RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 045521
(204 letters)
>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 = 265 bits (680), Expect = 7e-90
Identities = 110/248 (44%), Positives = 140/248 (56%), Gaps = 55/248 (22%)
Query: 2 GADAELIDSLPKLEIVATCSAGLDKIDLVKCKEKGIQVTNTPDVLTDDVADAAIGLTLAV 61
G A LI +LP LE++A+ G D IDL + +GI+VTNTP VLTDDVAD A+GL LAV
Sbjct: 53 GLSAALIAALPALELIASFGVGYDGIDLDAARARGIRVTNTPGVLTDDVADLAVGLLLAV 112
Query: 62 LR------RFVRSED-GEMGYKLTTKISGRSVGIIGLGRIGMAVAKRAEAFGCFISYRSR 114
LR RFVR+ + + LT K+SG+ VGI+GLGRIG A+A+R EAFG I+Y R
Sbjct: 113 LRRIPAADRFVRAGRWPKGAFPLTRKVSGKRVGIVGLGRIGRAIARRLEAFGMEIAYHGR 172
Query: 115 AEKPNTKYK------------------------------------------------GAL 126
KP+ Y+ G++
Sbjct: 173 RPKPDVPYRYYASLLELAAESDVLVVACPGGPATRHLVNAEVLEALGPDGVLVNVARGSV 232
Query: 127 VDESELVSALLEDRLAAAVLDVFEHEPQVPEELFGLENVVLLPHAASGTEETRKATADIV 186
VDE+ L++AL E R+A A LDVFE+EP VP L L+NVVL PH AS T ETR+A D+V
Sbjct: 233 VDEAALIAALQEGRIAGAGLDVFENEPNVPAALLDLDNVVLTPHIASATVETRRAMGDLV 292
Query: 187 IENLEACF 194
+ NLEA F
Sbjct: 293 LANLEAFF 300
>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 = 199 bits (510), Expect = 4e-64
Identities = 94/253 (37%), Positives = 120/253 (47%), Gaps = 63/253 (24%)
Query: 4 DAELIDSLPKLEIVATCSAGLDKIDLVKCKEKGIQVTNTPDVLTDDVADAAIGLTLAVLR 63
DAEL+D+ P L+++A S G D ID+ K +GI VTNTPDVLTD AD A L LA R
Sbjct: 56 DAELLDAAPPLKVIANYSVGYDHIDVDAAKARGIPVTNTPDVLTDATADLAFALLLAAAR 115
Query: 64 RFVRSED----------GEMGYKLTTKISGRSVGIIGLGRIGMAVAKRAEAFGCFISYRS 113
R V + L T + G+++GI+G+GRIG AVA+RA+ FG I Y +
Sbjct: 116 RVVEGDRFVRAGEWKGWSPTLL-LGTDLHGKTLGIVGMGRIGQAVARRAKGFGMKILYHN 174
Query: 114 RAEKP------NTKYK-------------------------------------------- 123
R+ KP +Y
Sbjct: 175 RSRKPEAEEELGARYVSLDELLAESDFVSLHCPLTPETRHLINAERLALMKPTAILINTA 234
Query: 124 -GALVDESELVSALLEDRLAAAVLDVFEHEPQVPE-ELFGLENVVLLPHAASGTEETRKA 181
G +VDE LV AL ++A A LDVFE EP + L L NVVLLPH S T ETR A
Sbjct: 235 RGGVVDEDALVEALKSGKIAGAGLDVFEPEPLPADHPLLTLPNVVLLPHIGSATVETRTA 294
Query: 182 TADIVIENLEACF 194
A++ +NL A
Sbjct: 295 MAELAADNLLAVL 307
>gnl|CDD|223980 COG1052, LdhA, Lactate dehydrogenase and related dehydrogenases
[Energy production and conversion / Coenzyme metabolism
/ General function prediction only].
Length = 324
Score = 192 bits (491), Expect = 4e-61
Identities = 94/268 (35%), Positives = 124/268 (46%), Gaps = 65/268 (24%)
Query: 1 VGADAELIDSLPKLEIVATCSAGLDKIDLVKCKEKGIQVTNTPDVLTDDVADAAIGLTLA 60
DAE+++ LP L+++AT SAG D +DL KE+GI VTN P T+ VA+ A+ L LA
Sbjct: 54 DRIDAEVLEKLPGLKLIATRSAGYDNVDLEAAKERGITVTNVPGYSTEAVAEHAVALILA 113
Query: 61 VLRRFVR----------SEDGEMGYKLTTKISGRSVGIIGLGRIGMAVAKRAEAFGCFIS 110
+ RR S G L + G+++GIIGLGRIG AVA+R + FG +
Sbjct: 114 LARRIHEGDRRVREGNWSLSGGPDPLLGFDLRGKTLGIIGLGRIGQAVARRLKGFGMKVL 173
Query: 111 YRSRAEKPNTKYK----------------------------------------------- 123
Y R+ P + +
Sbjct: 174 YYDRSPNPEAEKELGARYVDLDELLAESDIISLHCPLTPETRHLINAEELAKMKPGAILV 233
Query: 124 ----GALVDESELVSALLEDRLAAAVLDVFEHEP-QVPEELFGLEN---VVLLPHAASGT 175
G LVDE L+ AL ++A A LDVFE+EP L L+N VVL PH AS T
Sbjct: 234 NTARGGLVDEQALIDALKSGKIAGAGLDVFENEPALFDHPLLRLDNFPNVVLTPHIASAT 293
Query: 176 EETRKATADIVIENLEACFLNKPLLTPV 203
EE RKA A++ +ENLEA F V
Sbjct: 294 EEARKAMAELALENLEAFFDGGVPPNEV 321
>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 = 173 bits (442), Expect = 9e-54
Identities = 90/261 (34%), Positives = 120/261 (45%), Gaps = 61/261 (23%)
Query: 4 DAELIDSLPKLEIVATCSAGLDKIDLVKCKEKGIQVTNTPDVLTDDVADAAIGLTLAVLR 63
D E+ID+ L+I+A AG D ID+ KEKGI VTNTP V T+ A+ GL LA+ R
Sbjct: 56 DKEIIDAAKNLKIIANYGAGFDNIDVDYAKEKGIPVTNTPAVSTEPTAELTFGLILALAR 115
Query: 64 RFVR-----SEDGEMG----YKLTTKISGRSVGIIGLGRIGMAVAKRAEAFGCFISYRSR 114
R G +G + L +++G+++GIIG+GRIG AVA+RA+AFG I Y +R
Sbjct: 116 RIAEGDRLMRRGGFLGWAPLFFLGHELAGKTLGIIGMGRIGQAVARRAKAFGMKILYYNR 175
Query: 115 AEKP--------------------------NTKY-------------------------- 122
+ Y
Sbjct: 176 HRLSEETEKELGATYVDLDELLKESDFVSLHAPYTPETHHLIDAAAFKLMKPTAYLINAA 235
Query: 123 KGALVDESELVSALLEDRLAAAVLDVFEHEPQVPEELFGLENVVLLPHAASGTEETRKAT 182
+G LVDE LV AL +A A LDVFE EP+V EL L+NV+L PH + T E R A
Sbjct: 236 RGPLVDEKALVDALKTGEIAGAALDVFEFEPEVSPELKKLDNVILTPHIGNATVEARDAM 295
Query: 183 ADIVIENLEACFLNKPLLTPV 203
A +N+ + K V
Sbjct: 296 AKEAADNIISFLEGKRPKNIV 316
>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 = 169 bits (431), Expect = 2e-52
Identities = 85/249 (34%), Positives = 115/249 (46%), Gaps = 59/249 (23%)
Query: 3 ADAELIDSLPKLEIVATCSAGLDKIDLVKCKEKGIQVTNTPDVLTDDVADAAIGLTLAVL 62
AE++ PKL+ + AG+D IDL K++GI VTN P + VA+ A+GL LA+L
Sbjct: 53 VTAEVLAKAPKLKFIQVAGAGVDNIDLDAAKKRGITVTNVPGANAEAVAEHALGLLLALL 112
Query: 63 RRFVRSED----GEMGYKL---TTKISGRSVGIIGLGRIGMAVAKRAEAFGCFISYRSR- 114
RR R++ G ++ G++VGI+GLGRIG VAKR +AFG + Y R
Sbjct: 113 RRLPRADAAVRRGWGWLWAGFPGYELEGKTVGIVGLGRIGQRVAKRLQAFGMKVLYYDRT 172
Query: 115 -----AEKPNTKY---------------------------------------------KG 124
E + +G
Sbjct: 173 RKPEPEEDLGFRVVSLDELLAQSDVVVLHLPLTPETRHLINEEELALMKPGAVLVNTARG 232
Query: 125 ALVDESELVSALLEDRLAAAVLDVFEHEPQVPEE-LFGLENVVLLPHAASGTEETRKATA 183
LVDE L+ AL ++A A LDVFE EP + L L NV+L PH A TEE R+ A
Sbjct: 233 GLVDEDALLRALKSGKIAGAALDVFEPEPLPADHPLLELPNVILTPHIAGYTEEARERMA 292
Query: 184 DIVIENLEA 192
+I +ENLE
Sbjct: 293 EIAVENLER 301
>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 = 168 bits (428), Expect = 1e-51
Identities = 88/252 (34%), Positives = 123/252 (48%), Gaps = 61/252 (24%)
Query: 4 DAELIDSLPK-LEIVATCSAGLDKIDLVKCKEKGIQVTNTPDVLTDDVADAAIGLTLAVL 62
D ELI LP L+I+A AG D+ID+ ++GIQV+NTP + + AD A+ L L L
Sbjct: 66 DEELISPLPPSLKIIAHAGAGYDQIDVDALTKRGIQVSNTPGAVDEATADTALFLILGAL 125
Query: 63 RRFVRSE--------DGEMGYKLTTKISGRSVGIIGLGRIGMAVAKRAEAFGCFISY--R 112
R F R+E G + L G+++GI+GLG IG A+A++A AFG I Y R
Sbjct: 126 RNFSRAERSARAGKWRGFLDLTLAHDPRGKTLGILGLGGIGKAIARKAAAFGMKIIYHNR 185
Query: 113 SRA----EKPNTKY---------------------------------------------- 122
SR EK Y
Sbjct: 186 SRLPEELEKALATYYVSLDELLAQSDVVSLNCPLTAATRHLINKKEFAKMKDGVIIVNTA 245
Query: 123 KGALVDESELVSALLEDRLAAAVLDVFEHEPQVPEELFGLENVVLLPHAASGTEETRKAT 182
+GA++DE LV AL ++A+A LDVFE+EP+V L + NV LLPH + T ET++
Sbjct: 246 RGAVIDEDALVDALESGKVASAGLDVFENEPEVNPGLLKMPNVTLLPHMGTLTVETQEKM 305
Query: 183 ADIVIENLEACF 194
++V+EN+EA
Sbjct: 306 EELVLENIEAFL 317
>gnl|CDD|183914 PRK13243, PRK13243, glyoxylate reductase; Reviewed.
Length = 333
Score = 156 bits (395), Expect = 1e-46
Identities = 98/259 (37%), Positives = 122/259 (47%), Gaps = 76/259 (29%)
Query: 4 DAELIDSLPKLEIVATCSAGLDKIDLVKCKEKGIQVTNTPDVLTDDVADAAIGLTLAVLR 63
D E+ ++ P+L IVA + G D ID+ + +GI VTNTP VLT+ AD A L LA R
Sbjct: 58 DCEVFEAAPRLRIVANYAVGYDNIDVEEATRRGIYVTNTPGVLTEATADFAWALLLATAR 117
Query: 64 R------FVRSEDGE-------------MGYKLTTKISGRSVGIIGLGRIGMAVAKRAEA 104
R FVRS GE +GY + G+++GIIG GRIG AVA+RA+
Sbjct: 118 RLVEADHFVRS--GEWKRRGVAWHPLMFLGYDV----YGKTIGIIGFGRIGQAVARRAKG 171
Query: 105 FGCFISYRSRAEKP------NTKYK----------------------------------- 123
FG I Y SR KP +Y+
Sbjct: 172 FGMRILYYSRTRKPEAEKELGAEYRPLEELLRESDFVSLHVPLTKETYHMINEERLKLMK 231
Query: 124 ----------GALVDESELVSALLEDRLAAAVLDVFEHEPQVPEELFGLENVVLLPHAAS 173
G +VD LV AL E +A A LDVFE EP EELF L+NVVL PH S
Sbjct: 232 PTAILVNTARGKVVDTKALVKALKEGWIAGAGLDVFEEEPYYNEELFSLKNVVLAPHIGS 291
Query: 174 GTEETRKATADIVIENLEA 192
T E R+ A++V ENL A
Sbjct: 292 ATFEAREGMAELVAENLIA 310
>gnl|CDD|240649 cd12172, PGDH_like_2, Putative D-3-Phosphoglycerate Dehydrogenases,
NAD-binding and catalytic domains. Phosphoglycerate
dehydrogenases (PGDHs) catalyze the initial step in the
biosynthesis of L-serine from D-3-phosphoglycerate.
PGDHs come in 3 distinct structural forms, with this
first group being related to 2-hydroxy acid
dehydrogenases, sharing structural similarity to formate
and glycerate dehydrogenases of the D-specific
2-hydroxyacid dehydrogenase superfamily, which also
include groups such as L-alanine dehydrogenase and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. Many, not all, members of this family are
dimeric.
Length = 306
Score = 154 bits (391), Expect = 3e-46
Identities = 71/243 (29%), Positives = 108/243 (44%), Gaps = 56/243 (23%)
Query: 4 DAELIDSLPKLEIVATCSAGLDKIDLVKCKEKGIQVTNTPDVLTDDVADAAIGLTLAVLR 63
E++ + P+L++++ G D IDL K++GI VTNTP ++ VA+ IGL LA+ R
Sbjct: 59 TEEVLAAAPRLKVISRYGVGYDNIDLEAAKKRGIVVTNTPGANSNSVAELTIGLMLALAR 118
Query: 64 RFVRS----EDGEMGYKLTTKISGRSVGIIGLGRIGMAVAKRAEAFGCFI------SYRS 113
+ ++ G + T++ G+++GIIGLGRIG AVA+R FG +
Sbjct: 119 QIPQADREVRAGGWDRPVGTELYGKTLGIIGLGRIGKAVARRLSGFGMKVLAYDPYPDEE 178
Query: 114 RAEKPNTKY---------------------------------------------KGALVD 128
A++ ++ +G LVD
Sbjct: 179 FAKEHGVEFVSLEELLKESDFISLHLPLTPETRHLINAAELALMKPGAILINTARGGLVD 238
Query: 129 ESELVSALLEDRLAAAVLDVFEHEP-QVPEELFGLENVVLLPHAASGTEETRKATADIVI 187
E L AL R+A A LDVFE EP L L NV+L PH + T+E +
Sbjct: 239 EEALYEALKSGRIAGAALDVFEEEPPPADSPLLELPNVILTPHIGASTKEAVLRMGTMAA 298
Query: 188 ENL 190
+N+
Sbjct: 299 QNV 301
>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 = 142 bits (361), Expect = 8e-42
Identities = 70/265 (26%), Positives = 104/265 (39%), Gaps = 69/265 (26%)
Query: 4 DAELIDSLPKLEIVATCSAGLDKIDLVKCKEKGIQVTNTPDVLTDDVADAAIGLTLAVLR 63
AE++++ P L+++A G+D IDL E+GI VTN P T+ VA+ +GL LA+ R
Sbjct: 51 TAEVLEAAPGLKVIARRGVGVDNIDLDAATERGILVTNVPGYSTESVAELTVGLILALAR 110
Query: 64 RFVRSED----------GEMGYKLTTKISGRSVGIIGLGRIGMAVAKRAEAFGCFI---- 109
R ++ G +G +L G+++G+IG G IG A A+A G +
Sbjct: 111 RIPEADASVRAGDWKKGGPIGLELY----GKTLGVIGGGGIGGIGAAIAKALGMGVVAYD 166
Query: 110 SYRSRAEKPNTKY----------------------------------------------- 122
Y +
Sbjct: 167 PYPNPERAEEGGVEVLLLDLLLLDLKESDDLINLAPPTTMKTGHIIINEARGMLKDAVAI 226
Query: 123 ----KGALVDESELVSALLEDRLAAAVLDVFEHEPQVPEELFGLENVVLLPHAASGTEET 178
G +++E+ L + L E AAA+ V E P V L L NV+L PH A TEE
Sbjct: 227 NNARGGGVIEEAALDALLEEGIAAAALDVVEEEPPPVNSPLLDLPNVILTPHIAGATEEA 286
Query: 179 RKATADIVIENLEACFLNKPLLTPV 203
++ A+ ENL A V
Sbjct: 287 QENMAEEAAENLLAFLKGGTPPNAV 311
>gnl|CDD|223189 COG0111, SerA, Phosphoglycerate dehydrogenase and related
dehydrogenases [Amino acid transport and metabolism].
