RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 027408
(223 letters)
>gnl|CDD|178684 PLN03139, PLN03139, formate dehydrogenase; Provisional.
Length = 386
Score = 502 bits (1295), Expect = 0.0
Identities = 199/223 (89%), Positives = 213/223 (95%)
Query: 1 MRILILVRNFLPGHHQVISGEWNVAGVAYRAYDLEGKTVGTVGCGRIGKLLLQRLKPFNC 60
MRILIL+RNFLPG+HQV+SGEWNVAG+AYRAYDLEGKTVGTVG GRIG+LLLQRLKPFNC
Sbjct: 164 MRILILLRNFLPGYHQVVSGEWNVAGIAYRAYDLEGKTVGTVGAGRIGRLLLQRLKPFNC 223
Query: 61 NLLYHDRVKMDPQLEKETGAKFEEDLDTMLPKCDIVVVNTPLTEKTRGMFDKDRIAKMKK 120
NLLYHDR+KMDP+LEKETGAKFEEDLD MLPKCD+VV+NTPLTEKTRGMF+K+RIAKMKK
Sbjct: 224 NLLYHDRLKMDPELEKETGAKFEEDLDAMLPKCDVVVINTPLTEKTRGMFNKERIAKMKK 283
Query: 121 GVLIVNNARGAIMDTQAVVDACSSGHIAGYSGDVWNPQPAPKDHPWRYMPNQAMTPHVSG 180
GVLIVNNARGAIMDTQAV DACSSGHI GY GDVW PQPAPKDHPWRYMPN AMTPH+SG
Sbjct: 284 GVLIVNNARGAIMDTQAVADACSSGHIGGYGGDVWYPQPAPKDHPWRYMPNHAMTPHISG 343
Query: 181 TTIDAQLRYAAGVKDMLDRYFKGEDFPVQNYIVKAGELAPQYR 223
TTIDAQLRYAAGVKDMLDRYFKGEDFP QNYIVK G+LA QY+
Sbjct: 344 TTIDAQLRYAAGVKDMLDRYFKGEDFPAQNYIVKEGKLASQYQ 386
>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 = 411 bits (1059), Expect = e-146
Identities = 134/222 (60%), Positives = 171/222 (77%)
Query: 1 MRILILVRNFLPGHHQVISGEWNVAGVAYRAYDLEGKTVGTVGCGRIGKLLLQRLKPFNC 60
M ILILVRN++PGH Q I G WNVA V RAYDLEGKTVGTVG GRIG +L+RLKPF+
Sbjct: 127 MMILILVRNYVPGHEQAIEGGWNVADVVKRAYDLEGKTVGTVGAGRIGLRVLRRLKPFDV 186
Query: 61 NLLYHDRVKMDPQLEKETGAKFEEDLDTMLPKCDIVVVNTPLTEKTRGMFDKDRIAKMKK 120
+LLY+DR ++ ++EKE G DL+ M+ KCD+V +N PL +T G+F+K+ ++KMKK
Sbjct: 187 HLLYYDRHRLPEEVEKELGLTRHADLEDMVSKCDVVTINCPLHPETEGLFNKELLSKMKK 246
Query: 121 GVLIVNNARGAIMDTQAVVDACSSGHIAGYSGDVWNPQPAPKDHPWRYMPNQAMTPHVSG 180
G +VN ARG I D +AV +A SGH+AGY+GDVW PQPAPKDHPWR MPN AMTPH+SG
Sbjct: 247 GAYLVNTARGKICDREAVAEALESGHLAGYAGDVWFPQPAPKDHPWRTMPNNAMTPHISG 306
Query: 181 TTIDAQLRYAAGVKDMLDRYFKGEDFPVQNYIVKAGELAPQY 222
TT+DAQ RYAAG K++L+R+F+GE F + IV+ G+LA +
Sbjct: 307 TTLDAQARYAAGTKEILERFFEGEPFRPEYLIVQGGKLAGKG 348
>gnl|CDD|181041 PRK07574, PRK07574, formate dehydrogenase; Provisional.
Length = 385
Score = 326 bits (837), Expect = e-112
Identities = 111/219 (50%), Positives = 149/219 (68%)
Query: 1 MRILILVRNFLPGHHQVISGEWNVAGVAYRAYDLEGKTVGTVGCGRIGKLLLQRLKPFNC 60
M IL LVRN+ P H Q + G WN+A R+YDLEG TVG VG GRIG +L+RLKPF+
Sbjct: 157 MMILALVRNYEPSHRQAVEGGWNIADCVSRSYDLEGMTVGIVGAGRIGLAVLRRLKPFDV 216
Query: 61 NLLYHDRVKMDPQLEKETGAKFEEDLDTMLPKCDIVVVNTPLTEKTRGMFDKDRIAKMKK 120
L Y DR ++ ++E+E G + D+++ CD+V ++ PL +T +FD D +++MK+
Sbjct: 217 KLHYTDRHRLPEEVEQELGLTYHVSFDSLVSVCDVVTIHCPLHPETEHLFDADVLSRMKR 276
Query: 121 GVLIVNNARGAIMDTQAVVDACSSGHIAGYSGDVWNPQPAPKDHPWRYMPNQAMTPHVSG 180
G +VN ARG I+D AVV A SGH+AGY+GDVW PQPAP DHPWR MP MTPH+SG
Sbjct: 277 GSYLVNTARGKIVDRDAVVRALESGHLAGYAGDVWFPQPAPADHPWRTMPRNGMTPHISG 336
Query: 181 TTIDAQLRYAAGVKDMLDRYFKGEDFPVQNYIVKAGELA 219
TT+ AQ RYAAG +++L+ +F+G + IV G LA
Sbjct: 337 TTLSAQARYAAGTREILECFFEGRPIRDEYLIVDGGRLA 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 = 220 bits (564), Expect = 5e-72
Identities = 78/200 (39%), Positives = 122/200 (61%), Gaps = 3/200 (1%)
Query: 1 MRILILVRNFLPGHHQVISGEWNVAGVAYRAYDLEGKTVGTVGCGRIGKLLLQRLKPFNC 60
+L L+R V G W + Y+LEGKTVG VG GRIG+ + +RL+ F
Sbjct: 106 GLLLALLRRLPRADAAVRRG-WGWLWAGFPGYELEGKTVGIVGLGRIGQRVAKRLQAFGM 164
Query: 61 NLLYHDRVKMDPQLEKETGAKFEEDLDTMLPKCDIVVVNTPLTEKTRGMFDKDRIAKMKK 120
+LY+DR + P+ E++ G + LD +L + D+VV++ PLT +TR + +++ +A MK
Sbjct: 165 KVLYYDRTRK-PEPEEDLGFRVV-SLDELLAQSDVVVLHLPLTPETRHLINEEELALMKP 222
Query: 121 GVLIVNNARGAIMDTQAVVDACSSGHIAGYSGDVWNPQPAPKDHPWRYMPNQAMTPHVSG 180
G ++VN ARG ++D A++ A SG IAG + DV+ P+P P DHP +PN +TPH++G
Sbjct: 223 GAVLVNTARGGLVDEDALLRALKSGKIAGAALDVFEPEPLPADHPLLELPNVILTPHIAG 282
Query: 181 TTIDAQLRYAAGVKDMLDRY 200
T +A+ R A + L+R+
Sbjct: 283 YTEEARERMAEIAVENLERF 302
>gnl|CDD|223980 COG1052, LdhA, Lactate dehydrogenase and related dehydrogenases
[Energy production and conversion / Coenzyme metabolism
/ General function prediction only].
Length = 324
Score = 220 bits (563), Expect = 1e-71
Identities = 84/219 (38%), Positives = 127/219 (57%), Gaps = 10/219 (4%)
Query: 3 ILILVRNFLPGHHQVISGEWNVAGVAYR--AYDLEGKTVGTVGCGRIGKLLLQRLKPFNC 60
IL L R G +V G W+++G +DL GKT+G +G GRIG+ + +RLK F
Sbjct: 111 ILALARRIHEGDRRVREGNWSLSGGPDPLLGFDLRGKTLGIIGLGRIGQAVARRLKGFGM 170
Query: 61 NLLYHDRVKMDPQLEKETGAKFEEDLDTMLPKCDIVVVNTPLTEKTRGMFDKDRIAKMKK 120
+LY+DR +P+ EKE GA++ DLD +L + DI+ ++ PLT +TR + + + +AKMK
Sbjct: 171 KVLYYDRSP-NPEAEKELGARYV-DLDELLAESDIISLHCPLTPETRHLINAEELAKMKP 228
Query: 121 GVLIVNNARGAIMDTQAVVDACSSGHIAGYSGDVWNPQPAPKDHPWRYMPNQ---AMTPH 177
G ++VN ARG ++D QA++DA SG IAG DV+ +PA DHP + N +TPH
Sbjct: 229 GAILVNTARGGLVDEQALIDALKSGKIAGAGLDVFENEPALFDHPLLRLDNFPNVVLTPH 288
Query: 178 VSGTTIDAQLRYAAGVKDMLDRYFKGEDFPVQNYIVKAG 216
++ T +A+ A + L+ +F G V V
Sbjct: 289 IASATEEARKAMAELALENLEAFFDGG---VPPNEVNPE 324
>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 = 202 bits (516), Expect = 2e-66
Identities = 67/177 (37%), Positives = 104/177 (58%), Gaps = 5/177 (2%)
Query: 3 ILILVRNFLPGHHQVISGEWNVAGVAYRAYDLEGKTVGTVGCGRIGKLLLQRLKPFNCNL 62
+L L R QV +G W A +L GKTVG +G GRIG+ + +RLK F +
Sbjct: 4 LLALARRIPEADRQVRAGRWR--PDALLGRELSGKTVGIIGLGRIGRAVARRLKAFGMKV 61
Query: 63 LYHDRVKMDPQLEKETGAKFEEDLDTMLPKCDIVVVNTPLTEKTRGMFDKDRIAKMKKGV 122
+ +DR + GA++ LD +L + D+V ++ PLT +TR + + +R+A MK G
Sbjct: 62 IAYDRYPKAE--AEALGARYV-SLDELLAESDVVSLHLPLTPETRHLINAERLALMKPGA 118
Query: 123 LIVNNARGAIMDTQAVVDACSSGHIAGYSGDVWNPQPAPKDHPWRYMPNQAMTPHVS 179
+++N ARG ++D A++ A SG IAG + DV+ P+P P DHP +PN +TPH++
Sbjct: 119 ILINTARGGLVDEDALIAALKSGRIAGAALDVFEPEPLPPDHPLLELPNVILTPHIA 175
>gnl|CDD|223189 COG0111, SerA, Phosphoglycerate dehydrogenase and related
dehydrogenases [Amino acid transport and metabolism].
