RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13054
(1128 letters)
>gnl|CDD|240626 cd05301, GDH, D-glycerate dehydrogenase/hydroxypyruvate reductase
(GDH). D-glycerate dehydrogenase (GDH, also known as
hydroxypyruvate reductase, HPR) catalyzes the reversible
reaction of (R)-glycerate + NAD+ to hydroxypyruvate +
NADH + H+. In humans, HPR deficiency causes primary
hyperoxaluria type 2, characterized by over-excretion of
L-glycerate and oxalate in the urine, possibly due to an
imbalance in competition with L-lactate dehydrogenase,
another formate dehydrogenase (FDH)-like enzyme. GDH,
like FDH and other members of the D-specific hydroxyacid
dehydrogenase family that also includes L-alanine
dehydrogenase and S-adenosylhomocysteine hydrolase,
typically have a characteristic arrangement of 2 similar
subdomains of the alpha/beta Rossmann-fold NAD+ binding
form, despite often low sequence identity. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD is
bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of the
catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 309
Score = 313 bits (805), Expect = 4e-98
Identities = 118/249 (47%), Positives = 157/249 (63%), Gaps = 6/249 (2%)
Query: 875 NLKVITTFSVGYDHLELHEIKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRFQEGRKCI 934
LKVI +SVGYDH+++ KARGI V + + +D A+ L +A +RR EG + +
Sbjct: 65 PLKVIANYSVGYDHIDVDAAKARGIPVTNTPDVLTDATADLAFALLLAAARRVVEGDRFV 124
Query: 935 TSGEW-ALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSR-RVKE 992
+GEW T ++G L G T+GIVG+G IG A+ K F + KILY +R R E
Sbjct: 125 RAGEWKGWSPTLLLG---TDLHGKTLGIVGMGRIGQAVARRAKGFGM-KILYHNRSRKPE 180
Query: 993 EGTALGAQLVPLDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILVNTSRGGLLD 1052
LGA+ V LD L AESDF+ + C LT +T LI ++ +LMKPTAIL+NT+RGG++D
Sbjct: 181 AEEELGARYVSLDELLAESDFVSLHCPLTPETRHLINAERLALMKPTAILINTARGGVVD 240
Query: 1053 QEALVEFLKDKKIGGAGLDVMIPEPLPADHPLVQLDNCVLTPHTSSATKAVRDEKSSTSA 1112
++ALVE LK KI GAGLDV PEPLPADHPL+ L N VL PH SAT R + +A
Sbjct: 241 EDALVEALKSGKIAGAGLDVFEPEPLPADHPLLTLPNVVLLPHIGSATVETRTAMAELAA 300
Query: 1113 ENIIRGYKG 1121
+N++ G
Sbjct: 301 DNLLAVLAG 309
Score = 162 bits (414), Expect = 2e-44
Identities = 71/227 (31%), Positives = 108/227 (47%), Gaps = 50/227 (22%)
Query: 515 PKLFLTRDDYSRVP--AFEILGEMFDIITYPASEGQIPRDIFIEKLRGCSALLCTSRDRV 572
PK+ +TR R+P A +L E F++ + + +PR+ +E +G LLCT D++
Sbjct: 1 PKVLVTR----RLPEEALALLREGFEVEVWD-EDRPLPREELLEAAKGADGLLCTLTDKI 55
Query: 573 DKQVLDESGGYRCTEDFFGLDLDQMFRNPSKRHVNIETVLGVSFLIKNLKVITTFSVGYD 632
D ++LD + LKVI +SVGYD
Sbjct: 56 DAELLDAAP--------------------------------------PLKVIANYSVGYD 77
Query: 633 HLELHEIKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRFQEGRKCITSGEW-ALKQTHI 691
H+++ KARGI V + + +D A+ L +A +RR EG + + +GEW T +
Sbjct: 78 HIDVDAAKARGIPVTNTPDVLTDATADLAFALLLAAARRVVEGDRFVRAGEWKGWSPTLL 137
Query: 692 IGPNIMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRRVKEE 738
+G L G T+GIVG+G IG A+ K F + KILY +R K E
Sbjct: 138 LG---TDLHGKTLGIVGMGRIGQAVARRAKGFGM-KILYHNRSRKPE 180
Score = 162 bits (412), Expect = 4e-44
Identities = 59/95 (62%), Positives = 72/95 (75%)
Query: 306 ALGAQLVPLDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEA 365
LGA+ V LD L AESDF+ + C LT +T LI ++ +LMKPTAILINT+RGG++D++A
Sbjct: 184 ELGARYVSLDELLAESDFVSLHCPLTPETRHLINAERLALMKPTAILINTARGGVVDEDA 243
Query: 366 LVEFLKDKKIGGAGLDVMIPEPLPADHPLVQLDNC 400
LVE LK KI GAGLDV PEPLPADHPL+ L N
Sbjct: 244 LVEALKSGKIAGAGLDVFEPEPLPADHPLLTLPNV 278
Score = 111 bits (280), Expect = 1e-26
Identities = 44/124 (35%), Positives = 70/124 (56%), Gaps = 6/124 (4%)
Query: 40 SRLLVPESLSKLRFNSRFDIDTYPVSEGRMPRDIFIEKLKGCSALLCNPHQKVDKEVLDR 99
+R L E+L+ LR F+++ + + +PR+ +E KG LLC K+D E+LD
Sbjct: 6 TRRLPEEALALLR--EGFEVEVWD-EDRPLPREELLEAAKGADGLLCTLTDKIDAELLDA 62
Query: 100 SGENLKVIATFSVGHDHLHLDEIKSRGIRVG-TVGPVSSDTVAEYNIGLAIAVSRRFQQR 158
+ LKVIA +SVG+DH+ +D K+RGI V T V +D A+ L +A +RR +
Sbjct: 63 AP-PLKVIANYSVGYDHIDVDAAKARGIPVTNTPD-VLTDATADLAFALLLAAARRVVEG 120
Query: 159 HNWI 162
++
Sbjct: 121 DRFV 124
Score = 58.9 bits (144), Expect = 4e-09
Identities = 23/55 (41%), Positives = 31/55 (56%), Gaps = 5/55 (9%)
Query: 812 NGEW-ALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRN 865
GEW T ++G L G T+GIVG+G IG A+ K F + KILY +R+
Sbjct: 126 AGEWKGWSPTLLLG---TDLHGKTLGIVGMGRIGQAVARRAKGFGM-KILYHNRS 176
>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 = 266 bits (682), Expect = 6e-81
Identities = 105/251 (41%), Positives = 147/251 (58%), Gaps = 6/251 (2%)
Query: 868 KTPKRTENLKVITTFSVGYDHLELHEIKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRF 927
+ + LK I G D+++L K RGI V +V +++ VAE+ +GL +A+ RR
Sbjct: 56 EVLAKAPKLKFIQVAGAGVDNIDLDAAKKRGITVTNVPGANAEAVAEHALGLLLALLRRL 115
Query: 928 QEGRKCITSGEWALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTS 987
+ G L L+G TVGIVGLG IG AK L+AF + K+LY
Sbjct: 116 PRADAAVRRGWGWLWAGFPGY----ELEGKTVGIVGLGRIGQRVAKRLQAFGM-KVLYYD 170
Query: 988 RRVKEEGTA-LGAQLVPLDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILVNTS 1046
R K E LG ++V LD L A+SD + + LT +T LI ++ +LMKP A+LVNT+
Sbjct: 171 RTRKPEPEEDLGFRVVSLDELLAQSDVVVLHLPLTPETRHLINEEELALMKPGAVLVNTA 230
Query: 1047 RGGLLDQEALVEFLKDKKIGGAGLDVMIPEPLPADHPLVQLDNCVLTPHTSSATKAVRDE 1106
RGGL+D++AL+ LK KI GA LDV PEPLPADHPL++L N +LTPH + T+ R+
Sbjct: 231 RGGLVDEDALLRALKSGKIAGAALDVFEPEPLPADHPLLELPNVILTPHIAGYTEEARER 290
Query: 1107 KSSTSAENIIR 1117
+ + EN+ R
Sbjct: 291 MAEIAVENLER 301
Score = 133 bits (336), Expect = 3e-34
Identities = 50/94 (53%), Positives = 68/94 (72%)
Query: 307 LGAQLVPLDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEAL 366
LG ++V LD L A+SD + + LT +T LI ++ +LMKP A+L+NT+RGGL+D++AL
Sbjct: 181 LGFRVVSLDELLAQSDVVVLHLPLTPETRHLINEEELALMKPGAVLVNTARGGLVDEDAL 240
Query: 367 VEFLKDKKIGGAGLDVMIPEPLPADHPLVQLDNC 400
+ LK KI GA LDV PEPLPADHPL++L N
Sbjct: 241 LRALKSGKIAGAALDVFEPEPLPADHPLLELPNV 274
Score = 119 bits (300), Expect = 2e-29
Identities = 55/202 (27%), Positives = 78/202 (38%), Gaps = 47/202 (23%)
Query: 537 FDIITYPASEGQIPRDIFIEKLRGCSALLCTSRDRVDKQVLDESGGYRCTEDFFGLDLDQ 596
F++I D L AL+ +S V +VL ++
Sbjct: 22 FEVIVADDLLA----DELEALLADADALIVSSTTPVTAEVLAKA---------------- 61
Query: 597 MFRNPSKRHVNIETVLGVSFLIKNLKVITTFSVGYDHLELHEIKARGIRVGSVGHISSDT 656
LK I G D+++L K RGI V +V +++
Sbjct: 62 ----------------------PKLKFIQVAGAGVDNIDLDAAKKRGITVTNVPGANAEA 99
Query: 657 VAEYNIGLAIAVSRRFQEGRKCITSGEWALKQTHIIGPNIMGLKGATVGIVGLGNIGLET 716
VAE+ +GL +A+ RR + G L L+G TVGIVGLG IG
Sbjct: 100 VAEHALGLLLALLRRLPRADAAVRRGWGWLWAGFPGY----ELEGKTVGIVGLGRIGQRV 155
Query: 717 AKLLKAFKVSKILYTSRRVKEE 738
AK L+AF + K+LY R K E
Sbjct: 156 AKRLQAFGM-KVLYYDRTRKPE 176
Score = 80.0 bits (198), Expect = 5e-16
Identities = 35/126 (27%), Positives = 55/126 (43%), Gaps = 2/126 (1%)
Query: 41 RLLVPESLSKLRFNSRFDIDTYPV-SEGRMPRDIFIEKLKGCSALLCNPHQKVDKEVLDR 99
++LV E L + + V + D L AL+ + V EVL +
Sbjct: 1 KVLVLEPLFPPEALEALEATGFEVIVADDLLADELEALLADADALIVSSTTPVTAEVLAK 60
Query: 100 SGENLKVIATFSVGHDHLHLDEIKSRGIRVGTVGPVSSDTVAEYNIGLAIAVSRRFQQRH 159
+ LK I G D++ LD K RGI V V +++ VAE+ +GL +A+ RR +
Sbjct: 61 A-PKLKFIQVAGAGVDNIDLDAAKKRGITVTNVPGANAEAVAEHALGLLLALLRRLPRAD 119
Query: 160 NWIARL 165
+ R
Sbjct: 120 AAVRRG 125
Score = 51.1 bits (123), Expect = 1e-06
Identities = 25/69 (36%), Positives = 34/69 (49%), Gaps = 5/69 (7%)
Query: 812 NGEWALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRNKVKTPK 871
G L L+G TVGIVGLG IG AK L+AF + K+LY R + P+
Sbjct: 124 RGWGWLWAGFPGY----ELEGKTVGIVGLGRIGQRVAKRLQAFGM-KVLYYDRTRKPEPE 178
Query: 872 RTENLKVIT 880
+V++
Sbjct: 179 EDLGFRVVS 187
>gnl|CDD|223980 COG1052, LdhA, Lactate dehydrogenase and related dehydrogenases
[Energy production and conversion / Coenzyme metabolism /
General function prediction only].
Length = 324
Score = 262 bits (672), Expect = 3e-79
Identities = 112/259 (43%), Positives = 158/259 (61%), Gaps = 10/259 (3%)
Query: 871 KRTENLKVITTFSVGYDHLELHEIKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRFQEG 930
++ LK+I T S GYD+++L K RGI V +V S++ VAE+ + L +A++RR EG
Sbjct: 62 EKLPGLKLIATRSAGYDNVDLEAAKERGITVTNVPGYSTEAVAEHAVALILALARRIHEG 121
Query: 931 RKCITSGEWAL--KQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSR 988
+ + G W+L ++G ++ G T+GI+GLG IG A+ LK F + K+LY R
Sbjct: 122 DRRVREGNWSLSGGPDPLLGFDLRGK---TLGIIGLGRIGQAVARRLKGFGM-KVLYYDR 177
Query: 989 -RVKEEGTALGAQLVPLDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILVNTSR 1047
E LGA+ V LD L AESD I + C LT +T LI ++ + MKP AILVNT+R
Sbjct: 178 SPNPEAEKELGARYVDLDELLAESDIISLHCPLTPETRHLINAEELAKMKPGAILVNTAR 237
Query: 1048 GGLLDQEALVEFLKDKKIGGAGLDVMIPEPLPADHPLVQLDNC---VLTPHTSSATKAVR 1104
GGL+D++AL++ LK KI GAGLDV EP DHPL++LDN VLTPH +SAT+ R
Sbjct: 238 GGLVDEQALIDALKSGKIAGAGLDVFENEPALFDHPLLRLDNFPNVVLTPHIASATEEAR 297
Query: 1105 DEKSSTSAENIIRGYKGEP 1123
+ + EN+ + G
Sbjct: 298 KAMAELALENLEAFFDGGV 316
Score = 134 bits (339), Expect = 3e-34
Identities = 52/94 (55%), Positives = 67/94 (71%)
Query: 307 LGAQLVPLDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEAL 366
LGA+ V LD L AESD I + C LT +T LI ++ + MKP AIL+NT+RGGL+D++AL
Sbjct: 187 LGARYVDLDELLAESDIISLHCPLTPETRHLINAEELAKMKPGAILVNTARGGLVDEQAL 246
Query: 367 VEFLKDKKIGGAGLDVMIPEPLPADHPLVQLDNC 400
++ LK KI GAGLDV EP DHPL++LDN
Sbjct: 247 IDALKSGKIAGAGLDVFENEPALFDHPLLRLDNF 280
Score = 124 bits (314), Expect = 5e-31
Identities = 65/227 (28%), Positives = 100/227 (44%), Gaps = 48/227 (21%)
Query: 514 KPKLFLTRDDYSRVPAFEILGEMFDIITYPASEGQIPRDIFIEKLRGCSALLCTSRDRVD 573
K + TR E L E F++ Y P E+L+ A++ DR+D
Sbjct: 2 KIVVLSTRK-LPP-EVLERLKEKFEVERYEDDLT--PDTELAERLKDADAVITFVNDRID 57
Query: 574 KQVLDESGGYRCTEDFFGLDLDQMFRNPSKRHVNIETVLGVSFLIKNLKVITTFSVGYDH 633
+VL+ + P LK+I T S GYD+
Sbjct: 58 AEVLE--------------------KLP------------------GLKLIATRSAGYDN 79
Query: 634 LELHEIKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRFQEGRKCITSGEWAL--KQTHI 691
++L K RGI V +V S++ VAE+ + L +A++RR EG + + G W+L +
Sbjct: 80 VDLEAAKERGITVTNVPGYSTEAVAEHAVALILALARRIHEGDRRVREGNWSLSGGPDPL 139
Query: 692 IGPNIMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRRVKEE 738
+G ++ G T+GI+GLG IG A+ LK F + K+LY R E
Sbjct: 140 LGFDLRGK---TLGIIGLGRIGQAVARRLKGFGM-KVLYYDRSPNPE 182
Score = 88.4 bits (220), Expect = 9e-19
Identities = 39/123 (31%), Positives = 68/123 (55%), Gaps = 5/123 (4%)
Query: 40 SRLLVPESLSKLRFNSRFDIDTYPVSEGRMPRDIFIEKLKGCSALLCNPHQKVDKEVLDR 99
+R L PE L +L+ +F+++ Y E+LK A++ + ++D EVL++
Sbjct: 8 TRKLPPEVLERLKE--KFEVERYEDDLTPDT--ELAERLKDADAVITFVNDRIDAEVLEK 63
Query: 100 SGENLKVIATFSVGHDHLHLDEIKSRGIRVGTVGPVSSDTVAEYNIGLAIAVSRRFQQRH 159
LK+IAT S G+D++ L+ K RGI V V S++ VAE+ + L +A++RR +
Sbjct: 64 -LPGLKLIATRSAGYDNVDLEAAKERGITVTNVPGYSTEAVAEHAVALILALARRIHEGD 122
Query: 160 NWI 162
+
Sbjct: 123 RRV 125
Score = 53.0 bits (128), Expect = 4e-07
Identities = 21/58 (36%), Positives = 32/58 (55%), Gaps = 6/58 (10%)
Query: 810 TINGEWAL--KQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRN 865
G W+L ++G ++ G T+GI+GLG IG A+ LK F + K+LY R+
Sbjct: 125 VREGNWSLSGGPDPLLGFDLRGK---TLGIIGLGRIGQAVARRLKGFGM-KVLYYDRS 178
>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 = 258 bits (662), Expect = 5e-78
Identities = 104/252 (41%), Positives = 148/252 (58%), Gaps = 7/252 (2%)
Query: 874 ENLKVITTFSVGYDHLELHEIKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRFQEGRKC 933
L++I VG D ++L ARGI V ++ ++++VAE+ + L +A+ RR E +
Sbjct: 64 PRLRLIQQPGVGLDGVDLEAATARGIPVANIPGGNAESVAEHAVMLMLALLRRLPEADRE 123
Query: 934 ITSGEWALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRRVK-- 991
+ +G W + G L G TVGIVGLGNIG A+ L+ F V +++Y R
Sbjct: 124 LRAGRWGRPE----GRPSRELSGKTVGIVGLGNIGRAVARRLRGFGV-EVIYYDRFRDPE 178
Query: 992 EEGTALGAQLVPLDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILVNTSRGGLL 1051
E LG + V LD L AESD + + LT +T LIG ++ + MKP AIL+NT+RGGL+
Sbjct: 179 AEEKDLGVRYVELDELLAESDVVSLHVPLTPETRHLIGAEELAAMKPGAILINTARGGLV 238
Query: 1052 DQEALVEFLKDKKIGGAGLDVMIPEPLPADHPLVQLDNCVLTPHTSSATKAVRDEKSSTS 1111
D+EAL+ L+ + GAGLDV EPLP D PL++LDN +LTPH + T ++
Sbjct: 239 DEEALLAALRSGHLAGAGLDVFWQEPLPPDDPLLRLDNVILTPHIAGVTDESYQRMAAIV 298
Query: 1112 AENIIRGYKGEP 1123
AENI R +GEP
Sbjct: 299 AENIARLLRGEP 310
Score = 138 bits (349), Expect = 9e-36
Identities = 50/102 (49%), Positives = 66/102 (64%)
Query: 298 WFERSNGTALGAQLVPLDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSR 357
+ LG + V LD L AESD + + LT +T LIG ++ + MKP AILINT+R
Sbjct: 175 RDPEAEEKDLGVRYVELDELLAESDVVSLHVPLTPETRHLIGAEELAAMKPGAILINTAR 234
Query: 358 GGLLDQEALVEFLKDKKIGGAGLDVMIPEPLPADHPLVQLDN 399
GGL+D+EAL+ L+ + GAGLDV EPLP D PL++LDN
Sbjct: 235 GGLVDEEALLAALRSGHLAGAGLDVFWQEPLPPDDPLLRLDN 276
Score = 106 bits (268), Expect = 4e-25
Identities = 42/121 (34%), Positives = 65/121 (53%), Gaps = 5/121 (4%)
Query: 619 KNLKVITTFSVGYDHLELHEIKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRFQEGRKC 678
L++I VG D ++L ARGI V ++ ++++VAE+ + L +A+ RR E +
Sbjct: 64 PRLRLIQQPGVGLDGVDLEAATARGIPVANIPGGNAESVAEHAVMLMLALLRRLPEADRE 123
Query: 679 ITSGEWALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRRVKEE 738
+ +G W + G L G TVGIVGLGNIG A+ L+ F V +++Y R E
Sbjct: 124 LRAGRWGRPE----GRPSRELSGKTVGIVGLGNIGRAVARRLRGFGV-EVIYYDRFRDPE 178
Query: 739 G 739
Sbjct: 179 A 179
Score = 57.2 bits (139), Expect = 2e-08
Identities = 22/53 (41%), Positives = 28/53 (52%), Gaps = 5/53 (9%)
Query: 812 NGEWALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSR 864
G W + G L G TVGIVGLGNIG A+ L+ F V +++Y R
Sbjct: 126 AGRWGRPE----GRPSRELSGKTVGIVGLGNIGRAVARRLRGFGV-EVIYYDR 173
Score = 54.5 bits (132), Expect = 1e-07
Identities = 25/106 (23%), Positives = 46/106 (43%), Gaps = 7/106 (6%)
Query: 49 SKLRFNSRFDIDTYPVSEGRMPRDIFIEKLKGCSALLCNPHQKVDKEVLDRSGENLKVIA 108
+ L ++ T D L L+ + +D E+L L++I
Sbjct: 18 ALLPPAPGVEVVTAA------ELDEEAALLADADVLVPGMRKVIDAELLAA-APRLRLIQ 70
Query: 109 TFSVGHDHLHLDEIKSRGIRVGTVGPVSSDTVAEYNIGLAIAVSRR 154
VG D + L+ +RGI V + ++++VAE+ + L +A+ RR
Sbjct: 71 QPGVGLDGVDLEAATARGIPVANIPGGNAESVAEHAVMLMLALLRR 116
>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 = 254 bits (652), Expect = 1e-76
Identities = 99/249 (39%), Positives = 143/249 (57%), Gaps = 11/249 (4%)
Query: 871 KRTENLKVITTFSVGYDHLELHEIKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRFQEG 930
LKVI+ + VGYD+++L K RGI V + +S++VAE IGL +A++R+ +
Sbjct: 64 AAAPRLKVISRYGVGYDNIDLEAAKKRGIVVTNTPGANSNSVAELTIGLMLALARQIPQA 123
Query: 931 RKCITSGEWALKQTHIIGPNIMG--LKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSR 988
+ + +G W +G L G T+GI+GLG IG A+ L F + + Y
Sbjct: 124 DREVRAGGW---------DRPVGTELYGKTLGIIGLGRIGKAVARRLSGFGMKVLAYDPY 174
Query: 989 RVKEEGTALGAQLVPLDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILVNTSRG 1048
+E G + V L+ L ESDFI + LT +T LI + +LMKP AIL+NT+RG
Sbjct: 175 PDEEFAKEHGVEFVSLEELLKESDFISLHLPLTPETRHLINAAELALMKPGAILINTARG 234
Query: 1049 GLLDQEALVEFLKDKKIGGAGLDVMIPEPLPADHPLVQLDNCVLTPHTSSATKAVRDEKS 1108
GL+D+EAL E LK +I GA LDV EP PAD PL++L N +LTPH ++TK
Sbjct: 235 GLVDEEALYEALKSGRIAGAALDVFEEEPPPADSPLLELPNVILTPHIGASTKEAVLRMG 294
Query: 1109 STSAENIIR 1117
+ +A+N+I
Sbjct: 295 TMAAQNVID 303
Score = 140 bits (356), Expect = 1e-36
Identities = 50/95 (52%), Positives = 62/95 (65%)
Query: 306 ALGAQLVPLDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEA 365
G + V L+ L ESDFI + LT +T LI + +LMKP AILINT+RGGL+D+EA
Sbjct: 182 EHGVEFVSLEELLKESDFISLHLPLTPETRHLINAAELALMKPGAILINTARGGLVDEEA 241
Query: 366 LVEFLKDKKIGGAGLDVMIPEPLPADHPLVQLDNC 400
L E LK +I GA LDV EP PAD PL++L N
Sbjct: 242 LYEALKSGRIAGAALDVFEEEPPPADSPLLELPNV 276
Score = 102 bits (257), Expect = 1e-23
Identities = 57/232 (24%), Positives = 97/232 (41%), Gaps = 57/232 (24%)
Query: 510 KIMSKPKLFLTRDDYSRVPAFEILGEM-FDIITYPASEGQIPRDIFIEKLRGCSALLCTS 568
K++ P+ F + A E+L F+++ P + + IE L+ ++
Sbjct: 1 KVLVTPRSFSKYSE----EAKELLEAAGFEVVLNP-LGRPLTEEELIELLKDADGVI-AG 54
Query: 569 RDRVDKQVLDESGGYRCTEDFFGLDLDQMFRNPSKRHVNIETVLGVSFLIKNLKVITTFS 628
D + ++VL + LKVI+ +
Sbjct: 55 LDPITEEVLAAA--------------------------------------PRLKVISRYG 76
Query: 629 VGYDHLELHEIKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRFQEGRKCITSGEWALKQ 688
VGYD+++L K RGI V + +S++VAE IGL +A++R+ + + + +G W
Sbjct: 77 VGYDNIDLEAAKKRGIVVTNTPGANSNSVAELTIGLMLALARQIPQADREVRAGGW---- 132
Query: 689 THIIGPNIMG--LKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRRVKEE 738
+G L G T+GI+GLG IG A+ L F + K+L EE
Sbjct: 133 -----DRPVGTELYGKTLGIIGLGRIGKAVARRLSGFGM-KVLAYDPYPDEE 178
Score = 73.7 bits (182), Expect = 6e-14
Identities = 30/100 (30%), Positives = 49/100 (49%), Gaps = 2/100 (2%)
Query: 61 TYPVSEGRMPRDIFIEKLKGCSALLCNPHQKVDKEVLDRSGENLKVIATFSVGHDHLHLD 120
+ + IE LK ++ + +EVL LKVI+ + VG+D++ L+
Sbjct: 28 VLNPLGRPLTEEELIELLKDADGVIAG-LDPITEEVLAA-APRLKVISRYGVGYDNIDLE 85
Query: 121 EIKSRGIRVGTVGPVSSDTVAEYNIGLAIAVSRRFQQRHN 160
K RGI V +S++VAE IGL +A++R+ Q
Sbjct: 86 AAKKRGIVVTNTPGANSNSVAELTIGLMLALARQIPQADR 125
Score = 49.0 bits (118), Expect = 7e-06
Identities = 18/68 (26%), Positives = 28/68 (41%), Gaps = 12/68 (17%)
Query: 812 NGEWALKQTHIIGPNIMG--LKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRNKVKT 869
G W +G L G T+GI+GLG IG A+ L F + K+L +
Sbjct: 129 AGGW---------DRPVGTELYGKTLGIIGLGRIGKAVARRLSGFGM-KVLAYDPYPDEE 178
Query: 870 PKRTENLK 877
+ ++
Sbjct: 179 FAKEHGVE 186
>gnl|CDD|223189 COG0111, SerA, Phosphoglycerate dehydrogenase and related
dehydrogenases [Amino acid transport and metabolism].
Length = 324
Score = 247 bits (632), Expect = 1e-73
Identities = 105/283 (37%), Positives = 144/283 (50%), Gaps = 8/283 (2%)
Query: 844 GLETAKLLKAFKVSKILYTSRNKVK--TPKRTENLKVITTFSVGYDHLELHEIKARGIRV 901
L+ +LL+A + L S V NLK I G D+++L RGI V
Sbjct: 33 DLDEEELLEALADADALIVSVTPVTEEVLAAAPNLKAIGRAGAGVDNIDLEAATKRGILV 92
Query: 902 GSVGHISSDTVAEYNIGLAIAVSRRFQEGRKCITSGEWALKQTHIIGPNIMGLKGATVGI 961
+ ++ +VAE + L +A++RR + GEW K L G TVGI
Sbjct: 93 VNAPGGNAISVAELVLALLLALARRIPDADASQRRGEWDRKAFRGTE-----LAGKTVGI 147
Query: 962 VGLGNIGLETAKLLKAFKVSKILYTSRRVKEEGTALGAQLVP-LDTLCAESDFIFVTCAL 1020
+GLG IG AK LKAF + I Y +E G V LD L AE+D + + L
Sbjct: 148 IGLGRIGRAVAKRLKAFGMKVIGYDPYSPRERAGVDGVVGVDSLDELLAEADILTLHLPL 207
Query: 1021 TKDTEQLIGRKQFSLMKPTAILVNTSRGGLLDQEALVEFLKDKKIGGAGLDVMIPEPLPA 1080
T +T LI ++ + MKP AIL+N +RGG++D++AL+ L KI GA LDV EPLPA
Sbjct: 208 TPETRGLINAEELAKMKPGAILINAARGGVVDEDALLAALDSGKIAGAALDVFEEEPLPA 267
Query: 1081 DHPLVQLDNCVLTPHTSSATKAVRDEKSSTSAENIIRGYKGEP 1123
D PL L N +LTPH +T ++ + AENI+R G P
Sbjct: 268 DSPLWDLPNVILTPHIGGSTDEAQERVAEIVAENIVRYLAGGP 310
Score = 129 bits (326), Expect = 1e-32
Identities = 43/92 (46%), Positives = 57/92 (61%)
Query: 308 GAQLVPLDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALV 367
+ LD L AE+D + + LT +T LI ++ + MKP AILIN +RGG++D++AL+
Sbjct: 185 VVGVDSLDELLAEADILTLHLPLTPETRGLINAEELAKMKPGAILINAARGGVVDEDALL 244
Query: 368 EFLKDKKIGGAGLDVMIPEPLPADHPLVQLDN 399
L KI GA LDV EPLPAD PL L N
Sbjct: 245 AALDSGKIAGAALDVFEEEPLPADSPLWDLPN 276
Score = 96.6 bits (241), Expect = 2e-21
Identities = 42/128 (32%), Positives = 58/128 (45%), Gaps = 6/128 (4%)
Query: 619 KNLKVITTFSVGYDHLELHEIKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRFQEGRKC 678
NLK I G D+++L RGI V + ++ +VAE + L +A++RR +
Sbjct: 65 PNLKAIGRAGAGVDNIDLEAATKRGILVVNAPGGNAISVAELVLALLLALARRIPDADAS 124
Query: 679 ITSGEWALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRRVKEE 738
GEW K L G TVGI+GLG IG AK LKAF + K++ E
Sbjct: 125 QRRGEWDRKAFRGT-----ELAGKTVGIIGLGRIGRAVAKRLKAFGM-KVIGYDPYSPRE 178
Query: 739 GQLFSLVY 746
V
Sbjct: 179 RAGVDGVV 186
Score = 67.0 bits (164), Expect = 1e-11
Identities = 27/95 (28%), Positives = 42/95 (44%), Gaps = 2/95 (2%)
Query: 70 PRDIFIEKLKGCSALLCNPHQKVDKEVLDRSGENLKVIATFSVGHDHLHLDEIKSRGIRV 129
+ +E L AL+ + V +EVL NLK I G D++ L+ RGI V
Sbjct: 35 DEEELLEALADADALIVSV-TPVTEEVLAA-APNLKAIGRAGAGVDNIDLEAATKRGILV 92
Query: 130 GTVGPVSSDTVAEYNIGLAIAVSRRFQQRHNWIAR 164
++ +VAE + L +A++RR R
Sbjct: 93 VNAPGGNAISVAELVLALLLALARRIPDADASQRR 127
Score = 47.7 bits (114), Expect = 2e-05
Identities = 23/50 (46%), Positives = 25/50 (50%), Gaps = 5/50 (10%)
Query: 812 NGEWALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILY 861
GEW K L G TVGI+GLG IG AK LKAF + I Y
Sbjct: 127 RGEWDRKAFRGTE-----LAGKTVGIIGLGRIGRAVAKRLKAFGMKVIGY 171
>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 = 241 bits (618), Expect = 8e-72
Identities = 95/251 (37%), Positives = 142/251 (56%), Gaps = 6/251 (2%)
Query: 874 ENLKVITTFSVGYDHLELHEIKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRFQEGRKC 933
LKVI + VG D++++ RGI V +V ++ VA++ + L +A++R+ +
Sbjct: 64 PRLKVIVRYGVGVDNVDVAAATERGIPVCNVPDYCTEEVADHALALILALARKLPFLDRA 123
Query: 934 ITSGEWALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRRVKEE 993
+ +G W +G I L+G T+G+VG G IG AK KAF +++ V +
Sbjct: 124 VRAGGWDWT----VGGPIRRLRGLTLGLVGFGRIGRAVAKRAKAFGF-RVIAYDPYVPDG 178
Query: 994 GTAL-GAQLVPLDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILVNTSRGGLLD 1052
AL G ++V LD L A SD + + C LT +T LI + +LMKP A LVNT+RGGL+D
Sbjct: 179 VAALGGVRVVSLDELLARSDVVSLHCPLTPETRHLIDAEALALMKPGAFLVNTARGGLVD 238
Query: 1053 QEALVEFLKDKKIGGAGLDVMIPEPLPADHPLVQLDNCVLTPHTSSATKAVRDEKSSTSA 1112
+ AL LK +I GA LDV+ EP PAD PL+ N +LTPH + ++ E +A
Sbjct: 239 EAALARALKSGRIAGAALDVLEEEPPPADSPLLSAPNVILTPHAAWYSEESLAELRRKAA 298
Query: 1113 ENIIRGYKGEP 1123
E ++R +GEP
Sbjct: 299 EEVVRVLRGEP 309
Score = 141 bits (357), Expect = 9e-37
Identities = 45/93 (48%), Positives = 59/93 (63%)
Query: 308 GAQLVPLDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALV 367
G ++V LD L A SD + + C LT +T LI + +LMKP A L+NT+RGGL+D+ AL
Sbjct: 184 GVRVVSLDELLARSDVVSLHCPLTPETRHLIDAEALALMKPGAFLVNTARGGLVDEAALA 243
Query: 368 EFLKDKKIGGAGLDVMIPEPLPADHPLVQLDNC 400
LK +I GA LDV+ EP PAD PL+ N
Sbjct: 244 RALKSGRIAGAALDVLEEEPPPADSPLLSAPNV 276
Score = 85.3 bits (212), Expect = 9e-18
Identities = 37/112 (33%), Positives = 59/112 (52%), Gaps = 4/112 (3%)
Query: 619 KNLKVITTFSVGYDHLELHEIKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRFQEGRKC 678
LKVI + VG D++++ RGI V +V ++ VA++ + L +A++R+ +
Sbjct: 64 PRLKVIVRYGVGVDNVDVAAATERGIPVCNVPDYCTEEVADHALALILALARKLPFLDRA 123
Query: 679 ITSGEWALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILY 730
+ +G W +G I L+G T+G+VG G IG AK KAF I Y
Sbjct: 124 VRAGGWDWT----VGGPIRRLRGLTLGLVGFGRIGRAVAKRAKAFGFRVIAY 171
Score = 62.9 bits (154), Expect = 2e-10
Identities = 25/81 (30%), Positives = 41/81 (50%), Gaps = 2/81 (2%)
Query: 74 FIEKLKGCSALLCNPHQKVDKEVLDRSGENLKVIATFSVGHDHLHLDEIKSRGIRVGTVG 133
IE ALL + V EV++ LKVI + VG D++ + RGI V V
Sbjct: 38 LIEAAADADALLVQ-YAPVTAEVIEAL-PRLKVIVRYGVGVDNVDVAAATERGIPVCNVP 95
Query: 134 PVSSDTVAEYNIGLAIAVSRR 154
++ VA++ + L +A++R+
Sbjct: 96 DYCTEEVADHALALILALARK 116
Score = 45.2 bits (108), Expect = 1e-04
Identities = 20/49 (40%), Positives = 24/49 (48%), Gaps = 4/49 (8%)
Query: 813 GEWALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILY 861
G W +G I L+G T+G+VG G IG AK KAF I Y
Sbjct: 127 GGWDWT----VGGPIRRLRGLTLGLVGFGRIGRAVAKRAKAFGFRVIAY 171
>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 = 235 bits (601), Expect = 1e-69
Identities = 100/252 (39%), Positives = 148/252 (58%), Gaps = 11/252 (4%)
Query: 874 ENLKVITTFSVGYDHLELHEIKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRFQEGRKC 933
LKVI VG D++++ ARGI V + ++ +VAE+ I L +A++R +
Sbjct: 61 PRLKVIGRAGVGVDNIDVEAATARGILVVNAPGANTISVAEHTIALMLALARNIPQADAS 120
Query: 934 ITSGEWALKQTHIIGPNIMG--LKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRRVK 991
+ +G+W K+ MG L+G T+GIVGLG IG E A+ +AF + K+L +
Sbjct: 121 LRAGKWDRKKF-------MGVELRGKTLGIVGLGRIGREVARRARAFGM-KVLAYDPYIS 172
Query: 992 EEG-TALGAQLVPLDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILVNTSRGGL 1050
E A G +LV LD L AE+DFI + LT +T LI ++ + MKP AIL+NT+RGG+
Sbjct: 173 AERAAAGGVELVSLDELLAEADFISLHTPLTPETRGLINAEELAKMKPGAILINTARGGI 232
Query: 1051 LDQEALVEFLKDKKIGGAGLDVMIPEPLPADHPLVQLDNCVLTPHTSSATKAVRDEKSST 1110
+D+ AL + LK KI GA LDV EP PAD PL+ L N +LTPH ++T+ ++ +
Sbjct: 233 VDEAALADALKSGKIAGAALDVFEQEPPPADSPLLGLPNVILTPHLGASTEEAQERVAVD 292
Query: 1111 SAENIIRGYKGE 1122
+AE ++ GE
Sbjct: 293 AAEQVLAVLAGE 304
Score = 142 bits (360), Expect = 3e-37
Identities = 50/94 (53%), Positives = 63/94 (67%)
Query: 306 ALGAQLVPLDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEA 365
A G +LV LD L AE+DFI + LT +T LI ++ + MKP AILINT+RGG++D+ A
Sbjct: 178 AGGVELVSLDELLAEADFISLHTPLTPETRGLINAEELAKMKPGAILINTARGGIVDEAA 237
Query: 366 LVEFLKDKKIGGAGLDVMIPEPLPADHPLVQLDN 399
L + LK KI GA LDV EP PAD PL+ L N
Sbjct: 238 LADALKSGKIAGAALDVFEQEPPPADSPLLGLPN 271
Score = 83.2 bits (207), Expect = 3e-17
Identities = 39/107 (36%), Positives = 60/107 (56%), Gaps = 9/107 (8%)
Query: 619 KNLKVITTFSVGYDHLELHEIKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRFQEGRKC 678
LKVI VG D++++ ARGI V + ++ +VAE+ I L +A++R +
Sbjct: 61 PRLKVIGRAGVGVDNIDVEAATARGILVVNAPGANTISVAEHTIALMLALARNIPQADAS 120
Query: 679 ITSGEWALKQTHIIGPNIMG--LKGATVGIVGLGNIGLETAKLLKAF 723
+ +G+W K+ MG L+G T+GIVGLG IG E A+ +AF
Sbjct: 121 LRAGKWDRKKF-------MGVELRGKTLGIVGLGRIGREVARRARAF 160
Score = 62.0 bits (152), Expect = 4e-10
Identities = 32/125 (25%), Positives = 59/125 (47%), Gaps = 13/125 (10%)
Query: 41 RLLVPESLSK-----LRFNSRFDIDTYPVSEGRMPRDIFIEKLKGCSALLCNPHQKVDKE 95
++LV + + + LR + ++D P + + + + AL+ KV E
Sbjct: 1 KVLVTDPIDEEGLELLR-EAGIEVDVAP----GLSEEELLAIIADADALIVRSATKVTAE 55
Query: 96 VLDRSGENLKVIATFSVGHDHLHLDEIKSRGIRVGTVGPVS-SDTVAEYNIGLAIAVSRR 154
V++ LKVI VG D++ ++ +RGI V P + + +VAE+ I L +A++R
