RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 022672
(294 letters)
>gnl|CDD|177941 PLN02306, PLN02306, hydroxypyruvate reductase.
Length = 386
Score = 614 bits (1584), Expect = 0.0
Identities = 275/294 (93%), Positives = 289/294 (98%)
Query: 1 MAVGYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDG 60
MAVGYNNVDV AANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLY+G
Sbjct: 93 MAVGYNNVDVEAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYEG 152
Query: 61 WLPNLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQ 120
WLP+LFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQ+TRLEKFVTAYGQ
Sbjct: 153 WLPHLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQSTRLEKFVTAYGQ 212
Query: 121 FLKANGEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHLINKERLATMKKEAILVNCS 180
FLKANGEQPVTWKRASSM+EVLREADVISLHPVLDKTTYHLINKERLA MKKEA+LVN S
Sbjct: 213 FLKANGEQPVTWKRASSMEEVLREADVISLHPVLDKTTYHLINKERLALMKKEAVLVNAS 272
Query: 181 RGPVIDEVALVEHLKQNPMFRVGLDVFEDEPYMKPGLSEMKNAIVVPHIASASKWTREGM 240
RGPVIDEVALVEHLK NPMFRVGLDVFEDEPYMKPGL++MKNA+VVPHIASASKWTREGM
Sbjct: 273 RGPVIDEVALVEHLKANPMFRVGLDVFEDEPYMKPGLADMKNAVVVPHIASASKWTREGM 332
Query: 241 ATLAALNVLGKIKGYPIWGNPNQVEPFLNENAQPPAASPSIVNSKALGLPVSRL 294
ATLAALNVLGK+KGYP+WG+PN+VEPFLNENA PPAASPSIVN+KALGLPVS+L
Sbjct: 333 ATLAALNVLGKLKGYPVWGDPNRVEPFLNENAPPPAASPSIVNAKALGLPVSKL 386
>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 = 335 bits (861), Expect = e-115
Identities = 118/255 (46%), Positives = 156/255 (61%), Gaps = 18/255 (7%)
Query: 1 MAVGYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDG 60
+VGY+++DV+AA GI V NTP VLT+ TA+LA +L LAAARR+VE D F+RAG + G
Sbjct: 72 YSVGYDHIDVDAAKARGIPVTNTPDVLTDATADLAFALLLAAARRVVEGDRFVRAGEWKG 131
Query: 61 WLPNLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQ 120
W P L +G L G+T+G++G GRIG A AR GF M ++Y++ + E+ + A
Sbjct: 132 WSPTLLLGTDLHGKTLGIVGMGRIGQAVARRAK-GFGMKILYHNRSRKPEAEEELGAR-- 188
Query: 121 FLKANGEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHLINKERLATMKKEAILVNCS 180
S+DE+L E+D +SLH L T HLIN ERLA MK AIL+N +
Sbjct: 189 --------------YVSLDELLAESDFVSLHCPLTPETRHLINAERLALMKPTAILINTA 234
Query: 181 RGPVIDEVALVEHLKQNPMFRVGLDVFEDEPYMK-PGLSEMKNAIVVPHIASASKWTREG 239
RG V+DE ALVE LK + GLDVFE EP L + N +++PHI SA+ TR
Sbjct: 235 RGGVVDEDALVEALKSGKIAGAGLDVFEPEPLPADHPLLTLPNVVLLPHIGSATVETRTA 294
Query: 240 MATLAALNVLGKIKG 254
MA LAA N+L + G
Sbjct: 295 MAELAADNLLAVLAG 309
>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 = 248 bits (636), Expect = 1e-81
Identities = 103/253 (40%), Positives = 147/253 (58%), Gaps = 16/253 (6%)
Query: 2 AVGYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDGW 61
G++N+DV+ A + GI V NTP V TE TAEL L LA ARRI E D MR G + GW
Sbjct: 73 GAGFDNIDVDYAKEKGIPVTNTPAVSTEPTAELTFGLILALARRIAEGDRLMRRGGFLGW 132
Query: 62 LPNLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQF 121
P F+G+ L G+T+G+IG GRIG A AR + F M ++YY+ ++ + + G
Sbjct: 133 APLFFLGHELAGKTLGIIGMGRIGQAVARR-AKAFGMKILYYNRHRLSEETE--KELG-- 187
Query: 122 LKANGEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHLINKERLATMKKEAILVNCSR 181
T+ +DE+L+E+D +SLH T+HLI+ MK A L+N +R
Sbjct: 188 --------ATYV---DLDELLKESDFVSLHAPYTPETHHLIDAAAFKLMKPTAYLINAAR 236
Query: 182 GPVIDEVALVEHLKQNPMFRVGLDVFEDEPYMKPGLSEMKNAIVVPHIASASKWTREGMA 241
GP++DE ALV+ LK + LDVFE EP + P L ++ N I+ PHI +A+ R+ MA
Sbjct: 237 GPLVDEKALVDALKTGEIAGAALDVFEFEPEVSPELKKLDNVILTPHIGNATVEARDAMA 296
Query: 242 TLAALNVLGKIKG 254
AA N++ ++G
Sbjct: 297 KEAADNIISFLEG 309
>gnl|CDD|223980 COG1052, LdhA, Lactate dehydrogenase and related dehydrogenases
[Energy production and conversion / Coenzyme metabolism
/ General function prediction only].
