RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 021995
(304 letters)
>gnl|CDD|178684 PLN03139, PLN03139, formate dehydrogenase; Provisional.
Length = 386
Score = 554 bits (1430), Expect = 0.0
Identities = 224/248 (90%), Positives = 238/248 (95%)
Query: 57 AAAAAGLTVAEVTGSNVVSVAEDELMRILILVRNFLPGHHQVISGEWNVAGVAYRAYDLE 116
AAAAAGLTVAEVTGSNVVSVAEDELMRILIL+RNFLPG+HQV+SGEWNVAG+AYRAYDLE
Sbjct: 139 AAAAAGLTVAEVTGSNVVSVAEDELMRILILLRNFLPGYHQVVSGEWNVAGIAYRAYDLE 198
Query: 117 GKTVGTVGCGRIGKLLLQRLKPFNCNLLYHDRVKMDPQLEKETGAKFEEDLDTMLPKCDI 176
GKTVGTVG GRIG+LLLQRLKPFNCNLLYHDR+KMDP+LEKETGAKFEEDLD MLPKCD+
Sbjct: 199 GKTVGTVGAGRIGRLLLQRLKPFNCNLLYHDRLKMDPELEKETGAKFEEDLDAMLPKCDV 258
Query: 177 VVVNTPLTEKTRGMFDKDRIAKMKKGVLIVNNARGAIMDTQAVVDACSSGHIAGYSGDVW 236
VV+NTPLTEKTRGMF+K+RIAKMKKGVLIVNNARGAIMDTQAV DACSSGHI GY GDVW
Sbjct: 259 VVINTPLTEKTRGMFNKERIAKMKKGVLIVNNARGAIMDTQAVADACSSGHIGGYGGDVW 318
Query: 237 NPQPAPKDHPWRYMPNQAMTPHVSGTTIDAQLRYAAGVKDMLDRYFKGEDFPVQNYIVKA 296
PQPAPKDHPWRYMPN AMTPH+SGTTIDAQLRYAAGVKDMLDRYFKGEDFP QNYIVK
Sbjct: 319 YPQPAPKDHPWRYMPNHAMTPHISGTTIDAQLRYAAGVKDMLDRYFKGEDFPAQNYIVKE 378
Query: 297 GELAPQYR 304
G+LA QY+
Sbjct: 379 GKLASQYQ 386
Score = 68.7 bits (168), Expect = 4e-13
Identities = 33/69 (47%), Positives = 41/69 (59%), Gaps = 3/69 (4%)
Query: 2 AMKRVASSAINAFASS---GFLRSSSRFSRHYASSGSKKIVGVFYKGNEYASMNPNFLAA 58
AM+R A AI AF+SS L + S +AS+GSKKIVGVFYK EYA NPNF+
Sbjct: 1 AMRRAAQVAIRAFSSSSPAHLLTRALASSSLHASAGSKKIVGVFYKAGEYADKNPNFVGC 60
Query: 59 AAAGLTVAE 67
L + +
Sbjct: 61 VENALGIRD 69
>gnl|CDD|240627 cd05302, FDH, NAD-dependent Formate Dehydrogenase (FDH).
NAD-dependent formate dehydrogenase (FDH) catalyzes the
NAD+-dependent oxidation of a formate anion to carbon
dioxide coupled with the reduction of NAD+ to NADH.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxy acid dehydrogenase family have 2
highly similar subdomains of the alpha/beta form, with
NAD binding occurring in the cleft between subdomains.
NAD contacts are primarily to the Rossmann-fold
NAD-binding domain which is inserted within the linear
sequence of the more diverse flavodoxin-like catalytic
subdomain. Some related proteins have similar structural
subdomain but with a tandem arrangement of the catalytic
and NAD-binding subdomains in the linear sequence. FDHs
of this family contain no metal ions or prosthetic
groups. Catalysis occurs though direct transfer of the
hydride ion to NAD+ without the stages of acid-base
catalysis typically found in related dehydrogenases.
FDHs are found in all methylotrophic microorganisms in
energy production from C1 compounds such as methanol,
and in the stress responses of plants. NAD-dependent FDH
is useful in cofactor regeneration in asymmetrical
biocatalytic reduction processes, where FDH irreversibly
oxidizes formate to carbon dioxide, while reducing the
oxidized form of the cofactor to the reduced form.
Length = 348
Score = 460 bits (1185), Expect = e-164
Identities = 152/247 (61%), Positives = 191/247 (77%)
Query: 57 AAAAAGLTVAEVTGSNVVSVAEDELMRILILVRNFLPGHHQVISGEWNVAGVAYRAYDLE 116
AA G+TVAEVTGSNVVSVAE +M ILILVRN++PGH Q I G WNVA V RAYDLE
Sbjct: 102 AANDRGITVAEVTGSNVVSVAEHVVMMILILVRNYVPGHEQAIEGGWNVADVVKRAYDLE 161
Query: 117 GKTVGTVGCGRIGKLLLQRLKPFNCNLLYHDRVKMDPQLEKETGAKFEEDLDTMLPKCDI 176
GKTVGTVG GRIG +L+RLKPF+ +LLY+DR ++ ++EKE G DL+ M+ KCD+
Sbjct: 162 GKTVGTVGAGRIGLRVLRRLKPFDVHLLYYDRHRLPEEVEKELGLTRHADLEDMVSKCDV 221
Query: 177 VVVNTPLTEKTRGMFDKDRIAKMKKGVLIVNNARGAIMDTQAVVDACSSGHIAGYSGDVW 236
V +N PL +T G+F+K+ ++KMKKG +VN ARG I D +AV +A SGH+AGY+GDVW
Sbjct: 222 VTINCPLHPETEGLFNKELLSKMKKGAYLVNTARGKICDREAVAEALESGHLAGYAGDVW 281
Query: 237 NPQPAPKDHPWRYMPNQAMTPHVSGTTIDAQLRYAAGVKDMLDRYFKGEDFPVQNYIVKA 296
PQPAPKDHPWR MPN AMTPH+SGTT+DAQ RYAAG K++L+R+F+GE F + IV+
Sbjct: 282 FPQPAPKDHPWRTMPNNAMTPHISGTTLDAQARYAAGTKEILERFFEGEPFRPEYLIVQG 341
Query: 297 GELAPQY 303
G+LA +
Sbjct: 342 GKLAGKG 348
Score = 35.0 bits (81), Expect = 0.035
Identities = 9/21 (42%), Positives = 10/21 (47%)
Query: 36 KKIVGVFYKGNEYASMNPNFL 56
KIV V Y E+ PN L
Sbjct: 1 AKIVCVLYDDGEHGYKPPNLL 21
>gnl|CDD|181041 PRK07574, PRK07574, formate dehydrogenase; Provisional.
Length = 385
Score = 363 bits (933), Expect = e-125
Identities = 127/244 (52%), Positives = 169/244 (69%)
Query: 57 AAAAAGLTVAEVTGSNVVSVAEDELMRILILVRNFLPGHHQVISGEWNVAGVAYRAYDLE 116
AA+ G+TVAEVTGSN +SVAE +M IL LVRN+ P H Q + G WN+A R+YDLE
Sbjct: 132 AASEHGITVAEVTGSNSISVAEHVVMMILALVRNYEPSHRQAVEGGWNIADCVSRSYDLE 191
Query: 117 GKTVGTVGCGRIGKLLLQRLKPFNCNLLYHDRVKMDPQLEKETGAKFEEDLDTMLPKCDI 176
G TVG VG GRIG +L+RLKPF+ L Y DR ++ ++E+E G + D+++ CD+
Sbjct: 192 GMTVGIVGAGRIGLAVLRRLKPFDVKLHYTDRHRLPEEVEQELGLTYHVSFDSLVSVCDV 251
Query: 177 VVVNTPLTEKTRGMFDKDRIAKMKKGVLIVNNARGAIMDTQAVVDACSSGHIAGYSGDVW 236
V ++ PL +T +FD D +++MK+G +VN ARG I+D AVV A SGH+AGY+GDVW
Sbjct: 252 VTIHCPLHPETEHLFDADVLSRMKRGSYLVNTARGKIVDRDAVVRALESGHLAGYAGDVW 311
Query: 237 NPQPAPKDHPWRYMPNQAMTPHVSGTTIDAQLRYAAGVKDMLDRYFKGEDFPVQNYIVKA 296
PQPAP DHPWR MP MTPH+SGTT+ AQ RYAAG +++L+ +F+G + IV
Sbjct: 312 FPQPAPADHPWRTMPRNGMTPHISGTTLSAQARYAAGTREILECFFEGRPIRDEYLIVDG 371
Query: 297 GELA 300
G LA
Sbjct: 372 GRLA 375
>gnl|CDD|240622 cd05198, formate_dh_like, Formate/glycerate and related
dehydrogenases of the D-specific 2-hydroxy acid
dehydrogenase family. Formate dehydrogenase, D-specific
2-hydroxy acid dehydrogenase, Phosphoglycerate
Dehydrogenase, Lactate dehydrogenase, Thermostable
Phosphite Dehydrogenase, and Hydroxy(phenyl)pyruvate
reductase, among others, share a characteristic
arrangement of 2 similar subdomains of the alpha/beta
Rossmann fold NAD+ binding form. 2-hydroxyacid
dehydrogenases are enzymes that catalyze the conversion
of a wide variety of D-2-hydroxy acids to their
corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
The NAD+ binding domain is inserted within the linear
sequence of the mostly N-terminal catalytic domain,
which has a similar domain structure to the internal NAD
binding domain. Structurally, these domains are
connected by extended alpha helices and create a cleft
in which NAD is bound, primarily to the C-terminal
portion of the 2nd (internal) domain. Some related
proteins have similar structural subdomain but with a
tandem arrangement of the catalytic and NAD-binding
subdomains in the linear sequence. Formate dehydrogenase
(FDH) catalyzes the NAD+-dependent oxidation of formate
ion to carbon dioxide with the concomitant reduction of
NAD+ to NADH. FDHs of this family contain no metal ions
or prosthetic groups. Catalysis occurs though direct
transfer of hydride ion to NAD+ without the stages of
acid-base catalysis typically found in related
dehydrogenases. FDHs are found in all methylotrophic
microorganisms in energy production and in the stress
responses of plants. Formate/glycerate and related
dehydrogenases of the D-specific 2-hydroxyacid
dehydrogenase superfamily include groups such as formate
dehydrogenase, glycerate dehydrogenase, L-alanine
dehydrogenase, and S-Adenosylhomocysteine Hydrolase,
among others. While many members of this family are
dimeric, alanine DH is hexameric and phosphoglycerate DH
is tetrameric.
Length = 302
Score = 249 bits (637), Expect = 8e-82
Identities = 90/225 (40%), Positives = 137/225 (60%), Gaps = 3/225 (1%)
Query: 57 AAAAAGLTVAEVTGSNVVSVAEDELMRILILVRNFLPGHHQVISGEWNVAGVAYRAYDLE 116
AA G+TV V G+N +VAE L +L L+R V G W + Y+LE
Sbjct: 81 AAKKRGITVTNVPGANAEAVAEHALGLLLALLRRLPRADAAVRRG-WGWLWAGFPGYELE 139
Query: 117 GKTVGTVGCGRIGKLLLQRLKPFNCNLLYHDRVKMDPQLEKETGAKFEEDLDTMLPKCDI 176
GKTVG VG GRIG+ + +RL+ F +LY+DR + P+ E++ G + LD +L + D+
Sbjct: 140 GKTVGIVGLGRIGQRVAKRLQAFGMKVLYYDRTRK-PEPEEDLGFRVV-SLDELLAQSDV 197
Query: 177 VVVNTPLTEKTRGMFDKDRIAKMKKGVLIVNNARGAIMDTQAVVDACSSGHIAGYSGDVW 236
VV++ PLT +TR + +++ +A MK G ++VN ARG ++D A++ A SG IAG + DV+
Sbjct: 198 VVLHLPLTPETRHLINEEELALMKPGAVLVNTARGGLVDEDALLRALKSGKIAGAALDVF 257
Query: 237 NPQPAPKDHPWRYMPNQAMTPHVSGTTIDAQLRYAAGVKDMLDRY 281
P+P P DHP +PN +TPH++G T +A+ R A + L+R+
Sbjct: 258 EPEPLPADHPLLELPNVILTPHIAGYTEEARERMAEIAVENLERF 302
>gnl|CDD|223980 COG1052, LdhA, Lactate dehydrogenase and related dehydrogenases
[Energy production and conversion / Coenzyme metabolism
/ General function prediction only].
Length = 324
Score = 240 bits (615), Expect = 3e-78
Identities = 94/246 (38%), Positives = 141/246 (57%), Gaps = 10/246 (4%)
Query: 57 AAAAAGLTVAEVTGSNVVSVAEDELMRILILVRNFLPGHHQVISGEWNVAGVAYR--AYD 114
AA G+TV V G + +VAE + IL L R G +V G W+++G +D
Sbjct: 84 AAKERGITVTNVPGYSTEAVAEHAVALILALARRIHEGDRRVREGNWSLSGGPDPLLGFD 143
Query: 115 LEGKTVGTVGCGRIGKLLLQRLKPFNCNLLYHDRVKMDPQLEKETGAKFEEDLDTMLPKC 174
L GKT+G +G GRIG+ + +RLK F +LY+DR +P+ EKE GA++ DLD +L +
Sbjct: 144 LRGKTLGIIGLGRIGQAVARRLKGFGMKVLYYDRSP-NPEAEKELGARYV-DLDELLAES 201
Query: 175 DIVVVNTPLTEKTRGMFDKDRIAKMKKGVLIVNNARGAIMDTQAVVDACSSGHIAGYSGD 234
DI+ ++ PLT +TR + + + +AKMK G ++VN ARG ++D QA++DA SG IAG D
Sbjct: 202 DIISLHCPLTPETRHLINAEELAKMKPGAILVNTARGGLVDEQALIDALKSGKIAGAGLD 261
Query: 235 VWNPQPAPKDHPWRYMPNQ---AMTPHVSGTTIDAQLRYAAGVKDMLDRYFKGEDFPVQN 291
V+ +PA DHP + N +TPH++ T +A+ A + L+ +F G V
Sbjct: 262 VFENEPALFDHPLLRLDNFPNVVLTPHIASATEEARKAMAELALENLEAFFDGG---VPP 318
Query: 292 YIVKAG 297
V
Sbjct: 319 NEVNPE 324
>gnl|CDD|223189 COG0111, SerA, Phosphoglycerate dehydrogenase and related
dehydrogenases [Amino acid transport and metabolism].
Length = 324
Score = 219 bits (559), Expect = 8e-70
Identities = 85/229 (37%), Positives = 127/229 (55%), Gaps = 3/229 (1%)
Query: 57 AAAAAGLTVAEVTGSNVVSVAEDELMRILILVRNFLPGHHQVISGEWNVAGVAYRAYDLE 116
AA G+ V G N +SVAE L +L L R GEW+ A+R +L
Sbjct: 84 AATKRGILVVNAPGGNAISVAELVLALLLALARRIPDADASQRRGEWD--RKAFRGTELA 141
Query: 117 GKTVGTVGCGRIGKLLLQRLKPFNCNLLYHDRVKMDPQLEKETGAKFEEDLDTMLPKCDI 176
GKTVG +G GRIG+ + +RLK F ++ +D + G + LD +L + DI
Sbjct: 142 GKTVGIIGLGRIGRAVAKRLKAFGMKVIGYDPYSP-RERAGVDGVVGVDSLDELLAEADI 200
Query: 177 VVVNTPLTEKTRGMFDKDRIAKMKKGVLIVNNARGAIMDTQAVVDACSSGHIAGYSGDVW 236
+ ++ PLT +TRG+ + + +AKMK G +++N ARG ++D A++ A SG IAG + DV+
Sbjct: 201 LTLHLPLTPETRGLINAEELAKMKPGAILINAARGGVVDEDALLAALDSGKIAGAALDVF 260
Query: 237 NPQPAPKDHPWRYMPNQAMTPHVSGTTIDAQLRYAAGVKDMLDRYFKGE 285
+P P D P +PN +TPH+ G+T +AQ R A V + + RY G
Sbjct: 261 EEEPLPADSPLWDLPNVILTPHIGGSTDEAQERVAEIVAENIVRYLAGG 309
>gnl|CDD|240652 cd12175, 2-Hacid_dh_11, Putative D-isomer specific 2-hydroxyacid
dehydrogenases, NAD-binding and catalytic domains.
2-Hydroxyacid dehydrogenases catalyze the conversion of
a wide variety of D-2-hydroxy acids to their
corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 311
Score = 212 bits (541), Expect = 3e-67
Identities = 84/230 (36%), Positives = 134/230 (58%), Gaps = 2/230 (0%)
Query: 57 AAAAAGLTVAEVTGSNVVSVAEDELMRILILVRNFLPGHHQVISGEWNVAGVAYRAYDLE 116
AA A G+ VA + G N SVAE +M +L L+R ++ +G W + +L
Sbjct: 83 AATARGIPVANIPGGNAESVAEHAVMLMLALLRRLPEADRELRAGRWG-RPEGRPSRELS 141
Query: 117 GKTVGTVGCGRIGKLLLQRLKPFNCNLLYHDRVKMDPQLEKETGAKFEEDLDTMLPKCDI 176
GKTVG VG G IG+ + +RL+ F ++Y+DR + EK+ G ++ E LD +L + D+
Sbjct: 142 GKTVGIVGLGNIGRAVARRLRGFGVEVIYYDRFRDPEAEEKDLGVRYVE-LDELLAESDV 200
Query: 177 VVVNTPLTEKTRGMFDKDRIAKMKKGVLIVNNARGAIMDTQAVVDACSSGHIAGYSGDVW 236
V ++ PLT +TR + + +A MK G +++N ARG ++D +A++ A SGH+AG DV+
Sbjct: 201 VSLHVPLTPETRHLIGAEELAAMKPGAILINTARGGLVDEEALLAALRSGHLAGAGLDVF 260
Query: 237 NPQPAPKDHPWRYMPNQAMTPHVSGTTIDAQLRYAAGVKDMLDRYFKGED 286
+P P D P + N +TPH++G T ++ R AA V + + R +GE
Sbjct: 261 WQEPLPPDDPLLRLDNVILTPHIAGVTDESYQRMAAIVAENIARLLRGEP 310
>gnl|CDD|240650 cd12173, PGDH_4, Phosphoglycerate dehydrogenases, NAD-binding and
catalytic domains. Phosphoglycerate dehydrogenases
(PGDHs) catalyze the initial step in the biosynthesis of
L-serine from D-3-phosphoglycerate. PGDHs come in 3
distinct structural forms, with this first group being
related to 2-hydroxy acid dehydrogenases, sharing
structural similarity to formate and glycerate
dehydrogenases. PGDH in E. coli and Mycobacterium
tuberculosis form tetramers, with subunits containing a
Rossmann-fold NAD binding domain. Formate/glycerate and
related dehydrogenases of the D-specific 2-hydroxyacid
dehydrogenase superfamily include groups such as formate
dehydrogenase, glycerate dehydrogenase, L-alanine
dehydrogenase, and S-adenosylhomocysteine hydrolase.
Despite often low sequence identity, these proteins
typically have a characteristic arrangement of 2 similar
subdomains of the alpha/beta Rossmann fold NAD+ binding
form. The NAD+ binding domain is inserted within the
linear sequence of the mostly N-terminal catalytic
domain, which has a similar domain structure to the
internal NAD binding domain. Structurally, these domains
are connected by extended alpha helices and create a
cleft in which NAD is bound, primarily to the C-terminal
portion of the 2nd (internal) domain. Some related
proteins have similar structural subdomain but with a
tandem arrangement of the catalytic and NAD-binding
subdomains in the linear sequence.