Length = 324
Score = 205 bits (523), Expect = 1e-65
Identities = 74/202 (36%), Positives = 114/202 (56%), Gaps = 3/202 (1%)
Query: 3 ILILVRNFLPGHHQVISGEWNVAGVAYRAYDLEGKTVGTVGCGRIGKLLLQRLKPFNCNL 62
+L L R GEW+ A+R +L GKTVG +G GRIG+ + +RLK F +
Sbjct: 111 LLALARRIPDADASQRRGEWD--RKAFRGTELAGKTVGIIGLGRIGRAVAKRLKAFGMKV 168
Query: 63 LYHDRVKMDPQLEKETGAKFEEDLDTMLPKCDIVVVNTPLTEKTRGMFDKDRIAKMKKGV 122
+ +D + G + LD +L + DI+ ++ PLT +TRG+ + + +AKMK G
Sbjct: 169 IGYDPYSP-RERAGVDGVVGVDSLDELLAEADILTLHLPLTPETRGLINAEELAKMKPGA 227
Query: 123 LIVNNARGAIMDTQAVVDACSSGHIAGYSGDVWNPQPAPKDHPWRYMPNQAMTPHVSGTT 182
+++N ARG ++D A++ A SG IAG + DV+ +P P D P +PN +TPH+ G+T
Sbjct: 228 ILINAARGGVVDEDALLAALDSGKIAGAALDVFEEEPLPADSPLWDLPNVILTPHIGGST 287
Query: 183 IDAQLRYAAGVKDMLDRYFKGE 204
+AQ R A V + + RY G
Sbjct: 288 DEAQERVAEIVAENIVRYLAGG 309
>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 = 191 bits (487), Expect = 2e-60
Identities = 70/202 (34%), Positives = 112/202 (55%), Gaps = 4/202 (1%)
Query: 3 ILILVRNFLPGHHQVISGEWNVAGVAYRAYDLEGKTVGTVGCGRIGKLLLQRLKPFNCNL 62
+L L RN + +G+W+ + +L GKT+G VG GRIG+ + +R + F +
Sbjct: 107 MLALARNIPQADASLRAGKWDRK--KFMGVELRGKTLGIVGLGRIGREVARRARAFGMKV 164
Query: 63 LYHDRVKMDPQLEKETGAKFEEDLDTMLPKCDIVVVNTPLTEKTRGMFDKDRIAKMKKGV 122
L +D + + G + LD +L + D + ++TPLT +TRG+ + + +AKMK G
Sbjct: 165 LAYDPY-ISAERAAAGGVELV-SLDELLAEADFISLHTPLTPETRGLINAEELAKMKPGA 222
Query: 123 LIVNNARGAIMDTQAVVDACSSGHIAGYSGDVWNPQPAPKDHPWRYMPNQAMTPHVSGTT 182
+++N ARG I+D A+ DA SG IAG + DV+ +P P D P +PN +TPH+ +T
Sbjct: 223 ILINTARGGIVDEAALADALKSGKIAGAALDVFEQEPPPADSPLLGLPNVILTPHLGAST 282
Query: 183 IDAQLRYAAGVKDMLDRYFKGE 204
+AQ R A + + GE
Sbjct: 283 EEAQERVAVDAAEQVLAVLAGE 304
>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 = 187 bits (476), Expect = 1e-58
Identities = 72/205 (35%), Positives = 119/205 (58%), Gaps = 2/205 (0%)
Query: 1 MRILILVRNFLPGHHQVISGEWNVAGVAYRAYDLEGKTVGTVGCGRIGKLLLQRLKPFNC 60
M +L L+R ++ +G W + +L GKTVG VG G IG+ + +RL+ F
Sbjct: 108 MLMLALLRRLPEADRELRAGRWG-RPEGRPSRELSGKTVGIVGLGNIGRAVARRLRGFGV 166
Query: 61 NLLYHDRVKMDPQLEKETGAKFEEDLDTMLPKCDIVVVNTPLTEKTRGMFDKDRIAKMKK 120
++Y+DR + EK+ G ++ E LD +L + D+V ++ PLT +TR + + +A MK
Sbjct: 167 EVIYYDRFRDPEAEEKDLGVRYVE-LDELLAESDVVSLHVPLTPETRHLIGAEELAAMKP 225
Query: 121 GVLIVNNARGAIMDTQAVVDACSSGHIAGYSGDVWNPQPAPKDHPWRYMPNQAMTPHVSG 180
G +++N ARG ++D +A++ A SGH+AG DV+ +P P D P + N +TPH++G
Sbjct: 226 GAILINTARGGLVDEEALLAALRSGHLAGAGLDVFWQEPLPPDDPLLRLDNVILTPHIAG 285
Query: 181 TTIDAQLRYAAGVKDMLDRYFKGED 205
T ++ R AA V + + R +GE
Sbjct: 286 VTDESYQRMAAIVAENIARLLRGEP 310
>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 = 186 bits (474), Expect = 3e-58
Identities = 72/204 (35%), Positives = 111/204 (54%), Gaps = 8/204 (3%)
Query: 4 LIL--VRNFLPGHHQVISGEWNVAGVAYRAYDLEGKTVGTVGCGRIGKLLLQRLKPFNCN 61
LIL +RNF +G+W A+D GKT+G +G G IGK + ++ F
Sbjct: 120 LILGALRNFSRAERSARAGKWRGFLDLTLAHDPRGKTLGILGLGGIGKAIARKAAAFGMK 179
Query: 62 LLYHDRVKMDPQLEKETGAKFEEDLDTMLPKCDIVVVNTPLTEKTRGMFDKDRIAKMKKG 121
++YH+R ++ +LEK A + LD +L + D+V +N PLT TR + +K AKMK G
Sbjct: 180 IIYHNRSRLPEELEKAL-ATYYVSLDELLAQSDVVSLNCPLTAATRHLINKKEFAKMKDG 238
Query: 122 VLIVNNARGAIMDTQAVVDACSSGHIAGYSGDVWN--PQPAPKDHPWRYMPNQAMTPHVS 179
V+IVN ARGA++D A+VDA SG +A DV+ P+ P MPN + PH+
Sbjct: 239 VIIVNTARGAVIDEDALVDALESGKVASAGLDVFENEPEVNPG---LLKMPNVTLLPHMG 295
Query: 180 GTTIDAQLRYAAGVKDMLDRYFKG 203
T++ Q + V + ++ + +
Sbjct: 296 TLTVETQEKMEELVLENIEAFLET 319
>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 = 179 bits (457), Expect = 8e-56
Identities = 66/200 (33%), Positives = 106/200 (53%), Gaps = 6/200 (3%)
Query: 3 ILILVRNFLPGHHQVISGEWNVAGVAYRAYDLEGKTVGTVGCGRIGKLLLQRLKPFNCNL 62
+L L R +V +G W+ +L GKT+G +G GRIGK + +RL F +
Sbjct: 113 MLALARQIPQADREVRAGGWDRPV----GTELYGKTLGIIGLGRIGKAVARRLSGFGMKV 168
Query: 63 LYHDRVKMDPQLEKETGAKFEEDLDTMLPKCDIVVVNTPLTEKTRGMFDKDRIAKMKKGV 122
L +D D + KE G +F L+ +L + D + ++ PLT +TR + + +A MK G
Sbjct: 169 LAYDPYP-DEEFAKEHGVEFV-SLEELLKESDFISLHLPLTPETRHLINAAELALMKPGA 226
Query: 123 LIVNNARGAIMDTQAVVDACSSGHIAGYSGDVWNPQPAPKDHPWRYMPNQAMTPHVSGTT 182
+++N ARG ++D +A+ +A SG IAG + DV+ +P P D P +PN +TPH+ +T
Sbjct: 227 ILINTARGGLVDEEALYEALKSGRIAGAALDVFEEEPPPADSPLLELPNVILTPHIGAST 286
Query: 183 IDAQLRYAAGVKDMLDRYFK 202
+A LR +
Sbjct: 287 KEAVLRMGTMAAQNVIDVLA 306
>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 = 175 bits (447), Expect = 3e-54
Identities = 73/182 (40%), Positives = 109/182 (59%), Gaps = 6/182 (3%)
Query: 4 LIL--VRNFLPGHHQVISGEW-NVAGVAYRAYDLEGKTVGTVGCGRIGKLLLQRLKPFNC 60
L+L R + G V +GEW + DL GKT+G VG GRIG+ + +R K F
Sbjct: 109 LLLAAARRVVEGDRFVRAGEWKGWSPTLLLGTDLHGKTLGIVGMGRIGQAVARRAKGFGM 168
Query: 61 NLLYHDRVKMDPQLEKETGAKFEEDLDTMLPKCDIVVVNTPLTEKTRGMFDKDRIAKMKK 120
+LYH+R + P+ E+E GA++ LD +L + D V ++ PLT +TR + + +R+A MK
Sbjct: 169 KILYHNRSRK-PEAEEELGARYV-SLDELLAESDFVSLHCPLTPETRHLINAERLALMKP 226
Query: 121 GVLIVNNARGAIMDTQAVVDACSSGHIAGYSGDVWNPQPAPKDHPWRYMPNQAMTPHV-S 179
+++N ARG ++D A+V+A SG IAG DV+ P+P P DHP +PN + PH+ S
Sbjct: 227 TAILINTARGGVVDEDALVEALKSGKIAGAGLDVFEPEPLPADHPLLTLPNVVLLPHIGS 286
Query: 180 GT 181
T
Sbjct: 287 AT 288
>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 = 173 bits (441), Expect = 2e-53
Identities = 70/201 (34%), Positives = 104/201 (51%), Gaps = 4/201 (1%)
Query: 3 ILILVRNFLPGHHQVISGEWNVAGVAYRAY--DLEGKTVGTVGCGRIGKLLLQRLKPFNC 60
+L RN H + GEW Y Y +L GKTVG VG G IG+ + +RLK F
Sbjct: 112 MLAETRNIARAHAALKDGEWRKDYYNYDGYGPELRGKTVGIVGFGAIGRRVAKRLKAFGA 171
Query: 61 NLLYHDRVKMDPQLEKETGAKFEEDLDTMLPKCDIVVVNTPLTEKTRGMFDKDRIAKMKK 120
+L +D +DP+ + G K L+ +L + D+V ++ LT +TRGM + A MK
Sbjct: 172 EVLVYDPY-VDPEKIEADGVKKV-SLEELLKRSDVVSLHARLTPETRGMIGAEEFALMKP 229
Query: 121 GVLIVNNARGAIMDTQAVVDACSSGHIAGYSGDVWNPQPAPKDHPWRYMPNQAMTPHVSG 180
+N AR ++D A+++A G I G + DV+ +P P DHP + N +TPH++G
Sbjct: 230 TAYFINTARAGLVDEDALIEALEEGKIGGAALDVFPEEPLPADHPLLKLDNVTLTPHIAG 289
Query: 181 TTIDAQLRYAAGVKDMLDRYF 201
T D R + + L RY
Sbjct: 290 ATRDVAERSPEIIAEELKRYL 310
>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 = 171 bits (435), Expect = 1e-52
Identities = 56/202 (27%), Positives = 78/202 (38%), Gaps = 31/202 (15%)
Query: 1 MRILILVRNFLPGHHQVISGEWNVAGVAYRAYDLEGKTVGTVGCGRIGKLLLQRLKPFNC 60
I + PG A D+ GKTV VG G +GK Q L+
Sbjct: 138 QFIARFLEVQQPGR-------------LGGAPDVAGKTVVVVGAGVVGKEAAQMLRGLGA 184
Query: 61 NLLYHDRVKMDPQLEKETGAKFEEDLDTMLPKCDIVVVNTPLTEKTRGMF-DKDRIAKMK 119
+L D + +E G K E+L+ L + D++V T L K G+ ++ + +MK
Sbjct: 185 QVLITDINVEALEQLEELGGKNVEELEEALAEADVIVTTTLLPGKRAGILVPEELVEQMK 244
Query: 120 KGVLIVNNARGAIMDTQAVV-DACSSGHIAGYSGDVWNPQPAPKDHPWRYMPNQAMTPHV 178
G +IVN A GA+ QA+ GH + GDV P P
Sbjct: 245 PGSVIVNVAVGAVGCVQALHTQLLEEGHGVVHYGDVNMPGPGC----------------A 288
Query: 179 SGTTIDAQLRYAAGVKDMLDRY 200
G DA LR AA L +
Sbjct: 289 MGVPWDATLRLAANTLPALVKL 310
>gnl|CDD|237436 PRK13581, PRK13581, D-3-phosphoglycerate dehydrogenase;
Provisional.
Length = 526
Score = 166 bits (422), Expect = 1e-48
Identities = 74/216 (34%), Positives = 116/216 (53%), Gaps = 23/216 (10%)
Query: 3 ILILVRNFLPGHHQVISGEWNVAGVAYRAYDLEGKTVGTVGCGRIGKLLLQRLKPFNCNL 62
+L L RN H + +G+W + +L GKT+G +G GRIG + +R K F +
Sbjct: 109 MLALARNIPQAHASLKAGKWERK--KFMGVELYGKTLGIIGLGRIGSEVAKRAKAFGMKV 166
Query: 63 L-YHDRVKMDPQLEKETGAKFEE------DLDTMLPKCDIVVVNTPLTEKTRGMFDKDRI 115
+ Y DP + + + + LD +L + D + ++TPLT +TRG+ + +
Sbjct: 167 IAY------DPYI---SPERAAQLGVELVSLDELLARADFITLHTPLTPETRGLIGAEEL 217
Query: 116 AKMKKGVLIVNNARGAIMDTQAVVDACSSGHIAGYSGDVWNPQPAPKDHPWRYMPNQAMT 175
AKMK GV I+N ARG I+D A+ +A SG +AG + DV+ +P P D P +PN +T
Sbjct: 218 AKMKPGVRIINCARGGIIDEAALAEALKSGKVAGAALDVFEKEP-PTDSPLFELPNVVVT 276
Query: 176 PHVSGTTIDAQLRYAAGV-KDMLDRYFKGEDFPVQN 210
PH+ +T +AQ A V + ++D +G PV N
Sbjct: 277 PHLGASTAEAQENVAIQVAEQVID-ALRGG--PVPN 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 = 155 bits (395), Expect = 2e-46
Identities = 64/179 (35%), Positives = 92/179 (51%), Gaps = 7/179 (3%)
Query: 3 ILILVRNFLPGHHQVISGEWN--VAGVAYRAYDLEGKTVGTVGCGRIGKLLLQRLKPFNC 60
IL L R V +G W+ V G R L G T+G VG GRIG+ + +R K F
Sbjct: 110 ILALARKLPFLDRAVRAGGWDWTVGGPIRR---LRGLTLGLVGFGRIGRAVAKRAKAFGF 166
Query: 61 NLLYHDRVKMDPQLEKETGAKFEEDLDTMLPKCDIVVVNTPLTEKTRGMFDKDRIAKMKK 120
++ +D + G + LD +L + D+V ++ PLT +TR + D + +A MK
Sbjct: 167 RVIAYDPYV-PDGVAALGGVRVV-SLDELLARSDVVSLHCPLTPETRHLIDAEALALMKP 224
Query: 121 GVLIVNNARGAIMDTQAVVDACSSGHIAGYSGDVWNPQPAPKDHPWRYMPNQAMTPHVS 179
G +VN ARG ++D A+ A SG IAG + DV +P P D P PN +TPH +
Sbjct: 225 GAFLVNTARGGLVDEAALARALKSGRIAGAALDVLEEEPPPADSPLLSAPNVILTPHAA 283
>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 = 154 bits (390), Expect = 9e-46
Identities = 69/205 (33%), Positives = 111/205 (54%), Gaps = 4/205 (1%)
Query: 1 MRILILVRNFLPGHHQVISGEWNVAGVAYRAYDLEGKTVGTVGCGRIGKLLLQRLKP-FN 59
IL ++R V G+W + ++L GKTVG +G G IG + + LK FN
Sbjct: 113 ALILTVLRKINQASEAVKEGKWTER-ANFVGHELSGKTVGIIGYGNIGSRVAEILKEGFN 171
Query: 60 CNLLYHDRVKMDPQLEKETGAKFEEDLDTMLPKCDIVVVNTPLTEKTRGMFDKDRIAKMK 119
+L +D ++ K+ GAK L+ +L + DI+ ++ PLTE+T M ++ +KMK
Sbjct: 172 AKVLAYDPYV-SEEVIKKKGAKPV-SLEELLAESDIISLHAPLTEETYHMINEKAFSKMK 229
Query: 120 KGVLIVNNARGAIMDTQAVVDACSSGHIAGYSGDVWNPQPAPKDHPWRYMPNQAMTPHVS 179
KGV++VN ARG ++D +A+++A SG IAG DV +P DHP + N +TPH+
Sbjct: 230 KGVILVNTARGELIDEEALIEALKSGKIAGAGLDVLEEEPIKADHPLLHYENVVITPHIG 289
Query: 180 GTTIDAQLRYAAGVKDMLDRYFKGE 204
T ++ V D ++ + G+
Sbjct: 290 AYTYESLYGMGEKVVDDIEDFLAGK 314
>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 = 153 bits (389), Expect = 2e-45
Identities = 68/202 (33%), Positives = 105/202 (51%), Gaps = 3/202 (1%)
Query: 3 ILILVRNFLPGHHQVISGEWNVAGVAYRAYDLEGKTVGTVGCGRIGKLLLQRLKPFNCNL 62
IL+ +R +G L G+TVG VG GRIG+ +++ L+PF +
Sbjct: 117 ILLALRRIPRFAAAYRAGRDWGWPTRRGGRGLYGRTVGIVGFGRIGRAVVELLRPFGLRV 176
Query: 63 LYHDRVKMDPQLEKETGAKFEEDLDTMLPKCDIVVVNTPLTEKTRGMFDKDRIAKMKKGV 122
L +D + G + LD +L + D+V ++ PLT +TRGM D +A M+ G
Sbjct: 177 LVYDPY-LPAAEAAALGVE-LVSLDELLARSDVVSLHAPLTPETRGMIDARLLALMRDGA 234
Query: 123 LIVNNARGAIMDTQAVVDACSSGHIAGYSGDVWNPQPAPKDHPWRYMPNQAMTPHVSGTT 182
+N ARGA++D A++ SG + DV +P+P P D P R +PN +TPH++G+T
Sbjct: 235 TFINTARGALVDEAALLAELRSGRLRAAL-DVTDPEPLPPDSPLRTLPNVLLTPHIAGST 293
Query: 183 IDAQLRYAAGVKDMLDRYFKGE 204
D + R D L+R+ GE
Sbjct: 294 GDERRRLGDYALDELERFLAGE 315
>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 = 152 bits (387), Expect = 3e-45
Identities = 68/209 (32%), Positives = 106/209 (50%), Gaps = 9/209 (4%)
Query: 3 ILILVRNFLPGHHQVISGEWN-VAGVAYRAYDLEGKTVGTVGCGRIGKLLLQRLKPFNCN 61
IL L + + + + G W+ AG + +L GKTVG +G G IG+ + + LK F
Sbjct: 103 ILALAKRIVEYDNDLRRGIWHGRAGEEPESKELRGKTVGILGYGHIGREIARLLKAFGMR 162
Query: 62 LLYHDRVKMDPQLEKETGAKFEEDLDTMLPKCDIVVVNTPLTEKTRGMFDKDRIAKMKKG 121
++ R + + G DLD L + D+VVV PLT++TRG+ +A MK G
Sbjct: 163 VIGVSRSPKEDEGADFVG--TLSDLDEALEQADVVVVALPLTKQTRGLIGAAELAAMKPG 220
Query: 122 VLIVNNARGAIMDTQAVVDACSSGHIAGYSGDVW------NPQPAPKDHPWRYMPNQAMT 175
++VN RG ++D +A+ +A IAG + DVW AP +P+ +PN M+
Sbjct: 221 AILVNVGRGPVVDEEALYEALKERPIAGAAIDVWWRYPSRGDPVAPSRYPFHELPNVIMS 280
Query: 176 PHVSGTTIDAQLRYAAGVKDMLDRYFKGE 204
PH +G T + R + + RY +GE
Sbjct: 281 PHNAGWTEETFRRRIDEAAENIRRYLRGE 309
>gnl|CDD|183914 PRK13243, PRK13243, glyoxylate reductase; Reviewed.