Sbjct: 56 VIEA-APRLKVIGRAGVGVDNIDVEAATARGILV-VNAPGANTISVAEHTIALMLALARN 113
Query: 155 FQQRH 159
Q
Sbjct: 114 IPQAD 118
Score = 48.2 bits (116), Expect = 1e-05
Identities = 20/45 (44%), Positives = 26/45 (57%), Gaps = 9/45 (20%)
Query: 812 NGEWALKQTHIIGPNIMG--LKGATVGIVGLGNIGLETAKLLKAF 854
G+W K+ MG L+G T+GIVGLG IG E A+ +AF
Sbjct: 123 AGKWDRKKF-------MGVELRGKTLGIVGLGRIGREVARRARAF 160
>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 = 232 bits (593), Expect = 2e-68
Identities = 104/293 (35%), Positives = 154/293 (52%), Gaps = 24/293 (8%)
Query: 827 IMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRNKVKTPKRTENLKVITTFSVGY 886
+ LK A + I + T K+++A LK+I G
Sbjct: 41 LEALKDADILITHFAPV---TKKVIEAAP-------------------KLKLIGVCRGGP 78
Query: 887 DHLELHEIKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRFQEGRKCITSGEWALKQTHI 946
+++++ RGI V + +++ VAE+ +GL +A +R + GEW K +
Sbjct: 79 ENVDVEAATERGIPVLNTPGRNAEAVAEFTVGLMLAETRNIARAHAALKDGEW-RKDYYN 137
Query: 947 IGPNIMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRRVKEEGTALGAQLVPLDT 1006
L+G TVGIVG G IG AK LKAF ++Y E+ A G + V L+
Sbjct: 138 YDGYGPELRGKTVGIVGFGAIGRRVAKRLKAFGAEVLVYDPYVDPEKIEADGVKKVSLEE 197
Query: 1007 LCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILVNTSRGGLLDQEALVEFLKDKKIG 1066
L SD + + LT +T +IG ++F+LMKPTA +NT+R GL+D++AL+E L++ KIG
Sbjct: 198 LLKRSDVVSLHARLTPETRGMIGAEEFALMKPTAYFINTARAGLVDEDALIEALEEGKIG 257
Query: 1067 GAGLDVMIPEPLPADHPLVQLDNCVLTPHTSSATKAVRDEKSSTSAENIIRGY 1119
GA LDV EPLPADHPL++LDN LTPH + AT+ V E+S ++ Y
Sbjct: 258 GAALDVFPEEPLPADHPLLKLDNVTLTPHIAGATRDV-AERSPEIIAEELKRY 309
Score = 149 bits (379), Expect = 8e-40
Identities = 54/108 (50%), Positives = 72/108 (66%), Gaps = 6/108 (5%)
Query: 306 ALGAQLVPLDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEA 365
A G + V L+ L SD + + LT +T +IG ++F+LMKPTA INT+R GL+D++A
Sbjct: 187 ADGVKKVSLEELLKRSDVVSLHARLTPETRGMIGAEEFALMKPTAYFINTARAGLVDEDA 246
Query: 366 LVEFLKDKKIGGAGLDVMIPEPLPADHPLVQLDNC------GGAGLDV 407
L+E L++ KIGGA LDV EPLPADHPL++LDN GA DV
Sbjct: 247 LIEALEEGKIGGAALDVFPEEPLPADHPLLKLDNVTLTPHIAGATRDV 294
Score = 75.3 bits (186), Expect = 2e-14
Identities = 37/112 (33%), Positives = 56/112 (50%), Gaps = 1/112 (0%)
Query: 619 KNLKVITTFSVGYDHLELHEIKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRFQEGRKC 678
LK+I G +++++ RGI V + +++ VAE+ +GL +A +R
Sbjct: 66 PKLKLIGVCRGGPENVDVEAATERGIPVLNTPGRNAEAVAEFTVGLMLAETRNIARAHAA 125
Query: 679 ITSGEWALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILY 730
+ GEW K + L+G TVGIVG G IG AK LKAF ++Y
Sbjct: 126 LKDGEW-RKDYYNYDGYGPELRGKTVGIVGFGAIGRRVAKRLKAFGAEVLVY 176
Score = 49.8 bits (120), Expect = 4e-06
Identities = 25/100 (25%), Positives = 47/100 (47%), Gaps = 2/100 (2%)
Query: 65 SEGRMPRDIFIEKLKGCSALLCNPHQKVDKEVLDRSGENLKVIATFSVGHDHLHLDEIKS 124
E P + +E LK L+ + V K+V++ LK+I G +++ ++
Sbjct: 31 PEAVEPEEELLEALKDADILITH-FAPVTKKVIEA-APKLKLIGVCRGGPENVDVEAATE 88
Query: 125 RGIRVGTVGPVSSDTVAEYNIGLAIAVSRRFQQRHNWIAR 164
RGI V +++ VAE+ +GL +A +R + H +
Sbjct: 89 RGIPVLNTPGRNAEAVAEFTVGLMLAETRNIARAHAALKD 128
>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 = 224 bits (573), Expect = 1e-67
Identities = 83/181 (45%), Positives = 113/181 (62%), Gaps = 6/181 (3%)
Query: 917 IGLAIAVSRRFQEGRKCITSGEWALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLK 976
+ L +A++RR E + + +G W L G TVGI+GLG IG A+ LK
Sbjct: 1 LALLLALARRIPEADRQVRAGRWRPDALLGRE-----LSGKTVGIIGLGRIGRAVARRLK 55
Query: 977 AFKVSKILYTSRRVKEEGTALGAQLVPLDTLCAESDFIFVTCALTKDTEQLIGRKQFSLM 1036
AF + K++ R K E ALGA+ V LD L AESD + + LT +T LI ++ +LM
Sbjct: 56 AFGM-KVIAYDRYPKAEAEALGARYVSLDELLAESDVVSLHLPLTPETRHLINAERLALM 114
Query: 1037 KPTAILVNTSRGGLLDQEALVEFLKDKKIGGAGLDVMIPEPLPADHPLVQLDNCVLTPHT 1096
KP AIL+NT+RGGL+D++AL+ LK +I GA LDV PEPLP DHPL++L N +LTPH
Sbjct: 115 KPGAILINTARGGLVDEDALIAALKSGRIAGAALDVFEPEPLPPDHPLLELPNVILTPHI 174
Query: 1097 S 1097
+
Sbjct: 175 A 175
Score = 147 bits (374), Expect = 1e-40
Identities = 54/106 (50%), Positives = 73/106 (68%)
Query: 295 GYNWFERSNGTALGAQLVPLDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILIN 354
Y+ + ++ ALGA+ V LD L AESD + + LT +T LI ++ +LMKP AILIN
Sbjct: 63 AYDRYPKAEAEALGARYVSLDELLAESDVVSLHLPLTPETRHLINAERLALMKPGAILIN 122
Query: 355 TSRGGLLDQEALVEFLKDKKIGGAGLDVMIPEPLPADHPLVQLDNC 400
T+RGGL+D++AL+ LK +I GA LDV PEPLP DHPL++L N
Sbjct: 123 TARGGLVDEDALIAALKSGRIAGAALDVFEPEPLPPDHPLLELPNV 168
Score = 69.4 bits (171), Expect = 2e-13
Identities = 27/77 (35%), Positives = 39/77 (50%), Gaps = 6/77 (7%)
Query: 662 IGLAIAVSRRFQEGRKCITSGEWALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLK 721
+ L +A++RR E + + +G W L G TVGI+GLG IG A+ LK
Sbjct: 1 LALLLALARRIPEADRQVRAGRWRPDALLGRE-----LSGKTVGIIGLGRIGRAVARRLK 55
Query: 722 AFKVSKILYTSRRVKEE 738
AF + K++ R K E
Sbjct: 56 AFGM-KVIAYDRYPKAE 71
Score = 52.1 bits (126), Expect = 1e-07
Identities = 20/62 (32%), Positives = 26/62 (41%), Gaps = 6/62 (9%)
Query: 812 NGEWALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRNKVKTPK 871
G W L G TVGI+GLG IG A+ LKAF + K++ R +
Sbjct: 20 AGRWRPDALLGRE-----LSGKTVGIIGLGRIGRAVARRLKAFGM-KVIAYDRYPKAEAE 73
Query: 872 RT 873
Sbjct: 74 AL 75
>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 = 217 bits (556), Expect = 2e-63
Identities = 96/257 (37%), Positives = 146/257 (56%), Gaps = 10/257 (3%)
Query: 865 NKV----KTPKRTENLKVITTFSVGYDHLELHEIKARGIRVGSVGHISSDTVAEYNIGLA 920
NKV + + NLK+I + GY++++L K RGI V +V S+D+VA++ L
Sbjct: 51 NKVVLDAEVLAQLPNLKLIGVLATGYNNVDLAAAKERGITVTNVPGYSTDSVAQHTFALL 110
Query: 921 IAVSRRFQEGRKCITSGEWALKQTHI-IGPNIMGLKGATVGIVGLGNIGLETAKLLKAFK 979
+A++R + +GEW I+ L G T+GI+G GNIG A++ +AF
Sbjct: 111 LALARLVAYHNDVVKAGEWQKSPDFCFWDYPIIELAGKTLGIIGYGNIGQAVARIARAFG 170
Query: 980 VSKILYTSRRVKEEGTALGAQLVPLDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPT 1039
+ K+L+ R+ L V LD L A+SD I + C LT +T LI ++ + MKP
Sbjct: 171 M-KVLFAERKGAPP---LREGYVSLDELLAQSDVISLHCPLTPETRNLINAEELAKMKPG 226
Query: 1040 AILVNTSRGGLLDQEALVEFLKDKKIGGAGLDVMIPEPLPADHPLVQ-LDNCVLTPHTSS 1098
AIL+NT+RGGL+D++AL + L KI GAGLDV+ EP AD+PL++ N ++TPH +
Sbjct: 227 AILINTARGGLVDEQALADALNSGKIAGAGLDVLSQEPPRADNPLLKAAPNLIITPHIAW 286
Query: 1099 ATKAVRDEKSSTSAENI 1115
A++ R +NI
Sbjct: 287 ASREARQRLMDILVDNI 303
Score = 138 bits (350), Expect = 7e-36
Identities = 51/110 (46%), Positives = 67/110 (60%), Gaps = 3/110 (2%)
Query: 294 FGYN--WFERSNGTALGAQLVPLDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAI 351
FG + ER L V LD L A+SD I + C LT +T LI ++ + MKP AI
Sbjct: 169 FGMKVLFAERKGAPPLREGYVSLDELLAQSDVISLHCPLTPETRNLINAEELAKMKPGAI 228
Query: 352 LINTSRGGLLDQEALVEFLKDKKIGGAGLDVMIPEPLPADHPLVQ-LDNC 400
LINT+RGGL+D++AL + L KI GAGLDV+ EP AD+PL++ N
Sbjct: 229 LINTARGGLVDEQALADALNSGKIAGAGLDVLSQEPPRADNPLLKAAPNL 278
Score = 79.4 bits (197), Expect = 8e-16
Identities = 40/121 (33%), Positives = 66/121 (54%), Gaps = 2/121 (1%)
Query: 619 KNLKVITTFSVGYDHLELHEIKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRFQEGRKC 678
NLK+I + GY++++L K RGI V +V S+D+VA++ L +A++R
Sbjct: 64 PNLKLIGVLATGYNNVDLAAAKERGITVTNVPGYSTDSVAQHTFALLLALARLVAYHNDV 123
Query: 679 ITSGEWALKQTHI-IGPNIMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRRVKE 737
+ +GEW I+ L G T+GI+G GNIG A++ +AF + K+L+ R+
Sbjct: 124 VKAGEWQKSPDFCFWDYPIIELAGKTLGIIGYGNIGQAVARIARAFGM-KVLFAERKGAP 182
Query: 738 E 738
Sbjct: 183 P 183
Score = 47.1 bits (113), Expect = 3e-05
Identities = 32/115 (27%), Positives = 56/115 (48%), Gaps = 10/115 (8%)
Query: 48 LSKLRFNSRFDIDTYPVSEGRMPRDIFIEKLKGCSALLCNPHQKV--DKEVLDRSGENLK 105
LS ++ Y R + +E++K ++ N KV D EVL + NLK
Sbjct: 16 LSWDPLEFLGELTVYD----RTSPEEVVERIKDADIVITN---KVVLDAEVLAQL-PNLK 67
Query: 106 VIATFSVGHDHLHLDEIKSRGIRVGTVGPVSSDTVAEYNIGLAIAVSRRFQQRHN 160
+I + G++++ L K RGI V V S+D+VA++ L +A++R ++
Sbjct: 68 LIGVLATGYNNVDLAAAKERGITVTNVPGYSTDSVAQHTFALLLALARLVAYHND 122
Score = 45.5 bits (109), Expect = 9e-05
Identities = 14/40 (35%), Positives = 23/40 (57%)
Query: 827 IMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRNK 866
I+ L G T+GI+G GNIG A++ +AF + + +
Sbjct: 142 IIELAGKTLGIIGYGNIGQAVARIARAFGMKVLFAERKGA 181
>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 = 216 bits (553), Expect = 5e-63
Identities = 108/252 (42%), Positives = 151/252 (59%), Gaps = 10/252 (3%)
Query: 874 ENLKVITTFSVGYDHLELHEIKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRFQEGRKC 933
+NLK+I+ G DH++L K RGI V + S++ VAE IGLAI + R
Sbjct: 68 KNLKMISVAFTGVDHVDLEACKERGITVSNAAGYSTEAVAELTIGLAIDLLRNIVPCDAA 127
Query: 934 ITSGEWALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRRVKEE 993
+ +G + +IG L G TVGIVG G IGL A+L KAF K+L SR KEE
Sbjct: 128 VRAGG---TKAGLIGRE---LAGKTVGIVGTGAIGLRVARLFKAFG-CKVLAYSRSEKEE 180
Query: 994 GTALGAQLVPLDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILVNTSRGGLLDQ 1053
ALG + V LD L AESD + + L +T+ LIG+++ +LMK +AIL+NT+RG ++D
Sbjct: 181 AKALGIEYVSLDELLAESDIVSLHLPLNDETKGLIGKEKLALMKESAILINTARGPVVDN 240
Query: 1054 EALVEFLKDKKIGGAGLDV--MIPEPLPADHPLVQLDNCVLTPHTSSATKAVRDEKSSTS 1111
EAL + L + KI GAG+DV M P PLPAD+PL+ N +LTPH + AT+ ++++
Sbjct: 241 EALADALNEGKIAGAGIDVFDMEP-PLPADYPLLHAPNTILTPHVAFATEEAMEKRAEIV 299
Query: 1112 AENIIRGYKGEP 1123
+NI G+P
Sbjct: 300 FDNIEAWLAGKP 311
Score = 125 bits (317), Expect = 2e-31
Identities = 51/108 (47%), Positives = 71/108 (65%), Gaps = 3/108 (2%)
Query: 295 GYNWFERSNGTALGAQLVPLDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILIN 354
Y+ E+ ALG + V LD L AESD + + L +T+ LIG+++ +LMK +AILIN
Sbjct: 172 AYSRSEKEEAKALGIEYVSLDELLAESDIVSLHLPLNDETKGLIGKEKLALMKESAILIN 231
Query: 355 TSRGGLLDQEALVEFLKDKKIGGAGLDV--MIPEPLPADHPLVQLDNC 400
T+RG ++D EAL + L + KI GAG+DV M P PLPAD+PL+ N
Sbjct: 232 TARGPVVDNEALADALNEGKIAGAGIDVFDMEP-PLPADYPLLHAPNT 278
Score = 88.0 bits (219), Expect = 1e-18
Identities = 52/128 (40%), Positives = 68/128 (53%), Gaps = 7/128 (5%)
Query: 619 KNLKVITTFSVGYDHLELHEIKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRFQEGRKC 678
KNLK+I+ G DH++L K RGI V + S++ VAE IGLAI + R
Sbjct: 68 KNLKMISVAFTGVDHVDLEACKERGITVSNAAGYSTEAVAELTIGLAIDLLRNIVPCDAA 127
Query: 679 ITSGEWALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRRVKEE 738
+ +G + +IG L G TVGIVG G IGL A+L KAF K+L SR KEE
Sbjct: 128 VRAGG---TKAGLIGRE---LAGKTVGIVGTGAIGLRVARLFKAFG-CKVLAYSRSEKEE 180
Query: 739 GQLFSLVY 746
+ + Y
Sbjct: 181 AKALGIEY 188
Score = 48.8 bits (117), Expect = 1e-05
Identities = 25/64 (39%), Positives = 35/64 (54%), Gaps = 1/64 (1%)
Query: 94 KEVLDRSGENLKVIATFSVGHDHLHLDEIKSRGIRVGTVGPVSSDTVAEYNIGLAIAVSR 153
EV+ + +NLK+I+ G DH+ L+ K RGI V S++ VAE IGLAI + R
Sbjct: 61 GEVI-EACKNLKMISVAFTGVDHVDLEACKERGITVSNAAGYSTEAVAELTIGLAIDLLR 119
Query: 154 RFQQ 157
Sbjct: 120 NIVP 123
Score = 47.6 bits (114), Expect = 2e-05
Identities = 21/35 (60%), Positives = 23/35 (65%), Gaps = 1/35 (2%)
Query: 830 LKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSR 864
L G TVGIVG G IGL A+L KAF K+L SR
Sbjct: 142 LAGKTVGIVGTGAIGLRVARLFKAFG-CKVLAYSR 175
>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 = 212 bits (542), Expect = 1e-61
Identities = 83/272 (30%), Positives = 135/272 (49%), Gaps = 11/272 (4%)
Query: 859 ILYTSRNKVKTPKRTENLKVITTFSVGYDHLELHEIKARGIRVGSVGHISSDTVAEYNIG 918
+L + + L+ I + S G D L E+ R + + + I +AEY +G
Sbjct: 43 VLLGNPPLPELLPAAPRLRWIQSTSAGVDALLFPELLERDVVLTNARGIFGPPIAEYVLG 102
Query: 919 LAIAVSRRFQEGRKCITSGEWALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKAF 978
+A +R+ + W ++ + L G TV IVGLG+IG E A+ KAF
Sbjct: 103 YMLAFARKLPRYARNQAERRW--QRRGPVRE----LAGKTVLIVGLGDIGREIARRAKAF 156
Query: 979 KVSKILYTSRRVKEEGTALGAQLVP---LDTLCAESDFIFVTCALTKDTEQLIGRKQFSL 1035
+ +++ R + + ++ LD L E+D++ LT +T L ++F+
Sbjct: 157 GM-RVIGVRRSGRPAPPVVD-EVYTPDELDELLPEADYVVNALPLTPETRGLFNAERFAA 214
Query: 1036 MKPTAILVNTSRGGLLDQEALVEFLKDKKIGGAGLDVMIPEPLPADHPLVQLDNCVLTPH 1095
MKP A+L+N RG ++D++AL+E L+ +I GA LDV EPLPAD PL L N ++TPH
Sbjct: 215 MKPGAVLINVGRGSVVDEDALIEALESGRIAGAALDVFEEEPLPADSPLWDLPNVIITPH 274
Query: 1096 TSSATKAVRDEKSSTSAENIIRGYKGEPMIYE 1127
S + + + EN+ R GEP++
Sbjct: 275 ISGDSPSYPERVVEIFLENLRRYLAGEPLLNV 306
Score = 128 bits (325), Expect = 1e-32
Identities = 40/87 (45%), Positives = 55/87 (63%)
Query: 314 LDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLKDK 373
LD L E+D++ LT +T L ++F+ MKP A+LIN RG ++D++AL+E L+
Sbjct: 183 LDELLPEADYVVNALPLTPETRGLFNAERFAAMKPGAVLINVGRGSVVDEDALIEALESG 242
Query: 374 KIGGAGLDVMIPEPLPADHPLVQLDNC 400
+I GA LDV EPLPAD PL L N
Sbjct: 243 RIAGAALDVFEEEPLPADSPLWDLPNV 269
Score = 73.3 bits (181), Expect = 9e-14
Identities = 35/129 (27%), Positives = 58/129 (44%), Gaps = 7/129 (5%)
Query: 619 KNLKVITTFSVGYDHLELHEIKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRFQEGRKC 678
L+ I + S G D L E+ R + + + I +AEY +G +A +R+ +
Sbjct: 58 PRLRWIQSTSAGVDALLFPELLERDVVLTNARGIFGPPIAEYVLGYMLAFARKLPRYARN 117
Query: 679 ITSGEWALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRRVKEE 738
W ++ + L G TV IVGLG+IG E A+ KAF + +++ R +
Sbjct: 118 QAERRW--QRRGPVRE----LAGKTVLIVGLGDIGREIARRAKAFGM-RVIGVRRSGRPA 170
Query: 739 GQLFSLVYD 747
+ VY
Sbjct: 171 PPVVDEVYT 179
Score = 47.5 bits (114), Expect = 2e-05
Identities = 16/25 (64%), Positives = 18/25 (72%)
Query: 830 LKGATVGIVGLGNIGLETAKLLKAF 854
L G TV IVGLG+IG E A+ KAF
Sbjct: 132 LAGKTVLIVGLGDIGREIARRAKAF 156
Score = 47.1 bits (113), Expect = 3e-05
Identities = 24/94 (25%), Positives = 38/94 (40%), Gaps = 10/94 (10%)
Query: 74 FIEKLKGCSALLCNPHQKVDKEVLDRSGENLKVIATFSVGHDHLHLDEIKSRGIRVGTVG 133
E+L LL NP E+L + L+ I + S G D L E+ R + +
Sbjct: 34 LTEELADADVLLGNPP---LPELLPAA-PRLRWIQSTSAGVDALLFPELLERDVVLTNAR 89
Query: 134 PVSSDTVAEYNIGLAIAVSRRF------QQRHNW 161
+ +AEY +G +A +R+ Q W
Sbjct: 90 GIFGPPIAEYVLGYMLAFARKLPRYARNQAERRW 123
>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 = 210 bits (538), Expect = 5e-61
Identities = 103/257 (40%), Positives = 144/257 (56%), Gaps = 12/257 (4%)
Query: 875 NLKVITTFSVGYDHLELHEIKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRFQEG-RKC 933
NLK+I + G+D++++ K +GI V + +S++ AE GL +A++RR EG R
Sbjct: 65 NLKIIANYGAGFDNIDVDYAKEKGIPVTNTPAVSTEPTAELTFGLILALARRIAEGDRLM 124
Query: 934 ITSG--EWALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRRVK 991
G WA +G L G T+GI+G+G IG A+ KAF + KILY +R
Sbjct: 125 RRGGFLGWAP--LFFLGHE---LAGKTLGIIGMGRIGQAVARRAKAFGM-KILYYNRHRL 178
Query: 992 EEGT--ALGAQLVPLDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILVNTSRGG 1049
E T LGA V LD L ESDF+ + T +T LI F LMKPTA L+N +RG
Sbjct: 179 SEETEKELGATYVDLDELLKESDFVSLHAPYTPETHHLIDAAAFKLMKPTAYLINAARGP 238
Query: 1050 LLDQEALVEFLKDKKIGGAGLDVMIPEPLPADHPLVQLDNCVLTPHTSSATKAVRDEKSS 1109
L+D++ALV+ LK +I GA LDV EP + L +LDN +LTPH +AT RD +
Sbjct: 239 LVDEKALVDALKTGEIAGAALDVFEFEPEVSPE-LKKLDNVILTPHIGNATVEARDAMAK 297
Query: 1110 TSAENIIRGYKGEPMIY 1126
+A+NII +G+
Sbjct: 298 EAADNIISFLEGKRPKN 314
Score = 110 bits (278), Expect = 2e-26
Identities = 46/95 (48%), Positives = 57/95 (60%), Gaps = 1/95 (1%)
Query: 305 TALGAQLVPLDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQE 364
LGA V LD L ESDF+ + T +T LI F LMKPTA LIN +RG L+D++
Sbjct: 184 KELGATYVDLDELLKESDFVSLHAPYTPETHHLIDAAAFKLMKPTAYLINAARGPLVDEK 243
Query: 365 ALVEFLKDKKIGGAGLDVMIPEPLPADHPLVQLDN 399
ALV+ LK +I GA LDV EP + L +LDN
Sbjct: 244 ALVDALKTGEIAGAALDVFEFEPEVSPE-LKKLDN 277
Score = 101 bits (254), Expect = 3e-23
Identities = 63/228 (27%), Positives = 100/228 (43%), Gaps = 54/228 (23%)
Query: 516 KLFLTRDDYSRVP--AFEILGEMFDIITYPASEGQIPRDIFIEKLRGCSALLCTSRDRVD 573
K+ +T +P A E L E F++ Y G I ++ +E++ AL+ VD
Sbjct: 2 KVLVT----GWIPKEALEELEENFEVTYYD-GLGLISKEELLERIADYDALITPLSTPVD 56
Query: 574 KQVLDESGGYRCTEDFFGLDLDQMFRNPSKRHVNIETVLGVSFLIKNLKVITTFSVGYDH 633
K+++D + KNLK+I + G+D+
Sbjct: 57 KEIIDAA--------------------------------------KNLKIIANYGAGFDN 78
Query: 634 LELHEIKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRFQEG-RKCITSG--EWALKQTH 690
+++ K +GI V + +S++ AE GL +A++RR EG R G WA
Sbjct: 79 IDVDYAKEKGIPVTNTPAVSTEPTAELTFGLILALARRIAEGDRLMRRGGFLGWAP--LF 136
Query: 691 IIGPNIMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRRVKEE 738
+G L G T+GI+G+G IG A+ KAF + KILY +R E
Sbjct: 137 FLGHE---LAGKTLGIIGMGRIGQAVARRAKAFGM-KILYYNRHRLSE 180
Score = 75.7 bits (187), Expect = 1e-14
Identities = 35/112 (31%), Positives = 61/112 (54%), Gaps = 4/112 (3%)
Query: 43 LVPESLSKLRFNSRFDIDTYPVSEGRMPRDIFIEKLKGCSALLCNPHQKVDKEVLDRSGE 102
+ E+L +L F++ Y G + ++ +E++ AL+ VDKE++D +
Sbjct: 9 IPKEALEELE--ENFEVTYYD-GLGLISKEELLERIADYDALITPLSTPVDKEIIDA-AK 64
Query: 103 NLKVIATFSVGHDHLHLDEIKSRGIRVGTVGPVSSDTVAEYNIGLAIAVSRR 154
NLK+IA + G D++ +D K +GI V VS++ AE GL +A++RR
Sbjct: 65 NLKIIANYGAGFDNIDVDYAKEKGIPVTNTPAVSTEPTAELTFGLILALARR 116
Score = 47.6 bits (114), Expect = 2e-05
Identities = 19/45 (42%), Positives = 28/45 (62%), Gaps = 1/45 (2%)
Query: 830 LKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRNKVKTPKRTE 874
L G T+GI+G+G IG A+ KAF + KILY +R+++ E
Sbjct: 142 LAGKTLGIIGMGRIGQAVARRAKAFGM-KILYYNRHRLSEETEKE 185
>gnl|CDD|183914 PRK13243, PRK13243, glyoxylate reductase; Reviewed.
Length = 333
Score = 209 bits (533), Expect = 4e-60
Identities = 100/254 (39%), Positives = 145/254 (57%), Gaps = 11/254 (4%)
Query: 875 NLKVITTFSVGYDHLELHEIKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRFQEGRKCI 934
L+++ ++VGYD++++ E RGI V + + ++ A++ L +A +RR E +
Sbjct: 67 RLRIVANYAVGYDNIDVEEATRRGIYVTNTPGVLTEATADFAWALLLATARRLVEADHFV 126
Query: 935 TSGEWALKQT--HIIGPNIM---GLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRR 989
SGEW + H P + + G T+GI+G G IG A+ K F + +ILY SR
Sbjct: 127 RSGEWKRRGVAWH---PLMFLGYDVYGKTIGIIGFGRIGQAVARRAKGFGM-RILYYSRT 182
Query: 990 VKEEG-TALGAQLVPLDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILVNTSRG 1048
K E LGA+ PL+ L ESDF+ + LTK+T +I ++ LMKPTAILVNT+RG
Sbjct: 183 RKPEAEKELGAEYRPLEELLRESDFVSLHVPLTKETYHMINEERLKLMKPTAILVNTARG 242
Query: 1049 GLLDQEALVEFLKDKKIGGAGLDVMIPEPLPADHPLVQLDNCVLTPHTSSATKAVRDEKS 1108
++D +ALV+ LK+ I GAGLDV EP + L L N VL PH SAT R+ +
Sbjct: 243 KVVDTKALVKALKEGWIAGAGLDVFEEEPYY-NEELFSLKNVVLAPHIGSATFEAREGMA 301
Query: 1109 STSAENIIRGYKGE 1122
AEN+I +GE
Sbjct: 302 ELVAENLIAFKRGE 315
Score = 108 bits (272), Expect = 2e-25
Identities = 45/93 (48%), Positives = 61/93 (65%), Gaps = 1/93 (1%)
Query: 307 LGAQLVPLDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEAL 366
LGA+ PL+ L ESDF+ + LTK+T +I ++ LMKPTAIL+NT+RG ++D +AL
Sbjct: 191 LGAEYRPLEELLRESDFVSLHVPLTKETYHMINEERLKLMKPTAILVNTARGKVVDTKAL 250
Query: 367 VEFLKDKKIGGAGLDVMIPEPLPADHPLVQLDN 399
V+ LK+ I GAGLDV EP + L L N
Sbjct: 251 VKALKEGWIAGAGLDVFEEEPYY-NEELFSLKN 282
Score = 108 bits (272), Expect = 2e-25
Identities = 62/231 (26%), Positives = 106/231 (45%), Gaps = 50/231 (21%)
Query: 513 SKPKLFLTRDDYSRVPAFEILGEMFDIITYPASEGQIPRDIFIEKLRGCSALLCTSRDRV 572
KPK+F+TR+ E+L E F++ + E +IPR++ +EK+R AL+ +R+
Sbjct: 1 MKPKVFITREIPEN--GIEMLEEHFEVEVWE-DEREIPREVLLEKVRDVDALVTMLSERI 57
Query: 573 DKQVLDESGGYRCTEDFFGLDLDQMFRNPSKRHVNIETVLGVSFLIKNLKVITTFSVGYD 632
D +V + + L+++ ++VGYD
Sbjct: 58 DCEVFEAA--------------------------------------PRLRIVANYAVGYD 79
Query: 633 HLELHEIKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRFQEGRKCITSGEWALKQT--H 690
++++ E RGI V + + ++ A++ L +A +RR E + SGEW + H
Sbjct: 80 NIDVEEATRRGIYVTNTPGVLTEATADFAWALLLATARRLVEADHFVRSGEWKRRGVAWH 139
Query: 691 IIGPNIM---GLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRRVKEE 738
P + + G T+GI+G G IG A+ K F + +ILY SR K E
Sbjct: 140 ---PLMFLGYDVYGKTIGIIGFGRIGQAVARRAKGFGM-RILYYSRTRKPE 186
Score = 67.1 bits (164), Expect = 1e-11
Identities = 29/115 (25%), Positives = 64/115 (55%), Gaps = 4/115 (3%)
Query: 40 SRLLVPESLSKLRFNSRFDIDTYPVSEGRMPRDIFIEKLKGCSALLCNPHQKVDKEVLDR 99
+R + + L F+++ + E +PR++ +EK++ AL+ +++D EV +
Sbjct: 8 TREIPENGIEMLE--EHFEVEVWE-DEREIPREVLLEKVRDVDALVTMLSERIDCEVFEA 64
Query: 100 SGENLKVIATFSVGHDHLHLDEIKSRGIRVGTVGPVSSDTVAEYNIGLAIAVSRR 154
+ L+++A ++VG+D++ ++E RGI V V ++ A++ L +A +RR
Sbjct: 65 A-PRLRIVANYAVGYDNIDVEEATRRGIYVTNTPGVLTEATADFAWALLLATARR 118
Score = 42.1 bits (99), Expect = 0.001
Identities = 22/64 (34%), Positives = 32/64 (50%), Gaps = 9/64 (14%)
Query: 808 HGTINGEWALKQT--HIIGPNIM---GLKGATVGIVGLGNIGLETAKLLKAFKVSKILYT 862
H +GEW + H P + + G T+GI+G G IG A+ K F + +ILY
Sbjct: 124 HFVRSGEWKRRGVAWH---PLMFLGYDVYGKTIGIIGFGRIGQAVARRAKGFGM-RILYY 179
Query: 863 SRNK 866
SR +
Sbjct: 180 SRTR 183
>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 = 206 bits (527), Expect = 2e-59
Identities = 98/251 (39%), Positives = 139/251 (55%), Gaps = 9/251 (3%)
Query: 873 TENLKVITTFSVGYDHLELHEIKARGIRVGSV-GHISSDTVAEYNIGLAIAVSRRFQEGR 931
+ LK+I +GYD+++L G+ V V G + D VAE+ + L + V R+ +
Sbjct: 67 NDGLKLIARHGIGYDNVDLKAATEHGVIVTRVPGAVERDAVAEHAVALILTVLRKINQAS 126
Query: 932 KCITSGEWALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRRVK 991
+ + G+W + + L G TVGI+G GNIG A++LK +K+L V
Sbjct: 127 EAVKEGKWTERANFVGHE----LSGKTVGIIGYGNIGSRVAEILKEGFNAKVLAYDPYVS 182
Query: 992 EEG-TALGAQLVPLDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILVNTSRGGL 1050
EE GA+ V L+ L AESD I + LT++T +I K FS MK ILVNT+RG L
Sbjct: 183 EEVIKKKGAKPVSLEELLAESDIISLHAPLTEETYHMINEKAFSKMKKGVILVNTARGEL 242
Query: 1051 LDQEALVEFLKDKKIGGAGLDVMIPEPLPADHPLVQLDNCVLTPHTSSATK---AVRDEK 1107
+D+EAL+E LK KI GAGLDV+ EP+ ADHPL+ +N V+TPH + T EK
Sbjct: 243 IDEEALIEALKSGKIAGAGLDVLEEEPIKADHPLLHYENVVITPHIGAYTYESLYGMGEK 302
Query: 1108 SSTSAENIIRG 1118
E+ + G
Sbjct: 303 VVDDIEDFLAG 313
Score = 121 bits (306), Expect = 5e-30
Identities = 49/95 (51%), Positives = 64/95 (67%)
Query: 306 ALGAQLVPLDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEA 365
GA+ V L+ L AESD I + LT++T +I K FS MK IL+NT+RG L+D+EA
Sbjct: 188 KKGAKPVSLEELLAESDIISLHAPLTEETYHMINEKAFSKMKKGVILVNTARGELIDEEA 247
Query: 366 LVEFLKDKKIGGAGLDVMIPEPLPADHPLVQLDNC 400
L+E LK KI GAGLDV+ EP+ ADHPL+ +N
Sbjct: 248 LIEALKSGKIAGAGLDVLEEEPIKADHPLLHYENV 282
Score = 75.4 bits (186), Expect = 2e-14
Identities = 39/121 (32%), Positives = 61/121 (50%), Gaps = 5/121 (4%)
Query: 619 KNLKVITTFSVGYDHLELHEIKARGIRVGSV-GHISSDTVAEYNIGLAIAVSRRFQEGRK 677
LK+I +GYD+++L G+ V V G + D VAE+ + L + V R+ + +
Sbjct: 68 DGLKLIARHGIGYDNVDLKAATEHGVIVTRVPGAVERDAVAEHAVALILTVLRKINQASE 127
Query: 678 CITSGEWALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRRVKE 737
+ G+W + + L G TVGI+G GNIG A++LK +K+L V E
Sbjct: 128 AVKEGKWTERANFVGHE----LSGKTVGIIGYGNIGSRVAEILKEGFNAKVLAYDPYVSE 183
Query: 738 E 738
E
Sbjct: 184 E 184
Score = 42.3 bits (100), Expect = 0.001
Identities = 18/55 (32%), Positives = 26/55 (47%), Gaps = 4/55 (7%)
Query: 812 NGEWALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRNK 866
G+W + + L G TVGI+G GNIG A++LK +K+L
Sbjct: 131 EGKWTERANFVGHE----LSGKTVGIIGYGNIGSRVAEILKEGFNAKVLAYDPYV 181
Score = 38.5 bits (90), Expect = 0.015
Identities = 28/84 (33%), Positives = 44/84 (52%), Gaps = 2/84 (2%)
Query: 75 IEKLKGCSALLCNPHQKVDKEVLDRSGENLKVIATFSVGHDHLHLDEIKSRGIRVGTV-G 133
EKLKG ++ + DKE + + + LK+IA +G+D++ L G+ V V G
Sbjct: 42 AEKLKGYDIIIASVTPNFDKEFFEYN-DGLKLIARHGIGYDNVDLKAATEHGVIVTRVPG 100
Query: 134 PVSSDTVAEYNIGLAIAVSRRFQQ 157
V D VAE+ + L + V R+ Q
Sbjct: 101 AVERDAVAEHAVALILTVLRKINQ 124
>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 = 202 bits (516), Expect = 4e-58
Identities = 92/245 (37%), Positives = 140/245 (57%), Gaps = 12/245 (4%)
Query: 875 NLKVITTFSVGYDHLELHEIKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRFQEGRKCI 934
NLK+I VG D++++ K +GI+V + SS++VAE IGL ++++R + +
Sbjct: 63 NLKIIARAGVGLDNIDVEYAKKKGIKVINTPGASSNSVAELVIGLMLSLARFIHRANREM 122
Query: 935 TSGEWALKQTHIIGPNIMG--LKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRRVKE 992
G+W K+ G L+G T+GI+G G IG E AK+ +A + ++ K+
Sbjct: 123 KLGKWNKKK-------YKGIELRGKTLGIIGFGRIGREVAKIARALGM-NVIAYDPYPKD 174
Query: 993 EGTA-LGAQLVPLDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILVNTSRGGLL 1051
E LG + V L+ L SDFI + LT +T+ +I +K+ LMK AI++NTSRGG++
Sbjct: 175 EQAVELGVKTVSLEELLKNSDFISLHVPLTPETKHMINKKELELMKDGAIIINTSRGGVI 234
Query: 1052 DQEALVEFLKDKKIGGAGLDVMIPEPLPADHPLVQLDNCVLTPHTSSATKAVRDEKSSTS 1111
D+EAL+E LK K+ GA LDV EP P L++L N LTPH ++TK ++
Sbjct: 235 DEEALLEALKSGKLAGAALDVFENEPPPG-SKLLELPNVSLTPHIGASTKEAQERIGEEL 293
Query: 1112 AENII 1116
A II
Sbjct: 294 ANKII 298
Score = 117 bits (295), Expect = 9e-29
Identities = 45/94 (47%), Positives = 61/94 (64%), Gaps = 1/94 (1%)
Query: 307 LGAQLVPLDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEAL 366
LG + V L+ L SDFI + LT +T+ +I +K+ LMK AI+INTSRGG++D+EAL
Sbjct: 180 LGVKTVSLEELLKNSDFISLHVPLTPETKHMINKKELELMKDGAIIINTSRGGVIDEEAL 239
Query: 367 VEFLKDKKIGGAGLDVMIPEPLPADHPLVQLDNC 400
+E LK K+ GA LDV EP P L++L N
Sbjct: 240 LEALKSGKLAGAALDVFENEPPPG-SKLLELPNV 272
Score = 81.0 bits (201), Expect = 2e-16
Identities = 56/213 (26%), Positives = 95/213 (44%), Gaps = 53/213 (24%)
Query: 529 AFEILGEM-FDIITYPASEGQIPRDIFIEKLRGCSALLCTSRDRVDKQVLDESGGYRCTE 587
A E L E F++ P I ++ +EK++ L+ SR +V K+V+D +
Sbjct: 13 AIEKLEEAGFEVDYEPL----IAKEELLEKIKDYDVLIVRSRTKVTKEVIDAA------- 61
Query: 588 DFFGLDLDQMFRNPSKRHVNIETVLGVSFLIKNLKVITTFSVGYDHLELHEIKARGIRVG 647
KNLK+I VG D++++ K +GI+V
Sbjct: 62 -------------------------------KNLKIIARAGVGLDNIDVEYAKKKGIKVI 90
Query: 648 SVGHISSDTVAEYNIGLAIAVSRRFQEGRKCITSGEWALKQTHIIGPNIMG--LKGATVG 705
+ SS++VAE IGL ++++R + + G+W K+ G L+G T+G
Sbjct: 91 NTPGASSNSVAELVIGLMLSLARFIHRANREMKLGKWNKKK-------YKGIELRGKTLG 143
Query: 706 IVGLGNIGLETAKLLKAFKVSKILYTSRRVKEE 738
I+G G IG E AK+ +A + ++ K+E
Sbjct: 144 IIGFGRIGREVAKIARALGM-NVIAYDPYPKDE 175
Score = 68.7 bits (169), Expect = 2e-12
