RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 042102
(317 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 = 479 bits (1235), Expect = e-172
Identities = 161/299 (53%), Positives = 212/299 (70%)
Query: 10 VLMVCPVSNYLEQEIEKSFKVFKLWHFEDKEQFINTHKDSIQAVVGSAAAGADAELIESL 69
VL + P+ L E+E F V +LW D + H I+AVV + G A LI +L
Sbjct: 3 VLQLGPLPPELLAELEARFTVHRLWEAADPAALLAEHGGRIRAVVTNGETGLSAALIAAL 62
Query: 70 PKLEIVATCSVGLDKIDLARCKEKGIRVANTPDVLTDDVADLAIGLILAVLRRICESDRY 129
P LE++A+ VG D IDL + +GIRV NTP VLTDDVADLA+GL+LAVLRRI +DR+
Sbjct: 63 PALELIASFGVGYDGIDLDAARARGIRVTNTPGVLTDDVADLAVGLLLAVLRRIPAADRF 122
Query: 130 VRSGEWKKGEFKMTTKFTGKSVGILGMGRIGTAIAKRAEAFDCIIGYNSRTEKPNLNYKY 189
VR+G W KG F +T K +GK VGI+G+GRIG AIA+R EAF I Y+ R KP++ Y+Y
Sbjct: 123 VRAGRWPKGAFPLTRKVSGKRVGIVGLGRIGRAIARRLEAFGMEIAYHGRRPKPDVPYRY 182
Query: 190 YPNLIDLASNCQILVVACSLTEETQHIVNRQVINALGPKGVLINIGRGLLVDEHELVSAL 249
Y +L++LA+ +LVVAC T+H+VN +V+ ALGP GVL+N+ RG +VDE L++AL
Sbjct: 183 YASLLELAAESDVLVVACPGGPATRHLVNAEVLEALGPDGVLVNVARGSVVDEAALIAAL 242
Query: 250 LQGRLGGAGLDVFEHEPDVPEELIGLENVVLLPHVASATVETRKAMADLVVGNLQAHFG 308
+GR+ GAGLDVFE+EP+VP L+ L+NVVL PH+ASATVETR+AM DLV+ NL+A F
Sbjct: 243 QEGRIAGAGLDVFENEPNVPAALLDLDNVVLTPHIASATVETRRAMGDLVLANLEAFFA 301
>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 = 322 bits (827), Expect = e-110
Identities = 123/276 (44%), Positives = 171/276 (61%), Gaps = 7/276 (2%)
Query: 38 DKEQFINTHKDSIQAVVGSAAAGADAELIESLPKLEIVATCSVGLDKIDLARCKEKGIRV 97
+E+ + K ++ + DAEL+++ P L+++A SVG D ID+ K +GI V
Sbjct: 33 PREELLEAAKG-ADGLLCTLTDKIDAELLDAAPPLKVIANYSVGYDHIDVDAAKARGIPV 91
Query: 98 ANTPDVLTDDVADLAIGLILAVLRRICESDRYVRSGEWKK-GEFKMT-TKFTGKSVGILG 155
NTPDVLTD ADLA L+LA RR+ E DR+VR+GEWK + T GK++GI+G
Sbjct: 92 TNTPDVLTDATADLAFALLLAAARRVVEGDRFVRAGEWKGWSPTLLLGTDLHGKTLGIVG 151
Query: 156 MGRIGTAIAKRAEAFDCIIGYNSRTEKPNLNYK---YYPNLIDLASNCQILVVACSLTEE 212
MGRIG A+A+RA+ F I Y++R+ KP + Y +L +L + + + C LT E
Sbjct: 152 MGRIGQAVARRAKGFGMKILYHNRSRKPEAEEELGARYVSLDELLAESDFVSLHCPLTPE 211
Query: 213 TQHIVNRQVINALGPKGVLINIGRGLLVDEHELVSALLQGRLGGAGLDVFEHEPDVPE-E 271
T+H++N + + + P +LIN RG +VDE LV AL G++ GAGLDVFE EP +
Sbjct: 212 TRHLINAERLALMKPTAILINTARGGVVDEDALVEALKSGKIAGAGLDVFEPEPLPADHP 271
Query: 272 LIGLENVVLLPHVASATVETRKAMADLVVGNLQAHF 307
L+ L NVVLLPH+ SATVETR AMA+L NL A
Sbjct: 272 LLTLPNVVLLPHIGSATVETRTAMAELAADNLLAVL 307
>gnl|CDD|223980 COG1052, LdhA, Lactate dehydrogenase and related dehydrogenases
[Energy production and conversion / Coenzyme metabolism
/ General function prediction only].
Length = 324
Score = 301 bits (774), Expect = e-102
Identities = 121/320 (37%), Positives = 178/320 (55%), Gaps = 12/320 (3%)
Query: 8 IIVLMVCPVSNYLEQEIEKSFKVFKLWHFEDKEQFINTHKDSIQAVVGSAAAGADAELIE 67
I+VL + + + +++ F+V + + + AV+ DAE++E
Sbjct: 3 IVVLSTRKLPPEVLERLKEKFEVERYEDDLTPDTELAERLKDADAVITFVNDRIDAEVLE 62
Query: 68 SLPKLEIVATCSVGLDKIDLARCKEKGIRVANTPDVLTDDVADLAIGLILAVLRRICESD 127
LP L+++AT S G D +DL KE+GI V N P T+ VA+ A+ LILA+ RRI E D
Sbjct: 63 KLPGLKLIATRSAGYDNVDLEAAKERGITVTNVPGYSTEAVAEHAVALILALARRIHEGD 122
Query: 128 RYVRSGEWKK---GEFKMTTKFTGKSVGILGMGRIGTAIAKRAEAFDCIIGYNSRTEKP- 183
R VR G W + + GK++GI+G+GRIG A+A+R + F + Y R+ P
Sbjct: 123 RRVREGNWSLSGGPDPLLGFDLRGKTLGIIGLGRIGQAVARRLKGFGMKVLYYDRSPNPE 182
Query: 184 ---NLNYKYYPNLIDLASNCQILVVACSLTEETQHIVNRQVINALGPKGVLINIGRGLLV 240
L +Y L +L + I+ + C LT ET+H++N + + + P +L+N RG LV
Sbjct: 183 AEKELGARYVD-LDELLAESDIISLHCPLTPETRHLINAEELAKMKPGAILVNTARGGLV 241
Query: 241 DEHELVSALLQGRLGGAGLDVFEHEPD-VPEELIGLEN---VVLLPHVASATVETRKAMA 296
DE L+ AL G++ GAGLDVFE+EP L+ L+N VVL PH+ASAT E RKAMA
Sbjct: 242 DEQALIDALKSGKIAGAGLDVFENEPALFDHPLLRLDNFPNVVLTPHIASATEEARKAMA 301
Query: 297 DLVVGNLQAHFGKKPLLTPV 316
+L + NL+A F V
Sbjct: 302 ELALENLEAFFDGGVPPNEV 321
>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 = 272 bits (699), Expect = 5e-91
Identities = 100/257 (38%), Positives = 148/257 (57%), Gaps = 6/257 (2%)
Query: 52 AVVGSAAAGADAELIESLPKLEIVATCSVGLDKIDLARCKEKGIRVANTPDVLTDDVADL 111
A++ S+ AE++ PKL+ + G+D IDL K++GI V N P + VA+
Sbjct: 44 ALIVSSTTPVTAEVLAKAPKLKFIQVAGAGVDNIDLDAAKKRGITVTNVPGANAEAVAEH 103
Query: 112 AIGLILAVLRRICESDRYVRSGEWKKGEFKMTTKFTGKSVGILGMGRIGTAIAKRAEAFD 171
A+GL+LA+LRR+ +D VR G + GK+VGI+G+GRIG +AKR +AF
Sbjct: 104 ALGLLLALLRRLPRADAAVRRGWGWLWAGFPGYELEGKTVGIVGLGRIGQRVAKRLQAFG 163
Query: 172 C-IIGYNSRTEKPN---LNYKYYPNLIDLASNCQILVVACSLTEETQHIVNRQVINALGP 227
++ Y RT KP +L +L + ++V+ LT ET+H++N + + + P
Sbjct: 164 MKVLYY-DRTRKPEPEEDLGFRVVSLDELLAQSDVVVLHLPLTPETRHLINEEELALMKP 222
Query: 228 KGVLINIGRGLLVDEHELVSALLQGRLGGAGLDVFEHEPDVPEE-LIGLENVVLLPHVAS 286
VL+N RG LVDE L+ AL G++ GA LDVFE EP + L+ L NV+L PH+A
Sbjct: 223 GAVLVNTARGGLVDEDALLRALKSGKIAGAALDVFEPEPLPADHPLLELPNVILTPHIAG 282
Query: 287 ATVETRKAMADLVVGNL 303
T E R+ MA++ V NL
Sbjct: 283 YTEEARERMAEIAVENL 299
>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 = 248 bits (635), Expect = 5e-81
Identities = 106/298 (35%), Positives = 168/298 (56%), Gaps = 16/298 (5%)
Query: 23 EIEKSFKVFKLWHFEDKEQFIN---THK-DSIQAVV---GSAAAGA--DAELIESLPK-L 72
E+ +V +E+FI K A+ GSA D ELI LP L
Sbjct: 19 ELSSIAEVIYP-TSGTREEFIEALKEGKYGDFVAIYRTFGSAGETGPFDEELISPLPPSL 77
Query: 73 EIVATCSVGLDKIDLARCKEKGIRVANTPDVLTDDVADLAIGLILAVLRRICESDRYVRS 132
+I+A G D+ID+ ++GI+V+NTP + + AD A+ LIL LR ++R R+
Sbjct: 78 KIIAHAGAGYDQIDVDALTKRGIQVSNTPGAVDEATADTALFLILGALRNFSRAERSARA 137
Query: 133 GEWKKG-EFKMTTKFTGKSVGILGMGRIGTAIAKRAEAFDCIIGYNSRTEKPNL----NY 187
G+W+ + + GK++GILG+G IG AIA++A AF I Y++R+ P
Sbjct: 138 GKWRGFLDLTLAHDPRGKTLGILGLGGIGKAIARKAAAFGMKIIYHNRSRLPEELEKALA 197
Query: 188 KYYPNLIDLASNCQILVVACSLTEETQHIVNRQVINALGPKGVLINIGRGLLVDEHELVS 247
YY +L +L + ++ + C LT T+H++N++ + +++N RG ++DE LV
Sbjct: 198 TYYVSLDELLAQSDVVSLNCPLTAATRHLINKKEFAKMKDGVIIVNTARGAVIDEDALVD 257
Query: 248 ALLQGRLGGAGLDVFEHEPDVPEELIGLENVVLLPHVASATVETRKAMADLVVGNLQA 305
AL G++ AGLDVFE+EP+V L+ + NV LLPH+ + TVET++ M +LV+ N++A
Sbjct: 258 ALESGKVASAGLDVFENEPEVNPGLLKMPNVTLLPHMGTLTVETQEKMEELVLENIEA 315
>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 = 245 bits (628), Expect = 5e-80
Identities = 109/259 (42%), Positives = 145/259 (55%), Gaps = 9/259 (3%)
Query: 62 DAELIESLPKLEIVATCSVGLDKIDLARCKEKGIRVANTPDVLTDDVADLAIGLILAVLR 121
D E+I++ L+I+A G D ID+ KEKGI V NTP V T+ A+L GLILA+ R
Sbjct: 56 DKEIIDAAKNLKIIANYGAGFDNIDVDYAKEKGIPVTNTPAVSTEPTAELTFGLILALAR 115
Query: 122 RICESDRYVRSGEWKKGE--FKMTTKFTGKSVGILGMGRIGTAIAKRAEAFDCIIGYNSR 179
RI E DR +R G + F + + GK++GI+GMGRIG A+A+RA+AF I Y +R
Sbjct: 116 RIAEGDRLMRRGGFLGWAPLFFLGHELAGKTLGIIGMGRIGQAVARRAKAFGMKILYYNR 175
Query: 180 TEKP-----NLNYKYYPNLIDLASNCQILVVACSLTEETQHIVNRQVINALGPKGVLINI 234
L Y L +L + + T ET H+++ + P LIN
Sbjct: 176 HRLSEETEKELGATYVD-LDELLKESDFVSLHAPYTPETHHLIDAAAFKLMKPTAYLINA 234
Query: 235 GRGLLVDEHELVSALLQGRLGGAGLDVFEHEPDVPEELIGLENVVLLPHVASATVETRKA 294
RG LVDE LV AL G + GA LDVFE EP+V EL L+NV+L PH+ +ATVE R A
Sbjct: 235 ARGPLVDEKALVDALKTGEIAGAALDVFEFEPEVSPELKKLDNVILTPHIGNATVEARDA 294
Query: 295 MADLVVGNLQAHF-GKKPL 312
MA N+ + GK+P
Sbjct: 295 MAKEAADNIISFLEGKRPK 313
>gnl|CDD|183914 PRK13243, PRK13243, glyoxylate reductase; Reviewed.
Length = 333
Score = 245 bits (627), Expect = 9e-80
Identities = 124/295 (42%), Positives = 172/295 (58%), Gaps = 16/295 (5%)
Query: 24 IEKSFKVFKLWHFED---KEQFINTHKDSIQAVVGSAAAGADAELIESLPKLEIVATCSV 80
+E+ F+V ++W E +E + +D + A+V + D E+ E+ P+L IVA +V
Sbjct: 19 LEEHFEV-EVWEDEREIPREVLLEKVRD-VDALVTMLSERIDCEVFEAAPRLRIVANYAV 76
Query: 81 GLDKIDLARCKEKGIRVANTPDVLTDDVADLAIGLILAVLRRICESDRYVRSGEWKKGEF 140
G D ID+ +GI V NTP VLT+ AD A L+LA RR+ E+D +VRSGEWK+
Sbjct: 77 GYDNIDVEEATRRGIYVTNTPGVLTEATADFAWALLLATARRLVEADHFVRSGEWKRRGV 136
Query: 141 KMTTKF------TGKSVGILGMGRIGTAIAKRAEAFDCIIGYNSRTEKPN----LNYKYY 190
GK++GI+G GRIG A+A+RA+ F I Y SRT KP L +Y
Sbjct: 137 AWHPLMFLGYDVYGKTIGIIGFGRIGQAVARRAKGFGMRILYYSRTRKPEAEKELGAEYR 196
Query: 191 PNLIDLASNCQILVVACSLTEETQHIVNRQVINALGPKGVLINIGRGLLVDEHELVSALL 250
P L +L + + LT+ET H++N + + + P +L+N RG +VD LV AL
Sbjct: 197 P-LEELLRESDFVSLHVPLTKETYHMINEERLKLMKPTAILVNTARGKVVDTKALVKALK 255
Query: 251 QGRLGGAGLDVFEHEPDVPEELIGLENVVLLPHVASATVETRKAMADLVVGNLQA 305
+G + GAGLDVFE EP EEL L+NVVL PH+ SAT E R+ MA+LV NL A
Sbjct: 256 EGWIAGAGLDVFEEEPYYNEELFSLKNVVLAPHIGSATFEAREGMAELVAENLIA 310
>gnl|CDD|223189 COG0111, SerA, Phosphoglycerate dehydrogenase and related
dehydrogenases [Amino acid transport and metabolism].