Length = 304
Score = 211 bits (539), Expect = 5e-67
Identities = 81/229 (35%), Positives = 127/229 (55%), Gaps = 4/229 (1%)
Query: 57 AAAAAGLTVAEVTGSNVVSVAEDELMRILILVRNFLPGHHQVISGEWNVAGVAYRAYDLE 116
AA A G+ V G+N +SVAE + +L L RN + +G+W+ + +L
Sbjct: 80 AATARGILVVNAPGANTISVAEHTIALMLALARNIPQADASLRAGKWDRK--KFMGVELR 137
Query: 117 GKTVGTVGCGRIGKLLLQRLKPFNCNLLYHDRVKMDPQLEKETGAKFEEDLDTMLPKCDI 176
GKT+G VG GRIG+ + +R + F +L +D + + G + LD +L + D
Sbjct: 138 GKTLGIVGLGRIGREVARRARAFGMKVLAYDPY-ISAERAAAGGVELV-SLDELLAEADF 195
Query: 177 VVVNTPLTEKTRGMFDKDRIAKMKKGVLIVNNARGAIMDTQAVVDACSSGHIAGYSGDVW 236
+ ++TPLT +TRG+ + + +AKMK G +++N ARG I+D A+ DA SG IAG + DV+
Sbjct: 196 ISLHTPLTPETRGLINAEELAKMKPGAILINTARGGIVDEAALADALKSGKIAGAALDVF 255
Query: 237 NPQPAPKDHPWRYMPNQAMTPHVSGTTIDAQLRYAAGVKDMLDRYFKGE 285
+P P D P +PN +TPH+ +T +AQ R A + + GE
Sbjct: 256 EQEPPPADSPLLGLPNVILTPHLGASTEEAQERVAVDAAEQVLAVLAGE 304
>gnl|CDD|217244 pfam02826, 2-Hacid_dh_C, D-isomer specific 2-hydroxyacid
dehydrogenase, NAD binding domain. This domain is
inserted into the catalytic domain, the large
dehydrogenase and D-lactate dehydrogenase families in
SCOP. N-terminal portion of which is represented by
family pfam00389.
Length = 175
Score = 203 bits (518), Expect = 1e-65
Identities = 68/180 (37%), Positives = 105/180 (58%), Gaps = 5/180 (2%)
Query: 81 LMRILILVRNFLPGHHQVISGEWNVAGVAYRAYDLEGKTVGTVGCGRIGKLLLQRLKPFN 140
L +L L R QV +G W A +L GKTVG +G GRIG+ + +RLK F
Sbjct: 1 LALLLALARRIPEADRQVRAGRWR--PDALLGRELSGKTVGIIGLGRIGRAVARRLKAFG 58
Query: 141 CNLLYHDRVKMDPQLEKETGAKFEEDLDTMLPKCDIVVVNTPLTEKTRGMFDKDRIAKMK 200
++ +DR + GA++ LD +L + D+V ++ PLT +TR + + +R+A MK
Sbjct: 59 MKVIAYDRYPKAE--AEALGARYV-SLDELLAESDVVSLHLPLTPETRHLINAERLALMK 115
Query: 201 KGVLIVNNARGAIMDTQAVVDACSSGHIAGYSGDVWNPQPAPKDHPWRYMPNQAMTPHVS 260
G +++N ARG ++D A++ A SG IAG + DV+ P+P P DHP +PN +TPH++
Sbjct: 116 PGAILINTARGGLVDEDALIAALKSGRIAGAALDVFEPEPLPPDHPLLELPNVILTPHIA 175
>gnl|CDD|240631 cd12154, FDH_GDH_like, Formate/glycerate dehydrogenases, D-specific
2-hydroxy acid dehydrogenases and related
dehydrogenases. The formate/glycerate dehydrogenase
like family contains a diverse group of enzymes such as
formate dehydrogenase (FDH), glycerate dehydrogenase
(GDH), D-lactate dehydrogenase, L-alanine dehydrogenase,
and S-Adenosylhomocysteine hydrolase, that share a
common 2-domain structure. Despite often low sequence
identity, these proteins typically have a characteristic
arrangement of 2 similar domains of the alpha/beta
Rossmann fold NAD+ binding form. The NAD(P) binding
domain is inserted within the linear sequence of the
mostly N-terminal catalytic domain. Structurally, these
domains are connected by extended alpha helices and
create a cleft in which NAD(P) is bound, primarily to
the C-terminal portion of the 2nd (internal) domain.
While many members of this family are dimeric, alanine
DH is hexameric and phosphoglycerate DH is tetrameric.
2-hydroxyacid dehydrogenases are enzymes that catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate dehydrogenase (FDH) catalyzes the NAD+-dependent
oxidation of formate ion to carbon dioxide with the
concomitant reduction of NAD+ to NADH. FDHs of this
family contain no metal ions or prosthetic groups.
Catalysis occurs though direct transfer of a hydride ion
to NAD+ without the stages of acid-base catalysis
typically found in related dehydrogenases.
Length = 310
Score = 192 bits (490), Expect = 9e-60
Identities = 67/234 (28%), Positives = 91/234 (38%), Gaps = 38/234 (16%)
Query: 57 AAAAAGLTVAEVTG-------SNVVSVAEDELMRILILVRNFLPGHHQVISGEWNVAGVA 109
A A AGLT V G SN + E + I + PG
Sbjct: 106 ALARAGLTAIAVEGVELPLLTSNSIGAGELSVQFIARFLEVQQPGR-------------L 152
Query: 110 YRAYDLEGKTVGTVGCGRIGKLLLQRLKPFNCNLLYHDRVKMDPQLEKETGAKFEEDLDT 169
A D+ GKTV VG G +GK Q L+ +L D + +E G K E+L+
Sbjct: 153 GGAPDVAGKTVVVVGAGVVGKEAAQMLRGLGAQVLITDINVEALEQLEELGGKNVEELEE 212
Query: 170 MLPKCDIVVVNTPLTEKTRGMF-DKDRIAKMKKGVLIVNNARGAIMDTQAVV-DACSSGH 227
L + D++V T L K G+ ++ + +MK G +IVN A GA+ QA+ GH
Sbjct: 213 ALAEADVIVTTTLLPGKRAGILVPEELVEQMKPGSVIVNVAVGAVGCVQALHTQLLEEGH 272
Query: 228 IAGYSGDVWNPQPAPKDHPWRYMPNQAMTPHVSGTTIDAQLRYAAGVKDMLDRY 281
+ GDV P P G DA LR AA L +
Sbjct: 273 GVVHYGDVNMPGPGC----------------AMGVPWDATLRLAANTLPALVKL 310
>gnl|CDD|240649 cd12172, PGDH_like_2, Putative D-3-Phosphoglycerate Dehydrogenases,
NAD-binding and catalytic domains. Phosphoglycerate
dehydrogenases (PGDHs) catalyze the initial step in the
biosynthesis of L-serine from D-3-phosphoglycerate.
PGDHs come in 3 distinct structural forms, with this
first group being related to 2-hydroxy acid
dehydrogenases, sharing structural similarity to formate
and glycerate dehydrogenases of the D-specific
2-hydroxyacid dehydrogenase superfamily, which also
include groups such as L-alanine dehydrogenase and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. Many, not all, members of this family are
dimeric.
Length = 306
Score = 191 bits (489), Expect = 2e-59
Identities = 76/227 (33%), Positives = 119/227 (52%), Gaps = 6/227 (2%)
Query: 57 AAAAAGLTVAEVTGSNVVSVAEDELMRILILVRNFLPGHHQVISGEWNVAGVAYRAYDLE 116
AA G+ V G+N SVAE + +L L R +V +G W+ +L
Sbjct: 86 AAKKRGIVVTNTPGANSNSVAELTIGLMLALARQIPQADREVRAGGWDRPV----GTELY 141
Query: 117 GKTVGTVGCGRIGKLLLQRLKPFNCNLLYHDRVKMDPQLEKETGAKFEEDLDTMLPKCDI 176
GKT+G +G GRIGK + +RL F +L +D D + KE G +F L+ +L + D
Sbjct: 142 GKTLGIIGLGRIGKAVARRLSGFGMKVLAYDPYP-DEEFAKEHGVEFV-SLEELLKESDF 199
Query: 177 VVVNTPLTEKTRGMFDKDRIAKMKKGVLIVNNARGAIMDTQAVVDACSSGHIAGYSGDVW 236
+ ++ PLT +TR + + +A MK G +++N ARG ++D +A+ +A SG IAG + DV+
Sbjct: 200 ISLHLPLTPETRHLINAAELALMKPGAILINTARGGLVDEEALYEALKSGRIAGAALDVF 259
Query: 237 NPQPAPKDHPWRYMPNQAMTPHVSGTTIDAQLRYAAGVKDMLDRYFK 283
+P P D P +PN +TPH+ +T +A LR +
Sbjct: 260 EEEPPPADSPLLELPNVILTPHIGASTKEAVLRMGTMAAQNVIDVLA 306
>gnl|CDD|240645 cd12168, Mand_dh_like, D-Mandelate Dehydrogenase-like
dehydrogenases. D-Mandelate dehydrogenase (D-ManDH),
identified as an enzyme that interconverts
benzoylformate and D-mandelate, is a D-2-hydroxyacid
dehydrogenase family member that catalyzes the
conversion of c3-branched 2-ketoacids. D-ManDH exhibits
broad substrate specificities for 2-ketoacids with large
hydrophobic side chains, particularly those with
C3-branched side chains. 2-hydroxyacid dehydrogenases
catalyze the conversion of a wide variety of D-2-hydroxy
acids to their corresponding keto acids. The general
mechanism is (R)-lactate + acceptor to pyruvate +
reduced acceptor. Glycerate dehydrogenase catalyzes the
reaction (R)-glycerate + NAD+ to hydroxypyruvate + NADH
+ H+. Formate/glycerate and related dehydrogenases of
the D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain.
Length = 321
Score = 188 bits (481), Expect = 4e-58
Identities = 77/230 (33%), Positives = 121/230 (52%), Gaps = 6/230 (2%)
Query: 57 AAAAAGLTVAEVTGSNVVSVAEDELMRILILVRNFLPGHHQVISGEWNVAGVAYRAYDLE 116
A G+ V+ G+ + A+ L IL +RNF +G+W A+D
Sbjct: 94 ALTKRGIQVSNTPGAVDEATADTALFLILGALRNFSRAERSARAGKWRGFLDLTLAHDPR 153
Query: 117 GKTVGTVGCGRIGKLLLQRLKPFNCNLLYHDRVKMDPQLEKETGAKFEEDLDTMLPKCDI 176
GKT+G +G G IGK + ++ F ++YH+R ++ +LEK A + LD +L + D+
Sbjct: 154 GKTLGILGLGGIGKAIARKAAAFGMKIIYHNRSRLPEELEKAL-ATYYVSLDELLAQSDV 212
Query: 177 VVVNTPLTEKTRGMFDKDRIAKMKKGVLIVNNARGAIMDTQAVVDACSSGHIAGYSGDVW 236
V +N PLT TR + +K AKMK GV+IVN ARGA++D A+VDA SG +A DV+
Sbjct: 213 VSLNCPLTAATRHLINKKEFAKMKDGVIIVNTARGAVIDEDALVDALESGKVASAGLDVF 272
Query: 237 N--PQPAPKDHPWRYMPNQAMTPHVSGTTIDAQLRYAAGVKDMLDRYFKG 284
P+ P MPN + PH+ T++ Q + V + ++ + +
Sbjct: 273 ENEPEVNPG---LLKMPNVTLLPHMGTLTVETQEKMEELVLENIEAFLET 319
>gnl|CDD|240648 cd12171, 2-Hacid_dh_10, Putative D-isomer specific 2-hydroxyacid
dehydrogenases. 2-Hydroxyacid dehydrogenases catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 310
Score = 184 bits (470), Expect = 1e-56
Identities = 79/228 (34%), Positives = 116/228 (50%), Gaps = 4/228 (1%)
Query: 57 AAAAAGLTVAEVTGSNVVSVAEDELMRILILVRNFLPGHHQVISGEWNVAGVAYRAY--D 114
AA G+ V G N +VAE + +L RN H + GEW Y Y +
Sbjct: 85 AATERGIPVLNTPGRNAEAVAEFTVGLMLAETRNIARAHAALKDGEWRKDYYNYDGYGPE 144
Query: 115 LEGKTVGTVGCGRIGKLLLQRLKPFNCNLLYHDRVKMDPQLEKETGAKFEEDLDTMLPKC 174
L GKTVG VG G IG+ + +RLK F +L +D +DP+ + G K L+ +L +
Sbjct: 145 LRGKTVGIVGFGAIGRRVAKRLKAFGAEVLVYDPY-VDPEKIEADGVKKV-SLEELLKRS 202
Query: 175 DIVVVNTPLTEKTRGMFDKDRIAKMKKGVLIVNNARGAIMDTQAVVDACSSGHIAGYSGD 234
D+V ++ LT +TRGM + A MK +N AR ++D A+++A G I G + D
Sbjct: 203 DVVSLHARLTPETRGMIGAEEFALMKPTAYFINTARAGLVDEDALIEALEEGKIGGAALD 262
Query: 235 VWNPQPAPKDHPWRYMPNQAMTPHVSGTTIDAQLRYAAGVKDMLDRYF 282
V+ +P P DHP + N +TPH++G T D R + + L RY
Sbjct: 263 VFPEEPLPADHPLLKLDNVTLTPHIAGATRDVAERSPEIIAEELKRYL 310
>gnl|CDD|240626 cd05301, GDH, D-glycerate dehydrogenase/hydroxypyruvate reductase
(GDH). D-glycerate dehydrogenase (GDH, also known as
hydroxypyruvate reductase, HPR) catalyzes the reversible
reaction of (R)-glycerate + NAD+ to hydroxypyruvate +
NADH + H+. In humans, HPR deficiency causes primary
hyperoxaluria type 2, characterized by over-excretion of
L-glycerate and oxalate in the urine, possibly due to an
imbalance in competition with L-lactate dehydrogenase,
another formate dehydrogenase (FDH)-like enzyme. GDH,
like FDH and other members of the D-specific hydroxyacid
dehydrogenase family that also includes L-alanine
dehydrogenase and S-adenosylhomocysteine hydrolase,
typically have a characteristic arrangement of 2 similar
subdomains of the alpha/beta Rossmann-fold NAD+ binding
form, despite often low sequence identity. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 309
Score = 179 bits (456), Expect = 2e-54
Identities = 82/213 (38%), Positives = 123/213 (57%), Gaps = 14/213 (6%)
Query: 57 AAAAAGLTVAEVTGSN---VVSVAEDELMRILIL--VRNFLPGHHQVISGEW-NVAGVAY 110
AA A G+ V +N V++ A +L L+L R + G V +GEW +
Sbjct: 83 AAKARGIPV-----TNTPDVLTDATADLAFALLLAAARRVVEGDRFVRAGEWKGWSPTLL 137
Query: 111 RAYDLEGKTVGTVGCGRIGKLLLQRLKPFNCNLLYHDRVKMDPQLEKETGAKFEEDLDTM 170
DL GKT+G VG GRIG+ + +R K F +LYH+R + P+ E+E GA++ LD +
Sbjct: 138 LGTDLHGKTLGIVGMGRIGQAVARRAKGFGMKILYHNRSRK-PEAEEELGARYV-SLDEL 195
Query: 171 LPKCDIVVVNTPLTEKTRGMFDKDRIAKMKKGVLIVNNARGAIMDTQAVVDACSSGHIAG 230
L + D V ++ PLT +TR + + +R+A MK +++N ARG ++D A+V+A SG IAG
Sbjct: 196 LAESDFVSLHCPLTPETRHLINAERLALMKPTAILINTARGGVVDEDALVEALKSGKIAG 255
Query: 231 YSGDVWNPQPAPKDHPWRYMPNQAMTPHV-SGT 262
DV+ P+P P DHP +PN + PH+ S T
Sbjct: 256 AGLDVFEPEPLPADHPLLTLPNVVLLPHIGSAT 288
>gnl|CDD|237436 PRK13581, PRK13581, D-3-phosphoglycerate dehydrogenase;
Provisional.
Length = 526
Score = 178 bits (454), Expect = 5e-52
Identities = 82/243 (33%), Positives = 127/243 (52%), Gaps = 23/243 (9%)
Query: 57 AAAAAGLTVAEVTGSNVVSVAEDELMRILILVRNFLPGHHQVISGEWNVAGVAYRAYDLE 116
AA G+ V N +S AE + +L L RN H + +G+W + +L
Sbjct: 82 AATRRGIIVVNAPTGNTISAAEHTIALMLALARNIPQAHASLKAGKWERK--KFMGVELY 139
Query: 117 GKTVGTVGCGRIGKLLLQRLKPFNCNLL-YHDRVKMDPQLEKETGAKFEE------DLDT 169
GKT+G +G GRIG + +R K F ++ Y DP + + + + LD
Sbjct: 140 GKTLGIIGLGRIGSEVAKRAKAFGMKVIAY------DPYI---SPERAAQLGVELVSLDE 190
Query: 170 MLPKCDIVVVNTPLTEKTRGMFDKDRIAKMKKGVLIVNNARGAIMDTQAVVDACSSGHIA 229
+L + D + ++TPLT +TRG+ + +AKMK GV I+N ARG I+D A+ +A SG +A
Sbjct: 191 LLARADFITLHTPLTPETRGLIGAEELAKMKPGVRIINCARGGIIDEAALAEALKSGKVA 250
Query: 230 GYSGDVWNPQPAPKDHPWRYMPNQAMTPHVSGTTIDAQLRYAAGV-KDMLDRYFKGEDFP 288
G + DV+ +P P D P +PN +TPH+ +T +AQ A V + ++D +G P
Sbjct: 251 GAALDVFEKEP-PTDSPLFELPNVVVTPHLGASTAEAQENVAIQVAEQVID-ALRGG--P 306
Query: 289 VQN 291
V N
Sbjct: 307 VPN 309
>gnl|CDD|240624 cd05299, CtBP_dh, C-terminal binding protein (CtBP),
D-isomer-specific 2-hydroxyacid dehydrogenases related
repressor. The transcriptional corepressor CtBP is a
dehydrogenase with sequence and structural similarity to
the d2-hydroxyacid dehydrogenase family. CtBP was
initially identified as a protein that bound the PXDLS
sequence at the adenovirus E1A C terminus, causing the
loss of CR-1-mediated transactivation. CtBP binds NAD(H)
within a deep cleft, undergoes a conformational change
upon NAD binding, and has NAD-dependent dehydrogenase
activity.
Length = 312
Score = 167 bits (425), Expect = 6e-50
Identities = 72/206 (34%), Positives = 102/206 (49%), Gaps = 7/206 (3%)
Query: 57 AAAAAGLTVAEVTGSNVVSVAEDELMRILILVRNFLPGHHQVISGEWN--VAGVAYRAYD 114
AA G+ V V VA+ L IL L R V +G W+ V G R
Sbjct: 83 AATERGIPVCNVPDYCTEEVADHALALILALARKLPFLDRAVRAGGWDWTVGGPIRR--- 139
Query: 115 LEGKTVGTVGCGRIGKLLLQRLKPFNCNLLYHDRVKMDPQLEKETGAKFEEDLDTMLPKC 174
L G T+G VG GRIG+ + +R K F ++ +D + G + LD +L +
Sbjct: 140 LRGLTLGLVGFGRIGRAVAKRAKAFGFRVIAYDPYV-PDGVAALGGVRVV-SLDELLARS 197
Query: 175 DIVVVNTPLTEKTRGMFDKDRIAKMKKGVLIVNNARGAIMDTQAVVDACSSGHIAGYSGD 234
D+V ++ PLT +TR + D + +A MK G +VN ARG ++D A+ A SG IAG + D
Sbjct: 198 DVVSLHCPLTPETRHLIDAEALALMKPGAFLVNTARGGLVDEAALARALKSGRIAGAALD 257
Query: 235 VWNPQPAPKDHPWRYMPNQAMTPHVS 260
V +P P D P PN +TPH +
Sbjct: 258 VLEEEPPPADSPLLSAPNVILTPHAA 283
>gnl|CDD|240644 cd12167, 2-Hacid_dh_8, Putative D-isomer specific 2-hydroxyacid
dehydrogenases. 2-Hydroxyacid dehydrogenases catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 330
Score = 166 bits (424), Expect = 2e-49
Identities = 76/229 (33%), Positives = 115/229 (50%), Gaps = 3/229 (1%)
Query: 57 AAAAAGLTVAEVTGSNVVSVAEDELMRILILVRNFLPGHHQVISGEWNVAGVAYRAYDLE 116
A G+ V +N VAE L IL+ +R +G L
Sbjct: 90 AVWERGILVTSAADANAEPVAEFTLAAILLALRRIPRFAAAYRAGRDWGWPTRRGGRGLY 149
Query: 117 GKTVGTVGCGRIGKLLLQRLKPFNCNLLYHDRVKMDPQLEKETGAKFEEDLDTMLPKCDI 176
G+TVG VG GRIG+ +++ L+PF +L +D + G + LD +L + D+
Sbjct: 150 GRTVGIVGFGRIGRAVVELLRPFGLRVLVYDPY-LPAAEAAALGVE-LVSLDELLARSDV 207
Query: 177 VVVNTPLTEKTRGMFDKDRIAKMKKGVLIVNNARGAIMDTQAVVDACSSGHIAGYSGDVW 236
V ++ PLT +TRGM D +A M+ G +N ARGA++D A++ SG + DV
Sbjct: 208 VSLHAPLTPETRGMIDARLLALMRDGATFINTARGALVDEAALLAELRSGRLRAAL-DVT 266
Query: 237 NPQPAPKDHPWRYMPNQAMTPHVSGTTIDAQLRYAAGVKDMLDRYFKGE 285
+P+P P D P R +PN +TPH++G+T D + R D L+R+ GE
Sbjct: 267 DPEPLPPDSPLRTLPNVLLTPHIAGSTGDERRRLGDYALDELERFLAGE 315
>gnl|CDD|240654 cd12177, 2-Hacid_dh_12, Putative D-isomer specific 2-hydroxyacid
dehydrogenases, NAD-binding and catalytic domains.