Length = 333
Score = 151 bits (384), Expect = 1e-44
Identities = 74/210 (35%), Positives = 117/210 (55%), Gaps = 8/210 (3%)
Query: 3 ILILVRNFLPGHHQVISGEWNVAGVAYR-----AYDLEGKTVGTVGCGRIGKLLLQRLKP 57
+L R + H V SGEW GVA+ YD+ GKT+G +G GRIG+ + +R K
Sbjct: 112 LLATARRLVEADHFVRSGEWKRRGVAWHPLMFLGYDVYGKTIGIIGFGRIGQAVARRAKG 171
Query: 58 FNCNLLYHDRVKMDPQLEKETGAKFEEDLDTMLPKCDIVVVNTPLTEKTRGMFDKDRIAK 117
F +LY+ R + P+ EKE GA++ L+ +L + D V ++ PLT++T M +++R+
Sbjct: 172 FGMRILYYSRTR-KPEAEKELGAEYR-PLEELLRESDFVSLHVPLTKETYHMINEERLKL 229
Query: 118 MKKGVLIVNNARGAIMDTQAVVDACSSGHIAGYSGDVWNPQPAPKDHPWRYMPNQAMTPH 177
MK ++VN ARG ++DT+A+V A G IAG DV+ +P + + N + PH
Sbjct: 230 MKPTAILVNTARGKVVDTKALVKALKEGWIAGAGLDVFEEEPYY-NEELFSLKNVVLAPH 288
Query: 178 VSGTTIDAQLRYAAGVKDMLDRYFKGEDFP 207
+ 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 = 146 bits (370), Expect = 7e-43
Identities = 64/203 (31%), Positives = 108/203 (53%), Gaps = 3/203 (1%)
Query: 3 ILILVRNFLPGHHQVISGEWNVAGVAY-RAYDLEGKTVGTVGCGRIGKLLLQRLKPFNCN 61
IL L R G + G + + ++L GKT+G +G GRIG+ + +R K F
Sbjct: 110 ILALARRIAEGDRLMRRGGFLGWAPLFFLGHELAGKTLGIIGMGRIGQAVARRAKAFGMK 169
Query: 62 LLYHDRVKMDPQLEKETGAKFEEDLDTMLPKCDIVVVNTPLTEKTRGMFDKDRIAKMKKG 121
+LY++R ++ + EKE GA + DLD +L + D V ++ P T +T + D MK
Sbjct: 170 ILYYNRHRLSEETEKELGATYV-DLDELLKESDFVSLHAPYTPETHHLIDAAAFKLMKPT 228
Query: 122 VLIVNNARGAIMDTQAVVDACSSGHIAGYSGDVWNPQPAPKDHPWRYMPNQAMTPHVSGT 181
++N ARG ++D +A+VDA +G IAG + DV+ +P + + N +TPH+
Sbjct: 229 AYLINAARGPLVDEKALVDALKTGEIAGAALDVFEFEPEVSPE-LKKLDNVILTPHIGNA 287
Query: 182 TIDAQLRYAAGVKDMLDRYFKGE 204
T++A+ A D + + +G+
Sbjct: 288 TVEARDAMAKEAADNIISFLEGK 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 = 145 bits (369), Expect = 1e-42
Identities = 67/192 (34%), Positives = 96/192 (50%), Gaps = 2/192 (1%)
Query: 16 QVISGEWNVAGVAYRAYDLEGKTVGTVGCGRIGKLLLQRLKPFNCNLLYHDRVKMDPQLE 75
+ + W+ A L G TV VG G IG+ L+ L PF ++ +R +
Sbjct: 105 RARATTWDPAEEDDLVTLLRGSTVAIVGAGGIGRALIPLLAPFGAKVIAVNRSGRPVEGA 164
Query: 76 KETGAKFEEDLDTMLPKCDIVVVNTPLTEKTRGMFDKDRIAKMKKGVLIVNNARGAIMDT 135
ET + LD + P D VV+ PLT +TR + D +A MK +VN ARG ++DT
Sbjct: 165 DETVPA--DRLDEVWPDADHVVLAAPLTPETRHLVDAAALAAMKPHAWLVNVARGPLVDT 222
Query: 136 QAVVDACSSGHIAGYSGDVWNPQPAPKDHPWRYMPNQAMTPHVSGTTIDAQLRYAAGVKD 195
A+VDA SG IAG + DV +P+P P HP +PN +TPHV+ T + A V +
Sbjct: 223 DALVDALRSGEIAGAALDVTDPEPLPDGHPLWSLPNALITPHVANTPEVIRPLLAERVAE 282
Query: 196 MLDRYFKGEDFP 207
+ + GE
Sbjct: 283 NVRAFAAGEPLL 294
>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 = 145 bits (369), Expect = 1e-42
Identities = 70/200 (35%), Positives = 115/200 (57%), Gaps = 7/200 (3%)
Query: 6 LVRNFLPGHHQVISGEWNVAGVAYRAYDLEGKTVGTVGCGRIGKLLLQRLKPFNCNLLYH 65
L+RN +P V +G AG +L GKTVG VG G IG + + K F C +L +
Sbjct: 117 LLRNIVPCDAAVRAGG-TKAG--LIGRELAGKTVGIVGTGAIGLRVARLFKAFGCKVLAY 173
Query: 66 DRVKMDPQLEKETGAKFEEDLDTMLPKCDIVVVNTPLTEKTRGMFDKDRIAKMKKGVLIV 125
R + + K G ++ LD +L + DIV ++ PL ++T+G+ K+++A MK+ +++
Sbjct: 174 SRSE--KEEAKALGIEYV-SLDELLAESDIVSLHLPLNDETKGLIGKEKLALMKESAILI 230
Query: 126 NNARGAIMDTQAVVDACSSGHIAGYSGDVWNPQPA-PKDHPWRYMPNQAMTPHVSGTTID 184
N ARG ++D +A+ DA + G IAG DV++ +P P D+P + PN +TPHV+ T +
Sbjct: 231 NTARGPVVDNEALADALNEGKIAGAGIDVFDMEPPLPADYPLLHAPNTILTPHVAFATEE 290
Query: 185 AQLRYAAGVKDMLDRYFKGE 204
A + A V D ++ + G+
Sbjct: 291 AMEKRAEIVFDNIEAWLAGK 310
>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 = 149 bits (379), Expect = 2e-42
Identities = 74/208 (35%), Positives = 112/208 (53%), Gaps = 12/208 (5%)
Query: 1 MRILILVRNFLPGHHQVISGEWNVAGVAYRAYDLEGKTVGTVGCGRIGKLLLQRLKPFNC 60
+L RN + GEW+ A+ +L GKT+G +G GRIG ++ +R K F
Sbjct: 105 AMLLAAARNIPQADASLKEGEWDRK--AFMGTELYGKTLGVIGLGRIGSIVAKRAKAFGM 162
Query: 61 NLLYHDRVKMDPQLEKET----GAKFEEDLDTMLPKCDIVVVNTPLTEKTRGMFDKDRIA 116
+L +D P + E G + +DLD +L + D + V+TPLT +TRG+ + +A
Sbjct: 163 KVLAYD-----PYISPERAEQLGVELVDDLDELLARADFITVHTPLTPETRGLIGAEELA 217
Query: 117 KMKKGVLIVNNARGAIMDTQAVVDACSSGHIAGYSGDVWNPQPAPKDHPWRYMPNQAMTP 176
KMKKGV+IVN ARG I+D A+ +A GH+ + DV+ +P P D+P + N TP
Sbjct: 218 KMKKGVIIVNCARGGIIDEAALYEALEEGHVRAAALDVFEKEP-PTDNPLFDLDNVIATP 276
Query: 177 HVSGTTIDAQLRYAAGVKDMLDRYFKGE 204
H+ +T +AQ A V + + KG
Sbjct: 277 HLGASTREAQENVATQVAEQVLDALKGL 304
>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 = 141 bits (359), Expect = 2e-41
Identities = 60/199 (30%), Positives = 108/199 (54%), Gaps = 5/199 (2%)
Query: 3 ILILVRNFLPGHHQVISGEWNVAGVAYRAYDLEGKTVGTVGCGRIGKLLLQRLKPFNCNL 62
+L L R + ++ G+WN Y+ +L GKT+G +G GRIG+ + + + N+
Sbjct: 108 MLSLARFIHRANREMKLGKWNKK--KYKGIELRGKTLGIIGFGRIGREVAKIARALGMNV 165
Query: 63 LYHDRVKMDPQLEKETGAKFEEDLDTMLPKCDIVVVNTPLTEKTRGMFDKDRIAKMKKGV 122
+ +D D Q E G K L+ +L D + ++ PLT +T+ M +K + MK G
Sbjct: 166 IAYDPYPKDEQ-AVELGVKTV-SLEELLKNSDFISLHVPLTPETKHMINKKELELMKDGA 223
Query: 123 LIVNNARGAIMDTQAVVDACSSGHIAGYSGDVWNPQPAPKDHPWRYMPNQAMTPHVSGTT 182
+I+N +RG ++D +A+++A SG +AG + DV+ +P P +PN ++TPH+ +T
Sbjct: 224 IIINTSRGGVIDEEALLEALKSGKLAGAALDVFENEP-PPGSKLLELPNVSLTPHIGAST 282
Query: 183 IDAQLRYAAGVKDMLDRYF 201
+AQ R + + + +
Sbjct: 283 KEAQERIGEELANKIIEFL 301
>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 = 141 bits (359), Expect = 3e-41
Identities = 65/173 (37%), Positives = 97/173 (56%), Gaps = 3/173 (1%)
Query: 34 LEGKTVGTVGCGRIGKLLLQRLKPFNCNLLYHDR-VKMDPQLEKETGAKFEEDLDTMLPK 92
L GKTV VG G IG+ + +R K F ++ R + P + E ++LD +LP+
Sbjct: 132 LAGKTVLIVGLGDIGREIARRAKAFGMRVIGVRRSGRPAPPVVDEVYT--PDELDELLPE 189
Query: 93 CDIVVVNTPLTEKTRGMFDKDRIAKMKKGVLIVNNARGAIMDTQAVVDACSSGHIAGYSG 152
D VV PLT +TRG+F+ +R A MK G +++N RG+++D A+++A SG IAG +
Sbjct: 190 ADYVVNALPLTPETRGLFNAERFAAMKPGAVLINVGRGSVVDEDALIEALESGRIAGAAL 249
Query: 153 DVWNPQPAPKDHPWRYMPNQAMTPHVSGTTIDAQLRYAAGVKDMLDRYFKGED 205
DV+ +P P D P +PN +TPH+SG + R + L RY GE
Sbjct: 250 DVFEEEPLPADSPLWDLPNVIITPHISGDSPSYPERVVEIFLENLRRYLAGEP 302
>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 = 140 bits (356), Expect = 1e-40
Identities = 63/199 (31%), Positives = 109/199 (54%), Gaps = 13/199 (6%)
Query: 4 LIL-VRNFLPGHHQVI-SGEWNVAG----VAYRAYDLEGKTVGTVGCGRIGKLLLQRLKP 57
L+L + + H+ V+ +GEW + Y +L GKT+G +G G IG+ + + +
Sbjct: 109 LLLALARLVAYHNDVVKAGEWQKSPDFCFWDYPIIELAGKTLGIIGYGNIGQAVARIARA 168
Query: 58 FNCNLLYHDRVKMDPQLEKETGAKFEEDLDTMLPKCDIVVVNTPLTEKTRGMFDKDRIAK 117
F +L+ +R P E LD +L + D++ ++ PLT +TR + + + +AK
Sbjct: 169 FGMKVLFAERKGAPPLREGYV------SLDELLAQSDVISLHCPLTPETRNLINAEELAK 222
Query: 118 MKKGVLIVNNARGAIMDTQAVVDACSSGHIAGYSGDVWNPQPAPKDHP-WRYMPNQAMTP 176
MK G +++N ARG ++D QA+ DA +SG IAG DV + +P D+P + PN +TP
Sbjct: 223 MKPGAILINTARGGLVDEQALADALNSGKIAGAGLDVLSQEPPRADNPLLKAAPNLIITP 282
Query: 177 HVSGTTIDAQLRYAAGVKD 195
H++ + +A+ R + D
Sbjct: 283 HIAWASREARQRLMDILVD 301
>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 = 140 bits (354), Expect = 2e-40
Identities = 63/193 (32%), Positives = 98/193 (50%), Gaps = 9/193 (4%)
Query: 3 ILILVRNFLPGHHQVISGEWNVAGVAYRAYDLEGKTVGTVGCGRIGKLLLQRLKPFNCNL 62
++ L R+ L G V SG++ + L+GKTVG +G G +G+ + +RL F L
Sbjct: 111 LIGLGRHILAGDRFVRSGKFGGWRPKFYGTGLDGKTVGILGMGALGRAIARRLSGFGATL 170
Query: 63 LYHDRVKMDPQLEKETGAKFEEDLDTMLPKCDIVVVNTPLTEKTRGMFDKDRIAKMKKGV 122
LY+D +D E+ + E LD +L D +V+ PLT T + + + +AKMK G
Sbjct: 171 LYYDPHPLDQAEEQALNLRRVE-LDELLESSDFLVLALPLTPDTLHLINAEALAKMKPGA 229
Query: 123 LIVNNARGAIMDTQAVVDACSSGHIAGYSGDV-----WNPQPAPKDHPWRYM---PNQAM 174
L+VN RG+++D AV +A SGH+ GY+ DV W P+ P +
Sbjct: 230 LLVNPCRGSVVDEAAVAEALKSGHLGGYAADVFEMEDWARPDRPRSIPQELLDQHDRTVF 289
