RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 020160
(330 letters)
>gnl|CDD|240633 cd12156, HPPR, Hydroxy(phenyl)pyruvate Reductase, D-isomer-specific
2-hydroxyacid-related dehydrogenase.
Hydroxy(phenyl)pyruvate reductase (HPPR) catalyzes the
NADP-dependent reduction of hydroxyphenylpyruvates,
hydroxypyruvate, or pyruvate to its respective lactate.
HPPR acts as a dimer and is related to D-isomer-specific
2-hydroxyacid dehydrogenases, a superfamily that
includes groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-Adenosylhomocysteine Hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 301
Score = 396 bits (1020), Expect = e-139
Identities = 138/309 (44%), Positives = 191/309 (61%), Gaps = 10/309 (3%)
Query: 12 PQVLLLRK--PSGFAMLGEQFFTSNKFQYLKAYESALPLHEFLTLHAHSVKAIFSSAGAP 69
P VL L P A L +F + +E+A P L H ++A+ ++
Sbjct: 1 PDVLQLGPLPPELLAELEARF------TVHRLWEAADP-AALLAEHGGRIRAVVTNGETG 53
Query: 70 VTAEILRLLPEVRLVVATSAGLNHIDVVECRRRGVALANAGNVFSEDVADYALGLLIDVL 129
++A ++ LP + L+ + G + ID+ R RG+ + N V ++DVAD A+GLL+ VL
Sbjct: 54 LSAALIAALPALELIASFGVGYDGIDLDAARARGIRVTNTPGVLTDDVADLAVGLLLAVL 113
Query: 130 RKLSAADCFVRQGLWPINAEFPLGSKLGGKRVGIVGLGSIGSEVAKRLEAFGCCVSYNSR 189
R++ AAD FVR G WP FPL K+ GKRVGIVGLG IG +A+RLEAFG ++Y+ R
Sbjct: 114 RRIPAADRFVRAGRWP-KGAFPLTRKVSGKRVGIVGLGRIGRAIARRLEAFGMEIAYHGR 172
Query: 190 NKKPSVTYPFYPDVCELAANSDVLIICCALTDQTHHLINKQVLLALGKKGVIINVGRGAI 249
KP V Y +Y + ELAA SDVL++ C T HL+N +VL ALG GV++NV RG++
Sbjct: 173 RPKPDVPYRYYASLLELAAESDVLVVACPGGPATRHLVNAEVLEALGPDGVLVNVARGSV 232
Query: 250 IDEKEMVGCLLRGEIGGAGLDVFENEPDVPEQLFALDNVVLSPHSAVFTPESFKDVCELA 309
+DE ++ L G I GAGLDVFENEP+VP L LDNVVL+PH A T E+ + + +L
Sbjct: 233 VDEAALIAALQEGRIAGAGLDVFENEPNVPAALLDLDNVVLTPHIASATVETRRAMGDLV 292
Query: 310 VANLEAFFS 318
+ANLEAFF+
Sbjct: 293 LANLEAFFA 301
>gnl|CDD|223980 COG1052, LdhA, Lactate dehydrogenase and related dehydrogenases
[Energy production and conversion / Coenzyme metabolism
/ General function prediction only].
Length = 324
Score = 281 bits (722), Expect = 7e-94
Identities = 108/296 (36%), Positives = 161/296 (54%), Gaps = 9/296 (3%)
Query: 39 LKAYESALPLHEFLTLHAHSVKAIFSSAGAPVTAEILRLLPEVRLVVATSAGLNHIDVVE 98
++ YE L L A+ + + AE+L LP ++L+ SAG +++D+
Sbjct: 25 VERYEDDLTPDTELAERLKDADAVITFVNDRIDAEVLEKLPGLKLIATRSAGYDNVDLEA 84
Query: 99 CRRRGVALANAGNVFSEDVADYALGLLIDVLRKLSAADCFVRQGLWPINAE--FPLGSKL 156
+ RG+ + N +E VA++A+ L++ + R++ D VR+G W ++ LG L
Sbjct: 85 AKERGITVTNVPGYSTEAVAEHAVALILALARRIHEGDRRVREGNWSLSGGPDPLLGFDL 144
Query: 157 GGKRVGIVGLGSIGSEVAKRLEAFGCCVSYNSRNKKPSVTYPF---YPDVCELAANSDVL 213
GK +GI+GLG IG VA+RL+ FG V Y R+ P Y D+ EL A SD++
Sbjct: 145 RGKTLGIIGLGRIGQAVARRLKGFGMKVLYYDRSPNPEAEKELGARYVDLDELLAESDII 204
Query: 214 IICCALTDQTHHLINKQVLLALGKKGVIINVGRGAIIDEKEMVGCLLRGEIGGAGLDVFE 273
+ C LT +T HLIN + L + +++N RG ++DE+ ++ L G+I GAGLDVFE
Sbjct: 205 SLHCPLTPETRHLINAEELAKMKPGAILVNTARGGLVDEQALIDALKSGKIAGAGLDVFE 264
Query: 274 NEPD-VPEQLFALDN---VVLSPHSAVFTPESFKDVCELAVANLEAFFSNKPLLTP 325
NEP L LDN VVL+PH A T E+ K + ELA+ NLEAFF
Sbjct: 265 NEPALFDHPLLRLDNFPNVVLTPHIASATEEARKAMAELALENLEAFFDGGVPPNE 320
>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 = 255 bits (655), Expect = 6e-84
Identities = 118/320 (36%), Positives = 166/320 (51%), Gaps = 23/320 (7%)
Query: 12 PQVLLLRK--PSGFAMLGEQF-FTSNKFQYLKAYESALPLHEFLTLHAHSVKAIFSSAGA 68
P+VL+ R+ A+L E F + LP E L A + +
Sbjct: 1 PKVLVTRRLPEEALALLREGFEVEVW------DEDRPLPREELLE-AAKGADGLLCTLTD 53
Query: 69 PVTAEILRLLPEVRLVVAT-SAGLNHIDVVECRRRGVALANAGNVFSEDVADYALGLLID 127
+ AE+L P ++ V+A S G +HIDV + RG+ + N +V ++ AD A LL+
Sbjct: 54 KIDAELLDAAPPLK-VIANYSVGYDHIDVDAAKARGIPVTNTPDVLTDATADLAFALLLA 112
Query: 128 VLRKLSAADCFVRQGLW-PINAEFPLGSKLGGKRVGIVGLGSIGSEVAKRLEAFGCCVSY 186
R++ D FVR G W + LG+ L GK +GIVG+G IG VA+R + FG + Y
Sbjct: 113 AARRVVEGDRFVRAGEWKGWSPTLLLGTDLHGKTLGIVGMGRIGQAVARRAKGFGMKILY 172
Query: 187 NSRNKKPSVTYPF---YPDVCELAANSDVLIICCALTDQTHHLINKQVLLALGKKG-VII 242
++R++KP Y + EL A SD + + C LT +T HLIN + L AL K ++I
Sbjct: 173 HNRSRKPEAEEELGARYVSLDELLAESDFVSLHCPLTPETRHLINAERL-ALMKPTAILI 231
Query: 243 NVGRGAIIDEKEMVGCLLRGEIGGAGLDVFENEPDVPEQ-LFALDNVVLSPH--SAVFTP 299
N RG ++DE +V L G+I GAGLDVFE EP + L L NVVL PH SA T
Sbjct: 232 NTARGGVVDEDALVEALKSGKIAGAGLDVFEPEPLPADHPLLTLPNVVLLPHIGSA--TV 289
Query: 300 ESFKDVCELAVANLEAFFSN 319
E+ + ELA NL A +
Sbjct: 290 ETRTAMAELAADNLLAVLAG 309
>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 = 244 bits (624), Expect = 2e-79
Identities = 110/274 (40%), Positives = 158/274 (57%), Gaps = 5/274 (1%)
Query: 47 PLHEFLTLHAHSVKAIFSSAGAPVTAEILRLLPEVRLVVATSAGLNHIDVVECRRRGVAL 106
L + L A+ S+ PVTAE+L P+++ + AG+++ID+ ++RG+ +
Sbjct: 30 LLADELEALLADADALIVSSTTPVTAEVLAKAPKLKFIQVAGAGVDNIDLDAAKKRGITV 89
Query: 107 ANAGNVFSEDVADYALGLLIDVLRKLSAADCFVRQGLWPINAEFPLGSKLGGKRVGIVGL 166
N +E VA++ALGLL+ +LR+L AD VR+G G +L GK VGIVGL
Sbjct: 90 TNVPGANAEAVAEHALGLLLALLRRLPRADAAVRRGWG-WLWAGFPGYELEGKTVGIVGL 148
Query: 167 GSIGSEVAKRLEAFGCCVSYNSRNKKPSVTYPFYPDVC---ELAANSDVLIICCALTDQT 223
G IG VAKRL+AFG V Y R +KP V EL A SDV+++ LT +T
Sbjct: 149 GRIGQRVAKRLQAFGMKVLYYDRTRKPEPEEDLGFRVVSLDELLAQSDVVVLHLPLTPET 208
Query: 224 HHLINKQVLLALGKKGVIINVGRGAIIDEKEMVGCLLRGEIGGAGLDVFENEPDVPEQ-L 282
HLIN++ L + V++N RG ++DE ++ L G+I GA LDVFE EP + L
Sbjct: 209 RHLINEEELALMKPGAVLVNTARGGLVDEDALLRALKSGKIAGAALDVFEPEPLPADHPL 268
Query: 283 FALDNVVLSPHSAVFTPESFKDVCELAVANLEAF 316
L NV+L+PH A +T E+ + + E+AV NLE F
Sbjct: 269 LELPNVILTPHIAGYTEEARERMAEIAVENLERF 302
>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 = 242 bits (621), Expect = 8e-79
Identities = 111/320 (34%), Positives = 161/320 (50%), Gaps = 16/320 (5%)
Query: 12 PQVLLLRKPSGFAMLGEQFFTSNKFQYLKAYESALPLHEFLTLHAHSVKAIFSSAGA--- 68
P+VLLL P ++ + + Y + + AI+ + G+
Sbjct: 2 PKVLLLGDPIHAHDEWKELSSIAEVIYPTSGTREEFIEALKEGKYGDFVAIYRTFGSAGE 61
Query: 69 --PVTAEILRLLPE-VRLVVATSAGLNHIDVVECRRRGVALANAGNVFSEDVADYALGLL 125
P E++ LP ++++ AG + IDV +RG+ ++N E AD AL L+
Sbjct: 62 TGPFDEELISPLPPSLKIIAHAGAGYDQIDVDALTKRGIQVSNTPGAVDEATADTALFLI 121
Query: 126 IDVLRKLSAADCFVRQGLWPINAEFPLGSKLGGKRVGIVGLGSIGSEVAKRLEAFGCCVS 185
+ LR S A+ R G W + L GK +GI+GLG IG +A++ AFG +
Sbjct: 122 LGALRNFSRAERSARAGKWRGFLDLTLAHDPRGKTLGILGLGGIGKAIARKAAAFGMKII 181
Query: 186 YNSRNKKPS------VTYPFYPDVCELAANSDVLIICCALTDQTHHLINKQVLLALGKKG 239
Y++R++ P TY Y + EL A SDV+ + C LT T HLINK+ A K G
Sbjct: 182 YHNRSRLPEELEKALATY--YVSLDELLAQSDVVSLNCPLTAATRHLINKK-EFAKMKDG 238
Query: 240 VII-NVGRGAIIDEKEMVGCLLRGEIGGAGLDVFENEPDVPEQLFALDNVVLSPHSAVFT 298
VII N RGA+IDE +V L G++ AGLDVFENEP+V L + NV L PH T
Sbjct: 239 VIIVNTARGAVIDEDALVDALESGKVASAGLDVFENEPEVNPGLLKMPNVTLLPHMGTLT 298
Query: 299 PESFKDVCELAVANLEAFFS 318
E+ + + EL + N+EAF
Sbjct: 299 VETQEKMEELVLENIEAFLE 318
>gnl|CDD|223189 COG0111, SerA, Phosphoglycerate dehydrogenase and related
dehydrogenases [Amino acid transport and metabolism].
Length = 324
Score = 223 bits (571), Expect = 3e-71
Identities = 96/270 (35%), Positives = 141/270 (52%), Gaps = 9/270 (3%)
Query: 67 GAPVTAEILRLLPEVRLVVATSAGLNHIDVVECRRRGVALANAGNVFSEDVADYALGLLI 126
PVT E+L P ++ + AG+++ID+ +RG+ + NA + VA+ L LL+
Sbjct: 53 VTPVTEEVLAAAPNLKAIGRAGAGVDNIDLEAATKRGILVVNAPGGNAISVAELVLALLL 112
Query: 127 DVLRKLSAADCFVRQGLWPINAEFPLGSKLGGKRVGIVGLGSIGSEVAKRLEAFGCCVSY 186
+ R++ AD R+G W A G++L GK VGI+GLG IG VAKRL+AFG V
Sbjct: 113 ALARRIPDADASQRRGEWDRKAF--RGTELAGKTVGIIGLGRIGRAVAKRLKAFGMKVIG 170
Query: 187 NSRNKKPSV----TYPFYPDVCELAANSDVLIICCALTDQTHHLINKQVLLALGKKGVI- 241
+ EL A +D+L + LT +T LIN + LA K G I
Sbjct: 171 YDPYSPRERAGVDGVVGVDSLDELLAEADILTLHLPLTPETRGLINAE-ELAKMKPGAIL 229
Query: 242 INVGRGAIIDEKEMVGCLLRGEIGGAGLDVFENEPDVPE-QLFALDNVVLSPHSAVFTPE 300
IN RG ++DE ++ L G+I GA LDVFE EP + L+ L NV+L+PH T E
Sbjct: 230 INAARGGVVDEDALLAALDSGKIAGAALDVFEEEPLPADSPLWDLPNVILTPHIGGSTDE 289
Query: 301 SFKDVCELAVANLEAFFSNKPLLTPFAAVD 330
+ + V E+ N+ + + P++ VD
Sbjct: 290 AQERVAEIVAENIVRYLAGGPVVNNAPEVD 319
>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 = 222 bits (568), Expect = 5e-71
Identities = 105/300 (35%), Positives = 153/300 (51%), Gaps = 18/300 (6%)
Query: 38 YLKAYESALPLHEFLTLHAHSVKA---------IFSSAGAPVTAEILRLLPEVRLVVATS 88
L+A P E +T +A + + AE+L P +RL+
Sbjct: 15 LLRALLPPAPGVEVVTAAELDEEAALLADADVLVPGMRK-VIDAELLAAAPRLRLIQQPG 73
Query: 89 AGLNHIDVVECRRRGVALANAGNVFSEDVADYALGLLIDVLRKLSAADCFVRQGLWPINA 148
GL+ +D+ RG+ +AN +E VA++A+ L++ +LR+L AD +R G W
Sbjct: 74 VGLDGVDLEAATARGIPVANIPGGNAESVAEHAVMLMLALLRRLPEADRELRAGRWG-RP 132
Query: 149 EFPLGSKLGGKRVGIVGLGSIGSEVAKRLEAFGCCVSYNSRNKKPS----VTYPFYPDVC 204
E +L GK VGIVGLG+IG VA+RL FG V Y R + P Y ++
Sbjct: 133 EGRPSRELSGKTVGIVGLGNIGRAVARRLRGFGVEVIYYDRFRDPEAEEKDLGVRYVELD 192
Query: 205 ELAANSDVLIICCALTDQTHHLINKQVLLALGKKGVI-INVGRGAIIDEKEMVGCLLRGE 263
EL A SDV+ + LT +T HLI + L A+ K G I IN RG ++DE+ ++ L G
Sbjct: 193 ELLAESDVVSLHVPLTPETRHLIGAEELAAM-KPGAILINTARGGLVDEEALLAALRSGH 251
Query: 264 IGGAGLDVFENEPDVPEQ-LFALDNVVLSPHSAVFTPESFKDVCELAVANLEAFFSNKPL 322
+ GAGLDVF EP P+ L LDNV+L+PH A T ES++ + + N+ +P
Sbjct: 252 LAGAGLDVFWQEPLPPDDPLLRLDNVILTPHIAGVTDESYQRMAAIVAENIARLLRGEPP 311
>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 = 215 bits (550), Expect = 4e-68
Identities = 94/260 (36%), Positives = 139/260 (53%), Gaps = 7/260 (2%)
Query: 68 APVTAEILRLLPEVRLVVATSAGLNHIDVVECRRRGVALANAGNVFSEDVADYALGLLID 127
APVTAE++ LP ++++V G++++DV RG+ + N + +E+VAD+AL L++
Sbjct: 53 APVTAEVIEALPRLKVIVRYGVGVDNVDVAAATERGIPVCNVPDYCTEEVADHALALILA 112
Query: 128 VLRKLSAADCFVRQGLWPINAEFPLGSKLGGKRVGIVGLGSIGSEVAKRLEAFGCCVSYN 187
+ RKL D VR G W P+ +L G +G+VG G IG VAKR +AFG V
Sbjct: 113 LARKLPFLDRAVRAGGWDWTVGGPI-RRLRGLTLGLVGFGRIGRAVAKRAKAFGFRVIAY 171
Query: 188 SRNKKPSVTYPFYPDVC---ELAANSDVLIICCALTDQTHHLINKQVLLALGKKG-VIIN 243
V V EL A SDV+ + C LT +T HLI+ + L AL K G ++N
Sbjct: 172 DPYVPDGVAALGGVRVVSLDELLARSDVVSLHCPLTPETRHLIDAEAL-ALMKPGAFLVN 230
Query: 244 VGRGAIIDEKEMVGCLLRGEIGGAGLDVFENEPDVPEQ-LFALDNVVLSPHSAVFTPESF 302
RG ++DE + L G I GA LDV E EP + L + NV+L+PH+A ++ ES
Sbjct: 231 TARGGLVDEAALARALKSGRIAGAALDVLEEEPPPADSPLLSAPNVILTPHAAWYSEESL 290
Query: 303 KDVCELAVANLEAFFSNKPL 322
++ A + +P
Sbjct: 291 AELRRKAAEEVVRVLRGEPP 310
>gnl|CDD|240649 cd12172, PGDH_like_2, Putative D-3-Phosphoglycerate Dehydrogenases,
NAD-binding and catalytic domains. Phosphoglycerate
dehydrogenases (PGDHs) catalyze the initial step in the
biosynthesis of L-serine from D-3-phosphoglycerate.
PGDHs come in 3 distinct structural forms, with this
first group being related to 2-hydroxy acid
dehydrogenases, sharing structural similarity to formate
and glycerate dehydrogenases of the D-specific
2-hydroxyacid dehydrogenase superfamily, which also
include groups such as L-alanine dehydrogenase and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. Many, not all, members of this family are
dimeric.
Length = 306
Score = 213 bits (545), Expect = 2e-67
Identities = 87/250 (34%), Positives = 130/250 (52%), Gaps = 10/250 (4%)
Query: 69 PVTAEILRLLPEVRLVVATSAGLNHIDVVECRRRGVALANAGNVFSEDVADYALGLLIDV 128
P+T E+L P ++++ G ++ID+ ++RG+ + N S VA+ +GL++ +
Sbjct: 57 PITEEVLAAAPRLKVISRYGVGYDNIDLEAAKKRGIVVTNTPGANSNSVAELTIGLMLAL 116
Query: 129 LRKLSAADCFVRQGLWPINAEFPLGSKLGGKRVGIVGLGSIGSEVAKRLEAFGCCVSYNS 188
R++ AD VR G W P+G++L GK +GI+GLG IG VA+RL FG V
Sbjct: 117 ARQIPQADREVRAGGWDR----PVGTELYGKTLGIIGLGRIGKAVARRLSGFGMKVLAYD 172
Query: 189 RNKKPSVTYPF---YPDVCELAANSDVLIICCALTDQTHHLINKQVLLALGKKG-VIINV 244
+ + EL SD + + LT +T HLIN LAL K G ++IN
Sbjct: 173 PYPDEEFAKEHGVEFVSLEELLKESDFISLHLPLTPETRHLINAAE-LALMKPGAILINT 231
Query: 245 GRGAIIDEKEMVGCLLRGEIGGAGLDVFENEP-DVPEQLFALDNVVLSPHSAVFTPESFK 303
RG ++DE+ + L G I GA LDVFE EP L L NV+L+PH T E+
Sbjct: 232 ARGGLVDEEALYEALKSGRIAGAALDVFEEEPPPADSPLLELPNVILTPHIGASTKEAVL 291
Query: 304 DVCELAVANL 313
+ +A N+
Sbjct: 292 RMGTMAAQNV 301
>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 = 209 bits (533), Expect = 1e-65
Identities = 91/275 (33%), Positives = 144/275 (52%), Gaps = 11/275 (4%)
Query: 59 VKAIFSSAGAPVTAEILRLLPEVRLVVATSAGLNHIDVVECRRRGVALANAGNVFSEDVA 118
A+ + PV EI+ ++++ AG ++IDV + +G+ + N V +E A
Sbjct: 44 YDALITPLSTPVDKEIIDAAKNLKIIANYGAGFDNIDVDYAKEKGIPVTNTPAVSTEPTA 103
Query: 119 DYALGLLIDVLRKLSAADCFVRQGLWPINAE-FPLGSKLGGKRVGIVGLGSIGSEVAKRL 177
+ GL++ + R+++ D +R+G + A F LG +L GK +GI+G+G IG VA+R
Sbjct: 104 ELTFGLILALARRIAEGDRLMRRGGFLGWAPLFFLGHELAGKTLGIIGMGRIGQAVARRA 163
Query: 178 EAFGCCVSYNSRNKKPS-------VTYPFYPDVCELAANSDVLIICCALTDQTHHLINKQ 230
+AFG + Y +R++ TY D+ EL SD + + T +THHLI+
Sbjct: 164 KAFGMKILYYNRHRLSEETEKELGATYV---DLDELLKESDFVSLHAPYTPETHHLIDAA 220
Query: 231 VLLALGKKGVIINVGRGAIIDEKEMVGCLLRGEIGGAGLDVFENEPDVPEQLFALDNVVL 290
+ +IN RG ++DEK +V L GEI GA LDVFE EP+V +L LDNV+L
Sbjct: 221 AFKLMKPTAYLINAARGPLVDEKALVDALKTGEIAGAALDVFEFEPEVSPELKKLDNVIL 280
Query: 291 SPHSAVFTPESFKDVCELAVANLEAFFSNKPLLTP 325
+PH T E+ + + A N+ +F K
Sbjct: 281 TPHIGNATVEARDAMAKEAADNIISFLEGKRPKNI 315
>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 = 203 bits (518), Expect = 2e-63
Identities = 100/302 (33%), Positives = 151/302 (50%), Gaps = 26/302 (8%)
Query: 38 YLKAYESALPLHEFLTLHAHSVKAIFSSA----GAPVTAEILRLLPEVRLVVATSAGLNH 93
+L+ +A P E + A + + A G P E+L P +R + +TSAG++
Sbjct: 13 HLERLRAAAPGAELRVVTAEELTEELADADVLLGNPPLPELLPAAPRLRWIQSTSAGVDA 72
Query: 94 IDVVECRRRGVALANAGNVFSEDVADYALGLLIDVLRKLSAADCFVRQ---GLWPINAEF 150
+ E R V L NA +F +A+Y LG ++ RKL + R W
Sbjct: 73 LLFPELLERDVVLTNARGIFGPPIAEYVLGYMLAFARKL---PRYARNQAERRW--QRRG 127
Query: 151 PLGSKLGGKRVGIVGLGSIGSEVAKRLEAFGCCVSYNSRNKKPSVTYPFYPDVC------ 204
P+ L GK V IVGLG IG E+A+R +AFG V R+ +P+ P D
Sbjct: 128 PVRE-LAGKTVLIVGLGDIGREIARRAKAFGMRVIGVRRSGRPA---PPVVDEVYTPDEL 183
Query: 205 -ELAANSDVLIICCALTDQTHHLINKQVLLALGKKGVIINVGRGAIIDEKEMVGCLLRGE 263
EL +D ++ LT +T L N + A+ V+INVGRG+++DE ++ L G
Sbjct: 184 DELLPEADYVVNALPLTPETRGLFNAERFAAMKPGAVLINVGRGSVVDEDALIEALESGR 243
Query: 264 IGGAGLDVFENEPDVPEQ--LFALDNVVLSPHSAVFTPESFKDVCELAVANLEAFFSNKP 321
I GA LDVFE EP +P L+ L NV+++PH + +P + V E+ + NL + + +P
Sbjct: 244 IAGAALDVFEEEP-LPADSPLWDLPNVIITPHISGDSPSYPERVVEIFLENLRRYLAGEP 302
Query: 322 LL 323
LL
Sbjct: 303 LL 304
>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 = 198 bits (505), Expect = 1e-61
Identities = 77/277 (27%), Positives = 122/277 (44%), Gaps = 9/277 (3%)
Query: 56 AHSVKAIFSSAGAPVTAEILRLLPEVRLVVATSAGLNHIDVVECRRRGVALANAGNVFSE 115
A A+ + PVTAE+L P ++++ G+++ID+ RG+ + N +E
Sbjct: 36 AKDADALIVRSTTPVTAEVLEAAPGLKVIARRGVGVDNIDLDAATERGILVTNVPGYSTE 95
Query: 116 DVADYALGLLIDVLRKLSAADCFVRQGLWPINAEFPLGSKLGGKRVGIVGLGSIGSEVAK 175
VA+ +GL++ + R++ AD VR G W P+G +L GK +G++G G IG A
Sbjct: 96 SVAELTVGLILALARRIPEADASVRAGDW--KKGGPIGLELYGKTLGVIGGGGIGGIGAA 153
Query: 176 RLEAFGCCV----SYNSRNKKPSVTYPFYPDVCEL---AANSDVLIICCALTDQTHHLIN 228
+A G V Y + + L + D++ + T +T H+I
Sbjct: 154 IAKALGMGVVAYDPYPNPERAEEGGVEVLLLDLLLLDLKESDDLINLAPPTTMKTGHIII 213
Query: 229 KQVLLALGKKGVIINVGRGAIIDEKEMVGCLLRGEIGGAGLDVFENEPDVPEQLFALDNV 288
+ L I N G +I+E + L G A V E P V L L NV
Sbjct: 214 NEARGMLKDAVAINNARGGGVIEEAALDALLEEGIAAAALDVVEEEPPPVNSPLLDLPNV 273
Query: 289 VLSPHSAVFTPESFKDVCELAVANLEAFFSNKPLLTP 325
+L+PH A T E+ +++ E A NL AF
Sbjct: 274 ILTPHIAGATEEAQENMAEEAAENLLAFLKGGTPPNA 310
>gnl|CDD|183914 PRK13243, PRK13243, glyoxylate reductase; Reviewed.