2-Hydroxyacid dehydrogenases catalyze the conversion of
a wide variety of D-2-hydroxy acids to their
corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 321
Score = 163 bits (414), Expect = 3e-48
Identities = 78/231 (33%), Positives = 124/231 (53%), Gaps = 5/231 (2%)
Query: 57 AAAAAGLTVAEVTGS-NVVSVAEDELMRILILVRNFLPGHHQVISGEWNVAGVAYRAYDL 115
AA G+ V V G+ +VAE + IL ++R V G+W + ++L
Sbjct: 87 AATEHGVIVTRVPGAVERDAVAEHAVALILTVLRKINQASEAVKEGKWTER-ANFVGHEL 145
Query: 116 EGKTVGTVGCGRIGKLLLQRLKP-FNCNLLYHDRVKMDPQLEKETGAKFEEDLDTMLPKC 174
GKTVG +G G IG + + LK FN +L +D ++ K+ GAK L+ +L +
Sbjct: 146 SGKTVGIIGYGNIGSRVAEILKEGFNAKVLAYDPYV-SEEVIKKKGAKPV-SLEELLAES 203
Query: 175 DIVVVNTPLTEKTRGMFDKDRIAKMKKGVLIVNNARGAIMDTQAVVDACSSGHIAGYSGD 234
DI+ ++ PLTE+T M ++ +KMKKGV++VN ARG ++D +A+++A SG IAG D
Sbjct: 204 DIISLHAPLTEETYHMINEKAFSKMKKGVILVNTARGELIDEEALIEALKSGKIAGAGLD 263
Query: 235 VWNPQPAPKDHPWRYMPNQAMTPHVSGTTIDAQLRYAAGVKDMLDRYFKGE 285
V +P DHP + N +TPH+ T ++ V D ++ + G+
Sbjct: 264 VLEEEPIKADHPLLHYENVVITPHIGAYTYESLYGMGEKVVDDIEDFLAGK 314
>gnl|CDD|233358 TIGR01327, PGDH, D-3-phosphoglycerate dehydrogenase. This model
represents a long form of D-3-phosphoglycerate
dehydrogenase, the serA gene of one pathway of serine
biosynthesis. Shorter forms, scoring between trusted and
noise cutoff, include SerA from E. coli [Amino acid
biosynthesis, Serine family].
Length = 525
Score = 164 bits (418), Expect = 5e-47
Identities = 84/233 (36%), Positives = 124/233 (53%), Gaps = 12/233 (5%)
Query: 57 AAAAAGLTVAEVTGSNVVSVAEDELMRILILVRNFLPGHHQVISGEWNVAGVAYRAYDLE 116
AA A G+ V N +S AE L +L RN + GEW+ A+ +L
Sbjct: 80 AATARGILVVNAPTGNTISAAEHALAMLLAAARNIPQADASLKEGEWDRK--AFMGTELY 137
Query: 117 GKTVGTVGCGRIGKLLLQRLKPFNCNLLYHDRVKMDPQLEKET----GAKFEEDLDTMLP 172
GKT+G +G GRIG ++ +R K F +L +D P + E G + +DLD +L
Sbjct: 138 GKTLGVIGLGRIGSIVAKRAKAFGMKVLAYD-----PYISPERAEQLGVELVDDLDELLA 192
Query: 173 KCDIVVVNTPLTEKTRGMFDKDRIAKMKKGVLIVNNARGAIMDTQAVVDACSSGHIAGYS 232
+ D + V+TPLT +TRG+ + +AKMKKGV+IVN ARG I+D A+ +A GH+ +
Sbjct: 193 RADFITVHTPLTPETRGLIGAEELAKMKKGVIIVNCARGGIIDEAALYEALEEGHVRAAA 252
Query: 233 GDVWNPQPAPKDHPWRYMPNQAMTPHVSGTTIDAQLRYAAGVKDMLDRYFKGE 285
DV+ +P P D+P + N TPH+ +T +AQ A V + + KG
Sbjct: 253 LDVFEKEP-PTDNPLFDLDNVIATPHLGASTREAQENVATQVAEQVLDALKGL 304
>gnl|CDD|240642 cd12165, 2-Hacid_dh_6, Putative D-isomer specific 2-hydroxyacid
dehydrogenases. 2-Hydroxyacid dehydrogenases catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 314
Score = 158 bits (403), Expect = 1e-46
Identities = 73/221 (33%), Positives = 112/221 (50%), Gaps = 9/221 (4%)
Query: 72 NVVSVAEDELMRILILVRNFLPGHHQVISGEWN-VAGVAYRAYDLEGKTVGTVGCGRIGK 130
N +VAE L IL L + + + + G W+ AG + +L GKTVG +G G IG+
Sbjct: 91 NSPAVAEHALALILALAKRIVEYDNDLRRGIWHGRAGEEPESKELRGKTVGILGYGHIGR 150
Query: 131 LLLQRLKPFNCNLLYHDRVKMDPQLEKETGAKFEEDLDTMLPKCDIVVVNTPLTEKTRGM 190
+ + LK F ++ R + + G DLD L + D+VVV PLT++TRG+
Sbjct: 151 EIARLLKAFGMRVIGVSRSPKEDEGADFVG--TLSDLDEALEQADVVVVALPLTKQTRGL 208
Query: 191 FDKDRIAKMKKGVLIVNNARGAIMDTQAVVDACSSGHIAGYSGDVW------NPQPAPKD 244
+A MK G ++VN RG ++D +A+ +A IAG + DVW AP
Sbjct: 209 IGAAELAAMKPGAILVNVGRGPVVDEEALYEALKERPIAGAAIDVWWRYPSRGDPVAPSR 268
Query: 245 HPWRYMPNQAMTPHVSGTTIDAQLRYAAGVKDMLDRYFKGE 285
+P+ +PN M+PH +G T + R + + RY +GE
Sbjct: 269 YPFHELPNVIMSPHNAGWTEETFRRRIDEAAENIRRYLRGE 309
>gnl|CDD|240639 cd12162, 2-Hacid_dh_4, Putative D-isomer specific 2-hydroxyacid
dehydrogenases. 2-Hydroxyacid dehydrogenases catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine yydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 307
Score = 154 bits (393), Expect = 3e-45
Identities = 73/225 (32%), Positives = 119/225 (52%), Gaps = 11/225 (4%)
Query: 57 AAAAAGLTVAEVTGSNVVSVAEDELMRILILVRNFLPGHHQVISGEWNVAG----VAYRA 112
AA G+TV V G + SVA+ +L L R + V +GEW + Y
Sbjct: 83 AAKERGITVTNVPGYSTDSVAQHTFALLLALARLVAYHNDVVKAGEWQKSPDFCFWDYPI 142
Query: 113 YDLEGKTVGTVGCGRIGKLLLQRLKPFNCNLLYHDRVKMDPQLEKETGAKFEEDLDTMLP 172
+L GKT+G +G G IG+ + + + F +L+ +R P E LD +L
Sbjct: 143 IELAGKTLGIIGYGNIGQAVARIARAFGMKVLFAERKGAPPLREGYV------SLDELLA 196
Query: 173 KCDIVVVNTPLTEKTRGMFDKDRIAKMKKGVLIVNNARGAIMDTQAVVDACSSGHIAGYS 232
+ D++ ++ PLT +TR + + + +AKMK G +++N ARG ++D QA+ DA +SG IAG
Sbjct: 197 QSDVISLHCPLTPETRNLINAEELAKMKPGAILINTARGGLVDEQALADALNSGKIAGAG 256
Query: 233 GDVWNPQPAPKDHP-WRYMPNQAMTPHVSGTTIDAQLRYAAGVKD 276
DV + +P D+P + PN +TPH++ + +A+ R + D
Sbjct: 257 LDVLSQEPPRADNPLLKAAPNLIITPHIAWASREARQRLMDILVD 301
>gnl|CDD|240628 cd05303, PGDH_2, Phosphoglycerate dehydrogenase (PGDH) NAD-binding
and catalytic domains. Phosphoglycerate dehydrogenase
(PGDH) catalyzes the initial step in the biosynthesis of
L-serine from D-3-phosphoglycerate. PGDH comes in 3
distinct structural forms, with this first group being
related to 2-hydroxy acid dehydrogenases, sharing
structural similarity to formate and glycerate
dehydrogenases. PGDH in E. coli and Mycobacterium
tuberculosis form tetramers, with subunits containing a
Rossmann-fold NAD binding domain. Formate/glycerate and
related dehydrogenases of the D-specific 2-hydroxyacid
dehydrogenase superfamily include groups such as formate
dehydrogenase, glycerate dehydrogenase, L-alanine
dehydrogenase, and S-Adenosylhomocysteine Hydrolase.
Despite often low sequence identity, these proteins
typically have a characteristic arrangement of 2 similar
subdomains of the alpha/beta Rossmann fold NAD+ binding
form. The NAD+ binding domain is inserted within the
linear sequence of the mostly N-terminal catalytic
domain, which has a similar domain structure to the
internal NAD binding domain. Structurally, these domains
are connected by extended alpha helices and create a
cleft in which NAD is bound, primarily to the C-terminal
portion of the 2nd (internal) domain. Some related
proteins have similar structural subdomain but with a
tandem arrangement of the catalytic and NAD-binding
subdomains in the linear sequence.
Length = 301
Score = 153 bits (388), Expect = 1e-44
Identities = 68/226 (30%), Positives = 120/226 (53%), Gaps = 5/226 (2%)
Query: 57 AAAAAGLTVAEVTGSNVVSVAEDELMRILILVRNFLPGHHQVISGEWNVAGVAYRAYDLE 116
A G+ V G++ SVAE + +L L R + ++ G+WN Y+ +L
Sbjct: 81 YAKKKGIKVINTPGASSNSVAELVIGLMLSLARFIHRANREMKLGKWNKK--KYKGIELR 138
Query: 117 GKTVGTVGCGRIGKLLLQRLKPFNCNLLYHDRVKMDPQLEKETGAKFEEDLDTMLPKCDI 176
GKT+G +G GRIG+ + + + N++ +D D Q E G K L+ +L D
Sbjct: 139 GKTLGIIGFGRIGREVAKIARALGMNVIAYDPYPKDEQ-AVELGVKTV-SLEELLKNSDF 196
Query: 177 VVVNTPLTEKTRGMFDKDRIAKMKKGVLIVNNARGAIMDTQAVVDACSSGHIAGYSGDVW 236
+ ++ PLT +T+ M +K + MK G +I+N +RG ++D +A+++A SG +AG + DV+
Sbjct: 197 ISLHVPLTPETKHMINKKELELMKDGAIIINTSRGGVIDEEALLEALKSGKLAGAALDVF 256
Query: 237 NPQPAPKDHPWRYMPNQAMTPHVSGTTIDAQLRYAAGVKDMLDRYF 282
+P P +PN ++TPH+ +T +AQ R + + + +
Sbjct: 257 ENEP-PPGSKLLELPNVSLTPHIGASTKEAQERIGEELANKIIEFL 301
>gnl|CDD|240638 cd12161, GDH_like_1, Putative glycerate dehydrogenase and related
proteins of the D-specific 2-hydroxy dehydrogenase
family. This group contains a variety of proteins
variously identified as glycerate dehydrogenase (GDH,
aka Hydroxypyruvate Reductase) and other enzymes of the
2-hydroxyacid dehydrogenase family. GDH catalyzes the
reversible reaction of (R)-glycerate + NAD+ to
hydroxypyruvate + NADH + H+. 2-hydroxyacid
dehydrogenases catalyze the conversion of a wide variety
of D-2-hydroxy acids to their corresponding keto acids.
The general mechanism is (R)-lactate + acceptor to
pyruvate + reduced acceptor. Formate/glycerate and
related dehydrogenases of the D-specific 2-hydroxyacid
dehydrogenase superfamily include groups such as formate
dehydrogenase, glycerate dehydrogenase, L-alanine
dehydrogenase, and S-adenosylhomocysteine hydrolase.
Despite often low sequence identity, these proteins
typically have a characteristic arrangement of 2 similar
subdomains of the alpha/beta Rossmann-fold NAD+ binding
form. The NAD+ binding domain is inserted within the
linear sequence of the mostly N-terminal catalytic
domain, which has a similar domain structure to the
internal NAD binding domain. Structurally, these domains
are connected by extended alpha helices and create a
cleft in which NAD is bound, primarily to the C-terminal
portion of the 2nd (internal) domain. Some related
proteins have similar structural subdomain but with a
tandem arrangement of the catalytic and NAD-binding
subdomains in the linear sequence. While many members of
this family are dimeric, alanine DH is hexameric and
phosphoglycerate DH is tetrameric.
Length = 315
Score = 152 bits (386), Expect = 4e-44
Identities = 78/230 (33%), Positives = 129/230 (56%), Gaps = 7/230 (3%)
Query: 57 AAAAAGLTVAEVTGSNVVSVAEDELMRILILVRNFLPGHHQVISGEWNVAGVAYRAYDLE 116
A G+TV+ G + +VAE + + L+RN +P V +G AG +L
Sbjct: 87 ACKERGITVSNAAGYSTEAVAELTIGLAIDLLRNIVPCDAAVRAGG-TKAG--LIGRELA 143
Query: 117 GKTVGTVGCGRIGKLLLQRLKPFNCNLLYHDRVKMDPQLEKETGAKFEEDLDTMLPKCDI 176
GKTVG VG G IG + + K F C +L + R + + K G ++ LD +L + DI
Sbjct: 144 GKTVGIVGTGAIGLRVARLFKAFGCKVLAYSRSE--KEEAKALGIEYV-SLDELLAESDI 200
Query: 177 VVVNTPLTEKTRGMFDKDRIAKMKKGVLIVNNARGAIMDTQAVVDACSSGHIAGYSGDVW 236
V ++ PL ++T+G+ K+++A MK+ +++N ARG ++D +A+ DA + G IAG DV+
Sbjct: 201 VSLHLPLNDETKGLIGKEKLALMKESAILINTARGPVVDNEALADALNEGKIAGAGIDVF 260
Query: 237 NPQPA-PKDHPWRYMPNQAMTPHVSGTTIDAQLRYAAGVKDMLDRYFKGE 285
+ +P P D+P + PN +TPHV+ T +A + A V D ++ + G+
Sbjct: 261 DMEPPLPADYPLLHAPNTILTPHVAFATEEAMEKRAEIVFDNIEAWLAGK 310
>gnl|CDD|240636 cd12159, 2-Hacid_dh_2, Putative D-isomer specific 2-hydroxyacid
dehydrogenases. 2-Hydroxyacid dehydrogenases catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 303
Score = 151 bits (384), Expect = 6e-44
Identities = 73/214 (34%), Positives = 105/214 (49%), Gaps = 5/214 (2%)
Query: 75 SVAEDELMRILILVRNFLPGHHQVISGEWNVAGVAYRAYDLEGKTVGTVGCGRIGKLLLQ 134
+VAE L +L +R + + W+ A L G TV VG G IG+ L+
Sbjct: 86 TVAEHALALLLAGLRQL---PARARATTWDPAEEDDLVTLLRGSTVAIVGAGGIGRALIP 142
Query: 135 RLKPFNCNLLYHDRVKMDPQLEKETGAKFEEDLDTMLPKCDIVVVNTPLTEKTRGMFDKD 194
L PF ++ +R + ET + LD + P D VV+ PLT +TR + D
Sbjct: 143 LLAPFGAKVIAVNRSGRPVEGADETVPA--DRLDEVWPDADHVVLAAPLTPETRHLVDAA 200
Query: 195 RIAKMKKGVLIVNNARGAIMDTQAVVDACSSGHIAGYSGDVWNPQPAPKDHPWRYMPNQA 254
+A MK +VN ARG ++DT A+VDA SG IAG + DV +P+P P HP +PN
Sbjct: 201 ALAAMKPHAWLVNVARGPLVDTDALVDALRSGEIAGAALDVTDPEPLPDGHPLWSLPNAL 260
Query: 255 MTPHVSGTTIDAQLRYAAGVKDMLDRYFKGEDFP 288
+TPHV+ T + A V + + + GE
Sbjct: 261 ITPHVANTPEVIRPLLAERVAENVRAFAAGEPLL 294
>gnl|CDD|183914 PRK13243, PRK13243, glyoxylate reductase; Reviewed.
Length = 333
Score = 152 bits (385), Expect = 7e-44
Identities = 74/210 (35%), Positives = 117/210 (55%), Gaps = 8/210 (3%)
Query: 84 ILILVRNFLPGHHQVISGEWNVAGVAYR-----AYDLEGKTVGTVGCGRIGKLLLQRLKP 138
+L R + H V SGEW GVA+ YD+ GKT+G +G GRIG+ + +R K
Sbjct: 112 LLATARRLVEADHFVRSGEWKRRGVAWHPLMFLGYDVYGKTIGIIGFGRIGQAVARRAKG 171
Query: 139 FNCNLLYHDRVKMDPQLEKETGAKFEEDLDTMLPKCDIVVVNTPLTEKTRGMFDKDRIAK 198
F +LY+ R + P+ EKE GA++ L+ +L + D V ++ PLT++T M +++R+
Sbjct: 172 FGMRILYYSRTR-KPEAEKELGAEYR-PLEELLRESDFVSLHVPLTKETYHMINEERLKL 229
Query: 199 MKKGVLIVNNARGAIMDTQAVVDACSSGHIAGYSGDVWNPQPAPKDHPWRYMPNQAMTPH 258
MK ++VN ARG ++DT+A+V A G IAG DV+ +P + + N + PH
Sbjct: 230 MKPTAILVNTARGKVVDTKALVKALKEGWIAGAGLDVFEEEPYY-NEELFSLKNVVLAPH 288
Query: 259 VSGTTIDAQLRYAAGVKDMLDRYFKGEDFP 288
+ T +A+ A V + L + +GE P
Sbjct: 289 IGSATFEAREGMAELVAENLIAFKRGEVPP 318
>gnl|CDD|240655 cd12178, 2-Hacid_dh_13, Putative D-isomer specific 2-hydroxyacid
dehydrogenases, NAD-binding and catalytic domains.
2-Hydroxyacid dehydrogenases catalyze the conversion of
a wide variety of D-2-hydroxy acids to their
corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 317
Score = 151 bits (384), Expect = 1e-43
Identities = 69/230 (30%), Positives = 115/230 (50%), Gaps = 3/230 (1%)
Query: 57 AAAAAGLTVAEVTGSNVVSVAEDELMRILILVRNFLPGHHQVISGEWNVAGVAY-RAYDL 115
A G+ V + AE IL L R G + G + + ++L
Sbjct: 83 YAKEKGIPVTNTPAVSTEPTAELTFGLILALARRIAEGDRLMRRGGFLGWAPLFFLGHEL 142
Query: 116 EGKTVGTVGCGRIGKLLLQRLKPFNCNLLYHDRVKMDPQLEKETGAKFEEDLDTMLPKCD 175
GKT+G +G GRIG+ + +R K F +LY++R ++ + EKE GA + DLD +L + D
Sbjct: 143 AGKTLGIIGMGRIGQAVARRAKAFGMKILYYNRHRLSEETEKELGATYV-DLDELLKESD 201
Query: 176 IVVVNTPLTEKTRGMFDKDRIAKMKKGVLIVNNARGAIMDTQAVVDACSSGHIAGYSGDV 235
V ++ P T +T + D MK ++N ARG ++D +A+VDA +G IAG + DV
Sbjct: 202 FVSLHAPYTPETHHLIDAAAFKLMKPTAYLINAARGPLVDEKALVDALKTGEIAGAALDV 261
Query: 236 WNPQPAPKDHPWRYMPNQAMTPHVSGTTIDAQLRYAAGVKDMLDRYFKGE 285
+ +P + + N +TPH+ T++A+ A D + + +G+
Sbjct: 262 FEFEPEVSPE-LKKLDNVILTPHIGNATVEARDAMAKEAADNIISFLEGK 310
>gnl|CDD|240625 cd05300, 2-Hacid_dh_1, Putative D-isomer specific 2-hydroxyacid
dehydrogenase. 2-Hydroxyacid dehydrogenases catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomains but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric. Formate dehydrogenase (FDH) catalyzes the
NAD+-dependent oxidation of formate ion to carbon
dioxide with the concomitant reduction of NAD+ to NADH.