Identities = 36/113 (31%), Positives = 63/113 (55%), Gaps = 6/113 (5%)
Query: 45 PESLSKLRFNSRFDIDTYPVSEGRMPRDIFIEKLKGCSALLCNPHQKVDKEVLDRSGENL 104
++ KL + F++D P+ ++ +EK+K L+ KV KEV+D +NL
Sbjct: 11 EIAIEKLE-EAGFEVDYEPLI----AKEELLEKIKDYDVLIVRSRTKVTKEVIDA-AKNL 64
Query: 105 KVIATFSVGHDHLHLDEIKSRGIRVGTVGPVSSDTVAEYNIGLAIAVSRRFQQ 157
K+IA VG D++ ++ K +GI+V SS++VAE IGL ++++R +
Sbjct: 65 KIIARAGVGLDNIDVEYAKKKGIKVINTPGASSNSVAELVIGLMLSLARFIHR 117
Score = 42.5 bits (101), Expect = 7e-04
Identities = 18/71 (25%), Positives = 31/71 (43%), Gaps = 10/71 (14%)
Query: 812 NGEWALKQTHIIGPNIMG--LKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRNKVKT 869
G+W K+ G L+G T+GI+G G IG E AK+ +A + ++
Sbjct: 124 LGKWNKKK-------YKGIELRGKTLGIIGFGRIGREVAKIARALGM-NVIAYDPYPKDE 175
Query: 870 PKRTENLKVIT 880
+K ++
Sbjct: 176 QAVELGVKTVS 186
>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 = 201 bits (514), Expect = 9e-58
Identities = 93/263 (35%), Positives = 138/263 (52%), Gaps = 12/263 (4%)
Query: 872 RTENLKVITTFSVGYDHLELHEIKARGIRV-GSVGHISSDTVAEYNIGLAIAVSRRFQEG 930
+ LK+I S G DHL L + G+ V + G+ S VAE+ + L +A+++R E
Sbjct: 57 ALKRLKLIQVPSAGVDHLPLERLPE-GVVVANNHGN--SPAVAEHALALILALAKRIVEY 113
Query: 931 RKCITSGEWALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRRV 990
+ G W P L+G TVGI+G G+IG E A+LLKAF + I +
Sbjct: 114 DNDLRRGIW--HGRAGEEPESKELRGKTVGILGYGHIGREIARLLKAFGMRVIGVSRSPK 171
Query: 991 KEEGTALGAQLVPLDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILVNTSRGGL 1050
++EG L LD ++D + V LTK T LIG + + MKP AILVN RG +
Sbjct: 172 EDEGADFVGTLSDLDEALEQADVVVVALPLTKQTRGLIGAAELAAMKPGAILVNVGRGPV 231
Query: 1051 LDQEALVEFLKDKKIGGAGLDVMIPEP------LPADHPLVQLDNCVLTPHTSSATKAVR 1104
+D+EAL E LK++ I GA +DV P P+ +P +L N +++PH + T+
Sbjct: 232 VDEEALYEALKERPIAGAAIDVWWRYPSRGDPVAPSRYPFHELPNVIMSPHNAGWTEETF 291
Query: 1105 DEKSSTSAENIIRGYKGEPMIYE 1127
+ +AENI R +GEP++
Sbjct: 292 RRRIDEAAENIRRYLRGEPLLNL 314
Score = 100 bits (251), Expect = 6e-23
Identities = 37/92 (40%), Positives = 52/92 (56%), Gaps = 6/92 (6%)
Query: 314 LDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLKDK 373
LD ++D + V LTK T LIG + + MKP AIL+N RG ++D+EAL E LK++
Sbjct: 185 LDEALEQADVVVVALPLTKQTRGLIGAAELAAMKPGAILVNVGRGPVVDEEALYEALKER 244
Query: 374 KIGGAGLDVMIPEP------LPADHPLVQLDN 399
I GA +DV P P+ +P +L N
Sbjct: 245 PIAGAAIDVWWRYPSRGDPVAPSRYPFHELPN 276
Score = 85.0 bits (211), Expect = 1e-17
Identities = 45/130 (34%), Positives = 65/130 (50%), Gaps = 6/130 (4%)
Query: 619 KNLKVITTFSVGYDHLELHEIKARGIRV-GSVGHISSDTVAEYNIGLAIAVSRRFQEGRK 677
K LK+I S G DHL L + G+ V + G+ S VAE+ + L +A+++R E
Sbjct: 59 KRLKLIQVPSAGVDHLPLERLPE-GVVVANNHGN--SPAVAEHALALILALAKRIVEYDN 115
Query: 678 CITSGEWALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRRVKE 737
+ G W P L+G TVGI+G G+IG E A+LLKAF + I + ++
Sbjct: 116 DLRRGIW--HGRAGEEPESKELRGKTVGILGYGHIGREIARLLKAFGMRVIGVSRSPKED 173
Query: 738 EGQLFSLVYD 747
EG F
Sbjct: 174 EGADFVGTLS 183
Score = 48.8 bits (117), Expect = 9e-06
Identities = 26/92 (28%), Positives = 43/92 (46%), Gaps = 7/92 (7%)
Query: 70 PRDIFIEKLKGCSALLCNPHQKVDKEVLDRSGENLKVIATFSVGHDHLHLDEIKSRGIRV 129
P + E L+ L+ +E L + LK+I S G DHL L+ + G+ V
Sbjct: 30 PDEAAEEALEDADVLVGGR--LTKEEALAA-LKRLKLIQVPSAGVDHLPLERLPE-GVVV 85
Query: 130 -GTVGPVSSDTVAEYNIGLAIAVSRRFQQRHN 160
G +S VAE+ + L +A+++R + N
Sbjct: 86 ANNHG--NSPAVAEHALALILALAKRIVEYDN 115
Score = 47.6 bits (114), Expect = 2e-05
Identities = 20/43 (46%), Positives = 24/43 (55%), Gaps = 2/43 (4%)
Query: 812 NGEWALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKAF 854
G W P L+G TVGI+G G+IG E A+LLKAF
Sbjct: 119 RGIW--HGRAGEEPESKELRGKTVGILGYGHIGREIARLLKAF 159
>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 = 197 bits (502), Expect = 4e-56
Identities = 86/288 (29%), Positives = 135/288 (46%), Gaps = 12/288 (4%)
Query: 846 ETAKLLKAFKVSKILYTSRNKVKTP--KRTENLKVITTFSVGYDHLELHEIKARGIRVGS 903
E + K ++ S V + LKVI VG D+++L RGI V +
Sbjct: 31 ELLEAAKDADA--LIVRSTTPVTAEVLEAAPGLKVIARRGVGVDNIDLDAATERGILVTN 88
Query: 904 VGHISSDTVAEYNIGLAIAVSRRFQEGRKCITSGEWALKQTHIIGPNIMGLKGATVGIVG 963
V S+++VAE +GL +A++RR E + +G+W GP + L G T+G++G
Sbjct: 89 VPGYSTESVAELTVGLILALARRIPEADASVRAGDWKKG-----GPIGLELYGKTLGVIG 143
Query: 964 LGNIGLETAKLLKAFK---VSKILYTSRRVKEEGTALGAQLVPLDTLCAESDFIFVTCAL 1020
G IG A + KA V+ Y + EEG L L ESD +
Sbjct: 144 GGGIGGIGAAIAKALGMGVVAYDPYPNPERAEEGGVEVLLLDLLLLDLKESDDLINLAPP 203
Query: 1021 TKDTEQLIGRKQFSLMKPTAILVNTSRGGLLDQEALVEFLKDKKIGGAGLDVMIPEPLPA 1080
T I + M A+ +N +RGG + +EA ++ L ++ I A LDV+ EP P
Sbjct: 204 TTMKTGHIIINEARGMLKDAVAINNARGGGVIEEAALDALLEEGIAAAALDVVEEEPPPV 263
Query: 1081 DHPLVQLDNCVLTPHTSSATKAVRDEKSSTSAENIIRGYKGEPMIYEL 1128
+ PL+ L N +LTPH + AT+ ++ + +AEN++ KG +
Sbjct: 264 NSPLLDLPNVILTPHIAGATEEAQENMAEEAAENLLAFLKGGTPPNAV 311
Score = 115 bits (290), Expect = 5e-28
Identities = 55/223 (24%), Positives = 90/223 (40%), Gaps = 50/223 (22%)
Query: 531 EILGEMFDIITYPASEGQIPRDIFIEKLRGCSALLCTSRDRVDKQVLDESGGYRCTEDFF 590
E+L E ++ + + + +E + AL+ S V +VL+ +
Sbjct: 13 ELLKEGGEVEVHDE----LLTEELLEAAKDADALIVRSTTPVTAEVLEAA---------- 58
Query: 591 GLDLDQMFRNPSKRHVNIETVLGVSFLIKNLKVITTFSVGYDHLELHEIKARGIRVGSVG 650
LKVI VG D+++L RGI V +V
Sbjct: 59 ----------------------------PGLKVIARRGVGVDNIDLDAATERGILVTNVP 90
Query: 651 HISSDTVAEYNIGLAIAVSRRFQEGRKCITSGEWALKQTHIIGPNIMGLKGATVGIVGLG 710
S+++VAE +GL +A++RR E + +G+W GP + L G T+G++G G
Sbjct: 91 GYSTESVAELTVGLILALARRIPEADASVRAGDWKKG-----GPIGLELYGKTLGVIGGG 145
Query: 711 NIGLETAKLLKAFK---VSKILYTSRRVKEEGQLFSLVYDFCR 750
IG A + KA V+ Y + EEG + L+ D
Sbjct: 146 GIGGIGAAIAKALGMGVVAYDPYPNPERAEEGGVEVLLLDLLL 188
Score = 95.0 bits (237), Expect = 4e-21
Identities = 32/96 (33%), Positives = 49/96 (51%), Gaps = 1/96 (1%)
Query: 69 MPRDIFIEKLKGCSALLCNPHQKVDKEVLDRSGENLKVIATFSVGHDHLHLDEIKSRGIR 128
+ + +E K AL+ V EVL+ + LKVIA VG D++ LD RGI
Sbjct: 27 LLTEELLEAAKDADALIVRSTTPVTAEVLEAA-PGLKVIARRGVGVDNIDLDAATERGIL 85
Query: 129 VGTVGPVSSDTVAEYNIGLAIAVSRRFQQRHNWIAR 164
V V S+++VAE +GL +A++RR + +
Sbjct: 86 VTNVPGYSTESVAELTVGLILALARRIPEADASVRA 121
Score = 73.9 bits (182), Expect = 5e-14
Identities = 28/87 (32%), Positives = 41/87 (47%)
Query: 314 LDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLKDK 373
L ESD + T I + M A+ IN +RGG + +EA ++ L ++
Sbjct: 187 LLLDLKESDDLINLAPPTTMKTGHIIINEARGMLKDAVAINNARGGGVIEEAALDALLEE 246
Query: 374 KIGGAGLDVMIPEPLPADHPLVQLDNC 400
I A LDV+ EP P + PL+ L N
Sbjct: 247 GIAAAALDVVEEEPPPVNSPLLDLPNV 273
>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 = 194 bits (497), Expect = 1e-55
Identities = 88/238 (36%), Positives = 125/238 (52%), Gaps = 20/238 (8%)
Query: 875 NLKVITTFSVGYDHLELHEIKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRFQEGRKCI 934
L++I +F VGYD ++L +ARGIRV + + +D VA+ +GL +AV RR + +
Sbjct: 64 ALELIASFGVGYDGIDLDAARARGIRVTNTPGVLTDDVADLAVGLLLAVLRRIPAADRFV 123
Query: 935 TSGEWALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRRVKEEG 994
+G W P + G VGIVGLG IG A+ L+AF + +I Y RR K +
Sbjct: 124 RAGRWPKGAF----PLTRKVSGKRVGIVGLGRIGRAIARRLEAFGM-EIAYHGRRPKPD- 177
Query: 995 TALGAQLVPL---DTLC---AESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILVNTSRG 1048
VP +L AESD + V C T L+ + + P +LVN +RG
Sbjct: 178 -------VPYRYYASLLELAAESDVLVVACPGGPATRHLVNAEVLEALGPDGVLVNVARG 230
Query: 1049 GLLDQEALVEFLKDKKIGGAGLDVMIPEPLPADHPLVQLDNCVLTPHTSSATKAVRDE 1106
++D+ AL+ L++ +I GAGLDV EP L+ LDN VLTPH +SAT R
Sbjct: 231 SVVDEAALIAALQEGRIAGAGLDVFENEPNVPA-ALLDLDNVVLTPHIASATVETRRA 287
Score = 104 bits (263), Expect = 2e-24
Identities = 45/119 (37%), Positives = 66/119 (55%), Gaps = 5/119 (4%)
Query: 620 NLKVITTFSVGYDHLELHEIKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRFQEGRKCI 679
L++I +F VGYD ++L +ARGIRV + + +D VA+ +GL +AV RR + +
Sbjct: 64 ALELIASFGVGYDGIDLDAARARGIRVTNTPGVLTDDVADLAVGLLLAVLRRIPAADRFV 123
Query: 680 TSGEWALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRRVKEE 738
+G W P + G VGIVGLG IG A+ L+AF + +I Y RR K +
Sbjct: 124 RAGRWPKGAF----PLTRKVSGKRVGIVGLGRIGRAIARRLEAFGM-EIAYHGRRPKPD 177
Score = 85.2 bits (212), Expect = 7e-18
Identities = 31/83 (37%), Positives = 46/83 (55%), Gaps = 1/83 (1%)
Query: 317 LCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLKDKKIG 376
L AESD + V C T L+ + + P +L+N +RG ++D+ AL+ L++ +I
Sbjct: 189 LAAESDVLVVACPGGPATRHLVNAEVLEALGPDGVLVNVARGSVVDEAALIAALQEGRIA 248
Query: 377 GAGLDVMIPEPLPADHPLVQLDN 399
GAGLDV EP L+ LDN
Sbjct: 249 GAGLDVFENEPNVPA-ALLDLDN 270
Score = 74.0 bits (183), Expect = 4e-14
Identities = 26/80 (32%), Positives = 44/80 (55%), Gaps = 1/80 (1%)
Query: 83 ALLCNPHQKVDKEVLDRSGENLKVIATFSVGHDHLHLDEIKSRGIRVGTVGPVSSDTVAE 142
A++ N + ++ L++IA+F VG+D + LD ++RGIRV V +D VA+
Sbjct: 45 AVVTNGETGLSAALIAAL-PALELIASFGVGYDGIDLDAARARGIRVTNTPGVLTDDVAD 103
Query: 143 YNIGLAIAVSRRFQQRHNWI 162
+GL +AV RR ++
Sbjct: 104 LAVGLLLAVLRRIPAADRFV 123
Score = 49.8 bits (120), Expect = 3e-06
Identities = 17/38 (44%), Positives = 22/38 (57%), Gaps = 1/38 (2%)
Query: 830 LKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRNKV 867
+ G VGIVGLG IG A+ L+AF + +I Y R
Sbjct: 139 VSGKRVGIVGLGRIGRAIARRLEAFGM-EIAYHGRRPK 175
>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 = 193 bits (494), Expect = 4e-55
Identities = 96/251 (38%), Positives = 132/251 (52%), Gaps = 9/251 (3%)
Query: 872 RTENLKVITTFSVGYDHLELHEIKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRFQEGR 931
R NLK++ T + ++L K RGI V G AE L +A++R E
Sbjct: 66 RLPNLKLLVTTGMRNASIDLAAAKERGIVVCGTGG-GPTATAELTWALILALARNLPEED 124
Query: 932 KCITSGEWALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRRVK 991
+ +G W QT + G GL G T+GIVGLG IG A++ +AF + I ++S
Sbjct: 125 AALRAGGW---QTTL-G---TGLAGKTLGIVGLGRIGARVARIGQAFGMRVIAWSSNLTA 177
Query: 992 EEGTALGAQL-VPLDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILVNTSRGGL 1050
E A G + V + L A SD + + L+ T L+G + +LMKPTA+LVNTSRG L
Sbjct: 178 ERAAAAGVEAAVSKEELFATSDVVSLHLVLSDRTRGLVGAEDLALMKPTALLVNTSRGPL 237
Query: 1051 LDQEALVEFLKDKKIGGAGLDVMIPEPLPADHPLVQLDNCVLTPHTSSATKAVRDEKSST 1110
+D+ AL+ L+ +I GA LDV EPLPADHPL L N +LTPH T+ +
Sbjct: 238 VDEGALLAALRAGRIAGAALDVFDVEPLPADHPLRGLPNVLLTPHIGYVTEEAYEGFYGQ 297
Query: 1111 SAENIIRGYKG 1121
+ ENI G
Sbjct: 298 AVENIAAWLAG 308
Score = 114 bits (289), Expect = 6e-28
Identities = 45/95 (47%), Positives = 60/95 (63%), Gaps = 1/95 (1%)
Query: 306 ALGAQL-VPLDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQE 364
A G + V + L A SD + + L+ T L+G + +LMKPTA+L+NTSRG L+D+
Sbjct: 182 AAGVEAAVSKEELFATSDVVSLHLVLSDRTRGLVGAEDLALMKPTALLVNTSRGPLVDEG 241
Query: 365 ALVEFLKDKKIGGAGLDVMIPEPLPADHPLVQLDN 399
AL+ L+ +I GA LDV EPLPADHPL L N
Sbjct: 242 ALLAALRAGRIAGAALDVFDVEPLPADHPLRGLPN 276
Score = 69.1 bits (170), Expect = 2e-12
Identities = 37/104 (35%), Positives = 52/104 (50%), Gaps = 8/104 (7%)
Query: 620 NLKVITTFSVGYDHLELHEIKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRFQEGRKCI 679
NLK++ T + ++L K RGI V G AE L +A++R E +
Sbjct: 69 NLKLLVTTGMRNASIDLAAAKERGIVVCGTGG-GPTATAELTWALILALARNLPEEDAAL 127
Query: 680 TSGEWALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKAF 723
+G W QT + G GL G T+GIVGLG IG A++ +AF
Sbjct: 128 RAGGW---QTTL-G---TGLAGKTLGIVGLGRIGARVARIGQAF 164
Score = 43.7 bits (104), Expect = 3e-04
Identities = 25/90 (27%), Positives = 38/90 (42%), Gaps = 5/90 (5%)
Query: 70 PRDIFIEKLKGCSAL-LCNPHQKVDKEVLDRSGENLKVIATFSVGHDHLHLDEIKSRGIR 128
D E+L A+ L +L+R NLK++ T + + + L K RGI
Sbjct: 36 DEDALAERLAPFDAIVLMRERTPFPAALLERLP-NLKLLVTTGMRNASIDLAAAKERGIV 94
Query: 129 V-GTVGPVSSDTVAEYNIGLAIAVSRRFQQ 157
V GT G AE L +A++R +
Sbjct: 95 VCGTGG--GPTATAELTWALILALARNLPE 122
Score = 41.7 bits (99), Expect = 0.002
Identities = 15/27 (55%), Positives = 19/27 (70%)
Query: 828 MGLKGATVGIVGLGNIGLETAKLLKAF 854
GL G T+GIVGLG IG A++ +AF
Sbjct: 138 TGLAGKTLGIVGLGRIGARVARIGQAF 164
>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 = 185 bits (472), Expect = 3e-52
Identities = 77/235 (32%), Positives = 112/235 (47%), Gaps = 12/235 (5%)
Query: 894 IKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRFQEGRKCITSGEWALKQTHIIGPNIMG 953
I G R + ++TVAE+ + L +A R+ + W +
Sbjct: 69 ITDPGRRWTNAAGAYAETVAEHALALLLAGLRQL---PARARATTWDPA---EEDDLVTL 122
Query: 954 LKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRRVKEEGTALGAQLVPLDTL---CAE 1010
L+G+TV IVG G IG LL F I EG + VP D L +
Sbjct: 123 LRGSTVAIVGAGGIGRALIPLLAPFGAKVIAVNRSGRPVEG---ADETVPADRLDEVWPD 179
Query: 1011 SDFIFVTCALTKDTEQLIGRKQFSLMKPTAILVNTSRGGLLDQEALVEFLKDKKIGGAGL 1070
+D + + LT +T L+ + MKP A LVN +RG L+D +ALV+ L+ +I GA L
Sbjct: 180 ADHVVLAAPLTPETRHLVDAAALAAMKPHAWLVNVARGPLVDTDALVDALRSGEIAGAAL 239
Query: 1071 DVMIPEPLPADHPLVQLDNCVLTPHTSSATKAVRDEKSSTSAENIIRGYKGEPMI 1125
DV PEPLP HPL L N ++TPH ++ + +R + AEN+ GEP++
Sbjct: 240 DVTDPEPLPDGHPLWSLPNALITPHVANTPEVIRPLLAERVAENVRAFAAGEPLL 294
Score = 123 bits (311), Expect = 7e-31
Identities = 43/104 (41%), Positives = 58/104 (55%), Gaps = 4/104 (3%)
Query: 301 RSNGTALGA-QLVPLDTL---CAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTS 356
RS GA + VP D L ++D + + LT +T L+ + MKP A L+N +
Sbjct: 156 RSGRPVEGADETVPADRLDEVWPDADHVVLAAPLTPETRHLVDAAALAAMKPHAWLVNVA 215
Query: 357 RGGLLDQEALVEFLKDKKIGGAGLDVMIPEPLPADHPLVQLDNC 400
RG L+D +ALV+ L+ +I GA LDV PEPLP HPL L N
Sbjct: 216 RGPLVDTDALVDALRSGEIAGAALDVTDPEPLPDGHPLWSLPNA 259
Score = 50.3 bits (121), Expect = 2e-06
Identities = 25/95 (26%), Positives = 36/95 (37%), Gaps = 6/95 (6%)
Query: 639 IKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRFQEGRKCITSGEWALKQTHIIGPNIMG 698
I G R + ++TVAE+ + L +A R+ + W +
Sbjct: 69 ITDPGRRWTNAAGAYAETVAEHALALLLAGLRQL---PARARATTWDPA---EEDDLVTL 122
Query: 699 LKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSR 733
L+G+TV IVG G IG LL F I
Sbjct: 123 LRGSTVAIVGAGGIGRALIPLLAPFGAKVIAVNRS 157
Score = 36.5 bits (85), Expect = 0.064
Identities = 14/35 (40%), Positives = 16/35 (45%)
Query: 830 LKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSR 864
L+G+TV IVG G IG LL F I
Sbjct: 123 LRGSTVAIVGAGGIGRALIPLLAPFGAKVIAVNRS 157
>gnl|CDD|237436 PRK13581, PRK13581, D-3-phosphoglycerate dehydrogenase; Provisional.
Length = 526
Score = 189 bits (483), Expect = 2e-51
Identities = 103/275 (37%), Positives = 146/275 (53%), Gaps = 32/275 (11%)
Query: 863 SRNKVKTPK---RTENLKVITTFSVGYDHLELHEIKARGIRV-----GSVGHISSDTVAE 914
S KV T + +NLKVI VG D++++ RGI V G+ IS AE
Sbjct: 50 SATKV-TAEVLEAAKNLKVIGRAGVGVDNVDVPAATRRGIIVVNAPTGNT--IS---AAE 103
Query: 915 YNIGLAIAVSRRFQEGRKCITSGEWALKQTHIIGPNIMG--LKGATVGIVGLGNIGLETA 972
+ I L +A++R + + +G+W K MG L G T+GI+GLG IG E A
Sbjct: 104 HTIALMLALARNIPQAHASLKAGKWERK-------KFMGVELYGKTLGIIGLGRIGSEVA 156
Query: 973 KLLKAFKVSKILY----TSRRVKEEGTALGAQLVPLDTLCAESDFIFVTCALTKDTEQLI 1028
K KAF + I Y + R + LG +LV LD L A +DFI + LT +T LI
Sbjct: 157 KRAKAFGMKVIAYDPYISPERAAQ----LGVELVSLDELLARADFITLHTPLTPETRGLI 212
Query: 1029 GRKQFSLMKPTAILVNTSRGGLLDQEALVEFLKDKKIGGAGLDVMIPEPLPADHPLVQLD 1088
G ++ + MKP ++N +RGG++D+ AL E LK K+ GA LDV EP P D PL +L
Sbjct: 213 GAEELAKMKPGVRIINCARGGIIDEAALAEALKSGKVAGAALDVFEKEP-PTDSPLFELP 271
Query: 1089 NCVLTPHTSSATKAVRDEKSSTSAENIIRGYKGEP 1123
N V+TPH ++T ++ + AE +I +G P
Sbjct: 272 NVVVTPHLGASTAEAQENVAIQVAEQVIDALRGGP 306
Score = 128 bits (324), Expect = 8e-31
Identities = 45/93 (48%), Positives = 59/93 (63%), Gaps = 1/93 (1%)
Query: 307 LGAQLVPLDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEAL 366
LG +LV LD L A +DFI + LT +T LIG ++ + MKP +IN +RGG++D+ AL
Sbjct: 181 LGVELVSLDELLARADFITLHTPLTPETRGLIGAEELAKMKPGVRIINCARGGIIDEAAL 240
Query: 367 VEFLKDKKIGGAGLDVMIPEPLPADHPLVQLDN 399
E LK K+ GA LDV EP P D PL +L N
Sbjct: 241 AEALKSGKVAGAALDVFEKEP-PTDSPLFELPN 272
Score = 60.9 bits (149), Expect = 2e-09
Identities = 43/113 (38%), Positives = 58/113 (51%), Gaps = 19/113 (16%)
Query: 619 KNLKVITTFSVGYDHLELHEIKARGIRV-----GSVGHISSDTVAEYNIGLAIAVSRRFQ 673
KNLKVI VG D++++ RGI V G+ IS AE+ I L +A++R
Sbjct: 63 KNLKVIGRAGVGVDNVDVPAATRRGIIVVNAPTGNT--IS---AAEHTIALMLALARNIP 117
Query: 674 EGRKCITSGEWALKQTHIIGPNIMG--LKGATVGIVGLGNIGLETAKLLKAFK 724
+ + +G+W K MG L G T+GI+GLG IG E AK KAF
Sbjct: 118 QAHASLKAGKWERK-------KFMGVELYGKTLGIIGLGRIGSEVAKRAKAFG 163
Score = 45.8 bits (110), Expect = 1e-04
Identities = 21/46 (45%), Positives = 24/46 (52%), Gaps = 9/46 (19%)
Query: 812 NGEWALKQTHIIGPNIMG--LKGATVGIVGLGNIGLETAKLLKAFK 855
G+W K MG L G T+GI+GLG IG E AK KAF
Sbjct: 125 AGKWERK-------KFMGVELYGKTLGIIGLGRIGSEVAKRAKAFG 163
Score = 43.5 bits (104), Expect = 6e-04
Identities = 34/131 (25%), Positives = 58/131 (44%), Gaps = 22/131 (16%)
Query: 41 RLLVPESLSK-----LRFNSRFDIDTYPVSEGRMPRDIFIEKLKGCSALLCNPHQKVDKE 95
++LV + +S L+ ++D + ++ +E + AL+ KV E
Sbjct: 2 KVLVSDPISPAGLEILKDAPGVEVDVKT----GLDKEELLEIIGDYDALIVRSATKVTAE 57
Query: 96 VLDRSGENLKVIATFSVGHDHLHLDEIKSRGIRV------GTVGPVSSDTVAEYNIGLAI 149
VL+ +NLKVI VG D++ + RGI V T+ + AE+ I L +
Sbjct: 58 VLEA-AKNLKVIGRAGVGVDNVDVPAATRRGIIVVNAPTGNTI------SAAEHTIALML 110
Query: 150 AVSRRFQQRHN 160
A++R Q H
Sbjct: 111 ALARNIPQAHA 121
>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 = 183 bits (466), Expect = 4e-51
Identities = 82/235 (34%), Positives = 120/235 (51%), Gaps = 4/235 (1%)
Query: 893 EIKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRFQEGRKCITSGEWALKQTHIIGPNIM 952
+ RGI V S +++ VAE+ + + RR +G T G
Sbjct: 90 AVWERGILVTSAADANAEPVAEFTLAAILLALRRIPRFAAAYRAGRDWGWPTRRGGR--- 146
Query: 953 GLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRRVKEEGTALGAQLVPLDTLCAESD 1012
GL G TVGIVG G IG +LL+ F + ++Y E ALG +LV LD L A SD
Sbjct: 147 GLYGRTVGIVGFGRIGRAVVELLRPFGLRVLVYDPYLPAAEAAALGVELVSLDELLARSD 206
Query: 1013 FIFVTCALTKDTEQLIGRKQFSLMKPTAILVNTSRGGLLDQEALVEFLKDKKIGGAGLDV 1072
+ + LT +T +I + +LM+ A +NT+RG L+D+ AL+ L+ ++ A LDV
Sbjct: 207 VVSLHAPLTPETRGMIDARLLALMRDGATFINTARGALVDEAALLAELRSGRL-RAALDV 265
Query: 1073 MIPEPLPADHPLVQLDNCVLTPHTSSATKAVRDEKSSTSAENIIRGYKGEPMIYE 1127
PEPLP D PL L N +LTPH + +T R + + + R GEP+++E
Sbjct: 266 TDPEPLPPDSPLRTLPNVLLTPHIAGSTGDERRRLGDYALDELERFLAGEPLLHE 320
Score = 118 bits (297), Expect = 9e-29
Identities = 42/95 (44%), Positives = 57/95 (60%), Gaps = 1/95 (1%)
Query: 305 TALGAQLVPLDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQE 364
ALG +LV LD L A SD + + LT +T +I + +LM+ A INT+RG L+D+
Sbjct: 189 AALGVELVSLDELLARSDVVSLHAPLTPETRGMIDARLLALMRDGATFINTARGALVDEA 248
Query: 365 ALVEFLKDKKIGGAGLDVMIPEPLPADHPLVQLDN 399
AL+ L+ ++ A LDV PEPLP D PL L N
Sbjct: 249 ALLAELRSGRL-RAALDVTDPEPLPPDSPLRTLPN 282
Score = 59.5 bits (145), Expect = 3e-09
Identities = 29/93 (31%), Positives = 42/93 (45%), Gaps = 3/93 (3%)
Query: 638 EIKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRFQEGRKCITSGEWALKQTHIIGPNIM 697
+ RGI V S +++ VAE+ + + RR +G T G
Sbjct: 90 AVWERGILVTSAADANAEPVAEFTLAAILLALRRIPRFAAAYRAGRDWGWPTRRGGR--- 146
Query: 698 GLKGATVGIVGLGNIGLETAKLLKAFKVSKILY 730
GL G TVGIVG G IG +LL+ F + ++Y
Sbjct: 147 GLYGRTVGIVGFGRIGRAVVELLRPFGLRVLVY 179
Score = 41.0 bits (97), Expect = 0.003
Identities = 16/33 (48%), Positives = 21/33 (63%)
Query: 829 GLKGATVGIVGLGNIGLETAKLLKAFKVSKILY 861
GL G TVGIVG G IG +LL+ F + ++Y
Sbjct: 147 GLYGRTVGIVGFGRIGRAVVELLRPFGLRVLVY 179
Score = 37.9 bits (89), Expect = 0.025
Identities = 26/121 (21%), Positives = 49/121 (40%), Gaps = 17/121 (14%)
Query: 41 RLLVPESLSKLRFNSRFDI-DTYPVSEGRMPRDIFIEKLKGCSALLC---NPHQKVDKEV 96
P +L++L + ++ P ++ L G L+ P +D E+
Sbjct: 13 LFFGPAALARLA--ALAEVLPPTPDADFAAEE--LRALLAGVEVLVTGWGTPP--LDAEL 66
Query: 97 LDRSGENLKVI--ATFSVGHDHLHL-DEIKSRGIRVGTVGPVSSDTVAEYNIGLAIAVSR 153
L R+ L+ + A SV + D + RGI V + +++ VAE+ + + R
Sbjct: 67 LARAP-RLRAVVHAAGSVRG---LVTDAVWERGILVTSAADANAEPVAEFTLAAILLALR 122
Query: 154 R 154
R
Sbjct: 123 R 123
>gnl|CDD|185307 PRK15409, PRK15409, bifunctional glyoxylate/hydroxypyruvate reductase
B; Provisional.
Length = 323
Score = 182 bits (463), Expect = 8e-51
Identities = 100/283 (35%), Positives = 150/283 (53%), Gaps = 17/283 (6%)
Query: 848 AKLLKAFKVSKILYTSRNKV------KTPKRTENLKVITTFSVGYDHLELHEIKARGIRV 901
+ AF ++ L S KV K PK L+ +T SVGYD+ ++ + AR I +
Sbjct: 37 EQHAAAFAEAEGLLGSGEKVDAALLEKMPK----LRAASTISVGYDNFDVDALTARKILL 92
Query: 902 GSVGHISSDTVAEYNIGLAIAVSRRFQEGRKCITSGEWALKQTHIIGPNIMG--LKGATV 959
+ ++TVA+ + L ++ +RR E + + +GEW T IGP+ G + T+
Sbjct: 93 MHTPTVLTETVADTLMALVLSTARRVVEVAERVKAGEW----TASIGPDWFGTDVHHKTL 148
Query: 960 GIVGLGNIGLETAKLLKAFKVSKILYTSRRVKEEG-TALGAQLVPLDTLCAESDFIFVTC 1018
GIVG+G IG+ A+ ILY +RR +E A+ LDTL ESDF+ +
Sbjct: 149 GIVGMGRIGMALAQRAHFGFNMPILYNARRHHKEAEERFNARYCDLDTLLQESDFVCIIL 208
Query: 1019 ALTKDTEQLIGRKQFSLMKPTAILVNTSRGGLLDQEALVEFLKDKKIGGAGLDVMIPEPL 1078
LT +T L G +QF+ MK +AI +N RG ++D+ AL+ L+ +I AGLDV EPL
Sbjct: 209 PLTDETHHLFGAEQFAKMKSSAIFINAGRGPVVDENALIAALQKGEIHAAGLDVFEQEPL 268
Query: 1079 PADHPLVQLDNCVLTPHTSSATKAVRDEKSSTSAENIIRGYKG 1121
D PL+ L N V PH SAT R ++ + +N+I +G
Sbjct: 269 SVDSPLLSLPNVVAVPHIGSATHETRYNMAACAVDNLIDALQG 311
Score = 106 bits (266), Expect = 7e-25
Identities = 42/92 (45%), Positives = 56/92 (60%)
Query: 308 GAQLVPLDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALV 367
A+ LDTL ESDF+ + LT +T L G +QF+ MK +AI IN RG ++D+ AL+
Sbjct: 188 NARYCDLDTLLQESDFVCIILPLTDETHHLFGAEQFAKMKSSAIFINAGRGPVVDENALI 247
Query: 368 EFLKDKKIGGAGLDVMIPEPLPADHPLVQLDN 399
L+ +I AGLDV EPL D PL+ L N
Sbjct: 248 AALQKGEIHAAGLDVFEQEPLSVDSPLLSLPN 279
Score = 66.3 bits (162), Expect = 2e-11
Identities = 40/123 (32%), Positives = 67/123 (54%), Gaps = 6/123 (4%)
Query: 620 NLKVITTFSVGYDHLELHEIKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRFQEGRKCI 679
L+ +T SVGYD+ ++ + AR I + + ++TVA+ + L ++ +RR E + +
Sbjct: 66 KLRAASTISVGYDNFDVDALTARKILLMHTPTVLTETVADTLMALVLSTARRVVEVAERV 125
Query: 680 TSGEWALKQTHIIGPNIMG--LKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRRVKE 737
+GEW T IGP+ G + T+GIVG+G IG+ A+ ILY +RR +
Sbjct: 126 KAGEW----TASIGPDWFGTDVHHKTLGIVGMGRIGMALAQRAHFGFNMPILYNARRHHK 181
Query: 738 EGQ 740
E +
Sbjct: 182 EAE 184
Score = 37.8 bits (88), Expect = 0.029
Identities = 20/65 (30%), Positives = 39/65 (60%), Gaps = 1/65 (1%)
Query: 90 QKVDKEVLDRSGENLKVIATFSVGHDHLHLDEIKSRGIRVGTVGPVSSDTVAEYNIGLAI 149
+KVD +L++ L+ +T SVG+D+ +D + +R I + V ++TVA+ + L +
Sbjct: 54 EKVDAALLEKM-PKLRAASTISVGYDNFDVDALTARKILLMHTPTVLTETVADTLMALVL 112
Query: 150 AVSRR 154
+ +RR
Sbjct: 113 STARR 117
Score = 33.2 bits (76), Expect = 0.81
Identities = 21/54 (38%), Positives = 28/54 (51%), Gaps = 6/54 (11%)
Query: 813 GEWALKQTHIIGPNIMG--LKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSR 864
GEW T IGP+ G + T+GIVG+G IG+ A+ ILY +R
Sbjct: 128 GEW----TASIGPDWFGTDVHHKTLGIVGMGRIGMALAQRAHFGFNMPILYNAR 177
>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 = 181 bits (463), Expect = 8e-51
Identities = 83/257 (32%), Positives = 129/257 (50%), Gaps = 17/257 (6%)
Query: 874 ENLKVITTFSVGYDHLELHEIKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRFQEGRKC 933
+LK+I GYD +++ + RGI+V + + A+ + L + R F +
Sbjct: 75 PSLKIIAHAGAGYDQIDVDALTKRGIQVSNTPGAVDEATADTALFLILGALRNFSRAERS 134
Query: 934 ITSGEW----ALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRR 989
+G+W L H +G T+GI+GLG IG A+ AF + KI+Y +R
Sbjct: 135 ARAGKWRGFLDLTLAH-------DPRGKTLGILGLGGIGKAIARKAAAFGM-KIIYHNRS 186
Query: 990 VK--EEGTALGAQLVPLDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILVNTSR 1047
E AL V LD L A+SD + + C LT T LI +K+F+ MK I+VNT+R
Sbjct: 187 RLPEELEKALATYYVSLDELLAQSDVVSLNCPLTAATRHLINKKEFAKMKDGVIIVNTAR 246
Query: 1048 GGLLDQEALVEFLKDKKIGGAGLDVMIPEPLPADHP-LVQLDNCVLTPHTSSATKAVRDE 1106
G ++D++ALV+ L+ K+ AGLDV EP +P L+++ N L PH + T +++
Sbjct: 247 GAVIDEDALVDALESGKVASAGLDVFENEPEV--NPGLLKMPNVTLLPHMGTLTVETQEK 304
Query: 1107 KSSTSAENIIRGYKGEP 1123
ENI +
Sbjct: 305 MEELVLENIEAFLETGK 321
Score = 104 bits (262), Expect = 3e-24
Identities = 46/131 (35%), Positives = 67/131 (51%), Gaps = 11/131 (8%)
Query: 306 ALGAQLVPLDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEA 365
AL V LD L A+SD + + C LT T LI +K+F+ MK I++NT+RG ++D++A
Sbjct: 195 ALATYYVSLDELLAQSDVVSLNCPLTAATRHLINKKEFAKMKDGVIIVNTARGAVIDEDA 254
Query: 366 LVEFLKDKKIGGAGLDVMIPEPLP----ADHPLVQL-DNCGGAGLDVMIPEPLPADHPLV 420
LV+ L+ K+ AGLDV EP P V L + G ++ +
Sbjct: 255 LVDALESGKVASAGLDVFENEPEVNPGLLKMPNVTLLPHMGTLTVETQE------KMEEL 308
Query: 421 QLDNCEEFFEE 431
L+N E F E
Sbjct: 309 VLENIEAFLET 319
Score = 79.9 bits (198), Expect = 7e-16
Identities = 50/231 (21%), Positives = 85/231 (36%), Gaps = 55/231 (23%)
Query: 514 KPK-LFLTRDDYSRVPAFEILGEMFDIITYPASEGQIPRDIFIEKLR-----GCSALLCT 567
KPK L L ++ ++ L + ++I + R+ FIE L+ A+ T
Sbjct: 1 KPKVLLLGDPIHAH-DEWKELSSIAEVIYPTS----GTREEFIEALKEGKYGDFVAIYRT 55
Query: 568 SRDRVDKQVLDESGGYRCTEDFFGLDLDQMFRNPSKRHVNIETVLGVSFLIKNLKVITTF 627
+ E+ L +LK+I
Sbjct: 56 F-GSAGET-------GPFDEELISP------------------------LPPSLKIIAHA 83
Query: 628 SVGYDHLELHEIKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRFQEGRKCITSGEW--- 684
GYD +++ + RGI+V + + A+ + L + R F + +G+W
Sbjct: 84 GAGYDQIDVDALTKRGIQVSNTPGAVDEATADTALFLILGALRNFSRAERSARAGKWRGF 143
Query: 685 -ALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRR 734
L H +G T+GI+GLG IG A+ AF + KI+Y +R
Sbjct: 144 LDLTLAH-------DPRGKTLGILGLGGIGKAIARKAAAFGM-KIIYHNRS 186
Score = 46.4 bits (111), Expect = 5e-05
Identities = 22/59 (37%), Positives = 32/59 (54%), Gaps = 5/59 (8%)
Query: 831 KGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRNKVKTPKRTENLKVITTFSVGYDHL 889
+G T+GI+GLG IG A+ AF + KI+Y +R + E K + T+ V D L
Sbjct: 153 RGKTLGILGLGGIGKAIARKAAAFGM-KIIYHNR----SRLPEELEKALATYYVSLDEL 206
Score = 45.2 bits (108), Expect = 1e-04
Identities = 30/134 (22%), Positives = 49/134 (36%), Gaps = 25/134 (18%)