Length = 324
Score = 235 bits (602), Expect = 5e-76
Identities = 102/313 (32%), Positives = 166/313 (53%), Gaps = 7/313 (2%)
Query: 8 IIVLMVCPVSNYLEQEIEKSFKVFKLWHFEDKEQFINTHKDSIQAVVGSAAAGADAELIE 67
I VL+ P++ +E+ ++ V + E+ + A++ S E++
Sbjct: 4 IKVLVTDPLAPDALEELLAAYDVEVPDGPDLDEEELLEALADADALIVSVT-PVTEEVLA 62
Query: 68 SLPKLEIVATCSVGLDKIDLARCKEKGIRVANTPDVLTDDVADLAIGLILAVLRRICESD 127
+ P L+ + G+D IDL ++GI V N P VA+L + L+LA+ RRI ++D
Sbjct: 63 AAPNLKAIGRAGAGVDNIDLEAATKRGILVVNAPGGNAISVAELVLALLLALARRIPDAD 122
Query: 128 RYVRSGEWKKGEFKMTTKFTGKSVGILGMGRIGTAIAKRAEAFDC-IIGYN---SRTEKP 183
R GEW + F+ T GK+VGI+G+GRIG A+AKR +AF +IGY+ R
Sbjct: 123 ASQRRGEWDRKAFRGTELA-GKTVGIIGLGRIGRAVAKRLKAFGMKVIGYDPYSPRERAG 181
Query: 184 NLNYKYYPNLIDLASNCQILVVACSLTEETQHIVNRQVINALGPKGVLINIGRGLLVDEH 243
+L +L + IL + LT ET+ ++N + + + P +LIN RG +VDE
Sbjct: 182 VDGVVGVDSLDELLAEADILTLHLPLTPETRGLINAEELAKMKPGAILINAARGGVVDED 241
Query: 244 ELVSALLQGRLGGAGLDVFEHEPDVPE-ELIGLENVVLLPHVASATVETRKAMADLVVGN 302
L++AL G++ GA LDVFE EP + L L NV+L PH+ +T E ++ +A++V N
Sbjct: 242 ALLAALDSGKIAGAALDVFEEEPLPADSPLWDLPNVILTPHIGGSTDEAQERVAEIVAEN 301
Query: 303 LQAHFGKKPLLTP 315
+ + P++
Sbjct: 302 IVRYLAGGPVVNN 314
>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 = 231 bits (591), Expect = 1e-74
Identities = 90/247 (36%), Positives = 140/247 (56%), Gaps = 9/247 (3%)
Query: 62 DAELIESLPKLEIVATCSVGLDKIDLARCKEKGIRVANTPDVLTDDVADLAIGLILAVLR 121
E++ + P+L++++ VG D IDL K++GI V NTP ++ VA+L IGL+LA+ R
Sbjct: 59 TEEVLAAAPRLKVISRYGVGYDNIDLEAAKKRGIVVTNTPGANSNSVAELTIGLMLALAR 118
Query: 122 RICESDRYVRSGEWKKGEFKMTTKFTGKSVGILGMGRIGTAIAKRAEAFDC-IIGYN--- 177
+I ++DR VR+G W + + T+ GK++GI+G+GRIG A+A+R F ++ Y+
Sbjct: 119 QIPQADREVRAGGWDRP---VGTELYGKTLGIIGLGRIGKAVARRLSGFGMKVLAYDPYP 175
Query: 178 SRTEKPNLNYKYYPNLIDLASNCQILVVACSLTEETQHIVNRQVINALGPKGVLINIGRG 237
++ L +L + + LT ET+H++N + + P +LIN RG
Sbjct: 176 DEEFAKEHGVEFVS-LEELLKESDFISLHLPLTPETRHLINAAELALMKPGAILINTARG 234
Query: 238 LLVDEHELVSALLQGRLGGAGLDVFEHEP-DVPEELIGLENVVLLPHVASATVETRKAMA 296
LVDE L AL GR+ GA LDVFE EP L+ L NV+L PH+ ++T E M
Sbjct: 235 GLVDEEALYEALKSGRIAGAALDVFEEEPPPADSPLLELPNVILTPHIGASTKEAVLRMG 294
Query: 297 DLVVGNL 303
+ N+
Sbjct: 295 TMAAQNV 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 = 229 bits (587), Expect = 5e-74
Identities = 99/256 (38%), Positives = 150/256 (58%), Gaps = 5/256 (1%)
Query: 53 VVGSAAAGADAELIESLPKLEIVATCSVGLDKIDLARCKEKGIRVANTPDVLTDDVADLA 112
+V DAEL+ + P+L ++ VGLD +DL +GI VAN P + VA+ A
Sbjct: 47 LVPGMRKVIDAELLAAAPRLRLIQQPGVGLDGVDLEAATARGIPVANIPGGNAESVAEHA 106
Query: 113 IGLILAVLRRICESDRYVRSGEWKKGEFKMTTKFTGKSVGILGMGRIGTAIAKRAEAFDC 172
+ L+LA+LRR+ E+DR +R+G W + E + + + +GK+VGI+G+G IG A+A+R F
Sbjct: 107 VMLMLALLRRLPEADRELRAGRWGRPEGRPSRELSGKTVGIVGLGNIGRAVARRLRGFGV 166
Query: 173 IIGYNSRTEKPNLNYKYYPN----LIDLASNCQILVVACSLTEETQHIVNRQVINALGPK 228
+ Y R P K L +L + ++ + LT ET+H++ + + A+ P
Sbjct: 167 EVIYYDRFRDPEAEEKDLGVRYVELDELLAESDVVSLHVPLTPETRHLIGAEELAAMKPG 226
Query: 229 GVLINIGRGLLVDEHELVSALLQGRLGGAGLDVFEHEPDVPE-ELIGLENVVLLPHVASA 287
+LIN RG LVDE L++AL G L GAGLDVF EP P+ L+ L+NV+L PH+A
Sbjct: 227 AILINTARGGLVDEEALLAALRSGHLAGAGLDVFWQEPLPPDDPLLRLDNVILTPHIAGV 286
Query: 288 TVETRKAMADLVVGNL 303
T E+ + MA +V N+
Sbjct: 287 TDESYQRMAAIVAENI 302
>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 = 224 bits (573), Expect = 7e-72
Identities = 96/270 (35%), Positives = 144/270 (53%), Gaps = 15/270 (5%)
Query: 57 AAAGADA----------ELIESLPKLEIVATCSVGLDKIDLARCKEKGIRVANTPDVLTD 106
AAA ADA E+IE+LP+L+++ VG+D +D+A E+GI V N PD T+
Sbjct: 41 AAADADALLVQYAPVTAEVIEALPRLKVIVRYGVGVDNVDVAAATERGIPVCNVPDYCTE 100
Query: 107 DVADLAIGLILAVLRRICESDRYVRSGEWKKGEFKMTTKFTGKSVGILGMGRIGTAIAKR 166
+VAD A+ LILA+ R++ DR VR+G W + G ++G++G GRIG A+AKR
Sbjct: 101 EVADHALALILALARKLPFLDRAVRAGGWDWTVGGPIRRLRGLTLGLVGFGRIGRAVAKR 160
Query: 167 AEAFDC-IIGYNSRTEKPNLNYKYYP--NLIDLASNCQILVVACSLTEETQHIVNRQVIN 223
A+AF +I Y+ +L +L + ++ + C LT ET+H+++ + +
Sbjct: 161 AKAFGFRVIAYDPYVPDGVAALGGVRVVSLDELLARSDVVSLHCPLTPETRHLIDAEALA 220
Query: 224 ALGPKGVLINIGRGLLVDEHELVSALLQGRLGGAGLDVFEHEP-DVPEELIGLENVVLLP 282
+ P L+N RG LVDE L AL GR+ GA LDV E EP L+ NV+L P
Sbjct: 221 LMKPGAFLVNTARGGLVDEAALARALKSGRIAGAALDVLEEEPPPADSPLLSAPNVILTP 280
Query: 283 HVASATVETRKAMADLVVGNLQAHF-GKKP 311
H A + E+ + + G+ P
Sbjct: 281 HAAWYSEESLAELRRKAAEEVVRVLRGEPP 310
>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 = 218 bits (558), Expect = 1e-69
Identities = 95/314 (30%), Positives = 155/314 (49%), Gaps = 10/314 (3%)
Query: 10 VLMVCPVSNYLEQEIEKSFKVFKLWHFEDKEQFINTHKDSIQAVVGSAAAGADAELIESL 69
VL+ P+ + +++ +V ++ E+ + KD+ A++ + AE++E+
Sbjct: 1 VLITDPLRPEELELLKEGGEV-EVHDELLTEELLEAAKDA-DALIVRSTTPVTAEVLEAA 58
Query: 70 PKLEIVATCSVGLDKIDLARCKEKGIRVANTPDVLTDDVADLAIGLILAVLRRICESDRY 129
P L+++A VG+D IDL E+GI V N P T+ VA+L +GLILA+ RRI E+D
Sbjct: 59 PGLKVIARRGVGVDNIDLDAATERGILVTNVPGYSTESVAELTVGLILALARRIPEADAS 118
Query: 130 VRSGEWKKGEFKMTTKFTGKSVGILGMGRIGTAIAKRAEAFDC-IIGYNSRTEKPNLNYK 188
VR+G+WKKG + + GK++G++G G IG A A+A ++ Y+
Sbjct: 119 VRAGDWKKGGP-IGLELYGKTLGVIGGGGIGGIGAAIAKALGMGVVAYDPYPNPERAEEG 177
Query: 189 YYP------NLIDLASNCQILVVACSLTEETQHIVNRQVINALGPKGVLINIGRGLLVDE 242
L+DL + ++ +A T +T HI+ + L + N G +++E
Sbjct: 178 GVEVLLLDLLLLDLKESDDLINLAPPTTMKTGHIIINEARGMLKDAVAINNARGGGVIEE 237
Query: 243 HELVSALLQGRLGGAGLDVFEHEPDVPEELIGLENVVLLPHVASATVETRKAMADLVVGN 302
L + L +G A V E P V L+ L NV+L PH+A AT E ++ MA+ N
Sbjct: 238 AALDALLEEGIAAAALDVVEEEPPPVNSPLLDLPNVILTPHIAGATEEAQENMAEEAAEN 297
Query: 303 LQAHFGKKPLLTPV 316
L A V
Sbjct: 298 LLAFLKGGTPPNAV 311
>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 = 215 bits (551), Expect = 1e-68
Identities = 88/248 (35%), Positives = 143/248 (57%), Gaps = 5/248 (2%)
Query: 62 DAELIESLPKLEIVATCSVGLDKIDLARCKEKGIRVANTPDVLTDDVADLAIGLILAVLR 121
AE+IE+ P+L+++ VG+D ID+ +GI V N P T VA+ I L+LA+ R
Sbjct: 53 TAEVIEAAPRLKVIGRAGVGVDNIDVEAATARGILVVNAPGANTISVAEHTIALMLALAR 112
Query: 122 RICESDRYVRSGEWKKGEFKMTTKFTGKSVGILGMGRIGTAIAKRAEAFDC-IIGYNS-- 178
I ++D +R+G+W + +F M + GK++GI+G+GRIG +A+RA AF ++ Y+
Sbjct: 113 NIPQADASLRAGKWDRKKF-MGVELRGKTLGIVGLGRIGREVARRARAFGMKVLAYDPYI 171
Query: 179 RTEKPNLNYKYYPNLIDLASNCQILVVACSLTEETQHIVNRQVINALGPKGVLINIGRGL 238
E+ +L +L + + + LT ET+ ++N + + + P +LIN RG
Sbjct: 172 SAERAAAGGVELVSLDELLAEADFISLHTPLTPETRGLINAEELAKMKPGAILINTARGG 231
Query: 239 LVDEHELVSALLQGRLGGAGLDVFEHEPDVPE-ELIGLENVVLLPHVASATVETRKAMAD 297
+VDE L AL G++ GA LDVFE EP + L+GL NV+L PH+ ++T E ++ +A
Sbjct: 232 IVDEAALADALKSGKIAGAALDVFEQEPPPADSPLLGLPNVILTPHLGASTEEAQERVAV 291
Query: 298 LVVGNLQA 305
+ A
Sbjct: 292 DAAEQVLA 299
>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 = 212 bits (543), Expect = 1e-67
Identities = 95/303 (31%), Positives = 166/303 (54%), Gaps = 9/303 (2%)
Query: 10 VLMVCPVSNYLEQEIEKS-FKVFKLWHFEDKEQFINTHKDSIQAVVGSAAAGADAELIES 68
+L+ + +++E++ F+V KE+ + KD ++ + E+I++
Sbjct: 3 ILITDGIDEIAIEKLEEAGFEVDYE-PLIAKEELLEKIKD-YDVLIVRSRTKVTKEVIDA 60
Query: 69 LPKLEIVATCSVGLDKIDLARCKEKGIRVANTPDVLTDDVADLAIGLILAVLRRICESDR 128
L+I+A VGLD ID+ K+KGI+V NTP ++ VA+L IGL+L++ R I ++R
Sbjct: 61 AKNLKIIARAGVGLDNIDVEYAKKKGIKVINTPGASSNSVAELVIGLMLSLARFIHRANR 120
Query: 129 YVRSGEWKKGEFKMTTKFTGKSVGILGMGRIGTAIAKRAEAFDC-IIGYN---SRTEKPN 184
++ G+W K ++ + GK++GI+G GRIG +AK A A +I Y+ +
Sbjct: 121 EMKLGKWNKKKY-KGIELRGKTLGIIGFGRIGREVAKIARALGMNVIAYDPYPKDEQAVE 179
Query: 185 LNYKYYPNLIDLASNCQILVVACSLTEETQHIVNRQVINALGPKGVLINIGRGLLVDEHE 244
L K L +L N + + LT ET+H++N++ + + ++IN RG ++DE
Sbjct: 180 LGVKTVS-LEELLKNSDFISLHVPLTPETKHMINKKELELMKDGAIIINTSRGGVIDEEA 238
Query: 245 LVSALLQGRLGGAGLDVFEHEPDVPEELIGLENVVLLPHVASATVETRKAMADLVVGNLQ 304
L+ AL G+L GA LDVFE+EP +L+ L NV L PH+ ++T E ++ + + + +
Sbjct: 239 LLEALKSGKLAGAALDVFENEPPPGSKLLELPNVSLTPHIGASTKEAQERIGEELANKII 298
Query: 305 AHF 307
Sbjct: 299 EFL 301
>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 = 202 bits (517), Expect = 2e-63
Identities = 90/253 (35%), Positives = 140/253 (55%), Gaps = 12/253 (4%)
Query: 62 DAELIESLPKLEIVATCSVGLDKIDLARCKEKGIRVANTPDVLTDDVADLAIGLILAVLR 121
DAE++ LP L+++ + G + +DLA KE+GI V N P TD VA L+LA+ R
Sbjct: 56 DAEVLAQLPNLKLIGVLATGYNNVDLAAAKERGITVTNVPGYSTDSVAQHTFALLLALAR 115
Query: 122 RICESDRYVRSGEWKKGEF-----KMTTKFTGKSVGILGMGRIGTAIAKRAEAFDCIIGY 176
+ + V++GEW+K + GK++GI+G G IG A+A+ A AF + +
Sbjct: 116 LVAYHNDVVKAGEWQKSPDFCFWDYPIIELAGKTLGIIGYGNIGQAVARIARAFGMKVLF 175
Query: 177 NSRTEKPNLNYKYYPNLIDLASNCQILVVACSLTEETQHIVNRQVINALGPKGVLINIGR 236
R P L Y L +L + ++ + C LT ET++++N + + + P +LIN R
Sbjct: 176 AERKGAPPLREGYVS-LDELLAQSDVISLHCPLTPETRNLINAEELAKMKPGAILINTAR 234
Query: 237 GLLVDEHELVSALLQGRLGGAGLDVFEHEPDVPEE----LIGLENVVLLPHVASATVETR 292
G LVDE L AL G++ GAGLDV EP P L N+++ PH+A A+ E R
Sbjct: 235 GGLVDEQALADALNSGKIAGAGLDVLSQEP--PRADNPLLKAAPNLIITPHIAWASREAR 292
Query: 293 KAMADLVVGNLQA 305
+ + D++V N++A
Sbjct: 293 QRLMDILVDNIKA 305
>gnl|CDD|185307 PRK15409, PRK15409, bifunctional glyoxylate/hydroxypyruvate
reductase B; Provisional.