FDHs of this family contain no metal ions or prosthetic
groups. Catalysis occurs though direct transfer of the
hydride ion to NAD+ without the stages of acid-base
catalysis typically found in related dehydrogenases.
FDHs are found in all methylotrophic microorganisms in
energy production and in the stress responses of plants.
Length = 313
Score = 146 bits (371), Expect = 8e-42
Identities = 75/233 (32%), Positives = 112/233 (48%), Gaps = 6/233 (2%)
Query: 55 FLAAAAAGLTVAEVTGSNVVSVAEDELMRILILVRNFLPGHHQVISGEWNVAGVAYRAYD 114
F + + G +AE L +L R W G R +
Sbjct: 75 FPELLERDVVLTNARGIFGPPIAEYVLGYMLAFARKLPRYARNQAERRWQRRG-PVR--E 131
Query: 115 LEGKTVGTVGCGRIGKLLLQRLKPFNCNLLYHDR-VKMDPQLEKETGAKFEEDLDTMLPK 173
L GKTV VG G IG+ + +R K F ++ R + P + E ++LD +LP+
Sbjct: 132 LAGKTVLIVGLGDIGREIARRAKAFGMRVIGVRRSGRPAPPVVDEVYT--PDELDELLPE 189
Query: 174 CDIVVVNTPLTEKTRGMFDKDRIAKMKKGVLIVNNARGAIMDTQAVVDACSSGHIAGYSG 233
D VV PLT +TRG+F+ +R A MK G +++N RG+++D A+++A SG IAG +
Sbjct: 190 ADYVVNALPLTPETRGLFNAERFAAMKPGAVLINVGRGSVVDEDALIEALESGRIAGAAL 249
Query: 234 DVWNPQPAPKDHPWRYMPNQAMTPHVSGTTIDAQLRYAAGVKDMLDRYFKGED 286
DV+ +P P D P +PN +TPH+SG + R + L RY GE
Sbjct: 250 DVFEEEPLPADSPLWDLPNVIITPHISGDSPSYPERVVEIFLENLRRYLAGEP 302
>gnl|CDD|240661 cd12185, HGDH_LDH_like, Putative Lactate dehydrogenase and
(R)-2-Hydroxyglutarate Dehydrogenase-like proteins,
NAD-binding and catalytic domains. This group contains
various putative dehydrogenases related to D-lactate
dehydrogenase (LDH), (R)-2-hydroxyglutarate
dehydrogenase (HGDH), and related enzymes, members of
the 2-hydroxyacid dehydrogenases family. LDH catalyzes
the interconversion of pyruvate and lactate, and HGDH
catalyzes the NAD-dependent reduction of 2-oxoglutarate
to (R)-2-hydroxyglutarate. Despite often low sequence
identity within this 2-hydroxyacid dehydrogenase family,
these proteins typically have a characteristic
arrangement of 2 similar subdomains of the alpha/beta
Rossmann fold NAD+ binding form. The NAD+ binding domain
is inserted within the linear sequence of the mostly
N-terminal catalytic domain, which has a similar domain
structure to the internal NAD binding domain.
Structurally, these domains are connected by extended
alpha helices and create a cleft in which NAD is bound,
primarily to the C-terminal portion of the 2nd
(internal) domain.
Length = 322
Score = 145 bits (367), Expect = 3e-41
Identities = 72/218 (33%), Positives = 118/218 (54%), Gaps = 26/218 (11%)
Query: 57 AAAAAGLTVAEVTGS-NVVSVAEDELMRILILVRNFLPGHHQVISGEWNVAGVAYRAYDL 115
AA G+ V+ VT S N SVA+ +M +L+ +R + + ++++ G+ + +L
Sbjct: 86 AAKELGIKVSNVTYSPN--SVADYTVMLMLMALRKYKQIMKRAEVNDYSLGGL--QGREL 141
Query: 116 EGKTVGTVGCGRIGKLLLQRLKPFNCNLLYHDRVKMDPQLEKETGAKFEE--DLDTMLPK 173
TVG +G GRIG+ +++ L F C +L +D E K+ E DLDT+ +
Sbjct: 142 RNLTVGVIGTGRIGQAVIKNLSGFGCKILAYDP------YPNEEVKKYAEYVDLDTLYKE 195
Query: 174 CDIVVVNTPLTEKTRGMFDKDRIAKMKKGVLIVNNARGAIMDTQAVVDACSSGHIAGYSG 233
DI+ ++TPLTE+T + +K+ IAKMK GV+I+N ARG ++DT+A+++ SG I G +
Sbjct: 196 SDIITLHTPLTEETYHLINKESIAKMKDGVIIINTARGELIDTEALIEGLESGKIGGAAL 255
Query: 234 DVW---------NPQPAPKDHPW----RYMPNQAMTPH 258
DV + + + R PN +TPH
Sbjct: 256 DVIEGEDGIYYNDRKGDILSNRELAILRSFPNVILTPH 293
>gnl|CDD|240634 cd12157, PTDH, Thermostable Phosphite Dehydrogenase. Phosphite
dehydrogenase (PTDH), a member of the D-specific
2-hydroxyacid dehydrogenase family, catalyzes the
NAD-dependent formation of phosphate from phosphite
(hydrogen phosphonate). PTDH has been suggested as a
potential enzyme for cofactor regeneration systems. The
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD-binding
domain.
Length = 318
Score = 143 bits (362), Expect = 1e-40
Identities = 69/229 (30%), Positives = 109/229 (47%), Gaps = 25/229 (10%)
Query: 48 YASMNPNFLAAAAAGLTVAEVTGSNVVSVAEDELMRILILVRNFLPGHHQVISGEWNVAG 107
+ ++ P+ L A LT+ L+ + L R+ L G V SG++
Sbjct: 91 WVTIVPDLLTEPTAELTIG--------------LL--IGLGRHILAGDRFVRSGKFGGWR 134
Query: 108 VAYRAYDLEGKTVGTVGCGRIGKLLLQRLKPFNCNLLYHDRVKMDPQLEKETGAKFEEDL 167
+ L+GKTVG +G G +G+ + +RL F LLY+D +D E+ + E L
Sbjct: 135 PKFYGTGLDGKTVGILGMGALGRAIARRLSGFGATLLYYDPHPLDQAEEQALNLRRVE-L 193
Query: 168 DTMLPKCDIVVVNTPLTEKTRGMFDKDRIAKMKKGVLIVNNARGAIMDTQAVVDACSSGH 227
D +L D +V+ PLT T + + + +AKMK G L+VN RG+++D AV +A SGH
Sbjct: 194 DELLESSDFLVLALPLTPDTLHLINAEALAKMKPGALLVNPCRGSVVDEAAVAEALKSGH 253
Query: 228 IAGYSGDV-----WNPQPAPKDHPWRYM---PNQAMTPHVSGTTIDAQL 268
+ GY+ DV W P+ P + TPH+ + +L
Sbjct: 254 LGGYAADVFEMEDWARPDRPRSIPQELLDQHDRTVFTPHIGSAVDEVRL 302
>gnl|CDD|240651 cd12174, PGDH_like_3, Putative D-3-Phosphoglycerate Dehydrogenases,
NAD-binding and catalytic domains. Phosphoglycerate
dehydrogenases (PGDHs) catalyze the initial step in the
biosynthesis of L-serine from D-3-phosphoglycerate.
PGDHs come in 3 distinct structural forms, with this
first group being related to 2-hydroxy acid
dehydrogenases, sharing structural similarity to formate
and glycerate dehydrogenases of the D-specific
2-hydroxyacid dehydrogenase superfamily, which also
include groups such as L-alanine dehydrogenase and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. Many, not all, members of this family are
dimeric.
Length = 305
Score = 140 bits (354), Expect = 2e-39
Identities = 65/243 (26%), Positives = 116/243 (47%), Gaps = 20/243 (8%)
Query: 57 AAAAAGLTVAEVTGSNVVSVAEDELMRILILVRNFLPGHHQVISG---------EWNVAG 107
AA+ G+ V G+N +VAE + +L L RN + V +G E
Sbjct: 68 AASKRGIVVFNTPGANANAVAELVIAMMLALSRNIIQAIKWVTNGDGDDISKGVEKGKKQ 127
Query: 108 VAYRAYDLEGKTVGTVGCGRIGKLLLQRLKPFNCNLLYHDRVKMDPQLEKETGAKFE--E 165
+ +L GKT+G +G G IG+L+ ++ +D + + + + +
Sbjct: 128 --FVGTELRGKTLGVIGLGNIGRLVANAALALGMKVIGYDPY-LSVEAAWKLSVEVQRVT 184
Query: 166 DLDTMLPKCDIVVVNTPLTEKTRGMFDKDRIAKMKKGVLIVNNARGAIMDTQAVVDACSS 225
L+ +L D + ++ PLT++TRG+ + + +AKMK G +++N ARG I+D +A+++A
Sbjct: 185 SLEELLATADYITLHVPLTDETRGLINAELLAKMKPGAILLNFARGEIVDEEALLEALDE 244
Query: 226 GHIAGYSGDVWNPQPAPKDHPWRYMPNQAMTPHVSGTTIDAQLRYAAGVKDMLDRYFKGE 285
G + GY D P+PA H PN TPH+ +T +A+ A + + +
Sbjct: 245 GKLGGYVTDF--PEPALLGHL----PNVIATPHLGASTEEAEENCAVMAARQIMDFLETG 298
Query: 286 DFP 288
+
Sbjct: 299 NIT 301
>gnl|CDD|240643 cd12166, 2-Hacid_dh_7, Putative D-isomer specific 2-hydroxyacid
dehydrogenases. 2-Hydroxyacid dehydrogenases catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 300
Score = 138 bits (350), Expect = 5e-39
Identities = 79/234 (33%), Positives = 112/234 (47%), Gaps = 14/234 (5%)
Query: 54 NFLAAAAAGLTVAEVTGSNVVSVAEDELMRILILVRNFLPGHHQV-ISGEWNVAGVAYRA 112
L G+T+ G + S AE + IL +R P + G W
Sbjct: 73 GVLPLLPEGVTLCNARGVHDASTAELAVALILASLRGL-PRFVRAQARGRWEPRRTP--- 128
Query: 113 YDLEGKTVGTVGCGRIGKLLLQRLKPFNCNLLYHDRVKMDPQLEKETGAKFEEDLDTMLP 172
L + V VG G IG+ + +RL PF + RV + E +E L +LP
Sbjct: 129 -SLADRRVLIVGYGSIGRAIERRLAPFEVRVT---RVARTAR-PGEQVHGIDE-LPALLP 182
Query: 173 KCDIVVVNTPLTEKTRGMFDKDRIAKMKKGVLIVNNARGAIMDTQAVVDACSSGHI-AGY 231
+ D+VV+ PLT++TRG+ D + +A+M G L+VN ARG ++DT A+V +SG + A
Sbjct: 183 EADVVVLIVPLTDETRGLVDAEFLARMPDGALLVNVARGPVVDTDALVAELASGRLRAAL 242
Query: 232 SGDVWNPQPAPKDHPWRYMPNQAMTPHVSGTTIDAQLRYAAGVKDMLDRYFKGE 285
DV +P+P P HP P +TPHV G T R A V+ L RY GE
Sbjct: 243 --DVTDPEPLPPGHPLWSAPGVLITPHVGGATPAFLPRAYALVRRQLRRYAAGE 294
>gnl|CDD|240659 cd12183, LDH_like_2, D-Lactate and related Dehydrogenases,
NAD-binding and catalytic domains. D-Lactate
dehydrogenase (LDH) catalyzes the interconversion of
pyruvate and lactate, and is a member of the
2-hydroxyacid dehydrogenase family. LDH is homologous to
D-2-hydroxyisocaproic acid dehydrogenase (D-HicDH) and
shares the 2-domain structure of formate dehydrogenase.
D-2-hydroxyisocaproate dehydrogenase-like (HicDH)
proteins are NAD-dependent members of the
hydroxycarboxylate dehydrogenase family, and share the
Rossmann fold typical of many NAD binding proteins.
HicDH from Lactobacillus casei forms a monomer and
catalyzes the reaction R-CO-COO(-) + NADH + H+ to
R-COH-COO(-) + NAD+. D-HicDH, like the structurally
distinct L-HicDH, exhibits low side-chain R specificity,
accepting a wide range of 2-oxocarboxylic acid side
chains. Formate/glycerate and related dehydrogenases of
the D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain.
Length = 328
Score = 137 bits (349), Expect = 1e-38
Identities = 66/179 (36%), Positives = 108/179 (60%), Gaps = 5/179 (2%)
Query: 57 AAAAAGLTVAEVTGSNVVSVAEDELMRILILVRNFLPGHHQVISGEWNVAGVAYRAYDLE 116
AA G+TV V + +VAE + +L L R +++V G +++ G+ +DL
Sbjct: 86 AAKELGITVVRVPAYSPYAVAEHAVALLLALNRKIHRAYNRVREGNFSLDGLL--GFDLH 143
Query: 117 GKTVGTVGCGRIGKLLLQRLKPFNCNLLYHDRVKMDPQLEKETGAKFEEDLDTMLPKCDI 176
GKTVG +G G+IG+ + LK F C +L +D +P+L K G ++ DLD +L + DI
Sbjct: 144 GKTVGVIGTGKIGQAFARILKGFGCRVLAYD-PYPNPELAKL-GVEYV-DLDELLAESDI 200
Query: 177 VVVNTPLTEKTRGMFDKDRIAKMKKGVLIVNNARGAIMDTQAVVDACSSGHIAGYSGDV 235
+ ++ PLT +T + + + IAKMK GV+++N +RG ++DT+A+++A SG I G DV
Sbjct: 201 ISLHCPLTPETHHLINAETIAKMKDGVMLINTSRGGLIDTKALIEALKSGKIGGLGLDV 259
>gnl|CDD|240653 cd12176, PGDH_3, Phosphoglycerate dehydrogenases, NAD-binding and
catalytic domains. Phosphoglycerate dehydrogenases
(PGDHs) catalyze the initial step in the biosynthesis of
L-serine from D-3-phosphoglycerate. PGDHs come in 3
distinct structural forms, with this first group being
related to 2-hydroxy acid dehydrogenases, sharing
structural similarity to formate and glycerate
dehydrogenases. PGDH in E. coli and Mycobacterium
tuberculosis form tetramers, with subunits containing a
Rossmann-fold NAD binding domain. Formate/glycerate and
related dehydrogenases of the D-specific 2-hydroxyacid
dehydrogenase superfamily include groups such as formate
dehydrogenase, glycerate dehydrogenase, L-alanine
dehydrogenase, and S-adenosylhomocysteine hydrolase.
Despite often low sequence identity, these proteins
typically have a characteristic arrangement of 2 similar
subdomains of the alpha/beta Rossmann fold NAD+ binding
form. The NAD+ binding domain is inserted within the
linear sequence of the mostly N-terminal catalytic
domain, which has a similar domain structure to the
internal NAD binding domain. Structurally, these domains
are connected by extended alpha helices and create a
cleft in which NAD is bound, primarily to the C-terminal
portion of the 2nd (internal) domain. Some related
proteins have similar structural subdomain but with a
tandem arrangement of the catalytic and NAD-binding
subdomains in the linear sequence.
Length = 304
Score = 137 bits (347), Expect = 2e-38
Identities = 72/229 (31%), Positives = 118/229 (51%), Gaps = 10/229 (4%)
Query: 57 AAAAAGLTVAEVTGSNVVSVAEDELMRILILVRNFLPGHHQVISGEWNVAGVAYRAYDLE 116
AAA G+ V SN SVAE + I++L R + G WN A ++++
Sbjct: 82 AAAKRGIPVFNAPFSNTRSVAELVIGEIIMLARRLPDRNAAAHRGIWN--KSATGSHEVR 139
Query: 117 GKTVGTVGCGRIGKLLLQRLKPFNCNLLYHDRVKMDPQLEKETGAKFEEDLDTMLPKCDI 176
GKT+G +G G IG L + ++++D +L A+ L+ +L + D
Sbjct: 140 GKTLGIIGYGHIGSQLSVLAEALGMRVIFYDIA---EKLPLGN-ARQVSSLEELLAEADF 195
Query: 177 VVVNTPLTEKTRGMFDKDRIAKMKKGVLIVNNARGAIMDTQAVVDACSSGHIAGYSGDVW 236
V ++ P T T+ M + IA+MKKG +++N +RG ++D A+ +A SGH+AG + DV+
Sbjct: 196 VTLHVPATPSTKNMIGAEEIAQMKKGAILINASRGTVVDIDALAEALRSGHLAGAAVDVF 255
Query: 237 NPQPAPKDHPW----RYMPNQAMTPHVSGTTIDAQLRYAAGVKDMLDRY 281
+PA P+ + +PN +TPH+ G+T +AQ V L +Y
Sbjct: 256 PEEPASNGEPFSSPLQGLPNVILTPHIGGSTEEAQENIGLEVAGKLVKY 304
>gnl|CDD|240632 cd12155, PGDH_1, Phosphoglycerate Dehydrogenase, 2-hydroxyacid
dehydrogenase family. Phosphoglycerate Dehydrogenase
(PGDH) catalyzes the NAD-dependent conversion of
3-phosphoglycerate into 3-phosphohydroxypyruvate, which
is the first step in serine biosynthesis.
Over-expression of PGDH has been implicated as
supporting proliferation of certain breast cancers,
while PGDH deficiency is linked to defects in mammalian
central nervous system development. PGDH is a member of
the 2-hydroxyacid dehydrogenase family, enzymes that
catalyze the conversion of a wide variety of D-2-hydroxy
acids to their corresponding keto acids. The general
mechanism is (R)-lactate + acceptor to pyruvate +
reduced acceptor. Formate/glycerate and related
dehydrogenases of the D-specific 2-hydroxyacid
dehydrogenase superfamily include groups such as formate
dehydrogenase, glycerate dehydrogenase, L-alanine
dehydrogenase, and S-Adenosylhomocysteine Hydrolase.
Despite often low sequence identity, these proteins
typically have a characteristic arrangement of 2 similar
subdomains of the alpha/beta Rossmann-fold NAD+ binding
form. The NAD+ binding domain is inserted within the
linear sequence of the mostly N-terminal catalytic
domain, which has a similar domain structure to the
internal NAD binding domain. Structurally, these domains
are connected by extended alpha helices and create a
cleft in which NAD is bound, primarily to the C-terminal
portion of the 2nd (internal) domain. Some related
proteins have similar structural subdomain but with a
tandem arrangement of the catalytic and NAD-binding
subdomains in the linear sequence. While many members of
this family are dimeric, alanine DH is hexameric and
phosphoglycerate DH is tetrameric.
Length = 314
Score = 136 bits (345), Expect = 4e-38
Identities = 63/227 (27%), Positives = 103/227 (45%), Gaps = 27/227 (11%)
Query: 74 VSVAEDELMRILILVRNFLPGHHQVISGEWNVAGVAYRAYDLEGKTVGTVGCGRIGKLLL 133
+ +AE + IL + + + +W + L GKT+ +G G IG+ +
Sbjct: 95 IPIAEWIVGYILEIYKGLKKAYKNQKEKKWKMDSSLLE---LYGKTILFLGTGSIGQEIA 151
Query: 134 QRLKPFNCNLL----------YHDRVKMDPQLEKETGAKFEEDLDTMLPKCDIVVVNTPL 183
+RLK F ++ Y D+ E+LD +L + DIVV PL
Sbjct: 152 KRLKAFGMKVIGVNTSGRDVEYFDKCYPL------------EELDEVLKEADIVVNVLPL 199
Query: 184 TEKTRGMFDKDRIAKMKKGVLIVNNARGAIMDTQAVVDACSSGHIAGYSGDVWNPQPAPK 243
TE+T +FD+ +MKKG L +N RG +D A+++A + I G + DV+ +P PK
Sbjct: 200 TEETHHLFDEAFFEQMKKGALFINVGRGPSVDEDALIEALKNKQIRGAALDVFEEEPLPK 259
Query: 244 DHP-WRYMPNQAMTPHVSGTTIDAQLRYAAGVKDMLDRYFKGEDFPV 289
D P W + N +TPH+SG + R + L + + +
Sbjct: 260 DSPLWD-LDNVLITPHISGVSEHFNERLFDIFYENLKSFLEDGELLK 305
>gnl|CDD|240662 cd12186, LDH, D-Lactate dehydrogenase and D-2-Hydroxyisocaproic
acid dehydrogenase (D-HicDH), NAD-binding and catalytic
domains. D-Lactate dehydrogenase (LDH) catalyzes the
interconversion of pyruvate and lactate, and is a member
of the 2-hydroxyacid dehydrogenases family. LDH is
homologous to D-2-hydroxyisocaproic acid
dehydrogenase(D-HicDH) and shares the 2 domain structure
of formate dehydrogenase. D-HicDH is a NAD-dependent
member of the hydroxycarboxylate dehydrogenase family,
and shares the Rossmann fold typical of many NAD binding
proteins. HicDH from Lactobacillus casei forms a monomer
and catalyzes the reaction R-CO-COO(-) + NADH + H+ to
R-COH-COO(-) + NAD+. D-HicDH, like the structurally
distinct L-HicDH, exhibits low side-chain R specificity,
accepting a wide range of 2-oxocarboxylic acid side
chains. Formate/glycerate and related dehydrogenases of
the D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-Adenosylhomocysteine Hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain.
