RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5259
(294 letters)
>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 = 211 bits (541), Expect = 2e-67
Identities = 105/337 (31%), Positives = 148/337 (43%), Gaps = 105/337 (31%)
Query: 4 PKLLLTRNDYPRVSPAYDILEDMFDIITYPISEGRMPRDIFIEKLKGCSALLCNPHQKVD 63
PK+L+TR A +L + F++ + + +PR+ +E KG LLC K+D
Sbjct: 1 PKVLVTRRLPE---EALALLREGFEVEVWD-EDRPLPREELLEAAKGADGLLCTLTDKID 56
Query: 64 KEALDESGENLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVKN 123
E LD A
Sbjct: 57 AELLD---------------------------------------------------AAPP 65
Query: 124 LKVISTFSVGHDHLHLDQIKSRGIRVG-TVGPVSSDAVAEFNIGLAIAVSRRFQQGHNCI 182
LKVI+ +SVG+DH+ +D K+RGI V T V +DA A+ L +A +RR +G +
Sbjct: 66 LKVIANYSVGYDHIDVDAAKARGIPVTNTPD-VLTDATADLAFALLLAAARRVVEGDRFV 124
Query: 183 ASGEW-ALKQTQTVISDIIGLNGSTVGIVG------------------------------ 211
+GEW T + +D L+G T+GIVG
Sbjct: 125 RAGEWKGWSPTLLLGTD---LHGKTLGIVGMGRIGQAVARRAKGFGMKILYHNRSRKPEA 181
Query: 212 -TELGAQLVPLDTLCAQSDFIFVTCALTKDTEQLIGRKQF-------------RGGLLDQ 257
ELGA+ V LD L A+SDF+ + C LT +T LI ++ RGG++D+
Sbjct: 182 EEELGARYVSLDELLAESDFVSLHCPLTPETRHLINAERLALMKPTAILINTARGGVVDE 241
Query: 258 EALVEFLRDKKIGGAGLDVMIPEPMPADHPLVQLDNC 294
+ALVE L+ KI GAGLDV PEP+PADHPL+ L N
Sbjct: 242 DALVEALKSGKIAGAGLDVFEPEPLPADHPLLTLPNV 278
>gnl|CDD|223980 COG1052, LdhA, Lactate dehydrogenase and related dehydrogenases
[Energy production and conversion / Coenzyme metabolism
/ General function prediction only].
Length = 324
Score = 162 bits (413), Expect = 4e-48
Identities = 93/336 (27%), Positives = 138/336 (41%), Gaps = 101/336 (30%)
Query: 3 KPKLLLTRNDYPRVSPAYDILEDMFDIITYPISEGRMPRDIFIEKLKGCSALLCNPHQKV 62
K +L TR P + L++ F++ Y + P E+LK A++ + ++
Sbjct: 2 KIVVLSTR-KLPP--EVLERLKEKFEVERYE--DDLTPDTELAERLKDADAVITFVNDRI 56
Query: 63 DKEALDESGENLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVK 122
D E L E LK+I+T S G+D+ ++ A
Sbjct: 57 DAEVL-EKLPGLKLIATRSAGYDN--------------------------VDLEAA---- 85
Query: 123 NLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRRFQQGHNCI 182
K RGI V V S++AVAE + L +A++RR +G +
Sbjct: 86 --------------------KERGITVTNVPGYSTEAVAEHAVALILALARRIHEGDRRV 125
Query: 183 ASGEWALKQTQTVISDIIGLNGSTVGIVGT------------------------------ 212
G W+L + L G T+GI+G
Sbjct: 126 REGNWSLSGGPDPLL-GFDLRGKTLGIIGLGRIGQAVARRLKGFGMKVLYYDRSPNPEAE 184
Query: 213 -ELGAQLVPLDTLCAQSDFIFVTCALTKDTEQLIGRKQF-------------RGGLLDQE 258
ELGA+ V LD L A+SD I + C LT +T LI ++ RGGL+D++
Sbjct: 185 KELGARYVDLDELLAESDIISLHCPLTPETRHLINAEELAKMKPGAILVNTARGGLVDEQ 244
Query: 259 ALVEFLRDKKIGGAGLDVMIPEPMPADHPLVQLDNC 294
AL++ L+ KI GAGLDV EP DHPL++LDN
Sbjct: 245 ALIDALKSGKIAGAGLDVFENEPALFDHPLLRLDNF 280
>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 = 153 bits (388), Expect = 1e-44
Identities = 73/217 (33%), Positives = 99/217 (45%), Gaps = 48/217 (22%)
Query: 122 KNLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRRFQQGHNC 181
LK I G D++ LD K RGI V V +++AVAE +GL +A+ RR +
Sbjct: 62 PKLKFIQVAGAGVDNIDLDAAKKRGITVTNVPGANAEAVAEHALGLLLALLRRLPRADAA 121
Query: 182 IASGEWALKQTQTVISDIIGLNGSTVGIVGT----------------------------- 212
+ G L L G TVGIVG
Sbjct: 122 VRRGWGWLWAGFP----GYELEGKTVGIVGLGRIGQRVAKRLQAFGMKVLYYDRTRKPEP 177
Query: 213 --ELGAQLVPLDTLCAQSDFIFVTCALTKDTEQLIGRKQF-------------RGGLLDQ 257
+LG ++V LD L AQSD + + LT +T LI ++ RGGL+D+
Sbjct: 178 EEDLGFRVVSLDELLAQSDVVVLHLPLTPETRHLINEEELALMKPGAVLVNTARGGLVDE 237
Query: 258 EALVEFLRDKKIGGAGLDVMIPEPMPADHPLVQLDNC 294
+AL+ L+ KI GA LDV PEP+PADHPL++L N
Sbjct: 238 DALLRALKSGKIAGAALDVFEPEPLPADHPLLELPNV 274
>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 = 150 bits (381), Expect = 1e-43
Identities = 83/287 (28%), Positives = 123/287 (42%), Gaps = 78/287 (27%)
Query: 75 KVIST---FSVGHDHLHLDQIKSRGIRV---GTVGPVSSDAVAEFNIGLAIAV------- 121
KV+ T FS + + +++ G V P++ + + E + A V
Sbjct: 1 KVLVTPRSFSKYSEE-AKELLEAAGFEVVLNPLGRPLTEEELIEL-LKDADGVIAGLDPI 58
Query: 122 --------KNLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSR 173
LKVIS + VG+D++ L+ K RGI V +S++VAE IGL +A++R
Sbjct: 59 TEEVLAAAPRLKVISRYGVGYDNIDLEAAKKRGIVVTNTPGANSNSVAELTIGLMLALAR 118
Query: 174 RFQQGHNCIASGEWALKQTQTVISDIIG--LNGSTVGIVG-------------------- 211
+ Q + +G W +G L G T+GI+G
Sbjct: 119 QIPQADREVRAGGW---------DRPVGTELYGKTLGIIGLGRIGKAVARRLSGFGMKVL 169
Query: 212 -----------TELGAQLVPLDTLCAQSDFIFVTCALTKDTEQLIGRKQF---------- 250
E G + V L+ L +SDFI + LT +T LI +
Sbjct: 170 AYDPYPDEEFAKEHGVEFVSLEELLKESDFISLHLPLTPETRHLINAAELALMKPGAILI 229
Query: 251 ---RGGLLDQEALVEFLRDKKIGGAGLDVMIPEPMPADHPLVQLDNC 294
RGGL+D+EAL E L+ +I GA LDV EP PAD PL++L N
Sbjct: 230 NTARGGLVDEEALYEALKSGRIAGAALDVFEEEPPPADSPLLELPNV 276
>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 = 146 bits (370), Expect = 6e-42
Identities = 69/222 (31%), Positives = 102/222 (45%), Gaps = 49/222 (22%)
Query: 117 LAIAVKNLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRRFQ 176
L A L++I VG D + L+ +RGI V + ++++VAE + L +A+ RR
Sbjct: 59 LLAAAPRLRLIQQPGVGLDGVDLEAATARGIPVANIPGGNAESVAEHAVMLMLALLRRLP 118
Query: 177 QGHNCIASGEWALKQTQTVISDIIGLNGSTVGIVG------------------------- 211
+ + +G W + L+G TVGIVG
Sbjct: 119 EADRELRAGRWG----RPEGRPSRELSGKTVGIVGLGNIGRAVARRLRGFGVEVIYYDRF 174
Query: 212 -------TELGAQLVPLDTLCAQSDFIFVTCALTKDTEQLIGRKQF-------------R 251
+LG + V LD L A+SD + + LT +T LIG ++ R
Sbjct: 175 RDPEAEEKDLGVRYVELDELLAESDVVSLHVPLTPETRHLIGAEELAAMKPGAILINTAR 234
Query: 252 GGLLDQEALVEFLRDKKIGGAGLDVMIPEPMPADHPLVQLDN 293
GGL+D+EAL+ LR + GAGLDV EP+P D PL++LDN
Sbjct: 235 GGLVDEEALLAALRSGHLAGAGLDVFWQEPLPPDDPLLRLDN 276
>gnl|CDD|223189 COG0111, SerA, Phosphoglycerate dehydrogenase and related
dehydrogenases [Amino acid transport and metabolism].