Length = 323
Score = 201 bits (514), Expect = 6e-63
Identities = 110/297 (37%), Positives = 154/297 (51%), Gaps = 15/297 (5%)
Query: 20 LEQEIEKSFKV--FKLWHFEDKEQFINTHKDSIQAVVGSAAAG--ADAELIESLPKLEIV 75
L Q +E+ F V E EQ H + G +G DA L+E +PKL
Sbjct: 15 LLQRLEEHFTVTQVANLSPETVEQ----HAAAFAEAEGLLGSGEKVDAALLEKMPKLRAA 70
Query: 76 ATCSVGLDKIDLARCKEKGIRVANTPDVLTDDVADLAIGLILAVLRRICESDRYVRSGEW 135
+T SVG D D+ + I + +TP VLT+ VAD + L+L+ RR+ E V++GEW
Sbjct: 71 STISVGYDNFDVDALTARKILLMHTPTVLTETVADTLMALVLSTARRVVEVAERVKAGEW 130
Query: 136 KK--GEFKMTTKFTGKSVGILGMGRIGTAIAKRAE-AFDCIIGYNSRTEKPNLNYKY--- 189
G T K++GI+GMGRIG A+A+RA F+ I YN+R ++
Sbjct: 131 TASIGPDWFGTDVHHKTLGIVGMGRIGMALAQRAHFGFNMPILYNARRHHKEAEERFNAR 190
Query: 190 YPNLIDLASNCQILVVACSLTEETQHIVNRQVINALGPKGVLINIGRGLLVDEHELVSAL 249
Y +L L + + LT+ET H+ + + + IN GRG +VDE+ L++AL
Sbjct: 191 YCDLDTLLQESDFVCIILPLTDETHHLFGAEQFAKMKSSAIFINAGRGPVVDENALIAAL 250
Query: 250 LQGRLGGAGLDVFEHEP-DVPEELIGLENVVLLPHVASATVETRKAMADLVVGNLQA 305
+G + AGLDVFE EP V L+ L NVV +PH+ SAT ETR MA V NL
Sbjct: 251 QKGEIHAAGLDVFEQEPLSVDSPLLSLPNVVAVPHIGSATHETRYNMAACAVDNLID 307
>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 = 192 bits (491), Expect = 2e-61
Identities = 72/176 (40%), Positives = 110/176 (62%), Gaps = 4/176 (2%)
Query: 113 IGLILAVLRRICESDRYVRSGEWKKGEFKMTTKFTGKSVGILGMGRIGTAIAKRAEAFDC 172
+ L+LA+ RRI E+DR VR+G W+ + + +GK+VGI+G+GRIG A+A+R +AF
Sbjct: 1 LALLLALARRIPEADRQVRAGRWRPDAL-LGRELSGKTVGIIGLGRIGRAVARRLKAFGM 59
Query: 173 -IIGYN-SRTEKPNLNYKYYPNLIDLASNCQILVVACSLTEETQHIVNRQVINALGPKGV 230
+I Y+ + Y +L +L + ++ + LT ET+H++N + + + P +
Sbjct: 60 KVIAYDRYPKAEAEALGARYVSLDELLAESDVVSLHLPLTPETRHLINAERLALMKPGAI 119
Query: 231 LINIGRGLLVDEHELVSALLQGRLGGAGLDVFEHEPDVPE-ELIGLENVVLLPHVA 285
LIN RG LVDE L++AL GR+ GA LDVFE EP P+ L+ L NV+L PH+A
Sbjct: 120 LINTARGGLVDEDALIAALKSGRIAGAALDVFEPEPLPPDHPLLELPNVILTPHIA 175
>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 = 194 bits (496), Expect = 3e-60
Identities = 86/302 (28%), Positives = 147/302 (48%), Gaps = 19/302 (6%)
Query: 21 EQEIEKSFKVFKLWHFEDKEQFINTH--KDSIQ----AVVGSAAAGADAELIESLPKLEI 74
++ E +V + E ++++ + A ++IE+ PKL++
Sbjct: 13 DEPFEDLQEVILVVEKSGPEAVEPEEELLEALKDADILITHFAPVTK--KVIEAAPKLKL 70
Query: 75 VATCSVGLDKIDLARCKEKGIRVANTPDVLTDDVADLAIGLILAVLRRICESDRYVRSGE 134
+ C G + +D+ E+GI V NTP + VA+ +GL+LA R I + ++ GE
Sbjct: 71 IGVCRGGPENVDVEAATERGIPVLNTPGRNAEAVAEFTVGLMLAETRNIARAHAALKDGE 130
Query: 135 WKKGEF---KMTTKFTGKSVGILGMGRIGTAIAKRAEAFDC-IIGYN---SRTEKPNLNY 187
W+K + + GK+VGI+G G IG +AKR +AF ++ Y+ +
Sbjct: 131 WRKDYYNYDGYGPELRGKTVGIVGFGAIGRRVAKRLKAFGAEVLVYDPYVDPEKIEADGV 190
Query: 188 KYYPNLIDLASNCQILVVACSLTEETQHIVNRQVINALGPKGVLINIGRGLLVDEHELVS 247
K L +L ++ + LT ET+ ++ + + P IN R LVDE L+
Sbjct: 191 KKVS-LEELLKRSDVVSLHARLTPETRGMIGAEEFALMKPTAYFINTARAGLVDEDALIE 249
Query: 248 ALLQGRLGGAGLDVFEHEPDVPE--ELIGLENVVLLPHVASATVETRKAMADLVVGNLQA 305
AL +G++GGA LDVF EP +P L+ L+NV L PH+A AT + + +++ L+
Sbjct: 250 ALEEGKIGGAALDVFPEEP-LPADHPLLKLDNVTLTPHIAGATRDVAERSPEIIAEELKR 308
Query: 306 HF 307
+
Sbjct: 309 YL 310
>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 = 191 bits (488), Expect = 4e-59
Identities = 89/257 (34%), Positives = 131/257 (50%), Gaps = 16/257 (6%)
Query: 62 DAELIESLPKLEIVATCSVGLDKIDLARCKEKGIRVANTPDVLTDDVADLAIGLILAVLR 121
DA+ +++ P+L+I+A G D D+ C +GI V PD+LT+ A+L IGL++ + R
Sbjct: 57 DADFLDACPRLKIIACALKGYDNFDVEACTARGIWVTIVPDLLTEPTAELTIGLLIGLGR 116
Query: 122 RICESDRYVRSGEWKKGE-FKMTTKFTGKSVGILGMGRIGTAIAKRAEAFDCIIGYNSRT 180
I DR+VRSG++ T GK+VGILGMG +G AIA+R F + Y
Sbjct: 117 HILAGDRFVRSGKFGGWRPKFYGTGLDGKTVGILGMGALGRAIARRLSGFGATLLYYDPH 176
Query: 181 EKPN-----LNYKYYPNLIDLASNCQILVVACSLTEETQHIVNRQVINALGPKGVLINIG 235
LN + L +L + LV+A LT +T H++N + + + P +L+N
Sbjct: 177 PLDQAEEQALNLRRVE-LDELLESSDFLVLALPLTPDTLHLINAEALAKMKPGALLVNPC 235
Query: 236 RGLLVDEHELVSALLQGRLGGAGLDVFEHEP--------DVPEELIGLE-NVVLLPHVAS 286
RG +VDE + AL G LGG DVFE E +P+EL+ V PH+ S
Sbjct: 236 RGSVVDEAAVAEALKSGHLGGYAADVFEMEDWARPDRPRSIPQELLDQHDRTVFTPHIGS 295
Query: 287 ATVETRKAMADLVVGNL 303
A E R + N+
Sbjct: 296 AVDEVRLEIELEAALNI 312
>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 = 189 bits (482), Expect = 3e-58
Identities = 92/258 (35%), Positives = 145/258 (56%), Gaps = 16/258 (6%)
Query: 63 AELIESLPKLEIVATCSVGLDKIDLARCKEKGIRVANTPDVLTDDVADLAIGLILAVLRR 122
E+IE+ L++++ G+D +DL CKE+GI V+N T+ VA+L IGL + +LR
Sbjct: 61 GEVIEACKNLKMISVAFTGVDHVDLEACKERGITVSNAAGYSTEAVAELTIGLAIDLLRN 120
Query: 123 ICESDRYVRSGEWKKG----EFKMTTKFTGKSVGILGMGRIGTAIAKRAEAFDC-IIGYN 177
I D VR+G K G E GK+VGI+G G IG +A+ +AF C ++ Y+
Sbjct: 121 IVPCDAAVRAGGTKAGLIGRELA------GKTVGIVGTGAIGLRVARLFKAFGCKVLAYS 174
Query: 178 SRTEKPNLNYKY--YPNLIDLASNCQILVVACSLTEETQHIVNRQVINALGPKGVLINIG 235
R+EK Y +L +L + I+ + L +ET+ ++ ++ + + +LIN
Sbjct: 175 -RSEKEEAKALGIEYVSLDELLAESDIVSLHLPLNDETKGLIGKEKLALMKESAILINTA 233
Query: 236 RGLLVDEHELVSALLQGRLGGAGLDVFEHEPDVPEE--LIGLENVVLLPHVASATVETRK 293
RG +VD L AL +G++ GAG+DVF+ EP +P + L+ N +L PHVA AT E +
Sbjct: 234 RGPVVDNEALADALNEGKIAGAGIDVFDMEPPLPADYPLLHAPNTILTPHVAFATEEAME 293
Query: 294 AMADLVVGNLQAHFGKKP 311
A++V N++A KP
Sbjct: 294 KRAEIVFDNIEAWLAGKP 311
>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 = 187 bits (477), Expect = 2e-57
Identities = 88/314 (28%), Positives = 154/314 (49%), Gaps = 16/314 (5%)
Query: 10 VLMVCPVSNYLEQEIEKSFKVFKLWHFEDKEQFINTHKDSIQAVVGSAAAGADAELIESL 69
+L++ P+ + + + + E+ D ++G+ EL+ +
Sbjct: 3 ILVLSPLDDEHLERLRAAAPGA-ELRVVTAEELTEELAD-ADVLLGN---PPLPELLPAA 57
Query: 70 PKLEIVATCSVGLDKIDLARCKEKGIRVANTPDVLTDDVADLAIGLILAVLRRICESDRY 129
P+L + + S G+D + E+ + + N + +A+ +G +LA R++ R
Sbjct: 58 PRLRWIQSTSAGVDALLFPELLERDVVLTNARGIFGPPIAEYVLGYMLAFARKLPRYARN 117
Query: 130 VRSGEWKKGEFKMTTKFTGKSVGILGMGRIGTAIAKRAEAFDC-IIGYNSRTEKPNLNY- 187
W++ + GK+V I+G+G IG IA+RA+AF +IG R+ +P
Sbjct: 118 QAERRWQRRG--PVRELAGKTVLIVGLGDIGREIARRAKAFGMRVIGVR-RSGRPAPPVV 174
Query: 188 -KYYP--NLIDLASNCQILVVACSLTEETQHIVNRQVINALGPKGVLINIGRGLLVDEHE 244
+ Y L +L +V A LT ET+ + N + A+ P VLIN+GRG +VDE
Sbjct: 175 DEVYTPDELDELLPEADYVVNALPLTPETRGLFNAERFAAMKPGAVLINVGRGSVVDEDA 234
Query: 245 LVSALLQGRLGGAGLDVFEHEPDVPEE--LIGLENVVLLPHVASATVETRKAMADLVVGN 302
L+ AL GR+ GA LDVFE EP +P + L L NV++ PH++ + + + ++ + N
Sbjct: 235 LIEALESGRIAGAALDVFEEEP-LPADSPLWDLPNVIITPHISGDSPSYPERVVEIFLEN 293
Query: 303 LQAHFGKKPLLTPV 316
L+ + +PLL V
Sbjct: 294 LRRYLAGEPLLNVV 307
>gnl|CDD|237436 PRK13581, PRK13581, D-3-phosphoglycerate dehydrogenase;
Provisional.
Length = 526
Score = 184 bits (469), Expect = 4e-54
Identities = 81/236 (34%), Positives = 134/236 (56%), Gaps = 12/236 (5%)
Query: 62 DAELIESLPKLEIVATCSVGLDKIDLARCKEKGIRVANTPDVLTDDVADLAIGLILAVLR 121
AE++E+ L+++ VG+D +D+ +GI V N P T A+ I L+LA+ R
Sbjct: 55 TAEVLEAAKNLKVIGRAGVGVDNVDVPAATRRGIIVVNAPTGNTISAAEHTIALMLALAR 114
Query: 122 RICESDRYVRSGEWKKGEFKMTTKFTGKSVGILGMGRIGTAIAKRAEAFDC-IIGYN--- 177
I ++ +++G+W++ +F M + GK++GI+G+GRIG+ +AKRA+AF +I Y+
Sbjct: 115 NIPQAHASLKAGKWERKKF-MGVELYGKTLGIIGLGRIGSEVAKRAKAFGMKVIAYDPYI 173
Query: 178 --SRTEKPNLNYKYYPNLIDLASNCQILVVACSLTEETQHIVNRQVINALGPKGV-LINI 234
R + L + +L +L + + + LT ET+ ++ + + A GV +IN
Sbjct: 174 SPERAAQ--LGVELV-SLDELLARADFITLHTPLTPETRGLIGAEEL-AKMKPGVRIINC 229
Query: 235 GRGLLVDEHELVSALLQGRLGGAGLDVFEHEPDVPEELIGLENVVLLPHVASATVE 290
RG ++DE L AL G++ GA LDVFE EP L L NVV+ PH+ ++T E
Sbjct: 230 ARGGIIDEAALAEALKSGKVAGAALDVFEKEPPTDSPLFELPNVVVTPHLGASTAE 285
>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 = 177 bits (451), Expect = 1e-53
Identities = 90/306 (29%), Positives = 148/306 (48%), Gaps = 16/306 (5%)
Query: 20 LEQEIEKSFKVFKLWHFEDKEQFINTHKDSIQAVVGSAAAGADAELIESLPKLEIVATCS 79
L +E E + + E ++ + +VG E + +L +L+++ S
Sbjct: 11 LREEFEAALEGLYAEVPELPDEAAEEALEDADVLVGGR--LTKEEALAALKRLKLIQVPS 68
Query: 80 VGLDKIDLARCKEKGIRVANTPDVLTDDVADLAIGLILAVLRRICESDRYVRSGEWKK-- 137
G+D + L R E G+ VAN + VA+ A+ LILA+ +RI E D +R G W
Sbjct: 69 AGVDHLPLERLPE-GVVVANNHG-NSPAVAEHALALILALAKRIVEYDNDLRRGIWHGRA 126
Query: 138 GEFKMTTKFTGKSVGILGMGRIGTAIAKRAEAFDC-IIGYNSRTEKPNLNYKYYP--NLI 194
GE + + GK+VGILG G IG IA+ +AF +IG + ++ +L
Sbjct: 127 GEEPESKELRGKTVGILGYGHIGREIARLLKAFGMRVIGVSRSPKEDEGADFVGTLSDLD 186
Query: 195 DLASNCQILVVACSLTEETQHIVNRQVINALGPKGVLINIGRGLLVDEHELVSALLQGRL 254
+ ++VVA LT++T+ ++ + A+ P +L+N+GRG +VDE L AL + +
Sbjct: 187 EALEQADVVVVALPLTKQTRGLIGAAELAAMKPGAILVNVGRGPVVDEEALYEALKERPI 246
Query: 255 GGAGLDVFEHEPDVPEE-------LIGLENVVLLPHVASATVETRKAMADLVVGNLQAHF 307
GA +DV+ P + L NV++ PH A T ET + D N++ +
Sbjct: 247 AGAAIDVWWRYPSRGDPVAPSRYPFHELPNVIMSPHNAGWTEETFRRRIDEAAENIRRYL 306
Query: 308 GKKPLL 313
+PLL
Sbjct: 307 RGEPLL 312
>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 = 176 bits (450), Expect = 2e-53
Identities = 84/251 (33%), Positives = 132/251 (52%), Gaps = 9/251 (3%)
Query: 62 DAELIESLPKLEIVATCSVGLDKIDLARCKEKGIRVANTPDVLTDDVADLAIGLILAVLR 121
A L+E LP L+++ T + IDLA KE+GI V T A+L LILA+ R
Sbjct: 60 PAALLERLPNLKLLVTTGMRNASIDLAAAKERGIVVCGTGGG-PTATAELTWALILALAR 118
Query: 122 RICESDRYVRSGEWKKGEFKMTTKFTGKSVGILGMGRIGTAIAKRAEAFDC-IIGYNSR- 179
+ E D +R+G W+ + T GK++GI+G+GRIG +A+ +AF +I ++S
Sbjct: 119 NLPEEDAALRAGGWQTT---LGTGLAGKTLGIVGLGRIGARVARIGQAFGMRVIAWSSNL 175
Query: 180 -TEK-PNLNYKYYPNLIDLASNCQILVVACSLTEETQHIVNRQVINALGPKGVLINIGRG 237
E+ + + +L + ++ + L++ T+ +V + + + P +L+N RG
Sbjct: 176 TAERAAAAGVEAAVSKEELFATSDVVSLHLVLSDRTRGLVGAEDLALMKPTALLVNTSRG 235
Query: 238 LLVDEHELVSALLQGRLGGAGLDVFEHEP-DVPEELIGLENVVLLPHVASATVETRKAMA 296
LVDE L++AL GR+ GA LDVF+ EP L GL NV+L PH+ T E +
Sbjct: 236 PLVDEGALLAALRAGRIAGAALDVFDVEPLPADHPLRGLPNVLLTPHIGYVTEEAYEGFY 295
Query: 297 DLVVGNLQAHF 307
V N+ A
Sbjct: 296 GQAVENIAAWL 306
>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 = 176 bits (449), Expect = 3e-53
Identities = 84/259 (32%), Positives = 131/259 (50%), Gaps = 19/259 (7%)
Query: 62 DAELIESLPKLEIVATCSVGLDKIDLARCKEKGIRVANTPDVLTDDVADLAIGLILAVLR 121
DAEL++ P L+ ++ + G D IDL KE GI V N P+ + VA+ I LILA+LR
Sbjct: 58 DAELLDKAPGLKFISLRATGYDNIDLDYAKELGIGVTNVPEYSPNAVAEHTIALILALLR 117
Query: 122 RICESDRYVRSGEWKKGEFKMTTKFTGKSVGILGMGRIGTAIAKRAEAFDC-IIGYN--S 178
D ++ + + + ++VG++G G+IG A+A+RA+ F +I Y+
Sbjct: 118 NRKYIDERDKNQDLQDAGVIGR-ELEDQTVGVVGTGKIGRAVAQRAKGFGMKVIAYDPFR 176
Query: 179 RTEKPNLNYKYYPNLIDLASNCQILVVACSLTEETQHIVNRQVINALGPKGVLINIGRGL 238