Query: 52 RFNSRFDIDTYPVSEGRMPRDIFIEKLK-----GCSALLCNPHQK-----VDKEVLDRSG 101
+S ++ R+ FIE LK A+ D+E++
Sbjct: 19 ELSSIAEVIYPT----SGTREEFIEALKEGKYGDFVAIYRTFGSAGETGPFDEELISPLP 74
Query: 102 ENLKVIATFSVGHDHLHLDEIKSRGIRVGTVGPVSSDTVAEYNIGLAIAVSRRFQQRHNW 161
+LK+IA G+D + +D + RGI+V + A+ + L + R F
Sbjct: 75 PSLKIIAHAGAGYDQIDVDALTKRGIQVSNTPGAVDEATADTALFLILGALRNF------ 128
Query: 162 IARLSSFAEIQTRA 175
S AE RA
Sbjct: 129 -----SRAERSARA 137
>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 = 179 bits (457), Expect = 7e-50
Identities = 100/307 (32%), Positives = 153/307 (49%), Gaps = 37/307 (12%)
Query: 843 IGLETAKLLKAFKVSKILYTSRNKVKTPKRTENLKVITTFSVGYDHLELHEIKARGIRVG 902
+ + + K +V + SR + ++ LK+I T S G+DH++L + RGI V
Sbjct: 31 LLDDNVEEFKDAEVISVFVYSRLDAEVLEKLPRLKLIATRSTGFDHIDLEACRERGIAVC 90
Query: 903 SVGHISSDTVAEYNIGLAIAVSRRFQEGRKCITSGEWALKQTHIIGPNIMG--LKGATVG 960
+V TVAE+ L +A+SR+ +E + G+++ + G L G T+G
Sbjct: 91 NVPDYGEATVAEHAFALLLALSRKLREAIERTRRGDFSQA-------GLRGFELAGKTLG 143
Query: 961 IVGLGNIGLETAKLLKAFKVSKILYTSRRVKEEGTALGAQLVPLDTLCAESDFIFVTCAL 1020
+VG G IG A++ + F + + Y +E LG + V L+ L ESD I +
Sbjct: 144 VVGTGRIGRRVARIARGFGMKVLAYDVVPDEELAERLGFRYVSLEELLQESDIISLHVPY 203
Query: 1021 TKDTEQLIGRKQFSLMKPTAILVNTSRGGLLDQEALVEFLKDKKIGGAGLDV------MI 1074
T T LI R+ F+LMKP A+L+NT+RG ++D EALV LK+ K+ GAGLDV +
Sbjct: 204 TPQTHHLINRENFALMKPGAVLINTARGAVVDTEALVRALKEGKLAGAGLDVLEQEEVLR 263
Query: 1075 PE--------------PLPADHPLVQLDNCVLTPH----TSSATKAVRDEKSSTSAENII 1116
E L ADH L++ N ++TPH T A + + D T+ ENI
Sbjct: 264 EEAELFREDVSPEDLKKLLADHALLRKPNVIITPHVAYNTKEALERILD----TTVENIK 319
Query: 1117 RGYKGEP 1123
G+P
Sbjct: 320 AFAAGQP 326
Score = 100 bits (250), Expect = 1e-22
Identities = 47/118 (39%), Positives = 68/118 (57%), Gaps = 5/118 (4%)
Query: 307 LGAQLVPLDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEAL 366
LG + V L+ L ESD I + T T LI R+ F+LMKP A+LINT+RG ++D EAL
Sbjct: 180 LGFRYVSLEELLQESDIISLHVPYTPQTHHLINRENFALMKPGAVLINTARGAVVDTEAL 239
Query: 367 VEFLKDKKIGGAGLDVMIPEPLPADHPLVQLDNCGGAGLDVMIPEPLPADHPLVQLDN 424
V LK+ K+ GAGLDV+ E + + + ++ L ++ ADH L++ N
Sbjct: 240 VRALKEGKLAGAGLDVLEQEEVLREEAELFREDVSPEDLKKLL-----ADHALLRKPN 292
Score = 80.8 bits (200), Expect = 4e-16
Identities = 36/106 (33%), Positives = 57/106 (53%), Gaps = 9/106 (8%)
Query: 620 NLKVITTFSVGYDHLELHEIKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRFQEGRKCI 679
LK+I T S G+DH++L + RGI V +V TVAE+ L +A+SR+ +E +
Sbjct: 63 RLKLIATRSTGFDHIDLEACRERGIAVCNVPDYGEATVAEHAFALLLALSRKLREAIERT 122
Query: 680 TSGEWALKQTHIIGPNIMG--LKGATVGIVGLGNIGLETAKLLKAF 723
G+++ + G L G T+G+VG G IG A++ + F
Sbjct: 123 RRGDFSQA-------GLRGFELAGKTLGVVGTGRIGRRVARIARGF 161
Score = 65.4 bits (160), Expect = 4e-11
Identities = 30/89 (33%), Positives = 48/89 (53%), Gaps = 2/89 (2%)
Query: 89 HQKVDKEVLDRSGENLKVIATFSVGHDHLHLDEIKSRGIRVGTVGPVSSDTVAEYNIGLA 148
+ ++D EVL++ LK+IAT S G DH+ L+ + RGI V V TVAE+ L
Sbjct: 50 YSRLDAEVLEKL-PRLKLIATRSTGFDHIDLEACRERGIAVCNVPDYGEATVAEHAFALL 108
Query: 149 IAVSRRFQQRHNWIARLSSFAEIQTRALD 177
+A+SR+ ++ R F++ R +
Sbjct: 109 LALSRKLREAIE-RTRRGDFSQAGLRGFE 136
Score = 36.5 bits (85), Expect = 0.073
Identities = 11/25 (44%), Positives = 16/25 (64%)
Query: 830 LKGATVGIVGLGNIGLETAKLLKAF 854
L G T+G+VG G IG A++ + F
Sbjct: 137 LAGKTLGVVGTGRIGRRVARIARGF 161
>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 = 182 bits (464), Expect = 6e-49
Identities = 99/286 (34%), Positives = 147/286 (51%), Gaps = 14/286 (4%)
Query: 844 GLETAKLLKAFKVSKILYT-SRNKV--KTPKRTENLKVITTFSVGYDHLELHEIKARGIR 900
GL +LL+ L S KV + LKVI VG D++++ ARGI
Sbjct: 28 GLSREELLEIIPDYDALIVRSATKVTEEVIAAAPKLKVIGRAGVGVDNIDIEAATARGIL 87
Query: 901 VGSVGHISSDTVAEYNIGLAIAVSRRFQEGRKCITSGEWALKQTHIIGPNIMG--LKGAT 958
V + ++ + AE+ + + +A +R + + GEW K MG L G T
Sbjct: 88 VVNAPTGNTISAAEHALAMLLAAARNIPQADASLKEGEWDRKA-------FMGTELYGKT 140
Query: 959 VGIVGLGNIGLETAKLLKAFKVSKILYTSRRVKEEGTALGAQLVP-LDTLCAESDFIFVT 1017
+G++GLG IG AK KAF + + Y E LG +LV LD L A +DFI V
Sbjct: 141 LGVIGLGRIGSIVAKRAKAFGMKVLAYDPYISPERAEQLGVELVDDLDELLARADFITVH 200
Query: 1018 CALTKDTEQLIGRKQFSLMKPTAILVNTSRGGLLDQEALVEFLKDKKIGGAGLDVMIPEP 1077
LT +T LIG ++ + MK I+VN +RGG++D+ AL E L++ + A LDV EP
Sbjct: 201 TPLTPETRGLIGAEELAKMKKGVIIVNCARGGIIDEAALYEALEEGHVRAAALDVFEKEP 260
Query: 1078 LPADHPLVQLDNCVLTPHTSSATKAVRDEKSSTSAENIIRGYKGEP 1123
P D+PL LDN + TPH ++T+ ++ ++ AE ++ KG P
Sbjct: 261 -PTDNPLFDLDNVIATPHLGASTREAQENVATQVAEQVLDALKGLP 305
Score = 104 bits (261), Expect = 5e-23
Identities = 43/94 (45%), Positives = 59/94 (62%), Gaps = 2/94 (2%)
Query: 307 LGAQLVP-LDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEA 365
LG +LV LD L A +DFI V LT +T LIG ++ + MK I++N +RGG++D+ A
Sbjct: 179 LGVELVDDLDELLARADFITVHTPLTPETRGLIGAEELAKMKKGVIIVNCARGGIIDEAA 238
Query: 366 LVEFLKDKKIGGAGLDVMIPEPLPADHPLVQLDN 399
L E L++ + A LDV EP P D+PL LDN
Sbjct: 239 LYEALEEGHVRAAALDVFEKEP-PTDNPLFDLDN 271
Score = 63.9 bits (156), Expect = 3e-10
Identities = 37/114 (32%), Positives = 57/114 (50%), Gaps = 9/114 (7%)
Query: 619 KNLKVITTFSVGYDHLELHEIKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRFQEGRKC 678
LKVI VG D++++ ARGI V + ++ + AE+ + + +A +R +
Sbjct: 61 PKLKVIGRAGVGVDNIDIEAATARGILVVNAPTGNTISAAEHALAMLLAAARNIPQADAS 120
Query: 679 ITSGEWALKQTHIIGPNIMG--LKGATVGIVGLGNIGLETAKLLKAFKVSKILY 730
+ GEW K MG L G T+G++GLG IG AK KAF + + Y
Sbjct: 121 LKEGEWDRKA-------FMGTELYGKTLGVIGLGRIGSIVAKRAKAFGMKVLAY 167
Score = 48.5 bits (116), Expect = 2e-05
Identities = 24/94 (25%), Positives = 45/94 (47%), Gaps = 1/94 (1%)
Query: 66 EGRMPRDIFIEKLKGCSALLCNPHQKVDKEVLDRSGENLKVIATFSVGHDHLHLDEIKSR 125
+ + R+ +E + AL+ KV +EV+ LKVI VG D++ ++ +R
Sbjct: 26 QTGLSREELLEIIPDYDALIVRSATKVTEEVIAA-APKLKVIGRAGVGVDNIDIEAATAR 84
Query: 126 GIRVGTVGPVSSDTVAEYNIGLAIAVSRRFQQRH 159
GI V ++ + AE+ + + +A +R Q
Sbjct: 85 GILVVNAPTGNTISAAEHALAMLLAAARNIPQAD 118
Score = 41.2 bits (97), Expect = 0.003
Identities = 24/63 (38%), Positives = 31/63 (49%), Gaps = 14/63 (22%)
Query: 812 NGEWALKQTHIIGPNIMG--LKGATVGIVGLGNIGLETAKLLKAFKVSKIL----YTSRN 865
GEW K MG L G T+G++GLG IG AK KAF + K+L Y S
Sbjct: 123 EGEWDRKA-------FMGTELYGKTLGVIGLGRIGSIVAKRAKAFGM-KVLAYDPYISPE 174
Query: 866 KVK 868
+ +
Sbjct: 175 RAE 177
>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 = 170 bits (433), Expect = 6e-47
Identities = 91/258 (35%), Positives = 125/258 (48%), Gaps = 14/258 (5%)
Query: 874 ENLKVITTFSVGYDHLELHEIKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRFQEGRKC 933
LK+I GYD+ ++ ARGI V V + ++ AE IGL I + R G +
Sbjct: 65 PRLKIIACALKGYDNFDVEACTARGIWVTIVPDLLTEPTAELTIGLLIGLGRHILAGDRF 124
Query: 934 ITSGEWALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRR--VK 991
+ SG++ + G GL G TVGI+G+G +G A+ L F +LY +
Sbjct: 125 VRSGKFGGWRPKFYG---TGLDGKTVGILGMGALGRAIARRLSGFGA-TLLYYDPHPLDQ 180
Query: 992 EEGTALGAQLVPLDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILVNTSRGGLL 1051
E AL + V LD L SDF+ + LT DT LI + + MKP A+LVN RG ++
Sbjct: 181 AEEQALNLRRVELDELLESSDFLVLALPLTPDTLHLINAEALAKMKPGALLVNPCRGSVV 240
Query: 1052 DQEALVEFLKDKKIGGAGLDVMIPEPLP-ADHP-------LVQLDNCVLTPHTSSATKAV 1103
D+ A+ E LK +GG DV E D P L Q D V TPH SA V
Sbjct: 241 DEAAVAEALKSGHLGGYAADVFEMEDWARPDRPRSIPQELLDQHDRTVFTPHIGSAVDEV 300
Query: 1104 RDEKSSTSAENIIRGYKG 1121
R E +A NI++ +G
Sbjct: 301 RLEIELEAALNILQALQG 318
Score = 82.3 bits (204), Expect = 1e-16
Identities = 56/233 (24%), Positives = 90/233 (38%), Gaps = 52/233 (22%)
Query: 514 KPKLFLTRDDYSRVP--AFEILGEMFDIITYPASEGQIPRDIFIEKLRGCSALLCTSRDR 571
KPK+ +T +V E+L ++I+ ++ + R+ + + + L+ DR
Sbjct: 1 KPKVVIT----HKVHPEVLELLKPHCEVISNQ-TDEPLSREELLRRCKDADGLMAFMPDR 55
Query: 572 VDKQVLDESGGYRCTEDFFGLDLDQMFRNPSKRHVNIETVLGVSFLIKNLKVITTFSVGY 631
+D LD LK+I GY
Sbjct: 56 IDADFLDAC--------------------------------------PRLKIIACALKGY 77
Query: 632 DHLELHEIKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRFQEGRKCITSGEWALKQTHI 691
D+ ++ ARGI V V + ++ AE IGL I + R G + + SG++ +
Sbjct: 78 DNFDVEACTARGIWVTIVPDLLTEPTAELTIGLLIGLGRHILAGDRFVRSGKFGGWRPKF 137
Query: 692 IGPNIMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSR---RVKEEGQL 741
G GL G TVGI+G+G +G A+ L F +LY EE L
Sbjct: 138 YG---TGLDGKTVGILGMGALGRAIARRLSGFGA-TLLYYDPHPLDQAEEQAL 186
Score = 79.6 bits (197), Expect = 8e-16
Identities = 35/89 (39%), Positives = 47/89 (52%), Gaps = 1/89 (1%)
Query: 306 ALGAQLVPLDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEA 365
AL + V LD L SDF+ + LT DT LI + + MKP A+L+N RG ++D+ A
Sbjct: 185 ALNLRRVELDELLESSDFLVLALPLTPDTLHLINAEALAKMKPGALLVNPCRGSVVDEAA 244
Query: 366 LVEFLKDKKIGGAGLDVMIPEPLP-ADHP 393
+ E LK +GG DV E D P
Sbjct: 245 VAEALKSGHLGGYAADVFEMEDWARPDRP 273
Score = 57.3 bits (139), Expect = 2e-08
Identities = 28/109 (25%), Positives = 50/109 (45%), Gaps = 4/109 (3%)
Query: 45 PESLSKLRFNSRFDIDTYPVSEGRMPRDIFIEKLKGCSALLCNPHQKVDKEVLDRSGENL 104
PE L L+ + + + R+ + + K L+ ++D + LD + L
Sbjct: 12 PEVLELLKPHCEVISNQTDEP---LSREELLRRCKDADGLMAFMPDRIDADFLD-ACPRL 67
Query: 105 KVIATFSVGHDHLHLDEIKSRGIRVGTVGPVSSDTVAEYNIGLAIAVSR 153
K+IA G+D+ ++ +RGI V V + ++ AE IGL I + R
Sbjct: 68 KIIACALKGYDNFDVEACTARGIWVTIVPDLLTEPTAELTIGLLIGLGR 116
Score = 43.0 bits (102), Expect = 6e-04
Identities = 15/41 (36%), Positives = 22/41 (53%), Gaps = 1/41 (2%)
Query: 827 IMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRNKV 867
GL G TVGI+G+G +G A+ L F +LY + +
Sbjct: 139 GTGLDGKTVGILGMGALGRAIARRLSGFGA-TLLYYDPHPL 178
>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 = 165 bits (421), Expect = 3e-45
Identities = 96/294 (32%), Positives = 139/294 (47%), Gaps = 25/294 (8%)
Query: 846 ETAKLLKAFKVSKILYTSRNKVKTPKRTENLKVITTFSVGYDHLELHEIKARGIRVGSVG 905
ETA+L K +T + + + LK I+ + GYD+++L K GI V +V
Sbjct: 38 ETAELAKGADAILTAFTDKIDAELLDKAPGLKFISLRATGYDNIDLDYAKELGIGVTNVP 97
Query: 906 HISSDTVAEYNIGLAIAVSRRFQEGRKCIT--SGEWALKQTHIIGPNIMGLKGATVGIVG 963
S + VAE+ I L +A+ R RK I L+ +IG + TVG+VG
Sbjct: 98 EYSPNAVAEHTIALILALLRN----RKYIDERDKNQDLQDAGVIGRELEDQ---TVGVVG 150
Query: 964 LGNIGLETAKLLKAFKVSKILYTSRRVKEEGTALGAQLVPLDTLCAESDFIFVTCALTKD 1023
G IG A+ K F + I Y R E G + V L+ L SD I + LT +
Sbjct: 151 TGKIGRAVAQRAKGFGMKVIAYDPFR-NPELEDKGVKYVSLEELFKNSDIISLHVPLTPE 209
Query: 1024 TEQLIGRKQFSLMKPTAILVNTSRGGLLDQEALVEFLKDKKIGGAGLDVMIPE------- 1076
+I + F LMK I++NT+RG L+D EAL+E L KI GAGLDV+ E
Sbjct: 210 NHHMINEEAFKLMKKGVIIINTARGSLVDTEALIEALDSGKIFGAGLDVLEDETPDLLKD 269
Query: 1077 ------PLPADHPLVQLDNCVLTPHTSSAT-KAVRDEKSSTSAENIIRGYKGEP 1123
+ L + N ++TPHT+ T A+++ S ENI+ +GE
Sbjct: 270 LEGEIFKDALNALLGRRPNVIITPHTAFYTDDALKNMV-EISCENIVDFLEGEE 322
Score = 87.4 bits (217), Expect = 2e-18
Identities = 37/88 (42%), Positives = 48/88 (54%)
Query: 295 GYNWFERSNGTALGAQLVPLDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILIN 354
Y+ F G + V L+ L SD I + LT + +I + F LMK I+IN
Sbjct: 171 AYDPFRNPELEDKGVKYVSLEELFKNSDIISLHVPLTPENHHMINEEAFKLMKKGVIIIN 230
Query: 355 TSRGGLLDQEALVEFLKDKKIGGAGLDV 382
T+RG L+D EAL+E L KI GAGLDV
Sbjct: 231 TARGSLVDTEALIEALDSGKIFGAGLDV 258
Score = 73.9 bits (182), Expect = 6e-14
Identities = 39/114 (34%), Positives = 55/114 (48%), Gaps = 9/114 (7%)
Query: 619 KNLKVITTFSVGYDHLELHEIKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRFQEGRKC 678
LK I+ + GYD+++L K GI V +V S + VAE+ I L +A+ R RK
Sbjct: 66 PGLKFISLRATGYDNIDLDYAKELGIGVTNVPEYSPNAVAEHTIALILALLRN----RKY 121
Query: 679 IT--SGEWALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILY 730
I L+ +IG + TVG+VG G IG A+ K F + I Y
Sbjct: 122 IDERDKNQDLQDAGVIGRELEDQ---TVGVVGTGKIGRAVAQRAKGFGMKVIAY 172
Score = 64.6 bits (158), Expect = 6e-11
Identities = 32/93 (34%), Positives = 47/93 (50%), Gaps = 4/93 (4%)
Query: 72 DIFIEKLKGCSALLCNPHQKVDKEVLDRSGENLKVIATFSVGHDHLHLDEIKSRGIRVGT 131
D E KG A+L K+D E+LD++ LK I+ + G+D++ LD K GI V
Sbjct: 37 DETAELAKGADAILTAFTDKIDAELLDKA-PGLKFISLRATGYDNIDLDYAKELGIGVTN 95
Query: 132 VGPVSSDTVAEYNIGLAIAVSR---RFQQRHNW 161
V S + VAE+ I L +A+ R +R
Sbjct: 96 VPEYSPNAVAEHTIALILALLRNRKYIDERDKN 128
Score = 34.6 bits (80), Expect = 0.23
Identities = 15/40 (37%), Positives = 20/40 (50%), Gaps = 3/40 (7%)
Query: 822 IIGPNIMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILY 861
+IG + TVG+VG G IG A+ K F + I Y
Sbjct: 136 VIGRELEDQ---TVGVVGTGKIGRAVAQRAKGFGMKVIAY 172
>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 = 161 bits (410), Expect = 1e-43
Identities = 82/243 (33%), Positives = 122/243 (50%), Gaps = 10/243 (4%)
Query: 861 YTSRNKVKTPKRTENLKVITTFSVGYDHLELHEIKARGIRVGSVGHISSDTVAEYNIGLA 920
Y + ++ K NLK+ T +G DH++L RGI V V + +VAE+ + +
Sbjct: 73 YMTAERIAKAK---NLKLALTAGIGSDHVDLQAANDRGITVAEVTGSNVVSVAEHVVMMI 129
Query: 921 IAVSRRFQEGRKCITSGEWALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKAFKV 980
+ + R + G + G W + + L+G TVG VG G IGL + LK F V
Sbjct: 130 LILVRNYVPGHEQAIEGGWNVAD---VVKRAYDLEGKTVGTVGAGRIGLRVLRRLKPFDV 186
Query: 981 SKILYTSR-RVKEE-GTALGAQLVP-LDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMK 1037
+LY R R+ EE LG L+ + ++ D + + C L +TE L ++ S MK
Sbjct: 187 -HLLYYDRHRLPEEVEKELGLTRHADLEDMVSKCDVVTINCPLHPETEGLFNKELLSKMK 245
Query: 1038 PTAILVNTSRGGLLDQEALVEFLKDKKIGGAGLDVMIPEPLPADHPLVQLDNCVLTPHTS 1097
A LVNT+RG + D+EA+ E L+ + G DV P+P P DHP + N +TPH S
Sbjct: 246 KGAYLVNTARGKICDREAVAEALESGHLAGYAGDVWFPQPAPKDHPWRTMPNNAMTPHIS 305
Query: 1098 SAT 1100
T
Sbjct: 306 GTT 308
Score = 88.2 bits (219), Expect = 2e-18
Identities = 33/103 (32%), Positives = 52/103 (50%), Gaps = 1/103 (0%)
Query: 292 HYFGYNWFERSNGTALGAQLVP-LDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTA 350
Y+ + LG L+ + ++ D + + C L +TE L ++ S MK A
Sbjct: 189 LYYDRHRLPEEVEKELGLTRHADLEDMVSKCDVVTINCPLHPETEGLFNKELLSKMKKGA 248
Query: 351 ILINTSRGGLLDQEALVEFLKDKKIGGAGLDVMIPEPLPADHP 393
L+NT+RG + D+EA+ E L+ + G DV P+P P DHP
Sbjct: 249 YLVNTARGKICDREAVAEALESGHLAGYAGDVWFPQPAPKDHP 291
Score = 75.8 bits (187), Expect = 2e-14
Identities = 39/115 (33%), Positives = 57/115 (49%), Gaps = 4/115 (3%)
Query: 619 KNLKVITTFSVGYDHLELHEIKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRFQEGRKC 678
KNLK+ T +G DH++L RGI V V + +VAE+ + + + + R + G +
Sbjct: 83 KNLKLALTAGIGSDHVDLQAANDRGITVAEVTGSNVVSVAEHVVMMILILVRNYVPGHEQ 142
Query: 679 ITSGEWALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSR 733
G W + + L+G TVG VG G IGL + LK F V +LY R
Sbjct: 143 AIEGGWNVAD---VVKRAYDLEGKTVGTVGAGRIGLRVLRRLKPFDV-HLLYYDR 193
Score = 45.4 bits (108), Expect = 1e-04
Identities = 21/60 (35%), Positives = 28/60 (46%), Gaps = 4/60 (6%)
Query: 806 CYHGTINGEWALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRN 865
+ I G W + + L+G TVG VG G IGL + LK F V +LY R+
Sbjct: 139 GHEQAIEGGWNVAD---VVKRAYDLEGKTVGTVGAGRIGLRVLRRLKPFDV-HLLYYDRH 194
Score = 38.1 bits (89), Expect = 0.022
Identities = 23/85 (27%), Positives = 41/85 (48%), Gaps = 2/85 (2%)
Query: 94 KEVLDRSGENLKVIATFSVGHDHLHLDEIKSRGIRVGTVGPVSSDTVAEYNIGLAIAVSR 153
E + ++ +NLK+ T +G DH+ L RGI V V + +VAE+ + + + + R
Sbjct: 76 AERIAKA-KNLKLALTAGIGSDHVDLQAANDRGITVAEVTGSNVVSVAEHVVMMILILVR 134
Query: 154 RFQQRHNWIARLS-SFAEIQTRALD 177
+ H + A++ RA D
Sbjct: 135 NYVPGHEQAIEGGWNVADVVKRAYD 159
>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 = 158 bits (403), Expect = 7e-43
Identities = 86/247 (34%), Positives = 125/247 (50%), Gaps = 20/247 (8%)
Query: 859 ILYTSRNKVKT--PKRTENLKVITTFSVGYDHLELHEIKARGIRV--GSVGHISSDTVAE 914
ILY + +NLK I +S G D+L L IK +GI + S H S +AE
Sbjct: 42 ILYGYNPDFDELDLAKMKNLKWIQLYSAGVDYLPLEYIKKKGILLTNNSGIH--SIPIAE 99
Query: 915 YNIGLAIAVSRRFQEGRKCITSGEWALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKL 974
+ +G + + + ++ K +W + + + L G T+ +G G+IG E AK
Sbjct: 100 WIVGYILEIYKGLKKAYKNQKEKKWKMDSSL------LELYGKTILFLGTGSIGQEIAKR 153
Query: 975 LKAFKVSKI-LYTSRRVKE---EGTALGAQLVPLDTLCAESDFIFVTCALTKDTEQLIGR 1030
LKAF + I + TS R E + L LD + E+D + LT++T L
Sbjct: 154 LKAFGMKVIGVNTSGRDVEYFDKCYPLEE----LDEVLKEADIVVNVLPLTEETHHLFDE 209
Query: 1031 KQFSLMKPTAILVNTSRGGLLDQEALVEFLKDKKIGGAGLDVMIPEPLPADHPLVQLDNC 1090
F MK A+ +N RG +D++AL+E LK+K+I GA LDV EPLP D PL LDN
Sbjct: 210 AFFEQMKKGALFINVGRGPSVDEDALIEALKNKQIRGAALDVFEEEPLPKDSPLWDLDNV 269
Query: 1091 VLTPHTS 1097
++TPH S
Sbjct: 270 LITPHIS 276
Score = 99.2 bits (248), Expect = 2e-22
Identities = 39/86 (45%), Positives = 51/86 (59%)
Query: 314 LDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLKDK 373
LD + E+D + LT++T L F MK A+ IN RG +D++AL+E LK+K
Sbjct: 183 LDEVLKEADIVVNVLPLTEETHHLFDEAFFEQMKKGALFINVGRGPSVDEDALIEALKNK 242
Query: 374 KIGGAGLDVMIPEPLPADHPLVQLDN 399
+I GA LDV EPLP D PL LDN
Sbjct: 243 QIRGAALDVFEEEPLPKDSPLWDLDN 268
Score = 64.9 bits (159), Expect = 6e-11
Identities = 36/107 (33%), Positives = 55/107 (51%), Gaps = 10/107 (9%)
Query: 619 KNLKVITTFSVGYDHLELHEIKARGIRV--GSVGHISSDTVAEYNIGLAIAVSRRFQEGR 676
KNLK I +S G D+L L IK +GI + S H S +AE+ +G + + + ++
Sbjct: 59 KNLKWIQLYSAGVDYLPLEYIKKKGILLTNNSGIH--SIPIAEWIVGYILEIYKGLKKAY 116
Query: 677 KCITSGEWALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKAF 723
K +W + + + L G T+ +G G+IG E AK LKAF
Sbjct: 117 KNQKEKKWKMDSSL------LELYGKTILFLGTGSIGQEIAKRLKAF 157
Score = 39.9 bits (94), Expect = 0.006
Identities = 14/29 (48%), Positives = 20/29 (68%)
Query: 826 NIMGLKGATVGIVGLGNIGLETAKLLKAF 854
+++ L G T+ +G G+IG E AK LKAF
Sbjct: 129 SLLELYGKTILFLGTGSIGQEIAKRLKAF 157
Score = 38.7 bits (91), Expect = 0.011
Identities = 20/74 (27%), Positives = 35/74 (47%), Gaps = 6/74 (8%)
Query: 94 KEVLDRSGENLKVIATFSVGHDHLHLDEIKSRGIRVGTVGPVSSDTVAEYNIGLAIAVSR 153
E+ +NLK I +S G D+L L+ IK +GI + + S +AE+ +G + + +
Sbjct: 51 DELDLAKMKNLKWIQLYSAGVDYLPLEYIKKKGILLTNNSGIHSIPIAEWIVGYILEIYK 110
Query: 154 RF------QQRHNW 161
Q+ W
Sbjct: 111 GLKKAYKNQKEKKW 124
>gnl|CDD|180588 PRK06487, PRK06487, glycerate dehydrogenase; Provisional.
Length = 317
Score = 157 bits (398), Expect = 3e-42
Identities = 80/267 (29%), Positives = 143/267 (53%), Gaps = 14/267 (5%)
Query: 865 NKV----KTPKRTENLKVITTFSVGYDHLELHEIKARGIRVGSVGHISSDTVAEYNIGLA 920
NKV LK+I + G ++++L + RGI V + + +VA++ + L
Sbjct: 52 NKVALDAAALAAAPQLKLILVAATGTNNVDLAAARERGITVCNCQGYGTPSVAQHTLALL 111
Query: 921 IAVSRRFQEGRKCITSGEWALKQTHIIGPN--IMGLKGATVGIVGLGNIGLETAKLLKAF 978
+A++ R + ++ + +G W + + + I+ L+G T+G++G G +G A+L +AF
Sbjct: 112 LALATRLPDYQQAVAAGRWQ-QSSQFCLLDFPIVELEGKTLGLLGHGELGGAVARLAEAF 170
Query: 979 KVSKILYTSRRVKEEGTALGAQLVPLDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKP 1038
+ ++L G +PLD L + D + + C LT+ T LIG ++ +LMKP
Sbjct: 171 GM-RVLIGQL----PGRPARPDRLPLDELLPQVDALTLHCPLTEHTRHLIGARELALMKP 225
Query: 1039 TAILVNTSRGGLLDQEALVEFLKDKKIGGAGLDVMIPEPLPADHPLVQLD--NCVLTPHT 1096
A+L+NT+RGGL+D++AL + L+ +GGA DV+ EP +PL+ D ++TPH+
Sbjct: 226 GALLINTARGGLVDEQALADALRSGHLGGAATDVLSVEPPVNGNPLLAPDIPRLIVTPHS 285
Query: 1097 SSATKAVRDEKSSTSAENIIRGYKGEP 1123
+ ++ R AEN + G+P
Sbjct: 286 AWGSREARQRIVGQLAENARAFFAGKP 312
Score = 95.5 bits (238), Expect = 3e-21
Identities = 40/95 (42%), Positives = 59/95 (62%)
Query: 304 GTALGAQLVPLDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQ 363
G +PLD L + D + + C LT+ T LIG ++ +LMKP A+LINT+RGGL+D+
Sbjct: 181 GRPARPDRLPLDELLPQVDALTLHCPLTEHTRHLIGARELALMKPGALLINTARGGLVDE 240
Query: 364 EALVEFLKDKKIGGAGLDVMIPEPLPADHPLVQLD 398
+AL + L+ +GGA DV+ EP +PL+ D
Sbjct: 241 QALADALRSGHLGGAATDVLSVEPPVNGNPLLAPD 275
Score = 62.0 bits (151), Expect = 5e-10
Identities = 28/105 (26%), Positives = 60/105 (57%), Gaps = 3/105 (2%)
Query: 621 LKVITTFSVGYDHLELHEIKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRFQEGRKCIT 680
LK+I + G ++++L + RGI V + + +VA++ + L +A++ R + ++ +
Sbjct: 67 LKLILVAATGTNNVDLAAARERGITVCNCQGYGTPSVAQHTLALLLALATRLPDYQQAVA 126
Query: 681 SGEWALKQTHIIGPN--IMGLKGATVGIVGLGNIGLETAKLLKAF 723
+G W + + + I+ L+G T+G++G G +G A+L +AF
Sbjct: 127 AGRWQ-QSSQFCLLDFPIVELEGKTLGLLGHGELGGAVARLAEAF 170
Score = 33.9 bits (78), Expect = 0.38
Identities = 23/96 (23%), Positives = 44/96 (45%), Gaps = 6/96 (6%)
Query: 71 RDIFIEKLKGCSALLCNPHQKV--DKEVLDRSGENLKVIATFSVGHDHLHLDEIKSRGIR 128
+ E+L+G + N KV D L + + LK+I + G +++ L + RGI
Sbjct: 36 PEQVAERLRGAQVAISN---KVALDAAALAAAPQ-LKLILVAATGTNNVDLAAARERGIT 91
Query: 129 VGTVGPVSSDTVAEYNIGLAIAVSRRFQQRHNWIAR 164
V + +VA++ + L +A++ R +A
Sbjct: 92 VCNCQGYGTPSVAQHTLALLLALATRLPDYQQAVAA 127
Score = 32.4 bits (74), Expect = 1.3
Identities = 12/28 (42%), Positives = 20/28 (71%)
Query: 827 IMGLKGATVGIVGLGNIGLETAKLLKAF 854
I+ L+G T+G++G G +G A+L +AF
Sbjct: 143 IVELEGKTLGLLGHGELGGAVARLAEAF 170
>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 = 155 bits (395), Expect = 1e-41
Identities = 75/202 (37%), Positives = 111/202 (54%), Gaps = 18/202 (8%)
Query: 877 KVITTFSVGYDHLELHEIKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRFQEGRKCITS 936
K+I G+++++L K GI V V S VAE+ + L +A++R+ +
Sbjct: 70 KLIALRCAGFNNVDLKAAKELGITVVRVPAYSPYAVAEHAVALLLALNRKIHRAYNRVRE 129
Query: 937 GEWALKQTHIIGPNIMG--LKGATVGIVGLGNIGLETAKLLKAFKVSKIL----YTSRRV 990
G ++L ++G L G TVG++G G IG A++LK F ++L Y + +
Sbjct: 130 GNFSLD-------GLLGFDLHGKTVGVIGTGKIGQAFARILKGFGC-RVLAYDPYPNPEL 181
Query: 991 KEEGTALGAQLVPLDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILVNTSRGGL 1050
+ LG + V LD L AESD I + C LT +T LI + + MK +L+NTSRGGL
Sbjct: 182 AK----LGVEYVDLDELLAESDIISLHCPLTPETHHLINAETIAKMKDGVMLINTSRGGL 237
Query: 1051 LDQEALVEFLKDKKIGGAGLDV 1072
+D +AL+E LK KIGG GLDV
Sbjct: 238 IDTKALIEALKSGKIGGLGLDV 259
Score = 110 bits (279), Expect = 2e-26
Identities = 42/78 (53%), Positives = 51/78 (65%)
Query: 305 TALGAQLVPLDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQE 364
LG + V LD L AESD I + C LT +T LI + + MK +LINTSRGGL+D +
Sbjct: 182 AKLGVEYVDLDELLAESDIISLHCPLTPETHHLINAETIAKMKDGVMLINTSRGGLIDTK 241
Query: 365 ALVEFLKDKKIGGAGLDV 382
AL+E LK KIGG GLDV
Sbjct: 242 ALIEALKSGKIGGLGLDV 259
Score = 60.5 bits (148), Expect = 2e-09
Identities = 32/104 (30%), Positives = 53/104 (50%), Gaps = 9/104 (8%)
Query: 622 KVITTFSVGYDHLELHEIKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRFQEGRKCITS 681
K+I G+++++L K GI V V S VAE+ + L +A++R+ +
Sbjct: 70 KLIALRCAGFNNVDLKAAKELGITVVRVPAYSPYAVAEHAVALLLALNRKIHRAYNRVRE 129
Query: 682 GEWALKQTHIIGPNIMG--LKGATVGIVGLGNIGLETAKLLKAF 723
G ++L ++G L G TVG++G G IG A++LK F
Sbjct: 130 GNFSLD-------GLLGFDLHGKTVGVIGTGKIGQAFARILKGF 166
Score = 44.7 bits (107), Expect = 1e-04
Identities = 21/65 (32%), Positives = 35/65 (53%), Gaps = 1/65 (1%)
Query: 91 KVDKEVLDRSGEN-LKVIATFSVGHDHLHLDEIKSRGIRVGTVGPVSSDTVAEYNIGLAI 149
+D VL++ E +K+IA G +++ L K GI V V S VAE+ + L +
Sbjct: 55 DLDAPVLEKLAELGVKLIALRCAGFNNVDLKAAKELGITVVRVPAYSPYAVAEHAVALLL 114
Query: 150 AVSRR 154
A++R+
Sbjct: 115 ALNRK 119
Score = 39.3 bits (93), Expect = 0.009
Identities = 13/25 (52%), Positives = 17/25 (68%)
Query: 830 LKGATVGIVGLGNIGLETAKLLKAF 854
L G TVG++G G IG A++LK F
Sbjct: 142 LHGKTVGVIGTGKIGQAFARILKGF 166
>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 = 150 bits (382), Expect = 5e-40
Identities = 96/280 (34%), Positives = 143/280 (51%), Gaps = 30/280 (10%)
Query: 845 LETAKLLKAFKVSKILYTSR--NKVKTPKRTENLKVITTFSVGYDHLELHEIKARGIRVG 902
LE A L + + IL S+ ++ + +K I+T S+GYDH++L K GI+V
Sbjct: 36 LENAHLAEGYDGISILGKSKISAELLEKLKEAGVKYISTRSIGYDHIDLDAAKELGIKVS 95
Query: 903 SVGHISSDTVAEYNIGLAIAVSRRFQEGRKCITSGEWALKQTHIIGPNIMG--LKGATVG 960
+V + S ++VA+Y + L + R++++ K +++L + G L+ TVG
Sbjct: 96 NVTY-SPNSVADYTVMLMLMALRKYKQIMKRAEVNDYSL-------GGLQGRELRNLTVG 147
Query: 961 IVGLGNIGLETAKLLKAFKVSKILYTSRRVKEEGTALGAQLVPLDTLCAESDFIFVTCAL 1020
++G G IG K L F KIL EE A+ V LDTL ESD I + L
Sbjct: 148 VIGTGRIGQAVIKNLSGFG-CKILAYDPYPNEE-VKKYAEYVDLDTLYKESDIITLHTPL 205
Query: 1021 TKDTEQLIGRKQFSLMKPTAILVNTSRGGLLDQEALVEFLKDKKIGGAGLDVMIPE---- 1076
T++T LI ++ + MK I++NT+RG L+D EAL+E L+ KIGGA LDV+ E
Sbjct: 206 TEETYHLINKESIAKMKDGVIIINTARGELIDTEALIEGLESGKIGGAALDVIEGEDGIY 265
Query: 1077 -------PLPADHPLVQL---DNCVLTPHTSSATK-AVRD 1105
L + L L N +LTPH + T AV D
Sbjct: 266 YNDRKGDILS-NRELAILRSFPNVILTPHMAFYTDQAVSD 304
Score = 94.6 bits (236), Expect = 8e-21
Identities = 39/89 (43%), Positives = 53/89 (59%), Gaps = 1/89 (1%)
Query: 294 FGYNWFERSNGTALGAQLVPLDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILI 353
Y+ + A+ V LDTL ESD I + LT++T LI ++ + MK I+I
Sbjct: 170 LAYDPYPNEE-VKKYAEYVDLDTLYKESDIITLHTPLTEETYHLINKESIAKMKDGVIII 228
Query: 354 NTSRGGLLDQEALVEFLKDKKIGGAGLDV 382
NT+RG L+D EAL+E L+ KIGGA LDV
Sbjct: 229 NTARGELIDTEALIEGLESGKIGGAALDV 257
Score = 60.3 bits (147), Expect = 2e-09
Identities = 39/119 (32%), Positives = 62/119 (52%), Gaps = 11/119 (9%)
Query: 622 KVITTFSVGYDHLELHEIKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRFQEGRKCITS 681
K I+T S+GYDH++L K GI+V +V + S ++VA+Y + L + R++++ K
Sbjct: 70 KYISTRSIGYDHIDLDAAKELGIKVSNVTY-SPNSVADYTVMLMLMALRKYKQIMKRAEV 128
Query: 682 GEWALKQTHIIGPNIMG--LKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRRVKEE 738
+++L + G L+ TVG++G G IG K L F KIL EE
Sbjct: 129 NDYSL-------GGLQGRELRNLTVGVIGTGRIGQAVIKNLSGFG-CKILAYDPYPNEE 179
Score = 54.1 bits (131), Expect = 2e-07
Identities = 25/81 (30%), Positives = 43/81 (53%), Gaps = 2/81 (2%)
Query: 75 IEKLKGCSALLCNPHQKVDKEVLDRSGE-NLKVIATFSVGHDHLHLDEIKSRGIRVGTVG 133
+G + K+ E+L++ E +K I+T S+G+DH+ LD K GI+V V
Sbjct: 39 AHLAEGYDGISILGKSKISAELLEKLKEAGVKYISTRSIGYDHIDLDAAKELGIKVSNV- 97
Query: 134 PVSSDTVAEYNIGLAIAVSRR 154
S ++VA+Y + L + R+
Sbjct: 98 TYSPNSVADYTVMLMLMALRK 118
Score = 30.3 bits (69), Expect = 6.7
Identities = 12/32 (37%), Positives = 16/32 (50%), Gaps = 2/32 (6%)
Query: 825 PNIMG--LKGATVGIVGLGNIGLETAKLLKAF 854
+ G L+ TVG++G G IG K L F
Sbjct: 134 GGLQGRELRNLTVGVIGTGRIGQAVIKNLSGF 165
>gnl|CDD|235890 PRK06932, PRK06932, glycerate dehydrogenase; Provisional.