Length = 324
Score = 143 bits (363), Expect = 8e-41
Identities = 68/250 (27%), Positives = 102/250 (40%), Gaps = 58/250 (23%)
Query: 89 LDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVKNLKVISTFSVGHDHLHLDQIKSRGIR 148
L+ + + +V PV+ + +A A NLK I G D++ L+ RGI
Sbjct: 40 LEALADADALIVSVTPVTEEVLA--------AAPNLKAIGRAGAGVDNIDLEAATKRGIL 91
Query: 149 VGTVGPVSSDAVAEFNIGLAIAVSRRFQQGHNCIASGEWALKQTQTVISDIIGLNGSTVG 208
V ++ +VAE + L +A++RR GEW K + L G TVG
Sbjct: 92 VVNAPGGNAISVAELVLALLLALARRIPDADASQRRGEWDRKAFR-----GTELAGKTVG 146
Query: 209 IVGT--------------------------------ELGAQLVPLDTLCAQSDFIFVTCA 236
I+G + + LD L A++D + +
Sbjct: 147 IIGLGRIGRAVAKRLKAFGMKVIGYDPYSPRERAGVDGVVGVDSLDELLAEADILTLHLP 206
Query: 237 LTKDTEQLIGRKQF-------------RGGLLDQEALVEFLRDKKIGGAGLDVMIPEPMP 283
LT +T LI ++ RGG++D++AL+ L KI GA LDV EP+P
Sbjct: 207 LTPETRGLINAEELAKMKPGAILINAARGGVVDEDALLAALDSGKIAGAALDVFEEEPLP 266
Query: 284 ADHPLVQLDN 293
AD PL L N
Sbjct: 267 ADSPLWDLPN 276
>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 = 141 bits (359), Expect = 3e-40
Identities = 70/219 (31%), Positives = 101/219 (46%), Gaps = 45/219 (20%)
Query: 120 AVKNLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRRFQQGH 179
A LK+I G +++ ++ RGI V +++AVAEF +GL +A +R + H
Sbjct: 64 AAPKLKLIGVCRGGPENVDVEAATERGIPVLNTPGRNAEAVAEFTVGLMLAETRNIARAH 123
Query: 180 NCIASGEWALKQTQTVISDIIGLNGSTVGIVG---------------------------- 211
+ GEW K L G TVGIVG
Sbjct: 124 AALKDGEW-RKDYYNYDGYGPELRGKTVGIVGFGAIGRRVAKRLKAFGAEVLVYDPYVDP 182
Query: 212 ---TELGAQLVPLDTLCAQSDFIFVTCALTKDTEQLIGRKQF-------------RGGLL 255
G + V L+ L +SD + + LT +T +IG ++F R GL+
Sbjct: 183 EKIEADGVKKVSLEELLKRSDVVSLHARLTPETRGMIGAEEFALMKPTAYFINTARAGLV 242
Query: 256 DQEALVEFLRDKKIGGAGLDVMIPEPMPADHPLVQLDNC 294
D++AL+E L + KIGGA LDV EP+PADHPL++LDN
Sbjct: 243 DEDALIEALEEGKIGGAALDVFPEEPLPADHPLLKLDNV 281
>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 = 139 bits (352), Expect = 3e-39
Identities = 69/218 (31%), Positives = 98/218 (44%), Gaps = 49/218 (22%)
Query: 120 AVKNLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRRFQQGH 179
A LKVI VG D++ ++ +RGI V ++ +VAE I L +A++R Q
Sbjct: 59 AAPRLKVIGRAGVGVDNIDVEAATARGILVVNAPGANTISVAEHTIALMLALARNIPQAD 118
Query: 180 NCIASGEWALKQTQTVISDIIGLNGSTVGIVG---------------------------- 211
+ +G+W K+ V L G T+GIVG
Sbjct: 119 ASLRAGKWDRKKFMGV-----ELRGKTLGIVGLGRIGREVARRARAFGMKVLAYDPYISA 173
Query: 212 ---TELGAQLVPLDTLCAQSDFIFVTCALTKDTEQLIGRKQF-------------RGGLL 255
G +LV LD L A++DFI + LT +T LI ++ RGG++
Sbjct: 174 ERAAAGGVELVSLDELLAEADFISLHTPLTPETRGLINAEELAKMKPGAILINTARGGIV 233
Query: 256 DQEALVEFLRDKKIGGAGLDVMIPEPMPADHPLVQLDN 293
D+ AL + L+ KI GA LDV EP PAD PL+ L N
Sbjct: 234 DEAALADALKSGKIAGAALDVFEQEPPPADSPLLGLPN 271
>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 = 138 bits (351), Expect = 5e-39
Identities = 80/336 (23%), Positives = 126/336 (37%), Gaps = 105/336 (31%)
Query: 4 PKLLLTRNDYPRVSPAYDILEDM-FDIITYPISEGRMPRDIFIEKLKGCSALLCNPHQKV 62
PK+++T D+P + ++LE+ +++ R ++ IE ALL + V
Sbjct: 1 PKVVITDYDFPDLDIEREVLEEAGVELVDAQ---SRTEDEL-IEAAADADALLVQ-YAPV 55
Query: 63 DKEALDESGENLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVK 122
E ++ A+
Sbjct: 56 TAEVIE---------------------------------------------------ALP 64
Query: 123 NLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRRFQQGHNCI 182
LKVI + VG D++ + RGI V V ++ VA+ + L +A++R+ +
Sbjct: 65 RLKVIVRYGVGVDNVDVAAATERGIPVCNVPDYCTEEVADHALALILALARKLPFLDRAV 124
Query: 183 ASGEWALKQTQTVISDIIGLNGSTVGIVG------------------------------- 211
+G W TV I L G T+G+VG
Sbjct: 125 RAGGW----DWTVGGPIRRLRGLTLGLVGFGRIGRAVAKRAKAFGFRVIAYDPYVPDGVA 180
Query: 212 TELGAQLVPLDTLCAQSDFIFVTCALTKDTEQLIGRKQF-------------RGGLLDQE 258
G ++V LD L A+SD + + C LT +T LI + RGGL+D+
Sbjct: 181 ALGGVRVVSLDELLARSDVVSLHCPLTPETRHLIDAEALALMKPGAFLVNTARGGLVDEA 240
Query: 259 ALVEFLRDKKIGGAGLDVMIPEPMPADHPLVQLDNC 294
AL L+ +I GA LDV+ EP PAD PL+ N
Sbjct: 241 ALARALKSGRIAGAALDVLEEEPPPADSPLLSAPNV 276
>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 = 130 bits (329), Expect = 7e-36
Identities = 69/217 (31%), Positives = 100/217 (46%), Gaps = 42/217 (19%)
Query: 120 AVKNLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRRFQQGH 179
+ NLK+I + G++++ L K RGI V V S+D+VA+ L +A++R +
Sbjct: 62 QLPNLKLIGVLATGYNNVDLAAAKERGITVTNVPGYSTDSVAQHTFALLLALARLVAYHN 121
Query: 180 NCIASGEWALKQTQTVIS-DIIGLNGSTVGIVG--------------------------- 211
+ + +GEW II L G T+GI+G
Sbjct: 122 DVVKAGEWQKSPDFCFWDYPIIELAGKTLGIIGYGNIGQAVARIARAFGMKVLFAERKGA 181
Query: 212 TELGAQLVPLDTLCAQSDFIFVTCALTKDTEQLIGRKQF-------------RGGLLDQE 258
L V LD L AQSD I + C LT +T LI ++ RGGL+D++
Sbjct: 182 PPLREGYVSLDELLAQSDVISLHCPLTPETRNLINAEELAKMKPGAILINTARGGLVDEQ 241
Query: 259 ALVEFLRDKKIGGAGLDVMIPEPMPADHPLVQ-LDNC 294
AL + L KI GAGLDV+ EP AD+PL++ N
Sbjct: 242 ALADALNSGKIAGAGLDVLSQEPPRADNPLLKAAPNL 278
>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 = 126 bits (318), Expect = 9e-36
Identities = 52/173 (30%), Positives = 77/173 (44%), Gaps = 48/173 (27%)
Query: 165 IGLAIAVSRRFQQGHNCIASGEWALKQTQTVISDIIGLNGSTVGIVGT------------ 212
+ L +A++RR + + +G W L+G TVGI+G
Sbjct: 1 LALLLALARRIPEADRQVRAGRWRPDALL-----GRELSGKTVGIIGLGRIGRAVARRLK 55
Query: 213 ------------------ELGAQLVPLDTLCAQSDFIFVTCALTKDTEQLIGRKQF---- 250
LGA+ V LD L A+SD + + LT +T LI ++
Sbjct: 56 AFGMKVIAYDRYPKAEAEALGARYVSLDELLAESDVVSLHLPLTPETRHLINAERLALMK 115
Query: 251 ---------RGGLLDQEALVEFLRDKKIGGAGLDVMIPEPMPADHPLVQLDNC 294
RGGL+D++AL+ L+ +I GA LDV PEP+P DHPL++L N
Sbjct: 116 PGAILINTARGGLVDEDALIAALKSGRIAGAALDVFEPEPLPPDHPLLELPNV 168
>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 = 125 bits (315), Expect = 9e-34
Identities = 84/334 (25%), Positives = 128/334 (38%), Gaps = 103/334 (30%)
Query: 5 KLLLTRNDYPRVSPAYDILEDMFDIITYPISEGRMPRDIFIEKLKGCSALLCNPHQKVDK 64
K+L+T A + LE+ F++ Y G + ++ +E++ AL+ VDK
Sbjct: 2 KVLVT---GWIPKEALEELEENFEVTYYD-GLGLISKEELLERIADYDALITPLSTPVDK 57
Query: 65 EALDESGENLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVKNL 124
E +D + +NLK+I+ + G D++ +D K +GI V VS++ AE GL +A+
Sbjct: 58 EIID-AAKNLKIIANYGAGFDNIDVDYAKEKGIPVTNTPAVSTEPTAELTFGLILAL--- 113
Query: 125 KVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRRFQQGHNCIAS 184
+R I G G + + F GH
Sbjct: 114 -------------------ARRIAEGD---------RLMRRGGFLGWAPLFFLGHE---- 141
Query: 185 GEWALKQTQTVISDIIGLNGSTVGIVG--------------------------------T 212
L G T+GI+G
Sbjct: 142 -----------------LAGKTLGIIGMGRIGQAVARRAKAFGMKILYYNRHRLSEETEK 184
Query: 213 ELGAQLVPLDTLCAQSDFIFVTCALTKDTEQLIGRKQF-------------RGGLLDQEA 259
ELGA V LD L +SDF+ + T +T LI F RG L+D++A
Sbjct: 185 ELGATYVDLDELLKESDFVSLHAPYTPETHHLIDAAAFKLMKPTAYLINAARGPLVDEKA 244
Query: 260 LVEFLRDKKIGGAGLDVMIPEPMPADHPLVQLDN 293
LV+ L+ +I GA LDV EP + L +LDN
Sbjct: 245 LVDALKTGEIAGAALDVFEFEPEVSPE-LKKLDN 277
>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 = 124 bits (313), Expect = 2e-33
Identities = 70/223 (31%), Positives = 102/223 (45%), Gaps = 54/223 (24%)
Query: 120 AVKNLKVISTFSVGHDHLHLDQIKSRGIRVGTV-GPVSSDAVAEFNIGLAIAVSRRFQQG 178
LK+I+ +G+D++ L G+ V V G V DAVAE + L + V R+ Q
Sbjct: 66 YNDGLKLIARHGIGYDNVDLKAATEHGVIVTRVPGAVERDAVAEHAVALILTVLRKINQA 125
Query: 179 HNCIASGEWALKQTQTVISDIIG--LNGSTVGIVG------------------------- 211
+ G+W + +G L+G TVGI+G
Sbjct: 126 SEAVKEGKWTERAN------FVGHELSGKTVGIIGYGNIGSRVAEILKEGFNAKVLAYDP 179
Query: 212 -------TELGAQLVPLDTLCAQSDFIFVTCALTKDTEQLIGRKQF-------------R 251
+ GA+ V L+ L A+SD I + LT++T +I K F R
Sbjct: 180 YVSEEVIKKKGAKPVSLEELLAESDIISLHAPLTEETYHMINEKAFSKMKKGVILVNTAR 239
Query: 252 GGLLDQEALVEFLRDKKIGGAGLDVMIPEPMPADHPLVQLDNC 294
G L+D+EAL+E L+ KI GAGLDV+ EP+ ADHPL+ +N
Sbjct: 240 GELIDEEALIEALKSGKIAGAGLDVLEEEPIKADHPLLHYENV 282
>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 = 121 bits (305), Expect = 2e-32
Identities = 68/221 (30%), Positives = 105/221 (47%), Gaps = 54/221 (24%)
Query: 120 AVKNLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRRFQQGH 179
A KNLK+I+ VG D++ ++ K +GI+V SS++VAE IGL ++++R + +
Sbjct: 60 AAKNLKIIARAGVGLDNIDVEYAKKKGIKVINTPGASSNSVAELVIGLMLSLARFIHRAN 119
Query: 180 NCIASGEWALKQTQTVISDIIG--LNGSTVGIVG-------------------------- 211
+ G+W K+ G L G T+GI+G
Sbjct: 120 REMKLGKWNKKK-------YKGIELRGKTLGIIGFGRIGREVAKIARALGMNVIAYDPYP 172
Query: 212 -----TELGAQLVPLDTLCAQSDFIFVTCALTKDTEQLIGRKQF-------------RGG 253
ELG + V L+ L SDFI + LT +T+ +I +K+ RGG
Sbjct: 173 KDEQAVELGVKTVSLEELLKNSDFISLHVPLTPETKHMINKKELELMKDGAIIINTSRGG 232
Query: 254 LLDQEALVEFLRDKKIGGAGLDVMIPEPMPADHPLVQLDNC 294
++D+EAL+E L+ K+ GA LDV EP P L++L N
Sbjct: 233 VIDEEALLEALKSGKLAGAALDVFENEP-PPGSKLLELPNV 272
>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 = 121 bits (305), Expect = 2e-32
Identities = 77/222 (34%), Positives = 105/222 (47%), Gaps = 56/222 (25%)
Query: 120 AVKNLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRRFQQGH 179
A KNLK+IS G DH+ L+ K RGI V S++AVAE IGLAI + R
Sbjct: 66 ACKNLKMISVAFTGVDHVDLEACKERGITVSNAAGYSTEAVAELTIGLAIDLLRNIVPC- 124
Query: 180 NCIASGEWALKQTQTVISDIIG--LNGSTVGIVGT------------------------- 212
+ A++ T + +IG L G TVGIVGT
Sbjct: 125 ------DAAVRAGGT-KAGLIGRELAGKTVGIVGTGAIGLRVARLFKAFGCKVLAYSRSE 177
Query: 213 -----ELGAQLVPLDTLCAQSDFIFVTCALTKDTEQLIGRKQF-------------RGGL 254
LG + V LD L A+SD + + L +T+ LIG+++ RG +
Sbjct: 178 KEEAKALGIEYVSLDELLAESDIVSLHLPLNDETKGLIGKEKLALMKESAILINTARGPV 237
Query: 255 LDQEALVEFLRDKKIGGAGLDV--MIPEPMPADHPLVQLDNC 294
+D EAL + L + KI GAG+DV M P P+PAD+PL+ N
Sbjct: 238 VDNEALADALNEGKIAGAGIDVFDMEP-PLPADYPLLHAPNT 278
>gnl|CDD|183914 PRK13243, PRK13243, glyoxylate reductase; Reviewed.