Length = 324
Score = 140 bits (355), Expect = 8e-41
Identities = 76/248 (30%), Positives = 110/248 (44%), Gaps = 59/248 (23%)
Query: 4 DAELIDSLPKLEIVATCSAGLDKIDLVKCKEKGIQVTNTPDVLTDDVADAAIGLTLAVLR 63
E++ + P L+ + AG+D IDL ++GI V N P VA+ + L LA+ R
Sbjct: 57 TEEVLAAAPNLKAIGRAGAGVDNIDLEAATKRGILVVNAPGGNAISVAELVLALLLALAR 116
Query: 64 RFVRSEDGEMGYKLTTK------ISGRSVGIIGLGRIGMAVAKRAEAFGCFISY------ 111
R ++ + + K ++G++VGIIGLGRIG AVAKR +AFG +
Sbjct: 117 RIPDADASQRRGEWDRKAFRGTELAGKTVGIIGLGRIGRAVAKRLKAFGMKVIGYDPYSP 176
Query: 112 RSRAEK-----------------------PNTKYK-----------------------GA 125
R RA P T G
Sbjct: 177 RERAGVDGVVGVDSLDELLAEADILTLHLPLTPETRGLINAEELAKMKPGAILINAARGG 236
Query: 126 LVDESELVSALLEDRLAAAVLDVFEHEPQVPE-ELFGLENVVLLPHAASGTEETRKATAD 184
+VDE L++AL ++A A LDVFE EP + L+ L NV+L PH T+E ++ A+
Sbjct: 237 VVDEDALLAALDSGKIAGAALDVFEEEPLPADSPLWDLPNVILTPHIGGSTDEAQERVAE 296
Query: 185 IVIENLEA 192
IV EN+
Sbjct: 297 IVAENIVR 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 = 139 bits (354), Expect = 8e-41
Identities = 71/248 (28%), Positives = 106/248 (42%), Gaps = 57/248 (22%)
Query: 4 DAELIDSLPKLEIVATCSAGLDKIDLVKCKEKGIQVTNTPDVLTDDVADAAIGLTLAVLR 63
E+ID+ L+I+A GLD ID+ K+KGI+V NTP ++ VA+ IGL L++ R
Sbjct: 54 TKEVIDAAKNLKIIARAGVGLDNIDVEYAKKKGIKVINTPGASSNSVAELVIGLMLSLAR 113
Query: 64 ------RFVRSEDGEMGYKLTTKISGRSVGIIGLGRIGMAVAKRAEAFGCFISYRSRAEK 117
R ++ ++ G+++GIIG GRIG VAK A A G + K
Sbjct: 114 FIHRANREMKLGKWNKKKYKGIELRGKTLGIIGFGRIGREVAKIARALGMNVIAYDPYPK 173
Query: 118 -------------------------------PNTKY--------------------KGAL 126
P TK+ +G +
Sbjct: 174 DEQAVELGVKTVSLEELLKNSDFISLHVPLTPETKHMINKKELELMKDGAIIINTSRGGV 233
Query: 127 VDESELVSALLEDRLAAAVLDVFEHEPQVPEELFGLENVVLLPHAASGTEETRKATADIV 186
+DE L+ AL +LA A LDVFE+EP +L L NV L PH + T+E ++ + +
Sbjct: 234 IDEEALLEALKSGKLAGAALDVFENEPPPGSKLLELPNVSLTPHIGASTKEAQERIGEEL 293
Query: 187 IENLEACF 194
+
Sbjct: 294 ANKIIEFL 301
>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 = 135 bits (343), Expect = 4e-39
Identities = 79/256 (30%), Positives = 112/256 (43%), Gaps = 60/256 (23%)
Query: 4 DAELIDSLPKLEIVATCSAGLDKIDLVKCKEKGIQVTNTPDVLTDDVADAAIGLTLAVLR 63
DAEL+ + P+L ++ GLD +DL +GI V N P + VA+ A+ L LA+LR
Sbjct: 56 DAELLAAAPRLRLIQQPGVGLDGVDLEAATARGIPVANIPGGNAESVAEHAVMLMLALLR 115
Query: 64 RFVRS----EDGEMG---YKLTTKISGRSVGIIGLGRIGMAVAKRAEAFGCFISY--RSR 114
R + G G + + ++SG++VGI+GLG IG AVA+R FG + Y R R
Sbjct: 116 RLPEADRELRAGRWGRPEGRPSRELSGKTVGIVGLGNIGRAVARRLRGFGVEVIYYDRFR 175
Query: 115 AEKPNTKYKGA---------------------------LVDESE---------------- 131
+ K G L+ E
Sbjct: 176 DPEAEEKDLGVRYVELDELLAESDVVSLHVPLTPETRHLIGAEELAAMKPGAILINTARG 235
Query: 132 -------LVSALLEDRLAAAVLDVFEHEPQVPE-ELFGLENVVLLPHAASGTEETRKATA 183
L++AL LA A LDVF EP P+ L L+NV+L PH A T+E+ + A
Sbjct: 236 GLVDEEALLAALRSGHLAGAGLDVFWQEPLPPDDPLLRLDNVILTPHIAGVTDESYQRMA 295
Query: 184 DIVIENLEACFLNKPL 199
IV EN+ +P
Sbjct: 296 AIVAENIARLLRGEPP 311
>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 = 131 bits (332), Expect = 2e-37
Identities = 76/251 (30%), Positives = 117/251 (46%), Gaps = 57/251 (22%)
Query: 5 AELIDSLPKLEIVATCSAGLDKIDLVKCKEKGIQVTNTPDVLTDDVADAAIGLTLAVLRR 64
E+I++ L++++ G+D +DL CKE+GI V+N T+ VA+ IGL + +LR
Sbjct: 61 GEVIEACKNLKMISVAFTGVDHVDLEACKERGITVSNAAGYSTEAVAELTIGLAIDLLRN 120
Query: 65 FVRSED-----GEMGYKLTTKISGRSVGIIGLGRIGMAVAKRAEAFGCFISYRSRAEK-- 117
V + G + +++G++VGI+G G IG+ VA+ +AFGC + SR+EK
Sbjct: 121 IVPCDAAVRAGGTKAGLIGRELAGKTVGIVGTGAIGLRVARLFKAFGCKVLAYSRSEKEE 180
Query: 118 ----------------------------PNTK--------------------YKGALVDE 129
TK +G +VD
Sbjct: 181 AKALGIEYVSLDELLAESDIVSLHLPLNDETKGLIGKEKLALMKESAILINTARGPVVDN 240
Query: 130 SELVSALLEDRLAAAVLDVFEHEPQVPEE--LFGLENVVLLPHAASGTEETRKATADIVI 187
L AL E ++A A +DVF+ EP +P + L N +L PH A TEE + A+IV
Sbjct: 241 EALADALNEGKIAGAGIDVFDMEPPLPADYPLLHAPNTILTPHVAFATEEAMEKRAEIVF 300
Query: 188 ENLEACFLNKP 198
+N+EA KP
Sbjct: 301 DNIEAWLAGKP 311
>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 = 129 bits (326), Expect = 1e-36
Identities = 74/253 (29%), Positives = 105/253 (41%), Gaps = 67/253 (26%)
Query: 4 DAELIDSLPKLEIVATCSAGLDKIDLVKCKEKGIQVTNTPDVLTDDVADAAIGLTLAVLR 63
DAE++ LP L+++ + G + +DL KE+GI VTN P TD VA L LA+ R
Sbjct: 56 DAEVLAQLPNLKLIGVLATGYNNVDLAAAKERGITVTNVPGYSTDSVAQHTFALLLALAR 115
Query: 64 RFVRSED----GE---------MGYKLTTKISGRSVGIIGLGRIGMAVAKRAEAFG--CF 108
D GE Y + ++G+++GIIG G IG AVA+ A AFG
Sbjct: 116 LVAYHNDVVKAGEWQKSPDFCFWDYPIIE-LAGKTLGIIGYGNIGQAVARIARAFGMKVL 174
Query: 109 ISYRSRAEKPNTKY---------------------------------------------K 123
+ R A Y +
Sbjct: 175 FAERKGAPPLREGYVSLDELLAQSDVISLHCPLTPETRNLINAEELAKMKPGAILINTAR 234
Query: 124 GALVDESELVSALLEDRLAAAVLDVFEHEPQVPEE----LFGLENVVLLPHAASGTEETR 179
G LVDE L AL ++A A LDV EP P L N+++ PH A + E R
Sbjct: 235 GGLVDEQALADALNSGKIAGAGLDVLSQEP--PRADNPLLKAAPNLIITPHIAWASREAR 292
Query: 180 KATADIVIENLEA 192
+ DI+++N++A
Sbjct: 293 QRLMDILVDNIKA 305
>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 = 128 bits (325), Expect = 2e-36
Identities = 72/245 (29%), Positives = 106/245 (43%), Gaps = 60/245 (24%)
Query: 4 DAELIDSLPKLEIVATCSAGLDKIDLVKCKEKGIQVTNTPDVLTDDVADAAIGLTLAVLR 63
AE+I++ P+L+++ G+D ID+ +GI V N P T VA+ I L LA+ R
Sbjct: 53 TAEVIEAAPRLKVIGRAGVGVDNIDVEAATARGILVVNAPGANTISVAEHTIALMLALAR 112
Query: 64 RF------VRSEDGEMGYKLTTKISGRSVGIIGLGRIGMAVAKRAEAFGC-------FIS 110
+R+ + + ++ G+++GI+GLGRIG VA+RA AFG +IS
Sbjct: 113 NIPQADASLRAGKWDRKKFMGVELRGKTLGIVGLGRIGREVARRARAFGMKVLAYDPYIS 172
Query: 111 YRSRAEKPNTKYK---------------------------------------------GA 125
RA + G
Sbjct: 173 -AERAAAGGVELVSLDELLAEADFISLHTPLTPETRGLINAEELAKMKPGAILINTARGG 231
Query: 126 LVDESELVSALLEDRLAAAVLDVFEHEPQVPE-ELFGLENVVLLPHAASGTEETRKATAD 184
+VDE+ L AL ++A A LDVFE EP + L GL NV+L PH + TEE ++ A
Sbjct: 232 IVDEAALADALKSGKIAGAALDVFEQEPPPADSPLLGLPNVILTPHLGASTEEAQERVAV 291
Query: 185 IVIEN 189
E
Sbjct: 292 DAAEQ 296
>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 = 126 bits (318), Expect = 2e-35
Identities = 71/233 (30%), Positives = 101/233 (43%), Gaps = 59/233 (25%)
Query: 4 DAELIDSLPKLEIVATCSAGLDKIDLVKCKEKGIQVTNTPDVLTDDVADAAIGLTLAVLR 63
AE+I++LP+L+++ G+D +D+ E+GI V N PD T++VAD A+ L LA+ R
Sbjct: 56 TAEVIEALPRLKVIVRYGVGVDNVDVAAATERGIPVCNVPDYCTEEVADHALALILALAR 115
Query: 64 ------RFVRS-EDGEMGYKLTTKISGRSVGIIGLGRIGMAVAKRAEAFGCFISYRSRAE 116
R VR+ ++ G ++G++G GRIG AVAKRA+AFG +
Sbjct: 116 KLPFLDRAVRAGGWDWTVGGPIRRLRGLTLGLVGFGRIGRAVAKRAKAFGFRVIAYDPYV 175
Query: 117 KPNTKYKGA--------LVDESELVS------------------------ALL------- 137
G L+ S++VS A L
Sbjct: 176 PDGVAALGGVRVVSLDELLARSDVVSLHCPLTPETRHLIDAEALALMKPGAFLVNTARGG 235
Query: 138 ---EDRLAAAV---------LDVFEHEP-QVPEELFGLENVVLLPHAASGTEE 177
E LA A+ LDV E EP L NV+L PHAA +EE
Sbjct: 236 LVDEAALARALKSGRIAGAALDVLEEEPPPADSPLLSAPNVILTPHAAWYSEE 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 = 126 bits (318), Expect = 2e-35
Identities = 68/251 (27%), Positives = 103/251 (41%), Gaps = 64/251 (25%)
Query: 5 AELIDSLPKLEIVATCSAGLDKIDLVKCKEKGIQVTNTPDVLTDDVADAAIGLTLAVLRR 64
++I++ PKL+++ C G + +D+ E+GI V NTP + VA+ +GL LA R
Sbjct: 59 KKVIEAAPKLKLIGVCRGGPENVDVEAATERGIPVLNTPGRNAEAVAEFTVGLMLAETRN 118
Query: 65 FVRS----------EDGEMGYKLTTKISGRSVGIIGLGRIGMAVAKRAEAFGCFISY--- 111
R+ +D ++ G++VGI+G G IG VAKR +AFG +
Sbjct: 119 IARAHAALKDGEWRKDYYNYDGYGPELRGKTVGIVGFGAIGRRVAKRLKAFGAEVLVYDP 178
Query: 112 ---RSRAEKPNTKYK--------------------------------------------- 123
+ E K
Sbjct: 179 YVDPEKIEADGVKKVSLEELLKRSDVVSLHARLTPETRGMIGAEEFALMKPTAYFINTAR 238
Query: 124 GALVDESELVSALLEDRLAAAVLDVFEHEPQVPE--ELFGLENVVLLPHAASGTEETRKA 181
LVDE L+ AL E ++ A LDVF EP +P L L+NV L PH A T + +
Sbjct: 239 AGLVDEDALIEALEEGKIGGAALDVFPEEP-LPADHPLLKLDNVTLTPHIAGATRDVAER 297
Query: 182 TADIVIENLEA 192
+ +I+ E L+
Sbjct: 298 SPEIIAEELKR 308
>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 = 118 bits (299), Expect = 2e-32
Identities = 69/257 (26%), Positives = 101/257 (39%), Gaps = 70/257 (27%)
Query: 4 DAELIDSLPKLEIVATCSAGLDKIDLVKCKEKGIQVTNTPDVLTDDVADAAIGLTLAVLR 63
DAEL+D P L+ ++ + G D IDL KE GI VTN P+ + VA+ I L LA+LR
Sbjct: 58 DAELLDKAPGLKFISLRATGYDNIDLDYAKELGIGVTNVPEYSPNAVAEHTIALILALLR 117
Query: 64 R--FVRSEDGEMGYKLTT----KISGRSVGIIGLGRIGMAVAKRAEAFGC---------- 107
++ D + ++ ++VG++G G+IG AVA+RA+ FG
Sbjct: 118 NRKYIDERDKNQDLQDAGVIGRELEDQTVGVVGTGKIGRAVAQRAKGFGMKVIAYDPFRN 177
Query: 108 ---------------------FISYRSRAEKPNTKY-------------------KGALV 127
IS N +G+LV
Sbjct: 178 PELEDKGVKYVSLEELFKNSDIISLHVPLTPENHHMINEEAFKLMKKGVIIINTARGSLV 237
Query: 128 DESELVSALLEDRLAAAVLDVFEHEPQV--------------PEELFGLENVVLLPHAAS 173
D L+ AL ++ A LDV E E L NV++ PH A
Sbjct: 238 DTEALIEALDSGKIFGAGLDVLEDETPDLLKDLEGEIFKDALNALLGRRPNVIITPHTAF 297
Query: 174 GTEETRKATADIVIENL 190
T++ K +I EN+
Sbjct: 298 YTDDALKNMVEISCENI 314
>gnl|CDD|185307 PRK15409, PRK15409, bifunctional glyoxylate/hydroxypyruvate
reductase B; Provisional.