Length = 329
Score = 134 bits (341), Expect = 2e-37
Identities = 66/229 (28%), Positives = 109/229 (47%), Gaps = 37/229 (16%)
Query: 54 NFLAAAAAGLTVAEVTGSNV-----VSVAEDELMRILILVRNFLPGHHQVISGE--WNVA 106
+ A GL + +NV ++AE + + L L+RN +V G+ W
Sbjct: 83 DLDLAKENGLKI-----TNVPAYSPRAIAEFAVTQALNLLRNTPEIDRRVAKGDFRWAPG 137
Query: 107 GVAYRAYDLEGKTVGTVGCGRIGKLLLQRLKPFNCNLLYHDRVKMDPQLEKETGAKFEED 166
+ DL TVG +G GRIG + K F ++ +D +P+LEK +
Sbjct: 138 LIGREIRDL---TVGIIGTGRIGSAAAKIFKGFGAKVIAYDPYP-NPELEKFLLYY--DS 191
Query: 167 LDTMLPKCDIVVVNTPLTEKTRGMFDKDRIAKMKKGVLIVNNARGAIMDTQAVVDACSSG 226
L+ +L + DI+ ++ PLT++ + + + AKMK G ++VN ARG ++DT+A++DA SG
Sbjct: 192 LEDLLKQADIISLHVPLTKENHHLINAEAFAKMKDGAILVNAARGGLVDTKALIDALDSG 251
Query: 227 HIAGYSGDV-----------WNPQPAPKDHPWRY-----MPNQAMTPHV 259
IAG + D W+ + + MPN +TPH+
Sbjct: 252 KIAGAALDTYENETGYFNKDWSGKEIEDE---VLKELIAMPNVLITPHI 297
>gnl|CDD|240646 cd12169, PGDH_like_1, Putative D-3-Phosphoglycerate Dehydrogenases.
Phosphoglycerate dehydrogenases (PGDHs) catalyze the
initial step in the biosynthesis of L-serine from
D-3-phosphoglycerate. PGDHs come in 3 distinct
structural forms, with this first group being related to
2-hydroxy acid dehydrogenases, sharing structural
similarity to formate and glycerate dehydrogenases of
the D-specific 2-hydroxyacid dehydrogenase superfamily,
which also include groups such as L-alanine
dehydrogenase and S-adenosylhomocysteine hydrolase.
Despite often low sequence identity, these proteins
typically have a characteristic arrangement of 2 similar
subdomains of the alpha/beta Rossmann fold NAD+ binding
form. The NAD+ binding domain is inserted within the
linear sequence of the mostly N-terminal catalytic
domain, which has a similar domain structure to the
internal NAD binding domain. Structurally, these domains
are connected by extended alpha helices and create a
cleft in which NAD is bound, primarily to the C-terminal
portion of the 2nd (internal) domain. Some related
proteins have similar structural subdomain but with a
tandem arrangement of the catalytic and NAD-binding
subdomains in the linear sequence. Many, not all,
members of this family are dimeric.
Length = 308
Score = 128 bits (325), Expect = 4e-35
Identities = 65/228 (28%), Positives = 108/228 (47%), Gaps = 6/228 (2%)
Query: 57 AAAAAGLTVAEVTGSNVVSVAEDELMRILILVRNFLPGHHQVISGEWNVAGVAYRAYDLE 116
AA G+ V TG + AE IL L RN + +G W L
Sbjct: 87 AAKERGIVVCG-TGGGPTATAELTWALILALARNLPEEDAALRAGGWQTTL----GTGLA 141
Query: 117 GKTVGTVGCGRIGKLLLQRLKPFNCNLLYHDRVKMDPQLEKETGAKFEEDLDTMLPKCDI 176
GKT+G VG GRIG + + + F ++ + + G + + + D+
Sbjct: 142 GKTLGIVGLGRIGARVARIGQAFGMRVIAWSS-NLTAERAAAAGVEAAVSKEELFATSDV 200
Query: 177 VVVNTPLTEKTRGMFDKDRIAKMKKGVLIVNNARGAIMDTQAVVDACSSGHIAGYSGDVW 236
V ++ L+++TRG+ + +A MK L+VN +RG ++D A++ A +G IAG + DV+
Sbjct: 201 VSLHLVLSDRTRGLVGAEDLALMKPTALLVNTSRGPLVDEGALLAALRAGRIAGAALDVF 260
Query: 237 NPQPAPKDHPWRYMPNQAMTPHVSGTTIDAQLRYAAGVKDMLDRYFKG 284
+ +P P DHP R +PN +TPH+ T +A + + + + G
Sbjct: 261 DVEPLPADHPLRGLPNVLLTPHIGYVTEEAYEGFYGQAVENIAAWLAG 308
>gnl|CDD|240663 cd12187, LDH_like_1, D-Lactate and related Dehydrogenase like
proteins, NAD-binding and catalytic domains. D-Lactate
dehydrogenase (LDH) catalyzes the interconversion of
pyruvate and lactate, and is a member of the
2-hydroxyacid dehydrogenase family. LDH is homologous to
D-2-Hydroxyisocaproic acid dehydrogenase(D-HicDH) and
shares the 2 domain structure of formate dehydrogenase.
D-2-hydroxyisocaproate dehydrogenase-like (HicDH)
proteins are NAD-dependent members of the
hydroxycarboxylate dehydrogenase family, and share the
Rossmann fold typical of many NAD binding proteins.
HicDH from Lactobacillus casei forms a monomer and
catalyzes the reaction R-CO-COO(-) + NADH + H+ to
R-COH-COO(-) + NAD+. D-HicDH, like the structurally
distinct L-HicDH, exhibits low side-chain R specificity,
accepting a wide range of 2-oxocarboxylic acid side
chains. Formate/glycerate and related dehydrogenases of
the D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-Adenosylhomocysteine Hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain.
Length = 329
Score = 128 bits (324), Expect = 6e-35
Identities = 69/230 (30%), Positives = 114/230 (49%), Gaps = 24/230 (10%)
Query: 57 AAAAAGLTVAEVTGSNVVSVAEDELMRILILVRNFLPGHHQVISGEWNVAGVAYRAYDLE 116
A G+ V V +VAE +L L R + G+++ AG+ R ++L
Sbjct: 81 ACRERGIAVCNVPDYGEATVAEHAFALLLALSRKLREAIERTRRGDFSQAGL--RGFELA 138
Query: 117 GKTVGTVGCGRIGKLLLQRLKPFNCNLLYHDRVKMDPQLEKETGAKFEEDLDTMLPKCDI 176
GKT+G VG GRIG+ + + + F +L +D V D +L + G ++ L+ +L + DI
Sbjct: 139 GKTLGVVGTGRIGRRVARIARGFGMKVLAYDVVP-DEELAERLGFRYV-SLEELLQESDI 196
Query: 177 VVVNTPLTEKTRGMFDKDRIAKMKKGVLIVNNARGAIMDTQAVVDACSSGHIAGYSGDV- 235
+ ++ P T +T + +++ A MK G +++N ARGA++DT+A+V A G +AG DV
Sbjct: 197 ISLHVPYTPQTHHLINRENFALMKPGAVLINTARGAVVDTEALVRALKEGKLAGAGLDVL 256
Query: 236 ------------WNPQPAP-------KDHPWRYMPNQAMTPHVSGTTIDA 266
+ +P DH PN +TPHV+ T +A
Sbjct: 257 EQEEVLREEAELFREDVSPEDLKKLLADHALLRKPNVIITPHVAYNTKEA 306
>gnl|CDD|215893 pfam00389, 2-Hacid_dh, D-isomer specific 2-hydroxyacid
dehydrogenase, catalytic domain. This family represents
the largest portion of the catalytic domain of
2-hydroxyacid dehydrogenases as the NAD binding domain
is inserted within the structural domain.
Length = 312
Score = 127 bits (321), Expect = 1e-34
Identities = 65/230 (28%), Positives = 96/230 (41%), Gaps = 3/230 (1%)
Query: 57 AAAAAGLTVAEVTGSNVVSVAEDELMRILILVRNFLPGHHQVISGEWNVAGVAYRAYDLE 116
AA G+ V V G + SVAE + IL L R V +G+W +L
Sbjct: 78 AATERGILVTNVPGYSTESVAELTVGLILALARRIPEADASVRAGDWK--KGGPIGLELY 135
Query: 117 GKTVGTVGCGRIGKLLLQRLKPFNCN-LLYHDRVKMDPQLEKETGAKFEEDLDTMLPKCD 175
GKT+G +G G IG + K + Y + E + L L + D
Sbjct: 136 GKTLGVIGGGGIGGIGAAIAKALGMGVVAYDPYPNPERAEEGGVEVLLLDLLLLDLKESD 195
Query: 176 IVVVNTPLTEKTRGMFDKDRIAKMKKGVLIVNNARGAIMDTQAVVDACSSGHIAGYSGDV 235
++ P T G + M K + +NNARG + +A +DA IA + DV
Sbjct: 196 DLINLAPPTTMKTGHIIINEARGMLKDAVAINNARGGGVIEEAALDALLEEGIAAAALDV 255
Query: 236 WNPQPAPKDHPWRYMPNQAMTPHVSGTTIDAQLRYAAGVKDMLDRYFKGE 285
+P P + P +PN +TPH++G T +AQ A + L + KG
Sbjct: 256 VEEEPPPVNSPLLDLPNVILTPHIAGATEEAQENMAEEAAENLLAFLKGG 305
>gnl|CDD|240656 cd12179, 2-Hacid_dh_14, Putative D-isomer specific 2-hydroxyacid
dehydrogenases, NAD-binding and catalytic domains.
2-Hydroxyacid dehydrogenases catalyze the conversion of
a wide variety of D-2-hydroxy acids to their
corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 306
Score = 123 bits (311), Expect = 3e-33
Identities = 66/222 (29%), Positives = 106/222 (47%), Gaps = 24/222 (10%)
Query: 57 AAAAAGLTVAEVTGSNVVSVAEDELMRILILVRNFLPGHHQVISGEWNVAGVAYRAYDLE 116
A G+ + N +V E L +L L +V +G W+ G R +L
Sbjct: 80 YAKEKGIELFNAPEGNRDAVGEHALGMLLALFNKLNRADQEVRNGIWDREG--NRGVELM 137
Query: 117 GKTVGTVGCGRIGKLLLQRLKPFNCNLLYHDRVKMDPQLEKETGAKF--EEDLDTMLPKC 174
GKTVG +G G +GK +RL F C ++ +D+ K G + + L+T+ +
Sbjct: 138 GKTVGIIGYGNMGKAFAKRLSGFGCKVIAYDK-------YKNFGDAYAEQVSLETLFKEA 190
Query: 175 DIVVVNTPLTEKTRGMFDKDRIAKMKKGVLIVNNARGAIMDTQAVVDACSSGHIAGYSGD 234
DI+ ++ PLT +TRGM +K+ I+ KK +N ARG ++ T+ +V A SG I G D
Sbjct: 191 DILSLHIPLTPETRGMVNKEFISSFKKPFYFINTARGKVVVTKDLVKALKSGKILGACLD 250
Query: 235 VW--------NPQPAPKDHPWRYM---PNQAMTPHVSGTTID 265
V + P+ + Y+ P +TPH++G T +
Sbjct: 251 VLEYEKASFESIFNQPEA--FEYLIKSPKVILTPHIAGWTFE 290
>gnl|CDD|240657 cd12180, 2-Hacid_dh_15, Putative D-isomer specific 2-hydroxyacid
dehydrogenases, NAD-binding and catalytic domains.
2-Hydroxyacid dehydrogenases catalyze the conversion of
a wide variety of D-2-hydroxy acids to their
corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 308
Score = 122 bits (309), Expect = 7e-33
Identities = 65/229 (28%), Positives = 104/229 (45%), Gaps = 16/229 (6%)
Query: 61 AGLTVAEVTGSNVVSVAEDELMRILILVRNFLPGHHQVISGEWNVAGVAYRAYD----LE 116
G V G ++AE L IL + W V G + L
Sbjct: 84 EGPVVTCARGVAAEAIAEFVLAAILAAAKRL--------PEIW-VKGAEQWRREPLGSLA 134
Query: 117 GKTVGTVGCGRIGKLLLQRLKPFNCNLLYHDRVKMDPQLEKETGAKFEEDLDTMLPKCDI 176
G T+G VG G IG+ L +R +L ++ + G + DL + + D
Sbjct: 135 GSTLGIVGFGAIGQALARRALALGMRVL---ALRRSGRPSDVPGVEAAADLAELFARSDH 191
Query: 177 VVVNTPLTEKTRGMFDKDRIAKMKKGVLIVNNARGAIMDTQAVVDACSSGHIAGYSGDVW 236
+V+ PLT +TR + + D +A+ K G+ ++N ARG ++D +A+++A SG I+ S DV
Sbjct: 192 LVLAAPLTPETRHLINADVLAQAKPGLHLINIARGGLVDQEALLEALDSGRISLASLDVT 251
Query: 237 NPQPAPKDHPWRYMPNQAMTPHVSGTTIDAQLRYAAGVKDMLDRYFKGE 285
+P+P P+ HP P ++PH S D + A + L RY G+
Sbjct: 252 DPEPLPEGHPLYTHPRVRLSPHTSAIAPDGRRNLADRFLENLARYRAGQ 300
>gnl|CDD|180588 PRK06487, PRK06487, glycerate dehydrogenase; Provisional.
Length = 317
Score = 122 bits (309), Expect = 8e-33
Identities = 71/246 (28%), Positives = 115/246 (46%), Gaps = 13/246 (5%)
Query: 52 NPNFLAAAAAGLTVAEVTGSNVVSVAEDELMRILILVRNFLPGHHQVISGEWNVAG---- 107
N + AA G+TV G SVA+ L +L L V +G W +
Sbjct: 79 NVDLAAARERGITVCNCQGYGTPSVAQHTLALLLALATRLPDYQQAVAAGRWQQSSQFCL 138
Query: 108 VAYRAYDLEGKTVGTVGCGRIGKLLLQRLKPFNCNLLYHDRVKMDPQLEKETGAKFEEDL 167
+ + +LEGKT+G +G G +G + + + F +L QL L
Sbjct: 139 LDFPIVELEGKTLGLLGHGELGGAVARLAEAFGMRVLI-------GQLPGRPARPDRLPL 191
Query: 168 DTMLPKCDIVVVNTPLTEKTRGMFDKDRIAKMKKGVLIVNNARGAIMDTQAVVDACSSGH 227
D +LP+ D + ++ PLTE TR + +A MK G L++N ARG ++D QA+ DA SGH
Sbjct: 192 DELLPQVDALTLHCPLTEHTRHLIGARELALMKPGALLINTARGGLVDEQALADALRSGH 251
Query: 228 IAGYSGDVWNPQPAPKDHPWRY--MPNQAMTPHVSGTTIDAQLRYAAGVKDMLDRYFKGE 285
+ G + DV + +P +P +P +TPH + + +A+ R + + +F G+
Sbjct: 252 LGGAATDVLSVEPPVNGNPLLAPDIPRLIVTPHSAWGSREARQRIVGQLAENARAFFAGK 311
Query: 286 DFPVQN 291
V +
Sbjct: 312 PLRVVS 317
>gnl|CDD|240620 cd01619, LDH_like, D-Lactate and related Dehydrogenases,
NAD-binding and catalytic domains. D-Lactate
dehydrogenase (LDH) catalyzes the interconversion of
pyruvate and lactate, and is a member of the
2-hydroxyacid dehydrogenase family. LDH is homologous to
D-2-Hydroxyisocaproic acid dehydrogenase (D-HicDH) and
shares the 2 domain structure of formate dehydrogenase.
D-HicDH is a NAD-dependent member of the
hydroxycarboxylate dehydrogenase family, and shares the
Rossmann fold typical of many NAD binding proteins.
D-HicDH from Lactobacillus casei forms a monomer and
catalyzes the reaction R-CO-COO(-) + NADH + H+ to
R-COH-COO(-) + NAD+. Similar to the structurally
distinct L-HicDH, D-HicDH exhibits low side-chain R
specificity, accepting a wide range of 2-oxocarboxylic
acid side chains. (R)-2-hydroxyglutarate dehydrogenase
(HGDH) catalyzes the NAD-dependent reduction of
2-oxoglutarate to (R)-2-hydroxyglutarate.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain.
Length = 323
Score = 120 bits (304), Expect = 4e-32
Identities = 63/205 (30%), Positives = 103/205 (50%), Gaps = 18/205 (8%)
Query: 75 SVAEDELMRILILVRNFLPGHHQVISGEWNVAGVAYRAYDLEGKTVGTVGCGRIGKLLLQ 134
+VAE + IL L+RN + ++ +LE +TVG VG G+IG+ + Q
Sbjct: 103 AVAEHTIALILALLRNR--KYIDERDKNQDLQDAGVIGRELEDQTVGVVGTGKIGRAVAQ 160
Query: 135 RLKPFNCNLLYHDRVKMDPQLEKETGAKFEEDLDTMLPKCDIVVVNTPLTEKTRGMFDKD 194
R K F ++ +D + P+LE + G K+ L+ + DI+ ++ PLT + M +++
Sbjct: 161 RAKGFGMKVIAYDPFRN-PELEDK-GVKYVS-LEELFKNSDIISLHVPLTPENHHMINEE 217
Query: 195 RIAKMKKGVLIVNNARGAIMDTQAVVDACSSGHIAGYSGDV-----------WNPQ--PA 241
MKKGV+I+N ARG+++DT+A+++A SG I G DV +
Sbjct: 218 AFKLMKKGVIIINTARGSLVDTEALIEALDSGKIFGAGLDVLEDETPDLLKDLEGEIFKD 277
Query: 242 PKDHPWRYMPNQAMTPHVSGTTIDA 266
+ PN +TPH + T DA
Sbjct: 278 ALNALLGRRPNVIITPHTAFYTDDA 302
>gnl|CDD|240635 cd12158, ErythrP_dh, D-Erythronate-4-Phosphate Dehydrogenase
NAD-binding and catalytic domains.
D-Erythronate-4-phosphate Dehydrogenase (E. coli gene
PdxB), a D-specific 2-hydroxyacid dehydrogenase family
member, catalyzes the NAD-dependent oxidation of
erythronate-4-phosphate, which is followed by
transamination to form 4-hydroxy-L-threonine-4-phosphate
within the de novo biosynthesis pathway of vitamin B6.
D-Erythronate-4-phosphate dehydrogenase has the common
architecture shared with D-isomer specific 2-hydroxyacid
dehydrogenases but contains an additional C-terminal
dimerization domain in addition to an NAD-binding domain
and the "lid" domain. The lid domain corresponds to the
catalytic domain of phosphoglycerate dehydrogenase and
other proteins of the D-isomer specific 2-hydroxyacid
dehydrogenase family, which include groups such as
formate dehydrogenase, glycerate dehydrogenase,
L-alanine dehydrogenase, and S-adenosylhomocysteine
hydrolase. Despite often low sequence identity, these
proteins typically have a characteristic arrangement of
2 similar subdomains of the alpha/beta Rossmann fold
NAD+ binding form. The NAD+ binding domain is inserted
within the linear sequence of the mostly N-terminal
catalytic domain, which has a similar domain structure
to the internal NAD binding domain. Structurally, these
domains are connected by extended alpha helices and
create a cleft in which NAD is bound, primarily to the
C-terminal portion of the 2nd (internal) domain. Some
related proteins have similar structural subdomain but
with a tandem arrangement of the catalytic and
NAD-binding subdomains in the linear sequence.