Length = 324
Score = 239 bits (613), Expect = 4e-78
Identities = 108/259 (41%), Positives = 146/259 (56%), Gaps = 22/259 (8%)
Query: 1 MAVGYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDG 60
+ GY+NVD+ AA + GI V N PG TE AE A +L LA ARRI E D +R G +
Sbjct: 73 RSAGYDNVDLEAAKERGITVTNVPGYSTEAVAEHAVALILALARRIHEGDRRVREGNWSL 132
Query: 61 W-LPNLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAYG 119
P+ +G L+G+T+G+IG GRIG A AR + +GF M ++YYD EK
Sbjct: 133 SGGPDPLLGFDLRGKTLGIIGLGRIGQAVARRL-KGFGMKVLYYDRSPNPEAEK--ELGA 189
Query: 120 QFLKANGEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHLINKERLATMKKEAILVNC 179
+++ +DE+L E+D+ISLH L T HLIN E LA MK AILVN
Sbjct: 190 RYV--------------DLDELLAESDIISLHCPLTPETRHLINAEELAKMKPGAILVNT 235
Query: 180 SRGPVIDEVALVEHLKQNPMFRVGLDVFEDEPYMKP----GLSEMKNAIVVPHIASASKW 235
+RG ++DE AL++ LK + GLDVFE+EP + L N ++ PHIASA++
Sbjct: 236 ARGGLVDEQALIDALKSGKIAGAGLDVFENEPALFDHPLLRLDNFPNVVLTPHIASATEE 295
Query: 236 TREGMATLAALNVLGKIKG 254
R+ MA LA N+ G
Sbjct: 296 ARKAMAELALENLEAFFDG 314
>gnl|CDD|240649 cd12172, PGDH_like_2, Putative D-3-Phosphoglycerate Dehydrogenases,
NAD-binding and catalytic domains. Phosphoglycerate
dehydrogenases (PGDHs) catalyze the initial step in the
biosynthesis of L-serine from D-3-phosphoglycerate.
PGDHs come in 3 distinct structural forms, with this
first group being related to 2-hydroxy acid
dehydrogenases, sharing structural similarity to formate
and glycerate dehydrogenases of the D-specific
2-hydroxyacid dehydrogenase superfamily, which also
include groups such as L-alanine dehydrogenase and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. Many, not all, members of this family are
dimeric.
Length = 306
Score = 237 bits (608), Expect = 2e-77
Identities = 109/248 (43%), Positives = 144/248 (58%), Gaps = 23/248 (9%)
Query: 3 VGYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDGWL 62
VGY+N+D+ AA K GI V NTPG + + AEL L LA AR+I +AD +RAG GW
Sbjct: 77 VGYDNIDLEAAKKRGIVVTNTPGANSNSVAELTIGLMLALARQIPQADREVRAG---GWD 133
Query: 63 PNLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQFL 122
VG L G+T+G+IG GRIG A AR + GF M ++ YD Y +F
Sbjct: 134 R--PVGTELYGKTLGIIGLGRIGKAVARRLS-GFGMKVLAYDPYPDE----------EFA 180
Query: 123 KANGEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHLINKERLATMKKEAILVNCSRG 182
K +G + V S++E+L+E+D ISLH L T HLIN LA MK AIL+N +RG
Sbjct: 181 KEHGVEFV------SLEELLKESDFISLHLPLTPETRHLINAAELALMKPGAILINTARG 234
Query: 183 PVIDEVALVEHLKQNPMFRVGLDVFEDEPYMKPG-LSEMKNAIVVPHIASASKWTREGMA 241
++DE AL E LK + LDVFE+EP L E+ N I+ PHI +++K M
Sbjct: 235 GLVDEEALYEALKSGRIAGAALDVFEEEPPPADSPLLELPNVILTPHIGASTKEAVLRMG 294
Query: 242 TLAALNVL 249
T+AA NV+
Sbjct: 295 TMAAQNVI 302
>gnl|CDD|183914 PRK13243, PRK13243, glyoxylate reductase; Reviewed.