Length = 333
Score = 121 bits (305), Expect = 3e-32
Identities = 78/338 (23%), Positives = 138/338 (40%), Gaps = 102/338 (30%)
Query: 2 SKPKLLLTRNDYPRVSPAYDILEDMFDIITYPISEGRMPRDIFIEKLKGCSALLCNPHQK 61
KPK+ +TR ++LE+ F++ + E +PR++ +EK++ AL+ ++
Sbjct: 1 MKPKVFITREIPEN---GIEMLEEHFEVEVWE-DEREIPREVLLEKVRDVDALVTMLSER 56
Query: 62 VDKEALDESGENLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAV 121
+D E + A
Sbjct: 57 IDCEVFE---------------------------------------------------AA 65
Query: 122 KNLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRRFQQGHNC 181
L++++ ++VG+D++ +++ RGI V V ++A A+F L +A +RR + +
Sbjct: 66 PRLRIVANYAVGYDNIDVEEATRRGIYVTNTPGVLTEATADFAWALLLATARRLVEADHF 125
Query: 182 IASGEWALKQTQTVISDIIG--LNGSTVGIVG---------------------------- 211
+ SGEW + +G + G T+GI+G
Sbjct: 126 VRSGEWKRRGVAWHPLMFLGYDVYGKTIGIIGFGRIGQAVARRAKGFGMRILYYSRTRKP 185
Query: 212 ---TELGAQLVPLDTLCAQSDFIFVTCALTKDTEQLIGRKQF-------------RGGLL 255
ELGA+ PL+ L +SDF+ + LTK+T +I ++ RG ++
Sbjct: 186 EAEKELGAEYRPLEELLRESDFVSLHVPLTKETYHMINEERLKLMKPTAILVNTARGKVV 245
Query: 256 DQEALVEFLRDKKIGGAGLDVMIPEPMPADHPLVQLDN 293
D +ALV+ L++ I GAGLDV EP + L L N
Sbjct: 246 DTKALVKALKEGWIAGAGLDVFEEEPYY-NEELFSLKN 282
>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 = 119 bits (302), Expect = 6e-32
Identities = 56/220 (25%), Positives = 90/220 (40%), Gaps = 51/220 (23%)
Query: 120 AVKNLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRRFQQGH 179
A L+ I + S G D L ++ R + + + +AE+ +G +A +R+ +
Sbjct: 56 AAPRLRWIQSTSAGVDALLFPELLERDVVLTNARGIFGPPIAEYVLGYMLAFARKLPRYA 115
Query: 180 NCIASGEWALKQTQTVISDIIGLNGSTVGIVGT-ELGAQL-------------------- 218
A W ++ V L G TV IVG ++G ++
Sbjct: 116 RNQAERRW--QRRGPVRE----LAGKTVLIVGLGDIGREIARRAKAFGMRVIGVRRSGRP 169
Query: 219 VP-----------LDTLCAQSDFIFVTCALTKDTEQLIGRKQF-------------RGGL 254
P LD L ++D++ LT +T L ++F RG +
Sbjct: 170 APPVVDEVYTPDELDELLPEADYVVNALPLTPETRGLFNAERFAAMKPGAVLINVGRGSV 229
Query: 255 LDQEALVEFLRDKKIGGAGLDVMIPEPMPADHPLVQLDNC 294
+D++AL+E L +I GA LDV EP+PAD PL L N
Sbjct: 230 VDEDALIEALESGRIAGAALDVFEEEPLPADSPLWDLPNV 269
>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 = 115 bits (290), Expect = 2e-30
Identities = 70/252 (27%), Positives = 105/252 (41%), Gaps = 66/252 (26%)
Query: 88 HLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVKNLKVISTFSVGHDHLHLDQIKSRGI 147
H +I R + +S+ +A A+ L++I++F VG+D + LD ++RGI
Sbjct: 39 HGGRI--RAVVTNGETGLSAALIA--------ALPALELIASFGVGYDGIDLDAARARGI 88
Query: 148 RVGTVGPVSSDAVAEFNIGLAIAVSRRFQQGHNCIASGEWALKQ---TQTVISDIIGLNG 204
RV V +D VA+ +GL +AV RR + +G W T+ V +G
Sbjct: 89 RVTNTPGVLTDDVADLAVGLLLAVLRRIPAADRFVRAGRWPKGAFPLTRKV-------SG 141
Query: 205 STVGIVGTELG------AQ-LVPLDT-----------------------LCAQSDFIFVT 234
VGIVG LG A+ L L A+SD + V
Sbjct: 142 KRVGIVG--LGRIGRAIARRLEAFGMEIAYHGRRPKPDVPYRYYASLLELAAESDVLVVA 199
Query: 235 CALTKDTEQLIGRKQF-------------RGGLLDQEALVEFLRDKKIGGAGLDVMIPEP 281
C T L+ + RG ++D+ AL+ L++ +I GAGLDV EP
Sbjct: 200 CPGGPATRHLVNAEVLEALGPDGVLVNVARGSVVDEAALIAALQEGRIAGAGLDVFENEP 259
Query: 282 MPADHPLVQLDN 293
L+ LDN
Sbjct: 260 NVPA-ALLDLDN 270
>gnl|CDD|237436 PRK13581, PRK13581, D-3-phosphoglycerate dehydrogenase;
Provisional.
Length = 526
Score = 114 bits (288), Expect = 1e-28
Identities = 72/226 (31%), Positives = 100/226 (44%), Gaps = 66/226 (29%)
Query: 120 AVKNLKVISTFSVGHDHLHLDQIKSRGIRV------GTVGPVSSDAVAEFNIGLAIAVSR 173
A KNLKVI VG D++ + RGI V T+ + AE I L +A++R
Sbjct: 61 AAKNLKVIGRAGVGVDNVDVPAATRRGIIVVNAPTGNTI------SAAEHTIALMLALAR 114
Query: 174 RFQQGHNCIASGEWALKQTQTVISDIIG--LNGSTVGIVG-------------------- 211
Q H + +G+W K +G L G T+GI+G
Sbjct: 115 NIPQAHASLKAGKWERK-------KFMGVELYGKTLGIIGLGRIGSEVAKRAKAFGMKVI 167
Query: 212 -----------TELGAQLVPLDTLCAQSDFIFVTCALTKDTEQLIGRKQF---------- 250
+LG +LV LD L A++DFI + LT +T LIG ++
Sbjct: 168 AYDPYISPERAAQLGVELVSLDELLARADFITLHTPLTPETRGLIGAEELAKMKPGVRII 227
Query: 251 ---RGGLLDQEALVEFLRDKKIGGAGLDVMIPEPMPADHPLVQLDN 293
RGG++D+ AL E L+ K+ GA LDV EP P D PL +L N
Sbjct: 228 NCARGGIIDEAALAEALKSGKVAGAALDVFEKEP-PTDSPLFELPN 272
>gnl|CDD|215893 pfam00389, 2-Hacid_dh, D-isomer specific 2-hydroxyacid
dehydrogenase, catalytic domain. This family represents
the largest portion of the catalytic domain of
2-hydroxyacid dehydrogenases as the NAD binding domain
is inserted within the structural domain.
Length = 312
Score = 110 bits (277), Expect = 2e-28
Identities = 63/316 (19%), Positives = 104/316 (32%), Gaps = 97/316 (30%)
Query: 21 DILEDMFDIITYPISEGRMPRDIFIEKLKGCSALLCNPHQKVDKEALDESGENLKVISTF 80
++L++ ++ + + + +E K AL+ V E L+
Sbjct: 13 ELLKEGGEVEVHD----ELLTEELLEAAKDADALIVRSTTPVTAEVLE------------ 56
Query: 81 SVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVKNLKVISTFSVGHDHLHLD 140
A LKVI+ VG D++ LD
Sbjct: 57 ---------------------------------------AAPGLKVIARRGVGVDNIDLD 77
Query: 141 QIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRRFQQGHNCIASGEWALKQTQ------- 193
RGI V V S+++VAE +GL +A++RR + + +G+W
Sbjct: 78 AATERGILVTNVPGYSTESVAELTVGLILALARRIPEADASVRAGDWKKGGPIGLELYGK 137
Query: 194 TVISDIIGLNGSTVGIVGTELGAQLVPLD----------------------TLCAQSDFI 231
T+ G G + LG +V D +SD +
Sbjct: 138 TLGVIGGGGIGGIGAAIAKALGMGVVAYDPYPNPERAEEGGVEVLLLDLLLLDLKESDDL 197
Query: 232 FVTCALTKDTEQLIGRKQF-------------RGGLLDQEALVEFLRDKKIGGAGLDVMI 278
T I + RGG + +EA ++ L ++ I A LDV+
Sbjct: 198 INLAPPTTMKTGHIIINEARGMLKDAVAINNARGGGVIEEAALDALLEEGIAAAALDVVE 257
Query: 279 PEPMPADHPLVQLDNC 294
EP P + PL+ L N
Sbjct: 258 EEPPPVNSPLLDLPNV 273
>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 = 108 bits (273), Expect = 1e-27
Identities = 57/198 (28%), Positives = 80/198 (40%), Gaps = 48/198 (24%)
Query: 140 DQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRRFQQGHNCIASGEWALKQTQTVISDI 199
D + RGI V + +++ VAEF + + RR + +G T+
Sbjct: 89 DAVWERGILVTSAADANAEPVAEFTLAAILLALRRIPRFAAAYRAGRDWGWPTR---RGG 145
Query: 200 IGLNGSTVGIVG-------------------------------TELGAQLVPLDTLCAQS 228
GL G TVGIVG LG +LV LD L A+S
Sbjct: 146 RGLYGRTVGIVGFGRIGRAVVELLRPFGLRVLVYDPYLPAAEAAALGVELVSLDELLARS 205
Query: 229 DFIFVTCALTKDTEQLIGRKQF-------------RGGLLDQEALVEFLRDKKIGGAGLD 275
D + + LT +T +I + RG L+D+ AL+ LR ++ A LD
Sbjct: 206 DVVSLHAPLTPETRGMIDARLLALMRDGATFINTARGALVDEAALLAELRSGRL-RAALD 264
Query: 276 VMIPEPMPADHPLVQLDN 293
V PEP+P D PL L N
Sbjct: 265 VTDPEPLPPDSPLRTLPN 282
>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 = 107 bits (270), Expect = 2e-27
Identities = 67/240 (27%), Positives = 99/240 (41%), Gaps = 59/240 (24%)
Query: 105 VSSDAVAEFNIGLAIAVKNLKVISTFSVGHDHLHLDQIKSRGIRV-GTVGPVSSDAVAEF 163
V E + A+K LK+I S G DHL L+++ G+ V G +S AVAE
Sbjct: 45 VGGRLTKEEALA---ALKRLKLIQVPSAGVDHLPLERLPE-GVVVANNHG--NSPAVAEH 98
Query: 164 NIGLAIAVSRRFQQGHNCIASGEWALKQTQTVISDIIGLNGSTVGIVGT-----ELGAQL 218
+ L +A+++R + N + G W + + S L G TVGI+G E+ L
Sbjct: 99 ALALILALAKRIVEYDNDLRRGIWHGRAGEEPESKE--LRGKTVGILGYGHIGREIARLL 156
Query: 219 VP--------------------------LDTLCAQSDFIFVTCALTKDTEQLIGRKQF-- 250
LD Q+D + V LTK T LIG +
Sbjct: 157 KAFGMRVIGVSRSPKEDEGADFVGTLSDLDEALEQADVVVVALPLTKQTRGLIGAAELAA 216
Query: 251 -----------RGGLLDQEALVEFLRDKKIGGAGLDVMIPEP------MPADHPLVQLDN 293
RG ++D+EAL E L+++ I GA +DV P P+ +P +L N
Sbjct: 217 MKPGAILVNVGRGPVVDEEALYEALKERPIAGAAIDVWWRYPSRGDPVAPSRYPFHELPN 276
>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 = 107 bits (269), Expect = 3e-27