Length = 333
Score = 197 bits (502), Expect = 6e-61
Identities = 112/315 (35%), Positives = 163/315 (51%), Gaps = 16/315 (5%)
Query: 12 PQVLLLRK--PSGFAMLGEQFFTSNKFQYLKAYESALPLHEFLTLHAHSVKAIFSSAGAP 69
P+V + R+ +G ML E+ F ++ + E L V A+ +
Sbjct: 3 PKVFITREIPENGIEML-EEHFEVEVWE-----DEREIPREVLLEKVRDVDALVTMLSER 56
Query: 70 VTAEILRLLPEVRLVVATSAGLNHIDVVECRRRGVALANAGNVFSEDVADYALGLLIDVL 129
+ E+ P +R+V + G ++IDV E RRG+ + N V +E AD+A LL+
Sbjct: 57 IDCEVFEAAPRLRIVANYAVGYDNIDVEEATRRGIYVTNTPGVLTEATADFAWALLLATA 116
Query: 130 RKLSAADCFVRQGLWPIN--AEFP---LGSKLGGKRVGIVGLGSIGSEVAKRLEAFGCCV 184
R+L AD FVR G W A P LG + GK +GI+G G IG VA+R + FG +
Sbjct: 117 RRLVEADHFVRSGEWKRRGVAWHPLMFLGYDVYGKTIGIIGFGRIGQAVARRAKGFGMRI 176
Query: 185 SYNSRNKKPSVTYPF---YPDVCELAANSDVLIICCALTDQTHHLINKQVLLALGKKGVI 241
Y SR +KP Y + EL SD + + LT +T+H+IN++ L + ++
Sbjct: 177 LYYSRTRKPEAEKELGAEYRPLEELLRESDFVSLHVPLTKETYHMINEERLKLMKPTAIL 236
Query: 242 INVGRGAIIDEKEMVGCLLRGEIGGAGLDVFENEPDVPEQLFALDNVVLSPHSAVFTPES 301
+N RG ++D K +V L G I GAGLDVFE EP E+LF+L NVVL+PH T E+
Sbjct: 237 VNTARGKVVDTKALVKALKEGWIAGAGLDVFEEEPYYNEELFSLKNVVLAPHIGSATFEA 296
Query: 302 FKDVCELAVANLEAF 316
+ + EL NL AF
Sbjct: 297 REGMAELVAENLIAF 311
>gnl|CDD|240650 cd12173, PGDH_4, Phosphoglycerate dehydrogenases, NAD-binding and
catalytic domains. Phosphoglycerate dehydrogenases
(PGDHs) catalyze the initial step in the biosynthesis of
L-serine from D-3-phosphoglycerate. PGDHs come in 3
distinct structural forms, with this first group being
related to 2-hydroxy acid dehydrogenases, sharing
structural similarity to formate and glycerate
dehydrogenases. PGDH in E. coli and Mycobacterium
tuberculosis form tetramers, with subunits containing a
Rossmann-fold NAD binding domain. Formate/glycerate and
related dehydrogenases of the D-specific 2-hydroxyacid
dehydrogenase superfamily include groups such as formate
dehydrogenase, glycerate dehydrogenase, L-alanine
dehydrogenase, and S-adenosylhomocysteine hydrolase.
Despite often low sequence identity, these proteins
typically have a characteristic arrangement of 2 similar
subdomains of the alpha/beta Rossmann fold NAD+ binding
form. The NAD+ binding domain is inserted within the
linear sequence of the mostly N-terminal catalytic
domain, which has a similar domain structure to the
internal NAD binding domain. Structurally, these domains
are connected by extended alpha helices and create a
cleft in which NAD is bound, primarily to the C-terminal
portion of the 2nd (internal) domain. Some related
proteins have similar structural subdomain but with a
tandem arrangement of the catalytic and NAD-binding
subdomains in the linear sequence.
Length = 304
Score = 192 bits (491), Expect = 2e-59
Identities = 92/268 (34%), Positives = 134/268 (50%), Gaps = 32/268 (11%)
Query: 70 VTAEILRLLPEVRLVVATSAGLNHIDVVECRRRGVALANA--GNVFSEDVADYALGLLID 127
VTAE++ P ++++ G+++IDV RG+ + NA N S VA++ + L++
Sbjct: 52 VTAEVIEAAPRLKVIGRAGVGVDNIDVEAATARGILVVNAPGANTIS--VAEHTIALMLA 109
Query: 128 VLRKLSAADCFVRQGLWPINAEFPLGSKLGGKRVGIVGLGSIGSEVAKRLEAFGCCVSYN 187
+ R + AD +R G W F G +L GK +GIVGLG IG EVA+R AFG V
Sbjct: 110 LARNIPQADASLRAGKWDRKK-FM-GVELRGKTLGIVGLGRIGREVARRARAFGMKV--- 164
Query: 188 SRNKKPSVTY-PFYP------------DVCELAANSDVLIICCALTDQTHHLINKQVLLA 234
+ Y P+ + EL A +D + + LT +T LIN + LA
Sbjct: 165 -------LAYDPYISAERAAAGGVELVSLDELLAEADFISLHTPLTPETRGLINAE-ELA 216
Query: 235 LGKKGV-IINVGRGAIIDEKEMVGCLLRGEIGGAGLDVFENEPDVPE-QLFALDNVVLSP 292
K G +IN RG I+DE + L G+I GA LDVFE EP + L L NV+L+P
Sbjct: 217 KMKPGAILINTARGGIVDEAALADALKSGKIAGAALDVFEQEPPPADSPLLGLPNVILTP 276
Query: 293 HSAVFTPESFKDVCELAVANLEAFFSNK 320
H T E+ + V A + A + +
Sbjct: 277 HLGASTEEAQERVAVDAAEQVLAVLAGE 304
>gnl|CDD|240642 cd12165, 2-Hacid_dh_6, Putative D-isomer specific 2-hydroxyacid
dehydrogenases. 2-Hydroxyacid dehydrogenases catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 314
Score = 187 bits (477), Expect = 2e-57
Identities = 90/270 (33%), Positives = 141/270 (52%), Gaps = 15/270 (5%)
Query: 66 AGAPVTAEILRLLPEVRLVVATSAGLNHIDVVECRRRGVALAN-AGNVFSEDVADYALGL 124
G E L L ++L+ SAG++H+ + E GV +AN GN S VA++AL L
Sbjct: 46 GGRLTKEEALAALKRLKLIQVPSAGVDHLPL-ERLPEGVVVANNHGN--SPAVAEHALAL 102
Query: 125 LIDVLRKLSAADCFVRQGLWP-INAEFPLGSKLGGKRVGIVGLGSIGSEVAKRLEAFGCC 183
++ + +++ D +R+G+W E P +L GK VGI+G G IG E+A+ L+AFG
Sbjct: 103 ILALAKRIVEYDNDLRRGIWHGRAGEEPESKELRGKTVGILGYGHIGREIARLLKAFGMR 162
Query: 184 VSYNSRNKKPSVTYPF---YPDVCELAANSDVLIICCALTDQTHHLINKQVLLALGKKGV 240
V SR+ K F D+ E +DV+++ LT QT LI L A+ +
Sbjct: 163 VIGVSRSPKEDEGADFVGTLSDLDEALEQADVVVVALPLTKQTRGLIGAAELAAMKPGAI 222
Query: 241 IINVGRGAIIDEKEMVGCLLRGEIGGAGLDVFENEPDVPEQ-------LFALDNVVLSPH 293
++NVGRG ++DE+ + L I GA +DV+ P + L NV++SPH
Sbjct: 223 LVNVGRGPVVDEEALYEALKERPIAGAAIDVWWRYPSRGDPVAPSRYPFHELPNVIMSPH 282
Query: 294 SAVFTPESFKDVCELAVANLEAFFSNKPLL 323
+A +T E+F+ + A N+ + +PLL
Sbjct: 283 NAGWTEETFRRRIDEAAENIRRYLRGEPLL 312
>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 = 181 bits (462), Expect = 9e-57
Identities = 74/177 (41%), Positives = 99/177 (55%), Gaps = 5/177 (2%)
Query: 122 LGLLIDVLRKLSAADCFVRQGLWPINAEFPLGSKLGGKRVGIVGLGSIGSEVAKRLEAFG 181
L LL+ + R++ AD VR G W + LG +L GK VGI+GLG IG VA+RL+AFG
Sbjct: 1 LALLLALARRIPEADRQVRAGRW--RPDALLGRELSGKTVGIIGLGRIGRAVARRLKAFG 58
Query: 182 CCVSYNSR--NKKPSVTYPFYPDVCELAANSDVLIICCALTDQTHHLINKQVLLALGKKG 239
V R + Y + EL A SDV+ + LT +T HLIN + L +
Sbjct: 59 MKVIAYDRYPKAEAEALGARYVSLDELLAESDVVSLHLPLTPETRHLINAERLALMKPGA 118
Query: 240 VIINVGRGAIIDEKEMVGCLLRGEIGGAGLDVFENEPDVPEQ-LFALDNVVLSPHSA 295
++IN RG ++DE ++ L G I GA LDVFE EP P+ L L NV+L+PH A
Sbjct: 119 ILINTARGGLVDEDALIAALKSGRIAGAALDVFEPEPLPPDHPLLELPNVILTPHIA 175
>gnl|CDD|240648 cd12171, 2-Hacid_dh_10, Putative D-isomer specific 2-hydroxyacid
dehydrogenases. 2-Hydroxyacid dehydrogenases catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 310
Score = 184 bits (470), Expect = 3e-56
Identities = 87/269 (32%), Positives = 131/269 (48%), Gaps = 32/269 (11%)
Query: 68 APVTAEILRLLPEVRLVVATSAGLNHIDVVECRRRGVALANAGNVFSEDVADYALGLLID 127
APVT +++ P+++L+ G ++DV RG+ + N +E VA++ +GL++
Sbjct: 55 APVTKKVIEAAPKLKLIGVCRGGPENVDVEAATERGIPVLNTPGRNAEAVAEFTVGLMLA 114
Query: 128 VLRKLSAADCFVRQGLW---PINAEFPLGSKLGGKRVGIVGLGSIGSEVAKRLEAFGCCV 184
R ++ A ++ G W N + G +L GK VGIVG G+IG VAKRL+AFG V
Sbjct: 115 ETRNIARAHAALKDGEWRKDYYNYDG-YGPELRGKTVGIVGFGAIGRRVAKRLKAFGAEV 173
Query: 185 SYNSRNKKPSVTY-PFYP------------DVCELAANSDVLIICCALTDQTHHLINKQV 231
Y P+ + EL SDV+ + LT +T +I +
Sbjct: 174 LV----------YDPYVDPEKIEADGVKKVSLEELLKRSDVVSLHARLTPETRGMIGAE- 222
Query: 232 LLALGKKG-VIINVGRGAIIDEKEMVGCLLRGEIGGAGLDVFENEPDVPEQ--LFALDNV 288
AL K IN R ++DE ++ L G+IGGA LDVF EP +P L LDNV
Sbjct: 223 EFALMKPTAYFINTARAGLVDEDALIEALEEGKIGGAALDVFPEEP-LPADHPLLKLDNV 281
Query: 289 VLSPHSAVFTPESFKDVCELAVANLEAFF 317
L+PH A T + + E+ L+ +
Sbjct: 282 TLTPHIAGATRDVAERSPEIIAEELKRYL 310
>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 = 183 bits (466), Expect = 9e-56
Identities = 85/253 (33%), Positives = 128/253 (50%), Gaps = 7/253 (2%)
Query: 69 PVTAEILRLLPEVRLVVATSAGLNHIDVVECRRRGVALANAGNVFSEDVADYALGLLIDV 128
VT E++ ++++ GL++IDV +++G+ + N S VA+ +GL++ +
Sbjct: 52 KVTKEVIDAAKNLKIIARAGVGLDNIDVEYAKKKGIKVINTPGASSNSVAELVIGLMLSL 111
Query: 129 LRKLSAADCFVRQGLWPINAEFPLGSKLGGKRVGIVGLGSIGSEVAKRLEAFGCCVSYNS 188
R + A+ ++ G W N + G +L GK +GI+G G IG EVAK A G V
Sbjct: 112 ARFIHRANREMKLGKW--NKKKYKGIELRGKTLGIIGFGRIGREVAKIARALGMNVIAYD 169
Query: 189 RNKKPSVTYPFYPDVC---ELAANSDVLIICCALTDQTHHLINKQVLLALGKKGV-IINV 244
K EL NSD + + LT +T H+INK+ L L K G IIN
Sbjct: 170 PYPKDEQAVELGVKTVSLEELLKNSDFISLHVPLTPETKHMINKKEL-ELMKDGAIIINT 228
Query: 245 GRGAIIDEKEMVGCLLRGEIGGAGLDVFENEPDVPEQLFALDNVVLSPHSAVFTPESFKD 304
RG +IDE+ ++ L G++ GA LDVFENEP +L L NV L+PH T E+ +
Sbjct: 229 SRGGVIDEEALLEALKSGKLAGAALDVFENEPPPGSKLLELPNVSLTPHIGASTKEAQER 288
Query: 305 VCELAVANLEAFF 317
+ E + F
Sbjct: 289 IGEELANKIIEFL 301
>gnl|CDD|240639 cd12162, 2-Hacid_dh_4, Putative D-isomer specific 2-hydroxyacid
dehydrogenases. 2-Hydroxyacid dehydrogenases catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine yydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 307
Score = 183 bits (466), Expect = 9e-56
Identities = 87/258 (33%), Positives = 140/258 (54%), Gaps = 15/258 (5%)
Query: 69 PVTAEILRLLPEVRLVVATSAGLNHIDVVECRRRGVALANAGNVFSEDVADYALGLLIDV 128
+ AE+L LP ++L+ + G N++D+ + RG+ + N ++ VA + LL+ +
Sbjct: 54 VLDAEVLAQLPNLKLIGVLATGYNNVDLAAAKERGITVTNVPGYSTDSVAQHTFALLLAL 113
Query: 129 LRKLSAADCFVRQGLWPINAEF-----PLGSKLGGKRVGIVGLGSIGSEVAKRLEAFGCC 183
R ++ + V+ G W + +F P+ L GK +GI+G G+IG VA+ AFG
Sbjct: 114 ARLVAYHNDVVKAGEWQKSPDFCFWDYPIIE-LAGKTLGIIGYGNIGQAVARIARAFGMK 172
Query: 184 VSYNSRNKKPSVTYPFYPDVCELAANSDVLIICCALTDQTHHLINKQVLLALGKKGVI-I 242
V + R P + Y + EL A SDV+ + C LT +T +LIN + L A K G I I
Sbjct: 173 VLFAERKGAPPLREG-YVSLDELLAQSDVISLHCPLTPETRNLINAEEL-AKMKPGAILI 230
Query: 243 NVGRGAIIDEKEMVGCLLRGEIGGAGLDVFENEPDVPEQ----LFALDNVVLSPHSAVFT 298
N RG ++DE+ + L G+I GAGLDV EP P L A N++++PH A +
Sbjct: 231 NTARGGLVDEQALADALNSGKIAGAGLDVLSQEP--PRADNPLLKAAPNLIITPHIAWAS 288
Query: 299 PESFKDVCELAVANLEAF 316
E+ + + ++ V N++AF
Sbjct: 289 REARQRLMDILVDNIKAF 306
>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 = 183 bits (466), Expect = 1e-55
Identities = 94/266 (35%), Positives = 146/266 (54%), Gaps = 19/266 (7%)
Query: 66 AGAPVTAEILRLLPEVRLVVATSAGLNHIDVVECRRRGVALANAGNVFSEDVADYALGLL 125
A P+ E++ ++++ G++H+D+ C+ RG+ ++NA +E VA+ +GL
Sbjct: 55 ANMPLPGEVIEACKNLKMISVAFTGVDHVDLEACKERGITVSNAAGYSTEAVAELTIGLA 114
Query: 126 IDVLRKLSAADCFVR-----QGLWPINAEFPLGSKLGGKRVGIVGLGSIGSEVAKRLEAF 180
ID+LR + D VR GL +G +L GK VGIVG G+IG VA+ +AF
Sbjct: 115 IDLLRNIVPCDAAVRAGGTKAGL--------IGRELAGKTVGIVGTGAIGLRVARLFKAF 166
Query: 181 GCCVSYNSRNKKPSVTYPF--YPDVCELAANSDVLIICCALTDQTHHLINKQVLLALGKK 238
GC V SR++K Y + EL A SD++ + L D+T LI K+ LAL K+
Sbjct: 167 GCKVLAYSRSEKEEAKALGIEYVSLDELLAESDIVSLHLPLNDETKGLIGKE-KLALMKE 225
Query: 239 G-VIINVGRGAIIDEKEMVGCLLRGEIGGAGLDVFENEPDVPEQ--LFALDNVVLSPHSA 295
++IN RG ++D + + L G+I GAG+DVF+ EP +P L N +L+PH A
Sbjct: 226 SAILINTARGPVVDNEALADALNEGKIAGAGIDVFDMEPPLPADYPLLHAPNTILTPHVA 285
Query: 296 VFTPESFKDVCELAVANLEAFFSNKP 321
T E+ + E+ N+EA+ + KP
Sbjct: 286 FATEEAMEKRAEIVFDNIEAWLAGKP 311
>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 = 177 bits (451), Expect = 3e-53
Identities = 80/273 (29%), Positives = 126/273 (46%), Gaps = 6/273 (2%)
Query: 56 AHSVKAIFSSAGAP-VTAEILRLLPEVRLVVATSAGLNHIDVVECRRRGVALANAGNVFS 114
V+ + + G P + AE+L P +R VV + + + RG+ + +A + +
Sbjct: 47 LAGVEVLVTGWGTPPLDAELLARAPRLRAVVHAAGSVRGLVTDAVWERGILVTSAADANA 106
Query: 115 EDVADYALGLLIDVLRKLSAADCFVRQGLWPINAEFPLGSKLGGKRVGIVGLGSIGSEVA 174
E VA++ L ++ LR++ R G G L G+ VGIVG G IG V
Sbjct: 107 EPVAEFTLAAILLALRRIPRFAAAYRAGRDWGWPTRRGGRGLYGRTVGIVGFGRIGRAVV 166
Query: 175 KRLEAFGCCVSYNSRNKKPS-VTYPFYPDVC--ELAANSDVLIICCALTDQTHHLINKQV 231
+ L FG V + V EL A SDV+ + LT +T +I+ ++
Sbjct: 167 ELLRPFGLRVLVYDPYLPAAEAAALGVELVSLDELLARSDVVSLHAPLTPETRGMIDARL 226
Query: 232 LLALGKKGVIINVGRGAIIDEKEMVGCLLRGEIGGAGLDVFENEP-DVPEQLFALDNVVL 290
L + IN RGA++DE ++ L G + A LDV + EP L L NV+L
Sbjct: 227 LALMRDGATFINTARGALVDEAALLAELRSGRL-RAALDVTDPEPLPPDSPLRTLPNVLL 285
Query: 291 SPHSAVFTPESFKDVCELAVANLEAFFSNKPLL 323
+PH A T + + + + A+ LE F + +PLL
Sbjct: 286 TPHIAGSTGDERRRLGDYALDELERFLAGEPLL 318
>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 = 174 bits (442), Expect = 5e-52
Identities = 91/270 (33%), Positives = 141/270 (52%), Gaps = 9/270 (3%)
Query: 59 VKAIFSSAGAPVTAEILRLLPEVRLVVATSAGLNHIDVVECRRRGVALAN-AGNVFSEDV 117
I +S E ++L+ G +++D+ GV + G V + V
Sbjct: 48 YDIIIASVTPNFDKEFFEYNDGLKLIARHGIGYDNVDLKAATEHGVIVTRVPGAVERDAV 107
Query: 118 ADYALGLLIDVLRKLSAADCFVRQGLWPINAEFPLGSKLGGKRVGIVGLGSIGSEVAKRL 177
A++A+ L++ VLRK++ A V++G W A F +G +L GK VGI+G G+IGS VA+ L
Sbjct: 108 AEHAVALILTVLRKINQASEAVKEGKWTERANF-VGHELSGKTVGIIGYGNIGSRVAEIL 166
Query: 178 -EAFGCCVSYNSRNKKPSV---TYPFYPDVCELAANSDVLIICCALTDQTHHLINKQVLL 233
E F V V + EL A SD++ + LT++T+H+IN++
Sbjct: 167 KEGFNAKVLAYDPYVSEEVIKKKGAKPVSLEELLAESDIISLHAPLTEETYHMINEK-AF 225
Query: 234 ALGKKGVII-NVGRGAIIDEKEMVGCLLRGEIGGAGLDVFENEPDVPEQ-LFALDNVVLS 291
+ KKGVI+ N RG +IDE+ ++ L G+I GAGLDV E EP + L +NVV++
Sbjct: 226 SKMKKGVILVNTARGELIDEEALIEALKSGKIAGAGLDVLEEEPIKADHPLLHYENVVIT 285
Query: 292 PHSAVFTPESFKDVCELAVANLEAFFSNKP 321
PH +T ES + E V ++E F + K
Sbjct: 286 PHIGAYTYESLYGMGEKVVDDIEDFLAGKE 315
>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 = 172 bits (439), Expect = 7e-52
Identities = 83/266 (31%), Positives = 126/266 (47%), Gaps = 12/266 (4%)