Length = 333
Score = 235 bits (602), Expect = 2e-76
Identities = 119/258 (46%), Positives = 159/258 (61%), Gaps = 21/258 (8%)
Query: 1 MAVGYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYD- 59
AVGY+N+DV A + GI V NTPGVLTE TA+ A +L LA ARR+VEAD F+R+G +
Sbjct: 74 YAVGYDNIDVEEATRRGIYVTNTPGVLTEATADFAWALLLATARRLVEADHFVRSGEWKR 133
Query: 60 ---GWLPNLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVT 116
W P +F+G + G+T+G+IG GRIG A AR +GF M ++YY + EK +
Sbjct: 134 RGVAWHPLMFLGYDVYGKTIGIIGFGRIGQAVARR-AKGFGMRILYYSRTRKPEAEKELG 192
Query: 117 AYGQFLKANGEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHLINKERLATMKKEAIL 176
A ++E+LRE+D +SLH L K TYH+IN+ERL MK AIL
Sbjct: 193 A----------------EYRPLEELLRESDFVSLHVPLTKETYHMINEERLKLMKPTAIL 236
Query: 177 VNCSRGPVIDEVALVEHLKQNPMFRVGLDVFEDEPYMKPGLSEMKNAIVVPHIASASKWT 236
VN +RG V+D ALV+ LK+ + GLDVFE+EPY L +KN ++ PHI SA+
Sbjct: 237 VNTARGKVVDTKALVKALKEGWIAGAGLDVFEEEPYYNEELFSLKNVVLAPHIGSATFEA 296
Query: 237 REGMATLAALNVLGKIKG 254
REGMA L A N++ +G
Sbjct: 297 REGMAELVAENLIAFKRG 314
>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 = 225 bits (576), Expect = 1e-72
Identities = 99/250 (39%), Positives = 130/250 (52%), Gaps = 25/250 (10%)
Query: 3 VGYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDGWL 62
VG +N+DV AA GI V N PG T + AE +L LA AR I +AD +RAG W
Sbjct: 71 VGVDNIDVEAATARGILVVNAPGANTISVAEHTIALMLALARNIPQADASLRAG---KWD 127
Query: 63 PNLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLY-QATRLEKFVTAYGQF 121
F+G L+G+T+G++G GRIG AR F M ++ YD Y A R
Sbjct: 128 RKKFMGVELRGKTLGIVGLGRIGREVARRAR-AFGMKVLAYDPYISAERAAAGGV----- 181
Query: 122 LKANGEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHLINKERLATMKKEAILVNCSR 181
S+DE+L EAD ISLH L T LIN E LA MK AIL+N +R
Sbjct: 182 ------------ELVSLDELLAEADFISLHTPLTPETRGLINAEELAKMKPGAILINTAR 229
Query: 182 GPVIDEVALVEHLKQNPMFRVGLDVFEDEPYMKPG--LSEMKNAIVVPHIASASKWTREG 239
G ++DE AL + LK + LDVFE EP L + N I+ PH+ ++++ +E
Sbjct: 230 GGIVDEAALADALKSGKIAGAALDVFEQEP-PPADSPLLGLPNVILTPHLGASTEEAQER 288
Query: 240 MATLAALNVL 249
+A AA VL
Sbjct: 289 VAVDAAEQVL 298
>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 = 224 bits (574), Expect = 2e-72
Identities = 98/250 (39%), Positives = 133/250 (53%), Gaps = 20/250 (8%)
Query: 1 MAVGYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDG 60
G +N+D++AA K GI V N PG E AE A L LA RR+ AD +R G
Sbjct: 70 AGAGVDNIDLDAAKKRGITVTNVPGANAEAVAEHALGLLLALLRRLPRADAAVRRGWGWL 129
Query: 61 WLPNLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQ 120
W F G L+G+TVG++G GRIG A+ + + F M ++YYD + E+
Sbjct: 130 WAG--FPGYELEGKTVGIVGLGRIGQRVAKRL-QAFGMKVLYYDRTRKPEPEED------ 180
Query: 121 FLKANGEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHLINKERLATMKKEAILVNCS 180
R S+DE+L ++DV+ LH L T HLIN+E LA MK A+LVN +
Sbjct: 181 ----------LGFRVVSLDELLAQSDVVVLHLPLTPETRHLINEEELALMKPGAVLVNTA 230
Query: 181 RGPVIDEVALVEHLKQNPMFRVGLDVFEDEPYMKPG-LSEMKNAIVVPHIASASKWTREG 239
RG ++DE AL+ LK + LDVFE EP L E+ N I+ PHIA ++ RE
Sbjct: 231 RGGLVDEDALLRALKSGKIAGAALDVFEPEPLPADHPLLELPNVILTPHIAGYTEEARER 290
Query: 240 MATLAALNVL 249
MA +A N+
Sbjct: 291 MAEIAVENLE 300
>gnl|CDD|223189 COG0111, SerA, Phosphoglycerate dehydrogenase and related
dehydrogenases [Amino acid transport and metabolism].