Query: 175 TPHVSGTTIDAQL 187
TPH+ + +L
Sbjct: 290 TPHIGSAVDEVRL 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 = 135 bits (341), Expect = 2e-38
Identities = 61/192 (31%), Positives = 103/192 (53%), Gaps = 23/192 (11%)
Query: 1 MRILILVRNFLPGHHQVISGEWNVAGVAYRAYDLEGKTVGTVGCGRIGKLLLQRLKPFNC 60
M +L+ +R + + ++++ G+ + +L TVG +G GRIG+ +++ L F C
Sbjct: 110 MLMLMALRKYKQIMKRAEVNDYSLGGL--QGRELRNLTVGVIGTGRIGQAVIKNLSGFGC 167
Query: 61 NLLYHDRVKMDPQLEKETGAKFEE--DLDTMLPKCDIVVVNTPLTEKTRGMFDKDRIAKM 118
+L +D E K+ E DLDT+ + DI+ ++TPLTE+T + +K+ IAKM
Sbjct: 168 KILAYDP------YPNEEVKKYAEYVDLDTLYKESDIITLHTPLTEETYHLINKESIAKM 221
Query: 119 KKGVLIVNNARGAIMDTQAVVDACSSGHIAGYSGDVW---------NPQPAPKDHPW--- 166
K GV+I+N ARG ++DT+A+++ SG I G + DV + + +
Sbjct: 222 KDGVIIINTARGELIDTEALIEGLESGKIGGAALDVIEGEDGIYYNDRKGDILSNRELAI 281
Query: 167 -RYMPNQAMTPH 177
R PN +TPH
Sbjct: 282 LRSFPNVILTPH 293
>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 = 133 bits (336), Expect = 1e-37
Identities = 57/187 (30%), Positives = 90/187 (48%), Gaps = 22/187 (11%)
Query: 32 YDLEGKTVGTVGCGRIGKLLLQRLKPFNCNLL----------YHDRVKMDPQLEKETGAK 81
+L GKT+ +G G IG+ + +RLK F ++ Y D+
Sbjct: 131 LELYGKTILFLGTGSIGQEIAKRLKAFGMKVIGVNTSGRDVEYFDKCYPL---------- 180
Query: 82 FEEDLDTMLPKCDIVVVNTPLTEKTRGMFDKDRIAKMKKGVLIVNNARGAIMDTQAVVDA 141
E+LD +L + DIVV PLTE+T +FD+ +MKKG L +N RG +D A+++A
Sbjct: 181 --EELDEVLKEADIVVNVLPLTEETHHLFDEAFFEQMKKGALFINVGRGPSVDEDALIEA 238
Query: 142 CSSGHIAGYSGDVWNPQPAPKDHPWRYMPNQAMTPHVSGTTIDAQLRYAAGVKDMLDRYF 201
+ I G + DV+ +P PKD P + N +TPH+SG + R + L +
Sbjct: 239 LKNKQIRGAALDVFEEEPLPKDSPLWDLDNVLITPHISGVSEHFNERLFDIFYENLKSFL 298
Query: 202 KGEDFPV 208
+ +
Sbjct: 299 EDGELLK 305
>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 = 132 bits (334), Expect = 1e-37
Identities = 56/216 (25%), Positives = 102/216 (47%), Gaps = 20/216 (9%)
Query: 3 ILILVRNFLPGHHQVISG---------EWNVAGVAYRAYDLEGKTVGTVGCGRIGKLLLQ 53
+L L RN + V +G E + +L GKT+G +G G IG+L+
Sbjct: 95 MLALSRNIIQAIKWVTNGDGDDISKGVEKGKKQ--FVGTELRGKTLGVIGLGNIGRLVAN 152
Query: 54 RLKPFNCNLLYHDRVKMDPQLEKETGAKFE--EDLDTMLPKCDIVVVNTPLTEKTRGMFD 111
++ +D + + + + + L+ +L D + ++ PLT++TRG+ +
Sbjct: 153 AALALGMKVIGYDPY-LSVEAAWKLSVEVQRVTSLEELLATADYITLHVPLTDETRGLIN 211
Query: 112 KDRIAKMKKGVLIVNNARGAIMDTQAVVDACSSGHIAGYSGDVWNPQPAPKDHPWRYMPN 171
+ +AKMK G +++N ARG I+D +A+++A G + GY D P+PA H PN
Sbjct: 212 AELLAKMKPGAILLNFARGEIVDEEALLEALDEGKLGGYVTDF--PEPALLGHL----PN 265
Query: 172 QAMTPHVSGTTIDAQLRYAAGVKDMLDRYFKGEDFP 207
TPH+ +T +A+ A + + + +
Sbjct: 266 VIATPHLGASTEEAEENCAVMAARQIMDFLETGNIT 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 = 131 bits (333), Expect = 2e-37
Identities = 68/187 (36%), Positives = 95/187 (50%), Gaps = 12/187 (6%)
Query: 19 SGEWNVAGVAYRAYDLEGKTVGTVGCGRIGKLLLQRLKPFNCNLLYHDRVKMDPQLEKET 78
G W L + V VG G IG+ + +RL PF + RV + E
Sbjct: 119 RGRWEPRRTP----SLADRRVLIVGYGSIGRAIERRLAPFEVRVT---RVARTAR-PGEQ 170
Query: 79 GAKFEEDLDTMLPKCDIVVVNTPLTEKTRGMFDKDRIAKMKKGVLIVNNARGAIMDTQAV 138
+E L +LP+ D+VV+ PLT++TRG+ D + +A+M G L+VN ARG ++DT A+
Sbjct: 171 VHGIDE-LPALLPEADVVVLIVPLTDETRGLVDAEFLARMPDGALLVNVARGPVVDTDAL 229
Query: 139 VDACSSGHI-AGYSGDVWNPQPAPKDHPWRYMPNQAMTPHVSGTTIDAQLRYAAGVKDML 197
V +SG + A DV +P+P P HP P +TPHV G T R A V+ L
Sbjct: 230 VAELASGRLRAAL--DVTDPEPLPPGHPLWSAPGVLITPHVGGATPAFLPRAYALVRRQL 287
Query: 198 DRYFKGE 204
RY GE
Sbjct: 288 RRYAAGE 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 = 131 bits (332), Expect = 5e-37
Identities = 51/123 (41%), Positives = 81/123 (65%), Gaps = 3/123 (2%)
Query: 32 YDLEGKTVGTVGCGRIGKLLLQRLKPFNCNLLYHDRVKMDPQLEKETGAKFEEDLDTMLP 91
+DL GKTVG +G G+IG+ + LK F C +L +D +P+L K G ++ DLD +L
Sbjct: 140 FDLHGKTVGVIGTGKIGQAFARILKGFGCRVLAYD-PYPNPELAKL-GVEYV-DLDELLA 196
Query: 92 KCDIVVVNTPLTEKTRGMFDKDRIAKMKKGVLIVNNARGAIMDTQAVVDACSSGHIAGYS 151
+ DI+ ++ PLT +T + + + IAKMK GV+++N +RG ++DT+A+++A SG I G
Sbjct: 197 ESDIISLHCPLTPETHHLINAETIAKMKDGVMLINTSRGGLIDTKALIEALKSGKIGGLG 256
Query: 152 GDV 154
DV
Sbjct: 257 LDV 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 = 128 bits (323), Expect = 5e-36
Identities = 61/202 (30%), Positives = 105/202 (51%), Gaps = 10/202 (4%)
Query: 3 ILILVRNFLPGHHQVISGEWNVAGVAYRAYDLEGKTVGTVGCGRIGKLLLQRLKPFNCNL 62
I++L R + G WN A ++++ GKT+G +G G IG L + +
Sbjct: 109 IIMLARRLPDRNAAAHRGIWN--KSATGSHEVRGKTLGIIGYGHIGSQLSVLAEALGMRV 166
Query: 63 LYHDRVKMDPQLEKETGAKFEEDLDTMLPKCDIVVVNTPLTEKTRGMFDKDRIAKMKKGV 122
+++D +L A+ L+ +L + D V ++ P T T+ M + IA+MKKG
Sbjct: 167 IFYDIA---EKLPLGN-ARQVSSLEELLAEADFVTLHVPATPSTKNMIGAEEIAQMKKGA 222
Query: 123 LIVNNARGAIMDTQAVVDACSSGHIAGYSGDVWNPQPAPKDHPW----RYMPNQAMTPHV 178
+++N +RG ++D A+ +A SGH+AG + DV+ +PA P+ + +PN +TPH+
Sbjct: 223 ILINASRGTVVDIDALAEALRSGHLAGAAVDVFPEEPASNGEPFSSPLQGLPNVILTPHI 282
Query: 179 SGTTIDAQLRYAAGVKDMLDRY 200
G+T +AQ V L +Y
Sbjct: 283 GGSTEEAQENIGLEVAGKLVKY 304
>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 = 124 bits (313), Expect = 4e-34
Identities = 59/196 (30%), Positives = 96/196 (48%), Gaps = 27/196 (13%)
Query: 1 MRILILVRNFLPGHHQVISGE--WNVAGVAYRAYDLEGKTVGTVGCGRIGKLLLQRLKPF 58
+ L L+RN +V G+ W + DL TVG +G GRIG + K F
Sbjct: 111 TQALNLLRNTPEIDRRVAKGDFRWAPGLIGREIRDL---TVGIIGTGRIGSAAAKIFKGF 167
Query: 59 NCNLLYHDRVKMDPQLEKETGAKFEEDLDTMLPKCDIVVVNTPLTEKTRGMFDKDRIAKM 118
++ +D +P+LEK + L+ +L + DI+ ++ PLT++ + + + AKM
Sbjct: 168 GAKVIAYDPYP-NPELEKFLLYY--DSLEDLLKQADIISLHVPLTKENHHLINAEAFAKM 224
Query: 119 KKGVLIVNNARGAIMDTQAVVDACSSGHIAGYSGDV-----------WNPQPAPKDHPWR 167
K G ++VN ARG ++DT+A++DA SG IAG + D W+ + +
Sbjct: 225 KDGAILVNAARGGLVDTKALIDALDSGKIAGAALDTYENETGYFNKDWSGKEIEDE---V 281
Query: 168 Y-----MPNQAMTPHV 178
MPN +TPH+
Sbjct: 282 LKELIAMPNVLITPHI 297
>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 = 121 bits (305), Expect = 3e-33
Identities = 54/171 (31%), Positives = 89/171 (52%), Gaps = 3/171 (1%)
Query: 34 LEGKTVGTVGCGRIGKLLLQRLKPFNCNLLYHDRVKMDPQLEKETGAKFEEDLDTMLPKC 93
L G T+G VG G IG+ L +R +L ++ + G + DL + +
Sbjct: 133 LAGSTLGIVGFGAIGQALARRALALGMRVL---ALRRSGRPSDVPGVEAAADLAELFARS 189
Query: 94 DIVVVNTPLTEKTRGMFDKDRIAKMKKGVLIVNNARGAIMDTQAVVDACSSGHIAGYSGD 153
D +V+ PLT +TR + + D +A+ K G+ ++N ARG ++D +A+++A SG I+ S D
Sbjct: 190 DHLVLAAPLTPETRHLINADVLAQAKPGLHLINIARGGLVDQEALLEALDSGRISLASLD 249
Query: 154 VWNPQPAPKDHPWRYMPNQAMTPHVSGTTIDAQLRYAAGVKDMLDRYFKGE 204
V +P+P P+ HP P ++PH S D + A + L RY G+
Sbjct: 250 VTDPEPLPEGHPLYTHPRVRLSPHTSAIAPDGRRNLADRFLENLARYRAGQ 300
>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 = 120 bits (304), Expect = 6e-33
Identities = 62/203 (30%), Positives = 105/203 (51%), Gaps = 24/203 (11%)
Query: 3 ILILVRNFLPGHHQVISGEWNVAGVAYRAYDLEGKTVGTVGCGRIGKLLLQRLKPFNCNL 62
+L L R + G+++ AG+ R ++L GKT+G VG GRIG+ + + + F +
Sbjct: 108 LLALSRKLREAIERTRRGDFSQAGL--RGFELAGKTLGVVGTGRIGRRVARIARGFGMKV 165
Query: 63 LYHDRVKMDPQLEKETGAKFEEDLDTMLPKCDIVVVNTPLTEKTRGMFDKDRIAKMKKGV 122
L +D V D +L + G ++ L+ +L + DI+ ++ P T +T + +++ A MK G
Sbjct: 166 LAYDVVP-DEELAERLGFRYV-SLEELLQESDIISLHVPYTPQTHHLINRENFALMKPGA 223
Query: 123 LIVNNARGAIMDTQAVVDACSSGHIAGYSGDV-------------WNPQPAP-------K 162
+++N ARGA++DT+A+V A G +AG DV + +P
Sbjct: 224 VLINTARGAVVDTEALVRALKEGKLAGAGLDVLEQEEVLREEAELFREDVSPEDLKKLLA 283
Query: 163 DHPWRYMPNQAMTPHVSGTTIDA 185
DH PN +TPHV+ T +A
Sbjct: 284 DHALLRKPNVIITPHVAYNTKEA 306
>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 (301), Expect = 3e-32
Identities = 52/184 (28%), Positives = 89/184 (48%), Gaps = 29/184 (15%)