Length = 343
Score = 119 bits (302), Expect = 2e-31
Identities = 52/184 (28%), Positives = 89/184 (48%), Gaps = 29/184 (15%)
Query: 101 GEWNVAGVAYRAY----DLEGKTVGTVGCGRIGKLLLQRLKPFNCNLLYHDRVKMDPQLE 156
E+ ++ + A L+GKTVG VG G +G L +RL+ N+L D P+ E
Sbjct: 95 AEYVLSALLVLAQRQGFSLKGKTVGIVGVGNVGSRLARRLEALGMNVLLCD----PPRAE 150
Query: 157 KETGAKFEEDLDTMLPKCDIVVVNTPLTE----KTRGMFDKDRIAKMKKGVLIVNNARGA 212
E F L+ +L + DI+ ++ PLT T + D+D +A +K G +++N +RGA
Sbjct: 151 AEGDPGFV-SLEELLAEADIITLHVPLTRDGEHPTYHLLDEDFLAALKPGQILINASRGA 209
Query: 213 IMDTQAVVDACSSGHIAGYSGDVWNPQPAPKDHPWRYMPNQAM-------TPHVSGTTID 265
++D QA++ G DVW +P + + TPH++G +++
Sbjct: 210 VIDNQALLALLQRGKDLRVVLDVWENEPE---------IDLELLDKVDIATPHIAGYSLE 260
Query: 266 AQLR 269
+ R
Sbjct: 261 GKAR 264
>gnl|CDD|240633 cd12156, HPPR, Hydroxy(phenyl)pyruvate Reductase, D-isomer-specific
2-hydroxyacid-related dehydrogenase.
Hydroxy(phenyl)pyruvate reductase (HPPR) catalyzes the
NADP-dependent reduction of hydroxyphenylpyruvates,
hydroxypyruvate, or pyruvate to its respective lactate.
HPPR acts as a dimer and is related to D-isomer-specific
2-hydroxyacid dehydrogenases, a superfamily that
includes groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-Adenosylhomocysteine Hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 301
Score = 116 bits (294), Expect = 9e-31
Identities = 62/228 (27%), Positives = 105/228 (46%), Gaps = 11/228 (4%)
Query: 57 AAAAAGLTVAEVTGSNVVSVAEDELMRILILVRNFLPGHHQVISGEWNVAGVAYR-AYDL 115
AA A G+ V G VA+ + +L ++R V +G W A+ +
Sbjct: 82 AARARGIRVTNTPGVLTDDVADLAVGLLLAVLRRIPAADRFVRAGRW--PKGAFPLTRKV 139
Query: 116 EGKTVGTVGCGRIGKLLLQRLKPFNCNLLYHDRVKMDPQLEKETGAKFEEDLDTMLPKCD 175
GK VG VG GRIG+ + +RL+ F + YH R + ++ L + + D
Sbjct: 140 SGKRVGIVGLGRIGRAIARRLEAFGMEIAYHGRRPKP-----DVPYRYYASLLELAAESD 194
Query: 176 IVVVNTPLTEKTRGMFDKDRIAKM-KKGVLIVNNARGAIMDTQAVVDACSSGHIAGYSGD 234
++VV P TR + + + + + GVL+ N ARG+++D A++ A G IAG D
Sbjct: 195 VLVVACPGGPATRHLVNAEVLEALGPDGVLV-NVARGSVVDEAALIAALQEGRIAGAGLD 253
Query: 235 VWNPQPAPKDHPWRYMPNQAMTPHVSGTTIDAQLRYAAGVKDMLDRYF 282
V+ +P + N +TPH++ T++ + V L+ +F
Sbjct: 254 VFENEPNVPA-ALLDLDNVVLTPHIASATVETRRAMGDLVLANLEAFF 300
>gnl|CDD|185307 PRK15409, PRK15409, bifunctional glyoxylate/hydroxypyruvate
reductase B; Provisional.
Length = 323
Score = 115 bits (290), Expect = 5e-30
Identities = 67/206 (32%), Positives = 105/206 (50%), Gaps = 4/206 (1%)
Query: 75 SVAEDELMRILILVRNFLPGHHQVISGEWNVA-GVAYRAYDLEGKTVGTVGCGRIGKLLL 133
+VA+ + +L R + +V +GEW + G + D+ KT+G VG GRIG L
Sbjct: 102 TVADTLMALVLSTARRVVEVAERVKAGEWTASIGPDWFGTDVHHKTLGIVGMGRIGMALA 161
Query: 134 QRLK-PFNCNLLYHDRVKMDPQLEKETGAKFEEDLDTMLPKCDIVVVNTPLTEKTRGMFD 192
QR FN +LY+ R + + E+ A++ DLDT+L + D V + PLT++T +F
Sbjct: 162 QRAHFGFNMPILYNAR-RHHKEAEERFNARYC-DLDTLLQESDFVCIILPLTDETHHLFG 219
Query: 193 KDRIAKMKKGVLIVNNARGAIMDTQAVVDACSSGHIAGYSGDVWNPQPAPKDHPWRYMPN 252
++ AKMK + +N RG ++D A++ A G I DV+ +P D P +PN
Sbjct: 220 AEQFAKMKSSAIFINAGRGPVVDENALIAALQKGEIHAAGLDVFEQEPLSVDSPLLSLPN 279
Query: 253 QAMTPHVSGTTIDAQLRYAAGVKDML 278
PH+ T + + AA D L
Sbjct: 280 VVAVPHIGSATHETRYNMAACAVDNL 305
>gnl|CDD|240641 cd12164, GDH_like_2, Putative glycerate dehydrogenase and related
proteins of the D-specific 2-hydroxy dehydrogenase
family. This group contains a variety of proteins
variously identified as glycerate dehydrogenase (GDH,
also known as hydroxypyruvate reductase) and other
enzymes of the 2-hydroxyacid dehydrogenase family. GDH
catalyzes the reversible reaction of (R)-glycerate +
NAD+ to hydroxypyruvate + NADH + H+. 2-hydroxyacid
dehydrogenases catalyze the conversion of a wide variety
of D-2-hydroxy acids to their corresponding keto acids.
The general mechanism is (R)-lactate + acceptor to
pyruvate + reduced acceptor. Formate/glycerate and
related dehydrogenases of the D-specific 2-hydroxyacid
dehydrogenase superfamily include groups such as formate
dehydrogenase, glycerate dehydrogenase, L-alanine
dehydrogenase, and S-adenosylhomocysteine hydrolase.
Despite often low sequence identity, these proteins
typically have a characteristic arrangement of 2 similar
subdomains of the alpha/beta Rossmann-fold NAD+ binding
form. The NAD+ binding domain is inserted within the
linear sequence of the mostly N-terminal catalytic
domain, which has a similar domain structure to the
internal NAD binding domain. Structurally, these domains
are connected by extended alpha helices and create a
cleft in which NAD is bound, primarily to the C-terminal
portion of the 2nd (internal) domain. Some related
proteins have similar structural subdomain but with a
tandem arrangement of the catalytic and NAD-binding
subdomains in the linear sequence. While many members of
this family are dimeric, alanine DH is hexameric and
phosphoglycerate DH is tetrameric.
Length = 306
Score = 114 bits (287), Expect = 1e-29
Identities = 58/192 (30%), Positives = 88/192 (45%), Gaps = 16/192 (8%)
Query: 101 GEWNVAGVAYRAYDLEGKTVGTVGCGRIGKLLLQRLKPFNCNLLYHDRVKMDPQLEKETG 160
G W A + VG +G G +G + +RL + R D E
Sbjct: 120 GVWK-PLPQRPAAER---RVGVLGLGELGAAVARRLAALGFPVSGWSRSPKDI----EGV 171
Query: 161 AKF--EEDLDTMLPKCDIVVVNTPLTEKTRGMFDKDRIAKMKKGVLIVNNARGAIMDTQA 218
F EE LD L + DI+V PLT +TRG+ + + +A++ +G ++N RG +
Sbjct: 172 TCFHGEEGLDAFLAQTDILVCLLPLTPETRGILNAELLARLPRGAALINVGRGPHLVEAD 231
Query: 219 VVDACSSGHIAGYSGDVWNPQPAPKDHP-WRYMPNQAMTPHVSGTT-IDAQLRYAAGVKD 276
++ A SGH++G DV+ +P P DHP WR P +TPH++ T D+ A
Sbjct: 232 LLAALDSGHLSGAVLDVFEQEPLPADHPLWR-HPRVTVTPHIAAITDPDSAAAQVAEN-- 288
Query: 277 MLDRYFKGEDFP 288
+ R GE P
Sbjct: 289 -IRRLEAGEPLP 299
>gnl|CDD|235890 PRK06932, PRK06932, glycerate dehydrogenase; Provisional.
Length = 314
Score = 111 bits (278), Expect = 2e-28
Identities = 66/240 (27%), Positives = 114/240 (47%), Gaps = 14/240 (5%)
Query: 52 NPNFLAAAAAGLTVAEVTGSNVVSVAEDELMRILILVRNFLPGHHQVISGEWNVAG---- 107
N + +AA G+ V VTG + +V E L I L + + + +S W
Sbjct: 78 NVDLVAAKELGIAVKNVTGYSSTTVPEHVLGMIFALKHSLMGWYRDQLSDRWATCKQFCY 137
Query: 108 VAYRAYDLEGKTVGTVGCGRIGKLLLQRLKPFNCNLLYHDRVKMDPQLEKETGAKFEEDL 167
Y D+ G T+G G G +G + + + +LY + + +E FEE
Sbjct: 138 FDYPITDVRGSTLGVFGKGCLGTEVGRLAQALGMKVLYAEH--KGASVCREGYTPFEE-- 193
Query: 168 DTMLPKCDIVVVNTPLTEKTRGMFDKDRIAKMKKGVLIVNNARGAIMDTQAVVDACSSGH 227
+L + DIV ++ PLTE T+ + + + +A MK ++N RG ++D QA++DA +G
Sbjct: 194 --VLKQADIVTLHCPLTETTQNLINAETLALMKPTAFLINTGRGPLVDEQALLDALENGK 251
Query: 228 IAGYSGDVWNPQPAPKDHPW----RYMPNQAMTPHVSGTTIDAQLRYAAGVKDMLDRYFK 283
IAG + DV +P KD+P + +PN +TPH++ + A V ++ + +
Sbjct: 252 IAGAALDVLVKEPPEKDNPLIQAAKRLPNLLITPHIAWASDSAVTTLVNKVAQNIEEFVQ 311
>gnl|CDD|181414 PRK08410, PRK08410, 2-hydroxyacid dehydrogenase; Provisional.
Length = 311
Score = 109 bits (275), Expect = 5e-28
Identities = 58/245 (23%), Positives = 110/245 (44%), Gaps = 21/245 (8%)
Query: 52 NPNFLAAAAAGLTVAEVTGSNVVSVAEDELMRILILVRNFLPGHHQVISGEW-------N 104
N + A G+ V V G + SVA+ +L L+ V SGE+ +
Sbjct: 76 NVDIEYAKKKGIAVKNVAGYSTESVAQHTFAMLLSLLGRINYYDRYVKSGEYSESPIFTH 135
Query: 105 VAGVAYRAYDLEGKTVGTVGCGRIGKLLLQRLKPFNCNLLYHDRVKMDPQLEKETGAKFE 164
++ +++GK G +G G IGK + + + F ++Y+ K ++E
Sbjct: 136 ISRPLG---EIKGKKWGIIGLGTIGKRVAKIAQAFGAKVVYYSTSG------KNKNEEYE 186
Query: 165 E-DLDTMLPKCDIVVVNTPLTEKTRGMFDKDRIAKMKKGVLIVNNARGAIMDTQAVVDAC 223
L+ +L DI+ ++ PL EKT+ + + +K G +++N RG I++ + + A
Sbjct: 187 RVSLEELLKTSDIISIHAPLNEKTKNLIAYKELKLLKDGAILINVGRGGIVNEKDLAKAL 246
Query: 224 SSGHIAGYSGDVWNPQPAPKDHPWRYMPNQA---MTPHVSGTTIDAQLRYAAGVKDMLDR 280
I DV +P K+HP + N+ +TPH++ + +A+ VK+ +
Sbjct: 247 DEKDI-YAGLDVLEKEPMEKNHPLLSIKNKEKLLITPHIAWASKEARKTLIEKVKENIKD 305
Query: 281 YFKGE 285
+ +G
Sbjct: 306 FLEGG 310
>gnl|CDD|215501 PLN02928, PLN02928, oxidoreductase family protein.
Length = 347
Score = 108 bits (273), Expect = 2e-27
Identities = 73/222 (32%), Positives = 105/222 (47%), Gaps = 20/222 (9%)
Query: 57 AAAAAGLTVAEVTGS---NVVSVAEDELMRILILVRNFLPGHHQVISGEWNVAGVAYRAY 113
AA G+ VA + N S AE + +L L+R + +
Sbjct: 100 AATKHGIKVARIPSEGTGNAASCAEMAIYLMLGLLR-----KQNEMQISLKARRLGEPIG 154
Query: 114 D-LEGKTVGTVGCGRIGKLLLQRLKPFNCNLLYHDR---VKMDPQLEKETGAKFE----- 164
D L GKTV +G G IG L +RL+PF LL R + + L G +
Sbjct: 155 DTLFGKTVFILGYGAIGIELAKRLRPFGVKLLATRRSWTSEPEDGLLIPNGDVDDLVDEK 214
Query: 165 ---EDLDTMLPKCDIVVVNTPLTEKTRGMFDKDRIAKMKKGVLIVNNARGAIMDTQAVVD 221
ED+ + DIVV+ LT++T G+ + + ++ MKKG L+VN ARG ++D AV+
Sbjct: 215 GGHEDIYEFAGEADIVVLCCTLTKETAGIVNDEFLSSMKKGALLVNIARGGLLDYDAVLA 274
Query: 222 ACSSGHIAGYSGDVWNPQPAPKDHPWRYMPNQAMTPHVSGTT 263
A SGH+ G + DV +P D P PN +TPHV+G T
Sbjct: 275 ALESGHLGGLAIDVAWSEPFDPDDPILKHPNVIITPHVAGVT 316
>gnl|CDD|240660 cd12184, HGDH_like, (R)-2-Hydroxyglutarate Dehydrogenase and
related dehydrogenases, NAD-binding and catalytic
domains. (R)-2-hydroxyglutarate dehydrogenase (HGDH)
catalyzes the NAD-dependent reduction of 2-oxoglutarate
to (R)-2-hydroxyglutarate. HGDH is a member of the
D-2-hydroxyacid NAD(+)-dependent dehydrogenase family;
these proteins typically have a characteristic
arrangement of 2 similar subdomains of the alpha/beta
Rossmann fold NAD+ binding form. The NAD+ binding domain
is inserted within the linear sequence of the mostly
N-terminal catalytic domain, which has a similar domain
structure to the internal NAD binding domain.
Structurally, these domains are connected by extended
alpha helices and create a cleft in which NAD is bound,
primarily to the C-terminal portion of the 2nd
(internal) domain.
Length = 330
Score = 108 bits (271), Expect = 3e-27
Identities = 57/225 (25%), Positives = 102/225 (45%), Gaps = 20/225 (8%)
Query: 57 AAAAAGLTVAEVTGSNVVSVAEDELMRILILVRNFLPGHHQVISGEWNVAGVAYRAYDLE 116
AA G +A V + ++AE + L R+ + + + V + + ++
Sbjct: 86 AAKELGFKMARVPSYSPNAIAELAFTLAMTLSRHTAYTASRTANKNFKVDPFMF-SKEIR 144
Query: 117 GKTVGTVGCGRIGKLLLQRLKPFNCNLLYHDRVKMDPQLEKETGAKFEEDLDTMLPKCDI 176
TVG +G GRIG + K ++ +D + P + F LD +L K DI
Sbjct: 145 NSTVGIIGTGRIGLTAAKLFKGLGAKVIGYD---IYPSDAAKDVVTFV-SLDELLKKSDI 200
Query: 177 VVVNTP-LTEKTRGMFDKDRIAKMKKGVLIVNNARGAIMDTQAVVDACSSGHIAGYSGDV 235
+ ++ P + K + +K+ I+KMK G +++N ARG + D +A+++A SG +AG+ DV
Sbjct: 201 ISLHVPYIKGKNDKLINKEFISKMKDGAILINTARGELQDEEAILEALESGKLAGFGTDV 260
Query: 236 WNPQPAP--KDHPWRYMPNQA------------MTPHVSGTTIDA 266
N + KD + + +TPH+ T +A
Sbjct: 261 LNNEKEIFFKDFDGDKIEDPVVEKLLDLYPRVLLTPHIGSYTDEA 305
>gnl|CDD|240640 cd12163, 2-Hacid_dh_5, Putative D-isomer specific 2-hydroxyacid
dehydrogenases. 2-Hydroxyacid dehydrogenases catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 334
Score = 108 bits (271), Expect = 3e-27
Identities = 67/233 (28%), Positives = 104/233 (44%), Gaps = 22/233 (9%)
Query: 75 SVAEDELMRILILVRNFLPGHHQVISGEWNVAGVAYRAYDLEGKTVGTVGCGRIGKLLLQ 134
+AE + L+L +FL W AY D GK VG +G G IG+ +
Sbjct: 91 QIAEWVIGTWLVLSHHFLQYIELQKEQTWGRRQEAYSVEDSVGKRVGILGYGSIGRQTAR 150
Query: 135 RLKPFNCNLL-YHDRVKMDPQLEKETG--------------AKF-----EEDLDTML-PK 173
+ + Y + P+ K+ G + + + L L
Sbjct: 151 LAQALGMEVYAYTRSPRPTPESRKDDGYIVPGTGDPDGSIPSAWFSGTDKASLHEFLRQD 210
Query: 174 CDIVVVNTPLTEKTRGMFDKDRIAKM-KKGVLIVNNARGAIMDTQAVVDACSSGHIAGYS 232
D++VV+ PLT T+ + + + K+ + N ARG+++DT A+V A SG I G +
Sbjct: 211 LDLLVVSLPLTPATKHLLGAEEFEILAKRKTFVSNIARGSLVDTDALVAALESGQIRGAA 270
Query: 233 GDVWNPQPAPKDHPWRYMPNQAMTPHVSGTTIDAQLRYAAGVKDMLDRYFKGE 285
DV +P+P P DHP PN +TPHVS T + R +++ L+R KGE
Sbjct: 271 LDVTDPEPLPADHPLWSAPNVIITPHVSWQTQEYFDRALDVLEENLERLRKGE 323
>gnl|CDD|236985 PRK11790, PRK11790, D-3-phosphoglycerate dehydrogenase;
Provisional.
Length = 409
Score = 108 bits (273), Expect = 5e-27
Identities = 69/216 (31%), Positives = 112/216 (51%), Gaps = 12/216 (5%)
Query: 57 AAAAAGLTVAEVTGSNVVSVAEDELMRILILVRNFLPGHHQVISGEWNVAGVAYRAYDLE 116
AAA G+ V SN SVAE + I++L+R + + G WN A ++++
Sbjct: 93 AAAKRGIPVFNAPFSNTRSVAELVIGEIILLLRGIPEKNAKAHRGGWN--KSAAGSFEVR 150
Query: 117 GKTVGTVGCGRIGKLLLQRLKPFNCNLLYHDRVKMDPQLEKETG-AKFEEDLDTMLPKCD 175
GKT+G VG G IG L + + ++D P G A+ L+ +L + D
Sbjct: 151 GKTLGIVGYGHIGTQLSVLAESLGMRVYFYDIEDKLP-----LGNARQVGSLEELLAQSD 205
Query: 176 IVVVNTPLTEKTRGMFDKDRIAKMKKGVLIVNNARGAIMDTQAVVDACSSGHIAGYSGDV 235
+V ++ P T T+ M + +A MK G +++N +RG ++D A+ DA SGH+AG + DV
Sbjct: 206 VVSLHVPETPSTKNMIGAEELALMKPGAILINASRGTVVDIDALADALKSGHLAGAAIDV 265
Query: 236 WNPQPAPKDHPW----RYMPNQAMTPHVSGTTIDAQ 267
+ +P P+ R + N +TPH+ G+T +AQ
Sbjct: 266 FPVEPKSNGDPFESPLRGLDNVILTPHIGGSTQEAQ 301
>gnl|CDD|166874 PRK00257, PRK00257, erythronate-4-phosphate dehydrogenase;
Validated.