Length = 314
Score = 149 bits (379), Expect = 9e-40
Identities = 87/264 (32%), Positives = 143/264 (54%), Gaps = 13/264 (4%)
Query: 857 SKILYTSRNKVKTPKRTENLKVITTFSVGYDHLELHEIKARGIRVGSVGHISSDTVAEYN 916
SK+L+T + PK LK+I + G ++++L K GI V +V SS TV E+
Sbjct: 51 SKVLFTRETLAQLPK----LKLIAITATGTNNVDLVAAKELGIAVKNVTGYSSTTVPEHV 106
Query: 917 IGLAIAVSRRFQEGRKCITSGEWA-LKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLL 975
+G+ A+ + S WA KQ I ++G+T+G+ G G +G E +L
Sbjct: 107 LGMIFALKHSLMGWYRDQLSDRWATCKQFCYFDYPITDVRGSTLGVFGKGCLGTEVGRLA 166
Query: 976 KAFKVSKILYTSRRVKEEGTALGAQLVPLDTLCAESDFIFVTCALTKDTEQLIGRKQFSL 1035
+A + K+LY + + P + + ++D + + C LT+ T+ LI + +L
Sbjct: 167 QALGM-KVLYAEHK---GASVCREGYTPFEEVLKQADIVTLHCPLTETTQNLINAETLAL 222
Query: 1036 MKPTAILVNTSRGGLLDQEALVEFLKDKKIGGAGLDVMIPEPLPADHPLVQ----LDNCV 1091
MKPTA L+NT RG L+D++AL++ L++ KI GA LDV++ EP D+PL+Q L N +
Sbjct: 223 MKPTAFLINTGRGPLVDEQALLDALENGKIAGAALDVLVKEPPEKDNPLIQAAKRLPNLL 282
Query: 1092 LTPHTSSATKAVRDEKSSTSAENI 1115
+TPH + A+ + + A+NI
Sbjct: 283 ITPHIAWASDSAVTTLVNKVAQNI 306
Score = 96.0 bits (239), Expect = 2e-21
Identities = 39/97 (40%), Positives = 61/97 (62%)
Query: 300 ERSNGTALGAQLVPLDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGG 359
E + P + + ++D + + C LT+ T+ LI + +LMKPTA LINT RG
Sbjct: 177 EHKGASVCREGYTPFEEVLKQADIVTLHCPLTETTQNLINAETLALMKPTAFLINTGRGP 236
Query: 360 LLDQEALVEFLKDKKIGGAGLDVMIPEPLPADHPLVQ 396
L+D++AL++ L++ KI GA LDV++ EP D+PL+Q
Sbjct: 237 LVDEQALLDALENGKIAGAALDVLVKEPPEKDNPLIQ 273
Score = 56.3 bits (136), Expect = 3e-08
Identities = 35/115 (30%), Positives = 58/115 (50%), Gaps = 2/115 (1%)
Query: 621 LKVITTFSVGYDHLELHEIKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRFQEGRKCIT 680
LK+I + G ++++L K GI V +V SS TV E+ +G+ A+ +
Sbjct: 66 LKLIAITATGTNNVDLVAAKELGIAVKNVTGYSSTTVPEHVLGMIFALKHSLMGWYRDQL 125
Query: 681 SGEWA-LKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRR 734
S WA KQ I ++G+T+G+ G G +G E +L +A + K+LY +
Sbjct: 126 SDRWATCKQFCYFDYPITDVRGSTLGVFGKGCLGTEVGRLAQALGM-KVLYAEHK 179
Score = 35.2 bits (81), Expect = 0.19
Identities = 20/59 (33%), Positives = 31/59 (52%), Gaps = 1/59 (1%)
Query: 93 DKEVLDRSGENLKVIATFSVGHDHLHLDEIKSRGIRVGTVGPVSSDTVAEYNIGLAIAV 151
+E L + LK+IA + G +++ L K GI V V SS TV E+ +G+ A+
Sbjct: 56 TRETLAQL-PKLKLIAITATGTNNVDLVAAKELGIAVKNVTGYSSTTVPEHVLGMIFAL 113
Score = 33.2 bits (76), Expect = 0.73
Identities = 18/64 (28%), Positives = 30/64 (46%), Gaps = 2/64 (3%)
Query: 807 YHGTINGEWA-LKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRN 865
Y ++ WA KQ I ++G+T+G+ G G +G E +L +A + K+LY
Sbjct: 121 YRDQLSDRWATCKQFCYFDYPITDVRGSTLGVFGKGCLGTEVGRLAQALGM-KVLYAEHK 179
Query: 866 KVKT 869
Sbjct: 180 GASV 183
>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 = 149 bits (379), Expect = 2e-39
Identities = 80/266 (30%), Positives = 126/266 (47%), Gaps = 33/266 (12%)
Query: 875 NLKVITTFSVGYDHLELHEIKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRFQEGRKCI 934
+K I S G D ++L K G+++ +V S +AE+ + A+ + R E + +
Sbjct: 68 GIKQIALRSAGVDMIDLDLAKENGLKITNVPAYSPRAIAEFAVTQALNLLRNTPEIDRRV 127
Query: 935 TSGE--WALKQTHIIGPNIMG--LKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRRV 990
G+ WA P ++G ++ TVGI+G G IG AK+ K F +K++
Sbjct: 128 AKGDFRWA--------PGLIGREIRDLTVGIIGTGRIGSAAAKIFKGFG-AKVIAYDPYP 178
Query: 991 KEEGTALGAQLVPLDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILVNTSRGGL 1050
E L+ L ++D I + LTK+ LI + F+ MK AILVN +RGGL
Sbjct: 179 NPELEKFLLYYDSLEDLLKQADIISLHVPLTKENHHLINAEAFAKMKDGAILVNAARGGL 238
Query: 1051 LDQEALVEFLKDKKIGGAGLDVM---------------IPEPLPADHPLVQLDNCVLTPH 1095
+D +AL++ L KI GA LD I + + + L+ + N ++TPH
Sbjct: 239 VDTKALIDALDSGKIAGAALDTYENETGYFNKDWSGKEIEDEVLKE--LIAMPNVLITPH 296
Query: 1096 TSSATK-AVRD--EKSSTSAENIIRG 1118
+ T AV++ E S A II G
Sbjct: 297 IAFYTDTAVKNMVEISLDDALEIIEG 322
Score = 86.8 bits (216), Expect = 3e-18
Identities = 30/72 (41%), Positives = 43/72 (59%)
Query: 312 VPLDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLK 371
L+ L ++D I + LTK+ LI + F+ MK AIL+N +RGGL+D +AL++ L
Sbjct: 190 DSLEDLLKQADIISLHVPLTKENHHLINAEAFAKMKDGAILVNAARGGLVDTKALIDALD 249
Query: 372 DKKIGGAGLDVM 383
KI GA LD
Sbjct: 250 SGKIAGAALDTY 261
Score = 62.2 bits (152), Expect = 5e-10
Identities = 34/112 (30%), Positives = 55/112 (49%), Gaps = 14/112 (12%)
Query: 620 NLKVITTFSVGYDHLELHEIKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRFQEGRKCI 679
+K I S G D ++L K G+++ +V S +AE+ + A+ + R E + +
Sbjct: 68 GIKQIALRSAGVDMIDLDLAKENGLKITNVPAYSPRAIAEFAVTQALNLLRNTPEIDRRV 127
Query: 680 TSGE--WALKQTHIIGPNIMG--LKGATVGIVGLGNIGLETAKLLKAF--KV 725
G+ WA P ++G ++ TVGI+G G IG AK+ K F KV
Sbjct: 128 AKGDFRWA--------PGLIGREIRDLTVGIIGTGRIGSAAAKIFKGFGAKV 171
Score = 45.2 bits (108), Expect = 1e-04
Identities = 23/90 (25%), Positives = 41/90 (45%), Gaps = 4/90 (4%)
Query: 75 IEKLKGCSALLCNPHQKVDKEVLDRSGEN-LKVIATFSVGHDHLHLDEIKSRGIRVGTVG 133
++ KG ++ D+EV ++ E +K IA S G D + LD K G+++ V
Sbjct: 39 VDLAKGYDGVVVQQTLPYDEEVYEKLAEYGIKQIALRSAGVDMIDLDLAKENGLKITNVP 98
Query: 134 PVSSDTVAEYNIGLAIAVSRR---FQQRHN 160
S +AE+ + A+ + R +R
Sbjct: 99 AYSPRAIAEFAVTQALNLLRNTPEIDRRVA 128
Score = 39.4 bits (93), Expect = 0.008
Identities = 16/36 (44%), Positives = 22/36 (61%), Gaps = 4/36 (11%)
Query: 825 PNIMG--LKGATVGIVGLGNIGLETAKLLKAF--KV 856
P ++G ++ TVGI+G G IG AK+ K F KV
Sbjct: 136 PGLIGREIRDLTVGIIGTGRIGSAAAKIFKGFGAKV 171
>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 = 148 bits (376), Expect = 2e-39
Identities = 71/220 (32%), Positives = 107/220 (48%), Gaps = 13/220 (5%)
Query: 908 SSDTVAEYNIGLAIAVSRRFQEGRKCITS-GEWALKQTHIIGPNIMGLKGATVGIVGLGN 966
+++ +AE+ + +A ++R E + +W + +G L G+T+GIVG G
Sbjct: 95 AAEAIAEFVLAAILAAAKRLPEIW--VKGAEQWRRE---PLGS----LAGSTLGIVGFGA 145
Query: 967 IGLETAKLLKAFKVSKILYTSRRVKEEGTALGAQLVP-LDTLCAESDFIFVTCALTKDTE 1025
IG A+ A + ++L R + G + L L A SD + + LT +T
Sbjct: 146 IGQALARRALALGM-RVLALRRSGRPSDVP-GVEAAADLAELFARSDHLVLAAPLTPETR 203
Query: 1026 QLIGRKQFSLMKPTAILVNTSRGGLLDQEALVEFLKDKKIGGAGLDVMIPEPLPADHPLV 1085
LI + KP L+N +RGGL+DQEAL+E L +I A LDV PEPLP HPL
Sbjct: 204 HLINADVLAQAKPGLHLINIARGGLVDQEALLEALDSGRISLASLDVTDPEPLPEGHPLY 263
Query: 1086 QLDNCVLTPHTSSATKAVRDEKSSTSAENIIRGYKGEPMI 1125
L+PHTS+ R + EN+ R G+P+
Sbjct: 264 THPRVRLSPHTSAIAPDGRRNLADRFLENLARYRAGQPLH 303
Score = 98.2 bits (245), Expect = 3e-22
Identities = 40/88 (45%), Positives = 49/88 (55%), Gaps = 1/88 (1%)
Query: 308 GAQLVP-LDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEAL 366
G + L L A SD + + LT +T LI + KP LIN +RGGL+DQEAL
Sbjct: 175 GVEAAADLAELFARSDHLVLAAPLTPETRHLINADVLAQAKPGLHLINIARGGLVDQEAL 234
Query: 367 VEFLKDKKIGGAGLDVMIPEPLPADHPL 394
+E L +I A LDV PEPLP HPL
Sbjct: 235 LEALDSGRISLASLDVTDPEPLPEGHPL 262
Score = 41.9 bits (99), Expect = 0.001
Identities = 19/72 (26%), Positives = 35/72 (48%), Gaps = 10/72 (13%)
Query: 653 SSDTVAEYNIGLAIAVSRRFQEGRKCITS-GEWALKQTHIIGPNIMGLKGATVGIVGLGN 711
+++ +AE+ + +A ++R E + +W + +G L G+T+GIVG G
Sbjct: 95 AAEAIAEFVLAAILAAAKRLPEIW--VKGAEQWRRE---PLGS----LAGSTLGIVGFGA 145
Query: 712 IGLETAKLLKAF 723
IG A+ A
Sbjct: 146 IGQALARRALAL 157
Score = 31.9 bits (73), Expect = 1.5
Identities = 12/25 (48%), Positives = 15/25 (60%)
Query: 830 LKGATVGIVGLGNIGLETAKLLKAF 854
L G+T+GIVG G IG A+ A
Sbjct: 133 LAGSTLGIVGFGAIGQALARRALAL 157
>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 = 147 bits (373), Expect = 8e-39
Identities = 86/282 (30%), Positives = 129/282 (45%), Gaps = 28/282 (9%)
Query: 869 TPKRTENLKVITTFSVGYDHLELHE-IKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRF 927
+ NL+++ FS G DH H K + + + I +AE+ IG + +S F
Sbjct: 48 DAEDVPNLRLVQLFSAGADHWLGHPLYKDPEVPLCTASGIHGPQIAEWVIGTWLVLSHHF 107
Query: 928 QEGRKCITSGEWALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTS 987
+ + W ++ G VGI+G G+IG +TA+L +A + YT
Sbjct: 108 LQYIELQKEQTW---GRRQEAYSVEDSVGKRVGILGYGSIGRQTARLAQALGMEVYAYTR 164
Query: 988 R-RVKEE----------GTALGAQLVPL------------DTLCAESDFIFVTCALTKDT 1024
R E GT +P + L + D + V+ LT T
Sbjct: 165 SPRPTPESRKDDGYIVPGTGDPDGSIPSAWFSGTDKASLHEFLRQDLDLLVVSLPLTPAT 224
Query: 1025 EQLIGRKQFSLM-KPTAILVNTSRGGLLDQEALVEFLKDKKIGGAGLDVMIPEPLPADHP 1083
+ L+G ++F ++ K + N +RG L+D +ALV L+ +I GA LDV PEPLPADHP
Sbjct: 225 KHLLGAEEFEILAKRKTFVSNIARGSLVDTDALVAALESGQIRGAALDVTDPEPLPADHP 284
Query: 1084 LVQLDNCVLTPHTSSATKAVRDEKSSTSAENIIRGYKGEPMI 1125
L N ++TPH S T+ D EN+ R KGEP+I
Sbjct: 285 LWSAPNVIITPHVSWQTQEYFDRALDVLEENLERLRKGEPLI 326
Score = 90.0 bits (224), Expect = 3e-19
Identities = 36/85 (42%), Positives = 51/85 (60%), Gaps = 1/85 (1%)
Query: 317 LCAESDFIFVTCALTKDTEQLIGRKQFSLM-KPTAILINTSRGGLLDQEALVEFLKDKKI 375
L + D + V+ LT T+ L+G ++F ++ K + N +RG L+D +ALV L+ +I
Sbjct: 207 LRQDLDLLVVSLPLTPATKHLLGAEEFEILAKRKTFVSNIARGSLVDTDALVAALESGQI 266
Query: 376 GGAGLDVMIPEPLPADHPLVQLDNC 400
GA LDV PEPLPADHPL N
Sbjct: 267 RGAALDVTDPEPLPADHPLWSAPNV 291
Score = 54.6 bits (132), Expect = 1e-07
Identities = 31/118 (26%), Positives = 52/118 (44%), Gaps = 4/118 (3%)
Query: 617 LIKNLKVITTFSVGYDHLELHE-IKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRFQEG 675
+ NL+++ FS G DH H K + + + I +AE+ IG + +S F +
Sbjct: 51 DVPNLRLVQLFSAGADHWLGHPLYKDPEVPLCTASGIHGPQIAEWVIGTWLVLSHHFLQY 110
Query: 676 RKCITSGEWALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSR 733
+ W ++ G VGI+G G+IG +TA+L +A + YT
Sbjct: 111 IELQKEQTW---GRRQEAYSVEDSVGKRVGILGYGSIGRQTARLAQALGMEVYAYTRS 165
Score = 39.2 bits (92), Expect = 0.011
Identities = 16/40 (40%), Positives = 24/40 (60%), Gaps = 1/40 (2%)
Query: 832 GATVGIVGLGNIGLETAKLLKAFKVSKILYTSRNKVKTPK 871
G VGI+G G+IG +TA+L +A + YT + TP+
Sbjct: 133 GKRVGILGYGSIGRQTARLAQALGMEVYAYTRSPR-PTPE 171
Score = 32.2 bits (74), Expect = 1.4
Identities = 17/60 (28%), Positives = 27/60 (45%), Gaps = 1/60 (1%)
Query: 103 NLKVIATFSVGHDH-LHLDEIKSRGIRVGTVGPVSSDTVAEYNIGLAIAVSRRFQQRHNW 161
NL+++ FS G DH L K + + T + +AE+ IG + +S F Q
Sbjct: 54 NLRLVQLFSAGADHWLGHPLYKDPEVPLCTASGIHGPQIAEWVIGTWLVLSHHFLQYIEL 113
>gnl|CDD|181414 PRK08410, PRK08410, 2-hydroxyacid dehydrogenase; Provisional.
Length = 311
Score = 146 bits (371), Expect = 9e-39
Identities = 86/261 (32%), Positives = 143/261 (54%), Gaps = 16/261 (6%)
Query: 865 NKVKTPK----RTENLKVITTFSVGYDHLELHEIKARGIRVGSVGHISSDTVAEYNIGLA 920
NKV K + NLK+I + G +++++ K +GI V +V S+++VA++ +
Sbjct: 49 NKVVIDKEVLSQLPNLKLICITATGTNNVDIEYAKKKGIAVKNVAGYSTESVAQHTFAML 108
Query: 921 IAVSRRFQEGRKCITSGEWALKQ--THIIGPNIMG-LKGATVGIVGLGNIGLETAKLLKA 977
+++ R + + SGE++ THI P +G +KG GI+GLG IG AK+ +A
Sbjct: 109 LSLLGRINYYDRYVKSGEYSESPIFTHISRP--LGEIKGKKWGIIGLGTIGKRVAKIAQA 166
Query: 978 FKVSKILYTSRRVKEEGTALGAQLVPLDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMK 1037
F +K++Y S K + + V L+ L SD I + L + T+ LI K+ L+K
Sbjct: 167 FG-AKVVYYSTSGKNKNEEY--ERVSLEELLKTSDIISIHAPLNEKTKNLIAYKELKLLK 223
Query: 1038 PTAILVNTSRGGLLDQEALVEFLKDKKIGGAGLDVMIPEPLPADHPLVQL---DNCVLTP 1094
AIL+N RGG+++++ L + L +K I AGLDV+ EP+ +HPL+ + + ++TP
Sbjct: 224 DGAILINVGRGGIVNEKDLAKALDEKDI-YAGLDVLEKEPMEKNHPLLSIKNKEKLLITP 282
Query: 1095 HTSSATKAVRDEKSSTSAENI 1115
H + A+K R ENI
Sbjct: 283 HIAWASKEARKTLIEKVKENI 303
Score = 89.3 bits (222), Expect = 4e-19
Identities = 36/88 (40%), Positives = 54/88 (61%), Gaps = 1/88 (1%)
Query: 312 VPLDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLK 371
V L+ L SD I + L + T+ LI K+ L+K AILIN RGG+++++ L + L
Sbjct: 188 VSLEELLKTSDIISIHAPLNEKTKNLIAYKELKLLKDGAILINVGRGGIVNEKDLAKALD 247
Query: 372 DKKIGGAGLDVMIPEPLPADHPLVQLDN 399
+K I AGLDV+ EP+ +HPL+ + N
Sbjct: 248 EKDI-YAGLDVLEKEPMEKNHPLLSIKN 274
Score = 61.9 bits (151), Expect = 5e-10
Identities = 38/117 (32%), Positives = 68/117 (58%), Gaps = 6/117 (5%)
Query: 619 KNLKVITTFSVGYDHLELHEIKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRFQEGRKC 678
NLK+I + G +++++ K +GI V +V S+++VA++ + +++ R +
Sbjct: 62 PNLKLICITATGTNNVDIEYAKKKGIAVKNVAGYSTESVAQHTFAMLLSLLGRINYYDRY 121
Query: 679 ITSGEWALKQ--THIIGPNIMG-LKGATVGIVGLGNIGLETAKLLKAFKVSKILYTS 732
+ SGE++ THI P +G +KG GI+GLG IG AK+ +AF +K++Y S
Sbjct: 122 VKSGEYSESPIFTHISRP--LGEIKGKKWGIIGLGTIGKRVAKIAQAFG-AKVVYYS 175
Score = 40.4 bits (95), Expect = 0.003
Identities = 23/55 (41%), Positives = 34/55 (61%), Gaps = 6/55 (10%)
Query: 812 NGEWALKQ--THIIGPNIMG-LKGATVGIVGLGNIGLETAKLLKAFKVSKILYTS 863
+GE++ THI P +G +KG GI+GLG IG AK+ +AF +K++Y S
Sbjct: 124 SGEYSESPIFTHISRP--LGEIKGKKWGIIGLGTIGKRVAKIAQAFG-AKVVYYS 175
Score = 36.9 bits (86), Expect = 0.045
Identities = 29/112 (25%), Positives = 54/112 (48%), Gaps = 10/112 (8%)
Query: 52 RFNSRFDIDTYPVSEGRMPRDIFIEKLKGCSALLCNPHQKV--DKEVLDRSGENLKVIAT 109
F D YP + + IE++K + ++ N KV DKEVL NLK+I
Sbjct: 18 VFEEFGDFQIYPTT----SPEEVIERIKDANIIITN---KVVIDKEVLS-QLPNLKLICI 69
Query: 110 FSVGHDHLHLDEIKSRGIRVGTVGPVSSDTVAEYNIGLAIAVSRRFQQRHNW 161
+ G +++ ++ K +GI V V S+++VA++ + +++ R +
Sbjct: 70 TATGTNNVDIEYAKKKGIAVKNVAGYSTESVAQHTFAMLLSLLGRINYYDRY 121
>gnl|CDD|181041 PRK07574, PRK07574, formate dehydrogenase; Provisional.
Length = 385
Score = 148 bits (375), Expect = 1e-38
Identities = 83/238 (34%), Positives = 120/238 (50%), Gaps = 10/238 (4%)
Query: 869 TPKRTE---NLKVITTFSVGYDHLELHEIKARGIRVGSVGHISSDTVAEYNIGLAIAVSR 925
T +R NLK+ T +G DH++L GI V V +S +VAE+ + + +A+ R
Sbjct: 105 TAERIAKAPNLKLAITAGIGSDHVDLQAASEHGITVAEVTGSNSISVAEHVVMMILALVR 164
Query: 926 RFQEGRKCITSGEWALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILY 985
++ + G W + L+G TVGIVG G IGL + LK F V K+ Y
Sbjct: 165 NYEPSHRQAVEGGWNIAD---CVSRSYDLEGMTVGIVGAGRIGLAVLRRLKPFDV-KLHY 220
Query: 986 TSR-RVKEEGTA-LGAQLVP-LDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAIL 1042
T R R+ EE LG D+L + D + + C L +TE L S MK + L
Sbjct: 221 TDRHRLPEEVEQELGLTYHVSFDSLVSVCDVVTIHCPLHPETEHLFDADVLSRMKRGSYL 280
Query: 1043 VNTSRGGLLDQEALVEFLKDKKIGGAGLDVMIPEPLPADHPLVQLDNCVLTPHTSSAT 1100
VNT+RG ++D++A+V L+ + G DV P+P PADHP + +TPH S T
Sbjct: 281 VNTARGKIVDRDAVVRALESGHLAGYAGDVWFPQPAPADHPWRTMPRNGMTPHISGTT 338
Score = 77.8 bits (192), Expect = 6e-15
Identities = 31/82 (37%), Positives = 47/82 (57%)
Query: 312 VPLDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLK 371
V D+L + D + + C L +TE L S MK + L+NT+RG ++D++A+V L+
Sbjct: 240 VSFDSLVSVCDVVTIHCPLHPETEHLFDADVLSRMKRGSYLVNTARGKIVDRDAVVRALE 299
Query: 372 DKKIGGAGLDVMIPEPLPADHP 393
+ G DV P+P PADHP
Sbjct: 300 SGHLAGYAGDVWFPQPAPADHP 321
Score = 75.5 bits (186), Expect = 3e-14
Identities = 43/123 (34%), Positives = 63/123 (51%), Gaps = 5/123 (4%)
Query: 619 KNLKVITTFSVGYDHLELHEIKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRFQEGRKC 678
NLK+ T +G DH++L GI V V +S +VAE+ + + +A+ R ++ +
Sbjct: 113 PNLKLAITAGIGSDHVDLQAASEHGITVAEVTGSNSISVAEHVVMMILALVRNYEPSHRQ 172
Query: 679 ITSGEWALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSR-RVKE 737
G W + L+G TVGIVG G IGL + LK F V K+ YT R R+ E
Sbjct: 173 AVEGGWNIAD---CVSRSYDLEGMTVGIVGAGRIGLAVLRRLKPFDV-KLHYTDRHRLPE 228
Query: 738 EGQ 740
E +
Sbjct: 229 EVE 231
Score = 40.4 bits (95), Expect = 0.004
Identities = 19/60 (31%), Positives = 31/60 (51%)
Query: 103 NLKVIATFSVGHDHLHLDEIKSRGIRVGTVGPVSSDTVAEYNIGLAIAVSRRFQQRHNWI 162
NLK+ T +G DH+ L GI V V +S +VAE+ + + +A+ R ++ H
Sbjct: 114 NLKLAITAGIGSDHVDLQAASEHGITVAEVTGSNSISVAEHVVMMILALVRNYEPSHRQA 173
Score = 39.7 bits (93), Expect = 0.007
Identities = 22/58 (37%), Positives = 28/58 (48%), Gaps = 4/58 (6%)
Query: 807 YHGTINGEWALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSR 864
+ + G W + L+G TVGIVG G IGL + LK F V K+ YT R
Sbjct: 170 HRQAVEGGWNIAD---CVSRSYDLEGMTVGIVGAGRIGLAVLRRLKPFDV-KLHYTDR 223
>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 = 145 bits (367), Expect = 3e-38
Identities = 72/252 (28%), Positives = 111/252 (44%), Gaps = 19/252 (7%)
Query: 875 NLKVITTFSVGYDHLELHEIKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRFQEGRKCI 934
L+V+ T S GYD + + G+ + + + + AE + L +A R +
Sbjct: 60 RLRVVQTLSAGYDGV--LPLLPEGVTLCNARGVHDASTAELAVALILASLRGLPRFVRAQ 117
Query: 935 TSGEWALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRRVKEEG 994
G W ++T L V IVG G+IG + L F+V + +R +
Sbjct: 118 ARGRWEPRRTP-------SLADRRVLIVGYGSIGRAIERRLAPFEVR-VTRVARTARP-- 167
Query: 995 TALGAQLVP---LDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILVNTSRGGLL 1051
G Q+ L L E+D + + LT +T L+ + + M A+LVN +RG ++
Sbjct: 168 ---GEQVHGIDELPALLPEADVVVLIVPLTDETRGLVDAEFLARMPDGALLVNVARGPVV 224
Query: 1052 DQEALVEFLKDKKIGGAGLDVMIPEPLPADHPLVQLDNCVLTPHTSSATKAVRDEKSSTS 1111
D +ALV L ++ A LDV PEPLP HPL ++TPH AT A +
Sbjct: 225 DTDALVAELASGRLR-AALDVTDPEPLPPGHPLWSAPGVLITPHVGGATPAFLPRAYALV 283
Query: 1112 AENIIRGYKGEP 1123
+ R GEP
Sbjct: 284 RRQLRRYAAGEP 295
Score = 84.2 bits (209), Expect = 2e-17
Identities = 31/87 (35%), Positives = 46/87 (52%), Gaps = 1/87 (1%)
Query: 314 LDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLKDK 373
L L E+D + + LT +T L+ + + M A+L+N +RG ++D +ALV L
Sbjct: 177 LPALLPEADVVVLIVPLTDETRGLVDAEFLARMPDGALLVNVARGPVVDTDALVAELASG 236
Query: 374 KIGGAGLDVMIPEPLPADHPLVQLDNC 400
++ A LDV PEPLP HPL
Sbjct: 237 RL-RAALDVTDPEPLPPGHPLWSAPGV 262
Score = 54.1 bits (131), Expect = 1e-07
Identities = 27/109 (24%), Positives = 45/109 (41%), Gaps = 9/109 (8%)
Query: 618 IKNLKVITTFSVGYDHLELHEIKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRFQEGRK 677
+ L+V+ T S GYD + + G+ + + + + AE + L +A R +
Sbjct: 58 LPRLRVVQTLSAGYDGV--LPLLPEGVTLCNARGVHDASTAELAVALILASLRGLPRFVR 115
Query: 678 CITSGEWALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKAFKVS 726
G W ++T L V IVG G+IG + L F+V
Sbjct: 116 AQARGRWEPRRTP-------SLADRRVLIVGYGSIGRAIERRLAPFEVR 157
Score = 35.6 bits (83), Expect = 0.13
Identities = 18/67 (26%), Positives = 27/67 (40%), Gaps = 12/67 (17%)
Query: 103 NLKVIATFSVGHDHL--HLDEIKSRGIRVGTVGPVSSDTVAEYNIGLAIAVSRRF----- 155
L+V+ T S G+D + L E G+ + V + AE + L +A R
Sbjct: 60 RLRVVQTLSAGYDGVLPLLPE----GVTLCNARGVHDASTAELAVALILASLRGLPRFVR 115
Query: 156 -QQRHNW 161
Q R W
Sbjct: 116 AQARGRW 122
Score = 31.0 bits (71), Expect = 3.2
Identities = 19/85 (22%), Positives = 28/85 (32%), Gaps = 25/85 (29%)
Query: 773 LVVTVLHVHIGDLPAESFEDQVQTDGLKTLTELCYHGTINGEWALKQTHIIGPNIMGLKG 832
L V ++ + LP Q + G W ++T L
Sbjct: 98 LAVALILASLRGLP-RFVRAQAR-----------------GRWEPRRTP-------SLAD 132
Query: 833 ATVGIVGLGNIGLETAKLLKAFKVS 857
V IVG G+IG + L F+V
Sbjct: 133 RRVLIVGYGSIGRAIERRLAPFEVR 157
>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 = 137 bits (347), Expect = 2e-35
Identities = 70/233 (30%), Positives = 116/233 (49%), Gaps = 21/233 (9%)
Query: 874 ENLKVITTFSVGYDHLELHEIKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRFQEGRKC 933
+LK I G +++++ RGI V + +++ VAE I + +A+SR + K
Sbjct: 49 PSLKAIARAGAGVNNIDVDAASKRGIVVFNTPGANANAVAELVIAMMLALSRNIIQAIKW 108
Query: 934 ITSGEWAL-------KQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKAFKVSKIL-- 984
+T+G+ + +G L+G T+G++GLGNIG A A + K++
Sbjct: 109 VTNGDGDDISKGVEKGKKQFVGT---ELRGKTLGVIGLGNIGRLVANAALALGM-KVIGY 164
Query: 985 --YTSRRVKEEGTALGAQLVPLDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAIL 1042
Y S + + ++ L+ L A +D+I + LT +T LI + + MKP AIL
Sbjct: 165 DPYLSVEAAWKLSVEVQRVTSLEELLATADYITLHVPLTDETRGLINAELLAKMKPGAIL 224
Query: 1043 VNTSRGGLLDQEALVEFLKDKKIGGAGLDVMIPEPLPADHPLVQLDNCVLTPH 1095
+N +RG ++D+EAL+E L + K+GG D P L L N + TPH
Sbjct: 225 LNFARGEIVDEEALLEALDEGKLGGYVTDFPEPALLGH------LPNVIATPH 271
Score = 87.6 bits (218), Expect = 1e-18
Identities = 33/82 (40%), Positives = 48/82 (58%), Gaps = 1/82 (1%)
Query: 314 LDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLKDK 373
L+ L A +D+I + LT +T LI + + MKP AIL+N +RG ++D+EAL+E L +
Sbjct: 186 LEELLATADYITLHVPLTDETRGLINAELLAKMKPGAILLNFARGEIVDEEALLEALDEG 245
Query: 374 KIGGAGLDVMIPEPLPADHPLV 395
K+GG D P L P V
Sbjct: 246 KLGGYVTDFPEPALLGH-LPNV 266
Score = 57.6 bits (140), Expect = 1e-08
Identities = 31/112 (27%), Positives = 54/112 (48%), Gaps = 10/112 (8%)
Query: 619 KNLKVITTFSVGYDHLELHEIKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRFQEGRKC 678
+LK I G +++++ RGI V + +++ VAE I + +A+SR + K
Sbjct: 49 PSLKAIARAGAGVNNIDVDAASKRGIVVFNTPGANANAVAELVIAMMLALSRNIIQAIKW 108
Query: 679 ITSGEWAL-------KQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKAF 723
+T+G+ + +G L+G T+G++GLGNIG A A
Sbjct: 109 VTNGDGDDISKGVEKGKKQFVGT---ELRGKTLGVIGLGNIGRLVANAALAL 157
Score = 39.5 bits (93), Expect = 0.007
Identities = 12/26 (46%), Positives = 16/26 (61%)
Query: 829 GLKGATVGIVGLGNIGLETAKLLKAF 854
L+G T+G++GLGNIG A A
Sbjct: 132 ELRGKTLGVIGLGNIGRLVANAALAL 157
Score = 36.8 bits (86), Expect = 0.058
Identities = 21/66 (31%), Positives = 33/66 (50%), Gaps = 2/66 (3%)
Query: 102 ENLKVIATFSVGHDHLHLDEIKSRGIRV-GTVGPVSSDTVAEYNIGLAIAVSRRFQQRHN 160
+LK IA G +++ +D RGI V T G +++ VAE I + +A+SR Q
Sbjct: 49 PSLKAIARAGAGVNNIDVDAASKRGIVVFNTPGA-NANAVAELVIAMMLALSRNIIQAIK 107
Query: 161 WIARLS 166
W+
Sbjct: 108 WVTNGD 113
>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 = 131 bits (332), Expect = 1e-33
Identities = 81/264 (30%), Positives = 130/264 (49%), Gaps = 16/264 (6%)
Query: 845 LETAKLLKAFKVSKILYTSRNKVKTPKR----TENLKVITTFSVGYDHLELHEIKARGIR 900
L+ +L++A K +L R+K + + L I F +G + ++L RGI
Sbjct: 31 LDEDELIEALKDVHLLGI-RSKTQLTEEVLEAAPKLLAIGCFCIGTNQVDLDAAAKRGIP 89
Query: 901 VGSVGHISSDTVAEYNIGLAIAVSRRFQEGRKCITSGEWALKQTHIIGPNIMGLKGATVG 960
V + ++ +VAE IG I ++RR + G W ++ ++G T+G
Sbjct: 90 VFNAPFSNTRSVAELVIGEIIMLARRLPDRNAAAHRGIW--NKSAT---GSHEVRGKTLG 144
Query: 961 IVGLGNIGLETAKLLKAFKVSKILYTSRRVKEEGTALGAQLVPLDTLCAESDFIFVTCAL 1020
I+G G+IG + + L +A + I Y G A Q+ L+ L AE+DF+ +
Sbjct: 145 IIGYGHIGSQLSVLAEALGMRVIFYDIAEKLPLGNAR--QVSSLEELLAEADFVTLHVPA 202
Query: 1021 TKDTEQLIGRKQFSLMKPTAILVNTSRGGLLDQEALVEFLKDKKIGGAGLDVMIPEPL-- 1078
T T+ +IG ++ + MK AIL+N SRG ++D +AL E L+ + GA +DV EP
Sbjct: 203 TPSTKNMIGAEEIAQMKKGAILINASRGTVVDIDALAEALRSGHLAGAAVDVFPEEPASN 262
Query: 1079 --PADHPLVQLDNCVLTPHTSSAT 1100
P PL L N +LTPH +T
Sbjct: 263 GEPFSSPLQGLPNVILTPHIGGST 286
Score = 83.4 bits (207), Expect = 3e-17
Identities = 39/100 (39%), Positives = 55/100 (55%), Gaps = 6/100 (6%)
Query: 304 GTALGAQLVPLDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQ 363
G A Q+ L+ L AE+DF+ + T T+ +IG ++ + MK AILIN SRG ++D
Sbjct: 178 GNAR--QVSSLEELLAEADFVTLHVPATPSTKNMIGAEEIAQMKKGAILINASRGTVVDI 235
Query: 364 EALVEFLKDKKIGGAGLDVMIPEPL----PADHPLVQLDN 399
+AL E L+ + GA +DV EP P PL L N
Sbjct: 236 DALAEALRSGHLAGAAVDVFPEEPASNGEPFSSPLQGLPN 275
Score = 46.8 bits (112), Expect = 4e-05
Identities = 31/103 (30%), Positives = 47/103 (45%), Gaps = 6/103 (5%)
Query: 57 FDIDTYPVSEGRMPRDIFIEKLKGCSALLCNPHQKVDKEVLDRSGENLKVIATFSVGHDH 116
+++ G + D IE LK L ++ +EVL+ + L I F +G +
Sbjct: 22 IEVERLK---GALDEDELIEALKDVHLLGIRSKTQLTEEVLEAA-PKLLAIGCFCIGTNQ 77
Query: 117 LHLDEIKSRGIRVGTVGPVS-SDTVAEYNIGLAIAVSRRFQQR 158
+ LD RGI V P S + +VAE IG I ++RR R
Sbjct: 78 VDLDAAAKRGIPVFN-APFSNTRSVAELVIGEIIMLARRLPDR 119
Score = 46.8 bits (112), Expect = 4e-05
Identities = 41/203 (20%), Positives = 75/203 (36%), Gaps = 47/203 (23%)
Query: 529 AFEILGEM-FDIITYPASEGQIPRDIFIEKLRGCSALLCTSRDRVDKQVLDESGGYRCTE 587
A E+ ++ + D IE L+ L S+ ++ ++VL+ +
Sbjct: 13 ADELFRAGGIEVERLKGAL---DEDELIEALKDVHLLGIRSKTQLTEEVLEAA------- 62
Query: 588 DFFGLDLDQMFRNPSKRHVNIETVLGVSFLIKNLKVITTFSVGYDHLELHEIKARGIRVG 647
L I F +G + ++L RGI V
Sbjct: 63 -------------------------------PKLLAIGCFCIGTNQVDLDAAAKRGIPVF 91
Query: 648 SVGHISSDTVAEYNIGLAIAVSRRFQEGRKCITSGEWALKQTHIIGPNIMGLKGATVGIV 707
+ ++ +VAE IG I ++RR + G W ++ ++G T+GI+
Sbjct: 92 NAPFSNTRSVAELVIGEIIMLARRLPDRNAAAHRGIW--NKSAT---GSHEVRGKTLGII 146
Query: 708 GLGNIGLETAKLLKAFKVSKILY 730
G G+IG + + L +A + I Y
Sbjct: 147 GYGHIGSQLSVLAEALGMRVIFY 169
Score = 31.4 bits (72), Expect = 2.8
Identities = 13/37 (35%), Positives = 22/37 (59%)
Query: 830 LKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRNK 866
++G T+GI+G G+IG + + L +A + I Y K
Sbjct: 138 VRGKTLGIIGYGHIGSQLSVLAEALGMRVIFYDIAEK 174
>gnl|CDD|178684 PLN03139, PLN03139, formate dehydrogenase; Provisional.
Length = 386
Score = 131 bits (331), Expect = 8e-33
Identities = 78/258 (30%), Positives = 124/258 (48%), Gaps = 13/258 (5%)
Query: 871 KRTENLKVITTFSVGYDHLELHEIKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRFQEG 930
K+ +NL+++ T +G DH++L A G+ V V + +VAE + + + R F G
Sbjct: 117 KKAKNLELLLTAGIGSDHIDLPAAAAAGLTVAEVTGSNVVSVAEDELMRILILLRNFLPG 176
Query: 931 RKCITSGEWALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSR-- 988
+ SGEW + I L+G TVG VG G IG + LK F +LY R
Sbjct: 177 YHQVVSGEWNVAG---IAYRAYDLEGKTVGTVGAGRIGRLLLQRLKPFNC-NLLYHDRLK 232
Query: 989 ----RVKEEGTALGAQLVPLDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILVN 1044
KE G L D + + D + + LT+ T + +++ + MK ++VN
Sbjct: 233 MDPELEKETGAKFEEDL---DAMLPKCDVVVINTPLTEKTRGMFNKERIAKMKKGVLIVN 289
Query: 1045 TSRGGLLDQEALVEFLKDKKIGGAGLDVMIPEPLPADHPLVQLDNCVLTPHTSSATKAVR 1104
+RG ++D +A+ + IGG G DV P+P P DHP + N +TPH S T +
Sbjct: 290 NARGAIMDTQAVADACSSGHIGGYGGDVWYPQPAPKDHPWRYMPNHAMTPHISGTTIDAQ 349
Query: 1105 DEKSSTSAENIIRGYKGE 1122
++ + + R +KGE
Sbjct: 350 LRYAAGVKDMLDRYFKGE 367
Score = 64.5 bits (157), Expect = 1e-10
Identities = 25/80 (31%), Positives = 45/80 (56%)
Query: 314 LDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLKDK 373
LD + + D + + LT+ T + +++ + MK +++N +RG ++D +A+ +
Sbjct: 249 LDAMLPKCDVVVINTPLTEKTRGMFNKERIAKMKKGVLIVNNARGAIMDTQAVADACSSG 308
Query: 374 KIGGAGLDVMIPEPLPADHP 393
IGG G DV P+P P DHP
Sbjct: 309 HIGGYGGDVWYPQPAPKDHP 328
Score = 63.7 bits (155), Expect = 2e-10
Identities = 39/115 (33%), Positives = 56/115 (48%), Gaps = 4/115 (3%)
Query: 619 KNLKVITTFSVGYDHLELHEIKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRFQEGRKC 678
KNL+++ T +G DH++L A G+ V V + +VAE + + + R F G
Sbjct: 120 KNLELLLTAGIGSDHIDLPAAAAAGLTVAEVTGSNVVSVAEDELMRILILLRNFLPGYHQ 179
Query: 679 ITSGEWALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSR 733
+ SGEW + I L+G TVG VG G IG + LK F +LY R
Sbjct: 180 VVSGEWNVAG---IAYRAYDLEGKTVGTVGAGRIGRLLLQRLKPFNC-NLLYHDR 230
Score = 41.0 bits (96), Expect = 0.003
Identities = 23/61 (37%), Positives = 30/61 (49%), Gaps = 4/61 (6%)
Query: 807 YHGTINGEWALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRNK 866
YH ++GEW + I L+G TVG VG G IG + LK F +LY R K
Sbjct: 177 YHQVVSGEWNVAG---IAYRAYDLEGKTVGTVGAGRIGRLLLQRLKPFNC-NLLYHDRLK 232
Query: 867 V 867
+
Sbjct: 233 M 233
>gnl|CDD|177941 PLN02306, PLN02306, hydroxypyruvate reductase.