Length = 323
Score = 116 bits (292), Expect = 2e-31
Identities = 80/249 (32%), Positives = 114/249 (45%), Gaps = 62/249 (24%)
Query: 4 DAELIDSLPKLEIVATCSAGLDKIDLVKCKEKGIQVTNTPDVLTDDVADAAIGLTLAVLR 63
DA L++ +PKL +T S G D D+ + I + +TP VLT+ VAD + L L+ R
Sbjct: 57 DAALLEKMPKLRAASTISVGYDNFDVDALTARKILLMHTPTVLTETVADTLMALVLSTAR 116
Query: 64 RFV----RSEDGEMGYKLT-----TKISGRSVGIIGLGRIGMAVAKRAE-AFGCFISYRS 113
R V R + GE + T + +++GI+G+GRIGMA+A+RA F I Y +
Sbjct: 117 RVVEVAERVKAGEWTASIGPDWFGTDVHHKTLGIVGMGRIGMALAQRAHFGFNMPILYNA 176
Query: 114 R------AEKPNTKY--------------------------------------------- 122
R E+ N +Y
Sbjct: 177 RRHHKEAEERFNARYCDLDTLLQESDFVCIILPLTDETHHLFGAEQFAKMKSSAIFINAG 236
Query: 123 KGALVDESELVSALLEDRLAAAVLDVFEHEP-QVPEELFGLENVVLLPHAASGTEETRKA 181
+G +VDE+ L++AL + + AA LDVFE EP V L L NVV +PH S T ETR
Sbjct: 237 RGPVVDENALIAALQKGEIHAAGLDVFEQEPLSVDSPLLSLPNVVAVPHIGSATHETRYN 296
Query: 182 TADIVIENL 190
A ++NL
Sbjct: 297 MAACAVDNL 305
>gnl|CDD|237436 PRK13581, PRK13581, D-3-phosphoglycerate dehydrogenase;
Provisional.
Length = 526
Score = 115 bits (291), Expect = 3e-30
Identities = 71/236 (30%), Positives = 104/236 (44%), Gaps = 67/236 (28%)
Query: 4 DAELIDSLPKLEIVATCSAGLDKIDLVKCKEKGIQVTNTPDVLTDDVADAAIGLTLAVLR 63
AE++++ L+++ G+D +D+ +GI V N P T A+ I L LA+ R
Sbjct: 55 TAEVLEAAKNLKVIGRAGVGVDNVDVPAATRRGIIVVNAPTGNTISAAEHTIALMLALAR 114
Query: 64 RFVRS----EDGE------MGYKLTTKISGRSVGIIGLGRIGMAVAKRAEAFGC------ 107
++ + G+ MG +L G+++GIIGLGRIG VAKRA+AFG
Sbjct: 115 NIPQAHASLKAGKWERKKFMGVELY----GKTLGIIGLGRIGSEVAKRAKAFGMKVIAYD 170
Query: 108 -FISYRSRAEK-------------------------PNTKY------------------- 122
+IS RA + P T+
Sbjct: 171 PYIS-PERAAQLGVELVSLDELLARADFITLHTPLTPETRGLIGAEELAKMKPGVRIINC 229
Query: 123 -KGALVDESELVSALLEDRLAAAVLDVFEHEPQVPEELFGLENVVLLPHAASGTEE 177
+G ++DE+ L AL ++A A LDVFE EP LF L NVV+ PH + T E
Sbjct: 230 ARGGIIDEAALAEALKSGKVAGAALDVFEKEPPTDSPLFELPNVVVTPHLGASTAE 285
>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 = 115 bits (289), Expect = 5e-30
Identities = 73/244 (29%), Positives = 108/244 (44%), Gaps = 60/244 (24%)
Query: 4 DAELIDSLPKLEIVATCSAGLDKIDLVKCKEKGIQVTNTPDVLTDDVADAAIGLTLAVLR 63
E+I + PKL+++ G+D ID+ +GI V N P T A+ A+ + LA R
Sbjct: 53 TEEVIAAAPKLKVIGRAGVGVDNIDIEAATARGILVVNAPTGNTISAAEHALAMLLAAAR 112
Query: 64 RFVRSEDGEMGYK------LTTKISGRSVGIIGLGRIGMAVAKRAEAFGC-------FIS 110
+++ + + T++ G+++G+IGLGRIG VAKRA+AFG +IS
Sbjct: 113 NIPQADASLKEGEWDRKAFMGTELYGKTLGVIGLGRIGSIVAKRAKAFGMKVLAYDPYIS 172
Query: 111 YRSRAEK-----------------------PNTK-----------------------YKG 124
RAE+ P T +G
Sbjct: 173 -PERAEQLGVELVDDLDELLARADFITVHTPLTPETRGLIGAEELAKMKKGVIIVNCARG 231
Query: 125 ALVDESELVSALLEDRLAAAVLDVFEHEPQVPEELFGLENVVLLPHAASGTEETRKATAD 184
++DE+ L AL E + AA LDVFE EP LF L+NV+ PH + T E ++ A
Sbjct: 232 GIIDEAALYEALEEGHVRAAALDVFEKEPPTDNPLFDLDNVIATPHLGASTREAQENVAT 291
Query: 185 IVIE 188
V E
Sbjct: 292 QVAE 295
>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 = 110 bits (278), Expect = 2e-29
Identities = 66/256 (25%), Positives = 98/256 (38%), Gaps = 69/256 (26%)
Query: 4 DAELIDSLPKLEIVATCSAGLDKIDLVKCKEKGIQVTNTPDVLTDDVADAAIGLTLAVLR 63
DA+ +D+ P+L+I+A G D D+ C +GI VT PD+LT+ A+ IGL + + R
Sbjct: 57 DADFLDACPRLKIIACALKGYDNFDVEACTARGIWVTIVPDLLTEPTAELTIGLLIGLGR 116
Query: 64 ------RFVRSED--GEMGYKLTTKISGRSVGIIGLGRIGMAVAKRAEAFGCFISYRSRA 115
RFVRS G T + G++VGI+G+G +G A+A+R FG + Y
Sbjct: 117 HILAGDRFVRSGKFGGWRPKFYGTGLDGKTVGILGMGALGRAIARRLSGFGATLLYYDPH 176
Query: 116 EKPNTKYK---------------------------------------------------- 123
+ +
Sbjct: 177 PLDQAEEQALNLRRVELDELLESSDFLVLALPLTPDTLHLINAEALAKMKPGALLVNPCR 236
Query: 124 GALVDESELVSALLEDRLAAAVLDVFEHEP--------QVPEELFGLE-NVVLLPHAASG 174
G++VDE+ + AL L DVFE E +P+EL V PH S
Sbjct: 237 GSVVDEAAVAEALKSGHLGGYAADVFEMEDWARPDRPRSIPQELLDQHDRTVFTPHIGSA 296
Query: 175 TEETRKATADIVIENL 190
+E R N+
Sbjct: 297 VDEVRLEIELEAALNI 312
>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 = 108 bits (273), Expect = 8e-29
Identities = 62/261 (23%), Positives = 103/261 (39%), Gaps = 60/261 (22%)
Query: 2 GADAELIDSLPKLEIVATCSAGLDKIDLVKCKEKGIQVTNTPDVLTDDVADAAIGLTLAV 61
EL+ + P+L + + SAG+D + + E+ + +TN + +A+ +G LA
Sbjct: 48 PPLPELLPAAPRLRWIQSTSAGVDALLFPELLERDVVLTNARGIFGPPIAEYVLGYMLAF 107
Query: 62 LRRFVRSEDGEM-----GYKLTTKISGRSVGIIGLGRIGMAVAKRAEAFGCFIS-YRSRA 115
R+ R + +++G++V I+GLG IG +A+RA+AFG + R
Sbjct: 108 ARKLPRYARNQAERRWQRRGPVRELAGKTVLIVGLGDIGREIARRAKAFGMRVIGVRRSG 167
Query: 116 EK----------------------------PNTKYKGALVDESEL--------------- 132
P T L +
Sbjct: 168 RPAPPVVDEVYTPDELDELLPEADYVVNALPLTPETRGLFNAERFAAMKPGAVLINVGRG 227
Query: 133 --------VSALLEDRLAAAVLDVFEHEPQVPEE--LFGLENVVLLPHAASGTEETRKAT 182
+ AL R+A A LDVFE EP +P + L+ L NV++ PH + + +
Sbjct: 228 SVVDEDALIEALESGRIAGAALDVFEEEP-LPADSPLWDLPNVIITPHISGDSPSYPERV 286
Query: 183 ADIVIENLEACFLNKPLLTPV 203
+I +ENL +PLL V
Sbjct: 287 VEIFLENLRRYLAGEPLLNVV 307
>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 = 105 bits (265), Expect = 1e-27
Identities = 79/271 (29%), Positives = 115/271 (42%), Gaps = 86/271 (31%)
Query: 4 DAELIDSLPKLEIVATCSAGLDKIDLVKCKEKGIQVTNTPDVLTDDVADAAIGLTLAVLR 63
DAE+++ LP+L+++AT S G D IDL C+E+GI V N PD VA+ A L LA+ R
Sbjct: 54 DAEVLEKLPRLKLIATRSTGFDHIDLEACRERGIAVCNVPDYGEATVAEHAFALLLALSR 113
Query: 64 RFVRSED----------GEMGYKLTTKISGRSVGIIGLGRIGMAVAKRAEAFG----CF- 108
+ + + G G++L +G+++G++G GRIG VA+ A FG +
Sbjct: 114 KLREAIERTRRGDFSQAGLRGFEL----AGKTLGVVGTGRIGRRVARIARGFGMKVLAYD 169
Query: 109 ------------ISYRSRAE--------------KPNTKY-----------KGALV---- 127
Y S E P T + GA++
Sbjct: 170 VVPDEELAERLGFRYVSLEELLQESDIISLHVPYTPQTHHLINRENFALMKPGAVLINTA 229
Query: 128 -----DESELVSALLEDRLAAAVLDVFEHEPQVPEE---------------------LFG 161
D LV AL E +LA A LDV E E + EE L
Sbjct: 230 RGAVVDTEALVRALKEGKLAGAGLDVLEQEEVLREEAELFREDVSPEDLKKLLADHALLR 289
Query: 162 LENVVLLPHAASGTEETRKATADIVIENLEA 192
NV++ PH A T+E + D +EN++A
Sbjct: 290 KPNVIITPHVAYNTKEALERILDTTVENIKA 320
>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 = 104 bits (261), Expect = 5e-27
Identities = 81/251 (32%), Positives = 109/251 (43%), Gaps = 64/251 (25%)
Query: 4 DAELIDSLPKLEIVATCSAGLDKIDLVKCKEKGIQVTNTPDVLTDDVADAAIGLTLAVLR 63
A L++ LP L+++ T IDL KE+GI V T A+ L LA+ R
Sbjct: 60 PAALLERLPNLKLLVTTGMRNASIDLAAAKERGIVVCGTGGG-PTATAELTWALILALAR 118
Query: 64 RFVRSEDGEM--GYKLTT---KISGRSVGIIGLGRIGMAVAK------------------ 100
ED + G TT ++G+++GI+GLGRIG VA+
Sbjct: 119 NLPE-EDAALRAGGWQTTLGTGLAGKTLGIVGLGRIGARVARIGQAFGMRVIAWSSNLTA 177
Query: 101 -RAEAFG--------CFI------------SYRSR----AE-----KP-----NTKYKGA 125
RA A G S R+R AE KP NT +G
Sbjct: 178 ERAAAAGVEAAVSKEELFATSDVVSLHLVLSDRTRGLVGAEDLALMKPTALLVNTS-RGP 236
Query: 126 LVDESELVSALLEDRLAAAVLDVFEHEPQVPEE--LFGLENVVLLPHAASGTEETRKATA 183
LVDE L++AL R+A A LDVF+ EP +P + L GL NV+L PH TEE +
Sbjct: 237 LVDEGALLAALRAGRIAGAALDVFDVEP-LPADHPLRGLPNVLLTPHIGYVTEEAYEGFY 295
Query: 184 DIVIENLEACF 194
+EN+ A
Sbjct: 296 GQAVENIAAWL 306
>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 = 99.1 bits (248), Expect = 2e-26
Identities = 57/175 (32%), Positives = 76/175 (43%), Gaps = 57/175 (32%)
Query: 55 IGLTLAVLRRF------VRSEDGEMGYKLTTKISGRSVGIIGLGRIGMAVAKRAEAFGCF 108
+ L LA+ RR VR+ L ++SG++VGIIGLGRIG AVA+R +AFG
Sbjct: 1 LALLLALARRIPEADRQVRAGRWRPDALLGRELSGKTVGIIGLGRIGRAVARRLKAFGMK 60
Query: 109 ISY--RSRAEK----------------------------PNTKY---------------- 122
+ R + P T++
Sbjct: 61 VIAYDRYPKAEAEALGARYVSLDELLAESDVVSLHLPLTPETRHLINAERLALMKPGAIL 120
Query: 123 ----KGALVDESELVSALLEDRLAAAVLDVFEHEPQVPE-ELFGLENVVLLPHAA 172
+G LVDE L++AL R+A A LDVFE EP P+ L L NV+L PH A
Sbjct: 121 INTARGGLVDEDALIAALKSGRIAGAALDVFEPEPLPPDHPLLELPNVILTPHIA 175
>gnl|CDD|181414 PRK08410, PRK08410, 2-hydroxyacid dehydrogenase; Provisional.