Length = 381
Score = 90.1 bits (224), Expect = 2e-20
Identities = 55/184 (29%), Positives = 91/184 (49%), Gaps = 12/184 (6%)
Query: 111 RAYDLEGKTVGTVGCGRIGKLLLQRLKPFNCNLLYHDRVKMDPQLEKETGAKFEEDLDTM 170
DL +T G VG G +G L++ L+ +L D P+ E E F L+ +
Sbjct: 110 EGVDLAERTYGVVGAGHVGGRLVRVLRGLGWKVLVCD----PPRQEAEGDGDFV-SLERI 164
Query: 171 LPKCDIVVVNTPLTE----KTRGMFDKDRIAKMKKGVLIVNNARGAIMDTQAVVDACSSG 226
L +CD++ ++TPLT+ TR + D+ +A ++ G ++N +RGA++D QA+ +A SG
Sbjct: 165 LEECDVISLHTPLTKEGEHPTRHLLDEAFLASLRPGAWLINASRGAVVDNQALREALLSG 224
Query: 227 HIAGYSGDVWNPQPAPKDHPWRYMPNQAMTPHVSGTTIDAQLRYAAGVKDMLDRYFKGED 286
DVW + P+ TPH++G ++D + R A + L R+F G
Sbjct: 225 EDLDAVLDVWEGE--PQIDLELADLCTIATPHIAGYSLDGKARGTAQIYQALCRFF-GIP 281
Query: 287 FPVQ 290
V
Sbjct: 282 ARVS 285
>gnl|CDD|240637 cd12160, 2-Hacid_dh_3, Putative D-isomer specific 2-hydroxyacid
dehydrogenases. 2-Hydroxyacid dehydrogenases catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 310
Score = 79.7 bits (197), Expect = 4e-17
Identities = 64/217 (29%), Positives = 86/217 (39%), Gaps = 22/217 (10%)
Query: 60 AAGLT--VAEVTGSNVVS--VAEDELMRILILVRNFLPGHHQVISGEWNVA-------GV 108
AAG VA +G + VAE L IL VR W
Sbjct: 75 AAGFAPEVAVTSGRGLHDGTVAEHTLALILAAVRRLDEMREAQREHRWAGELGGLQPLRP 134
Query: 109 AYRAYDLEGKTVGTVGCGRIGKLLLQRLKPFNCNLLYHDRVKMDPQLEKETGAKF----E 164
A R L G V G G IG+ L L + R A F E
Sbjct: 135 AGRLTTLLGARVLIWGFGSIGQRLAPLLTALGARVTGVAR-------SAGERAGFPVVAE 187
Query: 165 EDLDTMLPKCDIVVVNTPLTEKTRGMFDKDRIAKMKKGVLIVNNARGAIMDTQAVVDACS 224
++L +LP+ D++V+ P T T D + +A + K +VN RGA +D A+V A
Sbjct: 188 DELPELLPETDVLVMILPATPSTAHALDAEVLAALPKHAWVVNVGRGATVDEDALVAALE 247
Query: 225 SGHIAGYSGDVWNPQPAPKDHPWRYMPNQAMTPHVSG 261
SG + G + DV +P P P PN +TPH +G
Sbjct: 248 SGRLGGAALDVTATEPLPASSPLWDAPNLILTPHAAG 284
>gnl|CDD|235800 PRK06436, PRK06436, glycerate dehydrogenase; Provisional.
Length = 303
Score = 75.3 bits (185), Expect = 1e-15
Identities = 58/262 (22%), Positives = 114/262 (43%), Gaps = 33/262 (12%)
Query: 41 VFYKGNEYASMNPNFLAAAAAGLTVAEVTG--SNVV----------SVAEDELMRILILV 88
+ KG + + +AG+ +V+G NVV SVAE +L
Sbjct: 38 ILIKGRYVPGKKTKMIQSLSAGVDHIDVSGIPENVVLCSNAGAYSISVAEHAFALLLAWA 97
Query: 89 RNFLPGHHQVISGEWNVAGVAYRAYD---LEGKTVGTVGCGRIGKLLLQRLKPFNCNLLY 145
+N + +N+ ++ L K++G +G G IG+ + K F N+
Sbjct: 98 KN-------ICENNYNMKNGNFKQSPTKLLYNKSLGILGYGGIGRRVALLAKAFGMNIYA 150
Query: 146 HDRVKMDPQLEKETGAKFEEDLDTMLPKCDIVVVNTPLTEKTRGMFDKDRIAKMKKGVLI 205
+ R + + + + ++ K D V+++ PLT++TRGM + ++ +KG+ I
Sbjct: 151 YTR-----SYVNDGISSIYMEPEDIMKKSDFVLISLPLTDETRGMINSKMLSLFRKGLAI 205
Query: 206 VNNARGAIMDTQAVVDACSSGHIAGYSGDVWNPQPAPKDHPWRYMPNQAMTPHVSGTTID 265
+N AR ++D +++ + + Y DVW +P + N ++PHV+G
Sbjct: 206 INVARADVVDKNDMLNFLRNHNDKYYLSDVWWNEPIITETNPD---NVILSPHVAGGMSG 262
Query: 266 A--QLRYAAGVKDMLDRYFKGE 285
Q A ++ + +F+G+
Sbjct: 263 EIMQPAVALAFEN-IKNFFEGK 283
>gnl|CDD|185335 PRK15438, PRK15438, erythronate-4-phosphate dehydrogenase PdxB;
Provisional.
Length = 378
Score = 70.7 bits (173), Expect = 7e-14
Identities = 63/266 (23%), Positives = 111/266 (41%), Gaps = 49/266 (18%)
Query: 15 ASSGFLRSSSRFSRHYASSGSKKIVGVFYKGNEYASMNPNFLAAAAAGLTVAEVTGSNVV 74
A + +RS ++ + + K VG G ++ ++ +L A G + A G N +
Sbjct: 38 ADALMVRSVTKVNESLLAGKPIKFVGTATAGTDH--VDEAWLKQAGIGFSAA--PGCNAI 93
Query: 75 SVAEDELMRILILVRNFLPGHHQVISGEWNVAGVAYRAYDLEGKTVGTVGCGRIGKLLLQ 134
+V E +L+L + L +TVG VG G +G+ L
Sbjct: 94 AVVEYVFSSLLMLAER--------------------DGFSLHDRTVGIVGVGNVGRRLQA 133
Query: 135 RLKPFNCNLLYHDRVKMDPQLEKETGAKFEEDLDTMLPKCDIVVVNTPLTE----KTRGM 190
RL+ L D P+ ++ F LD ++ + DI+ +TPL + KT +
Sbjct: 134 RLEALGIKTLLCD----PPRADRGDEGDFRS-LDELVQEADILTFHTPLFKDGPYKTLHL 188
Query: 191 FDKDRIAKMKKGVLIVNNARGAIMDTQAVVDACSSGHIAGYSGDVWNPQPAPKDHPWRYM 250
D+ I +K G +++N RGA++D A++ + G DVW +P
Sbjct: 189 ADEKLIRSLKPGAILINACRGAVVDNTALLTCLNEGQKLSVVLDVWEGEPE--------- 239
Query: 251 PNQAM-------TPHVSGTTIDAQLR 269
N + TPH++G T++ + R
Sbjct: 240 LNVELLKKVDIGTPHIAGYTLEGKAR 265
>gnl|CDD|185366 PRK15469, ghrA, bifunctional glyoxylate/hydroxypyruvate reductase
A; Provisional.
Length = 312
Score = 67.5 bits (165), Expect = 8e-13
Identities = 44/157 (28%), Positives = 79/157 (50%), Gaps = 6/157 (3%)
Query: 113 YDLEGKTVGTVGCGRIGKLLLQRLKPFNCNLLYHDRV-KMDPQLEKETGAKFEEDLDTML 171
Y E T+G +G G +G + Q L+ + L R K P ++ G E+L L
Sbjct: 132 YHREDFTIGILGAGVLGSKVAQSLQTWGFPLRCWSRSRKSWPGVQSFAGR---EELSAFL 188
Query: 172 PKCDIVVVNTPLTEKTRGMFDKDRIAKMKKGVLIVNNARGAIMDTQAVVDACSSGHIAGY 231
+ +++ P T +T G+ ++ + ++ G ++N ARG + ++ A SG + G
Sbjct: 189 SQTRVLINLLPNTPETVGIINQQLLEQLPDGAYLLNLARGVHVVEDDLLAALDSGKVKGA 248
Query: 232 SGDVWNPQPAPKDHP-WRYMPNQAMTPHVSGTTIDAQ 267
DV++ +P P + P W++ P A+TPHV+ T A+
Sbjct: 249 MLDVFSREPLPPESPLWQH-PRVAITPHVAAVTRPAE 284
>gnl|CDD|181499 PRK08605, PRK08605, D-lactate dehydrogenase; Validated.
Length = 332
Score = 66.3 bits (162), Expect = 2e-12
Identities = 45/188 (23%), Positives = 89/188 (47%), Gaps = 13/188 (6%)
Query: 54 NFLAAAAAGLTVAEVTGSNVVSVAEDELMRILILVRNFLPGHHQVISGEWNVA-GVAYRA 112
+ A L ++ V + S+AE + + + LVR+F Q E + +
Sbjct: 84 DLELATKYNLIISNVPSYSPESIAEFTVTQAINLVRHF--NQIQTKVREHDFRWEPPILS 141
Query: 113 YDLEGKTVGTVGCGRIGKLLLQRL-KPFNCNLLYHD---RVKMDPQLEKETGAKFEEDLD 168
++ V +G GRIG + + K + +++ +D K ++ +++ ++
Sbjct: 142 RSIKDLKVAVIGTGRIGLAVAKIFAKGYGSDVVAYDPFPNAKAATYVD------YKDTIE 195
Query: 169 TMLPKCDIVVVNTPLTEKTRGMFDKDRIAKMKKGVLIVNNARGAIMDTQAVVDACSSGHI 228
+ DIV ++ P T+ +F+ D KKG + VN ARG+++DT+A++DA +G I
Sbjct: 196 EAVEGADIVTLHMPATKYNHYLFNADLFKHFKKGAVFVNCARGSLVDTKALLDALDNGLI 255
Query: 229 AGYSGDVW 236
G + D +
Sbjct: 256 KGAALDTY 263
>gnl|CDD|177941 PLN02306, PLN02306, hydroxypyruvate reductase.
Length = 386
Score = 63.3 bits (154), Expect = 2e-11
Identities = 45/162 (27%), Positives = 82/162 (50%), Gaps = 18/162 (11%)
Query: 115 LEGKTVGTVGCGRIGKLLLQRL-KPFNCNLLYHDRVKMDPQLEKETGA------------ 161
L+G+TVG +G GRIG + + + F NL+Y+D + +LEK A
Sbjct: 163 LKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYD-LYQSTRLEKFVTAYGQFLKANGEQP 221
Query: 162 ---KFEEDLDTMLPKCDIVVVNTPLTEKTRGMFDKDRIAKMKKGVLIVNNARGAIMDTQA 218
K ++ +L + D++ ++ L + T + +K+R+A MKK ++VN +RG ++D A
Sbjct: 222 VTWKRASSMEEVLREADVISLHPVLDKTTYHLINKERLALMKKEAVLVNASRGPVIDEVA 281
Query: 219 VVDACSSGHIAGYSGDVWNPQPAPKDHPWRYMPNQAMTPHVS 260
+V+ + + DV+ +P K M N + PH++
Sbjct: 282 LVEHLKANPMFRVGLDVFEDEPYMKPG-LADMKNAVVVPHIA 322
>gnl|CDD|183550 PRK12480, PRK12480, D-lactate dehydrogenase; Provisional.
Length = 330
Score = 61.1 bits (148), Expect = 1e-10
Identities = 30/120 (25%), Positives = 58/120 (48%), Gaps = 8/120 (6%)
Query: 119 TVGTVGCGRIGKLLLQRLKPFNCNLLYHDRVKMDPQ--LEKETGAKFEEDLDTMLPKCDI 176
TV +G GRIG + F + +D L +++ + + DI
Sbjct: 148 TVAIIGTGRIGAATAKIYAGFGATITAYDAYPNKDLDFLT------YKDSVKEAIKDADI 201
Query: 177 VVVNTPLTEKTRGMFDKDRIAKMKKGVLIVNNARGAIMDTQAVVDACSSGHIAGYSGDVW 236
+ ++ P +++ +FDK +KKG ++VN ARGA+++T ++ A + G + G + D +
Sbjct: 202 ISLHVPANKESYHLFDKAMFDHVKKGAILVNAARGAVINTPDLIAAVNDGTLLGAAIDTY 261
>gnl|CDD|240647 cd12170, 2-Hacid_dh_9, Putative D-isomer specific 2-hydroxyacid
dehydrogenases. 2-Hydroxyacid dehydrogenases catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 294
Score = 51.9 bits (125), Expect = 1e-07
Identities = 35/170 (20%), Positives = 64/170 (37%), Gaps = 9/170 (5%)
Query: 112 AYDLEGKTVGTVGCGRIGKLLLQRLKPFNCNLLYHDRVKMDPQLEKETGAKFEEDLDTML 171
+L G VG +G G G+++ L F ++ Y+ R + P E + L+ +L
Sbjct: 133 PRELTGLKVGIIGLGTTGQMIADALSFFGADVYYYSRTR-KPDAEAKGIRYLP--LNELL 189
Query: 172 PKCDIVVVNTPLTEKTRGMFDKDRIAKMKKGVLIVNNARGAIMDTQAVVDACSSGHIAGY 231
D++ P K + ++ + G ++ N + G + +A+ + +
Sbjct: 190 KTVDVICTCLP---KNVILLGEEEFELLGDGKILFNTSLGPSFEVEALKKWLKASGYNIF 246
Query: 232 SGDVWNPQPAPKDHPWRYMPNQAMTPHVSGTTIDAQLRYAAGVKDMLDRY 281
D A D PN T +G T A R + V L+ Y
Sbjct: 247 DCDT---AGALGDEELLRYPNVICTNKSAGWTRQAFERLSQKVLANLEEY 293
>gnl|CDD|224626 COG1712, COG1712, Predicted dinucleotide-utilizing enzyme [General
function prediction only].
Length = 255
Score = 38.5 bits (90), Expect = 0.002
Identities = 21/64 (32%), Positives = 33/64 (51%), Gaps = 4/64 (6%)
Query: 119 TVGTVGCGRIGKLLLQRLK----PFNCNLLYHDRVKMDPQLEKETGAKFEEDLDTMLPKC 174
VG VGCG IGK LL+ ++ F +Y + +LE G + D+D ++ +
Sbjct: 2 KVGIVGCGAIGKFLLELVRDGRVDFELVAVYDRDEEKAKELEASVGRRCVSDIDELIAEV 61
Query: 175 DIVV 178
D+VV
Sbjct: 62 DLVV 65
>gnl|CDD|237343 PRK13304, PRK13304, L-aspartate dehydrogenase; Reviewed.
Length = 265
Score = 38.0 bits (89), Expect = 0.004
Identities = 20/63 (31%), Positives = 32/63 (50%), Gaps = 4/63 (6%)
Query: 120 VGTVGCGRIGKLLLQRLKP--FNCNLLY-HDR-VKMDPQLEKETGAKFEEDLDTMLPKCD 175
+G VGCG I L+ + + N L +DR ++ L +TGAK +D ++ D
Sbjct: 4 IGIVGCGAIASLITKAILSGRINAELYAFYDRNLEKAENLASKTGAKACLSIDELVEDVD 63
Query: 176 IVV 178
+VV
Sbjct: 64 LVV 66
>gnl|CDD|217691 pfam03720, UDPG_MGDP_dh_C, UDP-glucose/GDP-mannose dehydrogenase
family, UDP binding domain. The UDP-glucose/GDP-mannose
dehydrogenaseses are a small group of enzymes which
possesses the ability to catalyze the NAD-dependent
2-fold oxidation of an alcohol to an acid without the
release of an aldehyde intermediate.
Length = 103
Score = 32.9 bits (76), Expect = 0.039
Identities = 19/93 (20%), Positives = 38/93 (40%), Gaps = 14/93 (15%)
Query: 132 LLQRLKPFNCNLLYHD-RVKMDPQ-LEKETGAKFEEDLDTMLPKCDIVVVNTPLTE-KTR 188
+++ L ++ +D V + E G +DL+ L D +V+ T E ++
Sbjct: 22 IIEELLEEGAEVVVYDPYVPEEAIEALGEDGVTLVDDLEEALKGADAIVILTDHDEFRS- 80
Query: 189 GMFDKDRIAKMKKGVLIVNNARGAIMDTQAVVD 221
D +I K+ K ++ D + V+D
Sbjct: 81 --LDWAKIKKLMKPPVVF--------DGRNVLD 103
>gnl|CDD|201778 pfam01408, GFO_IDH_MocA, Oxidoreductase family, NAD-binding
Rossmann fold. This family of enzymes utilise NADP or
NAD. This family is called the GFO/IDH/MOCA family in
swiss-prot.
Length = 120
Score = 33.0 bits (76), Expect = 0.048
Identities = 22/75 (29%), Positives = 32/75 (42%), Gaps = 18/75 (24%)
Query: 120 VGTVGCGRIGKLLLQRLKPFNCNLLYHDRVK----MDP------QLEKETGAKFEEDLDT 169
VG VG G+IG+ L+ N + D + +DP + + G DL+
Sbjct: 3 VGIVGAGKIGRR---HLRALNES---QDGAELVGILDPDPARAEAVAESFGVPAYSDLEE 56
Query: 170 ML--PKCDIVVVNTP 182
+L P D V V TP
Sbjct: 57 LLADPDIDAVSVATP 71
>gnl|CDD|236326 PRK08655, PRK08655, prephenate dehydrogenase; Provisional.
Length = 437
Score = 33.8 bits (78), Expect = 0.087
Identities = 14/55 (25%), Positives = 27/55 (49%), Gaps = 6/55 (10%)
Query: 154 QLEKETGAKFEEDLDTMLPKCDIVVVNTPL--TEKTRGMFDKDRIAKMKKGVLIV 206
++ KE G ++ D DIV+++ P+ TE K+ +K+G L++
Sbjct: 39 EVAKELGVEYANDNIDAAKDADIVIISVPINVTEDVI----KEVAPHVKEGSLLM 89
>gnl|CDD|216527 pfam01488, Shikimate_DH, Shikimate / quinate 5-dehydrogenase. This
family contains both shikimate and quinate
dehydrogenases. Shikimate 5-dehydrogenase catalyzes the
conversion of shikimate to 5-dehydroshikimate. This
reaction is part of the shikimate pathway which is
involved in the biosynthesis of aromatic amino acids.
Quinate 5-dehydrogenase catalyzes the conversion of
quinate to 5-dehydroquinate. This reaction is part of
the quinate pathway where quinic acid is exploited as a
source of carbon in prokaryotes and microbial
eukaryotes. Both the shikimate and quinate pathways
share two common pathway metabolites 3-dehydroquinate
and dehydroshikimate.
Length = 133
Score = 31.9 bits (73), Expect = 0.17
Identities = 21/89 (23%), Positives = 38/89 (42%), Gaps = 14/89 (15%)
Query: 114 DLEGKTVGTVGCGRIGKLLLQRLKPFNCNLLY-----HDRVKMDPQLEKETGAKFE---- 164
DL+GK V +G G + +L + L + ++ K +L +E E
Sbjct: 9 DLKGKKVLLIGAGEMARLAAKHLLSKGAKKITIANRTLEKAK---ELAEEFPVGGEALPL 65
Query: 165 EDLDTMLPKCDIVVVNTPLTEK--TRGMF 191
++L+ +L + DIV+ T T+ M
Sbjct: 66 DELEELLAEADIVISATSAPTPIITKEMV 94
>gnl|CDD|214954 smart00984, UDPG_MGDP_dh_C, UDP binding domain. The
UDP-glucose/GDP-mannose dehydrogenases are a small group
of enzymes which possesses the ability to catalyse the
NAD-dependent 2-fold oxidation of an alcohol to an acid
without the release of an aldehyde intermediate.
Length = 99
Score = 30.9 bits (71), Expect = 0.23
Identities = 17/75 (22%), Positives = 34/75 (45%), Gaps = 4/75 (5%)
Query: 132 LLQRLKPFNCNLLYHDRVKMDPQLEKETGAKFEEDLDTMLPKCDIVVVNTPLTEKTRGMF 191
+++ L ++ +D M+ +E G + DL+ L D VV+ T E R +
Sbjct: 22 IIEELLEAGAEVVVYDPYAME--EAREYGLTYVSDLEEALKGADAVVIATEHDEF-RSL- 77
Query: 192 DKDRIAKMKKGVLIV 206
D + + + K ++V
Sbjct: 78 DPEELKDLMKKPVVV 92
>gnl|CDD|233242 TIGR01035, hemA, glutamyl-tRNA reductase. This enzyme, together
with glutamate-1-semialdehyde-2,1-aminomutase
(TIGR00713), leads to the production of
delta-amino-levulinic acid from Glu-tRNA [Biosynthesis
of cofactors, prosthetic groups, and carriers, Heme,
porphyrin, and cobalamin].