Length = 386
Score = 129 bits (325), Expect = 4e-32
Identities = 87/266 (32%), Positives = 143/266 (53%), Gaps = 22/266 (8%)
Query: 877 KVITTFSVGYDHLELHEIKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRFQEGRKCITS 936
K + +VGY+++++ GI VG+ + ++T AE L++A +RR E + + +
Sbjct: 88 KAFSNMAVGYNNVDVEAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRA 147
Query: 937 GEWALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLL-KAFKVSKI---LYTSRRVKE 992
G + H+ N+ LKG TVG++G G IG A+++ + FK++ I LY S R+++
Sbjct: 148 GLYEGWLPHLFVGNL--LKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQSTRLEK 205
Query: 993 EGTALGAQL-------------VPLDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPT 1039
TA G L ++ + E+D I + L K T LI +++ +LMK
Sbjct: 206 FVTAYGQFLKANGEQPVTWKRASSMEEVLREADVISLHPVLDKTTYHLINKERLALMKKE 265
Query: 1040 AILVNTSRGGLLDQEALVEFLKDKKIGGAGLDVMIPEPLPADHP-LVQLDNCVLTPHTSS 1098
A+LVN SRG ++D+ ALVE LK + GLDV E P P L + N V+ PH +S
Sbjct: 266 AVLVNASRGPVIDEVALVEHLKANPMFRVGLDVF--EDEPYMKPGLADMKNAVVVPHIAS 323
Query: 1099 ATKAVRDEKSSTSAENIIRGYKGEPM 1124
A+K R+ ++ +A N++ KG P+
Sbjct: 324 ASKWTREGMATLAALNVLGKLKGYPV 349
Score = 62.2 bits (151), Expect = 6e-10
Identities = 30/68 (44%), Positives = 42/68 (61%)
Query: 320 ESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLKDKKIGGAG 379
E+D I + L K T LI +++ +LMK A+L+N SRG ++D+ ALVE LK + G
Sbjct: 236 EADVISLHPVLDKTTYHLINKERLALMKKEAVLVNASRGPVIDEVALVEHLKANPMFRVG 295
Query: 380 LDVMIPEP 387
LDV EP
Sbjct: 296 LDVFEDEP 303
Score = 58.3 bits (141), Expect = 1e-08
Identities = 37/120 (30%), Positives = 68/120 (56%), Gaps = 6/120 (5%)
Query: 622 KVITTFSVGYDHLELHEIKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRFQEGRKCITS 681
K + +VGY+++++ GI VG+ + ++T AE L++A +RR E + + +
Sbjct: 88 KAFSNMAVGYNNVDVEAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRA 147
Query: 682 GEWALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLL-KAFKVSKI---LYTSRRVKE 737
G + H+ N+ LKG TVG++G G IG A+++ + FK++ I LY S R+++
Sbjct: 148 GLYEGWLPHLFVGNL--LKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQSTRLEK 205
Score = 33.3 bits (76), Expect = 0.77
Identities = 17/60 (28%), Positives = 32/60 (53%), Gaps = 2/60 (3%)
Query: 95 EVLDRSGENLKVIATFSVGHDHLHLDEIKSRGIRVGTVGPVSSDTVAEYNIGLAIAVSRR 154
L ++G K + +VG++++ ++ GI VG V ++T AE L++A +RR
Sbjct: 80 SALSKAGG--KAFSNMAVGYNNVDVEAANKYGIAVGNTPGVLTETTAELAASLSLAAARR 137
Score = 32.9 bits (75), Expect = 1.00
Identities = 15/33 (45%), Positives = 23/33 (69%), Gaps = 1/33 (3%)
Query: 830 LKGATVGIVGLGNIGLETAKLL-KAFKVSKILY 861
LKG TVG++G G IG A+++ + FK++ I Y
Sbjct: 163 LKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYY 195
>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 = 123 bits (310), Expect = 2e-30
Identities = 82/262 (31%), Positives = 124/262 (47%), Gaps = 33/262 (12%)
Query: 875 NLKVITTFSVGYDHLELHEIKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRFQEGRKCI 934
+K + T +VG++H++L K G ++ V S + +AE LA+ +SR
Sbjct: 68 GIKYVFTRTVGFNHIDLEAAKELGFKMARVPSYSPNAIAELAFTLAMTLSRHTAY----- 122
Query: 935 TSGEWALKQTHIIGPNIMG--LKGATVGIVGLGNIGLETAKLLKAFKVSKI---LYTSRR 989
+ + + P + ++ +TVGI+G G IGL AKL K I +Y S
Sbjct: 123 -TASRTANKNFKVDPFMFSKEIRNSTVGIIGTGRIGLTAAKLFKGLGAKVIGYDIYPSDA 181
Query: 990 VKEEGTALGAQLVPLDTLCAESDFIFVTCALTK-DTEQLIGRKQFSLMKPTAILVNTSRG 1048
K+ T V LD L +SD I + K ++LI ++ S MK AIL+NT+RG
Sbjct: 182 AKDVVT-----FVSLDELLKKSDIISLHVPYIKGKNDKLINKEFISKMKDGAILINTARG 236
Query: 1049 GLLDQEALVEFLKDKKIGGAGLDVMIPE-------------PLPADHPLVQLDNCVL-TP 1094
L D+EA++E L+ K+ G G DV+ E P L+ L VL TP
Sbjct: 237 ELQDEEAILEALESGKLAGFGTDVLNNEKEIFFKDFDGDKIEDPVVEKLLDLYPRVLLTP 296
Query: 1095 HTSSAT-KAVRDEKSSTSAENI 1115
H S T +A+ + TS EN+
Sbjct: 297 HIGSYTDEALSN-MIETSYENL 317
Score = 70.8 bits (174), Expect = 7e-13
Identities = 35/93 (37%), Positives = 51/93 (54%), Gaps = 2/93 (2%)
Query: 295 GYNWFERSNGTALGAQLVPLDTLCAESDFIFVTCALTK-DTEQLIGRKQFSLMKPTAILI 353
GY+ + + V LD L +SD I + K ++LI ++ S MK AILI
Sbjct: 173 GYDIYPSDAAKDV-VTFVSLDELLKKSDIISLHVPYIKGKNDKLINKEFISKMKDGAILI 231
Query: 354 NTSRGGLLDQEALVEFLKDKKIGGAGLDVMIPE 386
NT+RG L D+EA++E L+ K+ G G DV+ E
Sbjct: 232 NTARGELQDEEAILEALESGKLAGFGTDVLNNE 264
Score = 63.1 bits (154), Expect = 2e-10
Identities = 41/157 (26%), Positives = 69/157 (43%), Gaps = 25/157 (15%)
Query: 619 KNLKVITTFSVGYDHLELHEIKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRFQEGRKC 678
+K + T +VG++H++L K G ++ V S + +AE LA+ +SR
Sbjct: 67 YGIKYVFTRTVGFNHIDLEAAKELGFKMARVPSYSPNAIAELAFTLAMTLSRHTAY---- 122
Query: 679 ITSGEWALKQTHIIGPNIMG--LKGATVGIVGLGNIGLETAKLLKAFKVSKI---LYTSR 733
+ + + P + ++ +TVGI+G G IGL AKL K I +Y S
Sbjct: 123 --TASRTANKNFKVDPFMFSKEIRNSTVGIIGTGRIGLTAAKLFKGLGAKVIGYDIYPSD 180
Query: 734 RVKEEGQLFSLVYDFCRYSIGGVTIKRLVKKTFILSF 770
K D + V++ L+KK+ I+S
Sbjct: 181 AAK----------DVVTF----VSLDELLKKSDIISL 203
Score = 44.2 bits (105), Expect = 3e-04
Identities = 24/83 (28%), Positives = 41/83 (49%), Gaps = 1/83 (1%)
Query: 75 IEKLKGCSALLCNPHQKVDKEVLDRSGE-NLKVIATFSVGHDHLHLDEIKSRGIRVGTVG 133
+ KG A++ + DKE L+ E +K + T +VG +H+ L+ K G ++ V
Sbjct: 39 VHLAKGHDAVIVRGNCFADKENLEIYKEYGIKYVFTRTVGFNHIDLEAAKELGFKMARVP 98
Query: 134 PVSSDTVAEYNIGLAIAVSRRFQ 156
S + +AE LA+ +SR
Sbjct: 99 SYSPNAIAELAFTLAMTLSRHTA 121
Score = 40.4 bits (95), Expect = 0.004
Identities = 13/25 (52%), Positives = 17/25 (68%)
Query: 830 LKGATVGIVGLGNIGLETAKLLKAF 854
++ +TVGI+G G IGL AKL K
Sbjct: 143 IRNSTVGIIGTGRIGLTAAKLFKGL 167
>gnl|CDD|215501 PLN02928, PLN02928, oxidoreductase family protein.
Length = 347
Score = 121 bits (305), Expect = 1e-29
Identities = 79/246 (32%), Positives = 121/246 (49%), Gaps = 25/246 (10%)
Query: 872 RTENLKVITTFSVGYDHLELHEIKARGI---RVGSVGHISSDTVAEYNIGLAIAVSRRFQ 928
R +K+I F VG + +++ GI R+ S G ++ + AE I L + + R+
Sbjct: 79 RASQMKLIMQFGVGLEGVDVDAATKHGIKVARIPSEGTGNAASCAEMAIYLMLGLLRKQN 138
Query: 929 EGRKCITSGEWALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSR 988
E + +LK + P L G TV I+G G IG+E AK L+ F V K+L T R
Sbjct: 139 EMQI-------SLKARRLGEPIGDTLFGKTVFILGYGAIGIELAKRLRPFGV-KLLATRR 190
Query: 989 R-VKEEGTALGAQLVPLDTL------------CA-ESDFIFVTCALTKDTEQLIGRKQFS 1034
E L +D L A E+D + + C LTK+T ++ + S
Sbjct: 191 SWTSEPEDGLLIPNGDVDDLVDEKGGHEDIYEFAGEADIVVLCCTLTKETAGIVNDEFLS 250
Query: 1035 LMKPTAILVNTSRGGLLDQEALVEFLKDKKIGGAGLDVMIPEPLPADHPLVQLDNCVLTP 1094
MK A+LVN +RGGLLD +A++ L+ +GG +DV EP D P+++ N ++TP
Sbjct: 251 SMKKGALLVNIARGGLLDYDAVLAALESGHLGGLAIDVAWSEPFDPDDPILKHPNVIITP 310
Query: 1095 HTSSAT 1100
H + T
Sbjct: 311 HVAGVT 316
Score = 70.1 bits (172), Expect = 1e-12
Identities = 30/80 (37%), Positives = 49/80 (61%)
Query: 320 ESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLKDKKIGGAG 379
E+D + + C LTK+T ++ + S MK A+L+N +RGGLLD +A++ L+ +GG
Sbjct: 226 EADIVVLCCTLTKETAGIVNDEFLSSMKKGALLVNIARGGLLDYDAVLAALESGHLGGLA 285
Query: 380 LDVMIPEPLPADHPLVQLDN 399
+DV EP D P+++ N
Sbjct: 286 IDVAWSEPFDPDDPILKHPN 305
Score = 55.1 bits (133), Expect = 9e-08
Identities = 39/123 (31%), Positives = 59/123 (47%), Gaps = 11/123 (8%)
Query: 619 KNLKVITTFSVGYDHLELHEIKARGI---RVGSVGHISSDTVAEYNIGLAIAVSRRFQEG 675
+K+I F VG + +++ GI R+ S G ++ + AE I L + + R+ E
Sbjct: 81 SQMKLIMQFGVGLEGVDVDAATKHGIKVARIPSEGTGNAASCAEMAIYLMLGLLRKQNEM 140
Query: 676 RKCITSGEWALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRRV 735
+ +LK + P L G TV I+G G IG+E AK L+ F V K+L T R
Sbjct: 141 QI-------SLKARRLGEPIGDTLFGKTVFILGYGAIGIELAKRLRPFGV-KLLATRRSW 192
Query: 736 KEE 738
E
Sbjct: 193 TSE 195
Score = 43.1 bits (102), Expect = 6e-04
Identities = 22/50 (44%), Positives = 29/50 (58%), Gaps = 1/50 (2%)
Query: 816 ALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRN 865
+LK + P L G TV I+G G IG+E AK L+ F V K+L T R+
Sbjct: 143 SLKARRLGEPIGDTLFGKTVFILGYGAIGIELAKRLRPFGV-KLLATRRS 191
>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 = 118 bits (299), Expect = 3e-29
Identities = 75/260 (28%), Positives = 111/260 (42%), Gaps = 27/260 (10%)
Query: 875 NLKVITTFSVGYDHLELHEIKARGI---RVGSVGHISSDTVAEYNIGLAIAVSRRFQEGR 931
NLK I + G DHL + R+ V + +AEY + + + R
Sbjct: 58 NLKAIFSLGAGVDHLLADPD-LPDVPIVRL--VDPGLAQGMAEYVLAAVLRLHRDMDRYA 114
Query: 932 KCITSGEWALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKA--FKV---SKILYT 986
G W + P VG++GLG +G A+ L A F V S+
Sbjct: 115 AQQRRGVW---KPLPQRPA----AERRVGVLGLGELGAAVARRLAALGFPVSGWSR---- 163
Query: 987 SRRVKEEGTAL-GAQLVPLDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILVNT 1045
S + E T G + LD A++D + LT +T ++ + + + A L+N
Sbjct: 164 SPKDIEGVTCFHGEEG--LDAFLAQTDILVCLLPLTPETRGILNAELLARLPRGAALINV 221
Query: 1046 SRGGLLDQEALVEFLKDKKIGGAGLDVMIPEPLPADHPLVQLDNCVLTPHTSSATKAVRD 1105
RG L + L+ L + GA LDV EPLPADHPL + +TPH ++ T D
Sbjct: 222 GRGPHLVEADLLAALDSGHLSGAVLDVFEQEPLPADHPLWRHPRVTVTPHIAAIT--DPD 279
Query: 1106 EKSSTSAENIIRGYKGEPMI 1125
++ AENI R GEP+
Sbjct: 280 SAAAQVAENIRRLEAGEPLP 299
Score = 81.8 bits (203), Expect = 1e-16
Identities = 30/81 (37%), Positives = 42/81 (51%)
Query: 314 LDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLKDK 373
LD A++D + LT +T ++ + + + A LIN RG L + L+ L
Sbjct: 180 LDAFLAQTDILVCLLPLTPETRGILNAELLARLPRGAALINVGRGPHLVEADLLAALDSG 239
Query: 374 KIGGAGLDVMIPEPLPADHPL 394
+ GA LDV EPLPADHPL
Sbjct: 240 HLSGAVLDVFEQEPLPADHPL 260
Score = 36.3 bits (85), Expect = 0.071
Identities = 29/113 (25%), Positives = 42/113 (37%), Gaps = 15/113 (13%)
Query: 619 KNLKVITTFSVGYDHLELHEIKARGI---RVGSVGHISSDTVAEYNIGLAIAVSRRFQEG 675
NLK I + G DHL + R+ V + +AEY + + + R
Sbjct: 57 PNLKAIFSLGAGVDHLLADPD-LPDVPIVRL--VDPGLAQGMAEYVLAAVLRLHRDMDRY 113
Query: 676 RKCITSGEWALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKA--FKVS 726
G W + P VG++GLG +G A+ L A F VS
Sbjct: 114 AAQQRRGVW---KPLPQRPA----AERRVGVLGLGELGAAVARRLAALGFPVS 159
Score = 33.6 bits (78), Expect = 0.49
Identities = 12/26 (46%), Positives = 16/26 (61%), Gaps = 2/26 (7%)
Query: 834 TVGIVGLGNIGLETAKLLKA--FKVS 857
VG++GLG +G A+ L A F VS
Sbjct: 134 RVGVLGLGELGAAVARRLAALGFPVS 159
Score = 29.8 bits (68), Expect = 8.0
Identities = 19/66 (28%), Positives = 27/66 (40%), Gaps = 8/66 (12%)
Query: 103 NLKVIATFSVGHDHLHLDEIKSRGIR-VGTVGPVSSDTVAEYNIGLAIAVSRRF------ 155
NLK I + G DHL D + V V P + +AEY + + + R
Sbjct: 58 NLKAIFSLGAGVDHLLADPD-LPDVPIVRLVDPGLAQGMAEYVLAAVLRLHRDMDRYAAQ 116
Query: 156 QQRHNW 161
Q+R W
Sbjct: 117 QRRGVW 122
>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 = 116 bits (294), Expect = 3e-28
Identities = 69/227 (30%), Positives = 107/227 (47%), Gaps = 36/227 (15%)
Query: 875 NLKVITTFSVGYDHLELHEIKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRFQEGRKCI 934
+K + T ++G DH++ +K RGI + ++++VAEY + A+ Q
Sbjct: 57 KVKFVGTATIGTDHIDTDYLKERGIGFANAPGCNANSVAEY---VLSALLVLAQRQGF-- 111
Query: 935 TSGEWALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRRVKEEG 994
LKG TVGIVG+GN+G A+ L+A ++ +L R + EG
Sbjct: 112 ------------------SLKGKTVGIVGVGNVGSRLARRLEALGMNVLLCDPPRAEAEG 153
Query: 995 TALGAQLVPLDTLCAESDFIFVTCALTKD----TEQLIGRKQFSLMKPTAILVNTSRGGL 1050
V L+ L AE+D I + LT+D T L+ + +KP IL+N SRG +
Sbjct: 154 ---DPGFVSLEELLAEADIITLHVPLTRDGEHPTYHLLDEDFLAALKPGQILINASRGAV 210
Query: 1051 LDQEALVEFLKDKKIGGAGLDVMIPEPLPADHPLVQLDNCVL--TPH 1095
+D +AL+ L+ K LDV EP ++L + V TPH
Sbjct: 211 IDNQALLALLQRGKDLRVVLDVWENEP----EIDLELLDKVDIATPH 253
Score = 72.9 bits (180), Expect = 1e-13
Identities = 31/82 (37%), Positives = 43/82 (52%), Gaps = 4/82 (4%)
Query: 310 QLVPLDTLCAESDFIFVTCALTKD----TEQLIGRKQFSLMKPTAILINTSRGGLLDQEA 365
V L+ L AE+D I + LT+D T L+ + +KP ILIN SRG ++D +A
Sbjct: 156 GFVSLEELLAEADIITLHVPLTRDGEHPTYHLLDEDFLAALKPGQILINASRGAVIDNQA 215
Query: 366 LVEFLKDKKIGGAGLDVMIPEP 387
L+ L+ K LDV EP
Sbjct: 216 LLALLQRGKDLRVVLDVWENEP 237
Score = 60.6 bits (148), Expect = 2e-09
Identities = 44/202 (21%), Positives = 76/202 (37%), Gaps = 68/202 (33%)
Query: 529 AFEILGEMFDIITYPASEGQIPRDIFIEKLRGCSALLCTSRDRVDKQVLDESGGYRCTED 588
A E+ + ++ P R+I E L+ LL S +V++ +L+ S
Sbjct: 11 AEELFSPLGEVTYLPG------REITAEDLKDADVLLVRSVTKVNEALLEGS-------- 56
Query: 589 FFGLDLDQMFRNPSKRHVNIETVLGVSFLIKNLKVITTFSVGYDHLELHEIKARGIRVGS 648
+K + T ++G DH++ +K RGI +
Sbjct: 57 -------------------------------KVKFVGTATIGTDHIDTDYLKERGIGFAN 85
Query: 649 VGHISSDTVAEYNIGLAIAVSRRFQEGRKCITSGEWALKQTHIIGPNIMGLKGATVGIVG 708
++++VAEY + A+ Q LKG TVGIVG
Sbjct: 86 APGCNANSVAEY---VLSALLVLAQRQGF--------------------SLKGKTVGIVG 122
Query: 709 LGNIGLETAKLLKAFKVSKILY 730
+GN+G A+ L+A ++ +L
Sbjct: 123 VGNVGSRLARRLEALGMNVLLC 144
Score = 41.4 bits (98), Expect = 0.002
Identities = 26/77 (33%), Positives = 42/77 (54%), Gaps = 3/77 (3%)
Query: 68 RMP-RDIFIEKLKGCSALLCNPHQKVDKEVLDRSGENLKVIATFSVGHDHLHLDEIKSRG 126
+P R+I E LK LL KV++ +L+ S +K + T ++G DH+ D +K RG
Sbjct: 23 YLPGREITAEDLKDADVLLVRSVTKVNEALLEGS--KVKFVGTATIGTDHIDTDYLKERG 80
Query: 127 IRVGTVGPVSSDTVAEY 143
I ++++VAEY
Sbjct: 81 IGFANAPGCNANSVAEY 97
Score = 40.6 bits (96), Expect = 0.004
Identities = 16/32 (50%), Positives = 23/32 (71%)
Query: 830 LKGATVGIVGLGNIGLETAKLLKAFKVSKILY 861
LKG TVGIVG+GN+G A+ L+A ++ +L
Sbjct: 113 LKGKTVGIVGVGNVGSRLARRLEALGMNVLLC 144
>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 = 114 bits (286), Expect = 2e-27
Identities = 74/241 (30%), Positives = 109/241 (45%), Gaps = 12/241 (4%)
Query: 862 TSRNKVKTPKRTENLKVITTFSVGYDHLELHEIKARGIRVGSVGHISSDTVAEYNIGLAI 921
+S N +R L+ + + G D + L A + V S + TVAE+ + L +
Sbjct: 46 SSDNLADAARRLTRLRWVQALAAGPDAV-LAAGFAPEVAVTSGRGLHDGTVAEHTLALIL 104
Query: 922 AVSRRFQEGRKCITSGEWALK----QTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKA 977
A RR E R+ WA + Q + L GA V I G G+IG A LL A
Sbjct: 105 AAVRRLDEMREAQREHRWAGELGGLQPLRPAGRLTTLLGARVLIWGFGSIGQRLAPLLTA 164
Query: 978 FKVSKILYTSRRVKEEGTALGAQLVPLDTLCA---ESDFIFVTCALTKDTEQLIGRKQFS 1034
+++ +R G G +V D L E+D + + T T + + +
Sbjct: 165 LG-ARVTGVARS---AGERAGFPVVAEDELPELLPETDVLVMILPATPSTAHALDAEVLA 220
Query: 1035 LMKPTAILVNTSRGGLLDQEALVEFLKDKKIGGAGLDVMIPEPLPADHPLVQLDNCVLTP 1094
+ A +VN RG +D++ALV L+ ++GGA LDV EPLPA PL N +LTP
Sbjct: 221 ALPKHAWVVNVGRGATVDEDALVAALESGRLGGAALDVTATEPLPASSPLWDAPNLILTP 280
Query: 1095 H 1095
H
Sbjct: 281 H 281
Score = 68.6 bits (168), Expect = 4e-12
Identities = 33/97 (34%), Positives = 49/97 (50%), Gaps = 3/97 (3%)
Query: 301 RSNGTALGAQLVPLDTLCA---ESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSR 357
RS G G +V D L E+D + + T T + + + + A ++N R
Sbjct: 174 RSAGERAGFPVVAEDELPELLPETDVLVMILPATPSTAHALDAEVLAALPKHAWVVNVGR 233
Query: 358 GGLLDQEALVEFLKDKKIGGAGLDVMIPEPLPADHPL 394
G +D++ALV L+ ++GGA LDV EPLPA PL
Sbjct: 234 GATVDEDALVAALESGRLGGAALDVTATEPLPASSPL 270
Score = 45.1 bits (107), Expect = 1e-04
Identities = 26/72 (36%), Positives = 33/72 (45%), Gaps = 4/72 (5%)
Query: 656 TVAEYNIGLAIAVSRRFQEGRKCITSGEWALK----QTHIIGPNIMGLKGATVGIVGLGN 711
TVAE+ + L +A RR E R+ WA + Q + L GA V I G G+
Sbjct: 94 TVAEHTLALILAAVRRLDEMREAQREHRWAGELGGLQPLRPAGRLTTLLGARVLIWGFGS 153
Query: 712 IGLETAKLLKAF 723
IG A LL A
Sbjct: 154 IGQRLAPLLTAL 165
Score = 30.8 bits (70), Expect = 4.0
Identities = 13/25 (52%), Positives = 14/25 (56%)
Query: 830 LKGATVGIVGLGNIGLETAKLLKAF 854
L GA V I G G+IG A LL A
Sbjct: 141 LLGARVLIWGFGSIGQRLAPLLTAL 165
>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 = 110 bits (276), Expect = 4e-26
Identities = 70/256 (27%), Positives = 120/256 (46%), Gaps = 17/256 (6%)
Query: 871 KRTENLKVITTFSVGYDHLELHEIKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRFQEG 930
++ NLK I G ++++L K +GI + + + D V E+ +G+ +A+ +
Sbjct: 58 EKATNLKFIARAGAGLENIDLEYAKEKGIELFNAPEGNRDAVGEHALGMLLALFNKLNRA 117
Query: 931 RKCITSGEWALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRRV 990
+ + +G W + G + L G TVGI+G GN+G AK L F I Y +
Sbjct: 118 DQEVRNGIWDREGNR--G---VELMGKTVGIIGYGNMGKAFAKRLSGFGCKVIAYDKYKN 172
Query: 991 KEEGTALGAQLVPLDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILVNTSRGGL 1050
G A A+ V L+TL E+D + + LT +T ++ ++ S K +NT+RG +
Sbjct: 173 F--GDA-YAEQVSLETLFKEADILSLHIPLTPETRGMVNKEFISSFKKPFYFINTARGKV 229
Query: 1051 LDQEALVEFLKDKKIGGAGLDVMIPEPLPADHP---------LVQLDNCVLTPHTSSATK 1101
+ + LV+ LK KI GA LDV+ E + L++ +LTPH + T
Sbjct: 230 VVTKDLVKALKSGKILGACLDVLEYEKASFESIFNQPEAFEYLIKSPKVILTPHIAGWTF 289
Query: 1102 AVRDEKSSTSAENIIR 1117
++ + + I
Sbjct: 290 ESYEKIAEVLVDKIKA 305
Score = 59.2 bits (144), Expect = 4e-09
Identities = 28/75 (37%), Positives = 44/75 (58%)
Query: 309 AQLVPLDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVE 368
A+ V L+TL E+D + + LT +T ++ ++ S K INT+RG ++ + LV+
Sbjct: 178 AEQVSLETLFKEADILSLHIPLTPETRGMVNKEFISSFKKPFYFINTARGKVVVTKDLVK 237
Query: 369 FLKDKKIGGAGLDVM 383
LK KI GA LDV+
Sbjct: 238 ALKSGKILGACLDVL 252
Score = 58.8 bits (143), Expect = 5e-09
Identities = 39/152 (25%), Positives = 67/152 (44%), Gaps = 17/152 (11%)
Query: 619 KNLKVITTFSVGYDHLELHEIKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRFQEGRKC 678
NLK I G ++++L K +GI + + + D V E+ +G+ +A+ + +
Sbjct: 61 TNLKFIARAGAGLENIDLEYAKEKGIELFNAPEGNRDAVGEHALGMLLALFNKLNRADQE 120
Query: 679 ITSGEWALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRRVKEE 738
+ +G W + G + L G TVGI+G GN+G AK L F I Y + +
Sbjct: 121 VRNGIWDREGNR--G---VELMGKTVGIIGYGNMGKAFAKRLSGFGCKVIAYDKYKNFGD 175
Query: 739 GQLFSLVYDFCRYSIGGVTIKRLVKKTFILSF 770
+ V+++ L K+ ILS
Sbjct: 176 --------AYAEQ----VSLETLFKEADILSL 195
Score = 38.4 bits (90), Expect = 0.016
Identities = 16/32 (50%), Positives = 18/32 (56%)
Query: 830 LKGATVGIVGLGNIGLETAKLLKAFKVSKILY 861
L G TVGI+G GN+G AK L F I Y
Sbjct: 136 LMGKTVGIIGYGNMGKAFAKRLSGFGCKVIAY 167
Score = 36.9 bits (86), Expect = 0.046
Identities = 18/60 (30%), Positives = 33/60 (55%), Gaps = 1/60 (1%)
Query: 91 KVDKEVLDRSGENLKVIATFSVGHDHLHLDEIKSRGIRVGTVGPVSSDTVAEYNIGLAIA 150
+DKE +++ NLK IA G +++ L+ K +GI + + D V E+ +G+ +A
Sbjct: 51 PIDKEFIEK-ATNLKFIARAGAGLENIDLEYAKEKGIELFNAPEGNRDAVGEHALGMLLA 109
>gnl|CDD|236985 PRK11790, PRK11790, D-3-phosphoglycerate dehydrogenase; Provisional.
Length = 409
Score = 107 bits (271), Expect = 1e-24
Identities = 79/230 (34%), Positives = 114/230 (49%), Gaps = 19/230 (8%)
Query: 874 ENLKVITTFSVGYDHLELHEIKARGIRVGSVGHISSDT--VAEYNIGLAIAVSRRFQEGR 931
E L I F +G + ++L RGI V + S+T VAE IG I + R E
Sbjct: 74 EKLVAIGCFCIGTNQVDLDAAAKRGIPVFNAPF--SNTRSVAELVIGEIILLLRGIPEKN 131
Query: 932 KCITSGEWALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRRVK 991
G W K ++G T+GIVG G+IG + + L ++ + Y
Sbjct: 132 AKAHRGGW-NKSAA----GSFEVRGKTLGIVGYGHIGTQLSVLAESLGMRVYFYDI---- 182
Query: 992 EEGTALG-AQLVP-LDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILVNTSRGG 1049
E+ LG A+ V L+ L A+SD + + T T+ +IG ++ +LMKP AIL+N SRG
Sbjct: 183 EDKLPLGNARQVGSLEELLAQSDVVSLHVPETPSTKNMIGAEELALMKPGAILINASRGT 242
Query: 1050 LLDQEALVEFLKDKKIGGAGLDVMIPEPLPADH----PLVQLDNCVLTPH 1095
++D +AL + LK + GA +DV EP PL LDN +LTPH
Sbjct: 243 VVDIDALADALKSGHLAGAAIDVFPVEPKSNGDPFESPLRGLDNVILTPH 292
Score = 78.7 bits (195), Expect = 4e-15
Identities = 41/100 (41%), Positives = 57/100 (57%), Gaps = 6/100 (6%)
Query: 306 ALG-AQLVP-LDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQ 363
LG A+ V L+ L A+SD + + T T+ +IG ++ +LMKP AILIN SRG ++D
Sbjct: 187 PLGNARQVGSLEELLAQSDVVSLHVPETPSTKNMIGAEELALMKPGAILINASRGTVVDI 246
Query: 364 EALVEFLKDKKIGGAGLDVMIPEPLPADH----PLVQLDN 399
+AL + LK + GA +DV EP PL LDN
Sbjct: 247 DALADALKSGHLAGAAIDVFPVEPKSNGDPFESPLRGLDN 286
Score = 34.8 bits (81), Expect = 0.27
Identities = 35/114 (30%), Positives = 50/114 (43%), Gaps = 13/114 (11%)
Query: 602 SKRHVNIETVLGVSFLIKNLKVITTFSVGYDHLELHEIKARGIRVGSVGHISSDT--VAE 659
S+ + E VL + + L I F +G + ++L RGI V + S+T VAE
Sbjct: 61 SRTQLT-EEVLAAA---EKLVAIGCFCIGTNQVDLDAAAKRGIPVFNAPF--SNTRSVAE 114
Query: 660 YNIGLAIAVSRRFQEGRKCITSGEWALKQTHIIGPNIMGLKGATVGIVGLGNIG 713
IG I + R E G W K ++G T+GIVG G+IG
Sbjct: 115 LVIGEIILLLRGIPEKNAKAHRGGW-NKSAA----GSFEVRGKTLGIVGYGHIG 163
>gnl|CDD|235800 PRK06436, PRK06436, glycerate dehydrogenase; Provisional.
Length = 303
Score = 95.3 bits (237), Expect = 3e-21
Identities = 63/251 (25%), Positives = 120/251 (47%), Gaps = 15/251 (5%)
Query: 874 ENLKVITTFSVGYDHLELHEIKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRFQEGRKC 933
+ K+I + S G DH+++ I + + G S +VAE+ L +A ++ E
Sbjct: 48 KKTKMIQSLSAGVDHIDVSGIPENVVLCSNAGAYSI-SVAEHAFALLLAWAKNICENNYN 106
Query: 934 ITSGEWALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRRVKEE 993
+ +G + T + L ++GI+G G IG A L KAF ++ YT V +
Sbjct: 107 MKNGNFKQSPTKL-------LYNKSLGILGYGGIGRRVALLAKAFGMNIYAYTRSYVNDG 159
Query: 994 GTALGAQLVPLDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILVNTSRGGLLDQ 1053
+++ + P D + +SDF+ ++ LT +T +I K SL + ++N +R ++D+
Sbjct: 160 ISSIYME--PEDIM-KKSDFVLISLPLTDETRGMINSKMLSLFRKGLAIINVARADVVDK 216
Query: 1054 EALVEFLKDKKIGGAGLDVMIPEPLPADHPLVQLDNCVLTPHTSSA-TKAVRDEKSSTSA 1112
++ FL++ DV EP+ + DN +L+PH + + + + +
Sbjct: 217 NDMLNFLRNHNDKYYLSDVWWNEPIITET---NPDNVILSPHVAGGMSGEIMQPAVALAF 273
Query: 1113 ENIIRGYKGEP 1123
ENI ++G+P
Sbjct: 274 ENIKNFFEGKP 284
Score = 56.0 bits (135), Expect = 4e-08
Identities = 39/152 (25%), Positives = 63/152 (41%), Gaps = 8/152 (5%)
Query: 592 LDLDQMFRNPSKRHVNIETVLGVSFLIKNLKVITTFSVGYDHLELHEIKARGIRVGSVGH 651
LDLD + P + G K K+I + S G DH+++ I + + G
Sbjct: 21 LDLDDVHWYPDYYDAEAILIKGRYVPGKKTKMIQSLSAGVDHIDVSGIPENVVLCSNAGA 80
Query: 652 ISSDTVAEYNIGLAIAVSRRFQEGRKCITSGEWALKQTHIIGPNIMGLKGATVGIVGLGN 711
S +VAE+ L +A ++ E + +G + T + L ++GI+G G
Sbjct: 81 YSI-SVAEHAFALLLAWAKNICENNYNMKNGNFKQSPTKL-------LYNKSLGILGYGG 132
Query: 712 IGLETAKLLKAFKVSKILYTSRRVKEEGQLFS 743
IG A L KAF ++ YT V +
Sbjct: 133 IGRRVALLAKAFGMNIYAYTRSYVNDGISSIY 164
Score = 45.6 bits (108), Expect = 8e-05
Identities = 16/54 (29%), Positives = 32/54 (59%)
Query: 320 ESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLKDK 373
+SDF+ ++ LT +T +I K SL + +IN +R ++D+ ++ FL++
Sbjct: 173 KSDFVLISLPLTDETRGMINSKMLSLFRKGLAIINVARADVVDKNDMLNFLRNH 226
Score = 32.5 bits (74), Expect = 1.2
Identities = 14/33 (42%), Positives = 19/33 (57%)
Query: 830 LKGATVGIVGLGNIGLETAKLLKAFKVSKILYT 862
L ++GI+G G IG A L KAF ++ YT
Sbjct: 120 LYNKSLGILGYGGIGRRVALLAKAFGMNIYAYT 152
>gnl|CDD|166874 PRK00257, PRK00257, erythronate-4-phosphate dehydrogenase; Validated.
Length = 381
Score = 92.0 bits (229), Expect = 1e-19
Identities = 61/224 (27%), Positives = 97/224 (43%), Gaps = 34/224 (15%)
Query: 877 KVITTFSVGYDHLELHEIKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRFQEGRKCITS 936
+ + T ++G DHL+L GI S ++ V +Y +G + ++ R EG
Sbjct: 60 RFVGTCTIGTDHLDLDYFAEAGITWSSAPGCNARGVVDYVLGSLLTLAER--EG------ 111
Query: 937 GEWALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRRVKEEGTA 996
+ L T G+VG G++G ++L+ ++ R + EG
Sbjct: 112 ---------------VDLAERTYGVVGAGHVGGRLVRVLRGLGWKVLVCDPPRQEAEGDG 156
Query: 997 LGAQLVPLDTLCAESDFIFVTCALTKD----TEQLIGRKQFSLMKPTAILVNTSRGGLLD 1052
V L+ + E D I + LTK+ T L+ + ++P A L+N SRG ++D
Sbjct: 157 ---DFVSLERILEECDVISLHTPLTKEGEHPTRHLLDEAFLASLRPGAWLINASRGAVVD 213
Query: 1053 QEALVEFLKDKKIGGAGLDVMIPEPLPADHPLVQLDNCVL-TPH 1095
+AL E L + A LDV EP D L D C + TPH
Sbjct: 214 NQALREALLSGEDLDAVLDVWEGEPQ-IDLEL--ADLCTIATPH 254
Score = 58.5 bits (142), Expect = 1e-08
Identities = 29/80 (36%), Positives = 41/80 (51%), Gaps = 4/80 (5%)
Query: 312 VPLDTLCAESDFIFVTCALTKD----TEQLIGRKQFSLMKPTAILINTSRGGLLDQEALV 367
V L+ + E D I + LTK+ T L+ + ++P A LIN SRG ++D +AL
Sbjct: 159 VSLERILEECDVISLHTPLTKEGEHPTRHLLDEAFLASLRPGAWLINASRGAVVDNQALR 218
Query: 368 EFLKDKKIGGAGLDVMIPEP 387
E L + A LDV EP
Sbjct: 219 EALLSGEDLDAVLDVWEGEP 238
Score = 43.9 bits (104), Expect = 4e-04
Identities = 35/193 (18%), Positives = 60/193 (31%), Gaps = 68/193 (35%)
Query: 531 EILGEMFDIITYPASEGQIPRDIFIEKLRGCSALLCTSRDRVDKQVLDESGGYRCTEDFF 590
+I P R +R LL S RVD+ +L+ S
Sbjct: 14 AFFAGFGEIRRLPG------RAFDRAAVRDADVLLVRSVTRVDRALLEGS---------- 57
Query: 591 GLDLDQMFRNPSKRHVNIETVLGVSFLIKNLKVITTFSVGYDHLELHEIKARGIRVGSVG 650
++ + T ++G DHL+L GI S
Sbjct: 58 -----------------------------RVRFVGTCTIGTDHLDLDYFAEAGITWSSAP 88
Query: 651 HISSDTVAEYNIGLAIAVSRRFQEGRKCITSGEWALKQTHIIGPNIMGLKGATVGIVGLG 710
++ V +Y +G + ++ R EG + L T G+VG G
Sbjct: 89 GCNARGVVDYVLGSLLTLAER--EG---------------------VDLAERTYGVVGAG 125
Query: 711 NIGLETAKLLKAF 723
++G ++L+
Sbjct: 126 HVGGRLVRVLRGL 138
Score = 35.8 bits (83), Expect = 0.14
Identities = 18/61 (29%), Positives = 30/61 (49%), Gaps = 3/61 (4%)
Query: 68 RMP-RDIFIEKLKGCSALLCNPHQKVDKEVLDRSGENLKVIATFSVGHDHLHLDEIKSRG 126
R+P R ++ LL +VD+ +L+ G ++ + T ++G DHL LD G
Sbjct: 24 RLPGRAFDRAAVRDADVLLVRSVTRVDRALLE--GSRVRFVGTCTIGTDHLDLDYFAEAG 81
Query: 127 I 127
I
Sbjct: 82 I 82
Score = 30.0 bits (68), Expect = 8.0
Identities = 8/25 (32%), Positives = 14/25 (56%)
Query: 830 LKGATVGIVGLGNIGLETAKLLKAF 854
L T G+VG G++G ++L+
Sbjct: 114 LAERTYGVVGAGHVGGRLVRVLRGL 138
>gnl|CDD|183550 PRK12480, PRK12480, D-lactate dehydrogenase; Provisional.
Length = 330
Score = 78.8 bits (194), Expect = 2e-15
Identities = 63/278 (22%), Positives = 117/278 (42%), Gaps = 51/278 (18%)
Query: 870 PKRTE-NLKVITTFSVGYDHLELHEIKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRFQ 928
PK +K I + G+D +L K I + +V S +T+AEY++ +A+ + RRF
Sbjct: 63 PKLESYGIKQIAQRTAGFDMYDLDLAKKHNIVISNVPSYSPETIAEYSVSIALQLVRRFP 122
Query: 929 EGRKCITSGEWALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSR 988
+ + + + ++ + + P +K TV I+G G IG TAK+ F
Sbjct: 123 DIERRVQAHDFTWQAEIMSKP----VKNMTVAIIGTGRIGAATAKIYAGFG--------- 169
Query: 989 RVKEEGTALGAQLVPLDTL------------CAESDFIFVTCALTKDTEQLIGRKQFSLM 1036
T P L ++D I + K++ L + F +
Sbjct: 170 -----ATITAYDAYPNKDLDFLTYKDSVKEAIKDADIISLHVPANKESYHLFDKAMFDHV 224
Query: 1037 KPTAILVNTSRGGLLDQEALVEFLKDKKIGGAGLDVM---------------IPEPLPAD 1081
K AILVN +RG +++ L+ + D + GA +D I + +
Sbjct: 225 KKGAILVNAARGAVINTPDLIAAVNDGTLLGAAIDTYENEAAYFTNDWTNKDIDDKTLLE 284
Query: 1082 HPLVQLDNCVLTPHTS-SATKAVRD--EKSSTSAENII 1116
L++ + ++TPH + + +AV++ E +A ++I
Sbjct: 285 --LIEHERILVTPHIAFFSDEAVQNLVEGGLNAALSVI 320
Score = 51.5 bits (123), Expect = 1e-06
Identities = 30/103 (29%), Positives = 54/103 (52%), Gaps = 4/103 (3%)
Query: 621 LKVITTFSVGYDHLELHEIKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRFQEGRKCIT 680
+K I + G+D +L K I + +V S +T+AEY++ +A+ + RRF + + +
Sbjct: 70 IKQIAQRTAGFDMYDLDLAKKHNIVISNVPSYSPETIAEYSVSIALQLVRRFPDIERRVQ 129
Query: 681 SGEWALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKAF 723
+ ++ + + P +K TV I+G G IG TAK+ F
Sbjct: 130 AHDFTWQAEIMSKP----VKNMTVAIIGTGRIGAATAKIYAGF 168
Score = 43.7 bits (103), Expect = 4e-04
Identities = 17/63 (26%), Positives = 33/63 (52%)
Query: 319 AESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLKDKKIGGA 378
++D I + K++ L + F +K AIL+N +RG +++ L+ + D + GA
Sbjct: 197 KDADIISLHVPANKESYHLFDKAMFDHVKKGAILVNAARGAVINTPDLIAAVNDGTLLGA 256
Query: 379 GLD 381
+D
Sbjct: 257 AID 259
Score = 40.7 bits (95), Expect = 0.003
Identities = 28/102 (27%), Positives = 48/102 (47%), Gaps = 9/102 (8%)
Query: 75 IEKLKGCSALLCNPHQKVDKEVLDR-SGENLKVIATFSVGHDHLHLDEIKSRGIRVGTVG 133
+++LK + K++ +V + +K IA + G D LD K I + V
Sbjct: 40 VDQLKDYDGVTTMQFGKLENDVYPKLESYGIKQIAQRTAGFDMYDLDLAKKHNIVISNVP 99
Query: 134 PVSSDTVAEYNIGLAIAVSRRFQ------QRHN--WIARLSS 167
S +T+AEY++ +A+ + RRF Q H+ W A + S
Sbjct: 100 SYSPETIAEYSVSIALQLVRRFPDIERRVQAHDFTWQAEIMS 141
>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 = 76.9 bits (189), Expect = 6e-15
Identities = 48/219 (21%), Positives = 86/219 (39%), Gaps = 30/219 (13%)
Query: 875 NLKVITTFSVGYDHLELHE-IKARGIRV----GSVGHISSDT---VAEYNIGLAIAVSRR 926
+++ T+++G DH +L E + G+ G + + E ++
Sbjct: 87 GDRLLFTYTIGADHRDLTEALARAGLTAIAVEGVELPLLTSNSIGAGELSVQFIARFLEV 146
Query: 927 FQEGRKCITSGEWALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILYT 986
Q GR + G TV +VG G +G E A++L+ +++L T
Sbjct: 147 QQPGRL----------------GGAPDVAGKTVVVVGAGVVGKEAAQMLRGLG-AQVLIT 189
Query: 987 SRRV---KEEGTALGAQLVPLDTLCAESDFIFVTCALTKDTE-QLIGRKQFSLMKPTAIL 1042
V ++ G + L+ AE+D I T L L+ + MKP +++
Sbjct: 190 DINVEALEQLEELGGKNVEELEEALAEADVIVTTTLLPGKRAGILVPEELVEQMKPGSVI 249
Query: 1043 VNTSRGGLLDQEALVEF-LKDKKIGGAGLDVMIPEPLPA 1080
VN + G + +AL L++ DV +P P A
Sbjct: 250 VNVAVGAVGCVQALHTQLLEEGHGVVHYGDVNMPGPGCA 288
Score = 44.9 bits (106), Expect = 1e-04
Identities = 22/89 (24%), Positives = 37/89 (41%), Gaps = 2/89 (2%)
Query: 304 GTALGAQLVPLDTLCAESDFIFVTCALTKDTE-QLIGRKQFSLMKPTAILINTSRGGLLD 362
G + L+ AE+D I T L L+ + MKP ++++N + G +
Sbjct: 200 EELGGKNVEELEEALAEADVIVTTTLLPGKRAGILVPEELVEQMKPGSVIVNVAVGAVGC 259
Query: 363 QEALVEF-LKDKKIGGAGLDVMIPEPLPA 390
+AL L++ DV +P P A
Sbjct: 260 VQALHTQLLEEGHGVVHYGDVNMPGPGCA 288
Score = 42.2 bits (99), Expect = 0.001
Identities = 31/195 (15%), Positives = 66/195 (33%), Gaps = 39/195 (20%)
Query: 620 NLKVITTFSVGYDHLELHE-IKARGIRV----GSVGHISSDT---VAEYNIGLAIAVSRR 671
+++ T+++G DH +L E + G+ G + + E ++
Sbjct: 87 GDRLLFTYTIGADHRDLTEALARAGLTAIAVEGVELPLLTSNSIGAGELSVQFIARFLEV 146
Query: 672 FQEGRKCITSGEWALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILYT 731
Q GR + G TV +VG G +G E A++L+ +++L T
Sbjct: 147 QQPGRL----------------GGAPDVAGKTVVVVGAGVVGKEAAQMLRGLG-AQVLIT 189
Query: 732 SRRVKEEGQLFSLVYDFCRYSIGGVTIKRLVKKTFILSFGGLVVTVLHVHIGDLPAESFE 791
V+ QL L ++ + + ++ V + A
Sbjct: 190 DINVEALEQLEELGGKNV------EELEEALAEADVI--------VTTTLLPGKRAGILV 235
Query: 792 DQVQTDGLKTLTELC 806
+ + +K + +
Sbjct: 236 PEELVEQMKPGSVIV 250
Score = 33.7 bits (77), Expect = 0.54
Identities = 13/37 (35%), Positives = 22/37 (59%), Gaps = 1/37 (2%)
Query: 829 GLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRN 865
+ G TV +VG G +G E A++L+ +++L T N
Sbjct: 157 DVAGKTVVVVGAGVVGKEAAQMLRGLG-AQVLITDIN 192
>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 = 68.9 bits (169), Expect = 2e-12
Identities = 51/170 (30%), Positives = 74/170 (43%), Gaps = 23/170 (13%)
Query: 954 LKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRRVKEEGTALGAQLVPLDTLCAESDF 1013
L G VGI+GLG G A L F + + Y SR K + A G + +PL+ L D
Sbjct: 136 LTGLKVGIIGLGTTGQMIADALSFFG-ADVYYYSRTRKPDAEAKGIRYLPLNELLKTVDV 194
Query: 1014 IFVTCALTKDTEQLIGRKQFSLMKPTAILVNTSRGGLLDQEALVEFLKDKK--------I 1065
I TC L K+ L+G ++F L+ IL NTS G + EAL ++LK
Sbjct: 195 IC-TC-LPKNV-ILLGEEEFELLGDGKILFNTSLGPSFEVEALKKWLKASGYNIFDCDTA 251
Query: 1066 GGAGLDVMIPEPLPADHPLVQLDNCVLTPHTSSATKAVRDEKSSTSAENI 1115
G G D L++ N + T ++ T+ + S N+
Sbjct: 252 GALG-----------DEELLRYPNVICTNKSAGWTRQAFERLSQKVLANL 290
Score = 41.5 bits (98), Expect = 0.002
Identities = 24/62 (38%), Positives = 33/62 (53%), Gaps = 3/62 (4%)
Query: 313 PLDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLKD 372
PL+ L D I TC L K+ L+G ++F L+ IL NTS G + EAL ++LK
Sbjct: 184 PLNELLKTVDVIC-TC-LPKNV-ILLGEEEFELLGDGKILFNTSLGPSFEVEALKKWLKA 240
Query: 373 KK 374
Sbjct: 241 SG 242
Score = 32.7 bits (75), Expect = 0.96
Identities = 16/40 (40%), Positives = 20/40 (50%), Gaps = 1/40 (2%)
Query: 699 LKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRRVKEE 738
L G VGI+GLG G A L F + + Y SR K +
Sbjct: 136 LTGLKVGIIGLGTTGQMIADALSFFG-ADVYYYSRTRKPD 174
Score = 31.1 bits (71), Expect = 3.4
Identities = 15/35 (42%), Positives = 18/35 (51%), Gaps = 1/35 (2%)
Query: 830 LKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSR 864
L G VGI+GLG G A L F + + Y SR
Sbjct: 136 LTGLKVGIIGLGTTGQMIADALSFFG-ADVYYYSR 169
>gnl|CDD|181499 PRK08605, PRK08605, D-lactate dehydrogenase; Validated.