Length = 311
Score = 99.3 bits (248), Expect = 4e-25
Identities = 72/263 (27%), Positives = 106/263 (40%), Gaps = 76/263 (28%)
Query: 4 DAELIDSLPKLEIVATCSAGLDKIDLVKCKEKGIQVTNTPDVLTDDVADAAIGLTLAVLR 63
D E++ LP L+++ + G + +D+ K+KGI V N T+ VA + L++L
Sbjct: 54 DKEVLSQLPNLKLICITATGTNNVDIEYAKKKGIAVKNVAGYSTESVAQHTFAMLLSLLG 113
Query: 64 R------FVRSE-----------DGEMGYKLTTKISGRSVGIIGLGRIGMAVAKRAEAFG 106
R +V+S +G +I G+ GIIGLG IG VAK A+AFG
Sbjct: 114 RINYYDRYVKSGEYSESPIFTHISRPLG-----EIKGKKWGIIGLGTIGKRVAKIAQAFG 168
Query: 107 CFISYRSRAEK----------------------------PNTK----YK----------- 123
+ Y S + K TK YK
Sbjct: 169 AKVVYYSTSGKNKNEEYERVSLEELLKTSDIISIHAPLNEKTKNLIAYKELKLLKDGAIL 228
Query: 124 -----GALVDESELVSALLEDRLAAAVLDVFEHEPQVPEELF----GLENVVLLPHAASG 174
G +V+E +L AL E + A LDV E EP E +++ PH A
Sbjct: 229 INVGRGGIVNEKDLAKALDEKDIYAG-LDVLEKEPMEKNHPLLSIKNKEKLLITPHIAWA 287
Query: 175 TEETRKATADIVIENLEACFLNK 197
++E RK + V EN++ FL
Sbjct: 288 SKEARKTLIEKVKENIKD-FLEG 309
>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 = 98.9 bits (247), Expect = 5e-25
Identities = 69/256 (26%), Positives = 100/256 (39%), Gaps = 61/256 (23%)
Query: 4 DAELIDSLPKLEIVATCSAGLDKIDLVKCKEKGIQVTNTPD-VLTDDVADAAIGLTLAVL 62
D E + L+++A G D +DL E G+ VT P V D VA+ A+ L L VL
Sbjct: 60 DKEFFEYNDGLKLIARHGIGYDNVDLKAATEHGVIVTRVPGAVERDAVAEHAVALILTVL 119
Query: 63 RRFVRSEDGEMGYKLTTK-------ISGRSVGIIGLGRIGMAVAKRA-EAFGCFI----S 110
R+ ++ + K T + +SG++VGIIG G IG VA+ E F +
Sbjct: 120 RKINQASEAVKEGKWTERANFVGHELSGKTVGIIGYGNIGSRVAEILKEGFNAKVLAYDP 179
Query: 111 YRSRAEKPNTKYK----------------------------------------------- 123
Y S K
Sbjct: 180 YVSEEVIKKKGAKPVSLEELLAESDIISLHAPLTEETYHMINEKAFSKMKKGVILVNTAR 239
Query: 124 GALVDESELVSALLEDRLAAAVLDVFEHEPQVPEE-LFGLENVVLLPHAASGTEETRKAT 182
G L+DE L+ AL ++A A LDV E EP + L ENVV+ PH + T E+
Sbjct: 240 GELIDEEALIEALKSGKIAGAGLDVLEEEPIKADHPLLHYENVVITPHIGAYTYESLYGM 299
Query: 183 ADIVIENLEACFLNKP 198
+ V++++E K
Sbjct: 300 GEKVVDDIEDFLAGKE 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 = 95.8 bits (239), Expect = 6e-24
Identities = 66/264 (25%), Positives = 104/264 (39%), Gaps = 71/264 (26%)
Query: 5 AELIDSLPKLEIVATCSAGLDKIDLVKCKEKGIQVTNTPDVLTDDVADAAIGLTLAVLRR 64
E + +L +L+++ SAG+D + L + E G+ V N + VA+ A+ L LA+ +R
Sbjct: 52 EEALAALKRLKLIQVPSAGVDHLPLERLPE-GVVVANNHG-NSPAVAEHALALILALAKR 109
Query: 65 FVRSEDGEMGY----------KLTTKISGRSVGIIGLGRIGMAVAKRAEAFGC-FISYRS 113
V D ++ + ++ G++VGI+G G IG +A+ +AFG I
Sbjct: 110 IVEY-DNDLRRGIWHGRAGEEPESKELRGKTVGILGYGHIGREIARLLKAFGMRVIGVSR 168
Query: 114 RAEK---------------------------PNTKY-----------------------K 123
++ P TK +
Sbjct: 169 SPKEDEGADFVGTLSDLDEALEQADVVVVALPLTKQTRGLIGAAELAAMKPGAILVNVGR 228
Query: 124 GALVDESELVSALLEDRLAAAVLDVFEHEP-------QVPEELFGLENVVLLPHAASGTE 176
G +VDE L AL E +A A +DV+ P L NV++ PH A TE
Sbjct: 229 GPVVDEEALYEALKERPIAGAAIDVWWRYPSRGDPVAPSRYPFHELPNVIMSPHNAGWTE 288
Query: 177 ETRKATADIVIENLEACFLNKPLL 200
ET + D EN+ +PLL
Sbjct: 289 ETFRRRIDEAAENIRRYLRGEPLL 312
>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 = 95.1 bits (237), Expect = 1e-23
Identities = 69/257 (26%), Positives = 109/257 (42%), Gaps = 72/257 (28%)
Query: 4 DAELIDSLPKLEIVATCSAGLDKIDLVKCKEKGIQVTNTPDVLTDDVADAAIGLTLAVLR 63
D E I+ L+ +A AGL+ IDL KEKGI++ N P+ D V + A+G+ LA+
Sbjct: 53 DKEFIEKATNLKFIARAGAGLENIDLEYAKEKGIELFNAPEGNRDAVGEHALGMLLALFN 112
Query: 64 RFVRSE----------DGEMGYKLTTKISGRSVGIIGLGRIGMAVAKRAEAFGCFI---- 109
+ R++ +G G +L G++VGIIG G +G A AKR FGC +
Sbjct: 113 KLNRADQEVRNGIWDREGNRGVEL----MGKTVGIIGYGNMGKAFAKRLSGFGCKVIAYD 168
Query: 110 SYRSRAEK---------------------PNTKYKGALVDESE----------------- 131
Y++ + P T +V++
Sbjct: 169 KYKNFGDAYAEQVSLETLFKEADILSLHIPLTPETRGMVNKEFISSFKKPFYFINTARGK 228
Query: 132 ------LVSALLEDRLAAAVLDVFEHE----------PQVPEELFGLENVVLLPHAASGT 175
LV AL ++ A LDV E+E P+ E L V+L PH A T
Sbjct: 229 VVVTKDLVKALKSGKILGACLDVLEYEKASFESIFNQPEAFEYLIKSPKVILTPHIAGWT 288
Query: 176 EETRKATADIVIENLEA 192
E+ + A+++++ ++A
Sbjct: 289 FESYEKIAEVLVDKIKA 305
>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 = 92.5 bits (231), Expect = 1e-22
Identities = 71/277 (25%), Positives = 105/277 (37%), Gaps = 88/277 (31%)
Query: 3 ADAELIDSLPKLEI--VATCSAGLDKIDLVKCKEKGIQVTNTPDVLTDDVADAAIGLTLA 60
DA +++ L +L + +A AG + +DL KE GI V P VA+ A+ L LA
Sbjct: 56 LDAPVLEKLAELGVKLIALRCAGFNNVDLKAAKELGITVVRVPAYSPYAVAEHAVALLLA 115
Query: 61 VLRRFVR----------SEDGEMGYKLTTKISGRSVGIIGLGRIGMAVAKRAEAFGC--- 107
+ R+ R S DG +G+ L G++VG+IG G+IG A A+ + FGC
Sbjct: 116 LNRKIHRAYNRVREGNFSLDGLLGFDL----HGKTVGVIGTGKIGQAFARILKGFGCRVL 171
Query: 108 -------------FISYRSRAE--------------KPNTKY------------------ 122
+ Y E P T +
Sbjct: 172 AYDPYPNPELAKLGVEYVDLDELLAESDIISLHCPLTPETHHLINAETIAKMKDGVMLIN 231
Query: 123 --KGALVDESELVSALLEDRLAAAVLDVFEHEPQVPEELF------------------GL 162
+G L+D L+ AL ++ LDV+E E LF
Sbjct: 232 TSRGGLIDTKALIEALKSGKIGGLGLDVYEEE----AGLFFEDHSDEIIQDDVLARLLSF 287
Query: 163 ENVVLLPHAASGTEETRKATADIVIENLEACFLNKPL 199
NV++ H A T+E A+ +ENL+ KPL
Sbjct: 288 PNVLITGHQAFFTKEALTNIAETTLENLDDFEAGKPL 324
>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 = 90.7 bits (226), Expect = 4e-22
Identities = 65/260 (25%), Positives = 99/260 (38%), Gaps = 76/260 (29%)
Query: 3 ADAELIDSLPKLEIVATCSAGLDKIDLVKCKEKGIQVTNTPDVLTDDVADAAIGLTLAVL 62
+D P L+ +A AG++ ID+ ++GI V NTP + VA+ I + LA+
Sbjct: 40 DKLHDMDFAPSLKAIARAGAGVNNIDVDAASKRGIVVFNTPGANANAVAELVIAMMLALS 99
Query: 63 RRFVR-------------SEDGEMGYK--LTTKISGRSVGIIGLGRIGMAVAKRAEAFGC 107
R ++ S+ E G K + T++ G+++G+IGLG IG VA A A G
Sbjct: 100 RNIIQAIKWVTNGDGDDISKGVEKGKKQFVGTELRGKTLGVIGLGNIGRLVANAALALGM 159
Query: 108 -------FISYRSRAEK----------------------------PNTKY---------- 122
++S A K T+
Sbjct: 160 KVIGYDPYLS-VEAAWKLSVEVQRVTSLEELLATADYITLHVPLTDETRGLINAELLAKM 218
Query: 123 ----------KGALVDESELVSALLEDRLAAAVLDVFEHEPQVPEELFGLENVVLLPHAA 172
+G +VDE L+ AL E +L V D E P L L NV+ PH
Sbjct: 219 KPGAILLNFARGEIVDEEALLEALDEGKLGGYVTDFPE-----PALLGHLPNVIATPHLG 273
Query: 173 SGTEETRKATADIVIENLEA 192
+ TEE + A + +
Sbjct: 274 ASTEEAEENCAVMAARQIMD 293
>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 = 84.6 bits (210), Expect = 1e-19
Identities = 71/266 (26%), Positives = 103/266 (38%), Gaps = 83/266 (31%)
Query: 4 DAELIDSLPKLEI--VATCSAGLDKIDLVKCKEKGIQVTNTPDVLTDDVADAAIGLTLAV 61
AEL++ L + + ++T S G D IDL KE GI+V+N + VAD + L L
Sbjct: 57 SAELLEKLKEAGVKYISTRSIGYDHIDLDAAKELGIKVSNVT-YSPNSVADYTVMLMLMA 115
Query: 62 LRRF----VRSE------DGEMGYKLTTKISGRSVGIIGLGRIGMAVAKRAEAFGCFI-- 109
LR++ R+E G G +L +VG+IG GRIG AV K FGC I
Sbjct: 116 LRKYKQIMKRAEVNDYSLGGLQGRELRNL----TVGVIGTGRIGQAVIKNLSGFGCKILA 171
Query: 110 --SYRSRAEKPNTKY--------------------------------------------- 122
Y + K +Y
Sbjct: 172 YDPYPNEEVKKYAEYVDLDTLYKESDIITLHTPLTEETYHLINKESIAKMKDGVIIINTA 231
Query: 123 KGALVDESELVSALLEDRLAAAVLDVFEHEPQV------------PE--ELFGLENVVLL 168
+G L+D L+ L ++ A LDV E E + E L NV+L
Sbjct: 232 RGELIDTEALIEGLESGKIGGAALDVIEGEDGIYYNDRKGDILSNRELAILRSFPNVILT 291
Query: 169 PHAASGTEETRKATADIVIENLEACF 194
PH A T++ A +D+V ++E+
Sbjct: 292 PHMAFYTDQ---AVSDMVENSIESLV 314
>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 = 83.0 bits (206), Expect = 3e-19
Identities = 70/245 (28%), Positives = 99/245 (40%), Gaps = 63/245 (25%)
Query: 4 DAELIDSLPKLEIVATCSAGLDKIDLVKCKEKGIQVTNTPDVLTDDVADAAIGLTLAVLR 63
E++++ PKL + G +++DL ++GI V N P T VA+ IG + + R
Sbjct: 55 TEEVLEAAPKLLAIGCFCIGTNQVDLDAAAKRGIPVFNAPFSNTRSVAELVIGEIIMLAR 114
Query: 64 R-FVRSEDGEMG--YKLTTK---ISGRSVGIIGLGRIGMAVAKRAEAFGCFISYRSRAEK 117
R R+ G K T + G+++GIIG G IG ++ AEA G + + AEK
Sbjct: 115 RLPDRNAAAHRGIWNKSATGSHEVRGKTLGIIGYGHIGSQLSVLAEALGMRVIFYDIAEK 174
Query: 118 -----------------------------PNTK--------------------YKGALVD 128
P+TK +G +VD
Sbjct: 175 LPLGNARQVSSLEELLAEADFVTLHVPATPSTKNMIGAEEIAQMKKGAILINASRGTVVD 234
Query: 129 ESELVSALLEDRLAAAVLDVFEHEPQVPEELF-----GLENVVLLPHAASGTEETRKATA 183
L AL LA A +DVF EP E F GL NV+L PH TEE A
Sbjct: 235 IDALAEALRSGHLAGAAVDVFPEEPASNGEPFSSPLQGLPNVILTPHIGGSTEE---AQE 291
Query: 184 DIVIE 188
+I +E
Sbjct: 292 NIGLE 296
>gnl|CDD|180588 PRK06487, PRK06487, glycerate dehydrogenase; Provisional.
Length = 317
Score = 80.1 bits (198), Expect = 5e-18
Identities = 68/258 (26%), Positives = 103/258 (39%), Gaps = 63/258 (24%)
Query: 4 DAELIDSLPKLEIVATCSAGLDKIDLVKCKEKGIQVTNTPDVLTDDVADAAIGLTLAVLR 63
DA + + P+L+++ + G + +DL +E+GI V N T VA + L LA+
Sbjct: 57 DAAALAAAPQLKLILVAATGTNNVDLAAARERGITVCNCQGYGTPSVAQHTLALLLALAT 116
Query: 64 RFVRSE----DGEMGYKL--------TTKISGRSVGIIGLGRIGMAVAKRAEAFG----- 106
R + G ++ G+++G++G G +G AVA+ AEAFG
Sbjct: 117 RLPDYQQAVAAGRWQQSSQFCLLDFPIVELEGKTLGLLGHGELGGAVARLAEAFGMRVLI 176
Query: 107 ----------------------------CFISYRSR---------AEKP-----NTKYKG 124
C ++ +R KP NT +G
Sbjct: 177 GQLPGRPARPDRLPLDELLPQVDALTLHCPLTEHTRHLIGARELALMKPGALLINTA-RG 235
Query: 125 ALVDESELVSALLEDRLAAAVLDVFEHEPQV---PEELFGLENVVLLPHAASGTEETRKA 181
LVDE L AL L A DV EP V P + +++ PH+A G+ E R+
Sbjct: 236 GLVDEQALADALRSGHLGGAATDVLSVEPPVNGNPLLAPDIPRLIVTPHSAWGSREARQR 295
Query: 182 TADIVIENLEACFLNKPL 199
+ EN A F KPL
Sbjct: 296 IVGQLAENARAFFAGKPL 313
>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 = 77.9 bits (193), Expect = 2e-17
Identities = 63/267 (23%), Positives = 98/267 (36%), Gaps = 86/267 (32%)
Query: 4 DAELIDSLPKLEIVATCSAGLDKIDLVKCKEKGIQVTNTPDV---------LTDDVADAA 54
L+ LP L+ + + AG+D + + PDV L +A+
Sbjct: 49 PPGLLARLPNLKAIFSLGAGVDHLLADP---------DLPDVPIVRLVDPGLAQGMAEYV 99
Query: 55 IGLTLAVLRRFVR----SEDGEMGYKLTTKISGRSVGIIGLGRIGMAVAKRAEAFGCFIS 110
+ L + R R G + R VG++GLG +G AVA+R A G
Sbjct: 100 LAAVLRLHRDMDRYAAQQRRGVWKPLPQRPAAERRVGVLGLGELGAAVARRLAALG---- 155
Query: 111 YR----SRAEK-------------------------------PNTKY-----------KG 124
+ SR+ K P T+ +G
Sbjct: 156 FPVSGWSRSPKDIEGVTCFHGEEGLDAFLAQTDILVCLLPLTPETRGILNAELLARLPRG 215
Query: 125 A---------LVDESELVSALLEDRLAAAVLDVFEHEPQVPEE--LFGLENVVLLPHAAS 173
A + E++L++AL L+ AVLDVFE EP +P + L+ V + PH A+
Sbjct: 216 AALINVGRGPHLVEADLLAALDSGHLSGAVLDVFEQEP-LPADHPLWRHPRVTVTPHIAA 274
Query: 174 GTEETRKATADIVIENLEACFLNKPLL 200
T+ + A V EN+ +PL
Sbjct: 275 ITD--PDSAAAQVAENIRRLEAGEPLP 299
>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 = 74.6 bits (184), Expect = 3e-16
Identities = 64/257 (24%), Positives = 95/257 (36%), Gaps = 60/257 (23%)
Query: 6 ELIDSLPKLEIVATCSAGLDK-IDLVKCKEKGIQVTNTPDVLTDDVADAAIGLTLAVLRR 64
E + + P + V AG++ ++ + G + TN + VA+ A+ L LA LR+
Sbjct: 42 ERLPASPGVRWVQLPFAGVEAFVEAGVITDPGRRWTNAAGAYAETVAEHALALLLAGLRQ 101
Query: 65 FVR-----SEDGEMGYKLTTKISGRSVGIIGLGRIGMAVAKRAEAFGC-FISYRSRAEK- 117
+ D L T + G +V I+G G IG A+ FG I+
Sbjct: 102 LPARARATTWDPAEEDDLVTLLRGSTVAIVGAGGIGRALIPLLAPFGAKVIAVNRSGRPV 161
Query: 118 --------------------------PNTKYKGALVDESE-------------------- 131
P T LVD +
Sbjct: 162 EGADETVPADRLDEVWPDADHVVLAAPLTPETRHLVDAAALAAMKPHAWLVNVARGPLVD 221
Query: 132 ---LVSALLEDRLAAAVLDVFEHEPQVPEE--LFGLENVVLLPHAASGTEETRKATADIV 186
LV AL +A A LDV + EP +P+ L+ L N ++ PH A+ E R A+ V
Sbjct: 222 TDALVDALRSGEIAGAALDVTDPEP-LPDGHPLWSLPNALITPHVANTPEVIRPLLAERV 280
Query: 187 IENLEACFLNKPLLTPV 203
EN+ A +PLL V
Sbjct: 281 AENVRAFAAGEPLLGVV 297
>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 = 71.8 bits (177), Expect = 5e-15
Identities = 70/267 (26%), Positives = 102/267 (38%), Gaps = 84/267 (31%)
Query: 4 DAELIDSLPKLEI--VATCSAGLDKIDLVKCKEKGIQVTNTPDVLTDDVADAAIGLTLAV 61
D E+ + L + I +A SAG+D IDL KE G+++TN P +A+ A+ L +
Sbjct: 57 DEEVYEKLAEYGIKQIALRSAGVDMIDLDLAKENGLKITNVPAYSPRAIAEFAVTQALNL 116
Query: 62 LRRF------VRSEDGEMGYKLTTKISGR-----SVGIIGLGRIGMAVAKRAEAFGCF-- 108
LR V D ++ + GR +VGIIG GRIG A AK + FG
Sbjct: 117 LRNTPEIDRRVAKGD----FRWAPGLIGREIRDLTVGIIGTGRIGSAAAKIFKGFGAKVI 172
Query: 109 ---ISYRSRAEKPNTKY------------------------------------KGA---- 125
EK Y GA
Sbjct: 173 AYDPYPNPELEKFLLYYDSLEDLLKQADIISLHVPLTKENHHLINAEAFAKMKDGAILVN 232
Query: 126 -----LVDESELVSALLEDRLAAAVLDVFEHE--------------PQVPEELFGLENVV 166
LVD L+ AL ++A A LD +E+E +V +EL + NV+
Sbjct: 233 AARGGLVDTKALIDALDSGKIAGAALDTYENETGYFNKDWSGKEIEDEVLKELIAMPNVL 292
Query: 167 LLPHAASGTEETRKATADIVIENLEAC 193
+ PH A T+ A ++V +L+
Sbjct: 293 ITPHIAFYTDT---AVKNMVEISLDDA 316
>gnl|CDD|181499 PRK08605, PRK08605, D-lactate dehydrogenase; Validated.