Identities = 65/217 (29%), Positives = 90/217 (41%), Gaps = 55/217 (25%)
Query: 123 NLKVISTFSVGHDHLHLDQIKSRGIRV-GTVGPVSSDAVAEFNIGLAIAVSRRFQQGHNC 181
NLK++ T + + + L K RGI V GT G A AE L +A++R +
Sbjct: 69 NLKLLVTTGMRNASIDLAAAKERGIVVCGTGG--GPTATAELTWALILALARNLPEEDAA 126
Query: 182 IASGEWALKQTQTVISDIIGLNGSTVGIVG------------------------------ 211
+ +G W QT + GL G T+GIVG
Sbjct: 127 LRAGGW-----QT--TLGTGLAGKTLGIVGLGRIGARVARIGQAFGMRVIAWSSNLTAER 179
Query: 212 -TELGAQL-VPLDTLCAQSDFIFVTCALTKDTEQLIGRKQF-------------RGGLLD 256
G + V + L A SD + + L+ T L+G + RG L+D
Sbjct: 180 AAAAGVEAAVSKEELFATSDVVSLHLVLSDRTRGLVGAEDLALMKPTALLVNTSRGPLVD 239
Query: 257 QEALVEFLRDKKIGGAGLDVMIPEPMPADHPLVQLDN 293
+ AL+ LR +I GA LDV EP+PADHPL L N
Sbjct: 240 EGALLAALRAGRIAGAALDVFDVEPLPADHPLRGLPN 276
>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 = 104 bits (263), Expect = 3e-26
Identities = 58/219 (26%), Positives = 90/219 (41%), Gaps = 52/219 (23%)
Query: 122 KNLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRRFQQGHNC 181
+LK+I+ G+D + +D + RGI+V +A A+ + L + R F +
Sbjct: 75 PSLKIIAHAGAGYDQIDVDALTKRGIQVSNTPGAVDEATADTALFLILGALRNFSRAERS 134
Query: 182 IASGEWALKQTQTVISDIIGLNGSTVGIVG------------------------TELGAQ 217
+G+W + ++ G T+GI+G + L +
Sbjct: 135 ARAGKW---RGFLDLTLAHDPRGKTLGILGLGGIGKAIARKAAAFGMKIIYHNRSRLPEE 191
Query: 218 L--------VPLDTLCAQSDFIFVTCALTKDTEQLIGRKQF-------------RGGLLD 256
L V LD L AQSD + + C LT T LI +K+F RG ++D
Sbjct: 192 LEKALATYYVSLDELLAQSDVVSLNCPLTAATRHLINKKEFAKMKDGVIIVNTARGAVID 251
Query: 257 QEALVEFLRDKKIGGAGLDVMIPEPMP----ADHPLVQL 291
++ALV+ L K+ AGLDV EP P V L
Sbjct: 252 EDALVDALESGKVASAGLDVFENEPEVNPGLLKMPNVTL 290
>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 = 104 bits (262), Expect = 5e-26
Identities = 61/197 (30%), Positives = 91/197 (46%), Gaps = 52/197 (26%)
Query: 125 KVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRRFQQGHNCIAS 184
K+I+ G +++ L K GI V V S AVAE + L +A++R+ + +N +
Sbjct: 70 KLIALRCAGFNNVDLKAAKELGITVVRVPAYSPYAVAEHAVALLLALNRKIHRAYNRVRE 129
Query: 185 GEWALKQTQTVISDIIG--LNGSTVGIVGT------------------------------ 212
G ++L ++G L+G TVG++GT
Sbjct: 130 GNFSL-------DGLLGFDLHGKTVGVIGTGKIGQAFARILKGFGCRVLAYDPYPNPELA 182
Query: 213 ELGAQLVPLDTLCAQSDFIFVTCALTKDTEQLIGRKQF-------------RGGLLDQEA 259
+LG + V LD L A+SD I + C LT +T LI + RGGL+D +A
Sbjct: 183 KLGVEYVDLDELLAESDIISLHCPLTPETHHLINAETIAKMKDGVMLINTSRGGLIDTKA 242
Query: 260 LVEFLRDKKIGGAGLDV 276
L+E L+ KIGG GLDV
Sbjct: 243 LIEALKSGKIGGLGLDV 259
>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 = 101 bits (255), Expect = 3e-25
Identities = 49/182 (26%), Positives = 67/182 (36%), Gaps = 50/182 (27%)
Query: 157 SDAVAEFNIGLAIAVSRRFQQGHNCIASGEWALKQTQTVISDIIGLNGSTVGIVG----- 211
++ VAE + L +A R+ + W + L GSTV IVG
Sbjct: 84 AETVAEHALALLLAGLRQL---PARARATTWD---PAEEDDLVTLLRGSTVAIVGAGGIG 137
Query: 212 TELGAQLVP--------------------------LDTLCAQSDFIFVTCALTKDTEQLI 245
L L P LD + +D + + LT +T L+
Sbjct: 138 RALIPLLAPFGAKVIAVNRSGRPVEGADETVPADRLDEVWPDADHVVLAAPLTPETRHLV 197
Query: 246 GRKQF-------------RGGLLDQEALVEFLRDKKIGGAGLDVMIPEPMPADHPLVQLD 292
RG L+D +ALV+ LR +I GA LDV PEP+P HPL L
Sbjct: 198 DAAALAAMKPHAWLVNVARGPLVDTDALVDALRSGEIAGAALDVTDPEPLPDGHPLWSLP 257
Query: 293 NC 294
N
Sbjct: 258 NA 259
>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 = 100 bits (252), Expect = 1e-24
Identities = 64/235 (27%), Positives = 94/235 (40%), Gaps = 69/235 (29%)
Query: 123 NLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRRFQQGHNCI 182
LK+I+T S G DH+ L+ + RGI V V VAE L +A+SR+ ++
Sbjct: 63 RLKLIATRSTGFDHIDLEACRERGIAVCNVPDYGEATVAEHAFALLLALSRKLREAIERT 122
Query: 183 ASGEWALKQTQTVISDIIGLNGSTVGIVGT------------------------------ 212
G+++ + L G T+G+VGT
Sbjct: 123 RRGDFSQAGLRG-----FELAGKTLGVVGTGRIGRRVARIARGFGMKVLAYDVVPDEELA 177
Query: 213 -ELGAQLVPLDTLCAQSDFIFVTCALTKDTEQLIGRKQF-------------RGGLLDQE 258
LG + V L+ L +SD I + T T LI R+ F RG ++D E
Sbjct: 178 ERLGFRYVSLEELLQESDIISLHVPYTPQTHHLINRENFALMKPGAVLINTARGAVVDTE 237
Query: 259 ALVEFLRDKKIGGAGLDV------MIPE--------------PMPADHPLVQLDN 293
ALV L++ K+ GAGLDV + E + ADH L++ N
Sbjct: 238 ALVRALKEGKLAGAGLDVLEQEEVLREEAELFREDVSPEDLKKLLADHALLRKPN 292
>gnl|CDD|180588 PRK06487, PRK06487, glycerate dehydrogenase; Provisional.
Length = 317
Score = 99.0 bits (247), Expect = 4e-24
Identities = 75/252 (29%), Positives = 115/252 (45%), Gaps = 50/252 (19%)
Query: 84 HDHLHLDQIKSR--GIRVGTVGPVSSDAVAEFNIGLAIAVKNLKVISTFSVGHDHLHLDQ 141
HD +Q+ R G +V V+ DA A LA A LK+I + G +++ L
Sbjct: 31 HDATTPEQVAERLRGAQVAISNKVALDAAA-----LA-AAPQLKLILVAATGTNNVDLAA 84
Query: 142 IKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRRFQQGHNCIASGEWALKQTQTVISD--I 199
+ RGI V + +VA+ + L +A++ R +A+G W + +Q + D I
Sbjct: 85 ARERGITVCNCQGYGTPSVAQHTLALLLALATRLPDYQQAVAAGRWQ-QSSQFCLLDFPI 143
Query: 200 IGLNGSTVGIVGT-ELG----------------AQL---------VPLDTLCAQSDFIFV 233
+ L G T+G++G ELG QL +PLD L Q D + +
Sbjct: 144 VELEGKTLGLLGHGELGGAVARLAEAFGMRVLIGQLPGRPARPDRLPLDELLPQVDALTL 203
Query: 234 TCALTKDTEQLIGRKQF-------------RGGLLDQEALVEFLRDKKIGGAGLDVMIPE 280
C LT+ T LIG ++ RGGL+D++AL + LR +GGA DV+ E
Sbjct: 204 HCPLTEHTRHLIGARELALMKPGALLINTARGGLVDEQALADALRSGHLGGAATDVLSVE 263
Query: 281 PMPADHPLVQLD 292
P +PL+ D
Sbjct: 264 PPVNGNPLLAPD 275
>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 = 99.3 bits (248), Expect = 4e-24
Identities = 66/265 (24%), Positives = 104/265 (39%), Gaps = 61/265 (23%)
Query: 57 NPHQKVDKEALDESGENLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIG 116
+ +++KE L G ++++++ + L + + I + ++ + +
Sbjct: 10 DDELEIEKEILKAGGVDVEIVTYLLNDDETAELAK-GADAILTAFTDKIDAELLDKA--- 65
Query: 117 LAIAVKNLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRRFQ 176
LK IS + G+D++ LD K GI V V S +AVAE I L +A+ R
Sbjct: 66 -----PGLKFISLRATGYDNIDLDYAKELGIGVTNVPEYSPNAVAEHTIALILALLRN-- 118
Query: 177 QGHNCIASGEWALKQTQTVISDIIG--LNGSTVGIVGT---------------------- 212
+ K + +IG L TVG+VGT
Sbjct: 119 -----RKYIDERDKNQDLQDAGVIGRELEDQTVGVVGTGKIGRAVAQRAKGFGMKVIAYD 173
Query: 213 --------ELGAQLVPLDTLCAQSDFIFVTCALTKDTEQLIGRKQF-------------R 251
+ G + V L+ L SD I + LT + +I + F R
Sbjct: 174 PFRNPELEDKGVKYVSLEELFKNSDIISLHVPLTPENHHMINEEAFKLMKKGVIIINTAR 233
Query: 252 GGLLDQEALVEFLRDKKIGGAGLDV 276
G L+D EAL+E L KI GAGLDV
Sbjct: 234 GSLVDTEALIEALDSGKIFGAGLDV 258
>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 = 97.3 bits (243), Expect = 2e-23
Identities = 73/251 (29%), Positives = 111/251 (44%), Gaps = 51/251 (20%)
Query: 45 IEKLKGCSALLCNPHQKVDKEALDESGE-NLKVISTFSVGHDHLHLDQIKSRGIRVGTVG 103
+G + K+ E L++ E +K IST S+G+DH+ LD K GI+V V
Sbjct: 39 AHLAEGYDGISILGKSKISAELLEKLKEAGVKYISTRSIGYDHIDLDAAKELGIKVSNV- 97
Query: 104 PVSSDAVAEFNIGLAI-AVKNLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAE 162
S ++VA++ + L + A++ K I + +D+ L ++ R +R TVG + +
Sbjct: 98 TYSPNSVADYTVMLMLMALRKYKQIMKRAEVNDY-SLGGLQGRELRNLTVGVIGTG---- 152
Query: 163 FNIGLAIAVSRRFQQGHNCIASGEWALKQTQTVISDIIGL----NGSTVGIVGTELGAQL 218
IG A V + G C I+ N + A+
Sbjct: 153 -RIGQA--VIKNLS-GFGC----------------KILAYDPYPNEEV------KKYAEY 186
Query: 219 VPLDTLCAQSDFIFVTCALTKDTEQLIGRKQF-------------RGGLLDQEALVEFLR 265
V LDTL +SD I + LT++T LI ++ RG L+D EAL+E L
Sbjct: 187 VDLDTLYKESDIITLHTPLTEETYHLINKESIAKMKDGVIIINTARGELIDTEALIEGLE 246
Query: 266 DKKIGGAGLDV 276
KIGGA LDV
Sbjct: 247 SGKIGGAALDV 257
>gnl|CDD|185307 PRK15409, PRK15409, bifunctional glyoxylate/hydroxypyruvate
reductase B; Provisional.