Query: 20 GEWNVAGVAYRAY----DLEGKTVGTVGCGRIGKLLLQRLKPFNCNLLYHDRVKMDPQLE 75
E+ ++ + A L+GKTVG VG G +G L +RL+ N+L D P+ E
Sbjct: 95 AEYVLSALLVLAQRQGFSLKGKTVGIVGVGNVGSRLARRLEALGMNVLLCD----PPRAE 150
Query: 76 KETGAKFEEDLDTMLPKCDIVVVNTPLTE----KTRGMFDKDRIAKMKKGVLIVNNARGA 131
E F L+ +L + DI+ ++ PLT T + D+D +A +K G +++N +RGA
Sbjct: 151 AEGDPGFV-SLEELLAEADIITLHVPLTRDGEHPTYHLLDEDFLAALKPGQILINASRGA 209
Query: 132 IMDTQAVVDACSSGHIAGYSGDVWNPQPAPKDHPWRYMPNQAM-------TPHVSGTTID 184
++D QA++ G DVW +P + + TPH++G +++
Sbjct: 210 VIDNQALLALLQRGKDLRVVLDVWENEPE---------IDLELLDKVDIATPHIAGYSLE 260
Query: 185 AQLR 188
+ R
Sbjct: 261 GKAR 264
>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 = 117 bits (296), Expect = 6e-32
Identities = 57/201 (28%), Positives = 98/201 (48%), Gaps = 5/201 (2%)
Query: 3 ILILVRNFLPGHHQVISGEWNVAGVAYRAYDLEGKTVGTVGCGRIGKLLLQRLKPFNCNL 62
IL L RN + +G W L GKT+G VG GRIG + + + F +
Sbjct: 113 ILALARNLPEEDAALRAGGWQTTL----GTGLAGKTLGIVGLGRIGARVARIGQAFGMRV 168
Query: 63 LYHDRVKMDPQLEKETGAKFEEDLDTMLPKCDIVVVNTPLTEKTRGMFDKDRIAKMKKGV 122
+ + + G + + + D+V ++ L+++TRG+ + +A MK
Sbjct: 169 IAWSS-NLTAERAAAAGVEAAVSKEELFATSDVVSLHLVLSDRTRGLVGAEDLALMKPTA 227
Query: 123 LIVNNARGAIMDTQAVVDACSSGHIAGYSGDVWNPQPAPKDHPWRYMPNQAMTPHVSGTT 182
L+VN +RG ++D A++ A +G IAG + DV++ +P P DHP R +PN +TPH+ T
Sbjct: 228 LLVNTSRGPLVDEGALLAALRAGRIAGAALDVFDVEPLPADHPLRGLPNVLLTPHIGYVT 287
Query: 183 IDAQLRYAAGVKDMLDRYFKG 203
+A + + + + G
Sbjct: 288 EEAYEGFYGQAVENIAAWLAG 308
>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 = 117 bits (294), Expect = 1e-31
Identities = 60/195 (30%), Positives = 97/195 (49%), Gaps = 24/195 (12%)
Query: 3 ILILVRNFLPGHHQVISGEWNVAGVAYRAYDLEGKTVGTVGCGRIGKLLLQRLKPFNCNL 62
+L L +V +G W+ G R +L GKTVG +G G +GK +RL F C +
Sbjct: 107 LLALFNKLNRADQEVRNGIWDREG--NRGVELMGKTVGIIGYGNMGKAFAKRLSGFGCKV 164
Query: 63 LYHDRVKMDPQLEKETGAKF--EEDLDTMLPKCDIVVVNTPLTEKTRGMFDKDRIAKMKK 120
+ +D+ K G + + L+T+ + DI+ ++ PLT +TRGM +K+ I+ KK
Sbjct: 165 IAYDK-------YKNFGDAYAEQVSLETLFKEADILSLHIPLTPETRGMVNKEFISSFKK 217
Query: 121 GVLIVNNARGAIMDTQAVVDACSSGHIAGYSGDVW--------NPQPAPKDHPWRYM--- 169
+N ARG ++ T+ +V A SG I G DV + P+ + Y+
Sbjct: 218 PFYFINTARGKVVVTKDLVKALKSGKILGACLDVLEYEKASFESIFNQPEA--FEYLIKS 275
Query: 170 PNQAMTPHVSGTTID 184
P +TPH++G T +
Sbjct: 276 PKVILTPHIAGWTFE 290
>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 = 115 bits (289), Expect = 9e-31
Identities = 60/196 (30%), Positives = 98/196 (50%), Gaps = 18/196 (9%)
Query: 3 ILILVRNFLPGHHQVISGEWNVAGVAYRAYDLEGKTVGTVGCGRIGKLLLQRLKPFNCNL 62
IL L+RN + ++ +LE +TVG VG G+IG+ + QR K F +
Sbjct: 112 ILALLRNR--KYIDERDKNQDLQDAGVIGRELEDQTVGVVGTGKIGRAVAQRAKGFGMKV 169
Query: 63 LYHDRVKMDPQLEKETGAKFEEDLDTMLPKCDIVVVNTPLTEKTRGMFDKDRIAKMKKGV 122
+ +D + P+LE + G K+ L+ + DI+ ++ PLT + M +++ MKKGV
Sbjct: 170 IAYDPFRN-PELEDK-GVKYVS-LEELFKNSDIISLHVPLTPENHHMINEEAFKLMKKGV 226
Query: 123 LIVNNARGAIMDTQAVVDACSSGHIAGYSGDV-----------WNPQ--PAPKDHPWRYM 169
+I+N ARG+++DT+A+++A SG I G DV + +
Sbjct: 227 IIINTARGSLVDTEALIEALDSGKIFGAGLDVLEDETPDLLKDLEGEIFKDALNALLGRR 286
Query: 170 PNQAMTPHVSGTTIDA 185
PN +TPH + T DA
Sbjct: 287 PNVIITPHTAFYTDDA 302
>gnl|CDD|185307 PRK15409, PRK15409, bifunctional glyoxylate/hydroxypyruvate
reductase B; Provisional.
Length = 323
Score = 114 bits (287), Expect = 1e-30
Identities = 63/184 (34%), Positives = 96/184 (52%), Gaps = 4/184 (2%)
Query: 16 QVISGEWNVA-GVAYRAYDLEGKTVGTVGCGRIGKLLLQRLK-PFNCNLLYHDRVKMDPQ 73
+V +GEW + G + D+ KT+G VG GRIG L QR FN +LY+ R + +
Sbjct: 124 RVKAGEWTASIGPDWFGTDVHHKTLGIVGMGRIGMALAQRAHFGFNMPILYNAR-RHHKE 182
Query: 74 LEKETGAKFEEDLDTMLPKCDIVVVNTPLTEKTRGMFDKDRIAKMKKGVLIVNNARGAIM 133
E+ A++ DLDT+L + D V + PLT++T +F ++ AKMK + +N RG ++
Sbjct: 183 AEERFNARYC-DLDTLLQESDFVCIILPLTDETHHLFGAEQFAKMKSSAIFINAGRGPVV 241
Query: 134 DTQAVVDACSSGHIAGYSGDVWNPQPAPKDHPWRYMPNQAMTPHVSGTTIDAQLRYAAGV 193
D A++ A G I DV+ +P D P +PN PH+ T + + AA
Sbjct: 242 DENALIAALQKGEIHAAGLDVFEQEPLSVDSPLLSLPNVVAVPHIGSATHETRYNMAACA 301
Query: 194 KDML 197
D L
Sbjct: 302 VDNL 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 = 112 bits (283), Expect = 5e-30
Identities = 58/192 (30%), Positives = 88/192 (45%), Gaps = 16/192 (8%)
Query: 20 GEWNVAGVAYRAYDLEGKTVGTVGCGRIGKLLLQRLKPFNCNLLYHDRVKMDPQLEKETG 79
G W A + VG +G G +G + +RL + R D E
Sbjct: 120 GVWK-PLPQRPAAER---RVGVLGLGELGAAVARRLAALGFPVSGWSRSPKDI----EGV 171
Query: 80 AKF--EEDLDTMLPKCDIVVVNTPLTEKTRGMFDKDRIAKMKKGVLIVNNARGAIMDTQA 137
F EE LD L + DI+V PLT +TRG+ + + +A++ +G ++N RG +
Sbjct: 172 TCFHGEEGLDAFLAQTDILVCLLPLTPETRGILNAELLARLPRGAALINVGRGPHLVEAD 231
Query: 138 VVDACSSGHIAGYSGDVWNPQPAPKDHP-WRYMPNQAMTPHVSGTT-IDAQLRYAAGVKD 195
++ A SGH++G DV+ +P P DHP WR P +TPH++ T D+ A
Sbjct: 232 LLAALDSGHLSGAVLDVFEQEPLPADHPLWR-HPRVTVTPHIAAITDPDSAAAQVAEN-- 288
Query: 196 MLDRYFKGEDFP 207
+ R GE P
Sbjct: 289 -IRRLEAGEPLP 299
>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 = 109 bits (276), Expect = 4e-29
Identities = 54/201 (26%), Positives = 94/201 (46%), Gaps = 11/201 (5%)
Query: 3 ILILVRNFLPGHHQVISGEWNVAGVAYR-AYDLEGKTVGTVGCGRIGKLLLQRLKPFNCN 61
+L ++R V +G W A+ + GK VG VG GRIG+ + +RL+ F
Sbjct: 109 LLAVLRRIPAADRFVRAGRW--PKGAFPLTRKVSGKRVGIVGLGRIGRAIARRLEAFGME 166
Query: 62 LLYHDRVKMDPQLEKETGAKFEEDLDTMLPKCDIVVVNTPLTEKTRGMFDKDRIAKM-KK 120
+ YH R + ++ L + + D++VV P TR + + + + +
Sbjct: 167 IAYHGRRPKP-----DVPYRYYASLLELAAESDVLVVACPGGPATRHLVNAEVLEALGPD 221
Query: 121 GVLIVNNARGAIMDTQAVVDACSSGHIAGYSGDVWNPQPAPKDHPWRYMPNQAMTPHVSG 180
GVL+ N ARG+++D A++ A G IAG DV+ +P + N +TPH++
Sbjct: 222 GVLV-NVARGSVVDEAALIAALQEGRIAGAGLDVFENEPNVPA-ALLDLDNVVLTPHIAS 279
Query: 181 TTIDAQLRYAAGVKDMLDRYF 201
T++ + V L+ +F
Sbjct: 280 ATVETRRAMGDLVLANLEAFF 300
>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 = 110 bits (276), Expect = 5e-29
Identities = 55/203 (27%), Positives = 83/203 (40%), Gaps = 3/203 (1%)
Query: 3 ILILVRNFLPGHHQVISGEWNVAGVAYRAYDLEGKTVGTVGCGRIGKLLLQRLKPFNCN- 61
IL L R V +G+W +L GKT+G +G G IG + K
Sbjct: 105 ILALARRIPEADASVRAGDWK--KGGPIGLELYGKTLGVIGGGGIGGIGAAIAKALGMGV 162
Query: 62 LLYHDRVKMDPQLEKETGAKFEEDLDTMLPKCDIVVVNTPLTEKTRGMFDKDRIAKMKKG 121
+ Y + E + L L + D ++ P T G + M K
Sbjct: 163 VAYDPYPNPERAEEGGVEVLLLDLLLLDLKESDDLINLAPPTTMKTGHIIINEARGMLKD 222
Query: 122 VLIVNNARGAIMDTQAVVDACSSGHIAGYSGDVWNPQPAPKDHPWRYMPNQAMTPHVSGT 181
+ +NNARG + +A +DA IA + DV +P P + P +PN +TPH++G
Sbjct: 223 AVAINNARGGGVIEEAALDALLEEGIAAAALDVVEEEPPPVNSPLLDLPNVILTPHIAGA 282
Query: 182 TIDAQLRYAAGVKDMLDRYFKGE 204
T +AQ A + L + KG
Sbjct: 283 TEEAQENMAEEAAENLLAFLKGG 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 = 105 bits (264), Expect = 4e-27
Identities = 65/223 (29%), Positives = 100/223 (44%), Gaps = 22/223 (9%)
Query: 4 LILVRNFLPGHHQVISGEWNVAGVAYRAYDLEGKTVGTVGCGRIGKLLLQRLKPFNCNLL 63
L+L +FL W AY D GK VG +G G IG+ + + +
Sbjct: 101 LVLSHHFLQYIELQKEQTWGRRQEAYSVEDSVGKRVGILGYGSIGRQTARLAQALGMEVY 160
Query: 64 -YHDRVKMDPQLEKETG--------------AKF-----EEDLDTML-PKCDIVVVNTPL 102
Y + P+ K+ G + + + L L D++VV+ PL
Sbjct: 161 AYTRSPRPTPESRKDDGYIVPGTGDPDGSIPSAWFSGTDKASLHEFLRQDLDLLVVSLPL 220
Query: 103 TEKTRGMFDKDRIAKM-KKGVLIVNNARGAIMDTQAVVDACSSGHIAGYSGDVWNPQPAP 161
T T+ + + + K+ + N ARG+++DT A+V A SG I G + DV +P+P P
Sbjct: 221 TPATKHLLGAEEFEILAKRKTFVSNIARGSLVDTDALVAALESGQIRGAALDVTDPEPLP 280
Query: 162 KDHPWRYMPNQAMTPHVSGTTIDAQLRYAAGVKDMLDRYFKGE 204
DHP PN +TPHVS T + R +++ L+R KGE
Sbjct: 281 ADHPLWSAPNVIITPHVSWQTQEYFDRALDVLEENLERLRKGE 323
>gnl|CDD|215501 PLN02928, PLN02928, oxidoreductase family protein.