E + KY +L +L N I+ + LT E H++N + + ++IN RG
Sbjct: 177 NPELEDKGVKYV-SLEELFKNSDIISLHVPLTPENHHMINEEAFKLMKKGVIIINTARGS 235
Query: 239 LVDEHELVSALLQGRLGGAGLDVFEHE-PDVPE-------------ELIGLENVVLLPHV 284
LVD L+ AL G++ GAGLDV E E PD+ + L NV++ PH
Sbjct: 236 LVDTEALIEALDSGKIFGAGLDVLEDETPDLLKDLEGEIFKDALNALLGRRPNVIITPHT 295
Query: 285 ASATVETRKAMADLVVGNL 303
A T + K M ++ N+
Sbjct: 296 AFYTDDALKNMVEISCENI 314
>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 = 171 bits (435), Expect = 3e-51
Identities = 90/270 (33%), Positives = 143/270 (52%), Gaps = 11/270 (4%)
Query: 51 QAVVGSAAAGADAELIESLPKLEIVATCSVGLDKIDLARCKEKGIRVANTPD-VLTDDVA 109
++ S D E E L+++A +G D +DL E G+ V P V D VA
Sbjct: 49 DIIIASVTPNFDKEFFEYNDGLKLIARHGIGYDNVDLKAATEHGVIVTRVPGAVERDAVA 108
Query: 110 DLAIGLILAVLRRICESDRYVRSGEWKKGEFKMTTKFTGKSVGILGMGRIGTAIAKRA-E 168
+ A+ LIL VLR+I ++ V+ G+W + + + +GK+VGI+G G IG+ +A+ E
Sbjct: 109 EHAVALILTVLRKINQASEAVKEGKWTERANFVGHELSGKTVGIIGYGNIGSRVAEILKE 168
Query: 169 AFDC-IIGY--NSRTEKPNLNYKYYPNLIDLASNCQILVVACSLTEETQHIVNRQVINAL 225
F+ ++ Y E +L +L + I+ + LTEET H++N + + +
Sbjct: 169 GFNAKVLAYDPYVSEEVIKKKGAKPVSLEELLAESDIISLHAPLTEETYHMINEKAFSKM 228
Query: 226 GPKGVLINIGRGLLVDEHELVSALLQGRLGGAGLDVFEHEP---DVPEELIGLENVVLLP 282
+L+N RG L+DE L+ AL G++ GAGLDV E EP D P L+ ENVV+ P
Sbjct: 229 KKGVILVNTARGELIDEEALIEALKSGKIAGAGLDVLEEEPIKADHP--LLHYENVVITP 286
Query: 283 HVASATVETRKAMADLVVGNLQAHF-GKKP 311
H+ + T E+ M + VV +++ GK+P
Sbjct: 287 HIGAYTYESLYGMGEKVVDDIEDFLAGKEP 316
>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 = 174 bits (444), Expect = 2e-50
Identities = 83/255 (32%), Positives = 142/255 (55%), Gaps = 9/255 (3%)
Query: 52 AVVGSAAAGADAELIESLPKLEIVATCSVGLDKIDLARCKEKGIRVANTPDVLTDDVADL 111
A++ +A E+I + PKL+++ VG+D ID+ +GI V N P T A+
Sbjct: 43 ALIVRSATKVTEEVIAAAPKLKVIGRAGVGVDNIDIEAATARGILVVNAPTGNTISAAEH 102
Query: 112 AIGLILAVLRRICESDRYVRSGEWKKGEFKMTTKFTGKSVGILGMGRIGTAIAKRAEAFD 171
A+ ++LA R I ++D ++ GEW + F M T+ GK++G++G+GRIG+ +AKRA+AF
Sbjct: 103 ALAMLLAAARNIPQADASLKEGEWDRKAF-MGTELYGKTLGVIGLGRIGSIVAKRAKAFG 161
Query: 172 C-IIGYN-----SRTEKPNLNYKYYPNLIDLASNCQILVVACSLTEETQHIVNRQVINAL 225
++ Y+ R E+ L + +L +L + + V LT ET+ ++ + + +
Sbjct: 162 MKVLAYDPYISPERAEQ--LGVELVDDLDELLARADFITVHTPLTPETRGLIGAEELAKM 219
Query: 226 GPKGVLINIGRGLLVDEHELVSALLQGRLGGAGLDVFEHEPDVPEELIGLENVVLLPHVA 285
+++N RG ++DE L AL +G + A LDVFE EP L L+NV+ PH+
Sbjct: 220 KKGVIIVNCARGGIIDEAALYEALEEGHVRAAALDVFEKEPPTDNPLFDLDNVIATPHLG 279
Query: 286 SATVETRKAMADLVV 300
++T E ++ +A V
Sbjct: 280 ASTREAQENVATQVA 294
>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 = 161 bits (410), Expect = 2e-47
Identities = 95/273 (34%), Positives = 145/273 (53%), Gaps = 35/273 (12%)
Query: 62 DAELIESLPKLEIVATCSVGLDKIDLARCKEKGIRVANTPDVLTDDVADLAIGLILAVLR 121
DAE++E LP+L+++AT S G D IDL C+E+GI V N PD VA+ A L+LA+ R
Sbjct: 54 DAEVLEKLPRLKLIATRSTGFDHIDLEACRERGIAVCNVPDYGEATVAEHAFALLLALSR 113
Query: 122 RICESDRYVRSGEWKKGEFKMT--TKF--TGKSVGILGMGRIGTAIAKRAEAFDC-IIGY 176
++ E+ R+ ++G+F F GK++G++G GRIG +A+ A F ++ Y
Sbjct: 114 KLREA--IERT---RRGDFSQAGLRGFELAGKTLGVVGTGRIGRRVARIARGFGMKVLAY 168
Query: 177 NSRTEK---PNLNYKYYPNLIDLASNCQILVVACSLTEETQHIVNRQVINALGPKGVLIN 233
+ ++ L ++Y L +L I+ + T +T H++NR+ + P VLIN
Sbjct: 169 DVVPDEELAERLGFRYVS-LEELLQESDIISLHVPYTPQTHHLINRENFALMKPGAVLIN 227
Query: 234 IGRGLLVDEHELVSALLQGRLGGAGLDVFEHEPDVPEE---------------------L 272
RG +VD LV AL +G+L GAGLDV E E + EE L
Sbjct: 228 TARGAVVDTEALVRALKEGKLAGAGLDVLEQEEVLREEAELFREDVSPEDLKKLLADHAL 287
Query: 273 IGLENVVLLPHVASATVETRKAMADLVVGNLQA 305
+ NV++ PHVA T E + + D V N++A
Sbjct: 288 LRKPNVIITPHVAYNTKEALERILDTTVENIKA 320
>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 = 155 bits (394), Expect = 6e-45
Identities = 77/268 (28%), Positives = 124/268 (46%), Gaps = 22/268 (8%)
Query: 62 DAELIESLPKLEIVATCSVGLDKIDLARCKEKGIRVANTPDVLTDDVADLAIGLILAVLR 121
DAEL+ P+L V + + + E+GI V + D + VA+ + IL LR
Sbjct: 63 DAELLARAPRLRAVVHAAGSVRGLVTDAVWERGILVTSAADANAEPVAEFTLAAILLALR 122
Query: 122 RICESDRYVRSGE-WKKGEFKMTTKFTGKSVGILGMGRIGTAIAKRAEAFDC-IIGYNS- 178
RI R+G W + G++VGI+G GRIG A+ + F ++ Y+
Sbjct: 123 RIPRFAAAYRAGRDWGWPTRRGGRGLYGRTVGIVGFGRIGRAVVELLRPFGLRVLVYDPY 182
Query: 179 ---------RTEKPNLNYKYYPNLIDLASNCQILVVACSLTEETQHIVNRQVINALGPKG 229
E +L+ +L + ++ + LT ET+ +++ +++ +
Sbjct: 183 LPAAEAAALGVELVSLD--------ELLARSDVVSLHAPLTPETRGMIDARLLALMRDGA 234
Query: 230 VLINIGRGLLVDEHELVSALLQGRLGGAGLDVFEHEP-DVPEELIGLENVVLLPHVASAT 288
IN RG LVDE L++ L GRL A LDV + EP L L NV+L PH+A +T
Sbjct: 235 TFINTARGALVDEAALLAELRSGRL-RAALDVTDPEPLPPDSPLRTLPNVLLTPHIAGST 293
Query: 289 VETRKAMADLVVGNLQAHFGKKPLLTPV 316
+ R+ + D + L+ +PLL V
Sbjct: 294 GDERRRLGDYALDELERFLAGEPLLHEV 321
>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 = 154 bits (391), Expect = 8e-45
Identities = 79/288 (27%), Positives = 138/288 (47%), Gaps = 29/288 (10%)
Query: 43 INTHKDSIQAVVGSAAAGADA--------ELIESLPKLEIVATCSVGLDKIDLARCKEKG 94
+ K V A DA ++ P L+ +A G++ ID+ ++G
Sbjct: 14 LERFKKDKYEVKEDALEDPDALIVRSDKLHDMDFAPSLKAIARAGAGVNNIDVDAASKRG 73
Query: 95 IRVANTPDVLTDDVADLAIGLILAVLRRICESDRYV---------RSGEWKKGEFKMTTK 145
I V NTP + VA+L I ++LA+ R I ++ ++V + E K +F + T+
Sbjct: 74 IVVFNTPGANANAVAELVIAMMLALSRNIIQAIKWVTNGDGDDISKGVEKGKKQF-VGTE 132
Query: 146 FTGKSVGILGMGRIGTAIAKRAEAFDC-IIGYN---SRTEKPNLNYK--YYPNLIDLASN 199
GK++G++G+G IG +A A A +IGY+ S L+ + +L +L +
Sbjct: 133 LRGKTLGVIGLGNIGRLVANAALALGMKVIGYDPYLSVEAAWKLSVEVQRVTSLEELLAT 192
Query: 200 CQILVVACSLTEETQHIVNRQVINALGPKGVLINIGRGLLVDEHELVSALLQGRLGGAGL 259
+ + LT+ET+ ++N +++ + P +L+N RG +VDE L+ AL +G+LGG
Sbjct: 193 ADYITLHVPLTDETRGLINAELLAKMKPGAILLNFARGEIVDEEALLEALDEGKLGGYVT 252
Query: 260 DVFEHEPDVPEELIGLENVVLLPHVASATVETRKAMADLVVGNLQAHF 307
D E P L L NV+ PH+ ++T E + A + +
Sbjct: 253 DFPE-----PALLGHLPNVIATPHLGASTEEAEENCAVMAARQIMDFL 295
>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 = 153 bits (389), Expect = 2e-44
Identities = 88/256 (34%), Positives = 136/256 (53%), Gaps = 13/256 (5%)
Query: 62 DAELIESLPKLEIVATCSVGLDKIDLARCKEKGIRVANTPDVLTDDVADLAIGLILAVLR 121
D E IE L+ +A GL+ IDL KEKGI + N P+ D V + A+G++LA+
Sbjct: 53 DKEFIEKATNLKFIARAGAGLENIDLEYAKEKGIELFNAPEGNRDAVGEHALGMLLALFN 112
Query: 122 RICESDRYVRSGEWKKGEFKMTTKFTGKSVGILGMGRIGTAIAKRAEAFDC-IIGYNSRT 180
++ +D+ VR+G W + E + GK+VGI+G G +G A AKR F C +I Y+
Sbjct: 113 KLNRADQEVRNGIWDR-EGNRGVELMGKTVGIIGYGNMGKAFAKRLSGFGCKVIAYDKYK 171
Query: 181 EKPNLNYKYYPNLIDLASNCQILVVACSLTEETQHIVNRQVINALGPKGVLINIGRGLLV 240
+ + +L L IL + LT ET+ +VN++ I++ IN RG +V
Sbjct: 172 NFGDAYAEQV-SLETLFKEADILSLHIPLTPETRGMVNKEFISSFKKPFYFINTARGKVV 230
Query: 241 DEHELVSALLQGRLGGAGLDVFEHE----------PDVPEELIGLENVVLLPHVASATVE 290
+LV AL G++ GA LDV E+E P+ E LI V+L PH+A T E
Sbjct: 231 VTKDLVKALKSGKILGACLDVLEYEKASFESIFNQPEAFEYLIKSPKVILTPHIAGWTFE 290
Query: 291 TRKAMADLVVGNLQAH 306
+ + +A+++V ++A
Sbjct: 291 SYEKIAEVLVDKIKAL 306
>gnl|CDD|181414 PRK08410, PRK08410, 2-hydroxyacid dehydrogenase; Provisional.
Length = 311
Score = 152 bits (386), Expect = 5e-44
Identities = 83/255 (32%), Positives = 140/255 (54%), Gaps = 14/255 (5%)
Query: 62 DAELIESLPKLEIVATCSVGLDKIDLARCKEKGIRVANTPDVLTDDVADLAIGLILAVLR 121
D E++ LP L+++ + G + +D+ K+KGI V N T+ VA ++L++L
Sbjct: 54 DKEVLSQLPNLKLICITATGTNNVDIEYAKKKGIAVKNVAGYSTESVAQHTFAMLLSLLG 113
Query: 122 RICESDRYVRSGEWKKGEF-----KMTTKFTGKSVGILGMGRIGTAIAKRAEAFDCIIGY 176
RI DRYV+SGE+ + + + GK GI+G+G IG +AK A+AF + Y
Sbjct: 114 RINYYDRYVKSGEYSESPIFTHISRPLGEIKGKKWGIIGLGTIGKRVAKIAQAFGAKVVY 173
Query: 177 NSRTEKPNLNYKY-YPNLIDLASNCQILVVACSLTEETQHIVNRQVINALGPKGVLINIG 235
S T N N +Y +L +L I+ + L E+T++++ + + L +LIN+G
Sbjct: 174 YS-TSGKNKNEEYERVSLEELLKTSDIISIHAPLNEKTKNLIAYKELKLLKDGAILINVG 232
Query: 236 RGLLVDEHELVSALLQGRLGGAGLDVFEHEPDVPEE--LIGL---ENVVLLPHVASATVE 290
RG +V+E +L AL + + AGLDV E EP + + L+ + E +++ PH+A A+ E
Sbjct: 233 RGGIVNEKDLAKALDEKDI-YAGLDVLEKEP-MEKNHPLLSIKNKEKLLITPHIAWASKE 290
Query: 291 TRKAMADLVVGNLQA 305
RK + + V N++
Sbjct: 291 ARKTLIEKVKENIKD 305
>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 = 147 bits (373), Expect = 5e-42
Identities = 86/288 (29%), Positives = 143/288 (49%), Gaps = 12/288 (4%)
Query: 36 FEDKEQFINTHKDSIQAVVGSAAAGADAELIESLPKLEIVATCSVGLDKIDLARCKEKGI 95
FED+ +D I+ + G D + + L+ + S G+D + L K+KGI
Sbjct: 27 FEDELSDEEDLED-IEILYG-YNPDFDELDLAKMKNLKWIQLYSAGVDYLPLEYIKKKGI 84
Query: 96 RVANTPDVLTDDVADLAIGLILAVLRRICESDRYVRSGEWKKGEFKMTTKFTGKSVGILG 155
+ N + + +A+ +G IL + + + ++ + + +WK + GK++ LG
Sbjct: 85 LLTNNSGIHSIPIAEWIVGYILEIYKGLKKAYKNQKEKKWKMDSS--LLELYGKTILFLG 142
Query: 156 MGRIGTAIAKRAEAFDC-IIGYN-SRTEKPNLNYKYYP--NLIDLASNCQILVVACSLTE 211
G IG IAKR +AF +IG N S + + K YP L ++ I+V LTE
Sbjct: 143 TGSIGQEIAKRLKAFGMKVIGVNTSGRDVEYFD-KCYPLEELDEVLKEADIVVNVLPLTE 201
Query: 212 ETQHIVNRQVINALGPKGVLINIGRGLLVDEHELVSALLQGRLGGAGLDVFEHEPDVPEE 271
ET H+ + + + IN+GRG VDE L+ AL ++ GA LDVFE EP +P++
Sbjct: 202 ETHHLFDEAFFEQMKKGALFINVGRGPSVDEDALIEALKNKQIRGAALDVFEEEP-LPKD 260
Query: 272 --LIGLENVVLLPHVASATVETRKAMADLVVGNLQAHFGKKPLLTPVV 317
L L+NV++ PH++ + + + D+ NL++ LL VV
Sbjct: 261 SPLWDLDNVLITPHISGVSEHFNERLFDIFYENLKSFLEDGELLKNVV 308
>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 = 147 bits (372), Expect = 6e-42
Identities = 78/267 (29%), Positives = 125/267 (46%), Gaps = 11/267 (4%)
Query: 57 AAAGADAELIESLPKLEIVATCSVGLDK-IDLARCKEKGIRVANTPDVLTDDVADLAIGL 115
+ + E + + P + V G++ ++ + G R N + VA+ A+ L
Sbjct: 35 TGSAREPERLPASPGVRWVQLPFAGVEAFVEAGVITDPGRRWTNAAGAYAETVAEHALAL 94
Query: 116 ILAVLRRICESDRYVRSGEW-KKGEFKMTTKFTGKSVGILGMGRIGTAIAKRAEAFDC-I 173
+LA LR++ R+ W E + T G +V I+G G IG A+ F +
Sbjct: 95 LLAGLRQL---PARARATTWDPAEEDDLVTLLRGSTVAIVGAGGIGRALIPLLAPFGAKV 151
Query: 174 IGYNSRTEKPNLNYKYYP--NLIDLASNCQILVVACSLTEETQHIVNRQVINALGPKGVL 231
I N + P L ++ + +V+A LT ET+H+V+ + A+ P L
Sbjct: 152 IAVNRSGRPVEGADETVPADRLDEVWPDADHVVLAAPLTPETRHLVDAAALAAMKPHAWL 211
Query: 232 INIGRGLLVDEHELVSALLQGRLGGAGLDVFEHEPDVPEE--LIGLENVVLLPHVASATV 289
+N+ RG LVD LV AL G + GA LDV + EP +P+ L L N ++ PHVA+
Sbjct: 212 VNVARGPLVDTDALVDALRSGEIAGAALDVTDPEP-LPDGHPLWSLPNALITPHVANTPE 270
Query: 290 ETRKAMADLVVGNLQAHFGKKPLLTPV 316
R +A+ V N++A +PLL V
Sbjct: 271 VIRPLLAERVAENVRAFAAGEPLLGVV 297
>gnl|CDD|180588 PRK06487, PRK06487, glycerate dehydrogenase; Provisional.