Length = 332
Score = 70.2 bits (172), Expect = 2e-14
Identities = 61/249 (24%), Positives = 101/249 (40%), Gaps = 75/249 (30%)
Query: 17 VATCSAGLDKIDLVKCKEKGIQVTNTPDVLTDDVADAAIGLTLAVLRRF--VRSEDGEMG 74
+A SAG D DL + + ++N P + +A+ + + ++R F ++++ E
Sbjct: 73 IAQRSAGFDTYDLELATKYNLIISNVPSYSPESIAEFTVTQAINLVRHFNQIQTKVREHD 132
Query: 75 YKLTTKISGRS-----VGIIGLGRIGMAVAK-RAEAFGC---------------FISYRS 113
++ I RS V +IG GRIG+AVAK A+ +G ++ Y+
Sbjct: 133 FRWEPPILSRSIKDLKVAVIGTGRIGLAVAKIFAKGYGSDVVAYDPFPNAKAATYVDYKD 192
Query: 114 RAEK------------PNTKY-----------------------KGALVDESELVSALLE 138
E+ P TKY +G+LVD L+ AL
Sbjct: 193 TIEEAVEGADIVTLHMPATKYNHYLFNADLFKHFKKGAVFVNCARGSLVDTKALLDALDN 252
Query: 139 DRLAAAVLDVFEHE-PQVP-------------EELFGLENVVLLPHAASGTEETRKATAD 184
+ A LD +E E P P E L E+V+L PH A T+ A +
Sbjct: 253 GLIKGAALDTYEFERPLFPSDQRGQTINDPLLESLINREDVILTPHIAFYTDA---AVKN 309
Query: 185 IVIENLEAC 193
++++ L+A
Sbjct: 310 LIVDALDAT 318
>gnl|CDD|177941 PLN02306, PLN02306, hydroxypyruvate reductase.
Length = 386
Score = 70.3 bits (172), Expect = 2e-14
Identities = 64/249 (25%), Positives = 102/249 (40%), Gaps = 81/249 (32%)
Query: 21 SAGLDKIDLVKCKEKGIQVTNTPDVLTDDVADAAIGLTLAVLRRFVRSEDGEMG--YK-- 76
+ G + +D+ + GI V NTP VLT+ A+ A L+LA RR V +++ Y+
Sbjct: 94 AVGYNNVDVEAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYEGW 153
Query: 77 -----LTTKISGRSVGIIGLGRIG-----MAV--------------AKRAE----AFGCF 108
+ + G++VG+IG GRIG M V + R E A+G F
Sbjct: 154 LPHLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQSTRLEKFVTAYGQF 213
Query: 109 ISYRSRAEKP--------------------------NTKY-------------------- 122
+ ++ E+P T Y
Sbjct: 214 L--KANGEQPVTWKRASSMEEVLREADVISLHPVLDKTTYHLINKERLALMKKEAVLVNA 271
Query: 123 -KGALVDESELVSALLEDRLAAAVLDVFEHEPQVPEELFGLENVVLLPHAASGTEETRKA 181
+G ++DE LV L + + LDVFE EP + L ++N V++PH AS ++ TR+
Sbjct: 272 SRGPVIDEVALVEHLKANPMFRVGLDVFEDEPYMKPGLADMKNAVVVPHIASASKWTREG 331
Query: 182 TADIVIENL 190
A + N+
Sbjct: 332 MATLAALNV 340
>gnl|CDD|235890 PRK06932, PRK06932, glycerate dehydrogenase; Provisional.
Length = 314
Score = 69.8 bits (171), Expect = 2e-14
Identities = 64/255 (25%), Positives = 100/255 (39%), Gaps = 70/255 (27%)
Query: 4 DAELIDSLPKLEIVATCSAGLDKIDLVKCKEKGIQVTNTPDVLTDDVADAAIGLTLAV-- 61
E + LPKL+++A + G + +DLV KE GI V N + V + +G+ A+
Sbjct: 56 TRETLAQLPKLKLIAITATGTNNVDLVAAKELGIAVKNVTGYSSTTVPEHVLGMIFALKH 115
Query: 62 -LRRFVR-------SEDGEMGY--KLTTKISGRSVGIIGLGRIGMAVAKRAEAFGCFISY 111
L + R + + Y T + G ++G+ G G +G V + A+A G + Y
Sbjct: 116 SLMGWYRDQLSDRWATCKQFCYFDYPITDVRGSTLGVFGKGCLGTEVGRLAQALGMKVLY 175
Query: 112 RSR--------------------------------------AE-----KP-----NTKYK 123
AE KP NT +
Sbjct: 176 AEHKGASVCREGYTPFEEVLKQADIVTLHCPLTETTQNLINAETLALMKPTAFLINTG-R 234
Query: 124 GALVDESELVSALLEDRLAAAVLDVFEHEPQVPEE-------LFGLENVVLLPHAASGTE 176
G LVDE L+ AL ++A A LDV EP PE+ L N+++ PH A ++
Sbjct: 235 GPLVDEQALLDALENGKIAGAALDVLVKEP--PEKDNPLIQAAKRLPNLLITPHIAWASD 292
Query: 177 ETRKATADIVIENLE 191
+ V +N+E
Sbjct: 293 SAVTTLVNKVAQNIE 307
>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 = 69.9 bits (172), Expect = 3e-14
Identities = 59/225 (26%), Positives = 92/225 (40%), Gaps = 74/225 (32%)
Query: 4 DAELIDSLPKLEIVATCSAGLDKIDLVKCKEKGIQVTNTPDVLTDDVAD---AAIGLTLA 60
+ L++ K++ V T + G D ID KE+GI N P + VA+ +A+ L LA
Sbjct: 49 NEALLE-GSKVKFVGTATIGTDHIDTDYLKERGIGFANAPGCNANSVAEYVLSAL-LVLA 106
Query: 61 VLRRFVRSEDGEMGYKLTTKISGRSVGIIGLGRIGMAVAKRAEAFGC-FISY---RSRAE 116
+ F + G++VGI+G+G +G +A+R EA G + R+ AE
Sbjct: 107 QRQGF--------------SLKGKTVGIVGVGNVGSRLARRLEALGMNVLLCDPPRAEAE 152
Query: 117 K---------------------PNTK---YK-GALVDESELVS----------------- 134
P T+ + L+DE L +
Sbjct: 153 GDPGFVSLEELLAEADIITLHVPLTRDGEHPTYHLLDEDFLAALKPGQILINASRGAVID 212
Query: 135 --ALLE----DRLAAAVLDVFEHEPQVPEELFGLENVVLL-PHAA 172
ALL + VLDV+E+EP++ EL L+ V + PH A
Sbjct: 213 NQALLALLQRGKDLRVVLDVWENEPEIDLEL--LDKVDIATPHIA 255
>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 = 68.0 bits (167), Expect = 9e-14
Identities = 32/83 (38%), Positives = 48/83 (57%), Gaps = 3/83 (3%)
Query: 124 GALVDESELVSALLEDRLAAAVLDVFEHEPQVPEE--LFGLENVVLLPHAASGTEETRKA 181
G VDE L+ AL ++ A LDVFE EP +P++ L+ L+NV++ PH + +E +
Sbjct: 227 GPSVDEDALIEALKNKQIRGAALDVFEEEP-LPKDSPLWDLDNVLITPHISGVSEHFNER 285
Query: 182 TADIVIENLEACFLNKPLLTPVV 204
DI ENL++ + LL VV
Sbjct: 286 LFDIFYENLKSFLEDGELLKNVV 308
Score = 65.7 bits (161), Expect = 6e-13
Identities = 28/106 (26%), Positives = 55/106 (51%), Gaps = 5/106 (4%)
Query: 7 LIDSLPKLEIVATCSAGLDKIDLVKCKEKGIQVTNTPDVLTDDVADAAIGLTLAVLRRFV 66
+ + L+ + SAG+D + L K+KGI +TN + + +A+ +G L + +
Sbjct: 54 DLAKMKNLKWIQLYSAGVDYLPLEYIKKKGILLTNNSGIHSIPIAEWIVGYILEIYKGLK 113
Query: 67 RS--EDGEMGYKLTTK---ISGRSVGIIGLGRIGMAVAKRAEAFGC 107
++ E +K+ + + G+++ +G G IG +AKR +AFG
Sbjct: 114 KAYKNQKEKKWKMDSSLLELYGKTILFLGTGSIGQEIAKRLKAFGM 159
>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 = 67.6 bits (166), Expect = 1e-13
Identities = 63/230 (27%), Positives = 93/230 (40%), Gaps = 60/230 (26%)
Query: 1 VGADAELIDSLPKLEIVATCSAGLDKI-DLVKCKEKGIQVTNTPDVLTDDVADAAIGLTL 59
E + +LP+L +V T SAG D + L+ +G+ + N V A+ A+ L L
Sbjct: 48 APPVLEALRALPRLRVVQTLSAGYDGVLPLLP---EGVTLCNARGVHDASTAELAVALIL 104
Query: 60 AVLR---RFVRSED-GEMGYKLTTKISGRSVGIIGLGRIGMAVAKRAEAFGCFISYRSRA 115
A LR RFVR++ G + T ++ R V I+G G IG A+ +R F ++ +R
Sbjct: 105 ASLRGLPRFVRAQARGRWEPRRTPSLADRRVLIVGYGSIGRAIERRLAPFEVRVTRVART 164
Query: 116 EKPN----------------------------TKY-----------KGAL---------V 127
+P T+ GAL V
Sbjct: 165 ARPGEQVHGIDELPALLPEADVVVLIVPLTDETRGLVDAEFLARMPDGALLVNVARGPVV 224
Query: 128 DESELVSALLEDRLAAAVLDVFEHEPQVPEE--LFGLENVVLLPHAASGT 175
D LV+ L RL AA LDV + EP +P L+ V++ PH T
Sbjct: 225 DTDALVAELASGRLRAA-LDVTDPEP-LPPGHPLWSAPGVLITPHVGGAT 272
>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 = 66.4 bits (163), Expect = 4e-13
Identities = 35/81 (43%), Positives = 46/81 (56%), Gaps = 2/81 (2%)
Query: 124 GALVDESELVSALLEDRLAAAVLDVFEHEPQVPE-ELFGLENVVLLPHAASGTEETRKAT 182
GALVDE+ L++ L RL AA LDV + EP P+ L L NV+L PH A T + R+
Sbjct: 242 GALVDEAALLAELRSGRLRAA-LDVTDPEPLPPDSPLRTLPNVLLTPHIAGSTGDERRRL 300
Query: 183 ADIVIENLEACFLNKPLLTPV 203
D ++ LE +PLL V
Sbjct: 301 GDYALDELERFLAGEPLLHEV 321
Score = 58.7 bits (143), Expect = 2e-10
Identities = 51/167 (30%), Positives = 70/167 (41%), Gaps = 25/167 (14%)
Query: 4 DAELIDSLPKLEIVATCSAGLDKIDLVKCKEKGIQVTNTPDVLTDDVADAAIGLTLAVLR 63
DAEL+ P+L V + + + E+GI VT+ D + VA+ + L LR
Sbjct: 63 DAELLARAPRLRAVVHAAGSVRGLVTDAVWERGILVTSAADANAEPVAEFTLAAILLALR 122
Query: 64 R------FVRSEDGEMGYKL--TTKISGRSVGIIGLGRIGMAVAKRAEAFGCFIS----Y 111
R R+ + GR+VGI+G GRIG AV + FG + Y
Sbjct: 123 RIPRFAAAYRAGRDWGWPTRRGGRGLYGRTVGIVGFGRIGRAVVELLRPFGLRVLVYDPY 182
Query: 112 RSRAEKPNTKYKGALVDESELVSALLEDRLAAAVLD-VFEHEPQVPE 157
AE G ELVS L++ LA + D V H P PE
Sbjct: 183 LPAAE---AAALGV-----ELVS--LDELLARS--DVVSLHAPLTPE 217
>gnl|CDD|215501 PLN02928, PLN02928, oxidoreductase family protein.