Length = 347
Score = 105 bits (263), Expect = 6e-27
Identities = 60/160 (37%), Positives = 85/160 (53%), Gaps = 11/160 (6%)
Query: 34 LEGKTVGTVGCGRIGKLLLQRLKPFNCNLLYHDR---VKMDPQLEKETGAKFE------- 83
L GKTV +G G IG L +RL+PF LL R + + L G +
Sbjct: 157 LFGKTVFILGYGAIGIELAKRLRPFGVKLLATRRSWTSEPEDGLLIPNGDVDDLVDEKGG 216
Query: 84 -EDLDTMLPKCDIVVVNTPLTEKTRGMFDKDRIAKMKKGVLIVNNARGAIMDTQAVVDAC 142
ED+ + DIVV+ LT++T G+ + + ++ MKKG L+VN ARG ++D AV+ A
Sbjct: 217 HEDIYEFAGEADIVVLCCTLTKETAGIVNDEFLSSMKKGALLVNIARGGLLDYDAVLAAL 276
Query: 143 SSGHIAGYSGDVWNPQPAPKDHPWRYMPNQAMTPHVSGTT 182
SGH+ G + DV +P D P PN +TPHV+G T
Sbjct: 277 ESGHLGGLAIDVAWSEPFDPDDPILKHPNVIITPHVAGVT 316
>gnl|CDD|180588 PRK06487, PRK06487, glycerate dehydrogenase; Provisional.
Length = 317
Score = 104 bits (260), Expect = 1e-26
Identities = 60/216 (27%), Positives = 101/216 (46%), Gaps = 13/216 (6%)
Query: 1 MRILILVRNFLPGHHQVISGEWNVAG----VAYRAYDLEGKTVGTVGCGRIGKLLLQRLK 56
+L L V +G W + + + +LEGKT+G +G G +G + + +
Sbjct: 109 ALLLALATRLPDYQQAVAAGRWQQSSQFCLLDFPIVELEGKTLGLLGHGELGGAVARLAE 168
Query: 57 PFNCNLLYHDRVKMDPQLEKETGAKFEEDLDTMLPKCDIVVVNTPLTEKTRGMFDKDRIA 116
F +L QL LD +LP+ D + ++ PLTE TR + +A
Sbjct: 169 AFGMRVLI-------GQLPGRPARPDRLPLDELLPQVDALTLHCPLTEHTRHLIGARELA 221
Query: 117 KMKKGVLIVNNARGAIMDTQAVVDACSSGHIAGYSGDVWNPQPAPKDHPWRY--MPNQAM 174
MK G L++N ARG ++D QA+ DA SGH+ G + DV + +P +P +P +
Sbjct: 222 LMKPGALLINTARGGLVDEQALADALRSGHLGGAATDVLSVEPPVNGNPLLAPDIPRLIV 281
Query: 175 TPHVSGTTIDAQLRYAAGVKDMLDRYFKGEDFPVQN 210
TPH + + +A+ R + + +F G+ V +
Sbjct: 282 TPHSAWGSREARQRIVGQLAENARAFFAGKPLRVVS 317
>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 = 103 bits (258), Expect = 3e-26
Identities = 48/175 (27%), Positives = 83/175 (47%), Gaps = 26/175 (14%)
Query: 38 TVGTVGCGRIGKLLLQRLKPFNCNLLYHDRVKMDPQLEKETGAKFEEDLDTMLPKCDIVV 97
TVG +G GRIG + K ++ +D + P + F LD +L K DI+
Sbjct: 147 TVGIIGTGRIGLTAAKLFKGLGAKVIGYD---IYPSDAAKDVVTFV-SLDELLKKSDIIS 202
Query: 98 VNTP-LTEKTRGMFDKDRIAKMKKGVLIVNNARGAIMDTQAVVDACSSGHIAGYSGDVWN 156
++ P + K + +K+ I+KMK G +++N ARG + D +A+++A SG +AG+ DV N
Sbjct: 203 LHVPYIKGKNDKLINKEFISKMKDGAILINTARGELQDEEAILEALESGKLAGFGTDVLN 262
Query: 157 PQPAP--KDHPWRYMPNQA------------MTPHVSGTTIDAQLRYAAGVKDML 197
+ KD + + +TPH+ T +A + +M+
Sbjct: 263 NEKEIFFKDFDGDKIEDPVVEKLLDLYPRVLLTPHIGSYTDEA-------LSNMI 310
>gnl|CDD|181414 PRK08410, PRK08410, 2-hydroxyacid dehydrogenase; Provisional.
Length = 311
Score = 102 bits (256), Expect = 4e-26
Identities = 43/177 (24%), Positives = 85/177 (48%), Gaps = 11/177 (6%)
Query: 32 YDLEGKTVGTVGCGRIGKLLLQRLKPFNCNLLYHDRVKMDPQLEKETGAKFEE-DLDTML 90
+++GK G +G G IGK + + + F ++Y+ K ++E L+ +L
Sbjct: 141 GEIKGKKWGIIGLGTIGKRVAKIAQAFGAKVVYYSTSG------KNKNEEYERVSLEELL 194
Query: 91 PKCDIVVVNTPLTEKTRGMFDKDRIAKMKKGVLIVNNARGAIMDTQAVVDACSSGHIAGY 150
DI+ ++ PL EKT+ + + +K G +++N RG I++ + + A I
Sbjct: 195 KTSDIISIHAPLNEKTKNLIAYKELKLLKDGAILINVGRGGIVNEKDLAKALDEKDI-YA 253
Query: 151 SGDVWNPQPAPKDHPWRYMPNQA---MTPHVSGTTIDAQLRYAAGVKDMLDRYFKGE 204
DV +P K+HP + N+ +TPH++ + +A+ VK+ + + +G
Sbjct: 254 GLDVLEKEPMEKNHPLLSIKNKEKLLITPHIAWASKEARKTLIEKVKENIKDFLEGG 310
>gnl|CDD|236985 PRK11790, PRK11790, D-3-phosphoglycerate dehydrogenase;
Provisional.
Length = 409
Score = 99.1 bits (248), Expect = 2e-24
Identities = 58/189 (30%), Positives = 99/189 (52%), Gaps = 12/189 (6%)
Query: 3 ILILVRNFLPGHHQVISGEWNVAGVAYRAYDLEGKTVGTVGCGRIGKLLLQRLKPFNCNL 62
I++L+R + + G WN A ++++ GKT+G VG G IG L + +
Sbjct: 120 IILLLRGIPEKNAKAHRGGWN--KSAAGSFEVRGKTLGIVGYGHIGTQLSVLAESLGMRV 177
Query: 63 LYHDRVKMDPQLEKETG-AKFEEDLDTMLPKCDIVVVNTPLTEKTRGMFDKDRIAKMKKG 121
++D P G A+ L+ +L + D+V ++ P T T+ M + +A MK G
Sbjct: 178 YFYDIEDKLP-----LGNARQVGSLEELLAQSDVVSLHVPETPSTKNMIGAEELALMKPG 232
Query: 122 VLIVNNARGAIMDTQAVVDACSSGHIAGYSGDVWNPQPAPKDHPW----RYMPNQAMTPH 177
+++N +RG ++D A+ DA SGH+AG + DV+ +P P+ R + N +TPH
Sbjct: 233 AILINASRGTVVDIDALADALKSGHLAGAAIDVFPVEPKSNGDPFESPLRGLDNVILTPH 292
Query: 178 VSGTTIDAQ 186
+ G+T +AQ
Sbjct: 293 IGGSTQEAQ 301
>gnl|CDD|235890 PRK06932, PRK06932, glycerate dehydrogenase; Provisional.
Length = 314
Score = 92.9 bits (231), Expect = 1e-22
Identities = 53/197 (26%), Positives = 94/197 (47%), Gaps = 14/197 (7%)
Query: 14 HHQVISGEWNVAG----VAYRAYDLEGKTVGTVGCGRIGKLLLQRLKPFNCNLLYHDRVK 69
+ +S W Y D+ G T+G G G +G + + + +LY +
Sbjct: 121 YRDQLSDRWATCKQFCYFDYPITDVRGSTLGVFGKGCLGTEVGRLAQALGMKVLYAEH-- 178
Query: 70 MDPQLEKETGAKFEEDLDTMLPKCDIVVVNTPLTEKTRGMFDKDRIAKMKKGVLIVNNAR 129
+ +E FEE +L + DIV ++ PLTE T+ + + + +A MK ++N R
Sbjct: 179 KGASVCREGYTPFEE----VLKQADIVTLHCPLTETTQNLINAETLALMKPTAFLINTGR 234
Query: 130 GAIMDTQAVVDACSSGHIAGYSGDVWNPQPAPKDHPW----RYMPNQAMTPHVSGTTIDA 185
G ++D QA++DA +G IAG + DV +P KD+P + +PN +TPH++ + A
Sbjct: 235 GPLVDEQALLDALENGKIAGAALDVLVKEPPEKDNPLIQAAKRLPNLLITPHIAWASDSA 294
Query: 186 QLRYAAGVKDMLDRYFK 202
V ++ + +
Sbjct: 295 VTTLVNKVAQNIEEFVQ 311
>gnl|CDD|166874 PRK00257, PRK00257, erythronate-4-phosphate dehydrogenase;
Validated.
Length = 381
Score = 89.3 bits (222), Expect = 7e-21
Identities = 55/184 (29%), Positives = 91/184 (49%), Gaps = 12/184 (6%)
Query: 30 RAYDLEGKTVGTVGCGRIGKLLLQRLKPFNCNLLYHDRVKMDPQLEKETGAKFEEDLDTM 89
DL +T G VG G +G L++ L+ +L D P+ E E F L+ +
Sbjct: 110 EGVDLAERTYGVVGAGHVGGRLVRVLRGLGWKVLVCD----PPRQEAEGDGDFV-SLERI 164
Query: 90 LPKCDIVVVNTPLTE----KTRGMFDKDRIAKMKKGVLIVNNARGAIMDTQAVVDACSSG 145
L +CD++ ++TPLT+ TR + D+ +A ++ G ++N +RGA++D QA+ +A SG
Sbjct: 165 LEECDVISLHTPLTKEGEHPTRHLLDEAFLASLRPGAWLINASRGAVVDNQALREALLSG 224
Query: 146 HIAGYSGDVWNPQPAPKDHPWRYMPNQAMTPHVSGTTIDAQLRYAAGVKDMLDRYFKGED 205
DVW + P+ TPH++G ++D + R A + L R+F G
Sbjct: 225 EDLDAVLDVWEGE--PQIDLELADLCTIATPHIAGYSLDGKARGTAQIYQALCRFF-GIP 281
Query: 206 FPVQ 209
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 = 77.4 bits (191), Expect = 5e-17
Identities = 35/98 (35%), Positives = 53/98 (54%)
Query: 83 EEDLDTMLPKCDIVVVNTPLTEKTRGMFDKDRIAKMKKGVLIVNNARGAIMDTQAVVDAC 142
E++L +LP+ D++V+ P T T D + +A + K +VN RGA +D A+V A
Sbjct: 187 EDELPELLPETDVLVMILPATPSTAHALDAEVLAALPKHAWVVNVGRGATVDEDALVAAL 246
Query: 143 SSGHIAGYSGDVWNPQPAPKDHPWRYMPNQAMTPHVSG 180
SG + G + DV +P P P PN +TPH +G
Sbjct: 247 ESGRLGGAALDVTATEPLPASSPLWDAPNLILTPHAAG 284
>gnl|CDD|235800 PRK06436, PRK06436, glycerate dehydrogenase; Provisional.
Length = 303
Score = 73.0 bits (179), Expect = 3e-15
Identities = 42/173 (24%), Positives = 84/173 (48%), Gaps = 11/173 (6%)
Query: 34 LEGKTVGTVGCGRIGKLLLQRLKPFNCNLLYHDRVKMDPQLEKETGAKFEEDLDTMLPKC 93
L K++G +G G IG+ + K F N+ + R + + + + ++ K
Sbjct: 120 LYNKSLGILGYGGIGRRVALLAKAFGMNIYAYTR-----SYVNDGISSIYMEPEDIMKKS 174
Query: 94 DIVVVNTPLTEKTRGMFDKDRIAKMKKGVLIVNNARGAIMDTQAVVDACSSGHIAGYSGD 153
D V+++ PLT++TRGM + ++ +KG+ I+N AR ++D +++ + + Y D
Sbjct: 175 DFVLISLPLTDETRGMINSKMLSLFRKGLAIINVARADVVDKNDMLNFLRNHNDKYYLSD 234
Query: 154 VWNPQPAPKDHPWRYMPNQAMTPHVSGTTIDA--QLRYAAGVKDMLDRYFKGE 204
VW +P + N ++PHV+G Q A ++ + +F+G+
Sbjct: 235 VWWNEPIITETNPD---NVILSPHVAGGMSGEIMQPAVALAFEN-IKNFFEGK 283
>gnl|CDD|185366 PRK15469, ghrA, bifunctional glyoxylate/hydroxypyruvate reductase
A; Provisional.