Length = 323
Score = 96.7 bits (241), Expect = 3e-23
Identities = 61/218 (27%), Positives = 96/218 (44%), Gaps = 51/218 (23%)
Query: 123 NLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRRFQQGHNCI 182
L+ ST SVG+D+ +D + +R I + V ++ VA+ + L ++ +RR + +
Sbjct: 66 KLRAASTISVGYDNFDVDALTARKILLMHTPTVLTETVADTLMALVLSTARRVVEVAERV 125
Query: 183 ASGEWALKQTQTVISDIIGLN--GSTVGIVG----------------------------- 211
+GEW T ++ D G + T+GIVG
Sbjct: 126 KAGEW----TASIGPDWFGTDVHHKTLGIVGMGRIGMALAQRAHFGFNMPILYNARRHHK 181
Query: 212 ---TELGAQLVPLDTLCAQSDFIFVTCALTKDTEQLIGRKQF-------------RGGLL 255
A+ LDTL +SDF+ + LT +T L G +QF RG ++
Sbjct: 182 EAEERFNARYCDLDTLLQESDFVCIILPLTDETHHLFGAEQFAKMKSSAIFINAGRGPVV 241
Query: 256 DQEALVEFLRDKKIGGAGLDVMIPEPMPADHPLVQLDN 293
D+ AL+ L+ +I AGLDV EP+ D PL+ L N
Sbjct: 242 DENALIAALQKGEIHAAGLDVFEQEPLSVDSPLLSLPN 279
>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 = 97.8 bits (244), Expect = 8e-23
Identities = 66/221 (29%), Positives = 96/221 (43%), Gaps = 55/221 (24%)
Query: 120 AVKNLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRRFQQGH 179
A LKVI VG D++ ++ +RGI V ++ + AE + + +A +R Q
Sbjct: 59 AAPKLKVIGRAGVGVDNIDIEAATARGILVVNAPTGNTISAAEHALAMLLAAARNIPQAD 118
Query: 180 NCIASGEWALKQTQTVISDIIG--LNGSTVGIVG-------------------------- 211
+ GEW K +G L G T+G++G
Sbjct: 119 ASLKEGEWDRKA-------FMGTELYGKTLGVIGLGRIGSIVAKRAKAFGMKVLAYDPYI 171
Query: 212 -----TELGAQLVP-LDTLCAQSDFIFVTCALTKDTEQLIGRKQF-------------RG 252
+LG +LV LD L A++DFI V LT +T LIG ++ RG
Sbjct: 172 SPERAEQLGVELVDDLDELLARADFITVHTPLTPETRGLIGAEELAKMKKGVIIVNCARG 231
Query: 253 GLLDQEALVEFLRDKKIGGAGLDVMIPEPMPADHPLVQLDN 293
G++D+ AL E L + + A LDV EP P D+PL LDN
Sbjct: 232 GIIDEAALYEALEEGHVRAAALDVFEKEP-PTDNPLFDLDN 271
>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 = 93.4 bits (233), Expect = 4e-22
Identities = 58/218 (26%), Positives = 95/218 (43%), Gaps = 54/218 (24%)
Query: 122 KNLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRRFQQGHNC 181
KNLK I +S G D+L L+ IK +GI + + S +AE+ +G + + + ++ +
Sbjct: 59 KNLKWIQLYSAGVDYLPLEYIKKKGILLTNNSGIHSIPIAEWIVGYILEIYKGLKKAYKN 118
Query: 182 IASGEWALKQTQTVISDIIGLNGSTVGIVGTELGA------------------------- 216
+W + S ++ L G T+ +GT G+
Sbjct: 119 QKEKKWKMD------SSLLELYGKTILFLGT--GSIGQEIAKRLKAFGMKVIGVNTSGRD 170
Query: 217 -----QLVP---LDTLCAQSDFIFVTCALTKDTEQLIGRKQF-------------RGGLL 255
+ P LD + ++D + LT++T L F RG +
Sbjct: 171 VEYFDKCYPLEELDEVLKEADIVVNVLPLTEETHHLFDEAFFEQMKKGALFINVGRGPSV 230
Query: 256 DQEALVEFLRDKKIGGAGLDVMIPEPMPADHPLVQLDN 293
D++AL+E L++K+I GA LDV EP+P D PL LDN
Sbjct: 231 DEDALIEALKNKQIRGAALDVFEEEPLPKDSPLWDLDN 268
>gnl|CDD|181414 PRK08410, PRK08410, 2-hydroxyacid dehydrogenase; Provisional.
Length = 311
Score = 90.4 bits (225), Expect = 4e-21
Identities = 57/216 (26%), Positives = 98/216 (45%), Gaps = 43/216 (19%)
Query: 120 AVKNLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRRFQQGH 179
+ NLK+I + G +++ ++ K +GI V V S+++VA+ + +++ R
Sbjct: 60 QLPNLKLICITATGTNNVDIEYAKKKGIAVKNVAGYSTESVAQHTFAMLLSLLGRINYYD 119
Query: 180 NCIASGEWALKQTQTVISDIIG-LNGSTVGIVG------------TELGAQL-------- 218
+ SGE++ T IS +G + G GI+G GA++
Sbjct: 120 RYVKSGEYSESPIFTHISRPLGEIKGKKWGIIGLGTIGKRVAKIAQAFGAKVVYYSTSGK 179
Query: 219 --------VPLDTLCAQSDFIFVTCALTKDTEQLIGRKQF-------------RGGLLDQ 257
V L+ L SD I + L + T+ LI K+ RGG++++
Sbjct: 180 NKNEEYERVSLEELLKTSDIISIHAPLNEKTKNLIAYKELKLLKDGAILINVGRGGIVNE 239
Query: 258 EALVEFLRDKKIGGAGLDVMIPEPMPADHPLVQLDN 293
+ L + L +K I AGLDV+ EPM +HPL+ + N
Sbjct: 240 KDLAKALDEKDIY-AGLDVLEKEPMEKNHPLLSIKN 274
>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 = 90.8 bits (226), Expect = 5e-21
Identities = 56/212 (26%), Positives = 82/212 (38%), Gaps = 49/212 (23%)
Query: 122 KNLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRRFQQGHNC 181
KNLK+ T +G DH+ L RGI V V + +VAE + + + + R + GH
Sbjct: 83 KNLKLALTAGIGSDHVDLQAANDRGITVAEVTGSNVVSVAEHVVMMILILVRNYVPGHEQ 142
Query: 182 IASGEWALKQTQTVISDIIGLNGSTVGIVGT----------------------------- 212
G W + V+ L G TVG VG
Sbjct: 143 AIEGGWNVAD---VVKRAYDLEGKTVGTVGAGRIGLRVLRRLKPFDVHLLYYDRHRLPEE 199
Query: 213 ---ELGAQLVP-LDTLCAQSDFIFVTCALTKDTEQLIGRKQF-------------RGGLL 255
ELG L+ + ++ D + + C L +TE L ++ RG +
Sbjct: 200 VEKELGLTRHADLEDMVSKCDVVTINCPLHPETEGLFNKELLSKMKKGAYLVNTARGKIC 259
Query: 256 DQEALVEFLRDKKIGGAGLDVMIPEPMPADHP 287
D+EA+ E L + G DV P+P P DHP
Sbjct: 260 DREAVAEALESGHLAGYAGDVWFPQPAPKDHP 291
Score = 31.5 bits (72), Expect = 0.42
Identities = 16/44 (36%), Positives = 22/44 (50%)
Query: 69 ESGENLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAE 112
+NLK+ T +G DH+ L RGI V V + +VAE
Sbjct: 80 AKAKNLKLALTAGIGSDHVDLQAANDRGITVAEVTGSNVVSVAE 123
>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 = 89.7 bits (223), Expect = 9e-21
Identities = 73/302 (24%), Positives = 122/302 (40%), Gaps = 46/302 (15%)
Query: 3 KPKLLLTRNDYPRVSP-AYDILEDMFDIITYPISEGRMPRDIFIEKLKGCSALLCNPHQK 61
KPK+++T +V P ++L+ ++I+ ++ + R+ + + K L+ +
Sbjct: 1 KPKVVITH----KVHPEVLELLKPHCEVISNQ-TDEPLSREELLRRCKDADGLMAFMPDR 55
Query: 62 VDKEALDESGENLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAV 121
+D + LD LK+I+ G+D+ ++ +RGI V V + ++ AE IGL I +
Sbjct: 56 IDADFLDAC-PRLKIIACALKGYDNFDVEACTARGIWVTIVPDLLTEPTAELTIGLLIGL 114
Query: 122 KNLKVISTFSV--GHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRRFQQGH 179
+ V G + G+ TVG + A+ G AIA RR G
Sbjct: 115 GRHILAGDRFVRSGKFGGWRPKFYGTGLDGKTVGILGMGAL-----GRAIA--RRL-SGF 166
Query: 180 NCIASGEWALKQTQTVISDIIGLNGSTVGIVGTELGAQLVPLDTLCAQSDFIFVTCALTK 239
+ D L+ + L + V LD L SDF+ + LT
Sbjct: 167 GA-----------TLLYYDPHPLDQAE----EQALNLRRVELDELLESSDFLVLALPLTP 211
Query: 240 DTEQLIGRKQF-------------RGGLLDQEALVEFLRDKKIGGAGLDVMIPEPMP-AD 285
DT LI + RG ++D+ A+ E L+ +GG DV E D
Sbjct: 212 DTLHLINAEALAKMKPGALLVNPCRGSVVDEAAVAEALKSGHLGGYAADVFEMEDWARPD 271
Query: 286 HP 287
P
Sbjct: 272 RP 273
>gnl|CDD|235890 PRK06932, PRK06932, glycerate dehydrogenase; Provisional.
Length = 314
Score = 87.9 bits (218), Expect = 5e-20
Identities = 61/209 (29%), Positives = 94/209 (44%), Gaps = 43/209 (20%)
Query: 124 LKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRRFQQGHNCIA 183
LK+I+ + G +++ L K GI V V SS V E +G+ A+ +
Sbjct: 66 LKLIAITATGTNNVDLVAAKELGIAVKNVTGYSSTTVPEHVLGMIFALKHSLMGWYRDQL 125
Query: 184 SGEWALKQTQTVISD--IIGLNGSTVGIVG-----TELG--AQLV--------------- 219
S WA Q D I + GST+G+ G TE+G AQ +
Sbjct: 126 SDRWA-TCKQFCYFDYPITDVRGSTLGVFGKGCLGTEVGRLAQALGMKVLYAEHKGASVC 184
Query: 220 -----PLDTLCAQSDFIFVTCALTKDTEQLIGRKQF-------------RGGLLDQEALV 261
P + + Q+D + + C LT+ T+ LI + RG L+D++AL+
Sbjct: 185 REGYTPFEEVLKQADIVTLHCPLTETTQNLINAETLALMKPTAFLINTGRGPLVDEQALL 244
Query: 262 EFLRDKKIGGAGLDVMIPEPMPADHPLVQ 290
+ L + KI GA LDV++ EP D+PL+Q
Sbjct: 245 DALENGKIAGAALDVLVKEPPEKDNPLIQ 273
>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 = 85.5 bits (212), Expect = 3e-19
Identities = 51/180 (28%), Positives = 77/180 (42%), Gaps = 57/180 (31%)
Query: 155 VSSDAVAEFNIGLAIAVSRRFQQGHNCI---ASGEWALKQTQTVISDIIGLNGSTVGIVG 211
V+++A+AEF + +A ++R + I + +W + ++ GST+GIVG
Sbjct: 94 VAAEAIAEFVLAAILAAAKRLPE----IWVKGAEQWRREPLGSL-------AGSTLGIVG 142
Query: 212 ------------TELGAQLVPL------------------DTLCAQSDFIFVTCALTKDT 241
LG +++ L L A+SD + + LT +T
Sbjct: 143 FGAIGQALARRALALGMRVLALRRSGRPSDVPGVEAAADLAELFARSDHLVLAAPLTPET 202
Query: 242 EQLIGRKQF-------------RGGLLDQEALVEFLRDKKIGGAGLDVMIPEPMPADHPL 288
LI RGGL+DQEAL+E L +I A LDV PEP+P HPL
Sbjct: 203 RHLINADVLAQAKPGLHLINIARGGLVDQEALLEALDSGRISLASLDVTDPEPLPEGHPL 262
>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 = 84.6 bits (210), Expect = 9e-19
Identities = 63/243 (25%), Positives = 87/243 (35%), Gaps = 72/243 (29%)
Query: 121 VKNLKVISTFSVGHDH-LHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRRFQQGH 179
V NL+++ FS G DH L K + + T + +AE+ IG + +S F Q
Sbjct: 52 VPNLRLVQLFSAGADHWLGHPLYKDPEVPLCTASGIHGPQIAEWVIGTWLVLSHHFLQYI 111
Query: 180 NCIASGEWALKQTQTVISDIIGLNGSTVGIVG------------TELGAQL--------- 218
W +Q + D G VGI+G LG ++
Sbjct: 112 ELQKEQTWGRRQEAYSVED---SVGKRVGILGYGSIGRQTARLAQALGMEVYAYTRSPRP 168
Query: 219 -----------VP---------------------LDTLCAQSDFIFVTCA-LTKDTEQLI 245
VP L Q + V LT T+ L+
Sbjct: 169 TPESRKDDGYIVPGTGDPDGSIPSAWFSGTDKASLHEFLRQDLDLLVVSLPLTPATKHLL 228
Query: 246 GRKQF--------------RGGLLDQEALVEFLRDKKIGGAGLDVMIPEPMPADHPLVQL 291
G ++F RG L+D +ALV L +I GA LDV PEP+PADHPL
Sbjct: 229 GAEEFEILAKRKTFVSNIARGSLVDTDALVAALESGQIRGAALDVTDPEPLPADHPLWSA 288
Query: 292 DNC 294
N
Sbjct: 289 PNV 291
>gnl|CDD|181041 PRK07574, PRK07574, formate dehydrogenase; Provisional.