Length = 324
Score = 216 bits (553), Expect = 5e-69
Identities = 101/266 (37%), Positives = 139/266 (52%), Gaps = 22/266 (8%)
Query: 3 VGYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDGWL 62
G +N+D+ AA K GI V N PG + AEL +L LA ARRI +AD R G W
Sbjct: 75 AGVDNIDLEAATKRGILVVNAPGGNAISVAELVLALLLALARRIPDADASQRRG---EWD 131
Query: 63 PNLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQFL 122
F G L G+TVG+IG GRIG A A+ + + F M +I YD Y G
Sbjct: 132 RKAFRGTELAGKTVGIIGLGRIGRAVAKRL-KAFGMKVIGYDPYSPRERAGVDGVVG--- 187
Query: 123 KANGEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHLINKERLATMKKEAILVNCSRG 182
S+DE+L EAD+++LH L T LIN E LA MK AIL+N +RG
Sbjct: 188 ------------VDSLDELLAEADILTLHLPLTPETRGLINAEELAKMKPGAILINAARG 235
Query: 183 PVIDEVALVEHLKQNPMFRVGLDVFEDEPYMKPG--LSEMKNAIVVPHIASASKWTREGM 240
V+DE AL+ L + LDVFE+EP + L ++ N I+ PHI ++ +E +
Sbjct: 236 GVVDEDALLAALDSGKIAGAALDVFEEEP-LPADSPLWDLPNVILTPHIGGSTDEAQERV 294
Query: 241 ATLAALNVLGKIKGYPIWGNPNQVEP 266
A + A N++ + G P+ N +V+
Sbjct: 295 AEIVAENIVRYLAGGPVVNNAPEVDL 320
>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 = 206 bits (526), Expect = 3e-65
Identities = 92/247 (37%), Positives = 130/247 (52%), Gaps = 20/247 (8%)
Query: 3 VGYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDGWL 62
VG +N+DV A K GI V NTPG + + AEL L L+ AR I A+ M+ G W
Sbjct: 72 VGLDNIDVEYAKKKGIKVINTPGASSNSVAELVIGLMLSLARFIHRANREMKLG---KWN 128
Query: 63 PNLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQFL 122
+ G L+G+T+G+IG GRIG A++ MN+I YD Y +
Sbjct: 129 KKKYKGIELRGKTLGIIGFGRIGREVAKI-ARALGMNVIAYDPYPKDEQAVELGV----- 182
Query: 123 KANGEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHLINKERLATMKKEAILVNCSRG 182
+ S++E+L+ +D ISLH L T H+INK+ L MK AI++N SRG
Sbjct: 183 -----------KTVSLEELLKNSDFISLHVPLTPETKHMINKKELELMKDGAIIINTSRG 231
Query: 183 PVIDEVALVEHLKQNPMFRVGLDVFEDEPYMKPGLSEMKNAIVVPHIASASKWTREGMAT 242
VIDE AL+E LK + LDVFE+EP L E+ N + PHI +++K +E +
Sbjct: 232 GVIDEEALLEALKSGKLAGAALDVFENEPPPGSKLLELPNVSLTPHIGASTKEAQERIGE 291
Query: 243 LAALNVL 249
A ++
Sbjct: 292 ELANKII 298
>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 = 202 bits (515), Expect = 2e-63
Identities = 93/251 (37%), Positives = 136/251 (54%), Gaps = 17/251 (6%)
Query: 4 GYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDGWLP 63
GY+ +DV+A K GI V NTPG + E TA+ A L L A R A+ RAG + G+L
Sbjct: 86 GYDQIDVDALTKRGIQVSNTPGAVDEATADTALFLILGALRNFSRAERSARAGKWRGFLD 145
Query: 64 NLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQFLK 123
+ +G+T+G++G G IG A AR F M +IY++ + + A
Sbjct: 146 LTLAHDP-RGKTLGILGLGGIGKAIARKAA-AFGMKIIYHNRSRLPEELEKALA------ 197
Query: 124 ANGEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHLINKERLATMKKEAILVNCSRGP 183
S+DE+L ++DV+SL+ L T HLINK+ A MK I+VN +RG
Sbjct: 198 ---------TYYVSLDELLAQSDVVSLNCPLTAATRHLINKKEFAKMKDGVIIVNTARGA 248
Query: 184 VIDEVALVEHLKQNPMFRVGLDVFEDEPYMKPGLSEMKNAIVVPHIASASKWTREGMATL 243
VIDE ALV+ L+ + GLDVFE+EP + PGL +M N ++PH+ + + T+E M L
Sbjct: 249 VIDEDALVDALESGKVASAGLDVFENEPEVNPGLLKMPNVTLLPHMGTLTVETQEKMEEL 308
Query: 244 AALNVLGKIKG 254
N+ ++
Sbjct: 309 VLENIEAFLET 319
>gnl|CDD|240652 cd12175, 2-Hacid_dh_11, Putative D-isomer specific 2-hydroxyacid
dehydrogenases, NAD-binding and catalytic domains.