Length = 312
Score = 66.7 bits (163), Expect = 3e-13
Identities = 44/157 (28%), Positives = 79/157 (50%), Gaps = 6/157 (3%)
Query: 32 YDLEGKTVGTVGCGRIGKLLLQRLKPFNCNLLYHDRV-KMDPQLEKETGAKFEEDLDTML 90
Y E T+G +G G +G + Q L+ + L R K P ++ G E+L L
Sbjct: 132 YHREDFTIGILGAGVLGSKVAQSLQTWGFPLRCWSRSRKSWPGVQSFAGR---EELSAFL 188
Query: 91 PKCDIVVVNTPLTEKTRGMFDKDRIAKMKKGVLIVNNARGAIMDTQAVVDACSSGHIAGY 150
+ +++ P T +T G+ ++ + ++ G ++N ARG + ++ A SG + G
Sbjct: 189 SQTRVLINLLPNTPETVGIINQQLLEQLPDGAYLLNLARGVHVVEDDLLAALDSGKVKGA 248
Query: 151 SGDVWNPQPAPKDHP-WRYMPNQAMTPHVSGTTIDAQ 186
DV++ +P P + P W++ P A+TPHV+ T A+
Sbjct: 249 MLDVFSREPLPPESPLWQH-PRVAITPHVAAVTRPAE 284
>gnl|CDD|185335 PRK15438, PRK15438, erythronate-4-phosphate dehydrogenase PdxB;
Provisional.
Length = 378
Score = 66.1 bits (161), Expect = 8e-13
Identities = 46/168 (27%), Positives = 78/168 (46%), Gaps = 25/168 (14%)
Query: 32 YDLEGKTVGTVGCGRIGKLLLQRLKPFNCNLLYHDRVKMDPQLEKETGAKFEEDLDTMLP 91
+ L +TVG VG G +G+ L RL+ L D P+ ++ F LD ++
Sbjct: 112 FSLHDRTVGIVGVGNVGRRLQARLEALGIKTLLCD----PPRADRGDEGDFRS-LDELVQ 166
Query: 92 KCDIVVVNTPLTE----KTRGMFDKDRIAKMKKGVLIVNNARGAIMDTQAVVDACSSGHI 147
+ DI+ +TPL + KT + D+ I +K G +++N RGA++D A++ + G
Sbjct: 167 EADILTFHTPLFKDGPYKTLHLADEKLIRSLKPGAILINACRGAVVDNTALLTCLNEGQK 226
Query: 148 AGYSGDVWNPQPAPKDHPWRYMPNQAM-------TPHVSGTTIDAQLR 188
DVW +P N + TPH++G T++ + R
Sbjct: 227 LSVVLDVWEGEPE---------LNVELLKKVDIGTPHIAGYTLEGKAR 265
>gnl|CDD|181499 PRK08605, PRK08605, D-lactate dehydrogenase; Validated.
Length = 332
Score = 64.4 bits (157), Expect = 3e-12
Identities = 33/122 (27%), Positives = 64/122 (52%), Gaps = 10/122 (8%)
Query: 38 TVGTVGCGRIGKLLLQRL-KPFNCNLLYHD---RVKMDPQLEKETGAKFEEDLDTMLPKC 93
V +G GRIG + + K + +++ +D K ++ +++ ++ +
Sbjct: 148 KVAVIGTGRIGLAVAKIFAKGYGSDVVAYDPFPNAKAATYVD------YKDTIEEAVEGA 201
Query: 94 DIVVVNTPLTEKTRGMFDKDRIAKMKKGVLIVNNARGAIMDTQAVVDACSSGHIAGYSGD 153
DIV ++ P T+ +F+ D KKG + VN ARG+++DT+A++DA +G I G + D
Sbjct: 202 DIVTLHMPATKYNHYLFNADLFKHFKKGAVFVNCARGSLVDTKALLDALDNGLIKGAALD 261
Query: 154 VW 155
+
Sbjct: 262 TY 263
>gnl|CDD|177941 PLN02306, PLN02306, hydroxypyruvate reductase.
Length = 386
Score = 63.7 bits (155), Expect = 5e-12
Identities = 45/162 (27%), Positives = 82/162 (50%), Gaps = 18/162 (11%)
Query: 34 LEGKTVGTVGCGRIGKLLLQRL-KPFNCNLLYHDRVKMDPQLEKETGA------------ 80
L+G+TVG +G GRIG + + + F NL+Y+D + +LEK A
Sbjct: 163 LKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYD-LYQSTRLEKFVTAYGQFLKANGEQP 221
Query: 81 ---KFEEDLDTMLPKCDIVVVNTPLTEKTRGMFDKDRIAKMKKGVLIVNNARGAIMDTQA 137
K ++ +L + D++ ++ L + T + +K+R+A MKK ++VN +RG ++D A
Sbjct: 222 VTWKRASSMEEVLREADVISLHPVLDKTTYHLINKERLALMKKEAVLVNASRGPVIDEVA 281
Query: 138 VVDACSSGHIAGYSGDVWNPQPAPKDHPWRYMPNQAMTPHVS 179
+V+ + + DV+ +P K M N + PH++
Sbjct: 282 LVEHLKANPMFRVGLDVFEDEPYMKPG-LADMKNAVVVPHIA 322
>gnl|CDD|183550 PRK12480, PRK12480, D-lactate dehydrogenase; Provisional.
Length = 330
Score = 61.9 bits (150), Expect = 2e-11
Identities = 30/120 (25%), Positives = 58/120 (48%), Gaps = 8/120 (6%)
Query: 38 TVGTVGCGRIGKLLLQRLKPFNCNLLYHDRVKMDPQ--LEKETGAKFEEDLDTMLPKCDI 95
TV +G GRIG + F + +D L +++ + + DI
Sbjct: 148 TVAIIGTGRIGAATAKIYAGFGATITAYDAYPNKDLDFLT------YKDSVKEAIKDADI 201
Query: 96 VVVNTPLTEKTRGMFDKDRIAKMKKGVLIVNNARGAIMDTQAVVDACSSGHIAGYSGDVW 155
+ ++ 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 = 51.5 bits (124), Expect = 6e-08
Identities = 35/170 (20%), Positives = 64/170 (37%), Gaps = 9/170 (5%)
Query: 31 AYDLEGKTVGTVGCGRIGKLLLQRLKPFNCNLLYHDRVKMDPQLEKETGAKFEEDLDTML 90
+L G VG +G G G+++ L F ++ Y+ R + P E + L+ +L
Sbjct: 133 PRELTGLKVGIIGLGTTGQMIADALSFFGADVYYYSRTR-KPDAEAKGIRYLP--LNELL 189
Query: 91 PKCDIVVVNTPLTEKTRGMFDKDRIAKMKKGVLIVNNARGAIMDTQAVVDACSSGHIAGY 150
D++ P K + ++ + G ++ N + G + +A+ + +
Sbjct: 190 KTVDVICTCLP---KNVILLGEEEFELLGDGKILFNTSLGPSFEVEALKKWLKASGYNIF 246
Query: 151 SGDVWNPQPAPKDHPWRYMPNQAMTPHVSGTTIDAQLRYAAGVKDMLDRY 200
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 = 39.3 bits (92), Expect = 7e-04
Identities = 21/64 (32%), Positives = 33/64 (51%), Gaps = 4/64 (6%)
Query: 38 TVGTVGCGRIGKLLLQRLK----PFNCNLLYHDRVKMDPQLEKETGAKFEEDLDTMLPKC 93
VG VGCG IGK LL+ ++ F +Y + +LE G + D+D ++ +
Sbjct: 2 KVGIVGCGAIGKFLLELVRDGRVDFELVAVYDRDEEKAKELEASVGRRCVSDIDELIAEV 61
Query: 94 DIVV 97
D+VV
Sbjct: 62 DLVV 65
>gnl|CDD|237343 PRK13304, PRK13304, L-aspartate dehydrogenase; Reviewed.
Length = 265
Score = 38.8 bits (91), Expect = 0.001
Identities = 20/63 (31%), Positives = 32/63 (50%), Gaps = 4/63 (6%)
Query: 39 VGTVGCGRIGKLLLQRLKP--FNCNLLY-HDR-VKMDPQLEKETGAKFEEDLDTMLPKCD 94
+G VGCG I L+ + + N L +DR ++ L +TGAK +D ++ D
Sbjct: 4 IGIVGCGAIASLITKAILSGRINAELYAFYDRNLEKAENLASKTGAKACLSIDELVEDVD 63
Query: 95 IVV 97
+VV
Sbjct: 64 LVV 66
>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 = 33.7 bits (78), Expect = 0.023
Identities = 22/75 (29%), Positives = 32/75 (42%), Gaps = 18/75 (24%)
Query: 39 VGTVGCGRIGKLLLQRLKPFNCNLLYHDRVK----MDP------QLEKETGAKFEEDLDT 88
VG VG G+IG+ L+ N + D + +DP + + G DL+
Sbjct: 3 VGIVGAGKIGRR---HLRALNES---QDGAELVGILDPDPARAEAVAESFGVPAYSDLEE 56
Query: 89 ML--PKCDIVVVNTP 101
+L P D V V TP
Sbjct: 57 LLADPDIDAVSVATP 71
>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 = 32.5 bits (75), Expect = 0.045
Identities = 19/93 (20%), Positives = 38/93 (40%), Gaps = 14/93 (15%)
Query: 51 LLQRLKPFNCNLLYHD-RVKMDPQ-LEKETGAKFEEDLDTMLPKCDIVVVNTPLTE-KTR 107
+++ L ++ +D V + E G +DL+ L D +V+ T E ++
Sbjct: 22 IIEELLEEGAEVVVYDPYVPEEAIEALGEDGVTLVDDLEEALKGADAIVILTDHDEFRS- 80
Query: 108 GMFDKDRIAKMKKGVLIVNNARGAIMDTQAVVD 140
D +I K+ K ++ D + V+D
Sbjct: 81 --LDWAKIKKLMKPPVVF--------DGRNVLD 103
>gnl|CDD|236326 PRK08655, PRK08655, prephenate dehydrogenase; Provisional.
Length = 437
Score = 33.8 bits (78), Expect = 0.059
Identities = 14/55 (25%), Positives = 27/55 (49%), Gaps = 6/55 (10%)
Query: 73 QLEKETGAKFEEDLDTMLPKCDIVVVNTPL--TEKTRGMFDKDRIAKMKKGVLIV 125
++ 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 = 32.3 bits (74), Expect = 0.077
Identities = 21/89 (23%), Positives = 38/89 (42%), Gaps = 14/89 (15%)
Query: 33 DLEGKTVGTVGCGRIGKLLLQRLKPFNCNLLY-----HDRVKMDPQLEKETGAKFE---- 83
DL+GK V +G G + +L + L + ++ K +L +E E
Sbjct: 9 DLKGKKVLLIGAGEMARLAAKHLLSKGAKKITIANRTLEKAK---ELAEEFPVGGEALPL 65
Query: 84 EDLDTMLPKCDIVVVNTPLTEK--TRGMF 110
++L+ +L + DIV+ T T+ M
Sbjct: 66 DELEELLAEADIVISATSAPTPIITKEMV 94
>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 = 33.1 bits (76), Expect = 0.090
Identities = 25/99 (25%), Positives = 45/99 (45%), Gaps = 8/99 (8%)
Query: 33 DLEGKTVGTVGCGRIGKLLLQRLKPFNC-NLLYHDRVKMDPQ-LEKETGA---KFEEDLD 87
L+GK +G G +G+L+ + L +L +R + L KE G KFE DL+
Sbjct: 177 SLKGKKALLIGAGEMGELVAKHLLRKGVGKILIANRTYERAEDLAKELGGEAVKFE-DLE 235
Query: 88 TMLPKCDIVVVNTPLTEK--TRGMFDKDRIAKMKKGVLI 124
L + DIV+ +T ++ ++ + + +I
Sbjct: 236 EYLAEADIVISSTGAPHPIVSKEDVERALRERTRPLFII 274
>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 = 30.6 bits (70), Expect = 0.20
Identities = 17/75 (22%), Positives = 34/75 (45%), Gaps = 4/75 (5%)
Query: 51 LLQRLKPFNCNLLYHDRVKMDPQLEKETGAKFEEDLDTMLPKCDIVVVNTPLTEKTRGMF 110
+++ L ++ +D M+ +E G + DL+ L D VV+ T E R +
Sbjct: 22 IIEELLEAGAEVVVYDPYAME--EAREYGLTYVSDLEEALKGADAVVIATEHDEF-RSL- 77
Query: 111 DKDRIAKMKKGVLIV 125
D + + + K ++V
Sbjct: 78 DPEELKDLMKKPVVV 92
>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 = 30.7 bits (70), Expect = 0.53
Identities = 22/119 (18%), Positives = 46/119 (38%), Gaps = 22/119 (18%)
Query: 23 NVAGVAYRAYD--------LEGKTVGTVGCGRIGKLLLQRLKPFNCNLLY-----HDRVK 69
++ A + L+GK V +G G +G+L + L + ++R +
Sbjct: 157 GAVSISSAAVELAEKIFGNLKGKKVLVIGAGEMGELAAKHLAAKGVAEITIANRTYERAE 216
Query: 70 MDPQLEKETGAK---FEEDLDTMLPKCDIVVVNTPLTEKTRGMFDKDRIAKMKKGVLIV 125
+L KE G +E L+ +L + D+V+ T + + + K ++
Sbjct: 217 ---ELAKELGGNAVPLDELLE-LLNEADVVISATG-APHYAKIV-ERAMKKRSGKPRLI 269
>gnl|CDD|234592 PRK00045, hemA, glutamyl-tRNA reductase; Reviewed.
Length = 423
Score = 30.2 bits (69), Expect = 0.85
Identities = 20/75 (26%), Positives = 36/75 (48%), Gaps = 10/75 (13%)
Query: 33 DLEGKTVGTVGCGRIGKLLLQRLKPFNCNLLY-----HDRVKMDPQLEKETGAKFE--ED 85
DL GK V +G G +G+L+ + L + +R + +L +E G + ++
Sbjct: 179 DLSGKKVLVIGAGEMGELVAKHLAEKGVRKITVANRTLERAE---ELAEEFGGEAIPLDE 235
Query: 86 LDTMLPKCDIVVVNT 100
L L + DIV+ +T
Sbjct: 236 LPEALAEADIVISST 250
>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 = 0.99
Identities = 14/53 (26%), Positives = 21/53 (39%), Gaps = 2/53 (3%)
Query: 62 LLYHDRVKMDPQLEKETGAKFEEDLDTMLPKCDIVVVN--TPLTEKTRGMFDK 112
++ V P K ED+ +L D+ + N TPLT+K K
Sbjct: 7 IMLGRGVYDSPADRKYDFDPLFEDVKPLLRAADLAIGNLETPLTDKGSPAPSK 59
>gnl|CDD|235488 PRK05476, PRK05476, S-adenosyl-L-homocysteine hydrolase;
Provisional.