Query: 66 AGAPVTAEILRLLPEVRLVVATSAGLNH-IDVVECRRRGVALANAGNVFSEDVADYALGL 124
G+ E L P VR V AG+ ++ G NA ++E VA++AL L
Sbjct: 35 TGSAREPERLPASPGVRWVQLPFAGVEAFVEAGVITDPGRRWTNAAGAYAETVAEHALAL 94
Query: 125 LIDVLRKLSAADCFVRQGLWPINAEFPLGSKLGGKRVGIVGLGSIGSEVAKRLEAFGCCV 184
L+ LR+L R W E L + L G V IVG G IG + L FG V
Sbjct: 95 LLAGLRQLP---ARARATTWDPAEEDDLVTLLRGSTVAIVGAGGIGRALIPLLAPFGAKV 151
Query: 185 SYNSRNKKPS----VTYPFYPDVCELAANSDVLIICCALTDQTHHLINKQVLLALGKKGV 240
+R+ +P T P + E+ ++D +++ LT +T HL++ L A+
Sbjct: 152 IAVNRSGRPVEGADETVPAD-RLDEVWPDADHVVLAAPLTPETRHLVDAAALAAMKPHAW 210
Query: 241 IINVGRGAIIDEKEMVGCLLRGEIGGAGLDVFENEPDVPE--QLFALDNVVLSPHSAVFT 298
++NV RG ++D +V L GEI GA LDV + EP +P+ L++L N +++PH A
Sbjct: 211 LVNVARGPLVDTDALVDALRSGEIAGAALDVTDPEP-LPDGHPLWSLPNALITPHVANTP 269
Query: 299 PESFKDVCELAVANLEAFFSNKPLLT 324
+ E N+ AF + +PLL
Sbjct: 270 EVIRPLLAERVAENVRAFAAGEPLLG 295
>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 = 171 bits (436), Expect = 4e-51
Identities = 80/271 (29%), Positives = 137/271 (50%), Gaps = 32/271 (11%)
Query: 69 PVTAEILRLLPEVRLVVATSAGLNHIDVVECRRRGVALANAGNVFSEDVADYALGLLIDV 128
+ AE+L P ++ + + G ++ID+ + G+ + N VA++ + L++ +
Sbjct: 56 KIDAELLDKAPGLKFISLRATGYDNIDLDYAKELGIGVTNVPEYSPNAVAEHTIALILAL 115
Query: 129 LRKLSAADCFVRQGLWPINAEFPLGSKLGGKRVGIVGLGSIGSEVAKRLEAFGCCV-SYN 187
LR D R + +G +L + VG+VG G IG VA+R + FG V +Y+
Sbjct: 116 LRNRKYID--ERDKNQDLQDAGVIGRELEDQTVGVVGTGKIGRAVAQRAKGFGMKVIAYD 173
Query: 188 -SRNKKPSVTYPFYPDVC------ELAANSDVLIICCALTDQTHHLINKQVLLALGKKGV 240
RN + EL NSD++ + LT + HH+IN++ L KKGV
Sbjct: 174 PFRNPE------LEDKGVKYVSLEELFKNSDIISLHVPLTPENHHMINEEAF-KLMKKGV 226
Query: 241 I-INVGRGAIIDEKEMVGCLLRGEIGGAGLDVFENE-PDVPEQ-------------LFAL 285
I IN RG+++D + ++ L G+I GAGLDV E+E PD+ + L
Sbjct: 227 IIINTARGSLVDTEALIEALDSGKIFGAGLDVLEDETPDLLKDLEGEIFKDALNALLGRR 286
Query: 286 DNVVLSPHSAVFTPESFKDVCELAVANLEAF 316
NV+++PH+A +T ++ K++ E++ N+ F
Sbjct: 287 PNVIITPHTAFYTDDALKNMVEISCENIVDF 317
>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 = 166 bits (422), Expect = 4e-49
Identities = 74/242 (30%), Positives = 120/242 (49%), Gaps = 15/242 (6%)
Query: 70 VTAEILRLLPEVRLVVATSAGLNHIDVVECRRRGVALANAGNVFSEDVADYALGLLIDVL 129
+ A+ L P ++++ G ++ DV C RG+ + ++ +E A+ +GLLI +
Sbjct: 56 IDADFLDACPRLKIIACALKGYDNFDVEACTARGIWVTIVPDLLTEPTAELTIGLLIGLG 115
Query: 130 RKLSAADCFVRQGLWPINAEFPLGSKLGGKRVGIVGLGSIGSEVAKRLEAFGCCVSYNSR 189
R + A D FVR G + G+ L GK VGI+G+G++G +A+RL FG + Y
Sbjct: 116 RHILAGDRFVRSGKFGGWRPKFYGTGLDGKTVGILGMGALGRAIARRLSGFGATLLYYDP 175
Query: 190 NKKPSVTYPF----YPDVCELAANSDVLIICCALTDQTHHLINKQVLLALGKKGVIINVG 245
+ ++ EL +SD L++ LT T HLIN + L + +++N
Sbjct: 176 HPLDQAEEQALNLRRVELDELLESSDFLVLALPLTPDTLHLINAEALAKMKPGALLVNPC 235
Query: 246 RGAIIDEKEMVGCLLRGEIGGAGLDVFENEP--------DVPEQLFAL-DNVVLSPH--S 294
RG+++DE + L G +GG DVFE E +P++L D V +PH S
Sbjct: 236 RGSVVDEAAVAEALKSGHLGGYAADVFEMEDWARPDRPRSIPQELLDQHDRTVFTPHIGS 295
Query: 295 AV 296
AV
Sbjct: 296 AV 297
>gnl|CDD|237436 PRK13581, PRK13581, D-3-phosphoglycerate dehydrogenase;
Provisional.
Length = 526
Score = 170 bits (434), Expect = 7e-49
Identities = 88/241 (36%), Positives = 126/241 (52%), Gaps = 31/241 (12%)
Query: 69 PVTAEILRLLPEVRLVVATSAGLNHIDVVECRRRGVALANA--GNVFSEDVADYALGLLI 126
VTAE+L ++++ G++++DV RRG+ + NA GN S A++ + L++
Sbjct: 53 KVTAEVLEAAKNLKVIGRAGVGVDNVDVPAATRRGIIVVNAPTGNTIS--AAEHTIALML 110
Query: 127 DVLRKLSAADCFVRQGLWPINAEFPLGSKLGGKRVGIVGLGSIGSEVAKRLEAFGCCVSY 186
+ R + A ++ G W F +G +L GK +GI+GLG IGSEVAKR +AFG V
Sbjct: 111 ALARNIPQAHASLKAGKWERKK-F-MGVELYGKTLGIIGLGRIGSEVAKRAKAFGMKV-- 166
Query: 187 NSRNKKPSVTY-PFYP------------DVCELAANSDVLIICCALTDQTHHLINKQVLL 233
+ Y P+ + EL A +D + + LT +T LI + L
Sbjct: 167 --------IAYDPYISPERAAQLGVELVSLDELLARADFITLHTPLTPETRGLIGAE-EL 217
Query: 234 ALGKKGV-IINVGRGAIIDEKEMVGCLLRGEIGGAGLDVFENEPDVPEQLFALDNVVLSP 292
A K GV IIN RG IIDE + L G++ GA LDVFE EP LF L NVV++P
Sbjct: 218 AKMKPGVRIINCARGGIIDEAALAEALKSGKVAGAALDVFEKEPPTDSPLFELPNVVVTP 277
Query: 293 H 293
H
Sbjct: 278 H 278
>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 = 164 bits (419), Expect = 1e-48
Identities = 83/258 (32%), Positives = 124/258 (48%), Gaps = 14/258 (5%)
Query: 69 PVTAEILRLLPEVRLVVATSAGLNHIDVVECRRRGVALANAGNVFSEDVADYALGLLIDV 128
P A +L LP ++L+V T ID+ + RG+ + G A+ L++ +
Sbjct: 58 PFPAALLERLPNLKLLVTTGMRNASIDLAAAKERGIVVCGTGGG-PTATAELTWALILAL 116
Query: 129 LRKLSAADCFVRQGLWPINAEFPLGSKLGGKRVGIVGLGSIGSEVAKRLEAFGCCVSYNS 188
R L D +R G W LG+ L GK +GIVGLG IG+ VA+ +AFG V S
Sbjct: 117 ARNLPEEDAALRAGGWQTT----LGTGLAGKTLGIVGLGRIGARVARIGQAFGMRVIAWS 172
Query: 189 RNKKPS------VTYPFYPDVCELAANSDVLIICCALTDQTHHLINKQVLLALGKKGVII 242
N V EL A SDV+ + L+D+T L+ + L + +++
Sbjct: 173 SNLTAERAAAAGVEAA--VSKEELFATSDVVSLHLVLSDRTRGLVGAEDLALMKPTALLV 230
Query: 243 NVGRGAIIDEKEMVGCLLRGEIGGAGLDVFENEP-DVPEQLFALDNVVLSPHSAVFTPES 301
N RG ++DE ++ L G I GA LDVF+ EP L L NV+L+PH T E+
Sbjct: 231 NTSRGPLVDEGALLAALRAGRIAGAALDVFDVEPLPADHPLRGLPNVLLTPHIGYVTEEA 290
Query: 302 FKDVCELAVANLEAFFSN 319
++ AV N+ A+ +
Sbjct: 291 YEGFYGQAVENIAAWLAG 308
>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 = 167 bits (424), Expect = 2e-47
Identities = 93/252 (36%), Positives = 138/252 (54%), Gaps = 12/252 (4%)
Query: 61 AIFSSAGAPVTAEILRLLPEVRLVVATSAGLNHIDVVECRRRGVALANA--GNVFSEDVA 118
A+ + VT E++ P+++++ G+++ID+ RG+ + NA GN S A
Sbjct: 43 ALIVRSATKVTEEVIAAAPKLKVIGRAGVGVDNIDIEAATARGILVVNAPTGNTIS--AA 100
Query: 119 DYALGLLIDVLRKLSAADCFVRQGLWPINAEFPLGSKLGGKRVGIVGLGSIGSEVAKRLE 178
++AL +L+ R + AD +++G W A F +G++L GK +G++GLG IGS VAKR +
Sbjct: 101 EHALAMLLAAARNIPQADASLKEGEWDRKA-F-MGTELYGKTLGVIGLGRIGSIVAKRAK 158
Query: 179 AFGCCV----SYNSRNKKPSVTYPFYPDVCELAANSDVLIICCALTDQTHHLINKQVLLA 234
AFG V Y S + + D+ EL A +D + + LT +T LI + L A
Sbjct: 159 AFGMKVLAYDPYISPERAEQLGVELVDDLDELLARADFITVHTPLTPETRGLIGAEEL-A 217
Query: 235 LGKKGVII-NVGRGAIIDEKEMVGCLLRGEIGGAGLDVFENEPDVPEQLFALDNVVLSPH 293
KKGVII N RG IIDE + L G + A LDVFE EP LF LDNV+ +PH
Sbjct: 218 KMKKGVIIVNCARGGIIDEAALYEALEEGHVRAAALDVFEKEPPTDNPLFDLDNVIATPH 277
Query: 294 SAVFTPESFKDV 305
T E+ ++V
Sbjct: 278 LGASTREAQENV 289
>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 = 162 bits (411), Expect = 3e-47
Identities = 93/283 (32%), Positives = 138/283 (48%), Gaps = 40/283 (14%)
Query: 70 VTAEILRLLPEVRLVVATSAGLNHIDVVECRRRGVALANAGNVFSEDVADYALGLLIDVL 129
+ AE+L LP ++L+ S G +HID+ CR RG+A+ N + VA++A LL+ +
Sbjct: 53 LDAEVLEKLPRLKLIATRSTGFDHIDLEACRERGIAVCNVPDYGEATVAEHAFALLLALS 112
Query: 130 RKLSAA------DCFVRQGLWPINAEFPLGSKLGGKRVGIVGLGSIGSEVAKRLEAFGCC 183
RKL A F + GL G +L GK +G+VG G IG VA+ FG
Sbjct: 113 RKLREAIERTRRGDFSQAGL--------RGFELAGKTLGVVGTGRIGRRVARIARGFGMK 164
Query: 184 VSYNSRNKKPSV--TYPF-YPDVCELAANSDVLIICCALTDQTHHLINKQVLLALGKKGV 240
V + F Y + EL SD++ + T QTHHLIN++ AL K G
Sbjct: 165 VLAYDVVPDEELAERLGFRYVSLEELLQESDIISLHVPYTPQTHHLINRENF-ALMKPGA 223
Query: 241 I-INVGRGAIIDEKEMVGCLLRGEIGGAGLDVFENEPDVPE------------------- 280
+ IN RGA++D + +V L G++ GAGLDV E E + E
Sbjct: 224 VLINTARGAVVDTEALVRALKEGKLAGAGLDVLEQEEVLREEAELFREDVSPEDLKKLLA 283
Query: 281 --QLFALDNVVLSPHSAVFTPESFKDVCELAVANLEAFFSNKP 321
L NV+++PH A T E+ + + + V N++AF + +P
Sbjct: 284 DHALLRKPNVIITPHVAYNTKEALERILDTTVENIKAFAAGQP 326
>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 = 160 bits (407), Expect = 7e-47
Identities = 73/246 (29%), Positives = 135/246 (54%), Gaps = 13/246 (5%)
Query: 86 ATSAGLNHIDVVECRRRGVALANAGNVFSEDVADYALGLLIDVLRKLSAADCFVRQGLWP 145
SAG++++ + +++G+ L N + S +A++ +G ++++ + L A ++ W
Sbjct: 66 LYSAGVDYLPLEYIKKKGILLTNNSGIHSIPIAEWIVGYILEIYKGLKKAYKNQKEKKWK 125
Query: 146 INAEFPLGSKLGGKRVGIVGLGSIGSEVAKRLEAFGCCVSYNSRNKKP----SVTYPFYP 201
+++ +L GK + +G GSIG E+AKRL+AFG V + + + YP
Sbjct: 126 MDSS---LLELYGKTILFLGTGSIGQEIAKRLKAFGMKVIGVNTSGRDVEYFDKCYPL-E 181
Query: 202 DVCELAANSDVLIICCALTDQTHHLINKQVLLALGKKGVIINVGRGAIIDEKEMVGCLLR 261
++ E+ +D+++ LT++THHL ++ + K + INVGRG +DE ++ L
Sbjct: 182 ELDEVLKEADIVVNVLPLTEETHHLFDEAFFEQMKKGALFINVGRGPSVDEDALIEALKN 241
Query: 262 GEIGGAGLDVFENEP---DVPEQLFALDNVVLSPHSAVFTPESFKDVCELAVANLEAFFS 318
+I GA LDVFE EP D P L+ LDNV+++PH + + + + ++ NL++F
Sbjct: 242 KQIRGAALDVFEEEPLPKDSP--LWDLDNVLITPHISGVSEHFNERLFDIFYENLKSFLE 299
Query: 319 NKPLLT 324
+ LL
Sbjct: 300 DGELLK 305
>gnl|CDD|240659 cd12183, LDH_like_2, D-Lactate and related Dehydrogenases,
NAD-binding and catalytic domains. D-Lactate
dehydrogenase (LDH) catalyzes the interconversion of
pyruvate and lactate, and is a member of the
2-hydroxyacid dehydrogenase family. LDH is homologous to
D-2-hydroxyisocaproic acid dehydrogenase (D-HicDH) and
shares the 2-domain structure of formate dehydrogenase.
D-2-hydroxyisocaproate dehydrogenase-like (HicDH)
proteins are NAD-dependent members of the
hydroxycarboxylate dehydrogenase family, and share the
Rossmann fold typical of many NAD binding proteins.
HicDH from Lactobacillus casei forms a monomer and
catalyzes the reaction R-CO-COO(-) + NADH + H+ to
R-COH-COO(-) + NAD+. D-HicDH, like the structurally
distinct L-HicDH, exhibits low side-chain R specificity,
accepting a wide range of 2-oxocarboxylic acid side
chains. Formate/glycerate and related dehydrogenases of
the D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain.
Length = 328
Score = 156 bits (398), Expect = 3e-45
Identities = 99/281 (35%), Positives = 145/281 (51%), Gaps = 40/281 (14%)
Query: 70 VTAEILRLLPE--VRLVVATSAGLNHIDVVECRRRGVALANAGNVFSEDVADYALGLLID 127
+ A +L L E V+L+ AG N++D+ + G+ + VA++A+ LL+
Sbjct: 56 LDAPVLEKLAELGVKLIALRCAGFNNVDLKAAKELGITVVRVPAYSPYAVAEHAVALLLA 115
Query: 128 VLRKLSAADCFVRQ------GLWPINAEFPLGSKLGGKRVGIVGLGSIGSEVAKRLEAFG 181
+ RK+ A VR+ GL LG L GK VG++G G IG A+ L+ FG
Sbjct: 116 LNRKIHRAYNRVREGNFSLDGL--------LGFDLHGKTVGVIGTGKIGQAFARILKGFG 167
Query: 182 CCV-SY----NSRNKKPSVTYPFYPDVCELAANSDVLIICCALTDQTHHLINKQVLLALG 236
C V +Y N K V Y D+ EL A SD++ + C LT +THHLIN + +A
Sbjct: 168 CRVLAYDPYPNPELAKLGVEYV---DLDELLAESDIISLHCPLTPETHHLINAET-IAKM 223
Query: 237 KKGV-IINVGRGAIIDEKEMVGCLLRGEIGGAGLDVFENEP--------------DVPEQ 281
K GV +IN RG +ID K ++ L G+IGG GLDV+E E DV +
Sbjct: 224 KDGVMLINTSRGGLIDTKALIEALKSGKIGGLGLDVYEEEAGLFFEDHSDEIIQDDVLAR 283
Query: 282 LFALDNVVLSPHSAVFTPESFKDVCELAVANLEAFFSNKPL 322
L + NV+++ H A FT E+ ++ E + NL+ F + KPL
Sbjct: 284 LLSFPNVLITGHQAFFTKEALTNIAETTLENLDDFEAGKPL 324
>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 = 155 bits (394), Expect = 6e-45
Identities = 91/291 (31%), Positives = 139/291 (47%), Gaps = 36/291 (12%)
Query: 56 AHSVKAIFSSAGAPVTAEILRLLPE--VRLVVATSAGLNHIDVVECRRRGVALANAGNVF 113
A I + ++AE+L L E V+ + S G +HID+ + G+ ++N
Sbjct: 42 AEGYDGISILGKSKISAELLEKLKEAGVKYISTRSIGYDHIDLDAAKELGIKVSNV-TYS 100
Query: 114 SEDVADYALGLLIDVLRKLSAA-------DCFVRQGLWPINAEFPLGSKLGGKRVGIVGL 166
VADY + L++ LRK D + GL G +L VG++G
Sbjct: 101 PNSVADYTVMLMLMALRKYKQIMKRAEVND-YSLGGL--------QGRELRNLTVGVIGT 151
Query: 167 GSIGSEVAKRLEAFGC-CVSYNSRNKKPSVTYPFYPDVCELAANSDVLIICCALTDQTHH 225
G IG V K L FGC ++Y+ + Y Y D+ L SD++ + LT++T+H
Sbjct: 152 GRIGQAVIKNLSGFGCKILAYDPYPNEEVKKYAEYVDLDTLYKESDIITLHTPLTEETYH 211
Query: 226 LINKQVLLALGKKGV-IINVGRGAIIDEKEMVGCLLRGEIGGAGLDVFENEPDV------ 278
LINK+ + A K GV IIN RG +ID + ++ L G+IGGA LDV E E +
Sbjct: 212 LINKESI-AKMKDGVIIINTARGELIDTEALIEGLESGKIGGAALDVIEGEDGIYYNDRK 270
Query: 279 ------PE--QLFALDNVVLSPHSAVFTPESFKDVCELAVANLEAFFSNKP 321
E L + NV+L+PH A +T ++ D+ E ++ +L AF
Sbjct: 271 GDILSNRELAILRSFPNVILTPHMAFYTDQAVSDMVENSIESLVAFEKGGE 321
>gnl|CDD|181414 PRK08410, PRK08410, 2-hydroxyacid dehydrogenase; Provisional.
Length = 311
Score = 154 bits (391), Expect = 1e-44
Identities = 85/265 (32%), Positives = 141/265 (53%), Gaps = 21/265 (7%)
Query: 70 VTAEILRLLPEVRLVVATSAGLNHIDVVECRRRGVALANAGNVFSEDVADYALGLLIDVL 129
+ E+L LP ++L+ T+ G N++D+ +++G+A+ N +E VA + +L+ +L
Sbjct: 53 IDKEVLSQLPNLKLICITATGTNNVDIEYAKKKGIAVKNVAGYSTESVAQHTFAMLLSLL 112
Query: 130 RKLSAADCFVRQGLW---PI--NAEFPLGSKLGGKRVGIVGLGSIGSEVAKRLEAFGCCV 184
+++ D +V+ G + PI + PLG ++ GK+ GI+GLG+IG VAK +AFG V
Sbjct: 113 GRINYYDRYVKSGEYSESPIFTHISRPLG-EIKGKKWGIIGLGTIGKRVAKIAQAFGAKV 171
Query: 185 SYNS---RNKKPSVTYPFYPDVC--ELAANSDVLIICCALTDQTHHLINKQVLLALGKKG 239
Y S +NK Y V EL SD++ I L ++T +LI + L L
Sbjct: 172 VYYSTSGKNKNEE-----YERVSLEELLKTSDIISIHAPLNEKTKNLIAYKELKLLKDGA 226
Query: 240 VIINVGRGAIIDEKEMVGCLLRGEIGGAGLDVFENEPDVPEQLF----ALDNVVLSPHSA 295
++INVGRG I++EK++ L +I AGLDV E EP + ++++PH A
Sbjct: 227 ILINVGRGGIVNEKDLAKALDEKDI-YAGLDVLEKEPMEKNHPLLSIKNKEKLLITPHIA 285
Query: 296 VFTPESFKDVCELAVANLEAFFSNK 320
+ E+ K + E N++ F
Sbjct: 286 WASKEARKTLIEKVKENIKDFLEGG 310
>gnl|CDD|185307 PRK15409, PRK15409, bifunctional glyoxylate/hydroxypyruvate
reductase B; Provisional.