Length = 317
Score = 146 bits (370), Expect = 1e-41
Identities = 89/299 (29%), Positives = 146/299 (48%), Gaps = 12/299 (4%)
Query: 22 QEIEKSFKVFKLWHFEDKEQFINTHKDSIQAVVGSAAAGADAELIESLPKLEIVATCSVG 81
+E++F +L EQ + + A+ A DA + + P+L+++ + G
Sbjct: 19 SPLEQAFDELQLHDATTPEQVAERLRGAQVAISNKVAL--DAAALAAAPQLKLILVAATG 76
Query: 82 LDKIDLARCKEKGIRVANTPDVLTDDVADLAIGLILAVLRRICESDRYVRSGEWKK-GEF 140
+ +DLA +E+GI V N T VA + L+LA+ R+ + + V +G W++ +F
Sbjct: 77 TNNVDLAAARERGITVCNCQGYGTPSVAQHTLALLLALATRLPDYQQAVAAGRWQQSSQF 136
Query: 141 KM----TTKFTGKSVGILGMGRIGTAIAKRAEAFDCIIGYNSRTEKPNLNYKYYPNLIDL 196
+ + GK++G+LG G +G A+A+ AEAF + +P + L +L
Sbjct: 137 CLLDFPIVELEGKTLGLLGHGELGGAVARLAEAFGMRVLIGQLPGRPARPDRL--PLDEL 194
Query: 197 ASNCQILVVACSLTEETQHIVNRQVINALGPKGVLINIGRGLLVDEHELVSALLQGRLGG 256
L + C LTE T+H++ + + + P +LIN RG LVDE L AL G LGG
Sbjct: 195 LPQVDALTLHCPLTEHTRHLIGARELALMKPGALLINTARGGLVDEQALADALRSGHLGG 254
Query: 257 AGLDVFEHEPDV---PEELIGLENVVLLPHVASATVETRKAMADLVVGNLQAHFGKKPL 312
A DV EP V P + +++ PH A + E R+ + + N +A F KPL
Sbjct: 255 AATDVLSVEPPVNGNPLLAPDIPRLIVTPHSAWGSREARQRIVGQLAENARAFFAGKPL 313
>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 = 144 bits (366), Expect = 9e-41
Identities = 92/278 (33%), Positives = 135/278 (48%), Gaps = 35/278 (12%)
Query: 61 ADAELIESLPKLEI--VATCSVGLDKIDLARCKEKGIRVANTPDVLTDDVADLAIGLILA 118
DA ++E L +L + +A G + +DL KE GI V P VA+ A+ L+LA
Sbjct: 56 LDAPVLEKLAELGVKLIALRCAGFNNVDLKAAKELGITVVRVPAYSPYAVAEHAVALLLA 115
Query: 119 VLRRICESDRYVRSGEWKKGEFKMT--TKFT--GKSVGILGMGRIGTAIAKRAEAFDC-I 173
+ R+I + VR +G F + F GK+VG++G G+IG A A+ + F C +
Sbjct: 116 LNRKIHRAYNRVR-----EGNFSLDGLLGFDLHGKTVGVIGTGKIGQAFARILKGFGCRV 170
Query: 174 IGY----NSRTEKPNLNYKYYPNLIDLASNCQILVVACSLTEETQHIVNRQVINALGPKG 229
+ Y N K + Y +L +L + I+ + C LT ET H++N + I A G
Sbjct: 171 LAYDPYPNPELAKLGVEYV---DLDELLAESDIISLHCPLTPETHHLINAETI-AKMKDG 226
Query: 230 V-LINIGRGLLVDEHELVSALLQGRLGGAGLDVFEHEP--------------DVPEELIG 274
V LIN RG L+D L+ AL G++GG GLDV+E E DV L+
Sbjct: 227 VMLINTSRGGLIDTKALIEALKSGKIGGLGLDVYEEEAGLFFEDHSDEIIQDDVLARLLS 286
Query: 275 LENVVLLPHVASATVETRKAMADLVVGNLQAHFGKKPL 312
NV++ H A T E +A+ + NL KPL
Sbjct: 287 FPNVLITGHQAFFTKEALTNIAETTLENLDDFEAGKPL 324
>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 = 140 bits (355), Expect = 2e-39
Identities = 78/278 (28%), Positives = 121/278 (43%), Gaps = 43/278 (15%)
Query: 57 AAAGADAELIESLPKLEIVATCSVGLDKIDLARCKEKGIRVANTPDV---------LTDD 107
L+ LP L+ + + G+D + + PDV L
Sbjct: 44 LVWKPPPGLLARLPNLKAIFSLGAGVDHLLAD---------PDLPDVPIVRLVDPGLAQG 94
Query: 108 VADLAIGLILAVLRRICESDRYV---RSGEWKKGEFKMTTKFTGKSVGILGMGRIGTAIA 164
+A+ + +L + R + DRY R G WK + + VG+LG+G +G A+A
Sbjct: 95 MAEYVLAAVLRLHRDM---DRYAAQQRRGVWKPLPQRPAAERR---VGVLGLGELGAAVA 148
Query: 165 KRAEAFDCIIGYN----SRTEKPNLNYKYY---PNLIDLASNCQILVVACSLTEETQHIV 217
+R A G+ SR+ K + L + ILV LT ET+ I+
Sbjct: 149 RRLAAL----GFPVSGWSRSPKDIEGVTCFHGEEGLDAFLAQTDILVCLLPLTPETRGIL 204
Query: 218 NRQVINALGPKGVLINIGRGLLVDEHELVSALLQGRLGGAGLDVFEHEPDVPEE--LIGL 275
N +++ L LIN+GRG + E +L++AL G L GA LDVFE EP +P + L
Sbjct: 205 NAELLARLPRGAALINVGRGPHLVEADLLAALDSGHLSGAVLDVFEQEP-LPADHPLWRH 263
Query: 276 ENVVLLPHVASATVETRKAMADLVVGNLQAHFGKKPLL 313
V + PH+A+ T + A V N++ +PL
Sbjct: 264 PRVTVTPHIAAIT--DPDSAAAQVAENIRRLEAGEPLP 299
>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 = 137 bits (347), Expect = 2e-38
Identities = 82/264 (31%), Positives = 122/264 (46%), Gaps = 9/264 (3%)
Query: 52 AVVGSAAAGADAELIESLPKLEIVATCSVGLDKIDLARCKEKGIRVANTPDVLTDDVADL 111
V AA E + +LP+L +V T S G D + L E G+ + N V A+L
Sbjct: 41 VVPPYMAAPPVLEALRALPRLRVVQTLSAGYDGV-LPLLPE-GVTLCNARGVHDASTAEL 98
Query: 112 AIGLILAVLRRICESDRYVRSGEWKKGEFKMTTKFTGKSVGILGMGRIGTAIAKRAEAFD 171
A+ LILA LR + R G W+ T + V I+G G IG AI +R F+
Sbjct: 99 AVALILASLRGLPRFVRAQARGRWEPRR---TPSLADRRVLIVGYGSIGRAIERRLAPFE 155
Query: 172 CIIGYNSRTEKPNLNYKYYPNLIDLASNCQILVVACSLTEETQHIVNRQVINALGPKGVL 231
+ +RT +P L L ++V+ LT+ET+ +V+ + + + +L
Sbjct: 156 VRVTRVARTARPGEQVHGIDELPALLPEADVVVLIVPLTDETRGLVDAEFLARMPDGALL 215
Query: 232 INIGRGLLVDEHELVSALLQGRLGGAGLDVFEHEPDVPEE--LIGLENVVLLPHVASATV 289
+N+ RG +VD LV+ L GRL A LDV + EP +P L V++ PHV AT
Sbjct: 216 VNVARGPVVDTDALVAELASGRL-RAALDVTDPEP-LPPGHPLWSAPGVLITPHVGGATP 273
Query: 290 ETRKAMADLVVGNLQAHFGKKPLL 313
LV L+ + +PL
Sbjct: 274 AFLPRAYALVRRQLRRYAAGEPLE 297
>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 = 133 bits (336), Expect = 1e-36
Identities = 79/251 (31%), Positives = 127/251 (50%), Gaps = 13/251 (5%)
Query: 62 DAELIESLPKLEIVATCSVGLDKIDLARCKEKGIRVANTPDVLTDDVADLAIGLILAVLR 121
E++E+ PKL + +G +++DL ++GI V N P T VA+L IG I+ + R
Sbjct: 55 TEEVLEAAPKLLAIGCFCIGTNQVDLDAAAKRGIPVFNAPFSNTRSVAELVIGEIIMLAR 114
Query: 122 RICESDRYVRSGEWKK---GEFKMTTKFTGKSVGILGMGRIGTAIAKRAEAFDC-IIGYN 177
R+ + + G W K G ++ GK++GI+G G IG+ ++ AEA +I Y+
Sbjct: 115 RLPDRNAAAHRGIWNKSATGSHEV----RGKTLGIIGYGHIGSQLSVLAEALGMRVIFYD 170
Query: 178 SRTEKPNLNYKYYPNLIDLASNCQILVVACSLTEETQHIVNRQVINALGPKGVLINIGRG 237
+ P N + +L +L + + + T T++++ + I + +LIN RG
Sbjct: 171 IAEKLPLGNARQVSSLEELLAEADFVTLHVPATPSTKNMIGAEEIAQMKKGAILINASRG 230
Query: 238 LLVDEHELVSALLQGRLGGAGLDVFEHEP---DVP--EELIGLENVVLLPHVASATVETR 292
+VD L AL G L GA +DVF EP P L GL NV+L PH+ +T E +
Sbjct: 231 TVVDIDALAEALRSGHLAGAAVDVFPEEPASNGEPFSSPLQGLPNVILTPHIGGSTEEAQ 290
Query: 293 KAMADLVVGNL 303
+ + V G L
Sbjct: 291 ENIGLEVAGKL 301
>gnl|CDD|215501 PLN02928, PLN02928, oxidoreductase family protein.
Length = 347
Score = 133 bits (336), Expect = 2e-36
Identities = 82/271 (30%), Positives = 140/271 (51%), Gaps = 24/271 (8%)
Query: 62 DAELIESLPKLEIVATCSVGLDKIDLARCKEKGIRVANTPDVLT---DDVADLAIGLILA 118
DA++I +++++ VGL+ +D+ + GI+VA P T A++AI L+L
Sbjct: 73 DADIIARASQMKLIMQFGVGLEGVDVDAATKHGIKVARIPSEGTGNAASCAEMAIYLMLG 132
Query: 119 VLRRICESDRYVRSGEWKKGEFKMTTKFTGKSVGILGMGRIGTAIAKRAEAFDCIIGYNS 178
+LR+ E +++ + GE + GK+V ILG G IG +AKR F +
Sbjct: 133 LLRKQNEMQISLKAR--RLGE-PIGDTLFGKTVFILGYGAIGIELAKRLRPFGVKLLATR 189
Query: 179 R--TEKPN-------------LNYKYYP-NLIDLASNCQILVVACSLTEETQHIVNRQVI 222
R T +P ++ K ++ + A I+V+ C+LT+ET IVN + +
Sbjct: 190 RSWTSEPEDGLLIPNGDVDDLVDEKGGHEDIYEFAGEADIVVLCCTLTKETAGIVNDEFL 249
Query: 223 NALGPKGVLINIGRGLLVDEHELVSALLQGRLGGAGLDVFEHEPDVPEE-LIGLENVVLL 281
+++ +L+NI RG L+D +++AL G LGG +DV EP P++ ++ NV++
Sbjct: 250 SSMKKGALLVNIARGGLLDYDAVLAALESGHLGGLAIDVAWSEPFDPDDPILKHPNVIIT 309
Query: 282 PHVASATVETRKAMADLVVGN-LQAHFGKKP 311
PHVA T + ++M +V LQ H G+
Sbjct: 310 PHVAGVTEYSYRSMGKIVGDAALQLHAGRPL 340
>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 = 130 bits (329), Expect = 2e-35
Identities = 84/273 (30%), Positives = 126/273 (46%), Gaps = 31/273 (11%)
Query: 62 DAELIESLPKLEI--VATCSVGLDKIDLARCKEKGIRVANTPDVLTDDVADLAIGLILAV 119
AEL+E L + + ++T S+G D IDL KE GI+V+N + VAD + L+L
Sbjct: 57 SAELLEKLKEAGVKYISTRSIGYDHIDLDAAKELGIKVSNVT-YSPNSVADYTVMLMLMA 115
Query: 120 LRRI------CESDRYVRSGEWKKGEFKMTTKFTGKSVGILGMGRIGTAIAKRAEAFDC- 172
LR+ E + Y G + +VG++G GRIG A+ K F C
Sbjct: 116 LRKYKQIMKRAEVNDYSLGG-------LQGRELRNLTVGVIGTGRIGQAVIKNLSGFGCK 168
Query: 173 IIGYNSRTEKPNLNYKYYPNLIDLASNCQILVVACSLTEETQHIVNRQVINALGPKGVLI 232
I+ Y+ + Y Y +L L I+ + LTEET H++N++ I + ++I
Sbjct: 169 ILAYDPYPNEEVKKYAEYVDLDTLYKESDIITLHTPLTEETYHLINKESIAKMKDGVIII 228
Query: 233 NIGRGLLVDEHELVSALLQGRLGGAGLDVFEHEPDV-----------PEELIGLE---NV 278
N RG L+D L+ L G++GGA LDV E E + EL L NV
Sbjct: 229 NTARGELIDTEALIEGLESGKIGGAALDVIEGEDGIYYNDRKGDILSNRELAILRSFPNV 288
Query: 279 VLLPHVASATVETRKAMADLVVGNLQAHFGKKP 311
+L PH+A T + M + + +L A
Sbjct: 289 ILTPHMAFYTDQAVSDMVENSIESLVAFEKGGE 321
>gnl|CDD|181041 PRK07574, PRK07574, formate dehydrogenase; Provisional.