Length = 425
Score = 29.3 bits (67), Expect = 1.5
Identities = 29/113 (25%), Positives = 41/113 (36%), Gaps = 32/113 (28%)
Query: 30 RAYD--LEGKTVGTVGCGRIGKLLLQRLKPFNCNLLYHDRVKM---DP--QLEKETGAKF 82
RA + + GK V G G +GK QRL+ RV + DP L+ A
Sbjct: 204 RATNVLIAGKVVVVAGYGDVGKGCAQRLRGLGA------RVIVTEVDPICALQ----AAM 253
Query: 83 E----EDLDTMLPKCDIVVVNTPLTEKTRGMFD---KDRIAKMKKGVLIVNNA 128
+ ++ 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 = 28.1 bits (63), Expect = 1.6
Identities = 14/62 (22%), Positives = 20/62 (32%), Gaps = 6/62 (9%)
Query: 43 GCGRIGKLLLQRLK------PFNCNLLYHDRVKMDPQLEKETGAKFEEDLDTMLPKCDIV 96
GCG IG LL+ L P + + + DLD ++
Sbjct: 1 GCGAIGSGLLELLLRQQEEIPLELVAVADRDLLSKARAALLGDEPVTLDLDDLVADPRPD 60
Query: 97 VV 98
VV
Sbjct: 61 VV 62
>gnl|CDD|223450 COG0373, HemA, Glutamyl-tRNA reductase [Coenzyme metabolism].
Length = 414
Score = 29.1 bits (66), Expect = 1.9
Identities = 29/102 (28%), Positives = 50/102 (49%), Gaps = 14/102 (13%)
Query: 33 DLEGKTVGTVGCGRIGKLLLQRLKPFNCNLLY-----HDRVKMDPQLEKETGAKF--EED 85
L+ K V +G G +G+L+ + L + +R + +L K+ GA+ E+
Sbjct: 175 SLKDKKVLVIGAGEMGELVAKHLAEKGVKKITIANRTLERAE---ELAKKLGAEAVALEE 231
Query: 86 LDTMLPKCDIVVVNT--PLTEKTRGMFDKDRIAKMKKGVLIV 125
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 = 28.7 bits (64), Expect = 2.6
Identities = 20/74 (27%), Positives = 28/74 (37%), Gaps = 14/74 (18%)
Query: 39 VGTVGCGRIGKL----LLQRLKPFNCNLLYHDRVKMDPQLEKETGAKFE-----EDLDTM 89
VG +G G I L L + DR DP+ + +F DL+ +
Sbjct: 6 VGIIGAGGIAGKAHLPALAALGGGLELVAVVDR---DPERAEAFAEEFGIAKAYTDLEEL 62
Query: 90 L--PKCDIVVVNTP 101
L P D V + TP
Sbjct: 63 LADPDIDAVYIATP 76
>gnl|CDD|180709 PRK06815, PRK06815, hypothetical protein; Provisional.
Length = 317
Score = 28.1 bits (63), Expect = 3.2
Identities = 15/49 (30%), Positives = 19/49 (38%), Gaps = 8/49 (16%)
Query: 3 ILILVRNFLPGHHQVISGEWNVAGVAYRAY-----DLEGKTVGTVGCGR 46
I +R +I G AGVA A +GK V V CG+
Sbjct: 260 IKEAMRLIAETDRWLIEG---AAGVALAAALKLAPRYQGKKVAVVLCGK 305
>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 = 28.0 bits (63), Expect = 4.1
Identities = 28/135 (20%), Positives = 45/135 (33%), Gaps = 24/135 (17%)
Query: 24 VAGVAYRAYDLEG--KTVGTVGCGRIGKLLLQRLK----PFNCNLLY-HDRVKMDPQLEK 76
A +A R VG +GCG I + +L+ L +LY D + +
Sbjct: 118 SAALAARHLAAGRGFTRVGIIGCGPIAREILRFLLALGPEIRRVVLYDLDPARAE-AFAA 176
Query: 77 ETGAKFE------EDLDTMLPKCDIVVVNTPLTEKTRGMFDKDRIAKMKKGVLIVNN--- 127
+ L + D+VV T T + D + G L++N
Sbjct: 177 RCQELGPGKVTVAASAEAALRQADLVVTAT--VAGTPYIDDPAWF---QPGALVLNISLR 231
Query: 128 --ARGAIMDTQAVVD 140
A I+ +VD
Sbjct: 232 DLAPEVILKADNIVD 246
>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 = 28.0 bits (63), Expect = 4.8
Identities = 16/36 (44%), Positives = 18/36 (50%), Gaps = 4/36 (11%)
Query: 25 AGVAYRAYDL----EGKTVGTVGCGRIGKLLLQRLK 56
A VA A L G TV +G G IG L +Q LK
Sbjct: 145 AAVALHAVRLAGITLGDTVVVIGAGTIGLLAIQWLK 180
>gnl|CDD|223573 COG0499, SAM1, S-adenosylhomocysteine hydrolase [Coenzyme
metabolism].
Length = 420
Score = 27.6 bits (62), Expect = 6.4
Identities = 26/105 (24%), Positives = 43/105 (40%), Gaps = 19/105 (18%)
Query: 30 RAYD--LEGKTVGTVGCGRIGKLLLQRLKPFNCNLLYHDRVKMDP--QLEKETGAKFE-- 83
RA + L GK V G G +G+ + RL+ ++ ++DP LE A +
Sbjct: 201 RATNVLLAGKNVVVAGYGWVGRGIAMRLRGMGARVIV---TEVDPIRALE----AAMDGF 253
Query: 84 --EDLDTMLPKCDIVVVNTPLTEKTRGMFDKDRIAKMKKGVLIVN 126
++ DI V T + + K+ KMK G ++ N
Sbjct: 254 RVMTMEEAAKTGDIFVTAT----GNKDVIRKEHFEKMKDGAILAN 294
>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 = 26.9 bits (60), Expect = 7.0
Identities = 7/29 (24%), Positives = 12/29 (41%), Gaps = 1/29 (3%)
Query: 154 VWNPQPAPKDHPWRYMPN-QAMTPHVSGT 181
VW P +D Y+ + + +V G
Sbjct: 98 VWKKHPVHQDFLGFYVLDSHRFSSNVHGL 126
>gnl|CDD|214966 smart01002, AlaDh_PNT_C, Alanine dehydrogenase/PNT, C-terminal
domain. Alanine dehydrogenase catalyzes the
NAD-dependent reversible reductive amination of pyruvate
into alanine.
Length = 149
Score = 26.3 bits (59), Expect = 8.0
Identities = 17/66 (25%), Positives = 24/66 (36%), Gaps = 19/66 (28%)
Query: 73 QLEKETGAKFEEDLDTM------LPKCDIVVVNTPLTEK-------TRGMFDKDRIAKMK 119
QLE GA+F + + D+V+ L TR M + MK
Sbjct: 58 QLESLLGARFTTLYSQAELLEEAVKEADLVI-GAVLIPGAKAPKLVTREM-----VKSMK 111
Query: 120 KGVLIV 125
G +IV
Sbjct: 112 PGSVIV 117
>gnl|CDD|176918 cd08909, START_STARD13-like, C-terminal lipid-binding START domain
of mammalian STARD13 and related proteins, which also
have an N-terminal Rho GTPase-activating protein
(RhoGAP) domain. This subgroup includes the
steroidogenic acute regulatory protein (StAR)-related
lipid transfer (START) domains of STARD13 (also known as
DLC-2, Arhgap37, and SDCCAG13) and related proteins. It
belongs to the START domain family, and in turn to the
SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain
superfamily of proteins that bind hydrophobic ligands.
SRPBCC domains have a deep hydrophobic ligand-binding
pocket. Proteins belonging to this subfamily also have a
RhoGAP domain. The precise function of the START domain
in this subgroup is unclear.
Length = 205
Score = 26.8 bits (59), Expect = 8.0
Identities = 17/74 (22%), Positives = 37/74 (50%), Gaps = 3/74 (4%)
Query: 74 LEKETGAKFEEDLDTMLPKC--DIVVVNTPLTEKTRGMFDKDRIAKMKKGVLIVNNARGA 131
L+K+T ++ L+ M P D VV+ + T+ +G ++ + ++ R
Sbjct: 91 LDKQTEV-YQYVLNCMAPHPSRDFVVLRSWRTDLPKGACSLVSVSVEHEEAPLLGGVRAV 149
Query: 132 IMDTQAVVDACSSG 145
++D+Q +++ C SG
Sbjct: 150 VLDSQYLIEPCGSG 163
>gnl|CDD|176194 cd08232, idonate-5-DH, L-idonate 5-dehydrogenase. L-idonate
5-dehydrogenase (L-ido 5-DH ) catalyzes the conversion
of L-lodonate to 5-ketogluconate in the metabolism of
L-Idonate to 6-P-gluconate. In E. coli, this GntII
pathway is a subsidiary pathway to the canonical GntI
system, which also phosphorylates and transports
gluconate. L-ido 5-DH is found in an operon with a
regulator indR, transporter idnT, 5-keto-D-gluconate
5-reductase, and Gnt kinase. L-ido 5-DH is a
zinc-dependent alcohol dehydrogenase-like protein. The
alcohol dehydrogenase ADH-like family of proteins is a
diverse group of proteins related to the first
identified member, class I mammalian ADH. This group is
also called the medium chain dehydrogenases/reductase
family (MDR) which displays a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases(~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal GroES-like catalytic
domain. The MDR group contains a host of activities,
including the founding alcohol dehydrogenase (ADH),
quinone reductase, sorbitol dehydrogenase, formaldehyde
dehydrogenase, butanediol DH, ketose reductase, cinnamyl
reductase, and numerous others. The zinc-dependent
alcohol dehydrogenases (ADHs) catalyze the
NAD(P)(H)-dependent interconversion of alcohols to
aldehydes or ketones. ADH-like proteins typically form
dimers (typically higher plants, mammals) or tetramers
(yeast, bacteria), and generally have 2 tightly bound
zinc atoms per subunit. The active site zinc is
coordinated by a histidine, two cysteines, and a water
molecule. The second zinc seems to play a structural
role, affects subunit interactions, and is typically
coordinated by 4 cysteines.
Length = 339
Score = 27.2 bits (61), Expect = 8.4
Identities = 12/23 (52%), Positives = 14/23 (60%)
Query: 30 RAYDLEGKTVGTVGCGRIGKLLL 52
RA DL GK V G G IG L++
Sbjct: 160 RAGDLAGKRVLVTGAGPIGALVV 182
>gnl|CDD|177912 PLN02272, PLN02272, glyceraldehyde-3-phosphate dehydrogenase.
Length = 421
Score = 27.1 bits (60), Expect = 9.0
Identities = 11/20 (55%), Positives = 15/20 (75%), Gaps = 1/20 (5%)
Query: 35 EGKT-VGTVGCGRIGKLLLQ 53
GKT +G G GRIG+L+L+
Sbjct: 83 SGKTKIGINGFGRIGRLVLR 102
>gnl|CDD|223364 COG0287, TyrA, Prephenate dehydrogenase [Amino acid transport and
metabolism].
Length = 279
Score = 26.9 bits (60), Expect = 9.9
Identities = 22/95 (23%), Positives = 37/95 (38%), Gaps = 9/95 (9%)
Query: 37 KTVGTVGCGRIGKLL---LQRLKPFNCNLLYHDRVKMDPQLEKETGAKFEEDLDTM---L 90
VG VG G +G L L+ + DR + E G E + +
Sbjct: 4 MKVGIVGLGLMGGSLARALKEAGLVVRIIGR-DRSAATLKAALELGVIDELTVAGLAEAA 62
Query: 91 PKCDIVVVNTPLTEKTRGMFDKDRIAKMKKGVLIV 125
+ D+V+V P+ E T + + +KKG ++
Sbjct: 63 AEADLVIVAVPI-EATEEVLKE-LAPHLKKGAIVT 95
>gnl|CDD|236399 PRK09186, PRK09186, flagellin modification protein A;
Provisional.
Length = 256
Score = 26.5 bits (59), Expect = 9.9
Identities = 15/64 (23%), Positives = 31/64 (48%), Gaps = 3/64 (4%)
Query: 34 LEGKTVGTVG-CGRIGKLLLQRLKPFNCNLLYHD-RVKMDPQLEKETGAKFEEDLDTMLP 91
L+GKT+ G G IG L++ + ++ D + +L + G +F+ +++
Sbjct: 2 LKGKTILITGAGGLIGSALVKAILEAGGIVIAADIDKEALNELLESLGKEFKSKKLSLV- 60
Query: 92 KCDI 95
+ DI
Sbjct: 61 ELDI 64
>gnl|CDD|217556 pfam03435, Saccharop_dh, Saccharopine dehydrogenase. This family
comprised of three structural domains that can not be
separated in the linear sequence. In some organisms
this enzyme is found as a bifunctional polypeptide with
lysine ketoglutarate reductase. The saccharopine
dehydrogenase can also function as a saccharopine
reductase.
Length = 380
Score = 26.9 bits (60), Expect = 10.0
Identities = 14/68 (20%), Positives = 27/68 (39%), Gaps = 12/68 (17%)
Query: 42 VGCGRIGKLLLQRL-KPFNCNLLYHDRV--KMDPQLEKETGAKFE---------EDLDTM 89
+G G +G+ + L + + + DR K + G +F E L +
Sbjct: 4 IGAGGVGQGVAPLLARHGDLEITVADRSLEKAQALAAPKLGLRFIAIAVDADNYEALVAL 63
Query: 90 LPKCDIVV 97
L + D+V+
Sbjct: 64 LKEGDLVI 71
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
0.321 0.138 0.427
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: 11,735,513
Number of extensions: 1101558
Number of successful extensions: 1183
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1067
Number of HSP's successfully gapped: 103
Length of query: 223
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 130
Effective length of database: 6,812,680
Effective search space: 885648400
Effective search space used: 885648400
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: 57 (25.5 bits)