Length = 347
Score = 64.7 bits (158), Expect = 2e-12
Identities = 37/139 (26%), Positives = 65/139 (46%), Gaps = 9/139 (6%)
Query: 4 DAELIDSLPKLEIVATCSAGLDKIDLVKCKEKGIQVTNTPDVLT---DDVADAAIGLTLA 60
DA++I +++++ GL+ +D+ + GI+V P T A+ AI L L
Sbjct: 73 DADIIARASQMKLIMQFGVGLEGVDVDAATKHGIKVARIPSEGTGNAASCAEMAIYLMLG 132
Query: 61 VLRR----FVRSEDGEMGYKLTTKISGRSVGIIGLGRIGMAVAKRAEAFGCFISY--RSR 114
+LR+ + + +G + + G++V I+G G IG+ +AKR FG + RS
Sbjct: 133 LLRKQNEMQISLKARRLGEPIGDTLFGKTVFILGYGAIGIELAKRLRPFGVKLLATRRSW 192
Query: 115 AEKPNTKYKGALVDESELV 133
+P D +LV
Sbjct: 193 TSEPEDGLLIPNGDVDDLV 211
Score = 28.1 bits (63), Expect = 3.2
Identities = 20/67 (29%), Positives = 35/67 (52%), Gaps = 1/67 (1%)
Query: 123 KGALVDESELVSALLEDRLAAAVLDVFEHEPQVPEE-LFGLENVVLLPHAASGTEETRKA 181
+G L+D +++AL L +DV EP P++ + NV++ PH A TE + ++
Sbjct: 263 RGGLLDYDAVLAALESGHLGGLAIDVAWSEPFDPDDPILKHPNVIITPHVAGVTEYSYRS 322
Query: 182 TADIVIE 188
IV +
Sbjct: 323 MGKIVGD 329
>gnl|CDD|236985 PRK11790, PRK11790, D-3-phosphoglycerate dehydrogenase;
Provisional.
Length = 409
Score = 63.7 bits (156), Expect = 4e-12
Identities = 62/244 (25%), Positives = 98/244 (40%), Gaps = 63/244 (25%)
Query: 5 AELIDSLPKLEIVATCSAGLDKIDLVKCKEKGIQVTNTPDVLTDDVADAAIGLTLAVLRR 64
E++ + KL + G +++DL ++GI V N P T VA+ IG + +LR
Sbjct: 67 EEVLAAAEKLVAIGCFCIGTNQVDLDAAAKRGIPVFNAPFSNTRSVAELVIGEIILLLRG 126
Query: 65 -FVRSEDGEMGY--KLTT---KISGRSVGIIGLGRIGMAVAKRAEAFGCFISYRSRAEK- 117
++ G K ++ G+++GI+G G IG ++ AE+ G + + +K
Sbjct: 127 IPEKNAKAHRGGWNKSAAGSFEVRGKTLGIVGYGHIGTQLSVLAESLGMRVYFYDIEDKL 186
Query: 118 ----------------------------PNTKY-----------KGAL---------VDE 129
P+TK GA+ VD
Sbjct: 187 PLGNARQVGSLEELLAQSDVVSLHVPETPSTKNMIGAEELALMKPGAILINASRGTVVDI 246
Query: 130 SELVSALLEDRLAAAVLDVFEHEPQVPEELF-----GLENVVLLPHAASGTEETRKATAD 184
L AL LA A +DVF EP+ + F GL+NV+L PH T+E A +
Sbjct: 247 DALADALKSGHLAGAAIDVFPVEPKSNGDPFESPLRGLDNVILTPHIGGSTQE---AQEN 303
Query: 185 IVIE 188
I +E
Sbjct: 304 IGLE 307
>gnl|CDD|166874 PRK00257, PRK00257, erythronate-4-phosphate dehydrogenase;
Validated.
Length = 381
Score = 62.7 bits (153), Expect = 8e-12
Identities = 52/215 (24%), Positives = 75/215 (34%), Gaps = 71/215 (33%)
Query: 13 KLEIVATCSAGLDKIDLVKCKEKGIQVTNTPDVLTDDVADAAIG--LTLAVLRRFVRSED 70
++ V TC+ G D +DL E GI ++ P V D +G LTLA
Sbjct: 58 RVRFVGTCTIGTDHLDLDYFAEAGITWSSAPGCNARGVVDYVLGSLLTLAEREGV----- 112
Query: 71 GEMGYKLTTKISGRSVGIIGLGRIGMAVAKRAEAF-----------------GCFISYRS 113
++ R+ G++G G +G + + G F+S
Sbjct: 113 ---------DLAERTYGVVGAGHVGGRLVRVLRGLGWKVLVCDPPRQEAEGDGDFVSLER 163
Query: 114 RAEK--------PNTKY---------------------------KGALVDESELVSALLE 138
E+ P TK +GA+VD L ALL
Sbjct: 164 ILEECDVISLHTPLTKEGEHPTRHLLDEAFLASLRPGAWLINASRGAVVDNQALREALLS 223
Query: 139 DRLAAAVLDVFEHEPQVPEELFGLENVVL-LPHAA 172
AVLDV+E EPQ+ EL + + PH A
Sbjct: 224 GEDLDAVLDVWEGEPQIDLEL--ADLCTIATPHIA 256
>gnl|CDD|235800 PRK06436, PRK06436, glycerate dehydrogenase; Provisional.
Length = 303
Score = 58.7 bits (142), Expect = 2e-10
Identities = 59/253 (23%), Positives = 100/253 (39%), Gaps = 60/253 (23%)
Query: 3 ADAELIDSLP----KLEIVATCSAGLDKIDLVKCKEKGIQVTNTPDVLTDDVADAAIGLT 58
A+A LI K +++ + SAG+D ID+ E + +N + VA+ A L
Sbjct: 35 AEAILIKGRYVPGKKTKMIQSLSAGVDHIDVSGIPENVVLCSNA-GAYSISVAEHAFALL 93
Query: 59 LAVLRRFVRS----EDGEMGYKLTTKISGRSVGIIGLGRIGMAVAKRAEAFGCFISYRSR 114
LA + + ++G T + +S+GI+G G IG VA A+AFG I +R
Sbjct: 94 LAWAKNICENNYNMKNGNFKQSPTKLLYNKSLGILGYGGIGRRVALLAKAFGMNIYAYTR 153
Query: 115 AEK-------------------------PNTKY-----------------------KGAL 126
+ P T + +
Sbjct: 154 SYVNDGISSIYMEPEDIMKKSDFVLISLPLTDETRGMINSKMLSLFRKGLAIINVARADV 213
Query: 127 VDESELVSALLEDRLAAAVLDVFEHEPQVPEELFGLENVVLLPHAASG-TEETRKATADI 185
VD++++++ L + DV+ +EP + E +NV+L PH A G + E + +
Sbjct: 214 VDKNDMLNFLRNHNDKYYLSDVWWNEPIITETN--PDNVILSPHVAGGMSGEIMQPAVAL 271
Query: 186 VIENLEACFLNKP 198
EN++ F KP
Sbjct: 272 AFENIKNFFEGKP 284
>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 = 58.1 bits (141), Expect = 3e-10
Identities = 36/145 (24%), Positives = 66/145 (45%), Gaps = 15/145 (10%)
Query: 4 DAELIDSLPKLEIVATCSAGLDK----IDLVKCKEKGIQVTNTPDVLTDDVADAAIGLTL 59
D E++++ P ++ + C + + +D+ +E GI VT D + V + +
Sbjct: 59 DEEVLEACPNIKYIGMCCSLYSEESANVDIAAARENGITVTGIRDYGDEGVVE----YVI 114
Query: 60 AVLRRFVRSEDGEMGYKLTTKISGRSVGIIGLGRIGMAVAKRAEAFGCFISYRSRAEKPN 119
+ L R + G+ + +++G VGIIGLG G +A FG + Y SR KP+
Sbjct: 115 SELIRLLHGFGGKQWKEEPRELTGLKVGIIGLGTTGQMIADALSFFGADVYYYSRTRKPD 174
Query: 120 TKYKG-------ALVDESELVSALL 137
+ KG L+ +++ L
Sbjct: 175 AEAKGIRYLPLNELLKTVDVICTCL 199
>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 = 58.1 bits (141), Expect = 3e-10
Identities = 60/267 (22%), Positives = 89/267 (33%), Gaps = 84/267 (31%)
Query: 3 ADAELIDSLPKLEI--VATCSAGLDKIDLVKCKEKGIQVTNTPDVLTDDVADAAIGLTLA 60
AD E ++ + I V T + G + IDL KE G ++ P + +A+ A L +
Sbjct: 56 ADKENLEIYKEYGIKYVFTRTVGFNHIDLEAAKELGFKMARVPSYSPNAIAELAFTLAMT 115
Query: 61 VLRRFVRSEDGEMGYK------------LTTKISGRSVGIIGLGRIGMAVAKRAEAFGC- 107
+ R + + +I +VGIIG GRIG+ AK + G
Sbjct: 116 LSRHT-----AYTASRTANKNFKVDPFMFSKEIRNSTVGIIGTGRIGLTAAKLFKGLGAK 170
Query: 108 ---FISYRSRAEKPNTKY------------------------------------------ 122
+ Y S A K +
Sbjct: 171 VIGYDIYPSDAAKDVVTFVSLDELLKKSDIISLHVPYIKGKNDKLINKEFISKMKDGAIL 230
Query: 123 ----KGALVDESELVSALLEDRLAAAVLDVFEHEP--------------QVPEELFGL-E 163
+G L DE ++ AL +LA DV +E V E+L L
Sbjct: 231 INTARGELQDEEAILEALESGKLAGFGTDVLNNEKEIFFKDFDGDKIEDPVVEKLLDLYP 290
Query: 164 NVVLLPHAASGTEETRKATADIVIENL 190
V+L PH S T+E + ENL
Sbjct: 291 RVLLTPHIGSYTDEALSNMIETSYENL 317
>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 = 57.3 bits (139), Expect = 6e-10
Identities = 34/128 (26%), Positives = 56/128 (43%), Gaps = 10/128 (7%)
Query: 5 AELIDSLPKLEIVATCSAGLDKIDLVKCKEKGIQVTNTPDVLTDDVADAAIGLTLAVLRR 64
AE I L++ T G D +DL ++GI V VA+ + + L ++R
Sbjct: 76 AERIAKAKNLKLALTAGIGSDHVDLQAANDRGITVAEVTGSNVVSVAEHVVMMILILVRN 135
Query: 65 FVRS-----EDG----EMGYKLTTKISGRSVGIIGLGRIGMAVAKRAEAFGCFISYRSRA 115
+V E G ++ + + G++VG +G GRIG+ V +R + F + Y R
Sbjct: 136 YVPGHEQAIEGGWNVADVVKR-AYDLEGKTVGTVGAGRIGLRVLRRLKPFDVHLLYYDRH 194
Query: 116 EKPNTKYK 123
P K
Sbjct: 195 RLPEEVEK 202
>gnl|CDD|181041 PRK07574, PRK07574, formate dehydrogenase; Provisional.
Length = 385
Score = 57.0 bits (138), Expect = 8e-10
Identities = 37/118 (31%), Positives = 57/118 (48%), Gaps = 8/118 (6%)
Query: 5 AELIDSLPKLEIVATCSAGLDKIDLVKCKEKGIQVTNTPDVLTDDVADAAIGLTLAVLRR 64
AE I P L++ T G D +DL E GI V + VA+ + + LA++R
Sbjct: 106 AERIAKAPNLKLAITAGIGSDHVDLQAASEHGITVAEVTGSNSISVAEHVVMMILALVRN 165
Query: 65 FVRSEDGEM--GYKLTTKIS------GRSVGIIGLGRIGMAVAKRAEAFGCFISYRSR 114
+ S + G+ + +S G +VGI+G GRIG+AV +R + F + Y R
Sbjct: 166 YEPSHRQAVEGGWNIADCVSRSYDLEGMTVGIVGAGRIGLAVLRRLKPFDVKLHYTDR 223
>gnl|CDD|183550 PRK12480, PRK12480, D-lactate dehydrogenase; Provisional.
Length = 330
Score = 56.5 bits (136), Expect = 1e-09
Identities = 55/244 (22%), Positives = 94/244 (38%), Gaps = 75/244 (30%)
Query: 9 DSLPKLE-----IVATCSAGLDKIDLVKCKEKGIQVTNTPDVLTDDVADAAIGLTLAVLR 63
D PKLE +A +AG D DL K+ I ++N P + +A+ ++ + L ++R
Sbjct: 60 DVYPKLESYGIKQIAQRTAGFDMYDLDLAKKHNIVISNVPSYSPETIAEYSVSIALQLVR 119
Query: 64 RFVRSEDGEMGYKLT-------TKISGRSVGIIGLGRIGMAVAKRAEAFGC--------- 107
RF E + T + +V IIG GRIG A AK FG
Sbjct: 120 RFPDIERRVQAHDFTWQAEIMSKPVKNMTVAIIGTGRIGAATAKIYAGFGATITAYDAYP 179
Query: 108 -----FISYRSRAEK------------PNTK-----------------------YKGALV 127
F++Y+ ++ P K +GA++
Sbjct: 180 NKDLDFLTYKDSVKEAIKDADIISLHVPANKESYHLFDKAMFDHVKKGAILVNAARGAVI 239
Query: 128 DESELVSALLEDRLAAAVLDVFEHEP--------------QVPEELFGLENVVLLPHAAS 173
+ +L++A+ + L A +D +E+E + EL E +++ PH A
Sbjct: 240 NTPDLIAAVNDGTLLGAAIDTYENEAAYFTNDWTNKDIDDKTLLELIEHERILVTPHIAF 299
Query: 174 GTEE 177
++E
Sbjct: 300 FSDE 303
>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 = 54.7 bits (132), Expect = 4e-09
Identities = 32/79 (40%), Positives = 42/79 (53%), Gaps = 6/79 (7%)
Query: 123 KGALVDESELVSALLEDRLAAAVLDVFEHEPQVPEE--LFGLENVVLLPHAASGTEETRK 180
+GA VDE LV+AL RL A LDV EP +P L+ N++L PHAA G +
Sbjct: 233 RGATVDEDALVAALESGRLGGAALDVTATEP-LPASSPLWDAPNLILTPHAAGGRPQ--- 288
Query: 181 ATADIVIENLEACFLNKPL 199
+++ ENL A PL
Sbjct: 289 GAEELIAENLRAFLAGGPL 307
>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 = 53.5 bits (129), Expect = 1e-08
Identities = 53/223 (23%), Positives = 84/223 (37%), Gaps = 56/223 (25%)
Query: 36 GIQVTNTPDVLTDDVADAAIGLTLAVLRRFVRS---EDGEMGYKLTTKISGRSVGIIGLG 92
G VT V + +A+ + LA +R + + ++G ++GI+G G
Sbjct: 85 GPVVTCARGVAAEAIAEFVLAAILAAAKRLPEIWVKGAEQWRREPLGSLAGSTLGIVGFG 144
Query: 93 RIGMAVAKRAEAFGCFISYRSRAEKPN---------------------------TKYKGA 125
IG A+A+RA A G + R+ +P+ T
Sbjct: 145 AIGQALARRALALGMRVLALRRSGRPSDVPGVEAAADLAELFARSDHLVLAAPLTPETRH 204
Query: 126 LVDESELVS-------------------ALLE----DRLAAAVLDVFEHEPQVPEE--LF 160
L++ L ALLE R++ A LDV + EP +PE L+
Sbjct: 205 LINADVLAQAKPGLHLINIARGGLVDQEALLEALDSGRISLASLDVTDPEP-LPEGHPLY 263
Query: 161 GLENVVLLPHAASGTEETRKATADIVIENLEACFLNKPLLTPV 203
V L PH ++ + R+ AD +ENL +PL V
Sbjct: 264 THPRVRLSPHTSAIAPDGRRNLADRFLENLARYRAGQPLHDLV 306
>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 = 47.7 bits (114), Expect = 9e-07
Identities = 26/110 (23%), Positives = 43/110 (39%), Gaps = 13/110 (11%)
Query: 9 DSLPKLEIVATCSAGLDKI---DLVKCKEKGIQVTNTPDVLTDDVADAAIGLTLAVLRRF 65
+ +P L +V SAG D L K + + + + +A+ IG L + F
Sbjct: 50 EDVPNLRLVQLFSAGADHWLGHPLYK--DPEVPLCTASGIHGPQIAEWVIGTWLVLSHHF 107
Query: 66 VR--------SEDGEMGYKLTTKISGRSVGIIGLGRIGMAVAKRAEAFGC 107
++ + G+ VGI+G G IG A+ A+A G
Sbjct: 108 LQYIELQKEQTWGRRQEAYSVEDSVGKRVGILGYGSIGRQTARLAQALGM 157
Score = 46.1 bits (110), Expect = 4e-06
Identities = 30/83 (36%), Positives = 46/83 (55%), Gaps = 3/83 (3%)
Query: 123 KGALVDESELVSALLEDRLAAAVLDVFEHEPQVPE--ELFGLENVVLLPHAASGTEETRK 180
+G+LVD LV+AL ++ A LDV + EP +P L+ NV++ PH + T+E
Sbjct: 248 RGSLVDTDALVAALESGQIRGAALDVTDPEP-LPADHPLWSAPNVIITPHVSWQTQEYFD 306
Query: 181 ATADIVIENLEACFLNKPLLTPV 203
D++ ENLE +PL+ V
Sbjct: 307 RALDVLEENLERLRKGEPLINLV 329
>gnl|CDD|178684 PLN03139, PLN03139, formate dehydrogenase; Provisional.