Length = 385
Score = 130 bits (330), Expect = 4e-35
Identities = 76/259 (29%), Positives = 119/259 (45%), Gaps = 11/259 (4%)
Query: 63 AELIESLPKLEIVATCSVGLDKIDLARCKEKGIRVANTPDVLTDDVADLAIGLILAVLRR 122
AE I P L++ T +G D +DL E GI VA + VA+ + +ILA++R
Sbjct: 106 AERIAKAPNLKLAITAGIGSDHVDLQAASEHGITVAEVTGSNSISVAEHVVMMILALVRN 165
Query: 123 ICESDRYVRSGEWKKGE-FKMTTKFTGKSVGILGMGRIGTAIAKRAEAFDCIIGYNSRTE 181
S R G W + + G +VGI+G GRIG A+ +R + FD + Y R
Sbjct: 166 YEPSHRQAVEGGWNIADCVSRSYDLEGMTVGIVGAGRIGLAVLRRLKPFDVKLHYTDRHR 225
Query: 182 KP-----NLNYKYYPNLIDLASNCQILVVACSLTEETQHIVNRQVINALGPKGVLINIGR 236
P L Y+ + L S C ++ + C L ET+H+ + V++ + L+N R
Sbjct: 226 LPEEVEQELGLTYHVSFDSLVSVCDVVTIHCPLHPETEHLFDADVLSRMKRGSYLVNTAR 285
Query: 237 GLLVDEHELVSALLQGRLGGAGLDVFEHEP---DVPEELIGLENVVLLPHVASATVETRK 293
G +VD +V AL G L G DV+ +P D P + + PH++ T+ +
Sbjct: 286 GKIVDRDAVVRALESGHLAGYAGDVWFPQPAPADHPWR--TMPRNGMTPHISGTTLSAQA 343
Query: 294 AMADLVVGNLQAHFGKKPL 312
A L+ F +P+
Sbjct: 344 RYAAGTREILECFFEGRPI 362
>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 = 129 bits (326), Expect = 5e-35
Identities = 88/270 (32%), Positives = 129/270 (47%), Gaps = 30/270 (11%)
Query: 52 AVVGSAAAGADAELIESLPKLEI--VATCSVGLDKIDLARCKEKGIRVANTPDVLTDDVA 109
VV D E+ E L + I +A S G+D IDL KE G+++ N P +A
Sbjct: 47 GVVVQQTLPYDEEVYEKLAEYGIKQIALRSAGVDMIDLDLAKENGLKITNVPAYSPRAIA 106
Query: 110 DLAIGLILAVLRRICESDRYVRSGEWKKGEFKMTTKFTGK-----SVGILGMGRIGTAIA 164
+ A+ L +LR E DR V KG+F+ G+ +VGI+G GRIG+A A
Sbjct: 107 EFAVTQALNLLRNTPEIDRRVA-----KGDFRWAPGLIGREIRDLTVGIIGTGRIGSAAA 161
Query: 165 KRAEAFDC-IIGYNSRTEKPNLN--YKYYPNLIDLASNCQILVVACSLTEETQHIVNRQV 221
K + F +I Y P L YY +L DL I+ + LT+E H++N +
Sbjct: 162 KIFKGFGAKVIAY-DPYPNPELEKFLLYYDSLEDLLKQADIISLHVPLTKENHHLINAEA 220
Query: 222 INALGPKGVLINIGRGLLVDEHELVSALLQGRLGGAGLDVFEHE--------------PD 267
+ +L+N RG LVD L+ AL G++ GA LD +E+E +
Sbjct: 221 FAKMKDGAILVNAARGGLVDTKALIDALDSGKIAGAALDTYENETGYFNKDWSGKEIEDE 280
Query: 268 VPEELIGLENVVLLPHVASATVETRKAMAD 297
V +ELI + NV++ PH+A T K M +
Sbjct: 281 VLKELIAMPNVLITPHIAFYTDTAVKNMVE 310
>gnl|CDD|177941 PLN02306, PLN02306, hydroxypyruvate reductase.
Length = 386
Score = 129 bits (327), Expect = 9e-35
Identities = 89/303 (29%), Positives = 147/303 (48%), Gaps = 33/303 (10%)
Query: 37 EDKEQFINTHKDSIQAVVGSAAAGADAELIESLPKL--EIVATCSVGLDKIDLARCKEKG 94
ED I D V+G L +L K + + +VG + +D+ + G
Sbjct: 53 EDIIALIGDKCD---GVIGQLTEDWGETLFSALSKAGGKAFSNMAVGYNNVDVEAANKYG 109
Query: 95 IRVANTPDVLTDDVADLAIGLILAVLRRICESDRYVRSGEWKKGEFKMTTKFTG-----K 149
I V NTP VLT+ A+LA L LA RRI E+D ++R+G ++ + F G +
Sbjct: 110 IAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYEGW---LPHLFVGNLLKGQ 166
Query: 150 SVGILGMGRIGTAIAKR-AEAFDCIIGY-----NSRTEK--------------PNLNYKY 189
+VG++G GRIG+A A+ E F + Y ++R EK + +K
Sbjct: 167 TVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQSTRLEKFVTAYGQFLKANGEQPVTWKR 226
Query: 190 YPNLIDLASNCQILVVACSLTEETQHIVNRQVINALGPKGVLINIGRGLLVDEHELVSAL 249
++ ++ ++ + L + T H++N++ + + + VL+N RG ++DE LV L
Sbjct: 227 ASSMEEVLREADVISLHPVLDKTTYHLINKERLALMKKEAVLVNASRGPVIDEVALVEHL 286
Query: 250 LQGRLGGAGLDVFEHEPDVPEELIGLENVVLLPHVASATVETRKAMADLVVGNLQAHFGK 309
+ GLDVFE EP + L ++N V++PH+ASA+ TR+ MA L N+
Sbjct: 287 KANPMFRVGLDVFEDEPYMKPGLADMKNAVVVPHIASASKWTREGMATLAALNVLGKLKG 346
Query: 310 KPL 312
P+
Sbjct: 347 YPV 349
>gnl|CDD|235890 PRK06932, PRK06932, glycerate dehydrogenase; Provisional.
Length = 314
Score = 125 bits (316), Expect = 8e-34
Identities = 83/279 (29%), Positives = 132/279 (47%), Gaps = 17/279 (6%)
Query: 38 DKEQFINTHKDSIQAVVGSAAAGADAELIESLPKLEIVATCSVGLDKIDLARCKEKGIRV 97
EQ I KD+ +V ++ E + LPKL+++A + G + +DL KE GI V
Sbjct: 34 SAEQTIERAKDA--DIVITSKVLFTRETLAQLPKLKLIAITATGTNNVDLVAAKELGIAV 91
Query: 98 ANTPDVLTDDVADLAIGLILAVLRRICESDRYVRSGEW-KKGEFKMT----TKFTGKSVG 152
N + V + +G+I A+ + R S W +F T G ++G
Sbjct: 92 KNVTGYSSTTVPEHVLGMIFALKHSLMGWYRDQLSDRWATCKQFCYFDYPITDVRGSTLG 151
Query: 153 ILGMGRIGTAIAKRAEAFDCIIGYNSRTEKPNLNYKYYPNLIDLASNCQILVVACSLTEE 212
+ G G +GT + + A+A + Y Y P ++ I+ + C LTE
Sbjct: 152 VFGKGCLGTEVGRLAQALGMKVLYAEHKGASVCREGYTP-FEEVLKQADIVTLHCPLTET 210
Query: 213 TQHIVNRQVINALGPKGVLINIGRGLLVDEHELVSALLQGRLGGAGLDVFEHEPDVPEE- 271
TQ+++N + + + P LIN GRG LVDE L+ AL G++ GA LDV EP PE+
Sbjct: 211 TQNLINAETLALMKPTAFLINTGRGPLVDEQALLDALENGKIAGAALDVLVKEP--PEKD 268
Query: 272 --LIG----LENVVLLPHVASATVETRKAMADLVVGNLQ 304
LI L N+++ PH+A A+ + + V N++
Sbjct: 269 NPLIQAAKRLPNLLITPHIAWASDSAVTTLVNKVAQNIE 307
>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 = 125 bits (315), Expect = 2e-33
Identities = 69/258 (26%), Positives = 115/258 (44%), Gaps = 11/258 (4%)
Query: 63 AELIESLPKLEIVATCSVGLDKIDLARCKEKGIRVANTPDVLTDDVADLAIGLILAVLRR 122
AE I L++ T +G D +DL ++GI VA VA+ + +IL ++R
Sbjct: 76 AERIAKAKNLKLALTAGIGSDHVDLQAANDRGITVAEVTGSNVVSVAEHVVMMILILVRN 135
Query: 123 ICESDRYVRSGEWKKGEF-KMTTKFTGKSVGILGMGRIGTAIAKRAEAFDCIIGYNSRTE 181
G W + K GK+VG +G GRIG + +R + FD + Y R
Sbjct: 136 YVPGHEQAIEGGWNVADVVKRAYDLEGKTVGTVGAGRIGLRVLRRLKPFDVHLLYYDRHR 195
Query: 182 KP-----NLNYKYYPNLIDLASNCQILVVACSLTEETQHIVNRQVINALGPKGVLINIGR 236
P L + +L D+ S C ++ + C L ET+ + N+++++ + L+N R
Sbjct: 196 LPEEVEKELGLTRHADLEDMVSKCDVVTINCPLHPETEGLFNKELLSKMKKGAYLVNTAR 255
Query: 237 GLLVDEHELVSALLQGRLGGAGLDVFEHEP---DVPEELIGLENVVLLPHVASATVETRK 293
G + D + AL G L G DV+ +P D P + N + PH++ T++ +
Sbjct: 256 GKICDREAVAEALESGHLAGYAGDVWFPQPAPKDHPWRTMP--NNAMTPHISGTTLDAQA 313
Query: 294 AMADLVVGNLQAHFGKKP 311
A L+ F +P
Sbjct: 314 RYAAGTKEILERFFEGEP 331
>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 = 120 bits (302), Expect = 9e-32
Identities = 69/213 (32%), Positives = 108/213 (50%), Gaps = 9/213 (4%)
Query: 108 VADLAIGLILAVLRRICESDRYVRSGEWKKGEFKMTTKFTGKSVGILGMGRIGTAIAKRA 167
+A+ + ILA +R+ E + +W + G ++GI+G G IG A+A+RA
Sbjct: 99 IAEFVLAAILAAAKRLPEI-WVKGAEQW---RREPLGSLAGSTLGIVGFGAIGQALARRA 154
Query: 168 EAFDCIIGYNSRTEKPN--LNYKYYPNLIDLASNCQILVVACSLTEETQHIVNRQVINAL 225
A + R+ +P+ + +L +L + LV+A LT ET+H++N V+
Sbjct: 155 LALGMRVLALRRSGRPSDVPGVEAAADLAELFARSDHLVLAAPLTPETRHLINADVLAQA 214
Query: 226 GPKGVLINIGRGLLVDEHELVSALLQGRLGGAGLDVFEHEPDVPEE--LIGLENVVLLPH 283
P LINI RG LVD+ L+ AL GR+ A LDV + EP +PE L V L PH
Sbjct: 215 KPGLHLINIARGGLVDQEALLEALDSGRISLASLDVTDPEP-LPEGHPLYTHPRVRLSPH 273
Query: 284 VASATVETRKAMADLVVGNLQAHFGKKPLLTPV 316
++ + R+ +AD + NL + +PL V
Sbjct: 274 TSAIAPDGRRNLADRFLENLARYRAGQPLHDLV 306
>gnl|CDD|240635 cd12158, ErythrP_dh, D-Erythronate-4-Phosphate Dehydrogenase
NAD-binding and catalytic domains.
D-Erythronate-4-phosphate Dehydrogenase (E. coli gene
PdxB), a D-specific 2-hydroxyacid dehydrogenase family
member, catalyzes the NAD-dependent oxidation of
erythronate-4-phosphate, which is followed by
transamination to form 4-hydroxy-L-threonine-4-phosphate
within the de novo biosynthesis pathway of vitamin B6.
D-Erythronate-4-phosphate dehydrogenase has the common
architecture shared with D-isomer specific 2-hydroxyacid
dehydrogenases but contains an additional C-terminal
dimerization domain in addition to an NAD-binding domain
and the "lid" domain. The lid domain corresponds to the
catalytic domain of phosphoglycerate dehydrogenase and
other proteins of the D-isomer specific 2-hydroxyacid
dehydrogenase family, which include groups such as
formate dehydrogenase, glycerate dehydrogenase,
L-alanine dehydrogenase, and S-adenosylhomocysteine
hydrolase. Despite often low sequence identity, these
proteins typically have a characteristic arrangement of
2 similar subdomains of the alpha/beta Rossmann fold
NAD+ binding form. The NAD+ binding domain is inserted
within the linear sequence of the mostly N-terminal
catalytic domain, which has a similar domain structure
to the internal NAD binding domain. Structurally, these
domains are connected by extended alpha helices and
create a cleft in which NAD is bound, primarily to the
C-terminal portion of the 2nd (internal) domain. Some
related proteins have similar structural subdomain but
with a tandem arrangement of the catalytic and
NAD-binding subdomains in the linear sequence.
Length = 343
Score = 117 bits (296), Expect = 1e-30
Identities = 71/257 (27%), Positives = 126/257 (49%), Gaps = 31/257 (12%)
Query: 62 DAELIESLPKLEIVATCSVGLDKIDLARCKEKGIRVANTPDVLTDDVADLAIGLILAVLR 121
+ L+E K++ V T ++G D ID KE+GI AN P + VA+ + +L + +
Sbjct: 49 NEALLE-GSKVKFVGTATIGTDHIDTDYLKERGIGFANAPGCNANSVAEYVLSALLVLAQ 107
Query: 122 RICESDRYVRSGEWKKGEFKMTTKFTGKSVGILGMGRIGTAIAKRAEAFDC-IIGYNS-R 179
R S + GK+VGI+G+G +G+ +A+R EA ++ + R
Sbjct: 108 RQGFSLK-------------------GKTVGIVGVGNVGSRLARRLEALGMNVLLCDPPR 148
Query: 180 TEKPNLNYKYYPNLIDLASNCQILVVACSLTEE----TQHIVNRQVINALGPKGVLINIG 235
E + +L +L + I+ + LT + T H+++ + AL P +LIN
Sbjct: 149 AEAEGDPG--FVSLEELLAEADIITLHVPLTRDGEHPTYHLLDEDFLAALKPGQILINAS 206
Query: 236 RGLLVDEHELVSALLQGRLGGAGLDVFEHEPDVPEELIGLENVVLL-PHVASATVETRKA 294
RG ++D L++ L +G+ LDV+E+EP++ EL L+ V + PH+A ++E +
Sbjct: 207 RGAVIDNQALLALLQRGKDLRVVLDVWENEPEIDLEL--LDKVDIATPHIAGYSLEGKAR 264
Query: 295 MADLVVGNLQAHFGKKP 311
+++ L G K
Sbjct: 265 GTEMIYEALCQFLGLKA 281
>gnl|CDD|236985 PRK11790, PRK11790, D-3-phosphoglycerate dehydrogenase;
Provisional.
Length = 409
Score = 112 bits (283), Expect = 2e-28
Identities = 80/254 (31%), Positives = 129/254 (50%), Gaps = 21/254 (8%)
Query: 63 AELIESLPKLEIVATCSVGLDKIDLARCKEKGIRVANTPDVLTDDVADLAIGLILAVLRR 122
E++ + KL + +G +++DL ++GI V N P T VA+L IG I+ +LR
Sbjct: 67 EEVLAAAEKLVAIGCFCIGTNQVDLDAAAKRGIPVFNAPFSNTRSVAELVIGEIILLLRG 126
Query: 123 ICESDRYVRSGEWKK---GEFKMTTKFTGKSVGILGMGRIGTAIAKRAEAFDC-IIGYNS 178
I E + G W K G F++ GK++GI+G G IGT ++ AE+ + Y+
Sbjct: 127 IPEKNAKAHRGGWNKSAAGSFEVR----GKTLGIVGYGHIGTQLSVLAESLGMRVYFYDI 182
Query: 179 RTEKPNLNYKYYPNLIDLASNCQILVVACSL----TEETQHIVNRQVINALGPKGVLINI 234
+ P N + +L +L + ++ SL T T++++ + + + P +LIN
Sbjct: 183 EDKLPLGNARQVGSLEELLAQSDVV----SLHVPETPSTKNMIGAEELALMKPGAILINA 238
Query: 235 GRGLLVDEHELVSALLQGRLGGAGLDVFEHEPDVPEE-----LIGLENVVLLPHVASATV 289
RG +VD L AL G L GA +DVF EP + L GL+NV+L PH+ +T
Sbjct: 239 SRGTVVDIDALADALKSGHLAGAAIDVFPVEPKSNGDPFESPLRGLDNVILTPHIGGSTQ 298
Query: 290 ETRKAMADLVVGNL 303
E ++ + V G L
Sbjct: 299 EAQENIGLEVAGKL 312
>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 = 110 bits (278), Expect = 4e-28
Identities = 75/284 (26%), Positives = 119/284 (41%), Gaps = 38/284 (13%)
Query: 67 ESLPKLEIVATCSVGLDK-IDLARCKEKGIRVANTPDVLTDDVADLAIGLILAVLRRICE 125
E +P L +V S G D + K+ + + + +A+ IG L +
Sbjct: 50 EDVPNLRLVQLFSAGADHWLGHPLYKDPEVPLCTASGIHGPQIAEWVIGTWLVLSHHF-- 107
Query: 126 SDRYV---RSGEWKKGEFKMTTK-FTGKSVGILGMGRIGTAIAKRAEAFDC-IIGYNSR- 179
+Y+ + W + + + + GK VGILG G IG A+ A+A + Y
Sbjct: 108 -LQYIELQKEQTWGRRQEAYSVEDSVGKRVGILGYGSIGRQTARLAQALGMEVYAYTRSP 166
Query: 180 --TEKPNLNYKY-YPNLID---------------------LASNCQILVVACSLTEETQH 215
T + + Y P D L + +LVV+ LT T+H
Sbjct: 167 RPTPESRKDDGYIVPGTGDPDGSIPSAWFSGTDKASLHEFLRQDLDLLVVSLPLTPATKH 226
Query: 216 IVNRQVINALGPKG-VLINIGRGLLVDEHELVSALLQGRLGGAGLDVFEHEPDVPE--EL 272
++ + L + + NI RG LVD LV+AL G++ GA LDV + EP +P L
Sbjct: 227 LLGAEEFEILAKRKTFVSNIARGSLVDTDALVAALESGQIRGAALDVTDPEP-LPADHPL 285
Query: 273 IGLENVVLLPHVASATVETRKAMADLVVGNLQAHFGKKPLLTPV 316
NV++ PHV+ T E D++ NL+ +PL+ V
Sbjct: 286 WSAPNVIITPHVSWQTQEYFDRALDVLEENLERLRKGEPLINLV 329
>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 = 109 bits (274), Expect = 1e-27
Identities = 74/273 (27%), Positives = 123/273 (45%), Gaps = 19/273 (6%)
Query: 51 QAVVGSAAAGADAELIESLPKLEI--VATCSVGLDKIDLARCKEKGIRVANTPDVLTDDV 108
AV+ AD E +E + I V T +VG + IDL KE G ++A P + +
Sbjct: 46 DAVIVRGNCFADKENLEIYKEYGIKYVFTRTVGFNHIDLEAAKELGFKMARVPSYSPNAI 105
Query: 109 ADLAIGLILAVLRRICESDRYVRSGEWKKGEFKMTTKFTGKSVGILGMGRIGTAIAKRAE 168
A+LA L + + R + + +K F + + +VGI+G GRIG AK +
Sbjct: 106 AELAFTLAMTLSRHTAYTASRTANKNFKVDPFMFSKEIRNSTVGIIGTGRIGLTAAKLFK 165
Query: 169 AFDC-IIGYNSRTEKPNLNYKYYPNLIDLASNCQILVVACS-LTEETQHIVNRQVINALG 226
+IGY+ + + +L +L I+ + + + ++N++ I+ +
Sbjct: 166 GLGAKVIGYDIYPSDAAKDVVTFVSLDELLKKSDIISLHVPYIKGKNDKLINKEFISKMK 225
Query: 227 PKGVLINIGRGLLVDEHELVSALLQGRLGGAGLDVFEHEPDV--------------PEEL 272
+LIN RG L DE ++ AL G+L G G DV +E ++ E+L
Sbjct: 226 DGAILINTARGELQDEEAILEALESGKLAGFGTDVLNNEKEIFFKDFDGDKIEDPVVEKL 285
Query: 273 IGL-ENVVLLPHVASATVETRKAMADLVVGNLQ 304
+ L V+L PH+ S T E M + NL+
Sbjct: 286 LDLYPRVLLTPHIGSYTDEALSNMIETSYENLK 318
>gnl|CDD|235800 PRK06436, PRK06436, glycerate dehydrogenase; Provisional.