Length = 323
Score = 146 bits (371), Expect = 1e-41
Identities = 86/262 (32%), Positives = 127/262 (48%), Gaps = 8/262 (3%)
Query: 66 AGAPVTAEILRLLPEVRLVVATSAGLNHIDVVECRRRGVALANAGNVFSEDVADYALGLL 125
+G V A +L +P++R S G ++ DV R + L + V +E VAD + L+
Sbjct: 52 SGEKVDAALLEKMPKLRAASTISVGYDNFDVDALTARKILLMHTPTVLTETVADTLMALV 111
Query: 126 IDVLRKLSAADCFVRQGLW--PINAEFPLGSKLGGKRVGIVGLGSIGSEVAKRLE-AFGC 182
+ R++ V+ G W I ++ G+ + K +GIVG+G IG +A+R F
Sbjct: 112 LSTARRVVEVAERVKAGEWTASIGPDW-FGTDVHHKTLGIVGMGRIGMALAQRAHFGFNM 170
Query: 183 CVSYNSRNKKPSVTYPFYPDVCEL---AANSDVLIICCALTDQTHHLINKQVLLALGKKG 239
+ YN+R F C+L SD + I LTD+THHL + +
Sbjct: 171 PILYNARRHHKEAEERFNARYCDLDTLLQESDFVCIILPLTDETHHLFGAEQFAKMKSSA 230
Query: 240 VIINVGRGAIIDEKEMVGCLLRGEIGGAGLDVFENEP-DVPEQLFALDNVVLSPHSAVFT 298
+ IN GRG ++DE ++ L +GEI AGLDVFE EP V L +L NVV PH T
Sbjct: 231 IFINAGRGPVVDENALIAALQKGEIHAAGLDVFEQEPLSVDSPLLSLPNVVAVPHIGSAT 290
Query: 299 PESFKDVCELAVANLEAFFSNK 320
E+ ++ AV NL K
Sbjct: 291 HETRYNMAACAVDNLIDALQGK 312
>gnl|CDD|240656 cd12179, 2-Hacid_dh_14, Putative D-isomer specific 2-hydroxyacid
dehydrogenases, NAD-binding and catalytic domains.
2-Hydroxyacid dehydrogenases catalyze the conversion of
a wide variety of D-2-hydroxy acids to their
corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 306
Score = 142 bits (361), Expect = 3e-40
Identities = 83/252 (32%), Positives = 130/252 (51%), Gaps = 12/252 (4%)
Query: 69 PVTAEILRLLPEVRLVVATSAGLNHIDVVECRRRGVALANAGNVFSEDVADYALGLLIDV 128
P+ E + ++ + AGL +ID+ + +G+ L NA + V ++ALG+L+ +
Sbjct: 51 PIDKEFIEKATNLKFIARAGAGLENIDLEYAKEKGIELFNAPEGNRDAVGEHALGMLLAL 110
Query: 129 LRKLSAADCFVRQGLWPINAEFPLGSKLGGKRVGIVGLGSIGSEVAKRLEAFGCCVSYNS 188
KL+ AD VR G+W + E G +L GK VGI+G G++G AKRL FGC V
Sbjct: 111 FNKLNRADQEVRNGIW--DREGNRGVELMGKTVGIIGYGNMGKAFAKRLSGFGCKVIAYD 168
Query: 189 RNKKPSVTYPFYPDVCELAANSDVLIICCALTDQTHHLINKQVLLALGKKGVIINVGRGA 248
+ K Y + L +D+L + LT +T ++NK+ + + K IN RG
Sbjct: 169 KYKNFGDAYAEQVSLETLFKEADILSLHIPLTPETRGMVNKEFISSFKKPFYFINTARGK 228
Query: 249 IIDEKEMVGCLLRGEIGGAGLDVFENE----------PDVPEQLFALDNVVLSPHSAVFT 298
++ K++V L G+I GA LDV E E P+ E L V+L+PH A +T
Sbjct: 229 VVVTKDLVKALKSGKILGACLDVLEYEKASFESIFNQPEAFEYLIKSPKVILTPHIAGWT 288
Query: 299 PESFKDVCELAV 310
ES++ + E+ V
Sbjct: 289 FESYEKIAEVLV 300
>gnl|CDD|180588 PRK06487, PRK06487, glycerate dehydrogenase; Provisional.
Length = 317
Score = 137 bits (348), Expect = 3e-38
Identities = 81/262 (30%), Positives = 129/262 (49%), Gaps = 9/262 (3%)
Query: 68 APVTAEILRLLPEVRLVVATSAGLNHIDVVECRRRGVALANAGNVFSEDVADYALGLLID 127
+ A L P+++L++ + G N++D+ R RG+ + N + VA + L LL+
Sbjct: 54 VALDAAALAAAPQLKLILVAATGTNNVDLAAARERGITVCNCQGYGTPSVAQHTLALLLA 113
Query: 128 VLRKLSAADCFVRQGLWPINAEFPLGS----KLGGKRVGIVGLGSIGSEVAKRLEAFGCC 183
+ +L V G W +++F L +L GK +G++G G +G VA+ EAFG
Sbjct: 114 LATRLPDYQQAVAAGRWQQSSQFCLLDFPIVELEGKTLGLLGHGELGGAVARLAEAFGMR 173
Query: 184 VSYNSRNKKPSVTYPFYPDVCELAANSDVLIICCALTDQTHHLINKQVLLALGKKGVIIN 243
V +P P + EL D L + C LT+ T HLI + L + ++IN
Sbjct: 174 VLIGQLPGRP--ARPDRLPLDELLPQVDALTLHCPLTEHTRHLIGARELALMKPGALLIN 231
Query: 244 VGRGAIIDEKEMVGCLLRGEIGGAGLDVFENEPDVPEQ-LFALD--NVVLSPHSAVFTPE 300
RG ++DE+ + L G +GGA DV EP V L A D ++++PHSA + E
Sbjct: 232 TARGGLVDEQALADALRSGHLGGAATDVLSVEPPVNGNPLLAPDIPRLIVTPHSAWGSRE 291
Query: 301 SFKDVCELAVANLEAFFSNKPL 322
+ + + N AFF+ KPL
Sbjct: 292 ARQRIVGQLAENARAFFAGKPL 313
>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 = 134 bits (339), Expect = 6e-37
Identities = 77/265 (29%), Positives = 125/265 (47%), Gaps = 28/265 (10%)
Query: 73 EILRLLPEVRLVVATSAGLNHIDVVECRRRGVALANA--GNVFSEDVADYALGLLIDVLR 130
+ P ++ + AG+N+IDV +RG+ + N N + VA+ + +++ + R
Sbjct: 43 HDMDFAPSLKAIARAGAGVNNIDVDAASKRGIVVFNTPGAN--ANAVAELVIAMMLALSR 100
Query: 131 KLSAADCFV--------RQGLWPINAEFPLGSKLGGKRVGIVGLGSIGSEVAKRLEAFGC 182
+ A +V +G+ +F G++L GK +G++GLG+IG VA A G
Sbjct: 101 NIIQAIKWVTNGDGDDISKGVEKGKKQFV-GTELRGKTLGVIGLGNIGRLVANAALALGM 159
Query: 183 ----CVSYNSRN--KKPSVTYPFYPDVCELAANSDVLIICCALTDQTHHLINKQVLLALG 236
Y S K SV + EL A +D + + LTD+T LIN + LLA
Sbjct: 160 KVIGYDPYLSVEAAWKLSVEVQRVTSLEELLATADYITLHVPLTDETRGLINAE-LLAKM 218
Query: 237 KKGVI-INVGRGAIIDEKEMVGCLLRGEIGGAGLDVFENEPDVPEQLFALDNVVLSPHSA 295
K G I +N RG I+DE+ ++ L G++GG + F P L L NV+ +PH
Sbjct: 219 KPGAILLNFARGEIVDEEALLEALDEGKLGGY-VTDFPE----PALLGHLPNVIATPHLG 273
Query: 296 VFTPESFKDVCELAVAN-LEAFFSN 319
T E+ ++ C + A + F
Sbjct: 274 ASTEEA-EENCAVMAARQIMDFLET 297
>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 = 130 bits (329), Expect = 1e-35
Identities = 78/258 (30%), Positives = 120/258 (46%), Gaps = 8/258 (3%)
Query: 67 GAPVTAEILRLLPEVRLVVATSAGLNHIDVVECRRRGVALANAGNVFSEDVADYALGLLI 126
AP E LR LP +R+V SAG + V+ GV L NA V A+ A+ L++
Sbjct: 47 AAPPVLEALRALPRLRVVQTLSAGYDG--VLPLLPEGVTLCNARGVHDASTAELAVALIL 104
Query: 127 DVLRKLSAADCFVRQGLWPINAEFPLGSKLGGKRVGIVGLGSIGSEVAKRLEAFGCCVSY 186
LR L +G W E L +RV IVG GSIG + +RL F V+
Sbjct: 105 ASLRGLPRFVRAQARGRW----EPRRTPSLADRRVLIVGYGSIGRAIERRLAPFEVRVTR 160
Query: 187 NSRNKKPSVTYPFYPDVCELAANSDVLIICCALTDQTHHLINKQVLLALGKKGVIINVGR 246
+R +P ++ L +DV+++ LTD+T L++ + L + +++NV R
Sbjct: 161 VARTARPGEQVHGIDELPALLPEADVVVLIVPLTDETRGLVDAEFLARMPDGALLVNVAR 220
Query: 247 GAIIDEKEMVGCLLRGEIGGAGLDVFENEPDVPEQ-LFALDNVVLSPHSAVFTPESFKDV 305
G ++D +V L G + A LDV + EP P L++ V+++PH TP
Sbjct: 221 GPVVDTDALVAELASGRL-RAALDVTDPEPLPPGHPLWSAPGVLITPHVGGATPAFLPRA 279
Query: 306 CELAVANLEAFFSNKPLL 323
L L + + +PL
Sbjct: 280 YALVRRQLRRYAAGEPLE 297
>gnl|CDD|240662 cd12186, LDH, D-Lactate dehydrogenase and D-2-Hydroxyisocaproic
acid dehydrogenase (D-HicDH), NAD-binding and catalytic
domains. D-Lactate dehydrogenase (LDH) catalyzes the
interconversion of pyruvate and lactate, and is a member
of the 2-hydroxyacid dehydrogenases family. LDH is
homologous to D-2-hydroxyisocaproic acid
dehydrogenase(D-HicDH) and shares the 2 domain structure
of formate dehydrogenase. D-HicDH is a NAD-dependent
member of the hydroxycarboxylate dehydrogenase family,
and shares the Rossmann fold typical of many NAD binding
proteins. HicDH from Lactobacillus casei forms a monomer
and catalyzes the reaction R-CO-COO(-) + NADH + H+ to
R-COH-COO(-) + NAD+. D-HicDH, like the structurally
distinct L-HicDH, exhibits low side-chain R specificity,
accepting a wide range of 2-oxocarboxylic acid side
chains. Formate/glycerate and related dehydrogenases of
the D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-Adenosylhomocysteine Hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain.
Length = 329
Score = 131 bits (331), Expect = 1e-35
Identities = 76/275 (27%), Positives = 133/275 (48%), Gaps = 25/275 (9%)
Query: 68 APVTAEILRLLPEVRL-VVAT-SAGLNHIDVVECRRRGVALANAGNVFSEDVADYALGLL 125
P E+ L E + +A SAG++ ID+ + G+ + N +A++A+
Sbjct: 54 LPYDEEVYEKLAEYGIKQIALRSAGVDMIDLDLAKENGLKITNVPAYSPRAIAEFAVTQA 113
Query: 126 IDVLRKLSAADCFVRQGLWPINAEFPLGSKLGGKRVGIVGLGSIGSEVAKRLEAFGCCV- 184
+++LR D V +G + +G ++ VGI+G G IGS AK + FG V
Sbjct: 114 LNLLRNTPEIDRRVAKGDFRWAPGL-IGREIRDLTVGIIGTGRIGSAAAKIFKGFGAKVI 172
Query: 185 SYN-SRNK--KPSVTYPFYPDVCELAANSDVLIICCALTDQTHHLINKQVLLALGKKGVI 241
+Y+ N + + Y Y + +L +D++ + LT + HHLIN + A K G I
Sbjct: 173 AYDPYPNPELEKFLLY--YDSLEDLLKQADIISLHVPLTKENHHLINAEAF-AKMKDGAI 229
Query: 242 -INVGRGAIIDEKEMVGCLLRGEIGGAGLDVFENE--------------PDVPEQLFALD 286
+N RG ++D K ++ L G+I GA LD +ENE +V ++L A+
Sbjct: 230 LVNAARGGLVDTKALIDALDSGKIAGAALDTYENETGYFNKDWSGKEIEDEVLKELIAMP 289
Query: 287 NVVLSPHSAVFTPESFKDVCELAVANLEAFFSNKP 321
NV+++PH A +T + K++ E+++ +
Sbjct: 290 NVLITPHIAFYTDTAVKNMVEISLDDALEIIEGGT 324
>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 = 128 bits (325), Expect = 1e-34
Identities = 78/234 (33%), Positives = 113/234 (48%), Gaps = 32/234 (13%)
Query: 69 PVTAEILRLLPEVRLVVATSAGLNHIDVVECRRRGVALANAGNVFSEDVADYALGLLIDV 128
V +L V+ V + G +HID + RG+ ANA + VA+Y L L
Sbjct: 47 KVNEALLEGSK-VKFVGTATIGTDHIDTDYLKERGIGFANAPGCNANSVAEYVLSAL--- 102
Query: 129 LRKLSAADCFVRQGLWPINAEFPLGSKLGGKRVGIVGLGSIGSEVAKRLEAFGCCVSYNS 188
RQG L GK VGIVG+G++GS +A+RLEA G V
Sbjct: 103 ------LVLAQRQGF-----------SLKGKTVGIVGVGNVGSRLARRLEALGMNVLLCD 145
Query: 189 RNKKPSVTYPFYPDVCELAANSDVLIICC--ALTDQ----THHLINKQVLLALGKKGVII 242
+ + P + + EL A +D II LT T+HL+++ L AL ++I
Sbjct: 146 PPRAEAEGDPGFVSLEELLAEAD--IITLHVPLTRDGEHPTYHLLDEDFLAALKPGQILI 203
Query: 243 NVGRGAIIDEKEMVGCLLRGEIGGAGLDVFENEPDVPEQLFALDNVVL-SPHSA 295
N RGA+ID + ++ L RG+ LDV+ENEP++ +L LD V + +PH A
Sbjct: 204 NASRGAVIDNQALLALLQRGKDLRVVLDVWENEPEIDLEL--LDKVDIATPHIA 255
>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 = 125 bits (317), Expect = 7e-34
Identities = 84/238 (35%), Positives = 124/238 (52%), Gaps = 33/238 (13%)
Query: 96 VVECRRRGVALANAGNVFSEDVADYALGLLIDVLRKLSAADCFVRQGLWPINAEF----P 151
VV C R GVA +E +A++ L + L+AA +W AE P
Sbjct: 87 VVTCAR-GVA--------AEAIAEFVLAAI------LAAAKRL--PEIWVKGAEQWRREP 129
Query: 152 LGSKLGGKRVGIVGLGSIGSEVAKRLEAFGCCVSYNSRNKKPS----VTYPFYPDVCELA 207
LGS L G +GIVG G+IG +A+R A G V R+ +PS V D+ EL
Sbjct: 130 LGS-LAGSTLGIVGFGAIGQALARRALALGMRVLALRRSGRPSDVPGVEA--AADLAELF 186
Query: 208 ANSDVLIICCALTDQTHHLINKQVLLALGKKGV-IINVGRGAIIDEKEMVGCLLRGEIGG 266
A SD L++ LT +T HLIN V LA K G+ +IN+ RG ++D++ ++ L G I
Sbjct: 187 ARSDHLVLAAPLTPETRHLINADV-LAQAKPGLHLINIARGGLVDQEALLEALDSGRISL 245
Query: 267 AGLDVFENEPDVPEQ--LFALDNVVLSPHSAVFTPESFKDVCELAVANLEAFFSNKPL 322
A LDV + EP +PE L+ V LSPH++ P+ +++ + + NL + + +PL
Sbjct: 246 ASLDVTDPEP-LPEGHPLYTHPRVRLSPHTSAIAPDGRRNLADRFLENLARYRAGQPL 302
>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 = 122 bits (308), Expect = 2e-32
Identities = 73/284 (25%), Positives = 123/284 (43%), Gaps = 35/284 (12%)
Query: 75 LRLLPEVRLVVATSAGLNHI---DVVECRRRGVALANAGNVFSEDVADYALGLLIDVLRK 131
+P +RLV SAG +H + + V L A + +A++ +G + +
Sbjct: 49 AEDVPNLRLVQLFSAGADHWLGHPLY--KDPEVPLCTASGIHGPQIAEWVIGTWLVLSHH 106
Query: 132 LSAADCFVRQGLWPINAEFPLGSKLGGKRVGIVGLGSIGSEVAKRLEAFGCCV-SYNSRN 190
++ W E GKRVGI+G GSIG + A+ +A G V +Y
Sbjct: 107 FLQYIELQKEQTWGRRQEAYSVEDSVGKRVGILGYGSIGRQTARLAQALGMEVYAYTRSP 166
Query: 191 KK-----------------PSVTYP--FY-----PDVCE-LAANSDVLIICCALTDQTHH 225
+ P + P ++ + E L + D+L++ LT T H
Sbjct: 167 RPTPESRKDDGYIVPGTGDPDGSIPSAWFSGTDKASLHEFLRQDLDLLVVSLPLTPATKH 226
Query: 226 LINKQVLLALGKKG-VIINVGRGAIIDEKEMVGCLLRGEIGGAGLDVFENEPDVPEQ--L 282
L+ + L K+ + N+ RG+++D +V L G+I GA LDV + EP +P L
Sbjct: 227 LLGAEEFEILAKRKTFVSNIARGSLVDTDALVAALESGQIRGAALDVTDPEP-LPADHPL 285
Query: 283 FALDNVVLSPHSAVFTPESFKDVCELAVANLEAFFSNKPLLTPF 326
++ NV+++PH + T E F ++ NLE +PL+
Sbjct: 286 WSAPNVIITPHVSWQTQEYFDRALDVLEENLERLRKGEPLINLV 329
>gnl|CDD|215501 PLN02928, PLN02928, oxidoreductase family protein.
Length = 347
Score = 120 bits (303), Expect = 1e-31
Identities = 70/258 (27%), Positives = 128/258 (49%), Gaps = 28/258 (10%)
Query: 72 AEILRLLPEVRLVVATSAGLNHIDVVECRRRGVALAN-----AGNVFSEDVADYALGLLI 126
A+I+ +++L++ GL +DV + G+ +A GN S A+ A+ L++
Sbjct: 74 ADIIARASQMKLIMQFGVGLEGVDVDAATKHGIKVARIPSEGTGNAAS--CAEMAIYLML 131
Query: 127 DVLRKLSAADCFVRQGLWPINAEFPLGSKLGGKRVGIVGLGSIGSEVAKRLEAFGCCVSY 186
+LRK + ++ P+G L GK V I+G G+IG E+AKRL FG +
Sbjct: 132 GLLRKQNEMQISLKARRLGE----PIGDTLFGKTVFILGYGAIGIELAKRLRPFGVKLLA 187
Query: 187 NSRN--KKPSVTYPFYP--------------DVCELAANSDVLIICCALTDQTHHLINKQ 230
R+ +P D+ E A +D++++CC LT +T ++N +
Sbjct: 188 TRRSWTSEPEDGLLIPNGDVDDLVDEKGGHEDIYEFAGEADIVVLCCTLTKETAGIVNDE 247
Query: 231 VLLALGKKGVIINVGRGAIIDEKEMVGCLLRGEIGGAGLDVFENEPDVPE-QLFALDNVV 289
L ++ K +++N+ RG ++D ++ L G +GG +DV +EP P+ + NV+
Sbjct: 248 FLSSMKKGALLVNIARGGLLDYDAVLAALESGHLGGLAIDVAWSEPFDPDDPILKHPNVI 307
Query: 290 LSPHSAVFTPESFKDVCE 307
++PH A T S++ + +
Sbjct: 308 ITPHVAGVTEYSYRSMGK 325
>gnl|CDD|235890 PRK06932, PRK06932, glycerate dehydrogenase; Provisional.
Length = 314
Score = 117 bits (295), Expect = 1e-30
Identities = 77/262 (29%), Positives = 130/262 (49%), Gaps = 18/262 (6%)
Query: 71 TAEILRLLPEVRLVVATSAGLNHIDVVECRRRGVALANAGNVFSEDVADYALGLLIDVLR 130
T E L LP+++L+ T+ G N++D+V + G+A+ N S V ++ LG++ +
Sbjct: 56 TRETLAQLPKLKLIAITATGTNNVDLVAAKELGIAVKNVTGYSSTTVPEHVLGMIFALKH 115
Query: 131 KLSAADCFVRQGL---WPINAEF-----PLGSKLGGKRVGIVGLGSIGSEVAKRLEAFGC 182
L + R L W +F P+ + + G +G+ G G +G+EV + +A G
Sbjct: 116 SLMG---WYRDQLSDRWATCKQFCYFDYPI-TDVRGSTLGVFGKGCLGTEVGRLAQALGM 171
Query: 183 CVSYNSRNKKPSVTYPFYPDVCELAANSDVLIICCALTDQTHHLINKQVLLALGKKGVII 242
V Y + +K SV Y E+ +D++ + C LT+ T +LIN + L + +I
Sbjct: 172 KVLY-AEHKGASVCREGYTPFEEVLKQADIVTLHCPLTETTQNLINAETLALMKPTAFLI 230
Query: 243 NVGRGAIIDEKEMVGCLLRGEIGGAGLDVFENEP---DVPEQLFA--LDNVVLSPHSAVF 297
N GRG ++DE+ ++ L G+I GA LDV EP D P A L N++++PH A
Sbjct: 231 NTGRGPLVDEQALLDALENGKIAGAALDVLVKEPPEKDNPLIQAAKRLPNLLITPHIAWA 290
Query: 298 TPESFKDVCELAVANLEAFFSN 319
+ + + N+E F
Sbjct: 291 SDSAVTTLVNKVAQNIEEFVQQ 312
>gnl|CDD|235800 PRK06436, PRK06436, glycerate dehydrogenase; Provisional.