2-Hydroxyacid dehydrogenases catalyze the conversion of
a wide variety of D-2-hydroxy acids to their
corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 311
Score = 196 bits (500), Expect = 3e-61
Identities = 101/259 (38%), Positives = 135/259 (52%), Gaps = 23/259 (8%)
Query: 2 AVGYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDGW 61
VG + VD+ AA GI V N PG E+ AE A L LA RR+ EAD +RAG W
Sbjct: 73 GVGLDGVDLEAATARGIPVANIPGGNAESVAEHAVMLMLALLRRLPEADRELRAG---RW 129
Query: 62 -LPNLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQ 120
P L G+TVG++G G IG A AR + GF + +IYYD +
Sbjct: 130 GRPEGRPSRELSGKTVGIVGLGNIGRAVARRLR-GFGVEVIYYD---------------R 173
Query: 121 FLKANGEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHLINKERLATMKKEAILVNCS 180
F E+ R +DE+L E+DV+SLH L T HLI E LA MK AIL+N +
Sbjct: 174 FRDPEAEEKDLGVRYVELDELLAESDVVSLHVPLTPETRHLIGAEELAAMKPGAILINTA 233
Query: 181 RGPVIDEVALVEHLKQNPMFRVGLDVFEDEPYMKPG--LSEMKNAIVVPHIASASKWTRE 238
RG ++DE AL+ L+ + GLDVF EP + P L + N I+ PHIA + + +
Sbjct: 234 RGGLVDEEALLAALRSGHLAGAGLDVFWQEP-LPPDDPLLRLDNVILTPHIAGVTDESYQ 292
Query: 239 GMATLAALNVLGKIKGYPI 257
MA + A N+ ++G P
Sbjct: 293 RMAAIVAENIARLLRGEPP 311
>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 = 189 bits (482), Expect = 2e-60
Identities = 88/196 (44%), Positives = 109/196 (55%), Gaps = 24/196 (12%)
Query: 37 SLSLAAARRIVEADEFMRAGLYDGWLPNLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGF 96
+L LA ARRI EAD +RAG W P+ +G L G+TVG+IG GRIG A AR + + F
Sbjct: 2 ALLLALARRIPEADRQVRAG---RWRPDALLGRELSGKTVGIIGLGRIGRAVARRL-KAF 57
Query: 97 KMNLIYYDLYQATRLEKFVTAYGQFLKANGEQPVTWKRASSMDEVLREADVISLHPVLDK 156
M +I YD Y E Y S+DE+L E+DV+SLH L
Sbjct: 58 GMKVIAYDRYPKAEAEALGARY-----------------VSLDELLAESDVVSLHLPLTP 100
Query: 157 TTYHLINKERLATMKKEAILVNCSRGPVIDEVALVEHLKQNPMFRVGLDVFEDEPYMKPG 216
T HLIN ERLA MK AIL+N +RG ++DE AL+ LK + LDVFE EP P
Sbjct: 101 ETRHLINAERLALMKPGAILINTARGGLVDEDALIAALKSGRIAGAALDVFEPEPL-PPD 159
Query: 217 --LSEMKNAIVVPHIA 230
L E+ N I+ PHIA
Sbjct: 160 HPLLELPNVILTPHIA 175
>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 = 193 bits (492), Expect = 5e-60
Identities = 95/259 (36%), Positives = 131/259 (50%), Gaps = 24/259 (9%)
Query: 1 MAVGYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDG 60
VG +NVDV AA + GI V N P TE A+ A +L LA AR++ D +RAG +D
Sbjct: 72 YGVGVDNVDVAAATERGIPVCNVPDYCTEEVADHALALILALARKLPFLDRAVRAGGWDW 131
Query: 61 WLPNLFVGNL--LKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAY 118
+ G + L+G T+G++G GRIG A A+ + F +I YD Y
Sbjct: 132 TV----GGPIRRLRGLTLGLVGFGRIGRAVAKRA-KAFGFRVIAYDPY------------ 174
Query: 119 GQFLKANGEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHLINKERLATMKKEAILVN 178
+G + R S+DE+L +DV+SLH L T HLI+ E LA MK A LVN
Sbjct: 175 ----VPDGVAALGGVRVVSLDELLARSDVVSLHCPLTPETRHLIDAEALALMKPGAFLVN 230
Query: 179 CSRGPVIDEVALVEHLKQNPMFRVGLDVFEDEPYMKPG-LSEMKNAIVVPHIASASKWTR 237
+RG ++DE AL LK + LDV E+EP L N I+ PH A S+ +
Sbjct: 231 TARGGLVDEAALARALKSGRIAGAALDVLEEEPPPADSPLLSAPNVILTPHAAWYSEESL 290
Query: 238 EGMATLAALNVLGKIKGYP 256
+ AA V+ ++G P
Sbjct: 291 AELRRKAAEEVVRVLRGEP 309
>gnl|CDD|237436 PRK13581, PRK13581, D-3-phosphoglycerate dehydrogenase;
Provisional.