Length = 385
Score = 83.6 bits (207), Expect = 3e-18
Identities = 57/212 (26%), Positives = 82/212 (38%), Gaps = 49/212 (23%)
Query: 122 KNLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRRFQQGHNC 181
NLK+ T +G DH+ L GI V V +S +VAE + + +A+ R ++ H
Sbjct: 113 PNLKLAITAGIGSDHVDLQAASEHGITVAEVTGSNSISVAEHVVMMILALVRNYEPSHRQ 172
Query: 182 IASGEWALKQTQTVISDIIGLNGSTVGIVGT----------------------------- 212
G W + +S L G TVGIVG
Sbjct: 173 AVEGGWNIAD---CVSRSYDLEGMTVGIVGAGRIGLAVLRRLKPFDVKLHYTDRHRLPEE 229
Query: 213 ---ELGAQLVP-LDTLCAQSDFIFVTCALTKDTEQLIGRKQF-------------RGGLL 255
ELG D+L + D + + C L +TE L RG ++
Sbjct: 230 VEQELGLTYHVSFDSLVSVCDVVTIHCPLHPETEHLFDADVLSRMKRGSYLVNTARGKIV 289
Query: 256 DQEALVEFLRDKKIGGAGLDVMIPEPMPADHP 287
D++A+V L + G DV P+P PADHP
Sbjct: 290 DRDAVVRALESGHLAGYAGDVWFPQPAPADHP 321
>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 = 82.6 bits (205), Expect = 4e-18
Identities = 54/200 (27%), Positives = 82/200 (41%), Gaps = 51/200 (25%)
Query: 123 NLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRRFQQGHNCI 182
+K I+ S G D + LD K G+++ V S A+AEF + A+ + R + +
Sbjct: 68 GIKQIALRSAGVDMIDLDLAKENGLKITNVPAYSPRAIAEFAVTQALNLLRNTPEIDRRV 127
Query: 183 ASGEWALKQTQTVISDIIG--LNGSTVGIVGT------------ELGAQL---------- 218
A G++ +IG + TVGI+GT GA++
Sbjct: 128 AKGDF------RWAPGLIGREIRDLTVGIIGTGRIGSAAAKIFKGFGAKVIAYDPYPNPE 181
Query: 219 --------VPLDTLCAQSDFIFVTCALTKDTEQLIGRKQF-------------RGGLLDQ 257
L+ L Q+D I + LTK+ LI + F RGGL+D
Sbjct: 182 LEKFLLYYDSLEDLLKQADIISLHVPLTKENHHLINAEAFAKMKDGAILVNAARGGLVDT 241
Query: 258 EALVEFLRDKKIGGAGLDVM 277
+AL++ L KI GA LD
Sbjct: 242 KALIDALDSGKIAGAALDTY 261
>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 = 81.5 bits (202), Expect = 6e-18
Identities = 51/216 (23%), Positives = 81/216 (37%), Gaps = 51/216 (23%)
Query: 120 AVKNLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRRFQQGH 179
A+ L+V+ T S G+D + L + G+ + V + AE + L +A R +
Sbjct: 57 ALPRLRVVQTLSAGYDGV-LPLLP-EGVTLCNARGVHDASTAELAVALILASLRGLPRFV 114
Query: 180 NCIASGEWALKQTQTVISDIIGLNGSTVGIVG-----TELGAQLVP-------------- 220
A G W ++T + L V IVG + +L P
Sbjct: 115 RAQARGRWEPRRTPS-------LADRRVLIVGYGSIGRAIERRLAPFEVRVTRVARTARP 167
Query: 221 ---------LDTLCAQSDFIFVTCALTKDTEQLIGRKQF-------------RGGLLDQE 258
L L ++D + + LT +T L+ + RG ++D +
Sbjct: 168 GEQVHGIDELPALLPEADVVVLIVPLTDETRGLVDAEFLARMPDGALLVNVARGPVVDTD 227
Query: 259 ALVEFLRDKKIGGAGLDVMIPEPMPADHPLVQLDNC 294
ALV L ++ A LDV PEP+P HPL
Sbjct: 228 ALVAELASGRLR-AALDVTDPEPLPPGHPLWSAPGV 262
>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 = 74.9 bits (185), Expect = 1e-15
Identities = 74/289 (25%), Positives = 112/289 (38%), Gaps = 67/289 (23%)
Query: 54 LLCNPHQKVDKEALDESGENLKVISTFSVGHDHLH--LDQIKSRGIRVGTVGPVSSDAVA 111
LL N H D E G ++ + ++ D L L + GIR T ++ + +
Sbjct: 5 LLENIHPSAD-ELFRAGGIEVERLKG-ALDEDELIEALKDVHLLGIRSKTQ--LTEEVLE 60
Query: 112 EFNIGLAIAVKNLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVS-SDAVAEFNIGLAIA 170
A L I F +G + + LD RGI V P S + +VAE IG I
Sbjct: 61 --------AAPKLLAIGCFCIGTNQVDLDAAAKRGIPVFN-APFSNTRSVAELVIGEIIM 111
Query: 171 VSRRFQQGHNCIASGEWALKQTQTVISDIIGLNGSTVGIVG-TELGAQL----------- 218
++RR + G W + + G T+GI+G +G+QL
Sbjct: 112 LARRLPDRNAAAHRGIW-----NKSATGSHEVRGKTLGIIGYGHIGSQLSVLAEALGMRV 166
Query: 219 ----------------VP-LDTLCAQSDFIFVTCALTKDTEQLIGRKQF----------- 250
V L+ L A++DF+ + T T+ +IG ++
Sbjct: 167 IFYDIAEKLPLGNARQVSSLEELLAEADFVTLHVPATPSTKNMIGAEEIAQMKKGAILIN 226
Query: 251 --RGGLLDQEALVEFLRDKKIGGAGLDVMIPEPM----PADHPLVQLDN 293
RG ++D +AL E LR + GA +DV EP P PL L N
Sbjct: 227 ASRGTVVDIDALAEALRSGHLAGAAVDVFPEEPASNGEPFSSPLQGLPN 275
>gnl|CDD|178684 PLN03139, PLN03139, formate dehydrogenase; Provisional.
Length = 386
Score = 73.7 bits (181), Expect = 7e-15
Identities = 53/212 (25%), Positives = 85/212 (40%), Gaps = 49/212 (23%)
Query: 122 KNLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRRFQQGHNC 181
KNL+++ T +G DH+ L + G+ V V + +VAE + + + R F G++
Sbjct: 120 KNLELLLTAGIGSDHIDLPAAAAAGLTVAEVTGSNVVSVAEDELMRILILLRNFLPGYHQ 179
Query: 182 IASGEWALKQTQTVISDIIGLNGSTVGIVGT----------------------------- 212
+ SGEW + L G TVG VG
Sbjct: 180 VVSGEW---NVAGIAYRAYDLEGKTVGTVGAGRIGRLLLQRLKPFNCNLLYHDRLKMDPE 236
Query: 213 ---ELGAQLVP-LDTLCAQSDFIFVTCALTKDTEQLIGRKQF-------------RGGLL 255
E GA+ LD + + D + + LT+ T + +++ RG ++
Sbjct: 237 LEKETGAKFEEDLDAMLPKCDVVVINTPLTEKTRGMFNKERIAKMKKGVLIVNNARGAIM 296
Query: 256 DQEALVEFLRDKKIGGAGLDVMIPEPMPADHP 287
D +A+ + IGG G DV P+P P DHP
Sbjct: 297 DTQAVADACSSGHIGGYGGDVWYPQPAPKDHP 328
>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 = 70.3 bits (173), Expect = 6e-14
Identities = 54/218 (24%), Positives = 85/218 (38%), Gaps = 67/218 (30%)
Query: 122 KNLKVISTFSVGHDHLHLDQIKSRGIRV-GTVGPVSSDAVAEFNIGLAIAVSRRFQQGHN 180
+LK I+ G +++ +D RGI V T G +++AVAE I + +A+SR Q
Sbjct: 49 PSLKAIARAGAGVNNIDVDAASKRGIVVFNTPGA-NANAVAELVIAMMLALSRNIIQAIK 107
Query: 181 CIASG---------EWALKQTQTVISDIIGLNGSTVGIVGTELGA--------------- 216
+ +G E KQ L G T+G++G LG
Sbjct: 108 WVTNGDGDDISKGVEKGKKQ-----FVGTELRGKTLGVIG--LGNIGRLVANAALALGMK 160
Query: 217 ---------------------QLVPLDTLCAQSDFIFVTCALTKDTEQLIGRKQF----- 250
++ L+ L A +D+I + LT +T LI +
Sbjct: 161 VIGYDPYLSVEAAWKLSVEVQRVTSLEELLATADYITLHVPLTDETRGLINAELLAKMKP 220
Query: 251 --------RGGLLDQEALVEFLRDKKIGGAGLDVMIPE 280
RG ++D+EAL+E L + K+GG D P
Sbjct: 221 GAILLNFARGEIVDEEALLEALDEGKLGGYVTDFPEPA 258
>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 = 64.6 bits (158), Expect = 7e-12
Identities = 55/215 (25%), Positives = 83/215 (38%), Gaps = 65/215 (30%)
Query: 118 AIAVKNLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRRFQQ 177
+K + T +VG +H+ L+ K G ++ V S +A+AE LA+ +SR
Sbjct: 63 IYKEYGIKYVFTRTVGFNHIDLEAAKELGFKMARVPSYSPNAIAELAFTLAMTLSRHT-- 120
Query: 178 GHNCIASGEWALKQTQTVISDII--------GLNGSTVGIVGT------------ELGAQ 217
A ++T + + STVGI+GT LGA+
Sbjct: 121 ----------AYTASRTANKNFKVDPFMFSKEIRNSTVGIIGTGRIGLTAAKLFKGLGAK 170
Query: 218 -----------------LVPLDTLCAQSDFIFVTCALTK-DTEQLIGRKQF--------- 250
V LD L +SD I + K ++LI K+F
Sbjct: 171 VIGYDIYPSDAAKDVVTFVSLDELLKKSDIISLHVPYIKGKNDKLIN-KEFISKMKDGAI 229
Query: 251 -----RGGLLDQEALVEFLRDKKIGGAGLDVMIPE 280
RG L D+EA++E L K+ G G DV+ E
Sbjct: 230 LINTARGELQDEEAILEALESGKLAGFGTDVLNNE 264
>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 = 63.1 bits (154), Expect = 2e-11
Identities = 48/199 (24%), Positives = 84/199 (42%), Gaps = 46/199 (23%)
Query: 120 AVKNLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRRFQQGH 179
NLK I+ G +++ L+ K +GI + + DAV E +G+ +A+ + +
Sbjct: 59 KATNLKFIARAGAGLENIDLEYAKEKGIELFNAPEGNRDAVGEHALGMLLALFNKLNRAD 118
Query: 180 NCIASGEWALKQTQTVISDIIGLNGSTVGIVG---------------------------- 211
+ +G W + + V L G TVGI+G
Sbjct: 119 QEVRNGIWDREGNRGV-----ELMGKTVGIIGYGNMGKAFAKRLSGFGCKVIAYDKYKNF 173
Query: 212 TELGAQLVPLDTLCAQSDFIFVTCALTKDTEQLIG-------RKQF------RGGLLDQE 258
+ A+ V L+TL ++D + + LT +T ++ +K F RG ++ +
Sbjct: 174 GDAYAEQVSLETLFKEADILSLHIPLTPETRGMVNKEFISSFKKPFYFINTARGKVVVTK 233
Query: 259 ALVEFLRDKKIGGAGLDVM 277
LV+ L+ KI GA LDV+
Sbjct: 234 DLVKALKSGKILGACLDVL 252
Score = 35.3 bits (82), Expect = 0.028
Identities = 19/63 (30%), Positives = 34/63 (53%), Gaps = 1/63 (1%)
Query: 61 KVDKEALDESGENLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIA 120
+DKE ++ NLK I+ G +++ L+ K +GI + + DAV E +G+ +A
Sbjct: 51 PIDKEFIE-KATNLKFIARAGAGLENIDLEYAKEKGIELFNAPEGNRDAVGEHALGMLLA 109
Query: 121 VKN 123
+ N
Sbjct: 110 LFN 112
>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 = 62.2 bits (152), Expect = 4e-11