Length = 303
Score = 117 bits (294), Expect = 1e-30
Identities = 76/242 (31%), Positives = 125/242 (51%), Gaps = 10/242 (4%)
Query: 82 RLVVATSAGLNHIDVVECRRRGVALANAGNVFSEDVADYALGLLIDVLRKLSAADCFVRQ 141
+++ + SAG++HIDV V +NAG +S VA++A LL+ + + + ++
Sbjct: 51 KMIQSLSAGVDHIDVSGIPENVVLCSNAG-AYSISVAEHAFALLLAWAKNICENNYNMKN 109
Query: 142 GLWPINAEFPLGSKLGGKRVGIVGLGSIGSEVAKRLEAFGCCVSYNSRNKKPSVTYPFYP 201
G + + L L K +GI+G G IG VA +AFG + +R+ Y
Sbjct: 110 GNF-KQSPTKL---LYNKSLGILGYGGIGRRVALLAKAFGMNIYAYTRSYVNDGISSIYM 165
Query: 202 DVCELAANSDVLIICCALTDQTHHLINKQVLLALGKKGV-IINVGRGAIIDEKEMVGCLL 260
+ ++ SD ++I LTD+T +IN + +L+L +KG+ IINV R ++D+ +M+ L
Sbjct: 166 EPEDIMKKSDFVLISLPLTDETRGMINSK-MLSLFRKGLAIINVARADVVDKNDMLNFLR 224
Query: 261 RGEIGGAGLDVFENEPDVPEQLFALDNVVLSPH-SAVFTPESFKDVCELAVANLEAFFSN 319
DV+ NEP + E DNV+LSPH + + E + LA N++ FF
Sbjct: 225 NHNDKYYLSDVWWNEPIITETN--PDNVILSPHVAGGMSGEIMQPAVALAFENIKNFFEG 282
Query: 320 KP 321
KP
Sbjct: 283 KP 284
>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 = 117 bits (295), Expect = 1e-30
Identities = 89/272 (32%), Positives = 124/272 (45%), Gaps = 36/272 (13%)
Query: 72 AEILRLLPEVRLVVATSAGLNHI-------DVVECRRRGVALANAGNVFSEDVADYALGL 124
A+ R L +R V A +AG + + +V RG+ VA++ L L
Sbjct: 51 ADAARRLTRLRWVQALAAGPDAVLAAGFAPEVAVTSGRGL--------HDGTVAEHTLAL 102
Query: 125 LIDVLRKLSAADCFVRQGLWP--INAEFPLGSK-----LGGKRVGIVGLGSIGSEVAKRL 177
++ +R+L R+ W + PL L G RV I G GSIG +A L
Sbjct: 103 ILAAVRRLDEMREAQREHRWAGELGGLQPLRPAGRLTTLLGARVLIWGFGSIGQRLAPLL 162
Query: 178 EAFGCCV-----SYNSRNKKPSVTYPFYPDVCELAANSDVLIICCALTDQTHHLINKQVL 232
A G V S R P V P EL +DVL++ T T H ++ +VL
Sbjct: 163 TALGARVTGVARSAGERAGFPVVAEDELP---ELLPETDVLVMILPATPSTAHALDAEVL 219
Query: 233 LALGKKGVIINVGRGAIIDEKEMVGCLLRGEIGGAGLDVFENEPDVPEQ--LFALDNVVL 290
AL K ++NVGRGA +DE +V L G +GGA LDV EP +P L+ N++L
Sbjct: 220 AALPKHAWVVNVGRGATVDEDALVAALESGRLGGAALDVTATEP-LPASSPLWDAPNLIL 278
Query: 291 SPHSAVFTPESFKDVCELAVANLEAFFSNKPL 322
+PH+A P+ EL NL AF + PL
Sbjct: 279 TPHAAGGRPQG---AEELIAENLRAFLAGGPL 307
>gnl|CDD|177941 PLN02306, PLN02306, hydroxypyruvate reductase.
Length = 386
Score = 111 bits (280), Expect = 4e-28
Identities = 77/258 (29%), Positives = 126/258 (48%), Gaps = 25/258 (9%)
Query: 88 SAGLNHIDVVECRRRGVALANAGNVFSEDVADYALGLLIDVLRKLSAADCFVRQGLWPIN 147
+ G N++DV + G+A+ N V +E A+ A L + R++ AD F+R GL+
Sbjct: 94 AVGYNNVDVEAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLY--E 151
Query: 148 AEFP---LGSKLGGKRVGIVGLGSIGSEVAKRL-EAFGCCVSY-----NSR--------- 189
P +G+ L G+ VG++G G IGS A+ + E F + Y ++R
Sbjct: 152 GWLPHLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQSTRLEKFVTAYG 211
Query: 190 -----NKKPSVTYPFYPDVCELAANSDVLIICCALTDQTHHLINKQVLLALGKKGVIINV 244
N + VT+ + E+ +DV+ + L T+HLINK+ L + K+ V++N
Sbjct: 212 QFLKANGEQPVTWKRASSMEEVLREADVISLHPVLDKTTYHLINKERLALMKKEAVLVNA 271
Query: 245 GRGAIIDEKEMVGCLLRGEIGGAGLDVFENEPDVPEQLFALDNVVLSPHSAVFTPESFKD 304
RG +IDE +V L + GLDVFE+EP + L + N V+ PH A + + +
Sbjct: 272 SRGPVIDEVALVEHLKANPMFRVGLDVFEDEPYMKPGLADMKNAVVVPHIASASKWTREG 331
Query: 305 VCELAVANLEAFFSNKPL 322
+ LA N+ P+
Sbjct: 332 MATLAALNVLGKLKGYPV 349
>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 = 109 bits (276), Expect = 6e-28
Identities = 69/233 (29%), Positives = 116/233 (49%), Gaps = 14/233 (6%)
Query: 70 VTAEILRLLPEVRLVVATSAGLNHIDVVECRRRGVALANA--GNVFSEDVADYALGLLID 127
+T E+L P++ + G N +D+ +RG+ + NA N S VA+ +G +I
Sbjct: 54 LTEEVLEAAPKLLAIGCFCIGTNQVDLDAAAKRGIPVFNAPFSNTRS--VAELVIGEIIM 111
Query: 128 VLRKLSAADCFVRQGLWPINAEFPLGS-KLGGKRVGIVGLGSIGSEVAKRLEAFGCCVS- 185
+ R+L + +G+W +A GS ++ GK +GI+G G IGS+++ EA G V
Sbjct: 112 LARRLPDRNAAAHRGIWNKSAT---GSHEVRGKTLGIIGYGHIGSQLSVLAEALGMRVIF 168
Query: 186 YNSRNKKPSVTYPFYPDVCELAANSDVLIICCALTDQTHHLINKQVLLALGKKGVIINVG 245
Y+ K P + EL A +D + + T T ++I + + + K ++IN
Sbjct: 169 YDIAEKLPLGNARQVSSLEELLAEADFVTLHVPATPSTKNMIGAEEIAQMKKGAILINAS 228
Query: 246 RGAIIDEKEMVGCLLRGEIGGAGLDVFENEPDVPEQLFA-----LDNVVLSPH 293
RG ++D + L G + GA +DVF EP + F+ L NV+L+PH
Sbjct: 229 RGTVVDIDALAEALRSGHLAGAAVDVFPEEPASNGEPFSSPLQGLPNVILTPH 281
>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 = 108 bits (271), Expect = 6e-27
Identities = 70/263 (26%), Positives = 119/263 (45%), Gaps = 12/263 (4%)
Query: 68 APVTAEILRLLPEVRLVVATSAGLNHIDVVECRRRGVALANAGNVFSEDVADYALGLLID 127
A +TAE + ++L + G +H+D+ RG+ +A VA++ + +++
Sbjct: 72 AYMTAERIAKAKNLKLALTAGIGSDHVDLQAANDRGITVAEVTGSNVVSVAEHVVMMILI 131
Query: 128 VLRKLSAADCFVRQGLWPINAEFPLGSKLGGKRVGIVGLGSIGSEVAKRLEAFGCCVSYN 187
++R +G W + L GK VG VG G IG V +RL+ F + Y
Sbjct: 132 LVRNYVPGHEQAIEGGWNVADVVKRAYDLEGKTVGTVGAGRIGLRVLRRLKPFDVHLLYY 191
Query: 188 SRNKKPS-----VTYPFYPDVCELAANSDVLIICCALTDQTHHLINKQVLLALGKKGV-I 241
R++ P + + D+ ++ + DV+ I C L +T L NK+ LL+ KKG +
Sbjct: 192 DRHRLPEEVEKELGLTRHADLEDMVSKCDVVTINCPLHPETEGLFNKE-LLSKMKKGAYL 250
Query: 242 INVGRGAIIDEKEMVGCLLRGEIGGAGLDVFENEP---DVPEQLFALDNVVLSPHSAVFT 298
+N RG I D + + L G + G DV+ +P D P + N ++PH + T
Sbjct: 251 VNTARGKICDREAVAEALESGHLAGYAGDVWFPQPAPKDHP--WRTMPNNAMTPHISGTT 308
Query: 299 PESFKDVCELAVANLEAFFSNKP 321
++ LE FF +P
Sbjct: 309 LDAQARYAAGTKEILERFFEGEP 331
>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 = 106 bits (268), Expect = 1e-26
Identities = 81/274 (29%), Positives = 132/274 (48%), Gaps = 46/274 (16%)
Query: 72 AEILRLLPEVRLVVATSAGLNHI-------DVVECRRRGVALANAGNVFSEDVADYALGL 124
+L LP ++ + + AG++H+ DV R L + G ++ +A+Y L
Sbjct: 50 PGLLARLPNLKAIFSLGAGVDHLLADPDLPDVPIVR-----LVDPG--LAQGMAEYVLAA 102
Query: 125 LIDVLRKLSAADCFVRQGLW-----PINAEFPLGSKLGGKRVGIVGLGSIGSEVAKRLEA 179
++ + R + R+G+W AE RVG++GLG +G+ VA+RL A
Sbjct: 103 VLRLHRDMDRYAAQQRRGVWKPLPQRPAAER---------RVGVLGLGELGAAVARRLAA 153
Query: 180 FGCCVSYNSRNKK--PSVTYPFY-PDVCELA---ANSDVLIICCALTDQTHHLINKQVLL 233
G VS SR+ K VT F+ + L A +D+L+ LT +T ++N ++L
Sbjct: 154 LGFPVSGWSRSPKDIEGVT-CFHGEE--GLDAFLAQTDILVCLLPLTPETRGILNAELLA 210
Query: 234 ALGKKGVIINVGRGAIIDEKEMVGCLLRGEIGGAGLDVFENEP---DVPEQLFALDNVVL 290
L + +INVGRG + E +++ L G + GA LDVFE EP D P L+ V +
Sbjct: 211 RLPRGAALINVGRGPHLVEADLLAALDSGHLSGAVLDVFEQEPLPADHP--LWRHPRVTV 268
Query: 291 SPH-SAVFTPESFKDVCELAVANLEAFFSNKPLL 323
+PH +A+ P+S N+ + +PL
Sbjct: 269 TPHIAAITDPDS---AAAQVAENIRRLEAGEPLP 299
>gnl|CDD|181041 PRK07574, PRK07574, formate dehydrogenase; Provisional.
Length = 385
Score = 103 bits (258), Expect = 7e-25
Identities = 70/271 (25%), Positives = 120/271 (44%), Gaps = 10/271 (3%)
Query: 68 APVTAEILRLLPEVRLVVATSAGLNHIDVVECRRRGVALANAGNVFSEDVADYALGLLID 127
A +TAE + P ++L + G +H+D+ G+ +A S VA++ + +++
Sbjct: 102 AYLTAERIAKAPNLKLAITAGIGSDHVDLQAASEHGITVAEVTGSNSISVAEHVVMMILA 161
Query: 128 VLRKLSAADCFVRQGLWPINAEFPLGSKLGGKRVGIVGLGSIGSEVAKRLEAFGCCVSYN 187
++R + +G W I L G VGIVG G IG V +RL+ F + Y
Sbjct: 162 LVRNYEPSHRQAVEGGWNIADCVSRSYDLEGMTVGIVGAGRIGLAVLRRLKPFDVKLHYT 221
Query: 188 SRNKKPS-------VTYPFYPDVCELAANSDVLIICCALTDQTHHLINKQVLLALGKKGV 240
R++ P +TY + L + DV+ I C L +T HL + VL + +
Sbjct: 222 DRHRLPEEVEQELGLTY--HVSFDSLVSVCDVVTIHCPLHPETEHLFDADVLSRMKRGSY 279
Query: 241 IINVGRGAIIDEKEMVGCLLRGEIGGAGLDVFENEPDVPEQLF-ALDNVVLSPHSAVFTP 299
++N RG I+D +V L G + G DV+ +P + + + ++PH + T
Sbjct: 280 LVNTARGKIVDRDAVVRALESGHLAGYAGDVWFPQPAPADHPWRTMPRNGMTPHISGTTL 339
Query: 300 ESFKDVCELAVANLEAFFSNKPLLTPFAAVD 330
+ LE FF +P+ + VD
Sbjct: 340 SAQARYAAGTREILECFFEGRPIRDEYLIVD 370
>gnl|CDD|166874 PRK00257, PRK00257, erythronate-4-phosphate dehydrogenase;
Validated.
Length = 381
Score = 97.8 bits (244), Expect = 5e-23
Identities = 59/233 (25%), Positives = 96/233 (41%), Gaps = 30/233 (12%)
Query: 69 PVTAEILRLLPEVRLVVATSAGLNHIDVVECRRRGVALANAGNVFSEDVADYALG-LLID 127
V +L VR V + G +H+D+ G+ ++A + V DY LG LL
Sbjct: 48 RVDRALLEGSR-VRFVGTCTIGTDHLDLDYFAEAGITWSSAPGCNARGVVDYVLGSLLTL 106
Query: 128 VLRKLSAADCFVRQGLWPINAEFPLGSKLGGKRVGIVGLGSIGSEVAKRLEAFGCCVSYN 187
R+ G L + G+VG G +G + + L G V
Sbjct: 107 AERE---------------------GVDLAERTYGVVGAGHVGGRLVRVLRGLGWKVLVC 145
Query: 188 SRNKKPSVTYPFYPDVCELAANSDVLIICCALT----DQTHHLINKQVLLALGKKGVIIN 243
++ + + + + DV+ + LT T HL+++ L +L +IN
Sbjct: 146 DPPRQEAEGDGDFVSLERILEECDVISLHTPLTKEGEHPTRHLLDEAFLASLRPGAWLIN 205
Query: 244 VGRGAIIDEKEMVGCLLRGEIGGAGLDVFENEPDVPEQLFALDNVVL-SPHSA 295
RGA++D + + LL GE A LDV+E EP + +L D + +PH A
Sbjct: 206 ASRGAVVDNQALREALLSGEDLDAVLDVWEGEPQIDLEL--ADLCTIATPHIA 256
>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 = 97.0 bits (242), Expect = 6e-23
Identities = 78/312 (25%), Positives = 129/312 (41%), Gaps = 39/312 (12%)
Query: 34 NKFQY-LKAYESALPLHEFLTL-HAHSVK---AIFSSAGAPVTAEILRLLPE--VRLVVA 86
KF Y L E E+L + H K A+ E L + E ++ V
Sbjct: 21 KKFGYDLTLVE------EYLNDENVHLAKGHDAVIVRGNCFADKENLEIYKEYGIKYVFT 74
Query: 87 TSAGLNHIDVVECRRRGVALANAGNVFSEDVADYALGLLIDVLRKLSAADCFVRQGLWPI 146
+ G NHID+ + G +A + +A+ A L + + R + + +
Sbjct: 75 RTVGFNHIDLEAAKELGFKMARVPSYSPNAIAELAFTLAMTLSRHTAYTASRTANKNFKV 134
Query: 147 NAEFPLGSKLGGKRVGIVGLGSIGSEVAKRLEAFGCCV----SYNSRNKKPSVTYPFYPD 202
+ F ++ VGI+G G IG AK + G V Y S K VT+
Sbjct: 135 D-PFMFSKEIRNSTVGIIGTGRIGLTAAKLFKGLGAKVIGYDIYPSDAAKDVVTFV---S 190
Query: 203 VCELAANSDVLIICCA-LTDQTHHLINKQVLLALGKKGVI-INVGRGAIIDEKEMVGCLL 260
+ EL SD++ + + + LINK+ ++ K G I IN RG + DE+ ++ L
Sbjct: 191 LDELLKKSDIISLHVPYIKGKNDKLINKE-FISKMKDGAILINTARGELQDEEAILEALE 249
Query: 261 RGEIGGAGLDVFENEPDVPEQLFALDN---------------VVLSPHSAVFTPESFKDV 305
G++ G G DV NE ++ + F D V+L+PH +T E+ ++
Sbjct: 250 SGKLAGFGTDVLNNEKEIFFKDFDGDKIEDPVVEKLLDLYPRVLLTPHIGSYTDEALSNM 309
Query: 306 CELAVANLEAFF 317
E + NL+ +
Sbjct: 310 IETSYENLKEYL 321
>gnl|CDD|236985 PRK11790, PRK11790, D-3-phosphoglycerate dehydrogenase;
Provisional.
Length = 409
Score = 91.0 bits (227), Expect = 1e-20
Identities = 73/240 (30%), Positives = 115/240 (47%), Gaps = 28/240 (11%)
Query: 70 VTAEILRLLPEVRLVVATSAGLNHIDVVECRRRGVALANA--GNVFSEDVADYALGLLID 127
+T E+L ++ + G N +D+ +RG+ + NA N S VA+ +G +I
Sbjct: 65 LTEEVLAAAEKLVAIGCFCIGTNQVDLDAAAKRGIPVFNAPFSNTRS--VAELVIGEIIL 122
Query: 128 VLRKLSAADCFVRQGLWPINAEFPLGS-KLGGKRVGIVGLGSIGSEVAKRLEAFGCCVSY 186
+LR + + +G W +A GS ++ GK +GIVG G IG++++ E+ G V +
Sbjct: 123 LLRGIPEKNAKAHRGGWNKSAA---GSFEVRGKTLGIVGYGHIGTQLSVLAESLGMRVYF 179
Query: 187 ---NSR----NKKPSVTYPFYPDVCELAANSDVLIICCALTDQTHHLINKQVLLALGKKG 239
+ N + + EL A SDV+ + T T ++I + L AL K G
Sbjct: 180 YDIEDKLPLGNARQVGSLE------ELLAQSDVVSLHVPETPSTKNMIGAEEL-ALMKPG 232
Query: 240 VI-INVGRGAIIDEKEMVGCLLRGEIGGAGLDVFENEPDVPEQLF-----ALDNVVLSPH 293
I IN RG ++D + L G + GA +DVF EP F LDNV+L+PH
Sbjct: 233 AILINASRGTVVDIDALADALKSGHLAGAAIDVFPVEPKSNGDPFESPLRGLDNVILTPH 292
>gnl|CDD|178684 PLN03139, PLN03139, formate dehydrogenase; Provisional.
Length = 386
Score = 90.7 bits (225), Expect = 2e-20
Identities = 72/236 (30%), Positives = 110/236 (46%), Gaps = 14/236 (5%)
Query: 68 APVTAEILRLLPEVRLVVATSAGLNHIDVVECRRRG--VALANAGNVFSEDVADYALGLL 125
A VTAE ++ + L++ G +HID+ G VA NV S VA+ L +
Sbjct: 109 AYVTAERIKKAKNLELLLTAGIGSDHIDLPAAAAAGLTVAEVTGSNVVS--VAEDELMRI 166
Query: 126 IDVLRKLSAADCFVRQGLWPINAEFPLGSKLGGKRVGIVGLGSIGSEVAKRLEAFGCCVS 185
+ +LR V G W + L GK VG VG G IG + +RL+ F C +
Sbjct: 167 LILLRNFLPGYHQVVSGEWNVAGIAYRAYDLEGKTVGTVGAGRIGRLLLQRLKPFNCNLL 226
Query: 186 YNSRNKKPS-----VTYPFYPDVCELAANSDVLIICCALTDQTHHLINKQVLLALGKKGV 240
Y+ R K F D+ + DV++I LT++T + NK+ + + K +
Sbjct: 227 YHDRLKMDPELEKETGAKFEEDLDAMLPKCDVVVINTPLTEKTRGMFNKERIAKMKKGVL 286
Query: 241 IINVGRGAIIDEKEMVGCLLRGEIGGAGLDVFENEP---DVPEQLFALDNVVLSPH 293
I+N RGAI+D + + G IGG G DV+ +P D P + + N ++PH
Sbjct: 287 IVNNARGAIMDTQAVADACSSGHIGGYGGDVWYPQPAPKDHPWR--YMPNHAMTPH 340
>gnl|CDD|181499 PRK08605, PRK08605, D-lactate dehydrogenase; Validated.
Length = 332
Score = 82.9 bits (205), Expect = 6e-18
Identities = 66/267 (24%), Positives = 119/267 (44%), Gaps = 32/267 (11%)
Query: 69 PVTAEILRLLPE--VRLVVATSAGLNHIDVVECRRRGVALANAGNVFSEDVADYALGLLI 126
P++ I +LL E ++ + SAG + D+ + + ++N + E +A++ + I
Sbjct: 56 PLSEAIYKLLNELGIKQIAQRSAGFDTYDLELATKYNLIISNVPSYSPESIAEFTVTQAI 115
Query: 127 DVLRKLSAADCFVRQG--LW--PINAEFPLGSKLGGKRVGIVGLGSIGSEVAKRL-EAFG 181
+++R + VR+ W PI L + +V ++G G IG VAK + +G
Sbjct: 116 NLVRHFNQIQTKVREHDFRWEPPI-----LSRSIKDLKVAVIGTGRIGLAVAKIFAKGYG 170
Query: 182 CCVS----YNSRNKKPSVTYPFYPDVCELAANSDVLIICCALTDQTHHLINKQVLLALGK 237
V + + V Y + E +D++ + T H+L N + K
Sbjct: 171 SDVVAYDPFPNAKAATYVDYK--DTIEEAVEGADIVTLHMPATKYNHYLFNADLFKHFKK 228
Query: 238 KGVIINVGRGAIIDEKEMVGCLLRGEIGGAGLDVFENE-PDVP-------------EQLF 283
V +N RG+++D K ++ L G I GA LD +E E P P E L
Sbjct: 229 GAVFVNCARGSLVDTKALLDALDNGLIKGAALDTYEFERPLFPSDQRGQTINDPLLESLI 288
Query: 284 ALDNVVLSPHSAVFTPESFKDVCELAV 310
++V+L+PH A +T + K++ A+
Sbjct: 289 NREDVILTPHIAFYTDAAVKNLIVDAL 315
>gnl|CDD|183550 PRK12480, PRK12480, D-lactate dehydrogenase; Provisional.
Length = 330
Score = 81.9 bits (202), Expect = 1e-17
Identities = 49/243 (20%), Positives = 116/243 (47%), Gaps = 18/243 (7%)
Query: 81 VRLVVATSAGLNHIDVVECRRRGVALANAGNVFSEDVADYALGLLIDVLRKLSAADCFVR 140
++ + +AG + D+ ++ + ++N + E +A+Y++ + + ++R+ + V+
Sbjct: 70 IKQIAQRTAGFDMYDLDLAKKHNIVISNVPSYSPETIAEYSVSIALQLVRRFPDIERRVQ 129
Query: 141 QGLWPINAEFPLGSK-LGGKRVGIVGLGSIGSEVAKRLEAFGCCVSYNSRNKKPSVTYPF 199
+ A + SK + V I+G G IG+ AK FG ++ + +
Sbjct: 130 AHDFTWQA--EIMSKPVKNMTVAIIGTGRIGAATAKIYAGFGATITAYDAYPNKDLDFLT 187
Query: 200 YPDVCELA-ANSDVLIICCALTDQTHHLINKQVLLALGKKGVIINVGRGAIIDEKEMVGC 258
Y D + A ++D++ + +++HL +K + + K +++N RGA+I+ +++
Sbjct: 188 YKDSVKEAIKDADIISLHVPANKESYHLFDKAMFDHVKKGAILVNAARGAVINTPDLIAA 247
Query: 259 LLRGEIGGAGLDVFENEP--------------DVPEQLFALDNVVLSPHSAVFTPESFKD 304
+ G + GA +D +ENE +L + ++++PH A F+ E+ ++
Sbjct: 248 VNDGTLLGAAIDTYENEAAYFTNDWTNKDIDDKTLLELIEHERILVTPHIAFFSDEAVQN 307
Query: 305 VCE 307
+ E
Sbjct: 308 LVE 310
>gnl|CDD|185366 PRK15469, ghrA, bifunctional glyoxylate/hydroxypyruvate reductase
A; Provisional.