Length = 417
Score = 32.4 bits (74), Expect = 0.28
Identities = 25/99 (25%), Positives = 45/99 (45%), Gaps = 8/99 (8%)
Query: 114 DLEGKTVGTVGCGRIGKLLLQRLKPFNC-NLLYHDRVKMDPQ-LEKETGA---KFEEDLD 168
L+GK +G G +G+L+ + L +L +R + L KE G KFE DL+
Sbjct: 177 SLKGKKALLIGAGEMGELVAKHLLRKGVGKILIANRTYERAEDLAKELGGEAVKFE-DLE 235
Query: 169 TMLPKCDIVVVNTPLTEK--TRGMFDKDRIAKMKKGVLI 205
L + DIV+ +T ++ ++ + + +I
Sbjct: 236 EYLAEADIVISSTGAPHPIVSKEDVERALRERTRPLFII 274
>gnl|CDD|180709 PRK06815, PRK06815, hypothetical protein; Provisional.
Length = 317
Score = 32.0 bits (73), Expect = 0.38
Identities = 19/59 (32%), Positives = 25/59 (42%), Gaps = 11/59 (18%)
Query: 74 VSVAEDELMRILILVRNFLPGHHQVISGEWNVAGVAYRAY-----DLEGKTVGTVGCGR 127
V V+E+E I +R +I G AGVA A +GK V V CG+
Sbjct: 253 VLVSEEE---IKEAMRLIAETDRWLIEG---AAGVALAAALKLAPRYQGKKVAVVLCGK 305
>gnl|CDD|203422 pfam06304, DUF1048, Protein of unknown function (DUF1048). This
family consists of several hypothetical bacterial
proteins of unknown function.
Length = 92
Score = 29.2 bits (66), Expect = 0.84
Identities = 14/28 (50%), Positives = 17/28 (60%), Gaps = 1/28 (3%)
Query: 55 FLAAAAAGLTVAEVTGSNVVSVAEDELM 82
F AAA G +V EVTG +V + DEL
Sbjct: 46 FEEAAADGKSVLEVTGEDVAAFC-DELA 72
>gnl|CDD|215612 PLN03169, PLN03169, chalcone synthase family protein; Provisional.
Length = 391
Score = 30.1 bits (68), Expect = 1.4
Identities = 10/36 (27%), Positives = 19/36 (52%)
Query: 66 AEVTGSNVVSVAEDELMRILILVRNFLPGHHQVISG 101
A + G++ + V+E + ++ FLPG + I G
Sbjct: 225 AVIIGADPIPVSESPFFELHTAIQQFLPGTEKTIDG 260
>gnl|CDD|163624 cd07381, MPP_CapA, CapA and related proteins, metallophosphatase
domain. CapA is one of three membrane-associated
enzymes in Bacillus anthracis that is required for
synthesis of gamma-polyglutamic acid (PGA), a major
component of the bacterial capsule. The YwtB and PgsA
proteins of Bacillus subtilis are closely related to
CapA and are also included in this alignment model.
CapA belongs to the metallophosphatase (MPP)
superfamily. MPPs are functionally diverse, but all
share a conserved domain with an active site consisting
of two metal ions (usually manganese, iron, or zinc)
coordinated with octahedral geometry by a cage of
histidine, aspartate, and asparagine residues. The MPP
superfamily includes: Mre11/SbcD-like exonucleases,
Dbr1-like RNA lariat debranching enzymes, YfcE-like
phosphodiesterases, purple acid phosphatases (PAPs),
YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). The conserved domain is a
double beta-sheet sandwich with a di-metal active site
made up of residues located at the C-terminal side of
the sheets. This domain is thought to allow for
productive metal coordination.
Length = 239
Score = 29.5 bits (67), Expect = 1.6
Identities = 14/53 (26%), Positives = 21/53 (39%), Gaps = 2/53 (3%)
Query: 143 LLYHDRVKMDPQLEKETGAKFEEDLDTMLPKCDIVVVN--TPLTEKTRGMFDK 193
++ V P K ED+ +L D+ + N TPLT+K K
Sbjct: 7 IMLGRGVYDSPADRKYDFDPLFEDVKPLLRAADLAIGNLETPLTDKGSPAPSK 59
>gnl|CDD|133452 cd05213, NAD_bind_Glutamyl_tRNA_reduct, NADP-binding domain of
glutamyl-tRNA reductase. Glutamyl-tRNA reductase
catalyzes the conversion of glutamyl-tRNA to
glutamate-1-semialdehyde, initiating the synthesis of
tetrapyrrole. Whereas tRNAs are generally associated
with peptide bond formation in protein translation, here
the tRNA activates glutamate in the initiation of
tetrapyrrole biosynthesis in archaea, plants and many
bacteria. In the first step, activated glutamate is
reduced to glutamate-1-semi-aldehyde via the NADPH
dependent glutamyl-tRNA reductase. Glutamyl-tRNA
reductase forms a V-shaped dimer. Each monomer has 3
domains: an N-terminal catalytic domain, a classic
nucleotide binding domain, and a C-terminal dimerization
domain. Although the representative structure 1GPJ lacks
a bound NADPH, a theoretical binding pocket has been
described. (PMID 11172694). Amino acid dehydrogenase
(DH)-like NAD(P)-binding domains are members of the
Rossmann fold superfamily and include glutamate,
leucine, and phenylalanine DHs, methylene
tetrahydrofolate DH, methylene-tetrahydromethanopterin
DH, methylene-tetrahydropholate DH/cyclohydrolase,
Shikimate DH-like proteins, malate oxidoreductases, and
glutamyl tRNA reductase. Amino acid DHs catalyze the
deamination of amino acids to keto acids with NAD(P)+ as
a cofactor. The NAD(P)-binding Rossmann fold superfamily
includes a wide variety of protein families including
NAD(P)- binding domains of alcohol DHs,
tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate DH, lactate/malate DHs,
formate/glycerate DHs, siroheme synthases,
6-phosphogluconate DH, amino acid DHs, repressor rex,
NAD-binding potassium channel domain, CoA-binding, and
ornithine cyclodeaminase-like domains. These domains
have an alpha-beta-alpha configuration. NAD binding
involves numerous hydrogen and van der Waals contacts.
Length = 311
Score = 29.5 bits (67), Expect = 1.9
Identities = 21/118 (17%), Positives = 45/118 (38%), Gaps = 20/118 (16%)
Query: 104 NVAGVAYRAYD--------LEGKTVGTVGCGRIGKLLLQRLKPFNCNLLY-----HDRVK 150
++ A + L+GK V +G G +G+L + L + ++R +
Sbjct: 157 GAVSISSAAVELAEKIFGNLKGKKVLVIGAGEMGELAAKHLAAKGVAEITIANRTYERAE 216
Query: 151 MDPQLEKETGAKFE--EDLDTMLPKCDIVVVNTPLTEKTRGMFDKDRIAKMKKGVLIV 206
+L KE G ++L +L + D+V+ T + + + K ++
Sbjct: 217 ---ELAKELGGNAVPLDELLELLNEADVVISATG-APHYAKIV-ERAMKKRSGKPRLI 269
>gnl|CDD|234592 PRK00045, hemA, glutamyl-tRNA reductase; Reviewed.
Length = 423
Score = 29.8 bits (68), Expect = 2.1
Identities = 20/75 (26%), Positives = 36/75 (48%), Gaps = 10/75 (13%)
Query: 114 DLEGKTVGTVGCGRIGKLLLQRLKPFNCNLLY-----HDRVKMDPQLEKETGAKFE--ED 166
DL GK V +G G +G+L+ + L + +R + +L +E G + ++
Sbjct: 179 DLSGKKVLVIGAGEMGELVAKHLAEKGVRKITVANRTLERAE---ELAEEFGGEAIPLDE 235
Query: 167 LDTMLPKCDIVVVNT 181
L L + DIV+ +T
Sbjct: 236 LPEALAEADIVISST 250
>gnl|CDD|235488 PRK05476, PRK05476, S-adenosyl-L-homocysteine hydrolase;
Provisional.
Length = 425
Score = 29.7 bits (68), Expect = 2.1
Identities = 29/113 (25%), Positives = 41/113 (36%), Gaps = 32/113 (28%)
Query: 111 RAYD--LEGKTVGTVGCGRIGKLLLQRLKPFNCNLLYHDRVKM---DP--QLEKETGAKF 163
RA + + GK V G G +GK QRL+ RV + DP L+ A
Sbjct: 204 RATNVLIAGKVVVVAGYGDVGKGCAQRLRGLGA------RVIVTEVDPICALQ----AAM 253
Query: 164 E----EDLDTMLPKCDIVVVNTPLTEKTRGMFD---KDRIAKMKKGVLIVNNA 209
+ ++ DI V T G D + + MK G I+ N
Sbjct: 254 DGFRVMTMEEAAELGDIFVTAT-------GNKDVITAEHMEAMKDGA-ILANI 298
>gnl|CDD|217564 pfam03447, NAD_binding_3, Homoserine dehydrogenase, NAD binding
domain. This domain adopts a Rossmann NAD binding fold.
The C-terminal domain of homoserine dehydrogenase
contributes a single helix to this structural domain,
which is not included in the Pfam model.
Length = 116
Score = 27.7 bits (62), Expect = 3.1
Identities = 14/62 (22%), Positives = 20/62 (32%), Gaps = 6/62 (9%)
Query: 124 GCGRIGKLLLQRLK------PFNCNLLYHDRVKMDPQLEKETGAKFEEDLDTMLPKCDIV 177
GCG IG LL+ L P + + + DLD ++
Sbjct: 1 GCGAIGSGLLELLLRQQEEIPLELVAVADRDLLSKARAALLGDEPVTLDLDDLVADPRPD 60
Query: 178 VV 179
VV
Sbjct: 61 VV 62
>gnl|CDD|219588 pfam07805, HipA_N, HipA-like N-terminal domain. The members of
this family are similar to a region close to the
N-terminus of the HipA protein expressed by various
bacterial species. This protein is known to be involved
in high-frequency persistence to the lethal effects of
inhibition of either DNA or peptidoglycan synthesis.
When expressed alone, it is toxic to bacterial cells,
but it is usually tightly associated with HipB, and the
HipA-HipB complex may be involved in autoregulation of
the hip operon. The hip proteins may be involved in
cell division control and may interact with cell
division genes or their products.
Length = 81
Score = 26.8 bits (60), Expect = 3.8
Identities = 11/24 (45%), Positives = 11/24 (45%), Gaps = 4/24 (16%)
Query: 46 NEYASMNPNFLAAAAAGLTVAEVT 69
NEY M A AAGL V E
Sbjct: 45 NEYLCM----RLARAAGLEVPESR 64
>gnl|CDD|107205 cd01562, Thr-dehyd, Threonine dehydratase: The first step in amino
acid degradation is the removal of nitrogen. Although
the nitrogen atoms of most amino acids are transferred
to alpha-ketoglutarate before removal, the alpha-amino
group of threonine can be directly converted into NH4+.
The direct deamination is catalyzed by threonine
dehydratase, in which pyridoxal phosphate (PLP) is the
prosthetic group. Threonine dehydratase is widely
distributed in all three major phylogenetic divisions.
Length = 304
Score = 28.6 bits (65), Expect = 4.2
Identities = 18/57 (31%), Positives = 27/57 (47%), Gaps = 7/57 (12%)
Query: 73 VVSVAEDELMR-ILILVRNFLPGHHQVI--SGEWNVAGVAYRAYDLEGKTVGTVGCG 126
VV+V+EDE+ +L+L V +G +A + DL+GK V V G
Sbjct: 248 VVTVSEDEIAAAMLLLFER----EKLVAEPAGALALAALLSGKLDLKGKKVVVVLSG 300
>gnl|CDD|169427 PRK08402, PRK08402, replication factor A; Reviewed.
Length = 355
Score = 28.2 bits (63), Expect = 5.8
Identities = 25/87 (28%), Positives = 33/87 (37%), Gaps = 11/87 (12%)
Query: 47 EYASMNPNFLAAAAAGLTVAEVTGSNVVSVAEDELMRILILVRNFLPGHHQVISGEWNVA 106
E ++ AA L +AE G N+ E LM I LV PG V N+
Sbjct: 30 EIMKEEG--ISEHAAALLLAEELGVNLEGEEEAPLMHISDLV----PGMRGV-----NIV 78
Query: 107 GVAYRAYDLEGKTVGTVGCGRIGKLLL 133
G R Y T GR+ L++
Sbjct: 79 GRVLRKYPPREYTKKDGSTGRVASLII 105
>gnl|CDD|223450 COG0373, HemA, Glutamyl-tRNA reductase [Coenzyme metabolism].
Length = 414
Score = 28.4 bits (64), Expect = 5.8
Identities = 29/102 (28%), Positives = 50/102 (49%), Gaps = 14/102 (13%)
Query: 114 DLEGKTVGTVGCGRIGKLLLQRLKPFNCNLLY-----HDRVKMDPQLEKETGAKF--EED 166
L+ K V +G G +G+L+ + L + +R + +L K+ GA+ E+
Sbjct: 175 SLKDKKVLVIGAGEMGELVAKHLAEKGVKKITIANRTLERAE---ELAKKLGAEAVALEE 231
Query: 167 LDTMLPKCDIVVVNT--PLTEKTRGMFDKDRIAKMKKGVLIV 206
L L + D+V+ +T P TR M +R K++K +LIV
Sbjct: 232 LLEALAEADVVISSTSAPHPIITREMV--ERALKIRKRLLIV 271
>gnl|CDD|223745 COG0673, MviM, Predicted dehydrogenases and related proteins
[General function prediction only].
Length = 342
Score = 28.3 bits (63), Expect = 5.8
Identities = 20/74 (27%), Positives = 28/74 (37%), Gaps = 14/74 (18%)
Query: 120 VGTVGCGRIGKL----LLQRLKPFNCNLLYHDRVKMDPQLEKETGAKFE-----EDLDTM 170
VG +G G I L L + DR DP+ + +F DL+ +
Sbjct: 6 VGIIGAGGIAGKAHLPALAALGGGLELVAVVDR---DPERAEAFAEEFGIAKAYTDLEEL 62
Query: 171 L--PKCDIVVVNTP 182
L P D V + TP
Sbjct: 63 LADPDIDAVYIATP 76
>gnl|CDD|176198 cd08236, sugar_DH, NAD(P)-dependent sugar dehydrogenases. This
group contains proteins identified as sorbitol
dehydrogenases and other sugar dehydrogenases of the
medium-chain dehydrogenase/reductase family (MDR), which
includes zinc-dependent alcohol dehydrogenase and
related proteins. Sorbitol and aldose reductase are
NAD(+) binding proteins of the polyol pathway, which
interconverts glucose and fructose. Sorbitol
dehydrogenase is tetrameric and has a single catalytic
zinc per subunit. NAD(P)(H)-dependent oxidoreductases
are the major enzymes in the interconversion of alcohols
and aldehydes, or ketones. Related proteins include
threonine dehydrogenase, formaldehyde dehydrogenase, and
butanediol dehydrogenase. The medium chain alcohol
dehydrogenase family (MDR) has a NAD(P)(H)-binding
domain in a Rossmann fold of a beta-alpha form. The
N-terminal region typically has an all-beta catalytic
domain. These proteins typically form dimers (typically
higher plants, mammals) or tetramers (yeast, bacteria),
and have 2 tightly bound zinc atoms per subunit. Horse
liver alcohol dehydrogenase is a dimeric enzyme and each
subunit has two domains. The NAD binding domain is in a
Rossmann fold and the catalytic domain contains a zinc
ion to which substrates bind. There is a cleft between
the domains that closes upon formation of the ternary
complex.
Length = 343
Score = 27.6 bits (62), Expect = 7.7
Identities = 16/36 (44%), Positives = 18/36 (50%), Gaps = 4/36 (11%)
Query: 106 AGVAYRAYDL----EGKTVGTVGCGRIGKLLLQRLK 137
A VA A L G TV +G G IG L +Q LK
Sbjct: 145 AAVALHAVRLAGITLGDTVVVIGAGTIGLLAIQWLK 180
>gnl|CDD|148333 pfam06668, ITI_HC_C, Inter-alpha-trypsin inhibitor heavy chain
C-terminus. This family represents the C-terminal
region of inter-alpha-trypsin inhibitor heavy chains.
Inter-alpha-trypsin inhibitors are glycoproteins with a
high inhibitory activity against trypsin, built up from
different combinations of four polypeptides: bikunin and
the three heavy chains that belong to this family (HC1,
HC2, HC3). The heavy chains do not have any protease
inhibitory properties but have the capacity to interact
in vitro and in vivo with hyaluronic acid, which
promotes the stability of the extra-cellular matrix. All
family members contain the pfam00092 domain.
Length = 188
Score = 27.2 bits (61), Expect = 8.9
Identities = 7/29 (24%), Positives = 12/29 (41%), Gaps = 1/29 (3%)
Query: 235 VWNPQPAPKDHPWRYMPN-QAMTPHVSGT 262
VW P +D Y+ + + +V G
Sbjct: 98 VWKKHPVHQDFLGFYVLDSHRFSSNVHGL 126
>gnl|CDD|188459 TIGR03944, dehyd_SbnB_fam, 2,3-diaminopropionate biosynthesis
protein SbnB. Members of this protein family are
probable NAD-dependent dehydrogenases related to the
alanine dehydrogenase of Archaeoglobus fulgidus (see
TIGR02371, PDB structure 1OMO and PMID:15313611) and
more distantly to ornithine cyclodeaminase. Members
include the staphylobactin biosynthesis protein SbnB and
tend to occur in contexts suggesting non-ribosomal
peptide synthesis, always adjacent to (occasionally
fused with) a pyridoxal phosphate-dependent enzyme,
SbnA. The pair appears to provide 2,3-diaminopropionate
for biosynthesis of siderophores or other secondary
metabolites [Cellular processes, Biosynthesis of natural
products].
Length = 327
Score = 27.6 bits (62), Expect = 9.2
Identities = 28/135 (20%), Positives = 45/135 (33%), Gaps = 24/135 (17%)
Query: 105 VAGVAYRAYDLEG--KTVGTVGCGRIGKLLLQRLK----PFNCNLLY-HDRVKMDPQLEK 157
A +A R VG +GCG I + +L+ L +LY D + +
Sbjct: 118 SAALAARHLAAGRGFTRVGIIGCGPIAREILRFLLALGPEIRRVVLYDLDPARAE-AFAA 176
Query: 158 ETGAKFE------EDLDTMLPKCDIVVVNTPLTEKTRGMFDKDRIAKMKKGVLIVNN--- 208
+ L + D+VV T T + D + G L++N
Sbjct: 177 RCQELGPGKVTVAASAEAALRQADLVVTAT--VAGTPYIDDPAWF---QPGALVLNISLR 231
Query: 209 --ARGAIMDTQAVVD 221
A I+ +VD
Sbjct: 232 DLAPEVILKADNIVD 246
>gnl|CDD|223573 COG0499, SAM1, S-adenosylhomocysteine hydrolase [Coenzyme
metabolism].
Length = 420
Score = 27.6 bits (62), Expect = 10.0
Identities = 26/105 (24%), Positives = 43/105 (40%), Gaps = 19/105 (18%)
Query: 111 RAYD--LEGKTVGTVGCGRIGKLLLQRLKPFNCNLLYHDRVKMDP--QLEKETGAKFE-- 164
RA + L GK V G G +G+ + RL+ ++ ++DP LE A +
Sbjct: 201 RATNVLLAGKNVVVAGYGWVGRGIAMRLRGMGARVIV---TEVDPIRALE----AAMDGF 253
Query: 165 --EDLDTMLPKCDIVVVNTPLTEKTRGMFDKDRIAKMKKGVLIVN 207
++ DI V T + + K+ KMK G ++ N
Sbjct: 254 RVMTMEEAAKTGDIFVTAT----GNKDVIRKEHFEKMKDGAILAN 294
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 0.134 0.398
Gapped
Lambda K H
0.267 0.0831 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,766,933
Number of extensions: 1527154
Number of successful extensions: 1689
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1544
Number of HSP's successfully gapped: 104
Length of query: 304
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 208
Effective length of database: 6,679,618
Effective search space: 1389360544
Effective search space used: 1389360544
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 (21.8 bits)
S2: 59 (26.3 bits)