Identities = 69/282 (24%), Positives = 107/282 (37%), Gaps = 74/282 (26%)
Query: 19 AYDILEDMFDIITYPISEGRMPRDIFIEKLKGCSALLCNPHQKVDKEALDESGENLKVIS 78
A ++ + ++ P GR +I E LK LL KV++ L+ S +K +
Sbjct: 11 AEELFSPLGEVTYLP---GR---EITAEDLKDADVLLVRSVTKVNEALLEGS--KVKFVG 62
Query: 79 TFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVKNLKVISTFSVGHDHLH 138
T ++G DH+ D +K RGI ++++VAE+ V+S L
Sbjct: 63 TATIGTDHIDTDYLKERGIGFANAPGCNANSVAEY------------VLSALL----VLA 106
Query: 139 LDQIKS-RGIRVGTVGPVSSDAVAEFNIGLAIAVSRRFQQ-GHNCIASGEWALKQTQTVI 196
Q S +G VG VG V N+G +A RR + G N + +
Sbjct: 107 QRQGFSLKGKTVGIVG------VG--NVGSRLA--RRLEALGMNVLLCDPP--RAEA--- 151
Query: 197 SDIIGLNGSTVGIVGTELGAQLVPLDTLCAQSDFIFVTCALTKD----TEQLIGRKQF-- 250
E V L+ L A++D I + LT+D T L+
Sbjct: 152 ----------------EGDPGFVSLEELLAEADIITLHVPLTRDGEHPTYHLLDEDFLAA 195
Query: 251 -----------RGGLLDQEALVEFLRDKKIGGAGLDVMIPEP 281
RG ++D +AL+ L+ K LDV EP
Sbjct: 196 LKPGQILINASRGAVIDNQALLALLQRGKDLRVVLDVWENEP 237
>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 = 61.4 bits (150), Expect = 8e-11
Identities = 56/223 (25%), Positives = 80/223 (35%), Gaps = 63/223 (28%)
Query: 116 GLAIAVKNLKVISTFSVGHDHLHLDQIKSRGIR-VGTVGPVSSDAVAEFNIGLAIAVSRR 174
GL + NLK I + G DHL D + V V P + +AE+ + + + R
Sbjct: 51 GLLARLPNLKAIFSLGAGVDHLLADPD-LPDVPIVRLVDPGLAQGMAEYVLAAVLRLHRD 109
Query: 175 F-----QQGHNCIASGEWALKQTQTVISDIIGLNGSTVGIVGT-ELGA----QLVP---- 220
QQ G W Q ++ VG++G ELGA +L
Sbjct: 110 MDRYAAQQ-----RRGVWK-PLPQRPAAER------RVGVLGLGELGAAVARRLAALGFP 157
Query: 221 ----------------------LDTLCAQSDFIFVTCALTKDTEQLIGRKQF-------- 250
LD AQ+D + LT +T ++ +
Sbjct: 158 VSGWSRSPKDIEGVTCFHGEEGLDAFLAQTDILVCLLPLTPETRGILNAELLARLPRGAA 217
Query: 251 -----RGGLLDQEALVEFLRDKKIGGAGLDVMIPEPMPADHPL 288
RG L + L+ L + GA LDV EP+PADHPL
Sbjct: 218 LINVGRGPHLVEADLLAALDSGHLSGAVLDVFEQEPLPADHPL 260
>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 = 53.9 bits (130), Expect = 2e-08
Identities = 43/176 (24%), Positives = 63/176 (35%), Gaps = 47/176 (26%)
Query: 160 VAEFNIGLAIAVSRRFQQGHNCIASGEWALK----QTQTVISDIIGLNGSTVGIVG---- 211
VAE + L +A RR + WA + Q + L G+ V I G
Sbjct: 95 VAEHTLALILAAVRRLDEMREAQREHRWAGELGGLQPLRPAGRLTTLLGARVLIWGFGSI 154
Query: 212 --------TELGAQLVP------------------LDTLCAQSDFIFVTCALTKDTEQLI 245
T LGA++ L L ++D + + T T +
Sbjct: 155 GQRLAPLLTALGARVTGVARSAGERAGFPVVAEDELPELLPETDVLVMILPATPSTAHAL 214
Query: 246 GRKQF-------------RGGLLDQEALVEFLRDKKIGGAGLDVMIPEPMPADHPL 288
+ RG +D++ALV L ++GGA LDV EP+PA PL
Sbjct: 215 DAEVLAALPKHAWVVNVGRGATVDEDALVAALESGRLGGAALDVTATEPLPASSPL 270
>gnl|CDD|236985 PRK11790, PRK11790, D-3-phosphoglycerate dehydrogenase;
Provisional.
Length = 409
Score = 52.5 bits (127), Expect = 9e-08
Identities = 61/227 (26%), Positives = 87/227 (38%), Gaps = 65/227 (28%)
Query: 120 AVKNLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVS-SDAVAEFNIGLAIAVSRRFQQG 178
A + L I F +G + + LD RGI V P S + +VAE IG I + R +
Sbjct: 72 AAEKLVAIGCFCIGTNQVDLDAAAKRGIPVFN-APFSNTRSVAELVIGEIILLLRGIPEK 130
Query: 179 HNCIASGEWALKQTQTVISDIIGLNGS------TVGIVG-----TELG------------ 215
+ G W K GS T+GIVG T+L
Sbjct: 131 NAKAHRGGW-NKSA----------AGSFEVRGKTLGIVGYGHIGTQLSVLAESLGMRVYF 179
Query: 216 -----------AQLVP-LDTLCAQSDFIFVTCALTKDTEQLIGRKQF------------- 250
A+ V L+ L AQSD + + T T+ +IG ++
Sbjct: 180 YDIEDKLPLGNARQVGSLEELLAQSDVVSLHVPETPSTKNMIGAEELALMKPGAILINAS 239
Query: 251 RGGLLDQEALVEFLRDKKIGGAGLDVMIPEPMPADH----PLVQLDN 293
RG ++D +AL + L+ + GA +DV EP PL LDN
Sbjct: 240 RGTVVDIDALADALKSGHLAGAAIDVFPVEPKSNGDPFESPLRGLDN 286
>gnl|CDD|183550 PRK12480, PRK12480, D-lactate dehydrogenase; Provisional.
Length = 330
Score = 45.3 bits (107), Expect = 2e-05
Identities = 40/190 (21%), Positives = 70/190 (36%), Gaps = 38/190 (20%)
Query: 124 LKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRRFQ------Q 177
+K I+ + G D LD K I + V S + +AE+++ +A+ + RRF Q
Sbjct: 70 IKQIAQRTAGFDMYDLDLAKKHNIVISNVPSYSPETIAEYSVSIALQLVRRFPDIERRVQ 129
Query: 178 GHNCIASGEWALKQTQTVISDIIGLN--GSTVGIVGTELGAQLV-----PLDTL------ 224
H+ E K + + IIG G+ + GA + P L
Sbjct: 130 AHDFTWQAEIMSKPVKNMTVAIIGTGRIGAATAKIYAGFGATITAYDAYPNKDLDFLTYK 189
Query: 225 ------CAQSDFIFVTCALTKDTEQLIGRKQF-------------RGGLLDQEALVEFLR 265
+D I + K++ L + F RG +++ L+ +
Sbjct: 190 DSVKEAIKDADIISLHVPANKESYHLFDKAMFDHVKKGAILVNAARGAVINTPDLIAAVN 249
Query: 266 DKKIGGAGLD 275
D + GA +D
Sbjct: 250 DGTLLGAAID 259
Score = 28.7 bits (64), Expect = 3.4
Identities = 26/112 (23%), Positives = 50/112 (44%), Gaps = 6/112 (5%)
Query: 45 IEKLKGCSALLCNPHQKVDKEA---LDESGENLKVISTFSVGHDHLHLDQIKSRGIRVGT 101
+++LK + K++ + L+ G +K I+ + G D LD K I +
Sbjct: 40 VDQLKDYDGVTTMQFGKLENDVYPKLESYG--IKQIAQRTAGFDMYDLDLAKKHNIVISN 97
Query: 102 VGPVSSDAVAEFNIGLAIA-VKNLKVISTFSVGHDHLHLDQIKSRGIRVGTV 152
V S + +AE+++ +A+ V+ I HD +I S+ ++ TV
Sbjct: 98 VPSYSPETIAEYSVSIALQLVRRFPDIERRVQAHDFTWQAEIMSKPVKNMTV 149
>gnl|CDD|215501 PLN02928, PLN02928, oxidoreductase family protein.
Length = 347
Score = 42.4 bits (100), Expect = 2e-04
Identities = 24/80 (30%), Positives = 39/80 (48%), Gaps = 15/80 (18%)
Query: 228 SDFIFVTCALTKDTEQLIGRKQF--------------RGGLLDQEALVEFLRDKKIGGAG 273
+D + + C LTK+T ++ +F RGGLLD +A++ L +GG
Sbjct: 227 ADIVVLCCTLTKETAGIVN-DEFLSSMKKGALLVNIARGGLLDYDAVLAALESGHLGGLA 285
Query: 274 LDVMIPEPMPADHPLVQLDN 293
+DV EP D P+++ N
Sbjct: 286 IDVAWSEPFDPDDPILKHPN 305
>gnl|CDD|177941 PLN02306, PLN02306, hydroxypyruvate reductase.
Length = 386
Score = 40.6 bits (95), Expect = 6e-04
Identities = 48/218 (22%), Positives = 83/218 (38%), Gaps = 63/218 (28%)
Query: 125 KVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRRFQQGHNCIAS 184
K S +VG++++ ++ GI VG V ++ AE L++A +RR + + +
Sbjct: 88 KAFSNMAVGYNNVDVEAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRA 147
Query: 185 GEWALKQTQTVISDIIGLNGSTVGIVG----------------------------TEL-- 214
G + + ++ L G TVG++G T L
Sbjct: 148 GLYEGWLPHLFVGNL--LKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQSTRLEK 205
Query: 215 ------------GAQLV------PLDTLCAQSDFIFVTCALTKDTEQLIGRKQF------ 250
G Q V ++ + ++D I + L K T LI +++
Sbjct: 206 FVTAYGQFLKANGEQPVTWKRASSMEEVLREADVISLHPVLDKTTYHLINKERLALMKKE 265
Query: 251 -------RGGLLDQEALVEFLRDKKIGGAGLDVMIPEP 281
RG ++D+ ALVE L+ + GLDV EP
Sbjct: 266 AVLVNASRGPVIDEVALVEHLKANPMFRVGLDVFEDEP 303
>gnl|CDD|166874 PRK00257, PRK00257, erythronate-4-phosphate dehydrogenase;
Validated.
Length = 381
Score = 39.6 bits (93), Expect = 0.001
Identities = 41/202 (20%), Positives = 69/202 (34%), Gaps = 68/202 (33%)
Query: 125 KVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRRFQQGHNCIAS 184
+ + T ++G DHL LD GI + ++ V ++ +G + ++ R
Sbjct: 60 RFVGTCTIGTDHLDLDYFAEAGITWSSAPGCNARGVVDYVLGSLLTLAER---------- 109
Query: 185 GEWALKQTQTVISDIIGLNGSTVGIVGT-ELGAQL------------------------- 218
+ + L T G+VG +G +L
Sbjct: 110 -------------EGVDLAERTYGVVGAGHVGGRLVRVLRGLGWKVLVCDPPRQEAEGDG 156
Query: 219 --VPLDTLCAQSDFIFVTCALTKD----TEQLIGRKQF-------------RGGLLDQEA 259
V L+ + + D I + LTK+ T L+ RG ++D +A
Sbjct: 157 DFVSLERILEECDVISLHTPLTKEGEHPTRHLLDEAFLASLRPGAWLINASRGAVVDNQA 216
Query: 260 LVEFLRDKKIGGAGLDVMIPEP 281
L E L + A LDV EP
Sbjct: 217 LREALLSGEDLDAVLDVWEGEP 238
Score = 33.5 bits (77), Expect = 0.13
Identities = 18/61 (29%), Positives = 29/61 (47%), Gaps = 3/61 (4%)
Query: 38 RMP-RDIFIEKLKGCSALLCNPHQKVDKEALDESGENLKVISTFSVGHDHLHLDQIKSRG 96
R+P R ++ LL +VD+ L+ G ++ + T ++G DHL LD G
Sbjct: 24 RLPGRAFDRAAVRDADVLLVRSVTRVDRALLE--GSRVRFVGTCTIGTDHLDLDYFAEAG 81
Query: 97 I 97
I
Sbjct: 82 I 82
>gnl|CDD|235800 PRK06436, PRK06436, glycerate dehydrogenase; Provisional.