Length = 312
Score = 70.6 bits (173), Expect = 9e-14
Identities = 50/144 (34%), Positives = 79/144 (54%), Gaps = 8/144 (5%)
Query: 161 VGIVGLGSIGSEVAKRLEAFGCCVSYNSRNKK--PSVTYPFYPDVCELAA---NSDVLII 215
+GI+G G +GS+VA+ L+ +G + SR++K P V + EL+A + VLI
Sbjct: 139 IGILGAGVLGSKVAQSLQTWGFPLRCWSRSRKSWPGVQSFAGRE--ELSAFLSQTRVLIN 196
Query: 216 CCALTDQTHHLINKQVLLALGKKGVIINVGRGAIIDEKEMVGCLLRGEIGGAGLDVFENE 275
T +T +IN+Q+L L ++N+ RG + E +++ L G++ GA LDVF E
Sbjct: 197 LLPNTPETVGIINQQLLEQLPDGAYLLNLARGVHVVEDDLLAALDSGKVKGAMLDVFSRE 256
Query: 276 PDVPEQ-LFALDNVVLSPHSAVFT 298
P PE L+ V ++PH A T
Sbjct: 257 PLPPESPLWQHPRVAITPHVAAVT 280
>gnl|CDD|240647 cd12170, 2-Hacid_dh_9, Putative D-isomer specific 2-hydroxyacid
dehydrogenases. 2-Hydroxyacid dehydrogenases catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 294
Score = 63.1 bits (154), Expect = 2e-11
Identities = 65/276 (23%), Positives = 113/276 (40%), Gaps = 51/276 (18%)
Query: 61 AIFSSAGAPVTAEILRLLPEVR-------LVVATSAGLNHIDVVECRRRGVALANAGNVF 113
+ S + E+L P ++ L SA ++D+ R G+ + +
Sbjct: 49 CVLVSYTTQIDEEVLEACPNIKYIGMCCSLYSEESA---NVDIAAARENGITVTGIRDYG 105
Query: 114 SEDVADYALGLLIDVLRKLSAADCFVRQGLWPINAEFPLGSKLGGKRVGIVGLGSIGSEV 173
E V +Y + LI +L W E P +L G +VGI+GLG+ G +
Sbjct: 106 DEGVVEYVISELIRLLHGF-------GGKQW---KEEPR--ELTGLKVGIIGLGTTGQMI 153
Query: 174 AKRLEAFGCCVSYNSRNKKPSVT---YPFYPDVCELAANSDVLIICCALTDQTHHLINKQ 230
A L FG V Y SR +KP + P + EL DV+ C + K
Sbjct: 154 ADALSFFGADVYYYSRTRKPDAEAKGIRYLP-LNELLKTVDVICTC----------LPKN 202
Query: 231 VLL-------ALGKKGVIINVGRGAIIDEKEMVGCLLRGEIGGAGLDVF--ENEPDVPEQ 281
V+L LG ++ N G + + L+ + +G ++F + + ++
Sbjct: 203 VILLGEEEFELLGDGKILFNTSLGPSFEVEA-----LKKWLKASGYNIFDCDTAGALGDE 257
Query: 282 -LFALDNVVLSPHSAVFTPESFKDVCELAVANLEAF 316
L NV+ + SA +T ++F+ + + +ANLE +
Sbjct: 258 ELLRYPNVICTNKSAGWTRQAFERLSQKVLANLEEY 293
>gnl|CDD|185335 PRK15438, PRK15438, erythronate-4-phosphate dehydrogenase PdxB;
Provisional.
Length = 378
Score = 62.6 bits (152), Expect = 6e-11
Identities = 58/225 (25%), Positives = 102/225 (45%), Gaps = 27/225 (12%)
Query: 81 VRLVVATSAGLNHIDVVECRRRGVALANAGNVFSEDVADYALGLLIDVLRKLSAADCFVR 140
++ V +AG +H+D ++ G+ + A + V +Y L+ L+ D F
Sbjct: 59 IKFVGTATAGTDHVDEAWLKQAGIGFSAAPGCNAIAVVEYVFSSLL----MLAERDGFS- 113
Query: 141 QGLWPINAEFPLGSKLGGKRVGIVGLGSIGSEVAKRLEAFGCCVSYNSRNKKPSVTYPFY 200
L + VGIVG+G++G + RLEA G + +
Sbjct: 114 ---------------LHDRTVGIVGVGNVGRRLQARLEALGIKTLLCDPPRADRGDEGDF 158
Query: 201 PDVCELAANSDVLIICCALTD----QTHHLINKQVLLALGKKGVIINVGRGAIIDEKEMV 256
+ EL +D+L L +T HL +++++ +L ++IN RGA++D ++
Sbjct: 159 RSLDELVQEADILTFHTPLFKDGPYKTLHLADEKLIRSLKPGAILINACRGAVVDNTALL 218
Query: 257 GCLLRGEIGGAGLDVFENEPDVPEQLFALDNV-VLSPHSAVFTPE 300
CL G+ LDV+E EP++ +L L V + +PH A +T E
Sbjct: 219 TCLNEGQKLSVVLDVWEGEPELNVEL--LKKVDIGTPHIAGYTLE 261
>gnl|CDD|240631 cd12154, FDH_GDH_like, Formate/glycerate dehydrogenases, D-specific
2-hydroxy acid dehydrogenases and related
dehydrogenases. The formate/glycerate dehydrogenase
like family contains a diverse group of enzymes such as
formate dehydrogenase (FDH), glycerate dehydrogenase
(GDH), D-lactate dehydrogenase, L-alanine dehydrogenase,
and S-Adenosylhomocysteine hydrolase, that share a
common 2-domain structure. Despite often low sequence
identity, these proteins typically have a characteristic
arrangement of 2 similar domains of the alpha/beta
Rossmann fold NAD+ binding form. The NAD(P) binding
domain is inserted within the linear sequence of the
mostly N-terminal catalytic domain. Structurally, these
domains are connected by extended alpha helices and
create a cleft in which NAD(P) is bound, primarily to
the C-terminal portion of the 2nd (internal) domain.
While many members of this family are dimeric, alanine
DH is hexameric and phosphoglycerate DH is tetrameric.
2-hydroxyacid dehydrogenases are enzymes that catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate dehydrogenase (FDH) catalyzes the NAD+-dependent
oxidation of formate ion to carbon dioxide with the
concomitant reduction of NAD+ to NADH. FDHs of this
family contain no metal ions or prosthetic groups.
Catalysis occurs though direct transfer of a hydride ion
to NAD+ without the stages of acid-base catalysis
typically found in related dehydrogenases.
Length = 310
Score = 59.9 bits (145), Expect = 3e-10
Identities = 52/239 (21%), Positives = 85/239 (35%), Gaps = 25/239 (10%)
Query: 53 TLHAH--SVKAIFSSAGAPVTAEILRL-LPEVRLVVATSAGLNHIDVVEC-RRRGVALAN 108
TL S+ + AE + RL+ + G +H D+ E R G+
Sbjct: 57 TLAKALWSLDVVLKVKEPLTNAEYALIQKLGDRLLFTYTIGADHRDLTEALARAGLTAIA 116
Query: 109 AGNVFSEDVADYALG----LLIDVLRKLSAADCFVRQGLWPINAEFPLGSKLGGKRVGIV 164
V + ++G + + R L V+Q A + GK V +V
Sbjct: 117 VEGVELPLLTSNSIGAGELSVQFIARFLE-----VQQPGRLGGA-----PDVAGKTVVVV 166
Query: 165 GLGSIGSEVAKRLEAFGCCVSYNSRNKK-----PSVTYPFYPDVCELAANSDVLIICCAL 219
G G +G E A+ L G V N + + ++ E A +DV++ L
Sbjct: 167 GAGVVGKEAAQMLRGLGAQVLITDINVEALEQLEELGGKNVEELEEALAEADVIVTTTLL 226
Query: 220 TDQTHHLINKQVLLALGKKG-VIINVGRGAI-IDEKEMVGCLLRGEIGGAGLDVFENEP 276
+ ++ + L+ K G VI+NV GA+ + L G DV P
Sbjct: 227 PGKRAGILVPEELVEQMKPGSVIVNVAVGAVGCVQALHTQLLEEGHGVVHYGDVNMPGP 285
>gnl|CDD|224995 COG2084, MmsB, 3-hydroxyisobutyrate dehydrogenase and related
beta-hydroxyacid dehydrogenases [Lipid metabolism].
Length = 286
Score = 36.0 bits (84), Expect = 0.016
Identities = 23/98 (23%), Positives = 40/98 (40%), Gaps = 13/98 (13%)
Query: 159 KRVGIVGLGSIGSEVAKRLEAFGCCVSYNSRNKKPSVTYP------FYPDVCELAANSDV 212
++ +GLG +GS +A L G V+ +R + + E AA +DV
Sbjct: 1 MKIAFIGLGIMGSPMAANLLKAGHEVTVYNRTPEKAAELLAAAGATVAASPAEAAAEADV 60
Query: 213 LIICCALTDQTHHLINKQVLLALGKKGVIINVGRGAII 250
+I + VL G+ G++ + GAI+
Sbjct: 61 VITMLPDDAAV-----RAVL--FGENGLLEGLKPGAIV 91
>gnl|CDD|224011 COG1086, COG1086, Predicted nucleoside-diphosphate sugar epimerases
[Cell envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 588
Score = 36.5 bits (85), Expect = 0.019
Identities = 28/126 (22%), Positives = 49/126 (38%), Gaps = 20/126 (15%)
Query: 67 GAPV-----TAEILRLLPEVRLVVA----TSAGLNHIDVVECRRRGVALANAGNVFSEDV 117
G PV ++ L +++A + I ++ R G+A+ +
Sbjct: 160 GVPVLGRIEIERVVEELGIQLILIAIPSASQEERRRI-LLRLARTGIAVRILPQLTD--- 215
Query: 118 ADYALGLLIDVLRKLSAADCFVRQGLWPINAEFPLGSKLGGKRVGIVGL-GSIGSEVAKR 176
L L LR++ D R + +G+ L GK V + G GSIGSE+ ++
Sbjct: 216 ----LKDLNGQLREIEIEDLLGRPPVALDTEL--IGAMLTGKTVLVTGGGGSIGSELCRQ 269
Query: 177 LEAFGC 182
+ F
Sbjct: 270 ILKFNP 275
>gnl|CDD|237341 PRK13302, PRK13302, putative L-aspartate dehydrogenase;
Provisional.
Length = 271
Score = 34.1 bits (78), Expect = 0.068
Identities = 26/108 (24%), Positives = 53/108 (49%), Gaps = 17/108 (15%)
Query: 160 RVGIVGLGSIGSEVAKRLE--AFGCCVS---------YNSRNKKPSVTYPFYPDVCELAA 208
RV I GLG+IG +A+ L+ G +S + P P + +LA
Sbjct: 8 RVAIAGLGAIGKAIAQALDRGLPGLTLSAVAVRDPQRHADFIWGLRRPPPVVP-LDQLAT 66
Query: 209 NSDVLIICCALTDQTHHLINKQVLLALGKKGVIINVGRGAIIDEKEMV 256
++D +++ A ++ + +LA GKK ++++V GA++ ++++
Sbjct: 67 HAD-IVVEAAPASVLRAIV--EPVLAAGKKAIVLSV--GALLRNEDLI 109
>gnl|CDD|217563 pfam03446, NAD_binding_2, NAD binding domain of 6-phosphogluconate
dehydrogenase. The NAD binding domain of
6-phosphogluconate dehydrogenase adopts a Rossmann fold.
Length = 163
Score = 32.4 bits (75), Expect = 0.13
Identities = 26/100 (26%), Positives = 40/100 (40%), Gaps = 18/100 (18%)
Query: 159 KRVGIVGLGSIGSEVAKRLEAFGCCVS-YNSRNKKPSVTYPF-------YPDVCELAANS 210
++G +GLG +GS +A L G V+ YN R P E A++
Sbjct: 1 AKIGFIGLGVMGSPMALNLLKAGYTVTVYN-RT--PEKVEELVAEGAVGAASPAEFVASA 57
Query: 211 DVLIICCALTDQTHHLINKQVLLALGKKGVIINVGRGAII 250
DV+I +I LG+ G++ + G II
Sbjct: 58 DVVITMVPAGAAVDAVI-------LGEDGLLPGLKPGDII 90
>gnl|CDD|216180 pfam00899, ThiF, ThiF family. This family contains a repeated
domain in ubiquitin activating enzyme E1 and members of
the bacterial ThiF/MoeB/HesA family.
Length = 134
Score = 31.8 bits (73), Expect = 0.18
Identities = 10/24 (41%), Positives = 13/24 (54%)
Query: 159 KRVGIVGLGSIGSEVAKRLEAFGC 182
RV +VG G +GS A+ L G
Sbjct: 2 SRVLVVGAGGLGSPAAEYLARAGV 25
>gnl|CDD|133445 cd01076, NAD_bind_1_Glu_DH, NAD(P) binding domain of glutamate
dehydrogenase, subgroup 1. Amino acid dehydrogenase
(DH) is a widely distributed family of enzymes that
catalyzes the oxidative deamination of an amino acid to
its keto acid and ammonia with concomitant reduction of
NADP+. Glutamate DH is a multidomain enzyme that
catalyzes the reaction from glutamate to 2-oxyoglutarate
and ammonia in the presence of NAD or NADP. It is
present in all organisms. Enzymes involved in ammonia
assimilation are typically NADP+-dependent, while those
involved in glutamate catabolism are generally
NAD+-dependent. Amino acid DH-like NAD(P)-binding
domains are members of the Rossmann fold superfamily and
include glutamate, leucine, and phenylalanine DHs,
methylene tetrahydrofolate DH,
methylene-tetrahydromethanopterin DH,
methylene-tetrahydropholate DH/cyclohydrolase, Shikimate
DH-like proteins, malate oxidoreductases, and glutamyl
tRNA reductase. Amino acid DHs catalyze the deamination
of amino acids to keto acids with NAD(P)+ as a cofactor.
The NAD(P)-binding Rossmann fold superfamily includes a
wide variety of protein families including NAD(P)-
binding domains of alcohol DHs, tyrosine-dependent
oxidoreductases, glyceraldehyde-3-phosphate DH,
lactate/malate DHs, formate/glycerate DHs, siroheme
synthases, 6-phosphogluconate DH, amino acid DHs,
repressor rex, NAD-binding potassium channel domain,
CoA-binding, and ornithine cyclodeaminase-like domains.
These domains have an alpha -beta-alpha configuration.
NAD binding involves numerous hydrogen and van der Waals
contacts.
Length = 227
Score = 32.1 bits (74), Expect = 0.28
Identities = 14/31 (45%), Positives = 17/31 (54%)
Query: 152 LGSKLGGKRVGIVGLGSIGSEVAKRLEAFGC 182
LG L G RV I G G++GS A+ L G
Sbjct: 25 LGIGLAGARVAIQGFGNVGSHAARFLHEAGA 55
>gnl|CDD|223745 COG0673, MviM, Predicted dehydrogenases and related proteins
[General function prediction only].
Length = 342
Score = 32.1 bits (73), Expect = 0.33
Identities = 23/95 (24%), Positives = 36/95 (37%), Gaps = 15/95 (15%)
Query: 160 RVGIVGLGSIG--------SEVAKRLEAFGCCVSYNSRNKKPSVTYPF---YPDVCELAA 208
RVGI+G G I + + LE R + + + Y D+ EL A
Sbjct: 5 RVGIIGAGGIAGKAHLPALAALGGGLELVAVVDRDPERAEAFAEEFGIAKAYTDLEELLA 64
Query: 209 NSDVLIICCALTDQTHHLINKQVLLALG-KKGVII 242
+ D+ + A + H + L AL K V+
Sbjct: 65 DPDIDAVYIATPNALHA---ELALAALEAGKHVLC 96
>gnl|CDD|201778 pfam01408, GFO_IDH_MocA, Oxidoreductase family, NAD-binding
Rossmann fold. This family of enzymes utilise NADP or
NAD. This family is called the GFO/IDH/MOCA family in
swiss-prot.
Length = 120
Score = 30.6 bits (70), Expect = 0.42
Identities = 25/88 (28%), Positives = 35/88 (39%), Gaps = 10/88 (11%)
Query: 159 KRVGIVGLGSIGS-------EVAKRLEAFGCCVSYNSRNKKPSVTY--PFYPDVCELAAN 209
RVGIVG G IG E E G +R + + ++ P Y D+ EL A+
Sbjct: 1 LRVGIVGAGKIGRRHLRALNESQDGAELVGILDPDPARAEAVAESFGVPAYSDLEELLAD 60
Query: 210 SDVLIICCALTDQTHHLINKQVLLALGK 237
D+ + A H + L GK
Sbjct: 61 PDIDAVSVATPPGLHFELALA-ALEAGK 87
>gnl|CDD|224805 COG1893, ApbA, Ketopantoate reductase [Coenzyme metabolism].
Length = 307
Score = 31.9 bits (73), Expect = 0.44
Identities = 15/74 (20%), Positives = 28/74 (37%), Gaps = 16/74 (21%)
Query: 160 RVGIVGLGSIGSEVAKRLEAFGCCVSYNSRNKK----------------PSVTYPFYPDV 203
++ I+G G+IGS + RL G V+ R+++ T
Sbjct: 2 KILILGAGAIGSLLGARLAKAGHDVTLLVRSRRLEALKKKGLRIEDEGGNFTTPVVAATD 61
Query: 204 CELAANSDVLIICC 217
E +D++I+
Sbjct: 62 AEALGPADLVIVTV 75
>gnl|CDD|133444 cd01075, NAD_bind_Leu_Phe_Val_DH, NAD(P) binding domain of leucine
dehydrogenase, phenylalanine dehydrogenase, and valine
dehydrogenase. Amino acid dehydrogenase (DH) is a
widely distributed family of enzymes that catalyzes the
oxidative deamination of an amino acid to its keto acid
and ammonia with concomitant reduction of NADP+. For
example, leucine DH catalyzes the reversible oxidative
deamination of L-leucine and several other straight or
branched chain amino acids to the corresponding
2-oxoacid derivative. Amino acid DH -like NAD(P)-binding
domains are members of the Rossmann fold superfamily and
include glutamate, leucine, and phenylalanine DHs,
methylene tetrahydrofolate DH,
methylene-tetrahydromethanopterin DH,
methylene-tetrahydropholate DH/cyclohydrolase, Shikimate
DH-like proteins, malate oxidoreductases, and glutamyl
tRNA reductase. Amino acid DHs catalyze the deamination
of amino acids to keto acids with NAD(P)+ as a cofactor.
The NAD(P)-binding Rossmann fold superfamily includes a
wide variety of protein families including NAD(P)-
binding domains of alcohol DHs, tyrosine-dependent
oxidoreductases, glyceraldehyde-3-phosphate DH,
lactate/malate DHs, formate/glycerate DHs, siroheme
synthases, 6-phosphogluconate DH, amino acid DHs,
repressor rex, NAD-binding potassium channel domain,
CoA-binding, and ornithine cyclodeaminase-like domains.
These domains have an alpha-beta-alpha configuration.
NAD binding involves numerous hydrogen and van der Waals
contacts.
Length = 200
Score = 31.0 bits (71), Expect = 0.49
Identities = 15/35 (42%), Positives = 21/35 (60%), Gaps = 1/35 (2%)
Query: 148 AEFPLGSK-LGGKRVGIVGLGSIGSEVAKRLEAFG 181
AE LG+ L GK V + GLG +G ++A+ L G
Sbjct: 17 AEHLLGTDSLEGKTVAVQGLGKVGYKLAEHLLEEG 51
>gnl|CDD|198433 cd10035, UDG_like_3, Uncharacterized subfamily of Uracil-DNA
glycosylases. This is a subfamily of Uracil-DNA
glycosylase superfamily. Uracil-DNA glycosylases (UDG)
catalyze the removal of uracil from DNA to initiate DNA
base excision repair pathway. Uracil in DNA can arise as
a result of mis-incorporation of dUMP residues by DNA
polymerase or deamination of cytosine. Uracil mispaired
with guanine in DNA is one of the major pro-mutagenic
events, causing G:C->A:T mutations. UDG is an essential
enzyme for maintaining the integrity of genetic
information. This ubiquitously found enzyme hydrolyzes
the N-glycosidic bond of deoxyuridine in DNA.
Length = 133
Score = 30.4 bits (69), Expect = 0.52
Identities = 10/21 (47%), Positives = 14/21 (66%)
Query: 66 AGAPVTAEILRLLPEVRLVVA 86
AG AE+L LLP + +V+A
Sbjct: 88 AGLRYLAELLALLPRLAVVIA 108
>gnl|CDD|238760 cd01483, E1_enzyme_family, Superfamily of activating enzymes (E1)
of the ubiquitin-like proteins. This family includes
classical ubiquitin-activating enzymes E1,
ubiquitin-like (ubl) activating enzymes and other
mechanistic homologes, like MoeB, Thif1 and others. The
common reaction mechanism catalyzed by MoeB, ThiF and
the E1 enzymes begins with a nucleophilic attack of the
C-terminal carboxylate of MoaD, ThiS and ubiquitin,
respectively, on the alpha-phosphate of an ATP molecule
bound at the active site of the activating enzymes,
leading to the formation of a high-energy acyladenylate
intermediate and subsequently to the formation of a
thiocarboxylate at the C termini of MoaD and ThiS.
Length = 143
Score = 30.7 bits (70), Expect = 0.56
Identities = 12/23 (52%), Positives = 15/23 (65%)
Query: 160 RVGIVGLGSIGSEVAKRLEAFGC 182
RV +VGLG +GSE+A L G
Sbjct: 1 RVLLVGLGGLGSEIALNLARSGV 23
>gnl|CDD|236190 PRK08220, PRK08220, 2,3-dihydroxybenzoate-2,3-dehydrogenase;
Validated.
Length = 252
Score = 31.0 bits (71), Expect = 0.70
Identities = 18/59 (30%), Positives = 22/59 (37%), Gaps = 4/59 (6%)
Query: 158 GKRVGIVGLGS-IGSEVAKRLEAFGCCVSYNSRNKKPSVTYPFYP---DVCELAANSDV 212
GK V + G IG VA G V + YPF DV + AA + V
Sbjct: 8 GKTVWVTGAAQGIGYAVALAFVEAGAKVIGFDQAFLTQEDYPFATFVLDVSDAAAVAQV 66
>gnl|CDD|223643 COG0569, TrkA, K+ transport systems, NAD-binding component
[Inorganic ion transport and metabolism].