Length = 526
Score = 191 bits (488), Expect = 4e-57
Identities = 98/241 (40%), Positives = 126/241 (52%), Gaps = 33/241 (13%)
Query: 3 VGYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDGWL 62
VG +NVDV AA + GI V N P T + AE +L LA AR I +A ++AG W
Sbjct: 73 VGVDNVDVPAATRRGIIVVNAPTGNTISAAEHTIALMLALARNIPQAHASLKAGK---WE 129
Query: 63 PNLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLY----QATRLEKFVTAY 118
F+G L G+T+G+IG GRIGS A+ + F M +I YD Y +A +L
Sbjct: 130 RKKFMGVELYGKTLGIIGLGRIGSEVAKRA-KAFGMKVIAYDPYISPERAAQL------- 181
Query: 119 GQFLKANGEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHLINKERLATMKKEAILVN 178
G + V S+DE+L AD I+LH L T LI E LA MK ++N
Sbjct: 182 -------GVELV------SLDELLARADFITLHTPLTPETRGLIGAEELAKMKPGVRIIN 228
Query: 179 CSRGPVIDEVALVEHLKQNPMFRVGLDVFEDEP-YMKPGLSEMKNAIVVPHIASASKWTR 237
C+RG +IDE AL E LK + LDVFE EP P L E+ N +V PH+ AS T
Sbjct: 229 CARGGIIDEAALAEALKSGKVAGAALDVFEKEPPTDSP-LFELPNVVVTPHLG-AS--TA 284
Query: 238 E 238
E
Sbjct: 285 E 285
>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 = 185 bits (471), Expect = 8e-57
Identities = 95/258 (36%), Positives = 144/258 (55%), Gaps = 22/258 (8%)
Query: 3 VGYNNVDVNAANKYGIAVGNTPG-VLTETTAELAASLSLAAARRIVEADEFMRAGLYDGW 61
+GY+NVD+ AA ++G+ V PG V + AE A +L L R+I +A E ++ G +
Sbjct: 78 IGYDNVDLKAATEHGVIVTRVPGAVERDAVAEHAVALILTVLRKINQASEAVKEGKWT-- 135
Query: 62 LPNLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQF 121
FVG+ L G+TVG+IG G IGS A ++ EGF ++ YD Y + +
Sbjct: 136 ERANFVGHELSGKTVGIIGYGNIGSRVAEILKEGFNAKVLAYDPYVSE----------EV 185
Query: 122 LKANGEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHLINKERLATMKKEAILVNCSR 181
+K G +PV S++E+L E+D+ISLH L + TYH+IN++ + MKK ILVN +R
Sbjct: 186 IKKKGAKPV------SLEELLAESDIISLHAPLTEETYHMINEKAFSKMKKGVILVNTAR 239
Query: 182 GPVIDEVALVEHLKQNPMFRVGLDVFEDEPYMKPG--LSEMKNAIVVPHIASASKWTREG 239
G +IDE AL+E LK + GLDV E+EP +K L +N ++ PHI + + + G
Sbjct: 240 GELIDEEALIEALKSGKIAGAGLDVLEEEP-IKADHPLLHYENVVITPHIGAYTYESLYG 298
Query: 240 MATLAALNVLGKIKGYPI 257
M ++ + G
Sbjct: 299 MGEKVVDDIEDFLAGKEP 316
>gnl|CDD|240639 cd12162, 2-Hacid_dh_4, Putative D-isomer specific 2-hydroxyacid
dehydrogenases. 2-Hydroxyacid dehydrogenases catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine yydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 307
Score = 183 bits (468), Expect = 2e-56
Identities = 90/255 (35%), Positives = 132/255 (51%), Gaps = 30/255 (11%)
Query: 1 MAVGYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLY-- 58
+A GYNNVD+ AA + GI V N PG T++ A+ +L LA AR + ++ ++AG +
Sbjct: 72 LATGYNNVDLAAAKERGITVTNVPGYSTDSVAQHTFALLLALARLVAYHNDVVKAGEWQK 131
Query: 59 -DGWLPNLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRL-EKFVT 116
+ + L G+T+G+IG G IG A AR+ F M +++ + A L E +V
Sbjct: 132 SPDFCFWDYPIIELAGKTLGIIGYGNIGQAVARI-ARAFGMKVLFAERKGAPPLREGYV- 189
Query: 117 AYGQFLKANGEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHLINKERLATMKKEAIL 176
S+DE+L ++DVISLH L T +LIN E LA MK AIL
Sbjct: 190 --------------------SLDELLAQSDVISLHCPLTPETRNLINAEELAKMKPGAIL 229
Query: 177 VNCSRGPVIDEVALVEHLKQNPMFRVGLDVFEDEPYMKPG---LSEMKNAIVVPHIASAS 233
+N +RG ++DE AL + L + GLDV EP + L N I+ PHIA AS
Sbjct: 230 INTARGGLVDEQALADALNSGKIAGAGLDVLSQEP-PRADNPLLKAAPNLIITPHIAWAS 288