Length = 303
Score = 39.5 bits (92), Expect = 0.001
Identities = 41/199 (20%), Positives = 77/199 (38%), Gaps = 37/199 (18%)
Query: 104 PVSSDAVAEFNIGLAIAVKNLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEF 163
P DA A G + K K+I + S G DH+ + I + G S +VAE
Sbjct: 30 PDYYDAEAILIKGRYVPGKKTKMIQSLSAGVDHIDVSGIPENVVLCSNAGAYSI-SVAEH 88
Query: 164 NIGLAIAVSRRFQQGHNCIASGEWALKQTQTVISDIIGL-----NGSTVGIVGTELGAQL 218
L +A ++ + + + +G + T+ + + +G+ G V ++ G +
Sbjct: 89 AFALLLAWAKNICENNYNMKNGNFKQSPTKLLYNKSLGILGYGGIGRRVALLAKAFGMNI 148
Query: 219 V-----------------PLDTLCAQSDFIFVTCALTKDTEQLIGRKQF----------- 250
P D + +SDF+ ++ LT +T +I K
Sbjct: 149 YAYTRSYVNDGISSIYMEPEDIM-KKSDFVLISLPLTDETRGMINSKMLSLFRKGLAIIN 207
Query: 251 --RGGLLDQEALVEFLRDK 267
R ++D+ ++ FLR+
Sbjct: 208 VARADVVDKNDMLNFLRNH 226
Score = 27.9 bits (62), Expect = 7.0
Identities = 15/50 (30%), Positives = 23/50 (46%), Gaps = 1/50 (2%)
Query: 71 GENLKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIA 120
G+ K+I + S G DH+ + I + G S +VAE L +A
Sbjct: 47 GKKTKMIQSLSAGVDHIDVSGIPENVVLCSNAGAYSI-SVAEHAFALLLA 95
>gnl|CDD|181499 PRK08605, PRK08605, D-lactate dehydrogenase; Validated.
Length = 332
Score = 37.4 bits (87), Expect = 0.006
Identities = 54/216 (25%), Positives = 85/216 (39%), Gaps = 38/216 (17%)
Query: 74 LKVISTFSVGHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAI-AVKNLKVISTFSV 132
+K I+ S G D L+ + + V S +++AEF + AI V++ I T
Sbjct: 70 IKQIAQRSAGFDTYDLELATKYNLIISNVPSYSPESIAEFTVTQAINLVRHFNQIQTKVR 129
Query: 133 GHDHLHLDQIKSRGIRVGTVGPVSSDAVAEFNIGLAIAVSRRFQQGHNC------IASGE 186
HD I SR I+ V + + IGLA+A + F +G+
Sbjct: 130 EHDFRWEPPILSRSIKDLKVAVIGTG-----RIGLAVA--KIFAKGYGSDVVAYDPFPNA 182
Query: 187 WA---LKQTQTVISDIIGLNGSTVGIVGTELGAQLVPLDTLCAQSDF----IFVTCALTK 239
A + T+ + G + T+ + T+ L D F +FV CA
Sbjct: 183 KAATYVDYKDTIEEAVEGADIVTLHMPATKYNHYLFNADLF---KHFKKGAVFVNCA--- 236
Query: 240 DTEQLIGRKQFRGGLLDQEALVEFLRDKKIGGAGLD 275
RG L+D +AL++ L + I GA LD
Sbjct: 237 -----------RGSLVDTKALLDALDNGLIKGAALD 261
>gnl|CDD|185366 PRK15469, ghrA, bifunctional glyoxylate/hydroxypyruvate reductase
A; Provisional.
Length = 312
Score = 34.4 bits (79), Expect = 0.060
Identities = 28/100 (28%), Positives = 43/100 (43%), Gaps = 23/100 (23%)
Query: 189 LKQTQTVISDIIGLNGSTVGIVGTELGAQLVPLDTLCAQSDFIFVTCALTKDTEQLIGRK 248
L QT+ +I +++ TVGI+ +L QL D L+
Sbjct: 188 LSQTRVLI-NLLPNTPETVGIINQQLLEQL--------------------PDGAYLLNLA 226
Query: 249 QFRGGLLDQEALVEFLRDKKIGGAGLDVMIPEPMPADHPL 288
RG + ++ L+ L K+ GA LDV EP+P + PL
Sbjct: 227 --RGVHVVEDDLLAALDSGKVKGAMLDVFSREPLPPESPL 264
>gnl|CDD|227224 COG4887, COG4887, Uncharacterized metal-binding protein conserved
in archaea [General function prediction only].
Length = 191
Score = 33.0 bits (75), Expect = 0.10
Identities = 20/70 (28%), Positives = 33/70 (47%), Gaps = 4/70 (5%)
Query: 20 YDILEDMFDIITYPISEGRMPRDIF-IEKLK-GCSALLCNPHQKVDKEALDESGENLKVI 77
+IL F++ + +P+ ++KLK G +CNP L+E G +L ++
Sbjct: 85 CEILSRGFEVYSVCCKVCGVPKSKLSLKKLKPGGFEAVCNP--IGQARLLNEIGTDLNIL 142
Query: 78 STFSVGHDHL 87
VGHD L
Sbjct: 143 VGLCVGHDIL 152
>gnl|CDD|182753 PRK10814, PRK10814, outer membrane-specific lipoprotein transporter
subunit LolC; Provisional.
Length = 399
Score = 30.8 bits (70), Expect = 0.75
Identities = 23/66 (34%), Positives = 32/66 (48%), Gaps = 15/66 (22%)
Query: 159 AVAEFNI--GLAIAVSRRFQQGHNCIASGEWALKQTQTV----ISDIIGLNGSTVGIVGT 212
AVA FNI L + V + GE A+ QTQ + I + + G++ GI+G
Sbjct: 276 AVAAFNIITSLGLLVMEK---------QGEVAILQTQGLTRRQIMMVFMVQGASAGIIGA 326
Query: 213 ELGAQL 218
LGA L
Sbjct: 327 LLGALL 332
>gnl|CDD|185335 PRK15438, PRK15438, erythronate-4-phosphate dehydrogenase PdxB;
Provisional.
Length = 378
Score = 30.3 bits (68), Expect = 1.3
Identities = 20/73 (27%), Positives = 35/73 (47%), Gaps = 2/73 (2%)
Query: 41 RDIFIEKLKGCSALLCNPHQKVDKEALDESGENLKVISTFSVGHDHLHLDQIKSRGIRVG 100
R I + +L AL+ KV++ L +G+ +K + T + G DH+ +K GI
Sbjct: 28 RPIPVAQLADADALMVRSVTKVNESLL--AGKPIKFVGTATAGTDHVDEAWLKQAGIGFS 85
Query: 101 TVGPVSSDAVAEF 113
++ AV E+
Sbjct: 86 AAPGCNAIAVVEY 98
>gnl|CDD|239170 cd02769, MopB_DMSOR-BSOR-TMAOR, The MopB_DMSOR-BSOR-TMAOR CD
contains dimethylsulfoxide reductase (DMSOR), biotin
sulfoxide reductase (BSOR), trimethylamine N-oxide
reductase (TMAOR) and other related proteins. DMSOR
always catalyzes the reduction of DMSO to
dimethylsulfide, but its cellular location and
oligomerization state are organism-dependent. For
example, in Rhodobacter sphaeriodes and Rhodobacter
capsulatus, it is an 82-kDa monomeric soluble protein
found in the periplasmic space; in E. coli, it is
membrane-bound and exists as a heterotrimer. BSOR
catalyzes the reduction of biotin sulfixode to biotin,
and is unique among Mo enzymes because no additional
auxiliary proteins or cofactors are required. TMAOR is
similar to DMSOR, but its only natural substrate is
TMAO. Members of this CD belong to the
molybdopterin_binding (MopB) superfamily of proteins.
Length = 609
Score = 29.9 bits (68), Expect = 1.5
Identities = 14/48 (29%), Positives = 22/48 (45%), Gaps = 1/48 (2%)
Query: 118 AIAVKNLKVISTFSVGHDHL-HLDQIKSRGIRVGTVGPVSSDAVAEFN 164
A +KN ++ H +L +K RGIR ++ P+ D AE
Sbjct: 179 ADPLKNAQIAWGGIPDHQAYSYLKALKDRGIRFISISPLRDDTAAELG 226
Score = 28.4 bits (64), Expect = 4.7
Identities = 10/26 (38%), Positives = 14/26 (53%)
Query: 89 LDQIKSRGIRVGTVGPVSSDAVAEFN 114
L +K RGIR ++ P+ D AE
Sbjct: 201 LKALKDRGIRFISISPLRDDTAAELG 226
>gnl|CDD|218698 pfam05695, DUF825, Plant protein of unknown function (DUF825).
This family consists of several plant proteins greater
than 1000 residues in length. The function of this
family is unknown.
Length = 1127
Score = 29.1 bits (65), Expect = 3.7
Identities = 14/50 (28%), Positives = 22/50 (44%), Gaps = 7/50 (14%)
Query: 12 DYPRVSPAYDILEDMFDIITYPISEGRMP---RDIFIEKLKGCSALLCNP 58
D + L + I + +S G +P +I I +LKG + LCN
Sbjct: 526 DVSKFLL---FLSNSLPIF-FCVSFGNIPIHRSEIHIYELKGPNDQLCNQ 571
>gnl|CDD|225971 COG3437, COG3437, Response regulator containing a CheY-like
receiver domain and an HD-GYP domain [Transcription /
Signal transduction mechanisms].
Length = 360
Score = 27.7 bits (62), Expect = 7.4
Identities = 15/62 (24%), Positives = 26/62 (41%), Gaps = 2/62 (3%)
Query: 176 QQGHNCIA--SGEWALKQTQTVISDIIGLNGSTVGIVGTELGAQLVPLDTLCAQSDFIFV 233
G+ I +GE ALK Q D++ L+ + G E+ +L + + I +
Sbjct: 36 MIGYRVIEAENGEEALKLLQEEPPDLVLLDVRMPEMDGAEVLNKLKAMSPSTRRIPVILL 95
Query: 234 TC 235
T
Sbjct: 96 TA 97
>gnl|CDD|234487 TIGR04157, glyco_rSAM_CFB, glycosyltransferase, GG-Bacteroidales
peptide system. Members of this protein family are
predicted glycosyltransferases that occur in conserved
gene neighborhoods in various members of the
Bacteroidales. These neighborhoods feature a radical SAM
enzyme predicted to act in peptide modification (family
TIGR04148), peptides from family TIGR04149 with a
characteristic GG cleavage motif, and several other
proteins.
Length = 406
Score = 27.7 bits (62), Expect = 7.7
Identities = 7/32 (21%), Positives = 15/32 (46%)
Query: 20 YDILEDMFDIITYPISEGRMPRDIFIEKLKGC 51
+++ED + PI E R ++ ++L
Sbjct: 336 SEMIEDGLNGYKIPIKEYRDYVELDKKELVQK 367
>gnl|CDD|237773 PRK14636, PRK14636, hypothetical protein; Provisional.
Length = 176
Score = 27.1 bits (60), Expect = 8.6
Identities = 17/52 (32%), Positives = 24/52 (46%), Gaps = 4/52 (7%)
Query: 241 TEQLIGRKQFRGGLLDQEALVEFLRDKKIGGAGLDVMIPEPMPADHPLVQLD 292
+E L GRKQFRG L + + D K G +V++P L+ D
Sbjct: 106 SEPLDGRKQFRGELKGIDGDTVTIADNKAG----EVILPFAAIESAKLILTD 153
>gnl|CDD|235899 PRK06975, PRK06975, bifunctional uroporphyrinogen-III
synthetase/uroporphyrin-III C-methyltransferase;
Reviewed.
Length = 656
Score = 27.8 bits (62), Expect = 9.5
Identities = 11/28 (39%), Positives = 13/28 (46%)
Query: 88 HLDQIKSRGIRVGTVGPVSSDAVAEFNI 115
LD I + V VGP S A+A I
Sbjct: 73 RLDAIWPHALPVAVVGPGSVAALARHGI 100
Score = 27.8 bits (62), Expect = 9.5
Identities = 11/28 (39%), Positives = 13/28 (46%)
Query: 138 HLDQIKSRGIRVGTVGPVSSDAVAEFNI 165
LD I + V VGP S A+A I
Sbjct: 73 RLDAIWPHALPVAVVGPGSVAALARHGI 100
>gnl|CDD|107157 PHA02244, PHA02244, ATPase-like protein.
Length = 383
Score = 27.4 bits (60), Expect = 9.9
Identities = 14/53 (26%), Positives = 23/53 (43%), Gaps = 3/53 (5%)
Query: 220 PLDTLCAQSDFIFVTCALTKDT---EQLIGRKQFRGGLLDQEALVEFLRDKKI 269
+ + A DF ++ T + R + G LD+ A +EF D+KI
Sbjct: 212 ADERVTAHEDFRVISAGNTLGKGADHIYVARNKIDGATLDRFAPIEFDYDEKI 264
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
0.320 0.139 0.405
Gapped
Lambda K H
0.267 0.0596 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,089,457
Number of extensions: 1468859
Number of successful extensions: 1620
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1476
Number of HSP's successfully gapped: 145
Length of query: 294
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 198
Effective length of database: 6,679,618
Effective search space: 1322564364
Effective search space used: 1322564364
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 59 (26.8 bits)