVPIAAEVLKKAGVF 54
+ ++A+AEV KA I + PV + A E K AG
Sbjct: 42 FESVRAIAEVLKKAKIQALLRPVEHDIDAAVEAAKGAGAD 81
>gnl|CDD|239364 cd03066, PDI_b_Calsequestrin_middle, PDIb family, Calsequestrin
subfamily, Middle TRX-fold domain; Calsequestrin is the
major calcium storage protein in the sarcoplasmic
reticulum (SR) of skeletal and cardiac muscle. It stores
calcium ions in sufficient quantities (up to 20 mM) to
allow repetitive contractions and is essential to
maintain movement, respiration and heart beat. A
missense mutation in human cardiac calsequestrin is
associated with catecholamine-induced polymorphic
ventricular tachycardia (CPVT), a rare disease
characterized by seizures or sudden death in response to
physiologic or emotional stress. Calsequestrin is a
highly acidic protein with up to 50 calcium binding
sites formed simply by the clustering of two or more
acidic residues. The monomer contains three redox
inactive TRX-fold domains. Calsequestrin is condensed as
a linear polymer in the SR lumen and is
membrane-anchored through binding with intra-membrane
proteins triadin, junctin and ryanodine receptor (RyR)
Ca2+ release channel. In addition to its role as a
calcium ion buffer, calsequestrin also regulates the
activity of the RyR channel, coordinating the release of
calcium ions from the SR with the loading of the calcium
store.
Length = 102
Score = 25.8 bits (57), Expect = 7.7
Identities = 14/32 (43%), Positives = 20/32 (62%), Gaps = 4/32 (12%)
Query: 145 FEKERQQFSPFIKTFASFFSPQKNGIEKNLGL 176
FE+ ++F P+IK FA+F S + K LGL
Sbjct: 38 FEEAAEEFHPYIKFFATFDS----KVAKKLGL 65
>gnl|CDD|213839 TIGR03629, arch_S13P, archaeal ribosomal protein S13P. This model
describes exclusively the archaeal ribosomal protein
S13P. It excludes the homologous eukaryotic 40S
ribosomal protein S18 and bacterial 30S ribosomal
protein S13 [Protein synthesis, Ribosomal proteins:
synthesis and modification].
Length = 144
Score = 26.1 bits (58), Expect = 8.6
Identities = 11/30 (36%), Positives = 16/30 (53%)
Query: 169 GIEKNLGLGKLSDFEKELVKAAVPELKKNI 198
G++ N LG L D E E ++ AV + I
Sbjct: 42 GVDPNAKLGYLDDEEIEKLEEAVENYEYGI 71
>gnl|CDD|226044 COG3513, COG3513, Predicted CRISPR-associated nuclease, contains
McrA/HNH-nuclease and RuvC-like nuclease domain [Defense
mechanisms].
Length = 1088
Score = 27.2 bits (60), Expect = 8.7
Identities = 18/70 (25%), Positives = 25/70 (35%), Gaps = 5/70 (7%)
Query: 127 VSLKNGIEKNLGLGKLSDFEKERQQFSPFIKTFASFFSPQKNGIEKNLGLGKLSDFEKEL 186
V L E N G F + +K + +P K I + +G+ K FEK
Sbjct: 1013 VKLITKKEDNFG-----KFITLSANTNILLKNHNAMGAPAKFKIFETIGVRKRYSFEKYQ 1067
Query: 187 VKAAVPELKK 196
V A E
Sbjct: 1068 VDALGIEQSI 1077
>gnl|CDD|222238 pfam13580, SIS_2, SIS domain. SIS (Sugar ISomerase) domains are
found in many phosphosugar isomerases and phosphosugar
binding proteins. SIS domains are also found in proteins
that regulate the expression of genes involved in
synthesis of phosphosugars.
Length = 138
Score = 26.0 bits (58), Expect = 8.8
Identities = 12/40 (30%), Positives = 21/40 (52%), Gaps = 1/40 (2%)
Query: 16 DIIKAVAEVAPKALIGIISNPVNSTVPI-AAEVLKKAGVF 54
I + ++ P ++ +ISN + VPI AA K+ G+
Sbjct: 93 RQILRLYDIRPGDVLIVISNSGRNAVPIEAALAAKERGMK 132
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
0.316 0.135 0.369
Gapped
Lambda K H
0.267 0.0806 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,936,329
Number of extensions: 1071381
Number of successful extensions: 1236
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1209
Number of HSP's successfully gapped: 86
Length of query: 208
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 115
Effective length of database: 6,812,680
Effective search space: 783458200
Effective search space used: 783458200
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 (21.6 bits)
S2: 57 (25.6 bits)