Query: 234 KWTREGMATLAALNV 248
+ R+ + + N+
Sbjct: 289 REARQRLMDILVDNI 303
>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 = 183 bits (467), Expect = 2e-56
Identities = 94/247 (38%), Positives = 135/247 (54%), Gaps = 24/247 (9%)
Query: 3 VGYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDGWL 62
VGY+ +D++AA GI V NTPGVLT+ A+LA L LA RRI AD F+RAG W
Sbjct: 73 VGYDGIDLDAARARGIRVTNTPGVLTDDVADLAVGLLLAVLRRIPAADRFVRAG---RWP 129
Query: 63 PNLF-VGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQF 121
F + + G+ VG++G GRIG A AR +E F M + Y+ R K
Sbjct: 130 KGAFPLTRKVSGKRVGIVGLGRIGRAIAR-RLEAFGMEIAYHG-----RRPK-------- 175
Query: 122 LKANGEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHLINKERLATMKKEAILVNCSR 181
V ++ +S+ E+ E+DV+ + T HL+N E L + + +LVN +R
Sbjct: 176 ------PDVPYRYYASLLELAAESDVLVVACPGGPATRHLVNAEVLEALGPDGVLVNVAR 229
Query: 182 GPVIDEVALVEHLKQNPMFRVGLDVFEDEPYMKPGLSEMKNAIVVPHIASASKWTREGMA 241
G V+DE AL+ L++ + GLDVFE+EP + L ++ N ++ PHIASA+ TR M
Sbjct: 230 GSVVDEAALIAALQEGRIAGAGLDVFENEPNVPAALLDLDNVVLTPHIASATVETRRAMG 289
Query: 242 TLAALNV 248
L N+
Sbjct: 290 DLVLANL 296
>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 = 180 bits (460), Expect = 3e-55
Identities = 82/269 (30%), Positives = 123/269 (45%), Gaps = 35/269 (13%)
Query: 2 AVGYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDGW 61
A GY+N+D++ A + GI V N P AE +L LA R DE +
Sbjct: 75 ATGYDNIDLDYAKELGIGVTNVPEYSPNAVAEHTIALILALLRNRKYIDERDKNQDLQ-D 133
Query: 62 LPNLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQF 121
+ G L+ QTVGV+G G+IG A A+ +GF M +I YD ++ LE Y
Sbjct: 134 AGVI--GRELEDQTVGVVGTGKIGRAVAQRA-KGFGMKVIAYDPFRNPELEDKGVKY--- 187
Query: 122 LKANGEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHLINKERLATMKKEAILVNCSR 181
S++E+ + +D+ISLH L +H+IN+E MKK I++N +R
Sbjct: 188 --------------VSLEELFKNSDIISLHVPLTPENHHMINEEAFKLMKKGVIIINTAR 233
Query: 182 GPVIDEVALVEHLKQNPMFRVGLDVFEDEPYM--------------KPGLSEMKNAIVVP 227
G ++D AL+E L +F GLDV EDE L N I+ P
Sbjct: 234 GSLVDTEALIEALDSGKIFGAGLDVLEDETPDLLKDLEGEIFKDALNALLGRRPNVIITP 293
Query: 228 HIASASKWTREGMATLAALNVLGKIKGYP 256
H A + + M ++ N++ ++G
Sbjct: 294 HTAFYTDDALKNMVEISCENIVDFLEGEE 322
>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 = 178 bits (454), Expect = 2e-54
Identities = 80/233 (34%), Positives = 120/233 (51%), Gaps = 21/233 (9%)
Query: 4 GYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDGWLP 63
G NVDV AA + GI V NTPG E AE L LA R I A ++ G +
Sbjct: 77 GPENVDVEAATERGIPVLNTPGRNAEAVAEFTVGLMLAETRNIARAHAALKDGEWRKDYY 136
Query: 64 NL-FVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQFL 122
N G L+G+TVG++G G IG A+ + + F ++ YD +V + +
Sbjct: 137 NYDGYGPELRGKTVGIVGFGAIGRRVAKRL-KAFGAEVLVYD--------PYVDP--EKI 185
Query: 123 KANGEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHLINKERLATMKKEAILVNCSRG 182
+A+G + V S++E+L+ +DV+SLH L T +I E A MK A +N +R
Sbjct: 186 EADGVKKV------SLEELLKRSDVVSLHARLTPETRGMIGAEEFALMKPTAYFINTARA 239
Query: 183 PVIDEVALVEHLKQNPMFRVGLDVFEDEPYMKPG--LSEMKNAIVVPHIASAS 233
++DE AL+E L++ + LDVF +EP + L ++ N + PHIA A+
Sbjct: 240 GLVDEDALIEALEEGKIGGAALDVFPEEP-LPADHPLLKLDNVTLTPHIAGAT 291
>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 = 178 bits (455), Expect = 3e-54