Length = 225
Score = 30.7 bits (70), Expect = 0.73
Identities = 8/24 (33%), Positives = 13/24 (54%)
Query: 159 KRVGIVGLGSIGSEVAKRLEAFGC 182
++ I+G G +G VA+ L G
Sbjct: 1 MKIIIIGAGRVGRSVARELSEEGH 24
>gnl|CDD|133452 cd05213, NAD_bind_Glutamyl_tRNA_reduct, NADP-binding domain of
glutamyl-tRNA reductase. Glutamyl-tRNA reductase
catalyzes the conversion of glutamyl-tRNA to
glutamate-1-semialdehyde, initiating the synthesis of
tetrapyrrole. Whereas tRNAs are generally associated
with peptide bond formation in protein translation, here
the tRNA activates glutamate in the initiation of
tetrapyrrole biosynthesis in archaea, plants and many
bacteria. In the first step, activated glutamate is
reduced to glutamate-1-semi-aldehyde via the NADPH
dependent glutamyl-tRNA reductase. Glutamyl-tRNA
reductase forms a V-shaped dimer. Each monomer has 3
domains: an N-terminal catalytic domain, a classic
nucleotide binding domain, and a C-terminal dimerization
domain. Although the representative structure 1GPJ lacks
a bound NADPH, a theoretical binding pocket has been
described. (PMID 11172694). Amino acid dehydrogenase
(DH)-like NAD(P)-binding domains are members of the
Rossmann fold superfamily and include glutamate,
leucine, and phenylalanine DHs, methylene
tetrahydrofolate DH, methylene-tetrahydromethanopterin
DH, methylene-tetrahydropholate DH/cyclohydrolase,
Shikimate DH-like proteins, malate oxidoreductases, and
glutamyl tRNA reductase. Amino acid DHs catalyze the
deamination of amino acids to keto acids with NAD(P)+ as
a cofactor. The NAD(P)-binding Rossmann fold superfamily
includes a wide variety of protein families including
NAD(P)- binding domains of alcohol DHs,
tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate DH, lactate/malate DHs,
formate/glycerate DHs, siroheme synthases,
6-phosphogluconate DH, amino acid DHs, repressor rex,
NAD-binding potassium channel domain, CoA-binding, and
ornithine cyclodeaminase-like domains. These domains
have an alpha-beta-alpha configuration. NAD binding
involves numerous hydrogen and van der Waals contacts.
Length = 311
Score = 30.7 bits (70), Expect = 0.85
Identities = 12/28 (42%), Positives = 16/28 (57%)
Query: 156 LGGKRVGIVGLGSIGSEVAKRLEAFGCC 183
L GK+V ++G G +G AK L A G
Sbjct: 176 LKGKKVLVIGAGEMGELAAKHLAAKGVA 203
>gnl|CDD|183615 PRK12597, PRK12597, F0F1 ATP synthase subunit beta; Provisional.
Length = 461
Score = 31.0 bits (71), Expect = 0.91
Identities = 27/91 (29%), Positives = 41/91 (45%), Gaps = 22/91 (24%)
Query: 43 ESALP-LHEFLTLHAHSVKAIFSSAGAPVTAEILRLLPE--VR-LVVATSAGLNHIDVVE 98
E ALP +++ LT+H G P E+ + L E VR + + +++GL
Sbjct: 20 EGALPPINQALTVHDD---------GGPTLLEVKQHLDETTVRAIALGSTSGL------- 63
Query: 99 CRRRGVALANAGNVFSEDVADYALGLLIDVL 129
RG + N G V + LG L+DVL
Sbjct: 64 --ARGDEVRNTGGPIEVPVGEAVLGRLLDVL 92
>gnl|CDD|215144 PLN02256, PLN02256, arogenate dehydrogenase.
Length = 304
Score = 30.8 bits (70), Expect = 1.0
Identities = 20/66 (30%), Positives = 32/66 (48%), Gaps = 13/66 (19%)
Query: 160 RVGIVGLGSIGSEVAKRLEAFGCCVSYNSRN------KKPSVTYPFYPDV---CELAANS 210
++GIVG G+ G +AK G V SR+ + V+ F+ D CE +
Sbjct: 38 KIGIVGFGNFGQFLAKTFVKQGHTVLATSRSDYSDIAAELGVS--FFRDPDDFCE--EHP 93
Query: 211 DVLIIC 216
DV+++C
Sbjct: 94 DVVLLC 99
>gnl|CDD|202773 pfam03807, F420_oxidored, NADP oxidoreductase coenzyme
F420-dependent.
Length = 93
Score = 28.7 bits (65), Expect = 1.3
Identities = 18/66 (27%), Positives = 30/66 (45%), Gaps = 8/66 (12%)
Query: 160 RVGIVGLGSIGSEVAKRLEAFGCCVSY-NSRN-KKPSVTYPFYP------DVCELAANSD 211
++GI+G G++G +A+ L A G V NSRN +K + E +D
Sbjct: 1 KIGIIGAGNMGEALARGLAAAGHEVVIANSRNPEKAAALAEELGVKATAVSNEEAVEEAD 60
Query: 212 VLIICC 217
V+ +
Sbjct: 61 VVFLAV 66
>gnl|CDD|223411 COG0334, GdhA, Glutamate dehydrogenase/leucine dehydrogenase [Amino
acid transport and metabolism].
Length = 411
Score = 30.3 bits (69), Expect = 1.3
Identities = 12/30 (40%), Positives = 17/30 (56%)
Query: 152 LGSKLGGKRVGIVGLGSIGSEVAKRLEAFG 181
LG L G RV + G G++G A++L G
Sbjct: 201 LGDDLEGARVAVQGFGNVGQYAAEKLHELG 230
>gnl|CDD|99984 cd03813, GT1_like_3, This family is most closely related to the GT1
family of glycosyltransferases. Glycosyltransferases
catalyze the transfer of sugar moieties from activated
donor molecules to specific acceptor molecules, forming
glycosidic bonds. The acceptor molecule can be a lipid,
a protein, a heterocyclic compound, or another
carbohydrate residue. This group of glycosyltransferases
is most closely related to the previously defined
glycosyltransferase family 1 (GT1). The members of this
family may transfer UDP, ADP, GDP, or CMP linked sugars.
The diverse enzymatic activities among members of this
family reflect a wide range of biological functions. The
protein structure available for this family has the GTB
topology, one of the two protein topologies observed for
nucleotide-sugar-dependent glycosyltransferases. GTB
proteins have distinct N- and C- terminal domains each
containing a typical Rossmann fold. The two domains have
high structural homology despite minimal sequence
homology. The large cleft that separates the two domains
includes the catalytic center and permits a high degree
of flexibility. The members of this family are found
mainly in bacteria, while some of them are also found in
Archaea and eukaryotes.
Length = 475
Score = 30.3 bits (69), Expect = 1.6
Identities = 16/65 (24%), Positives = 25/65 (38%), Gaps = 7/65 (10%)
Query: 28 EQFFTSNKF--QYLKAYESALPLHEFLTLHAHSVKAIFSSAGAPVTAEILRLLPEVRLVV 85
F S +F + Y F+ +V+ + S P+ A I R LP+ +
Sbjct: 124 TDFLYSKEFWEMLTELYREYCTDPSFVDY-FWTVRNMLS----PLLAAIARPLPKADVYH 178
Query: 86 ATSAG 90
A S G
Sbjct: 179 AVSTG 183
>gnl|CDD|176186 cd05283, CAD1, Cinnamyl alcohol dehydrogenases (CAD). Cinnamyl
alcohol dehydrogenases (CAD), members of the medium
chain dehydrogenase/reductase family, reduce
cinnamaldehydes to cinnamyl alcohols in the last step of
monolignal metabolism in plant cells walls. CAD binds 2
zinc ions and is NADPH- dependent. CAD family members
are also found in non-plant species, e.g. in yeast where
they have an aldehyde reductase activity. The medium
chain dehydrogenases/reductase (MDR)/zinc-dependent
alcohol dehydrogenase-like family, which contains the
zinc-dependent alcohol dehydrogenase (ADH-Zn) and
related proteins, is a diverse group of proteins related
to the first identified member, class I mammalian ADH.
MDRs display a broad range of activities and are
distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases
(ADHs) catalyze the NAD(P)(H)-dependent interconversion
of alcohols to aldehydes or ketones. Active site zinc
has a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 337
Score = 29.8 bits (68), Expect = 1.8
Identities = 15/35 (42%), Positives = 21/35 (60%)
Query: 158 GKRVGIVGLGSIGSEVAKRLEAFGCCVSYNSRNKK 192
GKRVG+VG+G +G K +A G V+ SR+
Sbjct: 170 GKRVGVVGIGGLGHLAVKFAKALGAEVTAFSRSPS 204
>gnl|CDD|236122 PRK07877, PRK07877, hypothetical protein; Provisional.
Length = 722
Score = 30.0 bits (68), Expect = 1.9
Identities = 14/29 (48%), Positives = 19/29 (65%), Gaps = 1/29 (3%)
Query: 155 KLGGKRVGIVGLGSIGSEVAKRLEAFGCC 183
+LG R+G+VGL S+G +A L A G C
Sbjct: 104 RLGRLRIGVVGL-SVGHAIAHTLAAEGLC 131
>gnl|CDD|187627 cd05369, TER_DECR_SDR_a, Trans-2-enoyl-CoA reductase (TER) and
2,4-dienoyl-CoA reductase (DECR), atypical (a) SDR.
TTER is a peroxisomal protein with a proposed role in
fatty acid elongation. Fatty acid synthesis is known to
occur in the both endoplasmic reticulum and
mitochondria; peroxisomal TER has been proposed as an
additional fatty acid elongation system, it reduces the
double bond at C-2 as the last step of elongation. This
system resembles the mitochondrial system in that
acetyl-CoA is used as a carbon donor. TER may also
function in phytol metabolism, reducting phytenoyl-CoA
to phytanoyl-CoA in peroxisomes. DECR processes double
bonds in fatty acids to increase their utility in fatty
acid metabolism; it reduces 2,4-dienoyl-CoA to an
enoyl-CoA. DECR is active in mitochondria and
peroxisomes. This subgroup has the Gly-rich NAD-binding
motif of the classical SDR family, but does not display
strong identity to the canonical active site tetrad, and
lacks the characteristic Tyr at the usual position. SDRs
are a functionally diverse family of oxidoreductases
that have a single domain with a structurally conserved
Rossmann fold (alpha/beta folding pattern with a central
beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRS are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes have a
3-glycine N-terminal NAD(P)(H)-binding pattern
(typically, TGxxxGxG in classical SDRs and TGxxGxxG in
extended SDRs), while substrate binding is in the
C-terminal region. A critical catalytic Tyr residue
(Tyr-151, human 15-hydroxyprostaglandin dehydrogenase
(15-PGDH) numbering), is often found in a conserved
YXXXK pattern. In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) or additional
Ser, contributing to the active site. Substrates for
these enzymes include sugars, steroids, alcohols, and
aromatic compounds. The standard reaction mechanism is a
proton relay involving the conserved Tyr and Lys, as
well as Asn (or Ser). Some SDR family members, including
17 beta-hydroxysteroid dehydrogenase contain an
additional helix-turn-helix motif that is not generally
found among SDRs.
Length = 249
Score = 29.5 bits (67), Expect = 2.0
Identities = 13/37 (35%), Positives = 16/37 (43%), Gaps = 1/37 (2%)
Query: 156 LGGKRVGIVGLGS-IGSEVAKRLEAFGCCVSYNSRNK 191
L GK I G G+ IG +AK G V+ R
Sbjct: 1 LKGKVAFITGGGTGIGKAIAKAFAELGASVAIAGRKP 37
>gnl|CDD|181126 PRK07806, PRK07806, short chain dehydrogenase; Provisional.
Length = 248
Score = 29.3 bits (66), Expect = 2.4
Identities = 15/39 (38%), Positives = 18/39 (46%), Gaps = 1/39 (2%)
Query: 156 LGGKRVGIVGL-GSIGSEVAKRLEAFGCCVSYNSRNKKP 193
L GK + G IG++ AK L G V N R K P
Sbjct: 4 LPGKTALVTGSSRGIGADTAKILAGAGAHVVVNYRQKAP 42
>gnl|CDD|235783 PRK06349, PRK06349, homoserine dehydrogenase; Provisional.
Length = 426
Score = 29.7 bits (68), Expect = 2.4
Identities = 10/19 (52%), Positives = 16/19 (84%)
Query: 160 RVGIVGLGSIGSEVAKRLE 178
+VG++GLG++GS V + LE
Sbjct: 5 KVGLLGLGTVGSGVVRILE 23
>gnl|CDD|183197 PRK11559, garR, tartronate semialdehyde reductase; Provisional.
Length = 296
Score = 29.2 bits (66), Expect = 2.8
Identities = 24/97 (24%), Positives = 40/97 (41%), Gaps = 12/97 (12%)
Query: 159 KRVGIVGLGSIGSEVAKRLEAFGCCVSYNSRNKKP-----SVTYPFYPDVCELAANSDVL 213
+VG +GLG +G ++K L G + RN + + +A DV+
Sbjct: 3 MKVGFIGLGIMGKPMSKNLLKAGYSLVVYDRNPEAVAEVIAAGAETASTAKAVAEQCDVI 62
Query: 214 IICCALTDQTHHLINKQVLLALGKKGVIINVGRGAII 250
I L + H K+V LG+ G+I G ++
Sbjct: 63 IT--MLPNSPH---VKEVA--LGENGIIEGAKPGTVV 92
>gnl|CDD|223972 COG1042, COG1042, Acyl-CoA synthetase (NDP forming) [Energy
production and conversion].
Length = 598
Score = 29.6 bits (67), Expect = 2.9
Identities = 23/108 (21%), Positives = 40/108 (37%), Gaps = 16/108 (14%)
Query: 167 GSIGSEVAKRLEAFGCCVSYNSRNKKPSVT-YPFYPDVCELAANSDVLIICCALTDQTHH 225
G +G E+ + L +G Y K V Y V +L D+ +I
Sbjct: 23 GKLGYEILRNLLEYGQGKIYPVNPKYDEVLGVKAYTSVADLPDAPDLAVIV------VPA 76
Query: 226 LINKQVLLALGKKGVIINV---------GRGAIIDEKEMVGCLLRGEI 264
+ +++ LG+KGV + G + EKE+V + +
Sbjct: 77 KVVPEIVHELGEKGVKGAIVISAGFREAGEEGMELEKELVEAARKYGM 124
>gnl|CDD|238875 cd01837, SGNH_plant_lipase_like, SGNH_plant_lipase_like, a plant
specific subfamily of the SGNH-family of hydrolases, a
diverse family of lipases and esterases. The tertiary
fold of the enzyme is substantially different from that
of the alpha/beta hydrolase family and unique among all
known hydrolases; its active site closely resembles the
Ser-His-Asp(Glu) triad found in other serine hydrolases.
Length = 315
Score = 29.1 bits (66), Expect = 2.9
Identities = 18/92 (19%), Positives = 31/92 (33%), Gaps = 29/92 (31%)
Query: 155 KLGGKRVGIVGLGSIG---SEVAKRLEAFGCCVS--------YNS---------RNKKPS 194
LG ++ + GLG +G S+ G C+ +N+ R + P
Sbjct: 175 DLGARKFVVPGLGPLGCLPSQRTLFGGDGGGCLEELNELARLFNAKLKKLLAELRRELPG 234
Query: 195 VTY---PFYPDVCELAAN------SDVLIICC 217
+ Y + +L N + L CC
Sbjct: 235 AKFVYADIYNALLDLIQNPAKYGFENTLKACC 266
>gnl|CDD|177834 PLN02178, PLN02178, cinnamyl-alcohol dehydrogenase.
Length = 375
Score = 29.2 bits (65), Expect = 3.0
Identities = 16/39 (41%), Positives = 24/39 (61%)
Query: 154 SKLGGKRVGIVGLGSIGSEVAKRLEAFGCCVSYNSRNKK 192
+K GKR+G+ GLG +G K +AFG V+ SR+ +
Sbjct: 175 TKESGKRLGVNGLGGLGHIAVKIGKAFGLRVTVISRSSE 213
>gnl|CDD|187548 cd05237, UDP_invert_4-6DH_SDR_e, UDP-Glcnac (UDP-linked
N-acetylglucosamine) inverting 4,6-dehydratase, extended
(e) SDRs. UDP-Glcnac inverting 4,6-dehydratase was
identified in Helicobacter pylori as the hexameric flaA1
gene product (FlaA1). FlaA1 is hexameric, possesses
UDP-GlcNAc-inverting 4,6-dehydratase activity, and
catalyzes the first step in the creation of a
pseudaminic acid derivative in protein glycosylation.
Although this subgroup has the NADP-binding motif
characteristic of extended SDRs, its members tend to
have a Met substituted for the active site Tyr found in
most SDR families. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately 100
amino acids. Extended SDRs are a diverse collection of
proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 287
Score = 29.1 bits (66), Expect = 3.1
Identities = 11/26 (42%), Positives = 17/26 (65%), Gaps = 1/26 (3%)
Query: 158 GKRVGIVG-LGSIGSEVAKRLEAFGC 182
GK + + G GSIGSE+ +++ FG
Sbjct: 2 GKTILVTGGAGSIGSELVRQILKFGP 27
>gnl|CDD|235717 PRK06153, PRK06153, hypothetical protein; Provisional.
Length = 393
Score = 29.2 bits (66), Expect = 3.2
Identities = 11/20 (55%), Positives = 15/20 (75%)
Query: 152 LGSKLGGKRVGIVGLGSIGS 171
L +KL G+R+ I+GLG GS
Sbjct: 170 LSAKLEGQRIAIIGLGGTGS 189
>gnl|CDD|176198 cd08236, sugar_DH, NAD(P)-dependent sugar dehydrogenases. This
group contains proteins identified as sorbitol
dehydrogenases and other sugar dehydrogenases of the
medium-chain dehydrogenase/reductase family (MDR), which
includes zinc-dependent alcohol dehydrogenase and
related proteins. Sorbitol and aldose reductase are
NAD(+) binding proteins of the polyol pathway, which
interconverts glucose and fructose. Sorbitol
dehydrogenase is tetrameric and has a single catalytic
zinc per subunit. NAD(P)(H)-dependent oxidoreductases
are the major enzymes in the interconversion of alcohols
and aldehydes, or ketones. Related proteins include
threonine dehydrogenase, formaldehyde dehydrogenase, and
butanediol dehydrogenase. The medium chain alcohol
dehydrogenase family (MDR) has a NAD(P)(H)-binding
domain in a Rossmann fold of a beta-alpha form. The
N-terminal region typically has an all-beta catalytic
domain. These proteins typically form dimers (typically
higher plants, mammals) or tetramers (yeast, bacteria),
and have 2 tightly bound zinc atoms per subunit. Horse
liver alcohol dehydrogenase is a dimeric enzyme and each
subunit has two domains. The NAD binding domain is in a
Rossmann fold and the catalytic domain contains a zinc
ion to which substrates bind. There is a cleft between
the domains that closes upon formation of the ternary
complex.
Length = 343
Score = 29.1 bits (66), Expect = 3.3
Identities = 22/130 (16%), Positives = 40/130 (30%), Gaps = 33/130 (25%)
Query: 158 GKRVGIVGLGSIG------------SEV------AKRLE---AFGCCVSYNSRNKKPSVT 196
G V ++G G+IG V ++L G + N + +
Sbjct: 160 GDTVVVIGAGTIGLLAIQWLKILGAKRVIAVDIDDEKLAVARELGADDTINPKEEDVEKV 219
Query: 197 YPFYPDVCELAANSDVLIICCALTDQTHHLINKQVLLALGKKGVIINVG--RGAIIDEKE 254
+D++I +Q L G ++ VG G + +E
Sbjct: 220 RELTE-----GRGADLVIEAAGSPAT-----IEQALALARPGGKVVLVGIPYGDVTLSEE 269
Query: 255 MVGCLLRGEI 264
+LR E+
Sbjct: 270 AFEKILRKEL 279
>gnl|CDD|217105 pfam02558, ApbA, Ketopantoate reductase PanE/ApbA. This is a
family of 2-dehydropantoate 2-reductases also known as
ketopantoate reductases, EC:1.1.1.169. The reaction
catalyzed by this enzyme is: (R)-pantoate + NADP(+) <=>
2-dehydropantoate + NADPH. AbpA catalyzes the NADPH
reduction of ketopantoic acid to pantoic acid in the
alternative pyrimidine biosynthetic (APB) pathway. ApbA
and PanE are allelic. ApbA, the ketopantoate reductase
enzyme is required for the synthesis of thiamine via the
APB biosynthetic pathway.
Length = 150
Score = 28.4 bits (64), Expect = 3.4
Identities = 12/76 (15%), Positives = 24/76 (31%), Gaps = 21/76 (27%)
Query: 161 VGIVGLGSIGSEVA----------------KRLEAF---GCCVSYNSRNKKPSVTYPFYP 201
+ I+G G++GS + LEA G ++ +
Sbjct: 1 IAILGAGAVGSLYGARLARAGHDVTLIARGRHLEAIRENGLRITSPGGERTVPPPVATSA 60
Query: 202 DVCELAANSDVLIICC 217
E +D++I+
Sbjct: 61 S--EELGPADLVIVAV 74
>gnl|CDD|223552 COG0476, ThiF, Dinucleotide-utilizing enzymes involved in
molybdopterin and thiamine biosynthesis family 2
[Coenzyme metabolism].
Length = 254
Score = 28.9 bits (65), Expect = 3.4
Identities = 16/39 (41%), Positives = 18/39 (46%), Gaps = 2/39 (5%)
Query: 143 LWPINAEFPLGSKLGGKRVGIVGLGSIGSEVAKRLEAFG 181
L I E KL RV +VG G +GS AK L G
Sbjct: 17 LPGIGGEGQQ--KLKDSRVLVVGAGGLGSPAAKYLALAG 53
>gnl|CDD|169382 PRK08328, PRK08328, hypothetical protein; Provisional.
Length = 231
Score = 28.6 bits (64), Expect = 3.4
Identities = 13/27 (48%), Positives = 17/27 (62%)
Query: 155 KLGGKRVGIVGLGSIGSEVAKRLEAFG 181
KL +V +VG+G +GS VA L A G
Sbjct: 24 KLKKAKVAVVGVGGLGSPVAYYLAAAG 50
>gnl|CDD|180399 PRK06101, PRK06101, short chain dehydrogenase; Provisional.
Length = 240
Score = 28.7 bits (64), Expect = 3.5
Identities = 18/36 (50%), Positives = 22/36 (61%), Gaps = 6/36 (16%)
Query: 158 GKRVGIVGLGSIGSEVA-KRLEAFG---CCVSYNSR 189
G RV IVG SI SE+A R EA+G V+Y +R
Sbjct: 120 GHRVVIVG--SIASELALPRAEAYGASKAAVAYFAR 153
>gnl|CDD|107260 cd01575, PBP1_GntR, Ligand-binding domain of DNA transcription
repressor GntR specific for gluconate, a member of the
LacI-GalR family of bacterial transcription regulators.