Length = 332
Score = 67.1 bits (164), Expect = 1e-11
Identities = 57/246 (23%), Positives = 101/246 (41%), Gaps = 29/246 (11%)
Query: 876 LKVITTFSVGYDHLELHEIKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRFQEGRKCIT 935
+K I S G+D +L + + +V S +++AE+ + AI + R F + + +
Sbjct: 70 IKQIAQRSAGFDTYDLELATKYNLIISNVPSYSPESIAEFTVTQAINLVRHFNQIQTKVR 129
Query: 936 SGEWALKQTHIIGPNIMG--LKGATVGIVGLGNIGLETAKLLKAFKVSKIL----YTSRR 989
+ P I+ +K V ++G G IGL AK+ S ++ + + +
Sbjct: 130 ------EHDFRWEPPILSRSIKDLKVAVIGTGRIGLAVAKIFAKGYGSDVVAYDPFPNAK 183
Query: 990 VKEEGTALGAQLVPLDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILVNTSRGG 1049
++ +D + + TK L F K A+ VN +RG
Sbjct: 184 AATYVDYKDT----IEEAVEGADIVTLHMPATKYNHYLFNADLFKHFKKGAVFVNCARGS 239
Query: 1050 LLDQEALVEFLKDKKIGGAGLDVMIPEP--LPADH-----------PLVQLDNCVLTPHT 1096
L+D +AL++ L + I GA LD E P+D L+ ++ +LTPH
Sbjct: 240 LVDTKALLDALDNGLIKGAALDTYEFERPLFPSDQRGQTINDPLLESLINREDVILTPHI 299
Query: 1097 SSATKA 1102
+ T A
Sbjct: 300 AFYTDA 305
Score = 44.0 bits (104), Expect = 3e-04
Identities = 20/62 (32%), Positives = 31/62 (50%)
Query: 320 ESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLKDKKIGGAG 379
+D + + TK L F K A+ +N +RG L+D +AL++ L + I GA
Sbjct: 200 GADIVTLHMPATKYNHYLFNADLFKHFKKGAVFVNCARGSLVDTKALLDALDNGLIKGAA 259
Query: 380 LD 381
LD
Sbjct: 260 LD 261
Score = 39.7 bits (93), Expect = 0.007
Identities = 25/101 (24%), Positives = 46/101 (45%), Gaps = 8/101 (7%)
Query: 621 LKVITTFSVGYDHLELHEIKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRFQEGRKCIT 680
+K I S G+D +L + + +V S +++AE+ + AI + R F + + +
Sbjct: 70 IKQIAQRSAGFDTYDLELATKYNLIISNVPSYSPESIAEFTVTQAINLVRHFNQIQTKVR 129
Query: 681 SGEWALKQTHIIGPNIMG--LKGATVGIVGLGNIGLETAKL 719
+ P I+ +K V ++G G IGL AK+
Sbjct: 130 ------EHDFRWEPPILSRSIKDLKVAVIGTGRIGLAVAKI 164
Score = 29.7 bits (67), Expect = 8.1
Identities = 16/54 (29%), Positives = 26/54 (48%)
Query: 104 LKVIATFSVGHDHLHLDEIKSRGIRVGTVGPVSSDTVAEYNIGLAIAVSRRFQQ 157
+K IA S G D L+ + + V S +++AE+ + AI + R F Q
Sbjct: 70 IKQIAQRSAGFDTYDLELATKYNLIISNVPSYSPESIAEFTVTQAINLVRHFNQ 123
>gnl|CDD|185335 PRK15438, PRK15438, erythronate-4-phosphate dehydrogenase PdxB;
Provisional.
Length = 378
Score = 59.9 bits (145), Expect = 3e-09
Identities = 62/238 (26%), Positives = 96/238 (40%), Gaps = 46/238 (19%)
Query: 874 ENLKVITTFSVGYDHLELHEIKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRFQEGRKC 933
+ +K + T + G DH++ +K GI + ++ V EY + ++ R
Sbjct: 57 KPIKFVGTATAGTDHVDEAWLKQAGIGFSAAPGCNAIAVVEYVFSSLLMLAER------- 109
Query: 934 ITSGEWALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRRVK-- 991
+ L TVGIVG+GN+G L+A + +L R
Sbjct: 110 ----------------DGFSLHDRTVGIVGVGNVGRRLQARLEALGIKTLLCDPPRADRG 153
Query: 992 EEGTALGAQLVPLDTLCAESDFIFVTCALTKD---------TEQLIGRKQFSLMKPTAIL 1042
+EG LD L E+D + L KD E+LI +KP AIL
Sbjct: 154 DEG-----DFRSLDELVQEADILTFHTPLFKDGPYKTLHLADEKLIRS-----LKPGAIL 203
Query: 1043 VNTSRGGLLDQEALVEFLKDKKIGGAGLDVMIPEPLPADHPLVQLDNCVLTPHTSSAT 1100
+N RG ++D AL+ L + + LDV EP L ++D + TPH + T
Sbjct: 204 INACRGAVVDNTALLTCLNEGQKLSVVLDVWEGEPELNVELLKKVD--IGTPHIAGYT 259
Score = 42.6 bits (100), Expect = 0.001
Identities = 29/83 (34%), Positives = 38/83 (45%), Gaps = 14/83 (16%)
Query: 314 LDTLCAESDFIFVTCALTKD---------TEQLIGRKQFSLMKPTAILINTSRGGLLDQE 364
LD L E+D + L KD E+LI +KP AILIN RG ++D
Sbjct: 161 LDELVQEADILTFHTPLFKDGPYKTLHLADEKLIRS-----LKPGAILINACRGAVVDNT 215
Query: 365 ALVEFLKDKKIGGAGLDVMIPEP 387
AL+ L + + LDV EP
Sbjct: 216 ALLTCLNEGQKLSVVLDVWEGEP 238
Score = 33.7 bits (77), Expect = 0.47
Identities = 31/128 (24%), Positives = 50/128 (39%), Gaps = 25/128 (19%)
Query: 619 KNLKVITTFSVGYDHLELHEIKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRFQEGRKC 678
K +K + T + G DH++ +K GI + ++ V EY + ++ R
Sbjct: 57 KPIKFVGTATAGTDHVDEAWLKQAGIGFSAAPGCNAIAVVEYVFSSLLMLAER------- 109
Query: 679 ITSGEWALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRRVK-- 736
+ L TVGIVG+GN+G L+A + +L R
Sbjct: 110 ----------------DGFSLHDRTVGIVGVGNVGRRLQARLEALGIKTLLCDPPRADRG 153
Query: 737 EEGQLFSL 744
+EG SL
Sbjct: 154 DEGDFRSL 161
Score = 31.4 bits (71), Expect = 3.0
Identities = 20/73 (27%), Positives = 35/73 (47%), Gaps = 2/73 (2%)
Query: 71 RDIFIEKLKGCSALLCNPHQKVDKEVLDRSGENLKVIATFSVGHDHLHLDEIKSRGIRVG 130
R I + +L AL+ KV++ +L +G+ +K + T + G DH+ +K GI
Sbjct: 28 RPIPVAQLADADALMVRSVTKVNESLL--AGKPIKFVGTATAGTDHVDEAWLKQAGIGFS 85
Query: 131 TVGPVSSDTVAEY 143
++ V EY
Sbjct: 86 AAPGCNAIAVVEY 98
Score = 31.0 bits (70), Expect = 3.8
Identities = 13/31 (41%), Positives = 18/31 (58%)
Query: 830 LKGATVGIVGLGNIGLETAKLLKAFKVSKIL 860
L TVGIVG+GN+G L+A + +L
Sbjct: 114 LHDRTVGIVGVGNVGRRLQARLEALGIKTLL 144
>gnl|CDD|185366 PRK15469, ghrA, bifunctional glyoxylate/hydroxypyruvate reductase A;
Provisional.
Length = 312
Score = 54.8 bits (132), Expect = 9e-08
Identities = 44/166 (26%), Positives = 76/166 (45%), Gaps = 2/166 (1%)
Query: 958 TVGIVGLGNIGLETAKLLKAFKVSKILYTSRRVKEEGTALGAQLVPLDTLCAESDFIFVT 1017
T+GI+G G +G + A+ L+ + ++ R G A L +++ +
Sbjct: 138 TIGILGAGVLGSKVAQSLQTWGFPLRCWSRSRKSWPGVQSFAGREELSAFLSQTRVLINL 197
Query: 1018 CALTKDTEQLIGRKQFSLMKPTAILVNTSRGGLLDQEALVEFLKDKKIGGAGLDVMIPEP 1077
T +T +I ++ + A L+N +RG + ++ L+ L K+ GA LDV EP
Sbjct: 198 LPNTPETVGIINQQLLEQLPDGAYLLNLARGVHVVEDDLLAALDSGKVKGAMLDVFSREP 257
Query: 1078 LPADHPLVQLDNCVLTPHTSSATKAVRDEKSSTSAENIIRGYKGEP 1123
LP + PL Q +TPH ++ T+ E + I + KGE
Sbjct: 258 LPPESPLWQHPRVAITPHVAAVTRPA--EAVEYISRTIAQLEKGER 301
Score = 42.1 bits (99), Expect = 0.001
Identities = 22/64 (34%), Positives = 35/64 (54%)
Query: 331 TKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALVEFLKDKKIGGAGLDVMIPEPLPA 390
T +T +I ++ + A L+N +RG + ++ L+ L K+ GA LDV EPLP
Sbjct: 201 TPETVGIINQQLLEQLPDGAYLLNLARGVHVVEDDLLAALDSGKVKGAMLDVFSREPLPP 260
Query: 391 DHPL 394
+ PL
Sbjct: 261 ESPL 264
>gnl|CDD|214966 smart01002, AlaDh_PNT_C, Alanine dehydrogenase/PNT, C-terminal
domain. Alanine dehydrogenase catalyzes the
NAD-dependent reversible reductive amination of pyruvate
into alanine.
Length = 149
Score = 39.4 bits (93), Expect = 0.002
Identities = 23/102 (22%), Positives = 41/102 (40%), Gaps = 12/102 (11%)
Query: 953 GLKGATVGIVGLGNIGLETAKLLKAFKVS-KILYTSRRVKEEGTA-LGAQLV-------P 1003
G+ A V ++G G +GL A K +L + + LGA+
Sbjct: 17 GVPPAKVVVIGAGVVGLGAAATAKGLGAEVTVLDVRPARLRQLESLLGARFTTLYSQAEL 76
Query: 1004 LDTLCAESDFIFVTCAL--TKDTEQLIGRKQFSLMKPTAILV 1043
L+ E+D + + L +L+ R+ MKP +++V
Sbjct: 77 LEEAVKEAD-LVIGAVLIPGAKAPKLVTREMVKSMKPGSVIV 117
>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 = 37.6 bits (88), Expect = 0.027
Identities = 25/70 (35%), Positives = 34/70 (48%), Gaps = 6/70 (8%)
Query: 953 GLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSR---RVKEEGTALGAQLVPLDTLCA 1009
LKG V ++G G +G AK L A V++I +R R +E LG VPLD L
Sbjct: 175 NLKGKKVLVIGAGEMGELAAKHLAAKGVAEITIANRTYERAEELAKELGGNAVPLDELLE 234
Query: 1010 ---ESDFIFV 1016
E+D +
Sbjct: 235 LLNEADVVIS 244
Score = 34.5 bits (80), Expect = 0.24
Identities = 18/48 (37%), Positives = 25/48 (52%), Gaps = 4/48 (8%)
Query: 829 GLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRNKVKTPKRTENL 876
LKG V ++G G +G AK L A V++I +R T +R E L
Sbjct: 175 NLKGKKVLVIGAGEMGELAAKHLAAKGVAEITIANR----TYERAEEL 218
Score = 33.0 bits (76), Expect = 0.72
Identities = 14/36 (38%), Positives = 20/36 (55%)
Query: 698 GLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSR 733
LKG V ++G G +G AK L A V++I +R
Sbjct: 175 NLKGKKVLVIGAGEMGELAAKHLAAKGVAEITIANR 210
>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 = 37.6 bits (88), Expect = 0.029
Identities = 11/42 (26%), Positives = 18/42 (42%)
Query: 827 IMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRNKVK 868
G TV ++G G IGL + LK +++ + K
Sbjct: 155 AGITLGDTVVVIGAGTIGLLAIQWLKILGAKRVIAVDIDDEK 196
Score = 36.1 bits (84), Expect = 0.10
Identities = 13/52 (25%), Positives = 21/52 (40%), Gaps = 4/52 (7%)
Query: 951 IMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILYT---SRRVKEEGTALGA 999
G TV ++G G IGL + LK +++ ++ LGA
Sbjct: 155 AGITLGDTVVVIGAGTIGLLAIQWLKILGAKRVIAVDIDDEKL-AVARELGA 205
Score = 35.7 bits (83), Expect = 0.14
Identities = 10/34 (29%), Positives = 16/34 (47%)
Query: 696 IMGLKGATVGIVGLGNIGLETAKLLKAFKVSKIL 729
G TV ++G G IGL + LK +++
Sbjct: 155 AGITLGDTVVVIGAGTIGLLAIQWLKILGAKRVI 188
>gnl|CDD|240621 cd01620, Ala_dh_like, Alanine dehydrogenase and related
dehydrogenases. Alanine dehydrogenase/Transhydrogenase,
such as the hexameric L-alanine dehydrogenase of
Phormidium lapideum, contain 2 Rossmann fold-like domains
linked by an alpha helical region. Related proteins
include Saccharopine Dehydrogenase (SDH), bifunctional
lysine ketoglutarate reductase /saccharopine
dehydrogenase enzyme, N(5)-(carboxyethyl)ornithine
synthase, and Rubrum transdehydrogenase. Alanine
dehydrogenase (L-AlaDH) catalyzes the NAD-dependent
conversion of pyrucate to L-alanine via reductive
amination. Transhydrogenases found in bacterial and inner
mitochondrial membranes link NAD(P)(H)-dependent redox
reactions to proton translocation. The energy of the
proton electrochemical gradient (delta-p), generated by
the respiratory electron transport chain, is consumed by
transhydrogenase in NAD(P)+ reduction. Transhydrogenase
is likely involved in the regulation of the citric acid
cycle. Rubrum transhydrogenase has 3 components, dI, dII,
and dIII. dII spans the membrane while dI and dIII
protrude on the cytoplasmic/matirx side. DI contains 2
domains with Rossmann folds, linked by a long alpha
helix, and contains a NAD binding site. Two dI
polypeptides (represented in this sub-family)
spontaneously form a heterotrimer with one dIII in the
absence of dII. In the heterotrimer, both dI chains may
bind NAD, but only one is well-ordered. dIII also binds a
well-ordered NADP, but in a different orientation than
classical Rossmann domains.
Length = 317
Score = 37.4 bits (87), Expect = 0.035
Identities = 30/118 (25%), Positives = 48/118 (40%), Gaps = 11/118 (9%)
Query: 938 EWALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKAF----KVSKILYTSRR-VKE 992
E A Q +G G+ A V I+G G +GL AK+ K V I + V+
Sbjct: 145 ELARIQGGRMG-GAGGVPPAKVLIIGAGVVGLGAAKIAKKLGANVLVYDIKEEKLKGVET 203
Query: 993 EGTA--LGAQLVPLDTLCAESDFIFVTCAL--TKDTEQLIGRKQFSLMKPTAILVNTS 1046
G + +Q L+ ++D I + L LI + MK A++V+ +
Sbjct: 204 LGGSRLRYSQKEELEKELKQTD-ILINAILVDGPRAPILIMEELVGPMKRGAVIVDLA 260
Score = 35.1 bits (81), Expect = 0.20
Identities = 20/69 (28%), Positives = 28/69 (40%), Gaps = 7/69 (10%)
Query: 792 DQVQTDGLKTLTEL----CYHGTING--EWALKQTHIIGPNIMGLKGATVGIVGLGNIGL 845
+ ++ D L Y G G E A Q +G G+ A V I+G G +GL
Sbjct: 117 EDLENDFRPRLAPNSNIAGYAGVQLGAYELARIQGGRMG-GAGGVPPAKVLIIGAGVVGL 175
Query: 846 ETAKLLKAF 854
AK+ K
Sbjct: 176 GAAKIAKKL 184
Score = 34.7 bits (80), Expect = 0.25
Identities = 26/86 (30%), Positives = 39/86 (45%), Gaps = 3/86 (3%)
Query: 683 EWALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRRVKEEGQLF 742
E A Q +G G+ A V I+G G +GL AK+ K + +L + ++ +
Sbjct: 145 ELARIQGGRMG-GAGGVPPAKVLIIGAGVVGLGAAKIAKKLG-ANVLVYDIKEEKLKGVE 202
Query: 743 SLVYDFCRYSIGGVTIKRLVKKTFIL 768
+L RYS K L K+T IL
Sbjct: 203 TLGGSRLRYSQKEELEKEL-KQTDIL 227
>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 = 35.3 bits (82), Expect = 0.056
Identities = 32/133 (24%), Positives = 53/133 (39%), Gaps = 29/133 (21%)
Query: 958 TVGIVGLGNIGLETAKLL--KAFKVS---------KILYTSRRVKEE--GTALGAQLVP- 1003
+ ++G G+ G AK+L +V + + T+R + G L L
Sbjct: 1 KIAVLGAGSWGTALAKVLARNGHEVRLWGRDEELIEEINTTRENVKYLPGIKLPDNLRAT 60
Query: 1004 --LDTLCAESDFIFV---TCALTKDTEQLIGRKQFSLMKPTAILVNTSRG-----GLLDQ 1053
L+ +D I + + AL + +QL G L+ P AILV+ ++G L
Sbjct: 61 TDLEEAIKGADIIVLAVPSQALREVLKQLKG-----LLSPGAILVSLTKGIEPGTLKLLS 115
Query: 1054 EALVEFLKDKKIG 1066
E + E L I
Sbjct: 116 EIIEEELPINPIA 128
>gnl|CDD|240258 PTZ00075, PTZ00075, Adenosylhomocysteinase; Provisional.
Length = 476
Score = 36.9 bits (86), Expect = 0.058
Identities = 35/117 (29%), Positives = 52/117 (44%), Gaps = 24/117 (20%)
Query: 954 LKGATVGIVGLGNIGLETAKLLKAF----KVSKILYTSRRVKEEGTAL-----GAQLVPL 1004
+ G TV + G G++G A+ L+ F V++I + AL G Q+V L
Sbjct: 252 IAGKTVVVCGYGDVGKGCAQALRGFGARVVVTEI--------DPICALQAAMEGYQVVTL 303
Query: 1005 DTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILVNTSRGGLLDQEALVEFLK 1061
+ + +D IFVT KD +I + MK AI+ N G D E V L+
Sbjct: 304 EDVVETAD-IFVTATGNKD---IITLEHMRRMKNNAIVGNI---GHFDNEIQVAELE 353
>gnl|CDD|223450 COG0373, HemA, Glutamyl-tRNA reductase [Coenzyme metabolism].
Length = 414
Score = 35.7 bits (83), Expect = 0.13
Identities = 24/70 (34%), Positives = 33/70 (47%), Gaps = 6/70 (8%)
Query: 953 GLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSR---RVKEEGTALGAQLVPLDTL-- 1007
LK V ++G G +G AK L V KI +R R +E LGA+ V L+ L
Sbjct: 175 SLKDKKVLVIGAGEMGELVAKHLAEKGVKKITIANRTLERAEELAKKLGAEAVALEELLE 234
Query: 1008 -CAESDFIFV 1016
AE+D +
Sbjct: 235 ALAEADVVIS 244
Score = 33.0 bits (76), Expect = 0.92
Identities = 15/62 (24%), Positives = 22/62 (35%), Gaps = 6/62 (9%)
Query: 829 GLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRNKVKTPKRTENLKVITTFSVGYDH 888
LK V ++G G +G AK L V KI +R + ++
Sbjct: 175 SLKDKKVLVIGAGEMGELVAKHLAEKGVKKITIANRTLERAE------ELAKKLGAEAVA 228
Query: 889 LE 890
LE
Sbjct: 229 LE 230
>gnl|CDD|223411 COG0334, GdhA, Glutamate dehydrogenase/leucine dehydrogenase [Amino
acid transport and metabolism].
Length = 411
Score = 35.7 bits (83), Expect = 0.14
Identities = 21/90 (23%), Positives = 31/90 (34%), Gaps = 22/90 (24%)
Query: 952 MGLKGATVGIVGLGNIGLETAKLL--------------------KAFKVSKILYTSRRVK 991
L+GA V + G GN+G A+ L V +L R
Sbjct: 203 DDLEGARVAVQGFGNVGQYAAEKLHELGAKVVAVSDSKGGIYDEDGLDVEALLELKERRG 262
Query: 992 EEGTALGAQLVPLD-TLCAESDFIFVTCAL 1020
GA+ + + L + D I + CAL
Sbjct: 263 SVAEYAGAEYITNEELLEVDCD-ILIPCAL 291
Score = 30.7 bits (70), Expect = 4.5
Identities = 10/24 (41%), Positives = 14/24 (58%)
Query: 697 MGLKGATVGIVGLGNIGLETAKLL 720
L+GA V + G GN+G A+ L
Sbjct: 203 DDLEGARVAVQGFGNVGQYAAEKL 226
Score = 30.7 bits (70), Expect = 4.5
Identities = 10/24 (41%), Positives = 14/24 (58%)
Query: 828 MGLKGATVGIVGLGNIGLETAKLL 851
L+GA V + G GN+G A+ L
Sbjct: 203 DDLEGARVAVQGFGNVGQYAAEKL 226
>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 = 35.2 bits (82), Expect = 0.14
Identities = 18/46 (39%), Positives = 22/46 (47%), Gaps = 6/46 (13%)
Query: 675 GRKCITSGEWALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLL 720
GR + ALK+ I GL GA V I G GN+G A+ L
Sbjct: 11 GRGVAYATREALKKLGI------GLAGARVAIQGFGNVGSHAARFL 50
Score = 35.2 bits (82), Expect = 0.14
Identities = 18/46 (39%), Positives = 22/46 (47%), Gaps = 6/46 (13%)
Query: 930 GRKCITSGEWALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLL 975
GR + ALK+ I GL GA V I G GN+G A+ L
Sbjct: 11 GRGVAYATREALKKLGI------GLAGARVAIQGFGNVGSHAARFL 50
Score = 34.4 bits (80), Expect = 0.25
Identities = 16/38 (42%), Positives = 19/38 (50%), Gaps = 6/38 (15%)
Query: 814 EWALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLL 851
ALK+ I GL GA V I G GN+G A+ L
Sbjct: 19 REALKKLGI------GLAGARVAIQGFGNVGSHAARFL 50
>gnl|CDD|176195 cd08233, butanediol_DH_like, (2R,3R)-2,3-butanediol dehydrogenase.
(2R,3R)-2,3-butanediol dehydrogenase, a zinc-dependent
medium chain alcohol dehydrogenase, catalyzes the
NAD(+)-dependent oxidation of (2R,3R)-2,3-butanediol and
meso-butanediol to acetoin. BDH functions as a homodimer.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and aldehydes,
or ketones. The medium chain alcohol dehydrogenase
family (MDR) have 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. 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.
Length = 351
Score = 35.2 bits (82), Expect = 0.19
Identities = 22/63 (34%), Positives = 27/63 (42%), Gaps = 8/63 (12%)
Query: 954 LKGATVGIVGLGNIGLETAKLLKAFKVSKI----LYTSRRVKEEGTALGAQLV--PLDTL 1007
G T ++G G IGL T LKA SKI +RR E LGA +V P +
Sbjct: 171 KPGDTALVLGAGPIGLLTILALKAAGASKIIVSEPSEARRELAE--ELGATIVLDPTEVD 228
Query: 1008 CAE 1010
Sbjct: 229 VVA 231
Score = 34.8 bits (81), Expect = 0.24
Identities = 19/53 (35%), Positives = 24/53 (45%), Gaps = 4/53 (7%)
Query: 699 LKGATVGIVGLGNIGLETAKLLKAFKVSKI----LYTSRRVKEEGQLFSLVYD 747
G T ++G G IGL T LKA SKI +RR E ++V D
Sbjct: 171 KPGDTALVLGAGPIGLLTILALKAAGASKIIVSEPSEARRELAEELGATIVLD 223
Score = 32.9 bits (76), Expect = 0.82
Identities = 14/30 (46%), Positives = 16/30 (53%)
Query: 830 LKGATVGIVGLGNIGLETAKLLKAFKVSKI 859
G T ++G G IGL T LKA SKI
Sbjct: 171 KPGDTALVLGAGPIGLLTILALKAAGASKI 200
>gnl|CDD|187584 cd05323, ADH_SDR_c_like, insect type alcohol dehydrogenase
(ADH)-like, classical (c) SDRs. This subgroup contains
insect type ADH, and 15-hydroxyprostaglandin
dehydrogenase (15-PGDH) type I; these proteins are
classical SDRs. ADH catalyzes the NAD+-dependent
oxidation of alcohols to aldehydes/ketones. This subgroup
is distinct from the zinc-dependent alcohol
dehydrogenases of the medium chain
dehydrogenase/reductase family, and evolved in fruit
flies to allow the digestion of fermenting fruit. 15-PGDH
catalyzes the NAD-dependent interconversion of
(5Z,13E)-(15S)-11alpha,15-dihydroxy-9-oxoprost-13-enoate
and (5Z,13E)-11alpha-hydroxy-9,15-dioxoprost-13-enoate,
and has a typical SDR glycine-rich NAD-binding motif,
which is not fully present in ADH. 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 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 (15-PGDH) numbering). 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) 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. Extended SDRs have additional
elements in the C-terminal region, and typically have a
TGXXGXXG cofactor binding motif. 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. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity, dehalogenation,
Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction.
Length = 244
Score = 34.6 bits (80), Expect = 0.23
Identities = 22/84 (26%), Positives = 29/84 (34%), Gaps = 10/84 (11%)
Query: 963 GLGNIGLETAKLLKAFKVSKILYTSRRV-KEEGTALGAQLVPLDTLCAESDFIFVTCALT 1021
G IGL TAKLL K +K+ R L A + FV C +T
Sbjct: 8 GASGIGLATAKLL-LKKGAKVAILDRNENPGAAAELQAIN-------PKVKATFVQCDVT 59
Query: 1022 KDTEQLIG-RKQFSLMKPTAILVN 1044
+ +K IL+N
Sbjct: 60 SWEQLAAAFKKAIEKFGRVDILIN 83
>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 = 33.2 bits (77), Expect = 0.32
Identities = 28/118 (23%), Positives = 49/118 (41%), Gaps = 14/118 (11%)
Query: 957 ATVGIVGLGNIGLETAK-LLKA-FKVSKILY--TSRRVKEEGTALGAQLVPLDT---LCA 1009
A +G +GLG +G A LLKA + V+ +Y T +V+E + V + A
Sbjct: 1 AKIGFIGLGVMGSPMALNLLKAGYTVT--VYNRTPEKVEE---LVAEGAVGAASPAEFVA 55
Query: 1010 ESDFIFVTCALTKDTEQLIGRKQ--FSLMKPTAILVNTSRGGLLDQEALVEFLKDKKI 1065
+D + + +I + +KP I+++ S D + L +K I
Sbjct: 56 SADVVITMVPAGAAVDAVILGEDGLLPGLKPGDIIIDGSTSDPDDTRRRAKELAEKGI 113
>gnl|CDD|133450 cd05211, NAD_bind_Glu_Leu_Phe_Val, NAD(P) binding domain of
glutamate dehydrogenase, 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 NAD(P)+. This
subfamily includes glutamate, leucine, phenylalanine,
and valine DHs. Glutamate DH is a multi-domain 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. As in other NAD+-dependent
DHs, monomers in this family have 2 domains separated by
a deep cleft. Here the c-terminal domain contains a
modified NAD-binding Rossmann fold with 7 rather than
the usual 6 beta strands and one strand anti-parrallel
to the others. 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 = 217
Score = 33.3 bits (76), Expect = 0.44
Identities = 13/51 (25%), Positives = 21/51 (41%)
Query: 829 GLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRNKVKTPKRTENLKVI 879
L+G TV + GLGN+G AK L + + + ++I
Sbjct: 20 SLEGLTVAVQGLGNVGWGLAKKLAEEGGKVLAVSDPDGYIYDPGITTEELI 70
Score = 32.1 bits (73), Expect = 1.3
Identities = 25/87 (28%), Positives = 31/87 (35%), Gaps = 19/87 (21%)
Query: 953 GLKGATVGIVGLGNIGLETAKLL-----KAFKVS---KILYTSRRVKEEGTAL-----GA 999
L+G TV + GLGN+G AK L K VS +Y EE G+
Sbjct: 20 SLEGLTVAVQGLGNVGWGLAKKLAEEGGKVLAVSDPDGYIYDPGITTEELINYAVALGGS 79
Query: 1000 QLVPLDTLCAESDF------IFVTCAL 1020
V + IF CAL
Sbjct: 80 ARVKVQDYFPGEAILGLDVDIFAPCAL 106
Score = 31.8 bits (72), Expect = 1.7
Identities = 12/23 (52%), Positives = 15/23 (65%)
Query: 698 GLKGATVGIVGLGNIGLETAKLL 720
L+G TV + GLGN+G AK L
Sbjct: 20 SLEGLTVAVQGLGNVGWGLAKKL 42
>gnl|CDD|176244 cd08284, FDH_like_2, Glutathione-dependent formaldehyde dehydrogenase
related proteins, child 2. Glutathione-dependent
formaldehyde dehydrogenases (FDHs) are members of the
zinc-dependent/medium chain alcohol dehydrogenase family.
Formaldehyde dehydrogenase (FDH) is a member of the
zinc-dependent/medium chain alcohol dehydrogenase family.
FDH converts formaldehyde and NAD to formate and NADH.
The initial step in this process the spontaneous
formation of a S-(hydroxymethyl)glutathione adduct from
formaldehyde and glutathione, followed by FDH-mediated
oxidation (and detoxification) of the adduct to
S-formylglutathione. These tetrameric FDHs have a
catalytic zinc that resides between the catalytic and
NAD(H)binding domains and a structural zinc in a lobe of
the catalytic domain. 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.
Length = 344
Score = 33.8 bits (78), Expect = 0.51
Identities = 17/56 (30%), Positives = 28/56 (50%), Gaps = 6/56 (10%)
Query: 955 KGATVGIVGLGNIGL---ETAKLLKAFKVSKI-LYTSRRVKEEGTALGAQLVPLDT 1006
G TV ++G G +GL +A++L A +V + R E ALGA+ + +
Sbjct: 167 PGDTVAVIGCGPVGLCAVLSAQVLGAARVFAVDPVPERL--ERAAALGAEPINFED 220
>gnl|CDD|176238 cd08277, liver_alcohol_DH_like, Liver alcohol dehydrogenase.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. There are 7 vertebrate ADH 7
classes, 6 of which have been identified in humans.
Class III, glutathione-dependent formaldehyde
dehydrogenase, has been identified as the primordial
form and exists in diverse species, including plants,
micro-organisms, vertebrates, and invertebrates. Class
I, typified by liver dehydrogenase, is an evolving
form. Gene duplication and functional specialization of
ADH into ADH classes and subclasses created numerous
forms in vertebrates. For example, the A, B and C
(formerly alpha, beta, gamma) human class I subunits
have high overall structural similarity, but differ in
the substrate binding pocket and therefore in substrate
specificity. In human ADH catalysis, the zinc ion helps
coordinate the alcohol, followed by deprotonation of a
histidine (His-51), the ribose of NAD, a serine
(Ser-48) , then the alcohol, which allows the transfer
of a hydride to NAD+, creating NADH and a zinc-bound
aldehyde or ketone. In yeast and some bacteria, the
active site zinc binds an aldehyde, polarizing it, and
leading to the reverse reaction. ADH is a member of the
medium chain alcohol dehydrogenase family (MDR), which
has a NAD(P)(H)-binding domain in a Rossmann fold of an
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES.
These proteins typically form dimers (typically higher
plants, mammals) or tetramers (yeast, bacteria), and
have 2 tightly bound zinc atoms per subunit, a catalytic
zinc at the active site and a structural zinc in a lobe
of the catalytic domain. NAD(H) binding occurs in the
cleft between the catalytic and coenzyme-binding
domains at the active site, and coenzyme binding induces
a conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
Length = 365
Score = 33.5 bits (77), Expect = 0.56
Identities = 17/47 (36%), Positives = 24/47 (51%), Gaps = 6/47 (12%)
Query: 831 KGATVGIVGLGNIGL---ETAKLLKAFKVSKILYTSRNKVKTPKRTE 874
G+TV + GLG +GL AK+ A S+I+ N+ K K E
Sbjct: 184 PGSTVAVFGLGAVGLSAIMGAKIAGA---SRIIGVDINEDKFEKAKE 227
>gnl|CDD|234592 PRK00045, hemA, glutamyl-tRNA reductase; Reviewed.
Length = 423
Score = 33.6 bits (78), Expect = 0.62
Identities = 23/68 (33%), Positives = 32/68 (47%), Gaps = 6/68 (8%)
Query: 954 LKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSR---RVKEEGTALGAQLVPLDTLC-- 1008
L G V ++G G +G AK L V KI +R R +E G + +PLD L
Sbjct: 180 LSGKKVLVIGAGEMGELVAKHLAEKGVRKITVANRTLERAEELAEEFGGEAIPLDELPEA 239
Query: 1009 -AESDFIF 1015
AE+D +
Sbjct: 240 LAEADIVI 247
>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 = 33.2 bits (77), Expect = 0.70
Identities = 27/98 (27%), Positives = 39/98 (39%), Gaps = 15/98 (15%)
Query: 955 KGATVGIVGLGNIGLETAKLLKAF--KVSKILYTSRRVKEEGTALGAQLVP-------LD 1005
G VG+VG+G +G K KA +V+ S KE+ LGA +
Sbjct: 169 PGKRVGVVGIGGLGHLAVKFAKALGAEVT-AFSRSPSKKEDALKLGADEFIATKDPEAMK 227
Query: 1006 TLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILV 1043
D I T + + D + + SL+KP LV
Sbjct: 228 KAAGSLDLIIDTVSASHDLDPYL-----SLLKPGGTLV 260
>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 = 31.9 bits (73), Expect = 0.74
Identities = 25/100 (25%), Positives = 40/100 (40%), Gaps = 12/100 (12%)
Query: 953 GLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSR---RVKEEGTALGA--QLVPLD-- 1005
LKG V ++G G + AK L + KI +R + KE + +PLD
Sbjct: 9 DLKGKKVLLIGAGEMARLAAKHLLSKGAKKITIANRTLEKAKELAEEFPVGGEALPLDEL 68
Query: 1006 -TLCAESDFIFVTCALTKDTEQLIGRKQF-SLMKPTAILV 1043
L AE+D + T +I ++ +K +L
Sbjct: 69 EELLAEADIVISA---TSAPTPIITKEMVEEALKARPLLF 105
>gnl|CDD|233242 TIGR01035, hemA, glutamyl-tRNA reductase. This enzyme, together with
glutamate-1-semialdehyde-2,1-aminomutase (TIGR00713),
leads to the production of delta-amino-levulinic acid
from Glu-tRNA [Biosynthesis of cofactors, prosthetic
groups, and carriers, Heme, porphyrin, and cobalamin].
Length = 417
Score = 33.1 bits (76), Expect = 0.81
Identities = 22/69 (31%), Positives = 32/69 (46%), Gaps = 6/69 (8%)
Query: 954 LKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSR---RVKEEGTALGAQLVPLDTL--- 1007
LKG ++G G +G AK L V KIL +R R ++ LG + V + L
Sbjct: 178 LKGKKALLIGAGEMGELVAKHLLRKGVGKILIANRTYERAEDLAKELGGEAVKFEDLEEY 237
Query: 1008 CAESDFIFV 1016
AE+D +
Sbjct: 238 LAEADIVIS 246
Score = 31.2 bits (71), Expect = 3.8
Identities = 14/39 (35%), Positives = 19/39 (48%)
Query: 830 LKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRNKVK 868
LKG ++G G +G AK L V KIL +R +
Sbjct: 178 LKGKKALLIGAGEMGELVAKHLLRKGVGKILIANRTYER 216
Score = 29.7 bits (67), Expect = 9.2
Identities = 14/35 (40%), Positives = 18/35 (51%)
Query: 699 LKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSR 733
LKG ++G G +G AK L V KIL +R
Sbjct: 178 LKGKKALLIGAGEMGELVAKHLLRKGVGKILIANR 212
>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 = 32.2 bits (74), Expect = 0.95
Identities = 20/71 (28%), Positives = 31/71 (43%), Gaps = 6/71 (8%)
Query: 954 LKGATVGIVGLGNIGLETAKLLKA----FKVSKILYTSRRVKEEGTALGAQLVPLDTLCA 1009
L+G TV + GLG +G + A+ L V+ I V GA +V + + +
Sbjct: 26 LEGKTVAVQGLGKVGYKLAEHLLEEGAKLIVADIN--EEAVARAAELFGATVVAPEEIYS 83
Query: 1010 ESDFIFVTCAL 1020
+F CAL
Sbjct: 84 VDADVFAPCAL 94
>gnl|CDD|233844 TIGR02392, rpoH_proteo, alternative sigma factor RpoH. A sigma
factor is a DNA-binding protein protein that binds to
the DNA-directed RNA polymerase core to produce the
holoenzyme capable of initiating transcription at
specific sites. Different sigma factors act in
vegetative growth, heat shock, extracytoplasmic
functions (ECF), etc. This model represents the clade of
sigma factors called RpoH and further restricted to the
Proteobacteria. This protein may be called sigma-32,
sigma factor H, heat shock sigma factor, and alternative
sigma factor RpoH. Note that in some species the single
locus rpoH may be replaced by two or more differentially
regulated stress response sigma factors [Cellular
processes, Adaptations to atypical conditions,
Transcription, Transcription factors].