Length = 386
Score = 47.5 bits (113), Expect = 1e-06
Identities = 35/119 (29%), Positives = 53/119 (44%), Gaps = 10/119 (8%)
Query: 5 AELIDSLPKLEIVATCSAGLDKIDLVKCKEKGIQVTNTPDVLTDDVADAAIGLTLAVLRR 64
AE I LE++ T G D IDL G+ V VA+ + L +LR
Sbjct: 113 AERIKKAKNLELLLTAGIGSDHIDLPAAAAAGLTVAEVTGSNVVSVAEDELMRILILLRN 172
Query: 65 FV----RSEDGE-----MGYKLTTKISGRSVGIIGLGRIGMAVAKRAEAFGCFISYRSR 114
F+ + GE + Y+ + G++VG +G GRIG + +R + F C + Y R
Sbjct: 173 FLPGYHQVVSGEWNVAGIAYR-AYDLEGKTVGTVGAGRIGRLLLQRLKPFNCNLLYHDR 230
>gnl|CDD|185366 PRK15469, ghrA, bifunctional glyoxylate/hydroxypyruvate reductase
A; Provisional.
Length = 312
Score = 37.9 bits (88), Expect = 0.002
Identities = 24/62 (38%), Positives = 34/62 (54%), Gaps = 4/62 (6%)
Query: 123 KGALVDESELVSALLEDRLAAAVLDVFEHEPQVPEE-LFGLENVVLLPHAASGTEETRKA 181
+G V E +L++AL ++ A+LDVF EP PE L+ V + PH A+ TR A
Sbjct: 227 RGVHVVEDDLLAALDSGKVKGAMLDVFSREPLPPESPLWQHPRVAITPHVAA---VTRPA 283
Query: 182 TA 183
A
Sbjct: 284 EA 285
>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 = 36.8 bits (85), Expect = 0.004
Identities = 23/111 (20%), Positives = 44/111 (39%), Gaps = 6/111 (5%)
Query: 1 VGADAELIDSLPKLEIVATCSAGLDKIDLVKC-KEKGIQVTNTPDVLTDDVADAAIG--- 56
A+ LI L ++ T + G D DL + G+ V + +IG
Sbjct: 76 TNAEYALIQKLG-DRLLFTYTIGADHRDLTEALARAGLTAIAVEGVELPLLTSNSIGAGE 134
Query: 57 LTLAVLRRFVRSEDGEMGYKLTTKISGRSVGIIGLGRIGMAVAKRAEAFGC 107
L++ + RF+ + ++G++V ++G G +G A+ G
Sbjct: 135 LSVQFIARFLEVQQPGRLGGAPD-VAGKTVVVVGAGVVGKEAAQMLRGLGA 184
>gnl|CDD|185335 PRK15438, PRK15438, erythronate-4-phosphate dehydrogenase PdxB;
Provisional.
Length = 378
Score = 35.7 bits (82), Expect = 0.013
Identities = 36/147 (24%), Positives = 62/147 (42%), Gaps = 27/147 (18%)
Query: 3 ADAELIDSLPK----------LEIVATCSAGLDKIDLVKCKEKGIQVTNTPDVLTDDVAD 52
ADA ++ S+ K ++ V T +AG D +D K+ GI + P V +
Sbjct: 38 ADALMVRSVTKVNESLLAGKPIKFVGTATAGTDHVDEAWLKQAGIGFSAAPGCNAIAVVE 97
Query: 53 AAIGLTLAVLRRFVRSEDGEMGYKLTTKISGRSVGIIGLGRIGMAVAKRAEAFG-----C 107
L + R DG + R+VGI+G+G +G + R EA G C
Sbjct: 98 YVFSSLLMLAER-----DG-------FSLHDRTVGIVGVGNVGRRLQARLEALGIKTLLC 145
Query: 108 FISYRSRAEKPNTKYKGALVDESELVS 134
R ++ + + LV E+++++
Sbjct: 146 DPPRADRGDEGDFRSLDELVQEADILT 172
Score = 30.3 bits (68), Expect = 0.68
Identities = 24/76 (31%), Positives = 38/76 (50%), Gaps = 2/76 (2%)
Query: 123 KGALVDESELVSALLEDRLAAAVLDVFEHEPQVPEELFGLENVVLLPHAASGTEETRKAT 182
+GA+VD + L++ L E + + VLDV+E EP++ EL ++ PH A T E +
Sbjct: 208 RGAVVDNTALLTCLNEGQKLSVVLDVWEGEPELNVELLKKVDIG-TPHIAGYTLEGKARG 266
Query: 183 ADIVIENLEACFLNKP 198
V E F+
Sbjct: 267 TTQVFEAYSK-FIGHE 281
>gnl|CDD|177834 PLN02178, PLN02178, cinnamyl-alcohol dehydrogenase.
Length = 375
Score = 31.9 bits (72), Expect = 0.19
Identities = 21/62 (33%), Positives = 33/62 (53%)
Query: 73 MGYKLTTKISGRSVGIIGLGRIGMAVAKRAEAFGCFISYRSRAEKPNTKYKGALVDESEL 132
M Y TK SG+ +G+ GLG +G K +AFG ++ SR+ + + L +S L
Sbjct: 169 MKYYGMTKESGKRLGVNGLGGLGHIAVKIGKAFGLRVTVISRSSEKEREAIDRLGADSFL 228
Query: 133 VS 134
V+
Sbjct: 229 VT 230
>gnl|CDD|176184 cd05281, TDH, Threonine dehydrogenase. L-threonine dehydrogenase
(TDH) catalyzes the zinc-dependent formation of
2-amino-3-ketobutyrate from L-threonine via NAD(H)-
dependent oxidation. THD is a member of the
zinc-requiring, medium chain NAD(H)-dependent alcohol
dehydrogenase family (MDR). MDRs have a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. NAD(P)(H)-dependent oxidoreductases are
the major enzymes in the interconversion of alcohols and
aldehydes, or ketones. 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. Sorbitol and aldose reductase
are NAD(+) binding proteins of the polyol pathway, which
interconverts glucose and fructose.
Length = 341
Score = 31.4 bits (72), Expect = 0.25
Identities = 16/31 (51%), Positives = 19/31 (61%), Gaps = 3/31 (9%)
Query: 77 LTTKISGRSVGIIGLGRIGM---AVAKRAEA 104
L +SG+SV I G G IG+ AVAK A A
Sbjct: 158 LAGDVSGKSVLITGCGPIGLMAIAVAKAAGA 188
>gnl|CDD|223411 COG0334, GdhA, Glutamate dehydrogenase/leucine dehydrogenase [Amino
acid transport and metabolism].
Length = 411
Score = 30.7 bits (70), Expect = 0.49
Identities = 30/127 (23%), Positives = 46/127 (36%), Gaps = 22/127 (17%)
Query: 72 EMGYKLTTKISGRSVGIIGLGRIGMAVAKRAEAFG-----CFISYRSRAEKPNTKYKGAL 126
E L + G V + G G +G A++ G S KG +
Sbjct: 196 EALKALGDDLEGARVAVQGFGNVGQYAAEKLHELGAKVVAVSDS------------KGGI 243
Query: 127 VDESELVSALLEDR--LAAAVLDVFEHEPQVPEELFGLENVVLLPHAASG--TEET-RKA 181
DE L L + +V + E EEL ++ +L+P A TE+ +
Sbjct: 244 YDEDGLDVEALLELKERRGSVAEYAGAEYITNEELLEVDCDILIPCALENVITEDNADQL 303
Query: 182 TADIVIE 188
A IV+E
Sbjct: 304 KAKIVVE 310
>gnl|CDD|234828 PRK00742, PRK00742, chemotaxis-specific methylesterase;
Provisional.
Length = 354
Score = 30.5 bits (70), Expect = 0.58
Identities = 15/45 (33%), Positives = 24/45 (53%), Gaps = 8/45 (17%)
Query: 6 ELIDSLPKLEIVATCSAGLDKIDLVKCKEKGIQVTNTPDVLTDDV 50
E+++S P +E+V T GL+ + +K PDV+T DV
Sbjct: 21 EILNSDPDIEVVGTAPDGLEAREKIK--------KLNPDVITLDV 57
>gnl|CDD|176261 cd08301, alcohol_DH_plants, Plant alcohol dehydrogenase.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and aldehydes
or ketones. Alcohol dehydrogenase in the liver converts
ethanol and NAD+ to acetaldehyde and NADH, while in
yeast and some other microorganisms ADH catalyzes the
conversion acetaldehyde to ethanol in alcoholic
fermentation. There are 7 vertebrate ADH 7 classes, 6
of which have been identified in humans. Class III,
glutathione-dependent formaldehyde dehydrogenase, has
been identified as the primordial form and exists in
diverse species, including plants, micro-organisms,
vertebrates, and invertebrates. Class I, typified by
liver dehydrogenase, is an evolving form. Gene
duplication and functional specialization of ADH into
ADH classes and subclasses created numerous forms in
vertebrates. For example, the A, B and C (formerly
alpha, beta, gamma) human class I subunits have high
overall structural similarity, but differ in the
substrate binding pocket and therefore in substrate
specificity. In human ADH catalysis, the zinc ion helps
coordinate the alcohol, followed by deprotonation of a
histidine (His-51), the ribose of NAD, a serine
(Ser-48) , then the alcohol, which allows the transfer
of a hydride to NAD+, creating NADH and a zinc-bound
aldehyde or ketone. In yeast and some bacteria, the
active site zinc binds an aldehyde, polarizing it, and
leading to the reverse reaction. ADH is a member of the
medium chain alcohol dehydrogenase family (MDR), which
has a NAD(P)(H)-binding domain in a Rossmann fold of an
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES.
These proteins typically form dimers (typically higher
plants, mammals) or tetramers (yeast, bacteria), and
have 2 tightly bound zinc atoms per subunit, a catalytic
zinc at the active site and a structural zinc in a lobe
of the catalytic domain. NAD(H) binding occurs in the
cleft between the catalytic and coenzyme-binding
domains at the active site, and coenzyme binding induces
a conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
Length = 369
Score = 30.3 bits (69), Expect = 0.58
Identities = 12/25 (48%), Positives = 16/25 (64%)
Query: 83 GRSVGIIGLGRIGMAVAKRAEAFGC 107
G +V I GLG +G+AVA+ A G
Sbjct: 188 GSTVAIFGLGAVGLAVAEGARIRGA 212
>gnl|CDD|176186 cd05283, CAD1, Cinnamyl alcohol dehydrogenases (CAD). Cinnamyl
alcohol dehydrogenases (CAD), members of the medium
chain dehydrogenase/reductase family, reduce
cinnamaldehydes to cinnamyl alcohols in the last step of
monolignal metabolism in plant cells walls. CAD binds 2
zinc ions and is NADPH- dependent. CAD family members
are also found in non-plant species, e.g. in yeast where
they have an aldehyde reductase activity. The medium
chain dehydrogenases/reductase (MDR)/zinc-dependent
alcohol dehydrogenase-like family, which contains the
zinc-dependent alcohol dehydrogenase (ADH-Zn) and
related proteins, is a diverse group of proteins related
to the first identified member, class I mammalian ADH.
MDRs display a broad range of activities and are
distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases
(ADHs) catalyze the NAD(P)(H)-dependent interconversion
of alcohols to aldehydes or ketones. Active site zinc
has a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 337
Score = 30.2 bits (69), Expect = 0.60
Identities = 12/26 (46%), Positives = 19/26 (73%), Gaps = 2/26 (7%)
Query: 83 GRSVGIIGLGRIG-MAVAKRAEAFGC 107
G+ VG++G+G +G +AV K A+A G
Sbjct: 170 GKRVGVVGIGGLGHLAV-KFAKALGA 194
>gnl|CDD|131900 TIGR02853, spore_dpaA, dipicolinic acid synthetase, A subunit.
This predicted Rossman fold-containing protein is the A
subunit of dipicolinic acid synthetase as found in most,
though not all, endospore-forming low-GC Gram-positive
bacteria; it is absent in Clostridium. The B subunit is
represented by TIGR02852. This protein is also known as
SpoVFA [Cellular processes, Sporulation and
germination].
Length = 287
Score = 30.1 bits (68), Expect = 0.72
Identities = 12/37 (32%), Positives = 20/37 (54%)
Query: 81 ISGRSVGIIGLGRIGMAVAKRAEAFGCFISYRSRAEK 117
I G +V ++G GR GM +A+ A G + +R+
Sbjct: 149 IHGSNVMVLGFGRTGMTIARTFSALGARVFVGARSSA 185
>gnl|CDD|181371 PRK08306, PRK08306, dipicolinate synthase subunit A; Reviewed.
Length = 296
Score = 29.8 bits (68), Expect = 0.89
Identities = 11/27 (40%), Positives = 17/27 (62%)
Query: 81 ISGRSVGIIGLGRIGMAVAKRAEAFGC 107
I G +V ++G GR GM +A+ +A G
Sbjct: 150 IHGSNVLVLGFGRTGMTLARTLKALGA 176
>gnl|CDD|178341 PLN02740, PLN02740, Alcohol dehydrogenase-like.
Length = 381
Score = 29.4 bits (66), Expect = 1.1
Identities = 14/24 (58%), Positives = 17/24 (70%)
Query: 83 GRSVGIIGLGRIGMAVAKRAEAFG 106
G SV I GLG +G+AVA+ A A G
Sbjct: 199 GSSVAIFGLGAVGLAVAEGARARG 222
>gnl|CDD|188560 TIGR04045, MSMEG_0567_GNAT, putative N-acetyltransferase,
MSMEG_0567 N-terminal domain family. Members of this
family belong to the GNAT family (pfam00583), in which
numerous characterized examples, though not all, are are
shown to be N-acetyltransferases or to interact with
acetyl-CoA. This family occurs in a sparsely distributed
biosynthetic cluster that occurs in Actinobacteria,
Cyanobacteria, and Proteobacteria.
Length = 153
Score = 28.4 bits (64), Expect = 1.5
Identities = 17/45 (37%), Positives = 21/45 (46%), Gaps = 2/45 (4%)
Query: 64 RFVRSEDGE-MGYKLTTKISGRSVGIIGLGRIGMAVAKRAEAFGC 107
R E G G +L + R G IG G I +AV+ A A GC
Sbjct: 64 RIHEEEPGLWYGGRLAVHAAFRRQGRIGKGLIRLAVS-TAHALGC 107
>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 = 29.1 bits (66), Expect = 1.6
Identities = 8/25 (32%), Positives = 13/25 (52%)
Query: 83 GRSVGIIGLGRIGMAVAKRAEAFGC 107
G +V +IG G IG+ + + G
Sbjct: 160 GDTVVVIGAGTIGLLAIQWLKILGA 184
>gnl|CDD|224996 COG2085, COG2085, Predicted dinucleotide-binding enzymes [General
function prediction only].