Length = 303
Score = 98.4 bits (245), Expect = 9e-24
Identities = 70/256 (27%), Positives = 130/256 (50%), Gaps = 11/256 (4%)
Query: 61 ADAELIESLP----KLEIVATCSVGLDKIDLARCKEKGIRVANTPDVLTDDVADLAIGLI 116
A+A LI+ K +++ + S G+D ID++ E + +N + VA+ A L+
Sbjct: 35 AEAILIKGRYVPGKKTKMIQSLSAGVDHIDVSGIPENVVLCSNA-GAYSISVAEHAFALL 93
Query: 117 LAVLRRICESDRYVRSGEWKKGEFKMTTKFTGKSVGILGMGRIGTAIAKRAEAFDCIIGY 176
LA + ICE++ +++G +K+ K+ KS+GILG G IG +A A+AF I
Sbjct: 94 LAWAKNICENNYNMKNGNFKQSPTKL---LYNKSLGILGYGGIGRRVALLAKAFGMNIYA 150
Query: 177 NSRTEKPNLNYKYYPNLIDLASNCQILVVACSLTEETQHIVNRQVINALGPKGVLINIGR 236
+R+ + Y D+ ++++ LT+ET+ ++N ++++ +IN+ R
Sbjct: 151 YTRSYVNDGISSIYMEPEDIMKKSDFVLISLPLTDETRGMINSKMLSLFRKGLAIINVAR 210
Query: 237 GLLVDEHELVSALLQGRLGGAGLDVFEHEPDVPEELIGLENVVLLPHVASA-TVETRKAM 295
+VD++++++ L DV+ +EP + E +NV+L PHVA + E +
Sbjct: 211 ADVVDKNDMLNFLRNHNDKYYLSDVWWNEPIITETNP--DNVILSPHVAGGMSGEIMQPA 268
Query: 296 ADLVVGNLQAHFGKKP 311
L N++ F KP
Sbjct: 269 VALAFENIKNFFEGKP 284
>gnl|CDD|178684 PLN03139, PLN03139, formate dehydrogenase; Provisional.
Length = 386
Score = 98.8 bits (246), Expect = 2e-23
Identities = 73/244 (29%), Positives = 115/244 (47%), Gaps = 13/244 (5%)
Query: 63 AELIESLPKLEIVATCSVGLDKIDLARCKEKGIRVANTPDVLTDDVADLAIGLILAVLRR 122
AE I+ LE++ T +G D IDL G+ VA VA+ + IL +LR
Sbjct: 113 AERIKKAKNLELLLTAGIGSDHIDLPAAAAAGLTVAEVTGSNVVSVAEDELMRILILLRN 172
Query: 123 ICESDRYVRSGEWKKGEFKMTT-KFTGKSVGILGMGRIGTAIAKRAEAFDCIIGYNSRTE 181
V SGEW GK+VG +G GRIG + +R + F+C + Y+ R +
Sbjct: 173 FLPGYHQVVSGEWNVAGIAYRAYDLEGKTVGTVGAGRIGRLLLQRLKPFNCNLLYHDRLK 232
Query: 182 KP-----NLNYKYYPNLIDLASNCQILVVACSLTEETQHIVNRQVINALGPKGVLI-NIG 235
K+ +L + C ++V+ LTE+T+ + N++ I + KGVLI N
Sbjct: 233 MDPELEKETGAKFEEDLDAMLPKCDVVVINTPLTEKTRGMFNKERIAKM-KKGVLIVNNA 291
Query: 236 RGLLVDEHELVSALLQGRLGGAGLDVFEHEP---DVPEELIGLENVVLLPHVASATVETR 292
RG ++D + A G +GG G DV+ +P D P + N + PH++ T++ +
Sbjct: 292 RGAIMDTQAVADACSSGHIGGYGGDVWYPQPAPKDHPWRY--MPNHAMTPHISGTTIDAQ 349
Query: 293 KAMA 296
A
Sbjct: 350 LRYA 353
>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 = 97.4 bits (243), Expect = 2e-23
Identities = 83/289 (28%), Positives = 118/289 (40%), Gaps = 37/289 (12%)
Query: 46 HKDSIQAVVGSAAAGADAELIESLPKLEIVATCSVGLDKIDLARCKEKGIRVAN-TPDV- 103
H D+ VV ++ A+ L +L V + G D + A P+V
Sbjct: 34 HHDAEVLVVWGNSSDNLADAARRLTRLRWVQALAAGPD----------AVLAAGFAPEVA 83
Query: 104 ------LTD-DVADLAIGLILAVLRRICESDRYVRSGEWKK--------GEFKMTTKFTG 148
L D VA+ + LILA +RR+ E R W T G
Sbjct: 84 VTSGRGLHDGTVAEHTLALILAAVRRLDEMREAQREHRWAGELGGLQPLRPAGRLTTLLG 143
Query: 149 KSVGILGMGRIGTAIAKRAEAFDCIIGYNSRTEKPNLNYKYYP--NLIDLASNCQILVVA 206
V I G G IG +A A + +R+ + L +L +LV+
Sbjct: 144 ARVLIWGFGSIGQRLAPLLTALGARVTGVARSAGERAGFPVVAEDELPELLPETDVLVMI 203
Query: 207 CSLTEETQHIVNRQVINALGPKGVLINIGRGLLVDEHELVSALLQGRLGGAGLDVFEHEP 266
T T H ++ +V+ AL ++N+GRG VDE LV+AL GRLGGA LDV EP
Sbjct: 204 LPATPSTAHALDAEVLAALPKHAWVVNVGRGATVDEDALVAALESGRLGGAALDVTATEP 263
Query: 267 DVPEE--LIGLENVVLLPHVASATVETR-KAMADLVVGNLQAHFGKKPL 312
+P L N++L PH A R + +L+ NL+A PL
Sbjct: 264 -LPASSPLWDAPNLILTPHAAGG----RPQGAEELIAENLRAFLAGGPL 307
>gnl|CDD|181499 PRK08605, PRK08605, D-lactate dehydrogenase; Validated.
Length = 332
Score = 94.4 bits (235), Expect = 4e-22
Identities = 66/253 (26%), Positives = 109/253 (43%), Gaps = 30/253 (11%)
Query: 75 VATCSVGLDKIDLARCKEKGIRVANTPDVLTDDVADLAIGLILAVLRRICESDRYVRSGE 134
+A S G D DL + + ++N P + +A+ + + ++R + VR
Sbjct: 73 IAQRSAGFDTYDLELATKYNLIISNVPSYSPESIAEFTVTQAINLVRHFNQIQTKVR--- 129
Query: 135 WKKGEFKMTTKFTGKS-----VGILGMGRIGTAIAK-RAEAFDC-IIGYNSRTEKPNLNY 187
+ +F+ +S V ++G GRIG A+AK A+ + ++ Y+ Y
Sbjct: 130 --EHDFRWEPPILSRSIKDLKVAVIGTGRIGLAVAKIFAKGYGSDVVAYDPFPNAKAATY 187
Query: 188 KYYPNLIDLA-SNCQILVVACSLTEETQHIVNRQVINALGPKGVLINIGRGLLVDEHELV 246
Y + I+ A I+ + T+ ++ N + V +N RG LVD L+
Sbjct: 188 VDYKDTIEEAVEGADIVTLHMPATKYNHYLFNADLFKHFKKGAVFVNCARGSLVDTKALL 247
Query: 247 SALLQGRLGGAGLDVFEHE-PDVP-------------EELIGLENVVLLPHVASATVETR 292
AL G + GA LD +E E P P E LI E+V+L PH+A T
Sbjct: 248 DALDNGLIKGAALDTYEFERPLFPSDQRGQTINDPLLESLINREDVILTPHIAFYTDA-- 305
Query: 293 KAMADLVVGNLQA 305
A+ +L+V L A
Sbjct: 306 -AVKNLIVDALDA 317
>gnl|CDD|166874 PRK00257, PRK00257, erythronate-4-phosphate dehydrogenase;
Validated.
Length = 381
Score = 94.3 bits (235), Expect = 8e-22
Identities = 59/231 (25%), Positives = 99/231 (42%), Gaps = 31/231 (13%)
Query: 62 DAELIESLPKLEIVATCSVGLDKIDLARCKEKGIRVANTPDVLTDDVADLAIGLILAVLR 121
D L+E ++ V TC++G D +DL E GI ++ P V D +G +L +
Sbjct: 50 DRALLEG-SRVRFVGTCTIGTDHLDLDYFAEAGITWSSAPGCNARGVVDYVLGSLLTLAE 108
Query: 122 RICESDRYVRSGEWKKGEFKMTTKFTGKSVGILGMGRIGTAIAKRAEAFD--CIIGYNSR 179
R +G ++ G++G G +G + + ++ R
Sbjct: 109 R--------------EGV-----DLAERTYGVVGAGHVGGRLVRVLRGLGWKVLVCDPPR 149
Query: 180 TEKPNLNYKYYPNLIDLASNCQILVVACSLTEE----TQHIVNRQVINALGPKGVLINIG 235
E + +L + C ++ + LT+E T+H+++ + +L P LIN
Sbjct: 150 QEAEGDGD--FVSLERILEECDVISLHTPLTKEGEHPTRHLLDEAFLASLRPGAWLINAS 207
Query: 236 RGLLVDEHELVSALLQGRLGGAGLDVFEHEPDVPEELIGLENVVL-LPHVA 285
RG +VD L ALL G A LDV+E EP + EL + + PH+A
Sbjct: 208 RGAVVDNQALREALLSGEDLDAVLDVWEGEPQIDLEL--ADLCTIATPHIA 256
>gnl|CDD|183550 PRK12480, PRK12480, D-lactate dehydrogenase; Provisional.
Length = 330
Score = 93.4 bits (232), Expect = 1e-21
Identities = 67/260 (25%), Positives = 127/260 (48%), Gaps = 25/260 (9%)
Query: 67 ESLPKLE-----IVATCSVGLDKIDLARCKEKGIRVANTPDVLTDDVADLAIGLILAVLR 121
+ PKLE +A + G D DL K+ I ++N P + +A+ ++ + L ++R
Sbjct: 60 DVYPKLESYGIKQIAQRTAGFDMYDLDLAKKHNIVISNVPSYSPETIAEYSVSIALQLVR 119
Query: 122 RICESDRYVRSGEWKKGEFKMTTKFTGKSVGILGMGRIGTAIAKRAEAFDC-IIGYNSRT 180
R + +R V++ ++ M+ +V I+G GRIG A AK F I Y++
Sbjct: 120 RFPDIERRVQAHDFTWQAEIMSKPVKNMTVAIIGTGRIGAATAKIYAGFGATITAYDAYP 179
Query: 181 EKPNLNYKYYPNLIDLA-SNCQILVVACSLTEETQHIVNRQVINALGPKGVLINIGRGLL 239
K +L++ Y + + A + I+ + +E+ H+ ++ + + + +L+N RG +
Sbjct: 180 NK-DLDFLTYKDSVKEAIKDADIISLHVPANKESYHLFDKAMFDHVKKGAILVNAARGAV 238
Query: 240 VDEHELVSALLQGRLGGAGLDVFEHEP--------------DVPEELIGLENVVLLPHVA 285
++ +L++A+ G L GA +D +E+E ELI E +++ PH+A
Sbjct: 239 INTPDLIAAVNDGTLLGAAIDTYENEAAYFTNDWTNKDIDDKTLLELIEHERILVTPHIA 298
Query: 286 SATVETRKAMADLVVGNLQA 305
+ E A+ +LV G L A
Sbjct: 299 FFSDE---AVQNLVEGGLNA 315
>gnl|CDD|185366 PRK15469, ghrA, bifunctional glyoxylate/hydroxypyruvate reductase
A; Provisional.
Length = 312
Score = 72.9 bits (179), Expect = 1e-14
Identities = 56/182 (30%), Positives = 90/182 (49%), Gaps = 9/182 (4%)
Query: 112 AIGLILAVLRRICESDRYVRSGEWKKGEFKMTTKFTGKSVGILGMGRIGTAIAKRAEAFD 171
A+ +L RR + S W+ FT +GILG G +G+ +A+ + +
Sbjct: 103 AVSQVLHWFRRFDDYQALQNSSHWQPLPEYHREDFT---IGILGAGVLGSKVAQSLQTWG 159
Query: 172 CIIGYNSRTEK--PNL-NYKYYPNLIDLASNCQILVVACSLTEETQHIVNRQVINALGPK 228
+ SR+ K P + ++ L S ++L+ T ET I+N+Q++ L
Sbjct: 160 FPLRCWSRSRKSWPGVQSFAGREELSAFLSQTRVLINLLPNTPETVGIINQQLLEQLPDG 219
Query: 229 GVLINIGRGLLVDEHELVSALLQGRLGGAGLDVFEHEPDVPEE--LIGLENVVLLPHVAS 286
L+N+ RG+ V E +L++AL G++ GA LDVF EP +P E L V + PHVA+
Sbjct: 220 AYLLNLARGVHVVEDDLLAALDSGKVKGAMLDVFSREP-LPPESPLWQHPRVAITPHVAA 278
Query: 287 AT 288
T
Sbjct: 279 VT 280
>gnl|CDD|185335 PRK15438, PRK15438, erythronate-4-phosphate dehydrogenase PdxB;
Provisional.