Length = 270
Score = 32.6 bits (75), Expect = 1.0
Identities = 17/42 (40%), Positives = 20/42 (47%), Gaps = 9/42 (21%)
Query: 137 SDTVAEYNIGLAIAVSRRFQQRHNWIARLSSFA------EIQ 172
+D + E NIGL AV +RF RL SFA EI
Sbjct: 63 ADLIQEGNIGLMKAV-KRFDPERG--VRLVSFAVHWIKAEIH 101
>gnl|CDD|198065 smart00997, AdoHcyase_NAD, S-adenosyl-L-homocysteine hydrolase, NAD
binding domain.
Length = 162
Score = 31.7 bits (73), Expect = 1.1
Identities = 22/65 (33%), Positives = 31/65 (47%), Gaps = 7/65 (10%)
Query: 998 GAQLVPLDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILVNTSRGGLLDQEALV 1057
G +++ ++ +D IFVT KD I R+ F MK AIL N G D E V
Sbjct: 66 GFEVMKMEEAAKRAD-IFVTATGNKDV---ITREHFRAMKDGAILANA---GHFDVEIDV 118
Query: 1058 EFLKD 1062
L++
Sbjct: 119 AALEE 123
Score = 30.5 bits (70), Expect = 2.7
Identities = 22/65 (33%), Positives = 31/65 (47%), Gaps = 7/65 (10%)
Query: 308 GAQLVPLDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALV 367
G +++ ++ +D IFVT KD I R+ F MK AIL N G D E V
Sbjct: 66 GFEVMKMEEAAKRAD-IFVTATGNKDV---ITREHFRAMKDGAILANA---GHFDVEIDV 118
Query: 368 EFLKD 372
L++
Sbjct: 119 AALEE 123
>gnl|CDD|111576 pfam02691, VacA, Vacuolating cyotoxin. This family consists of
Vacuolating cyotoxin proteins form Proteobacteria. These
proteins are an important virulence determinate in H.
pylori and induce cytoplasmic vacuolation in a variety
of mammalian cell lines.
Length = 1002
Score = 32.8 bits (74), Expect = 1.5
Identities = 29/112 (25%), Positives = 47/112 (41%), Gaps = 21/112 (18%)
Query: 810 TINGEWALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRNKVKT 869
N E L + II ++G +GA +G N LE + FK LY + N++ T
Sbjct: 716 IKNKEHVLLKAKIIDYGLVGTQGANYDNIGASNTNLE-----EQFKERLALYNNNNRMDT 770
Query: 870 -PKRTENLKVITTFSVGYDHLELHEIKARGIRVGSVGHISSDTVAEYNIGLA 920
R +N L +IKA G+ +G+ +++ +Y G A
Sbjct: 771 CVVRKDN---------------LDDIKACGMAIGNQSMVNNPDNYKYLEGKA 807
>gnl|CDD|215382 PLN02712, PLN02712, arogenate dehydrogenase.
Length = 667
Score = 32.3 bits (73), Expect = 1.6
Identities = 22/87 (25%), Positives = 37/87 (42%), Gaps = 1/87 (1%)
Query: 959 VGIVGLGNIGLETAKLLKAFKVSKILYTSRRVKEEGTALGAQLVP-LDTLCAESDFIFVT 1017
+ IVG GN G AK + + + Y+ +E LG D LC E + +
Sbjct: 372 IAIVGFGNFGQFLAKTMVKQGHTVLAYSRSDYSDEAQKLGVSYFSDADDLCEEHPEVILL 431
Query: 1018 CALTKDTEQLIGRKQFSLMKPTAILVN 1044
C TE+++ F +K + + V+
Sbjct: 432 CTSILSTEKVLKSLPFQRLKRSTLFVD 458
>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 = 32.0 bits (74), Expect = 1.8
Identities = 22/65 (33%), Positives = 31/65 (47%), Gaps = 7/65 (10%)
Query: 998 GAQLVPLDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILVNTSRGGLLDQEALV 1057
G +++P++ D IFVT KD +I + F MK AIL N G D E V
Sbjct: 238 GFEVMPMEEAAKIGD-IFVTATGNKD---VIRGEHFEKMKDGAILCNA---GHFDVEIDV 290
Query: 1058 EFLKD 1062
L++
Sbjct: 291 AALEE 295
Score = 31.7 bits (73), Expect = 2.3
Identities = 22/65 (33%), Positives = 31/65 (47%), Gaps = 7/65 (10%)
Query: 308 GAQLVPLDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALV 367
G +++P++ D IFVT KD +I + F MK AIL N G D E V
Sbjct: 238 GFEVMPMEEAAKIGD-IFVTATGNKD---VIRGEHFEKMKDGAILCNA---GHFDVEIDV 290
Query: 368 EFLKD 372
L++
Sbjct: 291 AALEE 295
>gnl|CDD|223991 COG1063, Tdh, Threonine dehydrogenase and related Zn-dependent
dehydrogenases [Amino acid transport and metabolism /
General function prediction only].
Length = 350
Score = 32.0 bits (73), Expect = 1.9
Identities = 13/40 (32%), Positives = 18/40 (45%)
Query: 829 GLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRNKVK 868
G TV +VG G IGL L K S ++ R+ +
Sbjct: 166 VRPGGTVVVVGAGPIGLLAIALAKLLGASVVIVVDRSPER 205
Score = 32.0 bits (73), Expect = 2.0
Identities = 12/31 (38%), Positives = 14/31 (45%)
Query: 698 GLKGATVGIVGLGNIGLETAKLLKAFKVSKI 728
G TV +VG G IGL L K S +
Sbjct: 166 VRPGGTVVVVGAGPIGLLAIALAKLLGASVV 196
Score = 32.0 bits (73), Expect = 2.0
Identities = 12/31 (38%), Positives = 14/31 (45%)
Query: 953 GLKGATVGIVGLGNIGLETAKLLKAFKVSKI 983
G TV +VG G IGL L K S +
Sbjct: 166 VRPGGTVVVVGAGPIGLLAIALAKLLGASVV 196
>gnl|CDD|166227 PLN02586, PLN02586, probable cinnamyl alcohol dehydrogenase.
Length = 360
Score = 31.8 bits (72), Expect = 1.9
Identities = 19/50 (38%), Positives = 26/50 (52%), Gaps = 2/50 (4%)
Query: 952 MGLKGATVGIVGLGNIGLETAKLLKAF--KVSKILYTSRRVKEEGTALGA 999
M G +G+ GLG +G K+ KAF KV+ I +S + E LGA
Sbjct: 180 MTEPGKHLGVAGLGGLGHVAVKIGKAFGLKVTVISSSSNKEDEAINRLGA 229
>gnl|CDD|223842 COG0771, MurD, UDP-N-acetylmuramoylalanine-D-glutamate ligase [Cell
envelope biogenesis, outer membrane].
Length = 448
Score = 31.9 bits (73), Expect = 2.0
Identities = 17/96 (17%), Positives = 28/96 (29%), Gaps = 20/96 (20%)
Query: 826 NIMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILY----TSRNKVKTPKRTENLKVITT 881
+ +G V ++GLG GL A+ L + P E ++V
Sbjct: 1 MMEDFQGKKVLVLGLGKSGLAAARFLLKLGAEVTVSDDRPAPEGLAAQPLLLEGIEVELG 60
Query: 882 F----------------SVGYDHLELHEIKARGIRV 901
+ H + KA GI +
Sbjct: 61 SHDDEDLAEFDLVVKSPGIPPTHPLVEAAKAAGIEI 96
>gnl|CDD|224995 COG2084, MmsB, 3-hydroxyisobutyrate dehydrogenase and related
beta-hydroxyacid dehydrogenases [Lipid metabolism].
Length = 286
Score = 31.4 bits (72), Expect = 2.4
Identities = 23/95 (24%), Positives = 39/95 (41%), Gaps = 5/95 (5%)
Query: 957 ATVGIVGLGNIGLETAK-LLKA-FKVSKILYTSRRVKEEGTALGAQLVPLDT-LCAESDF 1013
+ +GLG +G A LLKA +V+ T + E A GA + AE+D
Sbjct: 1 MKIAFIGLGIMGSPMAANLLKAGHEVTVYNRTPEKAAELLAAAGATVAASPAEAAAEADV 60
Query: 1014 IFVTCALTKDTEQLIGRKQ--FSLMKPTAILVNTS 1046
+ ++ + +KP AI+++ S
Sbjct: 61 VITMLPDDAAVRAVLFGENGLLEGLKPGAIVIDMS 95
>gnl|CDD|184511 PRK14106, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
synthetase; Provisional.
Length = 450
Score = 31.5 bits (72), Expect = 2.8
Identities = 21/45 (46%), Positives = 22/45 (48%), Gaps = 3/45 (6%)
Query: 697 MGLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRRVKEEGQL 741
M LKG V +VG G GL AK LK IL KEE QL
Sbjct: 1 MELKGKKVLVVGAGVSGLALAKFLKKLGAKVILTDE---KEEDQL 42
Score = 31.5 bits (72), Expect = 2.9
Identities = 16/40 (40%), Positives = 19/40 (47%)
Query: 828 MGLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRNKV 867
M LKG V +VG G GL AK LK IL + +
Sbjct: 1 MELKGKKVLVVGAGVSGLALAKFLKKLGAKVILTDEKEED 40
Score = 31.1 bits (71), Expect = 3.9
Identities = 21/56 (37%), Positives = 25/56 (44%), Gaps = 3/56 (5%)
Query: 952 MGLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRR---VKEEGTALGAQLVPL 1004
M LKG V +VG G GL AK LK IL + +KE LG + L
Sbjct: 1 MELKGKKVLVVGAGVSGLALAKFLKKLGAKVILTDEKEEDQLKEALEELGELGIEL 56
>gnl|CDD|129609 TIGR00518, alaDH, alanine dehydrogenase. The family of known
L-alanine dehydrogenases includes representatives from
the Proteobacteria, Firmicutes, and Cyanobacteria, all
with about 50 % identity or better. An outlier to this
group in both sequence and gap pattern is the homolog
from Helicobacter pylori, an epsilon division
Proteobacteria, which must be considered a putative
alanine dehydrogenase. Related proteins include
saccharopine dehydrogenase and the N-terminal half of the
NAD(P) transhydrogenase alpha subunit. All of these
related proteins bind NAD and/or NADP [Energy metabolism,
Amino acids and amines].
Length = 370
Score = 31.4 bits (71), Expect = 2.9
Identities = 34/190 (17%), Positives = 71/190 (37%), Gaps = 18/190 (9%)
Query: 886 YDHLELHEIKARGIRVGSVGHISSDTVAEYNIGLAIAVSRRFQEGRKCITSGEWALKQTH 945
Y HL + I+ +TV + L + GR G + L++T
Sbjct: 93 YLHLAAERALTDALLDSGTTAIAYETVQTADGALPLLAPMSEVAGRLAAQVGAYHLEKTQ 152
Query: 946 ----IIGPNIMGLKGATVGIVGLGNIGLETAKLLKAF--KVSKILYTSRRVKEEGTALGA 999
++ + G++ V I+G G +G AK+ V+ + R+++ G
Sbjct: 153 GGRGVLLGGVPGVEPGDVTIIGGGVVGTNAAKMANGLGATVTILDINIDRLRQLDAEFGG 212
Query: 1000 QL-------VPLDTLCAESDFIFVTCALT-KDTEQLIGRKQFSLMKPTAILVNTSRGGLL 1051
++ ++ +D + + +L+ + MKP A++V+ + +
Sbjct: 213 RIHTRYSNAYEIEDAVKRADLLIGAVLIPGAKAPKLVSNSLVAQMKPGAVIVDVA----I 268
Query: 1052 DQEALVEFLK 1061
DQ VE +
Sbjct: 269 DQGGCVETSR 278
>gnl|CDD|223992 COG1064, AdhP, Zn-dependent alcohol dehydrogenases [General function
prediction only].
Length = 339
Score = 31.4 bits (72), Expect = 2.9
Identities = 20/65 (30%), Positives = 27/65 (41%), Gaps = 10/65 (15%)
Query: 940 ALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKAF--KVSKILYTSRRVKEEGTAL 997
ALK+ ++ P G V +VG G +G + KA +V I S E L
Sbjct: 158 ALKKANV-KP------GKWVAVVGAGGLGHMAVQYAKAMGAEVIAIT-RSEEKLELAKKL 209
Query: 998 GAQLV 1002
GA V
Sbjct: 210 GADHV 214
>gnl|CDD|234950 PRK01390, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
synthetase; Provisional.
Length = 460
Score = 31.4 bits (72), Expect = 3.2
Identities = 13/27 (48%), Positives = 16/27 (59%)
Query: 696 IMGLKGATVGIVGLGNIGLETAKLLKA 722
+ G G TV + GLG GL TA+ L A
Sbjct: 4 VTGFAGKTVAVFGLGGSGLATARALVA 30
Score = 31.4 bits (72), Expect = 3.2
Identities = 13/27 (48%), Positives = 16/27 (59%)
Query: 827 IMGLKGATVGIVGLGNIGLETAKLLKA 853
+ G G TV + GLG GL TA+ L A
Sbjct: 4 VTGFAGKTVAVFGLGGSGLATARALVA 30
Score = 31.4 bits (72), Expect = 3.2
Identities = 13/27 (48%), Positives = 16/27 (59%)
Query: 951 IMGLKGATVGIVGLGNIGLETAKLLKA 977
+ G G TV + GLG GL TA+ L A
Sbjct: 4 VTGFAGKTVAVFGLGGSGLATARALVA 30
>gnl|CDD|223536 COG0460, ThrA, Homoserine dehydrogenase [Amino acid transport and
metabolism].
Length = 333
Score = 31.0 bits (71), Expect = 3.3
Identities = 7/21 (33%), Positives = 13/21 (61%)
Query: 704 VGIVGLGNIGLETAKLLKAFK 724
VG++GLG +G ++L +
Sbjct: 6 VGLLGLGTVGSGVLEILAEKQ 26
Score = 31.0 bits (71), Expect = 3.3
Identities = 7/21 (33%), Positives = 13/21 (61%)
Query: 835 VGIVGLGNIGLETAKLLKAFK 855
VG++GLG +G ++L +
Sbjct: 6 VGLLGLGTVGSGVLEILAEKQ 26
Score = 31.0 bits (71), Expect = 3.3
Identities = 7/21 (33%), Positives = 13/21 (61%)
Query: 959 VGIVGLGNIGLETAKLLKAFK 979
VG++GLG +G ++L +
Sbjct: 6 VGLLGLGTVGSGVLEILAEKQ 26
>gnl|CDD|237342 PRK13303, PRK13303, L-aspartate dehydrogenase; Provisional.
Length = 265
Score = 30.7 bits (70), Expect = 3.5
Identities = 16/68 (23%), Positives = 28/68 (41%), Gaps = 7/68 (10%)
Query: 958 TVGIVGLGNIGLETAKLLKAFK---VSKILYTSRRVKEEGTALGAQLVPLDTLCA---ES 1011
V ++G G IG +LL+ V ++ + ALG + + ++ A
Sbjct: 3 KVAMIGFGAIGAAVLELLEHDPDLRVDWVIVPEHSIDAVRRALGEAVRVVSSVDALPQRP 62
Query: 1012 DFIFVTCA 1019
D + V CA
Sbjct: 63 DLV-VECA 69
>gnl|CDD|200461 cd11322, AmyAc_Glg_BE, Alpha amylase catalytic domain found in the
Glycogen branching enzyme (also called 1,4-alpha-glucan
branching enzyme). The glycogen branching enzyme
catalyzes the third step of glycogen biosynthesis by the
cleavage of an alpha-(1,4)-glucosidic linkage and the
formation a new alpha-(1,6)-branch by subsequent
transfer of cleaved oligosaccharide. They are part of a
group called branching enzymes which catalyze the
formation of alpha-1,6 branch points in either glycogen
or starch. This group includes proteins from bacteria,
eukaryotes, and archaea. The Alpha-amylase family
comprises the largest family of glycoside hydrolases
(GH), with the majority of enzymes acting on starch,
glycogen, and related oligo- and polysaccharides. These
proteins catalyze the transformation of alpha-1,4 and
alpha-1,6 glucosidic linkages with retention of the
anomeric center. The protein is described as having 3
domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a
loop between the beta 3 strand and alpha 3 helix of A; C
is the C-terminal extension characterized by a Greek
key. The majority of the enzymes have an active site
cleft found between domains A and B where a triad of
catalytic residues (Asp, Glu and Asp) performs
catalysis. Other members of this family have lost the
catalytic activity as in the case of the human 4F2hc, or
only have 2 residues that serve as the catalytic
nucleophile and the acid/base, such as Thermus A4
beta-galactosidase with 2 Glu residues (GH42) and human
alpha-galactosidase with 2 Asp residues (GH31). The
family members are quite extensive and include: alpha
amylase, maltosyltransferase, cyclodextrin
glycotransferase, maltogenic amylase, neopullulanase,
isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase,
4-alpha-glucotransferase, oligo-1,6-glucosidase,
amylosucrase, sucrose phosphorylase, and amylomaltase.
Length = 402
Score = 31.0 bits (71), Expect = 3.8
Identities = 9/23 (39%), Positives = 10/23 (43%)
Query: 281 KWRMGSKTDTNHYFGYNWFERSN 303
KW MG DT YF + R
Sbjct: 272 KWNMGWMNDTLDYFKTDPIYRKY 294
>gnl|CDD|213572 TIGR00936, ahcY, adenosylhomocysteinase. This enzyme hydrolyzes
adenosylhomocysteine as part of a cycle for the
regeneration of the methyl donor S-adenosylmethionine.
Species that lack this enzyme are likely to have
adenosylhomocysteine nucleosidase (EC 3.2.2.9), an enzyme
which also acts as 5'-methyladenosine nucleosidase (see
TIGR01704) [Energy metabolism, Amino acids and amines].
Length = 407
Score = 30.8 bits (70), Expect = 4.1
Identities = 29/113 (25%), Positives = 48/113 (42%), Gaps = 9/113 (7%)
Query: 950 NIMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRRVKE-EGTALGAQLVPLDTLC 1008
N++ + G TV + G G G A + I+ ++ E G +++ ++
Sbjct: 191 NLL-IAGKTVVVAGYGWCGKGIAMRARGMGARVIVTEVDPIRALEAAMDGFRVMTMEEAA 249
Query: 1009 AESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILVNTSRGGLLDQEALVEFLK 1061
D IF+T KD +I + F MK AI+ N G D E V+ L+
Sbjct: 250 KIGD-IFITATGNKD---VIRGEHFENMKDGAIVANI---GHFDVEIDVKALE 295
>gnl|CDD|235488 PRK05476, PRK05476, S-adenosyl-L-homocysteine hydrolase; Provisional.
Length = 425
Score = 30.5 bits (70), Expect = 5.2
Identities = 20/65 (30%), Positives = 28/65 (43%), Gaps = 7/65 (10%)
Query: 998 GAQLVPLDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILVNTSRGGLLDQEALV 1057
G +++ ++ D IFVT KD I + MK AIL N G D E V
Sbjct: 255 GFRVMTMEEAAELGD-IFVTATGNKDV---ITAEHMEAMKDGAILANI---GHFDNEIDV 307
Query: 1058 EFLKD 1062
L++
Sbjct: 308 AALEE 312
Score = 30.5 bits (70), Expect = 6.2
Identities = 20/65 (30%), Positives = 28/65 (43%), Gaps = 7/65 (10%)
Query: 308 GAQLVPLDTLCAESDFIFVTCALTKDTEQLIGRKQFSLMKPTAILINTSRGGLLDQEALV 367
G +++ ++ D IFVT KD I + MK AIL N G D E V
Sbjct: 255 GFRVMTMEEAAELGD-IFVTATGNKDV---ITAEHMEAMKDGAILANI---GHFDNEIDV 307
Query: 368 EFLKD 372
L++
Sbjct: 308 AALEE 312
>gnl|CDD|176260 cd08300, alcohol_DH_class_III, class III alcohol dehydrogenases.
Members identified as glutathione-dependent formaldehyde
dehydrogenase(FDH), a member of the zinc
dependent/medium chain alcohol dehydrogenase family.
FDH converts formaldehyde and NAD(P) to formate and
NAD(P)H. The initial step in this process the
spontaneous formation of a S-(hydroxymethyl)glutathione
adduct from formaldehyde and glutathione, followed by
FDH-mediated oxidation (and detoxification) of the
adduct to S-formylglutathione. MDH family uses NAD(H)
as a cofactor in the interconversion of alcohols and
aldehydes or ketones. Like many zinc-dependent alcohol
dehydrogenases (ADH) of the medium chain alcohol
dehydrogenase/reductase family (MDR), these FDHs form
dimers, with 4 zinc ions per dimer. The medium chain
alcohol dehydrogenase family (MDR) have 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. Alcohol dehydrogenase in the liver
converts ethanol and NAD+ to acetaldehyde and NADH,
while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which have a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES.
These proteins typically form dimers (typically higher
plants, mammals) or tetramers (yeast, bacteria), and
have 2 tightly bound zinc atoms per subunit, a catalytic
zinc at the active site and a structural zinc in a lobe
of the catalytic domain. NAD(H) binding occurs in the
cleft between the catalytic and coenzyme-binding
domains at the active site, and coenzyme binding induces
a conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
Length = 368
Score = 30.7 bits (70), Expect = 5.2
Identities = 14/41 (34%), Positives = 20/41 (48%)
Query: 831 KGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRNKVKTPK 871
G+TV + GLG +GL + KA S+I+ N K
Sbjct: 186 PGSTVAVFGLGAVGLAVIQGAKAAGASRIIGIDINPDKFEL 226
Score = 29.9 bits (68), Expect = 9.3
Identities = 12/30 (40%), Positives = 18/30 (60%)
Query: 700 KGATVGIVGLGNIGLETAKLLKAFKVSKIL 729
G+TV + GLG +GL + KA S+I+
Sbjct: 186 PGSTVAVFGLGAVGLAVIQGAKAAGASRII 215
Score = 29.9 bits (68), Expect = 9.3
Identities = 12/30 (40%), Positives = 18/30 (60%)
Query: 955 KGATVGIVGLGNIGLETAKLLKAFKVSKIL 984
G+TV + GLG +GL + KA S+I+
Sbjct: 186 PGSTVAVFGLGAVGLAVIQGAKAAGASRII 215
>gnl|CDD|176104 cd08412, PBP2_PAO1_like, The C-terminal substrate-binding domain of
putative LysR-type transcriptional regulator PAO1-like,
a member of the type 2 periplasmic binding fold protein
superfamily. This family includes the C-terminal
substrate domain of a putative LysR-type transcriptional
regulator from the plant pathogen Pseudomonas aeruginosa
PAO1and its closely related homologs. The LysR-type
transcriptional regulators (LTTRs) are composed of two
functional domains joined by a linker helix involved in
oligomerization: an N-terminal HTH (helix-turn-helix)
domain, which is responsible for the DNA-binding
specificity, and a C-terminal substrate-binding domain,
which is structurally homologous to the type 2
periplasmic binding proteins. As also observed in the
periplasmic binding proteins, the C-terminal domain of
the bacterial transcriptional repressor undergoes a
conformational change upon substrate binding which in
turn changes the DNA binding affinity of the repressor.
The genes controlled by the LTTRs have diverse
functional roles including amino acid biosynthesis, CO2
fixation, antibiotic resistance, degradation of aromatic
compounds, nodule formation of N2 fixing bacteria, and
synthesis of virulence factors, to a name a few. The
structural topology of this substrate-binding domain is
most similar to that of the type 2 periplasmic binding
proteins (PBP2), which are responsible for the uptake of
a variety of substrates such as phosphate, sulfate,
polysaccharides, lysine/arginine/ornithine, and
histidine. The PBP2 bind their ligand in the cleft
between these domains in a manner resembling a Venus
flytrap. After binding their specific ligand with high
affinity, they can interact with a cognate membrane
transport complex comprised of two integral membrane
domains and two cytoplasmically located ATPase domains.
This interaction triggers the ligand translocation
across the cytoplasmic membrane energized by ATP
hydrolysis. Besides transport proteins, the PBP2
superfamily includes the substrate-binding domains from
ionotropic glutamate receptors, LysR-like
transcriptional regulators, and unorthodox sensor
proteins involved in signal transduction.
Length = 198
Score = 29.8 bits (68), Expect = 5.2
Identities = 19/50 (38%), Positives = 21/50 (42%), Gaps = 11/50 (22%)
Query: 388 LPADHPLVQLDNCGGAGLDVMIPEPLPADHPLVQLDNCE--EFFEELFDK 435
LPADHPL D A L A PL+ LD E+F LF
Sbjct: 78 LPADHPLAGKDEVSLADL---------AAEPLILLDLPHSREYFLSLFAA 118
>gnl|CDD|215442 PLN02827, PLN02827, Alcohol dehydrogenase-like.
Length = 378
Score = 30.6 bits (69), Expect = 5.3
Identities = 16/41 (39%), Positives = 22/41 (53%)
Query: 831 KGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRNKVKTPK 871
KG++V I GLG +GL A+ K S+I+ N K K
Sbjct: 193 KGSSVVIFGLGTVGLSVAQGAKLRGASQIIGVDINPEKAEK 233
>gnl|CDD|215789 pfam00208, ELFV_dehydrog, Glutamate/Leucine/Phenylalanine/Valine
dehydrogenase.
Length = 237
Score = 30.2 bits (69), Expect = 5.6
Identities = 10/22 (45%), Positives = 14/22 (63%)
Query: 699 LKGATVGIVGLGNIGLETAKLL 720
L+G TV + G GN+G A+ L
Sbjct: 30 LEGKTVAVQGFGNVGSYAAEKL 51
Score = 30.2 bits (69), Expect = 5.6
Identities = 10/22 (45%), Positives = 14/22 (63%)
Query: 830 LKGATVGIVGLGNIGLETAKLL 851
L+G TV + G GN+G A+ L
Sbjct: 30 LEGKTVAVQGFGNVGSYAAEKL 51
Score = 30.2 bits (69), Expect = 5.6
Identities = 10/22 (45%), Positives = 14/22 (63%)
Query: 954 LKGATVGIVGLGNIGLETAKLL 975
L+G TV + G GN+G A+ L
Sbjct: 30 LEGKTVAVQGFGNVGSYAAEKL 51
>gnl|CDD|216396 pfam01262, AlaDh_PNT_C, Alanine dehydrogenase/PNT, C-terminal domain.
This family now also contains the lysine 2-oxoglutarate
reductases.
Length = 150
Score = 29.4 bits (67), Expect = 5.8
Identities = 29/100 (29%), Positives = 45/100 (45%), Gaps = 15/100 (15%)
Query: 957 ATVGIVGLGNIGL---ETAKLLKAFKVSKILYTSRRVKEEGTALGAQLVPLD-------- 1005
A V ++G G +GL TAK L A V+ IL E+ +L A+ V D
Sbjct: 21 AKVVVIGGGVVGLGAAATAKGLGA-PVT-ILDVRPERLEQLDSLFAEFVETDIFSNCEYL 78
Query: 1006 -TLCAESDFIFVTCALT-KDTEQLIGRKQFSLMKPTAILV 1043
AE+D + T + +L+ R+ MKP +++V
Sbjct: 79 AEAIAEADLVIGTVLIPGARAPKLVTREMVKTMKPGSVIV 118
>gnl|CDD|131865 TIGR02818, adh_III_F_hyde, S-(hydroxymethyl)glutathione
dehydrogenase/class III alcohol dehydrogenase. The
members of this protein family show dual function.
First, they remove formaldehyde, a toxic metabolite, by
acting as S-(hydroxymethyl)glutathione dehydrogenase
(1.1.1.284). S-(hydroxymethyl)glutathione can form
spontaneously from formaldehyde and glutathione, and so
this enzyme previously was designated
glutathione-dependent formaldehyde dehydrogenase. These
same proteins are also designated alcohol dehydrogenase
(EC 1.1.1.1) of class III, for activities that do not
require glutathione; they tend to show poor activity for
ethanol among their various substrate alcohols [Cellular
processes, Detoxification, Energy metabolism,
Fermentation].
Length = 368
Score = 30.2 bits (68), Expect = 6.0
Identities = 14/38 (36%), Positives = 20/38 (52%)
Query: 831 KGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRNKVK 868
+G TV + GLG IGL + + K S+I+ N K
Sbjct: 185 EGDTVAVFGLGGIGLSVIQGARMAKASRIIAIDINPAK 222
>gnl|CDD|176261 cd08301, alcohol_DH_plants, Plant alcohol dehydrogenase.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and aldehydes
or ketones. Alcohol dehydrogenase in the liver converts
ethanol and NAD+ to acetaldehyde and NADH, while in
yeast and some other microorganisms ADH catalyzes the
conversion acetaldehyde to ethanol in alcoholic
fermentation. There are 7 vertebrate ADH 7 classes, 6
of which have been identified in humans. Class III,
glutathione-dependent formaldehyde dehydrogenase, has
been identified as the primordial form and exists in
diverse species, including plants, micro-organisms,
vertebrates, and invertebrates. Class I, typified by
liver dehydrogenase, is an evolving form. Gene
duplication and functional specialization of ADH into
ADH classes and subclasses created numerous forms in
vertebrates. For example, the A, B and C (formerly
alpha, beta, gamma) human class I subunits have high
overall structural similarity, but differ in the
substrate binding pocket and therefore in substrate
specificity. In human ADH catalysis, the zinc ion helps
coordinate the alcohol, followed by deprotonation of a
histidine (His-51), the ribose of NAD, a serine
(Ser-48) , then the alcohol, which allows the transfer
of a hydride to NAD+, creating NADH and a zinc-bound
aldehyde or ketone. In yeast and some bacteria, the
active site zinc binds an aldehyde, polarizing it, and
leading to the reverse reaction. ADH is a member of the
medium chain alcohol dehydrogenase family (MDR), which
has a NAD(P)(H)-binding domain in a Rossmann fold of an
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES.
These proteins typically form dimers (typically higher
plants, mammals) or tetramers (yeast, bacteria), and
have 2 tightly bound zinc atoms per subunit, a catalytic
zinc at the active site and a structural zinc in a lobe
of the catalytic domain. NAD(H) binding occurs in the
cleft between the catalytic and coenzyme-binding
domains at the active site, and coenzyme binding induces
a conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
Length = 369
Score = 30.3 bits (69), Expect = 6.1
Identities = 15/38 (39%), Positives = 21/38 (55%)
Query: 831 KGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRNKVK 868
KG+TV I GLG +GL A+ + S+I+ N K
Sbjct: 187 KGSTVAIFGLGAVGLAVAEGARIRGASRIIGVDLNPSK 224
Score = 30.0 bits (68), Expect = 8.1
Identities = 13/30 (43%), Positives = 19/30 (63%)
Query: 700 KGATVGIVGLGNIGLETAKLLKAFKVSKIL 729
KG+TV I GLG +GL A+ + S+I+
Sbjct: 187 KGSTVAIFGLGAVGLAVAEGARIRGASRII 216
Score = 30.0 bits (68), Expect = 8.1
Identities = 13/30 (43%), Positives = 19/30 (63%)
Query: 955 KGATVGIVGLGNIGLETAKLLKAFKVSKIL 984
KG+TV I GLG +GL A+ + S+I+
Sbjct: 187 KGSTVAIFGLGAVGLAVAEGARIRGASRII 216
>gnl|CDD|176224 cd08263, Zn_ADH10, Alcohol dehydrogenases of the MDR family.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which have a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES. These
proteins typically form dimers (typically higher plants,
mammals) or tetramers (yeast, bacteria), and have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site and a structural zinc in a lobe of
the catalytic domain. NAD(H)-binding occurs in the
cleft between the catalytic and coenzyme-binding
domains at the active site, and coenzyme binding induces
a conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
In human ADH catalysis, the zinc ion helps coordinate
the alcohol, followed by deprotonation of a histidine,
the ribose of NAD, a serine, then the alcohol, which
allows the transfer of a hydride to NAD+, creating NADH
and a zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 367
Score = 30.0 bits (68), Expect = 6.9
Identities = 20/63 (31%), Positives = 27/63 (42%), Gaps = 8/63 (12%)
Query: 806 CYHGTINGEWALKQTHIIGPNIMGLKGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRN 865
C T G ALK + P G TV ++G+G +G +L KAF S I+
Sbjct: 170 CAGFTAYG--ALKHAADVRP------GETVAVIGVGGVGSSAIQLAKAFGASPIIAVDVR 221
Query: 866 KVK 868
K
Sbjct: 222 DEK 224
>gnl|CDD|176217 cd08255, 2-desacetyl-2-hydroxyethyl_bacteriochlorophyllide_like,
2-desacetyl-2-hydroxyethyl bacteriochlorophyllide and
other MDR family members. This subgroup of the medium
chain dehydrogenases/reductase (MDR)/zinc-dependent
alcohol dehydrogenase-like family has members identified
as 2-desacetyl-2-hydroxyethyl bacteriochlorophyllide A
dehydrogenase and alcohol dehydrogenases. 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.
Length = 277
Score = 29.9 bits (68), Expect = 7.1
Identities = 12/23 (52%), Positives = 15/23 (65%)
Query: 701 GATVGIVGLGNIGLETAKLLKAF 723
G V +VGLG +GL A+L KA
Sbjct: 98 GERVAVVGLGLVGLLAAQLAKAA 120
Score = 29.9 bits (68), Expect = 7.1
Identities = 12/23 (52%), Positives = 15/23 (65%)
Query: 832 GATVGIVGLGNIGLETAKLLKAF 854
G V +VGLG +GL A+L KA
Sbjct: 98 GERVAVVGLGLVGLLAAQLAKAA 120
Score = 29.9 bits (68), Expect = 7.1
Identities = 12/23 (52%), Positives = 15/23 (65%)
Query: 956 GATVGIVGLGNIGLETAKLLKAF 978
G V +VGLG +GL A+L KA
Sbjct: 98 GERVAVVGLGLVGLLAAQLAKAA 120
>gnl|CDD|202773 pfam03807, F420_oxidored, NADP oxidoreductase coenzyme
F420-dependent.
Length = 93
Score = 27.9 bits (63), Expect = 7.4
Identities = 18/67 (26%), Positives = 31/67 (46%), Gaps = 7/67 (10%)
Query: 958 TVGIVGLGNIGLETAKLLKAFKVSKILYTSRRVKEEGTAL------GAQLVPLDTLCAES 1011
+GI+G GN+G A+ L A +++ + R E+ AL A V + E+
Sbjct: 1 KIGIIGAGNMGEALARGLAAAG-HEVVIANSRNPEKAAALAEELGVKATAVSNEEAVEEA 59
Query: 1012 DFIFVTC 1018
D +F+
Sbjct: 60 DVVFLAV 66
>gnl|CDD|176197 cd08235, iditol_2_DH_like, L-iditol 2-dehydrogenase. Putative
L-iditol 2-dehydrogenase based on annotation of some
members in this subgroup. L-iditol 2-dehydrogenase
catalyzes the NAD+-dependent conversion of L-iditol to
L-sorbose in fructose and mannose metabolism. This
enzyme is related to sorbitol dehydrogenase, alcohol
dehydrogenase, and other medium chain
dehydrogenase/reductases. The zinc-dependent alcohol
dehydrogenase (ADH-Zn)-like family of proteins is a
diverse group of proteins related to the first
identified member, class I mammalian ADH. This group is
also called the medium chain dehydrogenases/reductase
family (MDR) to highlight its broad range of activities
and to distinguish from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal GroES-like catalytic
domain. The MDR group contains a host of activities,
including the founding alcohol dehydrogenase (ADH),
quinone reductase, sorbitol dehydrogenase, formaldehyde
dehydrogenase, butanediol DH, ketose reductase, cinnamyl
reductase, and numerous others. The zinc-dependent
alcohol dehydrogenases (ADHs) catalyze the
NAD(P)(H)-dependent interconversion of alcohols to
aldehydes or ketones. 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 = 343
Score = 29.9 bits (68), Expect = 7.9
Identities = 14/36 (38%), Positives = 20/36 (55%)
Query: 831 KGATVGIVGLGNIGLETAKLLKAFKVSKILYTSRNK 866
G TV ++G G IGL A L KA K++ + N+
Sbjct: 165 PGDTVLVIGAGPIGLLHAMLAKASGARKVIVSDLNE 200
Score = 29.9 bits (68), Expect = 8.0
Identities = 13/30 (43%), Positives = 17/30 (56%)
Query: 700 KGATVGIVGLGNIGLETAKLLKAFKVSKIL 729
G TV ++G G IGL A L KA K++
Sbjct: 165 PGDTVLVIGAGPIGLLHAMLAKASGARKVI 194
Score = 29.9 bits (68), Expect = 8.0
Identities = 13/30 (43%), Positives = 17/30 (56%)
Query: 955 KGATVGIVGLGNIGLETAKLLKAFKVSKIL 984
G TV ++G G IGL A L KA K++
Sbjct: 165 PGDTVLVIGAGPIGLLHAMLAKASGARKVI 194
>gnl|CDD|203593 pfam07200, Mod_r, Modifier of rudimentary (Mod(r)) protein. This
family represents a conserved region approximately 150
residues long within a number of eukaryotic proteins
that show homology with Drosophila melanogaster Modifier
of rudimentary (Mod(r)) proteins. The N-terminal half of
Mod(r) proteins is acidic, whereas the C-terminal half
is basic, and both of these regions are represented in
this family. Members of this family include the Vps37
subunit of the endosomal sorting complex ESCRT-I, a
complex involved in recruiting transport machinery for
protein sorting at the multivesicular body (MVB). The
yeast ESCRT-I complex consists of three proteins (Vps23,
Vps28 and Vps37). The mammalian homologue of Vps37
interacts with Tsg101 (Pfam: PF05743) through its mod(r)
domain and its function is essential for lysosomal
sorting of EGF receptors.
Length = 150
Score = 28.8 bits (65), Expect = 8.9
Identities = 13/29 (44%), Positives = 17/29 (58%), Gaps = 2/29 (6%)
Query: 710 GNIGLETAKLLKAFKVSKILYTSRRVKEE 738
G I L+T L+ +K + LY RR KEE
Sbjct: 122 GEIDLDT--FLQKYKDKRTLYHLRRAKEE 148
Score = 28.8 bits (65), Expect = 8.9
Identities = 13/29 (44%), Positives = 17/29 (58%), Gaps = 2/29 (6%)
Query: 965 GNIGLETAKLLKAFKVSKILYTSRRVKEE 993
G I L+T L+ +K + LY RR KEE
Sbjct: 122 GEIDLDT--FLQKYKDKRTLYHLRRAKEE 148
>gnl|CDD|199859 cd06235, M14_Nna1_like_2, Peptidase M14-like domain of human
Nna1/AGTPBP-1, AGBL2 -5, and related proteins. Subgroup
of the Peptidase M14-like domain of Nna-1 (Nervous
system Nuclear protein induced by Axotomy), also known
as ATP/GTP binding protein (AGTPBP-1) and cytosolic
carboxypeptidase (CCP), and related proteins. The
Peptidase M14 family of metallocarboxypeptidases are
zinc-binding carboxypeptidases (CPs) which hydrolyze
single, C-terminal amino acids from polypeptide chains,
and have a recognition site for the free C-terminal
carboxyl group, which is a key determinant of
specificity. This eukaryotic subgroup includes the human
Nna1/AGTPBP-1 and AGBL -2, -3, -4, and -5, and the mouse
Nna1/CCP-1 and CCP -2 through -6. Nna1-like proteins are
active metallopeptidases that are thought to act on
cytosolic proteins such as alpha-tubulin, to remove a
C-terminal tyrosine. Nna1 is widely expressed in the
developing and adult nervous systems, including
cerebellar Purkinje and granule neurons, miral cells of
the olfactory bulb and retinal photoreceptors. Nna1 is
also induced in axotomized motor neurons. Mutations in
Nna1 cause Purkinje cell degeneration (pcd). The Nna1 CP
domain is required to prevent the retinal photoreceptor
loss and cerebellar ataxia phenotypes of pcd mice, and a
functional zinc-binding domain is needed for Nna-1 to
support neuron survival in these mice. Nna1-like
proteins from the different phyla are highly diverse,
but they all contain a unique N-terminal conserved
domain right before the CP domain. It has been suggested
that this N-terminal domain might act as a folding
domain.
Length = 258
Score = 29.5 bits (67), Expect = 9.3
Identities = 15/42 (35%), Positives = 22/42 (52%), Gaps = 4/42 (9%)
Query: 581 GGYRCTEDFFGLDLDQMFRNPSKRHVNIETVLGVSFLIKNLK 622
G YRC G+DL++ ++NP K+ + V LIK L
Sbjct: 102 GNYRC--SLSGIDLNRQWKNPDKKL--HPEIYSVKQLIKKLS 139
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.320 0.138 0.404
Gapped
Lambda K H
0.267 0.0831 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 57,130,218
Number of extensions: 5738775
Number of successful extensions: 5960
Number of sequences better than 10.0: 1
Number of HSP's gapped: 5691
Number of HSP's successfully gapped: 419
Length of query: 1128
Length of database: 10,937,602
Length adjustment: 107
Effective length of query: 1021
Effective length of database: 6,191,724
Effective search space: 6321750204
Effective search space used: 6321750204
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 64 (28.2 bits)