This group represents the ligand-binding domain of DNA
transcription repressor GntR specific for gluconate, a
member of the LacI-GalR family of bacterial
transcription regulators. The ligand-binding domain of
GntR is structurally homologous to the periplasmic
sugar-binding domain of ABC-type transporters and both
domains contain the type I periplasmic binding
protein-like fold. The LacI-GalR family repressors are
composed of two functional domains: an N-terminal HTH
(helix-turn-helix) domain, which is responsible for the
DNA-binding specificity, and a C-terminal ligand-binding
domain, which is homologous to the type I periplasmic
binding proteins. As also observed in the periplasmic
binding proteins, the C-terminal domain of the bacterial
transcription repressor undergoes a conformational
change upon ligand binding, which in turn changes the
DNA binding affinity of the repressor.
Length = 268
Score = 28.6 bits (65), Expect = 4.0
Identities = 17/76 (22%), Positives = 32/76 (42%), Gaps = 13/76 (17%)
Query: 37 QYLKAYESALPLHEFLTLHAHSVKAIFS-SAGAPVTAEILRLLPEVRLVVATSAGLNHID 95
Q L+ + +AL + S + G + AE+L P++ V ++ D
Sbjct: 133 QRLEGFRAALRAAGLDPPLVVTTPEPSSFALGRELLAELLARWPDLDAVFCSN------D 186
Query: 96 VV------ECRRRGVA 105
+ EC+RRG++
Sbjct: 187 DLALGALFECQRRGIS 202
>gnl|CDD|215463 PLN02858, PLN02858, fructose-bisphosphate aldolase.
Length = 1378
Score = 29.0 bits (65), Expect = 4.2
Identities = 23/73 (31%), Positives = 34/73 (46%), Gaps = 13/73 (17%)
Query: 159 KRVGIVGLGSIGSEVAKRLEAFGCCV-SYNSRNKKPSVTYPFYPDVCELAANS------- 210
KR+G +GLG++G +A L V Y+ KP++ + + LA NS
Sbjct: 325 KRIGFIGLGAMGFGMASHLLKSNFSVCGYDV--YKPTLVR--FENAGGLAGNSPAEVAKD 380
Query: 211 -DVLIICCALTDQ 222
DVL+I A Q
Sbjct: 381 VDVLVIMVANEVQ 393
>gnl|CDD|236241 PRK08324, PRK08324, short chain dehydrogenase; Validated.
Length = 681
Score = 29.0 bits (66), Expect = 4.5
Identities = 13/27 (48%), Positives = 15/27 (55%), Gaps = 2/27 (7%)
Query: 160 RVGIV--GLGSIGSEVAKRLEAFGCCV 184
+V +V G IG AKRL A G CV
Sbjct: 423 KVALVTGAAGGIGKATAKRLAAEGACV 449
>gnl|CDD|237771 PRK14619, PRK14619, NAD(P)H-dependent glycerol-3-phosphate
dehydrogenase; Provisional.
Length = 308
Score = 28.4 bits (64), Expect = 4.7
Identities = 16/61 (26%), Positives = 28/61 (45%), Gaps = 8/61 (13%)
Query: 159 KRVGIVGLGSIGSEVAKRLEAFGCCVSYNSRNKKPSVTYPFYPDVCELAANSDVLIICCA 218
K + I+G G+ GS +A A G V SR S+ + A++DV++ +
Sbjct: 5 KTIAILGAGAWGSTLAGLASANGHRVRVWSRRSGLSLA--------AVLADADVIVSAVS 56
Query: 219 L 219
+
Sbjct: 57 M 57
>gnl|CDD|137204 PRK09310, aroDE, bifunctional 3-dehydroquinate
dehydratase/shikimate dehydrogenase protein; Reviewed.
Length = 477
Score = 28.6 bits (64), Expect = 4.8
Identities = 11/36 (30%), Positives = 15/36 (41%)
Query: 156 LGGKRVGIVGLGSIGSEVAKRLEAFGCCVSYNSRNK 191
L + V IVG G +A L G + +R K
Sbjct: 330 LNNQHVAIVGAGGAAKAIATTLARAGAELLIFNRTK 365
>gnl|CDD|198065 smart00997, AdoHcyase_NAD, S-adenosyl-L-homocysteine hydrolase, NAD
binding domain.
Length = 162
Score = 27.8 bits (63), Expect = 5.0
Identities = 13/29 (44%), Positives = 15/29 (51%)
Query: 156 LGGKRVGIVGLGSIGSEVAKRLEAFGCCV 184
L GK V + G G +G VA RL G V
Sbjct: 21 LAGKNVVVAGYGDVGKGVAARLRGLGARV 49
>gnl|CDD|238579 cd01174, ribokinase, Ribokinase catalyses the phosphorylation of
ribose to ribose-5-phosphate using ATP. This reaction is
the first step in the ribose metabolism. It traps ribose
within the cell after uptake and also prepares the sugar
for use in the synthesis of nucleotides and histidine,
and for entry into the pentose phosphate pathway.
Ribokinase is dimeric in solution.
Length = 292
Score = 28.3 bits (64), Expect = 5.1
Identities = 22/70 (31%), Positives = 32/70 (45%), Gaps = 10/70 (14%)
Query: 198 PFYPDVCELAANSDVLI---ICCAL------TDQTHHLINKQVLLALGKKGVIINVG-RG 247
P P EL A D+L+ AL TD+ ++LLA G K VI+ +G +G
Sbjct: 164 PARPLPAELLALVDILVPNETEAALLTGIEVTDEEDAEKAARLLLAKGVKNVIVTLGAKG 223
Query: 248 AIIDEKEMVG 257
A++ V
Sbjct: 224 ALLASGGEVE 233
>gnl|CDD|223536 COG0460, ThrA, Homoserine dehydrogenase [Amino acid transport and
metabolism].
Length = 333
Score = 28.3 bits (64), Expect = 5.1
Identities = 9/22 (40%), Positives = 15/22 (68%)
Query: 160 RVGIVGLGSIGSEVAKRLEAFG 181
+VG++GLG++GS V + L
Sbjct: 5 KVGLLGLGTVGSGVLEILAEKQ 26
>gnl|CDD|240619 cd00401, SAHH, S-Adenosylhomocysteine Hydrolase, NAD-binding and
catalytic domains. S-adenosyl-L-homocysteine hydrolase
(SAHH, AdoHycase) catalyzes the hydrolysis of
S-adenosyl-L-homocysteine (AdoHyc) to form adenosine
(Ado) and homocysteine (Hcy). The equilibrium lies far
on the side of AdoHyc synthesis, but in nature the
removal of Ado and Hyc is sufficiently fast, so that the
net reaction is in the direction of hydrolysis. Since
AdoHyc is a potent inhibitor of S-adenosyl-L-methionine
dependent methyltransferases, AdoHycase plays a critical
role in the modulation of the activity of various
methyltransferases. The enzyme forms homotetramers, with
each monomer binding one molecule of NAD+.
Length = 402
Score = 28.6 bits (65), Expect = 5.3
Identities = 10/29 (34%), Positives = 13/29 (44%)
Query: 156 LGGKRVGIVGLGSIGSEVAKRLEAFGCCV 184
+ GK V + G G +G A R G V
Sbjct: 193 IAGKVVVVAGYGWVGKGCAMRARGLGARV 221
>gnl|CDD|181371 PRK08306, PRK08306, dipicolinate synthase subunit A; Reviewed.
Length = 296
Score = 28.3 bits (64), Expect = 5.3
Identities = 11/33 (33%), Positives = 18/33 (54%)
Query: 158 GKRVGIVGLGSIGSEVAKRLEAFGCCVSYNSRN 190
G V ++G G G +A+ L+A G V+ +R
Sbjct: 152 GSNVLVLGFGRTGMTLARTLKALGANVTVGARK 184
>gnl|CDD|215789 pfam00208, ELFV_dehydrog, Glutamate/Leucine/Phenylalanine/Valine
dehydrogenase.
Length = 237
Score = 28.3 bits (64), Expect = 5.4
Identities = 13/32 (40%), Positives = 18/32 (56%)
Query: 153 GSKLGGKRVGIVGLGSIGSEVAKRLEAFGCCV 184
G L GK V + G G++GS A++L G V
Sbjct: 27 GDSLEGKTVAVQGFGNVGSYAAEKLLELGAKV 58
>gnl|CDD|238769 cd01492, Aos1_SUMO, Ubiquitin activating enzyme (E1) subunit Aos1.
Aos1 is part of the heterodimeric activating enzyme
(E1), specific for the SUMO family of ubiquitin-like
proteins (Ubls). E1 enzymes are part of a conjugation
cascade to attach Ub or Ubls, covalently to substrate
proteins consisting of activating (E1), conjugating
(E2), and/or ligating (E3) enzymes. E1 activates
ubiquitin by C-terminal adenylation, and subsequently
forms a highly reactive thioester bond between its
catalytic cysteine and Ubls C-terminus. The E1 also
associates with E2 and promotes ubiquitin transfer to
the E2's catalytic cysteine. Post-translational
modification by SUMO family of ubiquitin-like proteins
(Ublps) is involved in cell division, nuclear transport,
the stress response and signal transduction. Aos1
contains part of the adenylation domain.
Length = 197
Score = 28.0 bits (63), Expect = 5.5
Identities = 12/35 (34%), Positives = 21/35 (60%), Gaps = 4/35 (11%)
Query: 143 LWPINAEFPLGSKLGGKRVGIVGLGSIGSEVAKRL 177
LW + A+ +L R+ ++GL +G+E+AK L
Sbjct: 10 LWGLEAQ----KRLRSARILLIGLKGLGAEIAKNL 40
>gnl|CDD|237342 PRK13303, PRK13303, L-aspartate dehydrogenase; Provisional.
Length = 265
Score = 28.0 bits (63), Expect = 5.8
Identities = 8/21 (38%), Positives = 14/21 (66%)
Query: 159 KRVGIVGLGSIGSEVAKRLEA 179
+V ++G G+IG+ V + LE
Sbjct: 2 MKVAMIGFGAIGAAVLELLEH 22
>gnl|CDD|180970 PRK07417, PRK07417, arogenate dehydrogenase; Reviewed.
Length = 279
Score = 27.9 bits (63), Expect = 6.1
Identities = 22/101 (21%), Positives = 47/101 (46%), Gaps = 14/101 (13%)
Query: 160 RVGIVGLGSIGSEVAKRLEAFG---CCVSYNSRNKKPSVTYPFYPDV-CELA--ANSDVL 213
++GIVGLG IG + L + G VS + ++ + +L+ + D++
Sbjct: 2 KIGIVGLGLIGGSLGLDLRSLGHTVYGVSRRESTCERAIERGLVDEASTDLSLLKDCDLV 61
Query: 214 IICCALTDQTHHLIN--KQVLLALGKKGVIINVG--RGAII 250
I+ + L+ +Q++ AL + ++ +VG + I+
Sbjct: 62 ILALPIGL----LLPPSEQLIPALPPEAIVTDVGSVKAPIV 98
>gnl|CDD|236541 PRK09496, trkA, potassium transporter peripheral membrane
component; Reviewed.
Length = 453
Score = 28.2 bits (64), Expect = 6.2
Identities = 14/24 (58%), Positives = 16/24 (66%)
Query: 159 KRVGIVGLGSIGSEVAKRLEAFGC 182
KRV IVG G+IG +AK LE G
Sbjct: 232 KRVMIVGGGNIGYYLAKLLEKEGY 255
>gnl|CDD|237343 PRK13304, PRK13304, L-aspartate dehydrogenase; Reviewed.
Length = 265
Score = 28.0 bits (63), Expect = 6.4
Identities = 28/108 (25%), Positives = 47/108 (43%), Gaps = 24/108 (22%)
Query: 160 RVGIVGLGSIGSEVAK---------RLEAFGCCVSYNSRNKKPS-----VTYPFYPDVCE 205
++GIVG G+I S + K L AF Y+ +K + E
Sbjct: 3 KIGIVGCGAIASLITKAILSGRINAELYAF-----YDRNLEKAENLASKTGAKACLSIDE 57
Query: 206 LAANSDVLIICCALTDQTHHLINKQVLLALGKKGVIINVGRGAIIDEK 253
L + D L++ CA + ++ K L GK +I++V GA+ D++
Sbjct: 58 LVEDVD-LVVECASVNAVEEVVPK--SLENGKDVIIMSV--GALADKE 100
>gnl|CDD|130488 TIGR01421, gluta_reduc_1, glutathione-disulfide reductase,
animal/bacterial. The tripeptide glutathione is an
important reductant, e.g., for maintaining the cellular
thiol/disulfide status and for protecting against
reactive oxygen species such as hydrogen peroxide.
Glutathione-disulfide reductase regenerates reduced
glutathione from oxidized glutathione (glutathione
disulfide) + NADPH. This model represents one of two
closely related subfamilies of glutathione-disulfide
reductase. Both are closely related to trypanothione
reductase, and separate models are built so each of the
three can describe proteins with conserved function.
This model describes glutathione-disulfide reductases of
animals, yeast, and a number of animal-resident bacteria
[Energy metabolism, Electron transport].
Length = 450
Score = 28.3 bits (63), Expect = 6.5
Identities = 21/76 (27%), Positives = 29/76 (38%), Gaps = 12/76 (15%)
Query: 130 RKLSAADCFVRQGLWPINAEFPLGSKLGG------------KRVGIVGLGSIGSEVAKRL 177
R +A + G P E G++LG KRV IVG G I E+A L
Sbjct: 126 RDYTAPHILIATGGKPSFPENIPGAELGTDSDGFFALEELPKRVVIVGAGYIAVELAGVL 185
Query: 178 EAFGCCVSYNSRNKKP 193
G R+++
Sbjct: 186 HGLGSETHLVIRHERV 201
>gnl|CDD|234710 PRK00278, trpC, indole-3-glycerol-phosphate synthase; Reviewed.
Length = 260
Score = 27.8 bits (63), Expect = 6.6
Identities = 10/35 (28%), Positives = 15/35 (42%)
Query: 70 VTAEILRLLPEVRLVVATSAGLNHIDVVECRRRGV 104
T + L+P RLVV+ S D+ + G
Sbjct: 200 TTERLAPLIPSDRLVVSESGIFTPEDLKRLAKAGA 234
>gnl|CDD|216527 pfam01488, Shikimate_DH, Shikimate / quinate 5-dehydrogenase. This
family contains both shikimate and quinate
dehydrogenases. Shikimate 5-dehydrogenase catalyzes the
conversion of shikimate to 5-dehydroshikimate. This
reaction is part of the shikimate pathway which is
involved in the biosynthesis of aromatic amino acids.
Quinate 5-dehydrogenase catalyzes the conversion of
quinate to 5-dehydroquinate. This reaction is part of
the quinate pathway where quinic acid is exploited as a
source of carbon in prokaryotes and microbial
eukaryotes. Both the shikimate and quinate pathways
share two common pathway metabolites 3-dehydroquinate
and dehydroshikimate.
Length = 133
Score = 27.3 bits (61), Expect = 7.0
Identities = 10/30 (33%), Positives = 15/30 (50%)
Query: 153 GSKLGGKRVGIVGLGSIGSEVAKRLEAFGC 182
L GK+V ++G G + AK L + G
Sbjct: 7 FGDLKGKKVLLIGAGEMARLAAKHLLSKGA 36
>gnl|CDD|216949 pfam02254, TrkA_N, TrkA-N domain. This domain is found in a wide
variety of proteins. These protein include potassium
channels, phosphoesterases, and various other
transporters. This domain binds to NAD.
Length = 116
Score = 26.8 bits (60), Expect = 7.4
Identities = 17/74 (22%), Positives = 26/74 (35%), Gaps = 17/74 (22%)
Query: 163 IVGLGSIGSEVAKRLEAFGCCVSYNSRNKKPSVTYPFYPDVCELAANSDVLIICCALTDQ 222
I+G G +G +A+ L G V V P+ E V ++ TD+
Sbjct: 3 IIGYGRVGRSLAEELREGGPDV----------VVIDKDPERVEELREEGVPVVVGDATDE 52
Query: 223 THHLINKQVLLALG 236
+VL G
Sbjct: 53 -------EVLEEAG 59
>gnl|CDD|240258 PTZ00075, PTZ00075, Adenosylhomocysteinase; Provisional.
Length = 476
Score = 28.1 bits (63), Expect = 7.5
Identities = 11/29 (37%), Positives = 15/29 (51%)
Query: 156 LGGKRVGIVGLGSIGSEVAKRLEAFGCCV 184
+ GK V + G G +G A+ L FG V
Sbjct: 252 IAGKTVVVCGYGDVGKGCAQALRGFGARV 280
>gnl|CDD|193585 cd08824, LOTUS, LOTUS is an uncharacterized small globular domain
found in Limkain b1, Oskar and Tudor-containing
proteins 5 and 7. LOTUS is an uncharacterized small
globular domain found in Limkain b1, Oskar and
Tudor-containing proteins 5 and 7. The LOTUS containing
proteins are germline-specific and are found in the
nuage/polar granules of germ cells. Tudor-containing
protein 5 and 7 belong to the evolutionary conserved
Tudor domain-containing protein (TDRD) family involved
in germ cell development. In mice, TDRD5 and TDRD7 are
components of the intermitochondrial cements (IMCs) and
the chromatoid bodies (CBs), which are cytoplasmic
ribonucleoprotein granules involved in RNA processing
for spermatogenesis. Oskar protein is a critical
component of the pole plasm in the Drosophila oocyte,
which is required for germ cell formation. Limkain b1
is a novel human autoantigen, localized to a subset of
ABCD3 and PXF marked peroxisomes. Limkain b1 may be a
relatively common target of human autoantibodies
reactive to cytoplasmic vesicle-like structures.
Limkain b1 contains multiple copies of LOTUS domains
and a conserved RNA recognition motif. The exact
molecular function of LOTUS domain remains to be
characterized. Its occurrence in proteins associated
with RNA metabolism suggests that it might be involved
in RNA binding function. The presence of several basic
residues and RNA fold recognition motifs support this
hypothesis. The RNA binding function might be the first
step of regulating mRNA translation or localization.
Length = 70
Score = 26.0 bits (58), Expect = 7.7
Identities = 13/48 (27%), Positives = 21/48 (43%), Gaps = 2/48 (4%)
Query: 39 LKAYESALPLHEFLTLHAHSVKAIF--SSAGAPVTAEILRLLPEVRLV 84
L++Y LPL + L+ S G +++L LP V +V
Sbjct: 12 LQSYPGGLPLSKLPQLYKKKFGKPLDLSEYGFSKLSDLLEALPGVVIV 59
>gnl|CDD|224996 COG2085, COG2085, Predicted dinucleotide-binding enzymes [General
function prediction only].
Length = 211
Score = 27.7 bits (62), Expect = 8.3
Identities = 12/32 (37%), Positives = 16/32 (50%)
Query: 159 KRVGIVGLGSIGSEVAKRLEAFGCCVSYNSRN 190
+ I+G G+IGS +A RL G V S
Sbjct: 2 MIIAIIGTGNIGSALALRLAKAGHEVIIGSSR 33
>gnl|CDD|215382 PLN02712, PLN02712, arogenate dehydrogenase.
Length = 667
Score = 28.0 bits (62), Expect = 8.3
Identities = 19/67 (28%), Positives = 37/67 (55%), Gaps = 9/67 (13%)
Query: 160 RVGIVGLGSIGSEVAKRLEAFGCCVSYNSRN------KKPSVTYPFYP-DVCELAANSDV 212
++ I+G G+ G +AK L + G V +SR+ + V++ P D+CE + DV
Sbjct: 54 KIAIIGFGNYGQFLAKTLISQGHTVLAHSRSDHSLAARSLGVSFFLDPHDLCE--RHPDV 111
Query: 213 LIICCAL 219
+++C ++
Sbjct: 112 ILLCTSI 118
>gnl|CDD|232919 TIGR00322, diphth2_R, diphthamide biosynthesis enzyme Dph1/Dph2
domain. Archaea and Eukaryotes, but not Eubacteria,
share the property of having a covalently modified
residue,
2'-[3-carboxamido-3-(trimethylammonio)propyl]histidine,
as a part of a cytosolic protein. The modified His,
termed diphthamide, is part of translation elongation
factor EF-2 and is the site for ADP-ribosylation by
diphtheria toxin. This model includes both Dph1 and Dph2
from Saccharomyces cerevisiae, although only Dph2 is
found in the Archaea (see TIGR03682). Dph2 has been
shown to act analogously to the radical SAM (rSAM)
family (pfam04055), with 4Fe-4S-assisted cleavage of
S-adenosylmethionine to create a free radical, but a
different organic radical than in rSAM.
Length = 319
Score = 27.6 bits (62), Expect = 8.9
Identities = 13/46 (28%), Positives = 24/46 (52%), Gaps = 2/46 (4%)
Query: 215 ICCALTDQTHHLIN--KQVLLALGKKGVIINVGRGAIIDEKEMVGC 258
I T Q H ++ K++L G + VII G+ ++ +++GC
Sbjct: 119 IALVTTVQYIHALDEVKKILEEAGYEPVIIPQGKPRVLSPGQVLGC 164
>gnl|CDD|183114 PRK11388, PRK11388, DNA-binding transcriptional regulator DhaR;
Provisional.
Length = 638
Score = 27.7 bits (62), Expect = 9.1
Identities = 10/44 (22%), Positives = 22/44 (50%), Gaps = 2/44 (4%)
Query: 64 SSAGAPVTAEILRLLPEVRLVVATSAGLNHIDV-VECRRRGVAL 106
+S G +T E+L L ++ + + L H++V E + + +
Sbjct: 242 ASQGRAIT-ELLTLPAVLQQAIKQAHPLKHVEVTFESQGQFIDA 284
>gnl|CDD|201664 pfam01210, NAD_Gly3P_dh_N, NAD-dependent glycerol-3-phosphate
dehydrogenase N-terminus. NAD-dependent
glycerol-3-phosphate dehydrogenase (GPDH) catalyzes the
interconversion of dihydroxyacetone phosphate and
L-glycerol-3-phosphate. This family represents the
N-terminal NAD-binding domain.
Length = 157
Score = 27.2 bits (61), Expect = 9.2
Identities = 23/102 (22%), Positives = 42/102 (41%), Gaps = 22/102 (21%)
Query: 160 RVGIVGLGSIGSEVAKRLEAFGCCVSYNSRNKK---------------PSVTYP----FY 200
++ ++G GS G+ +AK L G V R+++ P + P
Sbjct: 1 KIAVLGAGSWGTALAKVLARNGHEVRLWGRDEELIEEINTTRENVKYLPGIKLPDNLRAT 60
Query: 201 PDVCELAANSDVLIICCALTDQTHHLINKQVLLALGKKGVII 242
D+ E +D++++ A+ Q + KQ L L G I+
Sbjct: 61 TDLEEAIKGADIIVL--AVPSQALREVLKQ-LKGLLSPGAIL 99
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
0.323 0.139 0.413
Gapped
Lambda K H
0.267 0.0864 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 17,150,430
Number of extensions: 1707558
Number of successful extensions: 2174
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1987
Number of HSP's successfully gapped: 172
Length of query: 330
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 233
Effective length of database: 6,635,264
Effective search space: 1546016512
Effective search space used: 1546016512
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 59 (26.3 bits)