Length = 211
Score = 28.8 bits (65), Expect = 1.7
Identities = 24/82 (29%), Positives = 28/82 (34%), Gaps = 7/82 (8%)
Query: 84 RSVGIIGLGRIGMAVAKRAEAFGCFISYRSR----AEKPNTKYKGALVDESELVSALLED 139
+ IIG G IG A+A R G + S A G L+ A
Sbjct: 2 MIIAIIGTGNIGSALALRLAKAGHEVIIGSSRGPKALAAAAAALGPLITGGSNEDAA--A 59
Query: 140 RLAAAVLDV-FEHEPQVPEELF 160
VL V FE P V EL
Sbjct: 60 LADVVVLAVPFEAIPDVLAELR 81
>gnl|CDD|132409 TIGR03366, HpnZ_proposed, putative phosphonate catabolism
associated alcohol dehydrogenase. This clade of
zinc-binding alcohol dehydrogenases (members of
pfam00107) are repeatedly associated with genes proposed
to be involved with the catabolism of phosphonate
compounds.
Length = 280
Score = 28.6 bits (64), Expect = 2.1
Identities = 20/74 (27%), Positives = 27/74 (36%), Gaps = 16/74 (21%)
Query: 36 GIQVTNTPDVLTDDV---ADAAIGLTLAVLRRFVRSEDGEMGYKLTTKISGRSVGIIGLG 92
G + PD L D V A A +A L + GR V ++G G
Sbjct: 84 GTAIVPVPDDLPDAVAAPAGCATATVMAALEAAGD-------------LKGRRVLVVGAG 130
Query: 93 RIGMAVAKRAEAFG 106
+G+ A A A G
Sbjct: 131 MLGLTAAAAAAAAG 144
>gnl|CDD|223990 COG1062, AdhC, Zn-dependent alcohol dehydrogenases, class III
[Energy production and conversion].
Length = 366
Score = 28.0 bits (63), Expect = 3.3
Identities = 10/25 (40%), Positives = 16/25 (64%)
Query: 83 GRSVGIIGLGRIGMAVAKRAEAFGC 107
G +V + GLG +G+A + A+A G
Sbjct: 186 GDTVAVFGLGGVGLAAIQGAKAAGA 210
>gnl|CDD|236582 PRK09599, PRK09599, 6-phosphogluconate dehydrogenase-like protein;
Reviewed.
Length = 301
Score = 27.8 bits (63), Expect = 3.4
Identities = 9/16 (56%), Positives = 14/16 (87%)
Query: 86 VGIIGLGRIGMAVAKR 101
+G+IGLGR+G +A+R
Sbjct: 3 LGMIGLGRMGGNMARR 18
>gnl|CDD|133445 cd01076, NAD_bind_1_Glu_DH, NAD(P) binding domain of glutamate
dehydrogenase, subgroup 1. Amino acid dehydrogenase
(DH) is a widely distributed family of enzymes that
catalyzes the oxidative deamination of an amino acid to
its keto acid and ammonia with concomitant reduction of
NADP+. Glutamate DH is a multidomain enzyme that
catalyzes the reaction from glutamate to 2-oxyoglutarate
and ammonia in the presence of NAD or NADP. It is
present in all organisms. Enzymes involved in ammonia
assimilation are typically NADP+-dependent, while those
involved in glutamate catabolism are generally
NAD+-dependent. Amino acid 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 = 227
Score = 27.9 bits (63), Expect = 3.7
Identities = 28/114 (24%), Positives = 45/114 (39%), Gaps = 12/114 (10%)
Query: 80 KISGRSVGIIGLGRIGMAVAKRAEAFGCFISYRSRAEKPNTKYKGALVDESEL-VSALLE 138
++G V I G G +G A+ G + S + G + + L V ALL
Sbjct: 28 GLAGARVAIQGFGNVGSHAARFLHEAGAKVVAVSDS-------DGTIYNPDGLDVPALLA 80
Query: 139 DRLA-AAVLDVFEHEPQVPEELFGLENVVLLPHAASGT---EETRKATADIVIE 188
+ +VL E EEL L+ +L+P A + + A I++E
Sbjct: 81 YKKEHGSVLGFPGAERITNEELLELDCDILIPAALENQITADNADRIKAKIIVE 134
>gnl|CDD|177398 PHA02569, 39, DNA topoisomerase II large subunit; Provisional.
Length = 602
Score = 28.2 bits (63), Expect = 3.8
Identities = 13/34 (38%), Positives = 15/34 (44%), Gaps = 2/34 (5%)
Query: 13 KLEIVATCSAGLDKIDL--VKCKEKGIQVTNTPD 44
K E+ CS G + I K KG VT PD
Sbjct: 152 KNEVTVNCSNGAENISWSTKPGKGKGTSVTFIPD 185
>gnl|CDD|180054 PRK05396, tdh, L-threonine 3-dehydrogenase; Validated.
Length = 341
Score = 27.9 bits (63), Expect = 4.0
Identities = 13/31 (41%), Positives = 16/31 (51%), Gaps = 3/31 (9%)
Query: 77 LTTKISGRSVGIIGLGRIGM---AVAKRAEA 104
L+ + G V I G G IG+ AVAK A
Sbjct: 158 LSFDLVGEDVLITGAGPIGIMAAAVAKHVGA 188
>gnl|CDD|132208 TIGR03164, UHCUDC, OHCU decarboxylase. Previously thought to only
proceed spontaneously, the decarboxylation of
2-oxo-4-hydroxy-4-carboxy--5-ureidoimidazoline (OHCU)
has been recently been shown to be catalyzed by this
enzyme in Mus musculus. Homologs of this enzyme are
found adjacent to and fused with uricase in a number of
prokaryotes and are represented by this model.
Length = 157
Score = 27.3 bits (61), Expect = 4.1
Identities = 8/25 (32%), Positives = 12/25 (48%)
Query: 139 DRLAAAVLDVFEHEPQVPEELFGLE 163
AA+ D+FEH P + E +
Sbjct: 4 ADFVAALGDIFEHSPWIAERAWAQR 28
>gnl|CDD|235297 PRK04423, PRK04423, organic solvent tolerance protein; Provisional.
Length = 798
Score = 27.9 bits (62), Expect = 4.7
Identities = 10/14 (71%), Positives = 13/14 (92%)
Query: 60 AVLRRFVRSEDGEM 73
A++RRFVR+ DGEM
Sbjct: 728 ALVRRFVRNRDGEM 741
>gnl|CDD|237613 PRK14109, PRK14109, bifunctional glutamine-synthetase
adenylyltransferase/deadenyltransferase; Provisional.
Length = 1007
Score = 27.9 bits (63), Expect = 4.8
Identities = 15/47 (31%), Positives = 23/47 (48%), Gaps = 8/47 (17%)
Query: 49 DVADAAIGLTLAVLRRFVRSEDGEMGYKLTTKISGRSVGIIGLGRIG 95
DV DA + L R V +E G+ +I+ +IG+GR+G
Sbjct: 695 DVWDAVLEAALRAAIRAVEAEGGDP---APARIA-----VIGMGRLG 733
>gnl|CDD|223643 COG0569, TrkA, K+ transport systems, NAD-binding component
[Inorganic ion transport and metabolism].
Length = 225
Score = 27.2 bits (61), Expect = 5.3
Identities = 9/22 (40%), Positives = 13/22 (59%)
Query: 86 VGIIGLGRIGMAVAKRAEAFGC 107
+ IIG GR+G +VA+ G
Sbjct: 3 IIIIGAGRVGRSVARELSEEGH 24
>gnl|CDD|166227 PLN02586, PLN02586, probable cinnamyl alcohol dehydrogenase.
Length = 360
Score = 27.5 bits (61), Expect = 5.9
Identities = 16/46 (34%), Positives = 21/46 (45%), Gaps = 3/46 (6%)
Query: 83 GRSVGIIGLGRIGMAVAKRAEAFG---CFISYRSRAEKPNTKYKGA 125
G+ +G+ GLG +G K +AFG IS S E GA
Sbjct: 184 GKHLGVAGLGGLGHVAVKIGKAFGLKVTVISSSSNKEDEAINRLGA 229
>gnl|CDD|129775 TIGR00692, tdh, L-threonine 3-dehydrogenase. This protein is a
tetrameric, zinc-binding, NAD-dependent enzyme of
threonine catabolism. Closely related proteins include
sorbitol dehydrogenase, xylitol dehydrogenase, and
benzyl alcohol dehydrogenase. Eukaryotic examples of
this enzyme have been demonstrated experimentally but do
not appear in database search results.E. coli His-90
modulates substrate specificity and is believed part of
the active site [Energy metabolism, Amino acids and
amines].
Length = 340
Score = 27.1 bits (60), Expect = 6.2
Identities = 19/48 (39%), Positives = 25/48 (52%), Gaps = 7/48 (14%)
Query: 77 LTTKISGRSVGIIGLGRIGM---AVAKRAEAFGCFIS----YRSRAEK 117
L ISG+SV + G G IG+ AVAK + A+ +S YR K
Sbjct: 156 LAGPISGKSVLVTGAGPIGLMAIAVAKASGAYPVIVSDPNEYRLELAK 203
>gnl|CDD|223954 COG1023, Gnd, Predicted 6-phosphogluconate dehydrogenase
[Carbohydrate transport and metabolism].
Length = 300
Score = 27.4 bits (61), Expect = 6.4
Identities = 8/17 (47%), Positives = 13/17 (76%)
Query: 86 VGIIGLGRIGMAVAKRA 102
+G+IGLGR+G + +R
Sbjct: 3 IGMIGLGRMGANLVRRL 19
>gnl|CDD|225350 COG2740, COG2740, Predicted nucleic-acid-binding protein implicated
in transcription termination [Transcription].
Length = 95
Score = 26.2 bits (58), Expect = 6.4
Identities = 13/42 (30%), Positives = 19/42 (45%), Gaps = 1/42 (2%)
Query: 62 LRRFVRSEDGEMGYKLTTKISGRSVGIIGLGR-IGMAVAKRA 102
L RFV ++GE+ T K+ GR + I A K+
Sbjct: 23 LLRFVAVKEGEVVIDPTGKLPGRGAYVCPDRECIEKAKKKKL 64
>gnl|CDD|217684 pfam03710, GlnE, Glutamate-ammonia ligase adenylyltransferase.
Conserved repeated domain found in GlnE proteins. These
proteins adenylate and deadenylate glutamine synthases:
ATP + {L-Glutamate:ammonia ligase (ADP-forming)} =
Diphosphate + Adenylyl-{L-Glutamate:Ammonia ligase
(ADP-forming)}. The family is related to the pfam01909
domain.
Length = 251
Score = 26.9 bits (60), Expect = 7.5
Identities = 13/47 (27%), Positives = 21/47 (44%), Gaps = 3/47 (6%)
Query: 49 DVADAAIGLTLAVLRRFVRSEDGEMGYKLTTKISGRSVGIIGLGRIG 95
D+ADA I L R E G + + + +IG+G++G
Sbjct: 95 DLADAIIDAALDWA---WRQVCAEGGTPGHLQGEPQGLAVIGMGKLG 138
>gnl|CDD|133426 cd05290, LDH_3, A subgroup of L-lactate dehydrogenases. L-lactate
dehydrogenases (LDH) are tetrameric enzymes catalyzing
the last step of glycolysis in which pyruvate is
converted to L-lactate. This subgroup is composed of
some bacterial LDHs from firmicutes,
gammaproteobacteria, and actinobacteria. Vertebrate LDHs
are non-allosteric, but some bacterial LDHs are
activated by an allosteric effector such as
fructose-1,6-bisphosphate. LDHs are part of the
NAD(P)-binding Rossmann fold superfamily, which includes
a wide variety of protein families including the
NAD(P)-binding domains of alcohol dehydrogenases,
tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate dehydrogenases,
formate/glycerate dehydrogenases, siroheme synthases,
6-phosphogluconate dehydrogenase, aminoacid
dehydrogenases, repressor rex, and NAD-binding potassium
channel domains, among others.
Length = 307
Score = 26.9 bits (60), Expect = 7.5
Identities = 10/23 (43%), Positives = 13/23 (56%)
Query: 86 VGIIGLGRIGMAVAKRAEAFGCF 108
+ +IG G +G AV A A G F
Sbjct: 2 LVVIGAGHVGSAVLNYALALGLF 24
>gnl|CDD|182318 PRK10225, PRK10225, DNA-binding transcriptional repressor UxuR;
Provisional.
Length = 257
Score = 26.9 bits (59), Expect = 7.9
Identities = 13/48 (27%), Positives = 26/48 (54%), Gaps = 1/48 (2%)
Query: 119 NTKYKGA-LVDESELVSALLEDRLAAAVLDVFEHEPQVPEELFGLENV 165
++ Y+ L D ++++AL++ AA L +++H V + L NV
Sbjct: 190 DSLYRKEWLGDHKQILAALIKKDARAAKLAMWQHLENVKQRLLEFSNV 237
>gnl|CDD|223364 COG0287, TyrA, Prephenate dehydrogenase [Amino acid transport and
metabolism].
Length = 279
Score = 26.5 bits (59), Expect = 8.8
Identities = 16/63 (25%), Positives = 24/63 (38%), Gaps = 3/63 (4%)
Query: 86 VGIIGLGRIGMAVA---KRAEAFGCFISYRSRAEKPNTKYKGALVDESELVSALLEDRLA 142
VGI+GLG +G ++A K A I A + ++DE + A
Sbjct: 6 VGIVGLGLMGGSLARALKEAGLVVRIIGRDRSAATLKAALELGVIDELTVAGLAEAAAEA 65
Query: 143 AAV 145
V
Sbjct: 66 DLV 68
>gnl|CDD|133037 cd04194, GT8_A4GalT_like, A4GalT_like proteins catalyze the
addition of galactose or glucose residues to the
lipooligosaccharide (LOS) or lipopolysaccharide (LPS) of
the bacterial cell surface. The members of this family
of glycosyltransferases catalyze the addition of
galactose or glucose residues to the lipooligosaccharide
(LOS) or lipopolysaccharide (LPS) of the bacterial cell
surface. The enzymes exhibit broad substrate
specificities. The known functions found in this family
include: Alpha-1,4-galactosyltransferase,
LOS-alpha-1,3-D-galactosyltransferase,
UDP-glucose:(galactosyl) LPS
alpha1,2-glucosyltransferase, UDP-galactose: (glucosyl)
LPS alpha1,2-galactosyltransferase, and
UDP-glucose:(glucosyl) LPS alpha1,2-glucosyltransferase.
Alpha-1,4-galactosyltransferase from N. meningitidis
adds an alpha-galactose from UDP-Gal (the donor) to a
terminal lactose (the acceptor) of the LOS structure of
outer membrane. LOSs are virulence factors that enable
the organism to evade the immune system of host cells.
In E. coli, the three alpha-1,2-glycosyltransferases,
that are involved in the synthesis of the outer core
region of the LPS, are all members of this family. The
three enzymes share 40 % of sequence identity, but have
different sugar donor or acceptor specificities,
representing the structural diversity of LPS.
Length = 248
Score = 26.4 bits (59), Expect = 9.3
Identities = 15/36 (41%), Positives = 18/36 (50%), Gaps = 1/36 (2%)
Query: 130 SELVSALLEDRLAAAVLDVF-EHEPQVPEELFGLEN 164
SEL L D L AAV D F E E + L G ++
Sbjct: 113 SELFDIDLGDNLLAAVRDPFIEQEKKRKRRLGGYDD 148
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
0.317 0.136 0.375
Gapped
Lambda K H
0.267 0.0864 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,610,197
Number of extensions: 1029588
Number of successful extensions: 1389
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1279
Number of HSP's successfully gapped: 195
Length of query: 204
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 112
Effective length of database: 6,857,034
Effective search space: 767987808
Effective search space used: 767987808
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 57 (25.5 bits)