Length = 378
Score = 64.2 bits (156), Expect = 1e-11
Identities = 65/260 (25%), Positives = 113/260 (43%), Gaps = 39/260 (15%)
Query: 50 IQAVVG-----SAAAGADAELIESLPK----------LEIVATCSVGLDKIDLARCKEKG 94
++AV G + A ADA ++ S+ K ++ V T + G D +D A K+ G
Sbjct: 22 VKAVPGRPIPVAQLADADALMVRSVTKVNESLLAGKPIKFVGTATAGTDHVDEAWLKQAG 81
Query: 95 IRVANTPDVLTDDVADLAIGLILAVLRRICESDRYVRSGEWKKGEFKMTTKFTGKSVGIL 154
I + P V + + + L + E D + ++VGI+
Sbjct: 82 IGFSAAPGCNAIAVVEY----VFSSLLMLAERDGFS---------------LHDRTVGIV 122
Query: 155 GMGRIGTAIAKRAEAFDCIIGYNSRTEKPNLNYKYYPNLIDLASNCQILVVACSLTEE-- 212
G+G +G + R EA + + +L +L IL L ++
Sbjct: 123 GVGNVGRRLQARLEALGIKTLLCDPPRADRGDEGDFRSLDELVQEADILTFHTPLFKDGP 182
Query: 213 --TQHIVNRQVINALGPKGVLINIGRGLLVDEHELVSALLQGRLGGAGLDVFEHEPDVPE 270
T H+ + ++I +L P +LIN RG +VD L++ L +G+ LDV+E EP++
Sbjct: 183 YKTLHLADEKLIRSLKPGAILINACRGAVVDNTALLTCLNEGQKLSVVLDVWEGEPELNV 242
Query: 271 ELIGLENVVLLPHVASATVE 290
EL+ ++ PH+A T+E
Sbjct: 243 ELLKKVDIG-TPHIAGYTLE 261
>gnl|CDD|240647 cd12170, 2-Hacid_dh_9, Putative D-isomer specific 2-hydroxyacid
dehydrogenases. 2-Hydroxyacid dehydrogenases catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 294
Score = 60.4 bits (147), Expect = 2e-10
Identities = 66/280 (23%), Positives = 109/280 (38%), Gaps = 35/280 (12%)
Query: 37 EDKEQFINTHKDSIQAVVGSAAAGADAELIESLPKLEIVATCSVGLDK----IDLARCKE 92
E E+ I D+ V+ S D E++E+ P ++ + C + +D+A +E
Sbjct: 35 ESDEEIIERIGDA-DCVLVSYTTQIDEEVLEACPNIKYIGMCCSLYSEESANVDIAAARE 93
Query: 93 KGIRVANTPDVLTDDVADLAIGLILAVLRRICESDRYV---RSGEWKKGEFKMTTKFTGK 149
GI V D + V + I E R + +WK+ + TG
Sbjct: 94 NGITVTGIRDYGDEGVVEYVI----------SELIRLLHGFGGKQWKE----EPRELTGL 139
Query: 150 SVGILGMGRIGTAIAKRAEAFDCIIGYNSRTEKPNL---NYKYYPNLIDLASNCQILVVA 206
VGI+G+G G IA F + Y SRT KP+ +Y P L +L ++
Sbjct: 140 KVGIIGLGTTGQMIADALSFFGADVYYYSRTRKPDAEAKGIRYLP-LNELLKTVDVI--- 195
Query: 207 CSLTEETQHIVNRQVINALGPKGVLINIGRGLLVDEHELVSALLQ--GRLGGAGLDVFEH 264
C+ + ++ + LG +L N G + V AL + G D
Sbjct: 196 CTCLPKNVILLGEEEFELLGDGKILFNTSLGPSFE----VEALKKWLKASGYNIFDCDTA 251
Query: 265 EPDVPEELIGLENVVLLPHVASATVETRKAMADLVVGNLQ 304
EEL+ NV+ A T + + ++ V+ NL+
Sbjct: 252 GALGDEELLRYPNVICTNKSAGWTRQAFERLSQKVLANLE 291
>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 = 46.1 bits (109), Expect = 1e-05
Identities = 36/212 (16%), Positives = 73/212 (34%), Gaps = 15/212 (7%)
Query: 53 VVGSAAAGADAELIESLPKLEIVATCSVGLDKIDLARC-KEKGIRVANTPDVLTDDVADL 111
V A+ LI+ L ++ T ++G D DL G+ V +
Sbjct: 70 KVKEPLTNAEYALIQKLG-DRLLFTYTIGADHRDLTEALARAGLTAIAVEGVELPLLTSN 128
Query: 112 AIGLILAVLRRIC-ESDRYVRSGEWKKGEFKMTTKFTGKSVGILGMGRIGTAIAKRAEAF 170
+IG ++ I + + GK+V ++G G +G A+
Sbjct: 129 SIGAGELSVQFIARFLEVQQPGRLGGAPDVA------GKTVVVVGAGVVGKEAAQMLRGL 182
Query: 171 DCIIGYN-----SRTEKPNLNYKYYPNLIDLASNCQILVVACSLTEETQHIVN-RQVINA 224
+ + + L K L + + ++V L + I+ +++
Sbjct: 183 GAQVLITDINVEALEQLEELGGKNVEELEEALAEADVIVTTTLLPGKRAGILVPEELVEQ 242
Query: 225 LGPKGVLINIGRGLLVDEHELVSALLQGRLGG 256
+ P V++N+ G + L + LL+ G
Sbjct: 243 MKPGSVIVNVAVGAVGCVQALHTQLLEEGHGV 274
>gnl|CDD|223318 COG0240, GpsA, Glycerol-3-phosphate dehydrogenase [Energy
production and conversion].
Length = 329
Score = 37.9 bits (89), Expect = 0.005
Identities = 26/131 (19%), Positives = 48/131 (36%), Gaps = 29/131 (22%)
Query: 149 KSVGILGMGRIGTAIAK--------------RAEAFDCIIGYNSRTEKPNL-------NY 187
+ ++G G GTA+AK E I +R L N
Sbjct: 2 MKIAVIGAGSWGTALAKVLARNGHEVRLWGRDEEIVAEIN--ETRENPKYLPGILLPPNL 59
Query: 188 KYYPNLIDLASNCQILVVACSLTEETQHIVN--RQVINALGPKGVLINIGRGLLVDEHEL 245
K +L + I+V+A +Q + RQ+ L ++++ +GL + L
Sbjct: 60 KATTDLAEALDGADIIVIAVP----SQALREVLRQLKPLLLKDAIIVSATKGLEPETGRL 115
Query: 246 VSALLQGRLGG 256
+S +++ L
Sbjct: 116 LSEIIEEELPD 126
>gnl|CDD|234828 PRK00742, PRK00742, chemotaxis-specific methylesterase;
Provisional.
Length = 354
Score = 30.5 bits (70), Expect = 0.97
Identities = 14/45 (31%), Positives = 22/45 (48%), Gaps = 8/45 (17%)
Query: 64 ELIESLPKLEIVATCSVGLDKIDLARCKEKGIRVANTPDVLTDDV 108
E++ S P +E+V T GL+ + + PDV+T DV
Sbjct: 21 EILNSDPDIEVVGTAPDGLEAREKIK--------KLNPDVITLDV 57
>gnl|CDD|223842 COG0771, MurD, UDP-N-acetylmuramoylalanine-D-glutamate ligase [Cell
envelope biogenesis, outer membrane].
Length = 448
Score = 29.2 bits (66), Expect = 3.6
Identities = 11/24 (45%), Positives = 15/24 (62%)
Query: 142 MTTKFTGKSVGILGMGRIGTAIAK 165
M F GK V +LG+G+ G A A+
Sbjct: 1 MMEDFQGKKVLVLGLGKSGLAAAR 24
>gnl|CDD|236668 PRK10252, entF, enterobactin synthase subunit F; Provisional.
Length = 1296
Score = 29.2 bits (66), Expect = 3.8
Identities = 13/56 (23%), Positives = 19/56 (33%), Gaps = 20/56 (35%)
Query: 109 ADLAIGLILAVLRRICESDRYVRSGEWKKGEFKMTTKFTGKSVGILGMGRIGTAIA 164
DLA+ L+ L R+C Y G + M R+G+A
Sbjct: 252 PDLALALVALWLGRLCGRMDYA--------------------AGFIFMRRLGSAAL 287
>gnl|CDD|234142 TIGR03187, DGQHR, DGQHR domain. This highly divergent,
uncharacterized domain has several absolutely conserved
residues, including a QR pair and FxxxN motif. Its most
striking feature, however, is a near invariant
pentapeptide motif DGQHR. Several different subfamilies
occur specifically as a part of DNA phosphorothioation
systems, previously called DND (DNA instability during
electrophoresis), while others (e.g. CPS_2936) occur in
other contexts suggestive of lateral gene transfer
(sporadic distribution of helicase-containing
cassettes). The region described by this model is about
280 amino acids in length; additional sequences show
local sequence similarity.
Length = 271
Score = 28.4 bits (64), Expect = 4.2
Identities = 13/69 (18%), Positives = 24/69 (34%), Gaps = 5/69 (7%)
Query: 96 RVANTPDVLTDDVADLAIGLILAVLRRICESDRYVRSGEWKKGEFKMTTKFTGKSVGILG 155
R+ P + D+ + ++ + E W K K + T VGI
Sbjct: 208 RLLGKPPGVKDENDEEIAQILNNFWTAVAEVFPE----AWLKVPRKGDSILT-HGVGIQA 262
Query: 156 MGRIGTAIA 164
+G +G +
Sbjct: 263 LGLLGRELL 271
>gnl|CDD|173621 PTZ00431, PTZ00431, pyrroline carboxylate reductase; Provisional.
Length = 260
Score = 28.4 bits (63), Expect = 4.7
Identities = 28/92 (30%), Positives = 50/92 (54%), Gaps = 8/92 (8%)
Query: 151 VGILGMGRIGTAIAKRAEAFDCI----IGYNSRTEKPNLNYKYYPNLIDLASNCQILVVA 206
VG +G+G++G+A+A E + I I Y++ ++K N + Y + +LA C I+V
Sbjct: 6 VGFIGLGKMGSALAYGIENSNIIGKENIYYHTPSKK-NTPFVYLQSNEELAKTCDIIV-- 62
Query: 207 CSLTEETQHIVNRQVINALGPKGVLINIGRGL 238
++ + V ++ LG K +LI+I GL
Sbjct: 63 LAVKPDLAGKVLLEIKPYLGSK-LLISICGGL 93
>gnl|CDD|143587 cd07197, nitrilase, Nitrilase superfamily, including nitrile- or
amide-hydrolyzing enzymes and amide-condensing enzymes.
This superfamily (also known as the C-N hydrolase
superfamily) contains hydrolases that break
carbon-nitrogen bonds; it includes nitrilases, cyanide
dihydratases, aliphatic amidases, N-terminal amidases,
beta-ureidopropionases, biotinidases, pantotheinase,
N-carbamyl-D-amino acid amidohydrolases, the glutaminase
domain of glutamine-dependent NAD+ synthetase,
apolipoprotein N-acyltransferases, and
N-carbamoylputrescine amidohydrolases, among others.
These enzymes depend on a Glu-Lys-Cys catalytic triad,
and work through a thiol acylenzyme intermediate.
Members of this superfamily generally form homomeric
complexes, the basic building block of which is a
homodimer. These oligomers include dimers, tetramers,
hexamers, octamers, tetradecamers, octadecamers, as well
as variable length helical arrangements and
homo-oligomeric spirals. These proteins have roles in
vitamin and co-enzyme metabolism, in detoxifying small
molecules, in the synthesis of signaling molecules, and
in the post-translational modification of proteins. They
are used industrially, as biocatalysts in the fine
chemical and pharmaceutical industry, in cyanide
remediation, and in the treatment of toxic effluent.
This superfamily has been classified previously in the
literature, based on global and structure-based sequence
analysis, into thirteen different enzyme classes
(referred to as 1-13). This hierarchy includes those
thirteen classes and a few additional subfamilies. A
putative distant relative, the plasmid-borne TraB
family, has not been included in the hierarchy.
Length = 253
Score = 28.1 bits (63), Expect = 5.4
Identities = 11/40 (27%), Positives = 19/40 (47%), Gaps = 2/40 (5%)
Query: 193 LIDLASNCQILVVACSLTEETQHIVNRQVINALGPKGVLI 232
L +LA I +VA ++ + N V+ + P G +I
Sbjct: 68 LAELAKELGIYIVAGIAEKDGDKLYNTAVV--IDPDGEII 105
>gnl|CDD|224996 COG2085, COG2085, Predicted dinucleotide-binding enzymes [General
function prediction only].
Length = 211
Score = 28.1 bits (63), Expect = 5.6
Identities = 14/36 (38%), Positives = 20/36 (55%), Gaps = 3/36 (8%)
Query: 149 KSVGILGMGRIGTAIAKRAEA--FDCIIGYNSRTEK 182
+ I+G G IG+A+A R + IIG +SR K
Sbjct: 2 MIIAIIGTGNIGSALALRLAKAGHEVIIG-SSRGPK 36
>gnl|CDD|237612 PRK14108, PRK14108, bifunctional glutamine-synthetase
adenylyltransferase/deadenyltransferase; Provisional.
Length = 986
Score = 28.4 bits (64), Expect = 5.7
Identities = 17/53 (32%), Positives = 22/53 (41%), Gaps = 14/53 (26%)
Query: 109 ADLAIGLILAVLRRICESDRYVRSGEWKKGEFKMT-TKFTGKSVGILGMGRIG 160
ADLA +I A L + E EF + G V IL MG++G
Sbjct: 672 ADLAELIIGAALDAVEE-------------EFARAHGRIKGGRVAILAMGKLG 711
>gnl|CDD|202773 pfam03807, F420_oxidored, NADP oxidoreductase coenzyme
F420-dependent.
Length = 93
Score = 26.4 bits (59), Expect = 7.3
Identities = 12/34 (35%), Positives = 20/34 (58%), Gaps = 3/34 (8%)
Query: 151 VGILGMGRIGTAIAKRAEA--FDCIIGYNSRTEK 182
+GI+G G +G A+A+ A + +I NSR +
Sbjct: 2 IGIIGAGNMGEALARGLAAAGHEVVIA-NSRNPE 34
>gnl|CDD|232943 TIGR00367, TIGR00367, K+-dependent Na+/Ca+ exchanger
related-protein. This model models a family of
bacterial and archaeal proteins that is homologous,
except for lacking a central region of ~ 250 amino acids
and an N-terminal region of > 100 residues, to a
functionally proven potassium-dependent sodium-calcium
exchanger of the rat [Unknown function, General].
Length = 307
Score = 27.7 bits (62), Expect = 7.8
Identities = 12/39 (30%), Positives = 21/39 (53%), Gaps = 3/39 (7%)
Query: 267 DVPEELIGLENVVL---LPHVASATVETRKAMADLVVGN 302
+ E++IGL + + LP + + RK + D+ VGN
Sbjct: 201 GISEKIIGLTLLAIGTSLPELVVSLAAARKGLGDIAVGN 239
>gnl|CDD|183714 PRK12742, PRK12742, oxidoreductase; Provisional.
Length = 237
Score = 27.8 bits (62), Expect = 7.8
Identities = 13/24 (54%), Positives = 15/24 (62%), Gaps = 1/24 (4%)
Query: 144 TKFTGKSVGILGMGR-IGTAIAKR 166
FTGK V +LG R IG AI +R
Sbjct: 2 GAFTGKKVLVLGGSRGIGAAIVRR 25
>gnl|CDD|178341 PLN02740, PLN02740, Alcohol dehydrogenase-like.
Length = 381
Score = 27.8 bits (62), Expect = 8.1
Identities = 16/37 (43%), Positives = 21/37 (56%), Gaps = 2/37 (5%)
Query: 148 GKSVGILGMGRIGTAIAK--RAEAFDCIIGYNSRTEK 182
G SV I G+G +G A+A+ RA IIG + EK
Sbjct: 199 GSSVAIFGLGAVGLAVAEGARARGASKIIGVDINPEK 235
>gnl|CDD|238358 cd00669, Asp_Lys_Asn_RS_core, Asp_Lys_Asn_tRNA synthetase class II
core domain. This domain is the core catalytic domain of
class II aminoacyl-tRNA synthetases of the subgroup
containing aspartyl, lysyl, and asparaginyl tRNA
synthetases. It is primarily responsible for
ATP-dependent formation of the enzyme bound
aminoacyl-adenylate. Class II assignment is based upon
its structure and the presence of three characteristic
sequence motifs. Nearly all class II tRNA synthetases
are dimers and enzymes in this subgroup are homodimers.
These enzymes attach a specific amino acid to the 3' OH
group of ribose of the appropriate tRNA.
Length = 269
Score = 27.4 bits (61), Expect = 9.2
Identities = 21/87 (24%), Positives = 35/87 (40%), Gaps = 14/87 (16%)
Query: 29 KVFKL-WHFEDKEQFINTHKDSIQAVVGSAAA----------GADAELIESLPKLEIVAT 77
K+ K F D F+ +Q + G A A G D L S P+L
Sbjct: 6 KIIKAIRDFMDDRGFLEVETPMLQKITGGAGARPFLVKYNALGLDYYLRIS-PQLFKKRL 64
Query: 78 CSVGLDKI-DLARC-KEKGIRVANTPD 102
GLD++ ++ R + + +R + P+
Sbjct: 65 MVGGLDRVFEINRNFRNEDLRARHQPE 91
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.319 0.137 0.395
Gapped
Lambda K H
0.267 0.0781 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 16,309,735
Number of extensions: 1612603
Number of successful extensions: 1855
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1684
Number of HSP's successfully gapped: 102
Length of query: 317
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 220
Effective length of database: 6,635,264
Effective search space: 1459758080
Effective search space used: 1459758080
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 59 (26.4 bits)