Identities = 82/242 (33%), Positives = 120/242 (49%), Gaps = 34/242 (14%)
Query: 3 VGYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDGWL 62
G + +D++ A + G+ + N P AE A + +L R E D + G + W
Sbjct: 77 AGVDMIDLDLAKENGLKITNVPAYSPRAIAEFAVTQALNLLRNTPEIDRRVAKGDFR-WA 135
Query: 63 PNLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQFL 122
P L +G ++ TVG+IG GRIGSA A++ +GF +I YD Y LEKF+ Y
Sbjct: 136 PGL-IGREIRDLTVGIIGTGRIGSAAAKIF-KGFGAKVIAYDPYPNPELEKFLLYY---- 189
Query: 123 KANGEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHLINKERLATMKKEAILVNCSRG 182
S++++L++AD+ISLH L K +HLIN E A MK AILVN +RG
Sbjct: 190 -------------DSLEDLLKQADIISLHVPLTKENHHLINAEAFAKMKDGAILVNAARG 236
Query: 183 PVIDEVALVEHLKQNPMFRVGLDVFEDE-PYMKPGLS-------------EMKNAIVVPH 228
++D AL++ L + LD +E+E Y S M N ++ PH
Sbjct: 237 GLVDTKALIDALDSGKIAGAALDTYENETGYFNKDWSGKEIEDEVLKELIAMPNVLITPH 296
Query: 229 IA 230
IA
Sbjct: 297 IA 298
>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 = 178 bits (453), Expect = 3e-54
Identities = 84/256 (32%), Positives = 120/256 (46%), Gaps = 16/256 (6%)
Query: 1 MAVGYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDG 60
VG +N+D++AA + GI V N PG TE+ AEL L LA ARRI EAD +RAG +
Sbjct: 67 RGVGVDNIDLDAATERGILVTNVPGYSTESVAELTVGLILALARRIPEADASVRAGDWKK 126
Query: 61 WLPNLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQ 120
P L G+T+GVIG G IG A + + M ++ YD Y +
Sbjct: 127 GGPIGL---ELYGKTLGVIGGGGIGGIGAAIA-KALGMGVVAYDPYPNPERAEEGGVEVL 182
Query: 121 FLKANGEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHLINKERLATMKKEAILVNCS 180
L + ++ D+I+L P T H+I E +K + N
Sbjct: 183 LLDLL------------LLDLKESDDLINLAPPTTMKTGHIIINEARGMLKDAVAINNAR 230
Query: 181 RGPVIDEVALVEHLKQNPMFRVGLDVFEDEPYMKPGLSEMKNAIVVPHIASASKWTREGM 240
G VI+E AL L++ V E+ P + L ++ N I+ PHIA A++ +E M
Sbjct: 231 GGGVIEEAALDALLEEGIAAAALDVVEEEPPPVNSPLLDLPNVILTPHIAGATEEAQENM 290
Query: 241 ATLAALNVLGKIKGYP 256
A AA N+L +KG
Sbjct: 291 AEEAAENLLAFLKGGT 306
>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 = 179 bits (457), Expect = 9e-53
Identities = 101/281 (35%), Positives = 146/281 (51%), Gaps = 37/281 (13%)
Query: 3 VGYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDGWL 62
VG +N+D+ AA GI V N P T + AE A ++ LAAAR I +AD ++ G W
Sbjct: 71 VGVDNIDIEAATARGILVVNAPTGNTISAAEHALAMLLAAARNIPQADASLKEG---EWD 127
Query: 63 PNLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLY----QATRLEKFVTAY 118
F+G L G+T+GVIG GRIGS A+ + F M ++ YD Y +A +L
Sbjct: 128 RKAFMGTELYGKTLGVIGLGRIGSIVAKR-AKAFGMKVLAYDPYISPERAEQL------- 179
Query: 119 GQFLKANGEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHLINKERLATMKKEAILVN 178
+ +DE+L AD I++H L T LI E LA MKK I+VN
Sbjct: 180 ------------GVELVDDLDELLARADFITVHTPLTPETRGLIGAEELAKMKKGVIIVN 227
Query: 179 CSRGPVIDEVALVEHLKQNPMFRVGLDVFEDEPYMKPGLSEMKNAIVVPHIASASKWTRE 238
C+RG +IDE AL E L++ + LDVFE EP L ++ N I PH+ ++++ +E
Sbjct: 228 CARGGIIDEAALYEALEEGHVRAAALDVFEKEPPTDNPLFDLDNVIATPHLGASTREAQE 287
Query: 239 GMATLAALNVLGKIKGYPIWGNPN----------QVEPFLN 269
+AT A VL +KG P+ N +++P+L+
Sbjct: 288 NVATQVAEQVLDALKGLPVPNAVNAPGIDADVMEKLKPYLD 328
>gnl|CDD|185307 PRK15409, PRK15409, bifunctional glyoxylate/hydroxypyruvate
reductase B; Provisional.
Length = 323
Score = 174 bits (443), Expect = 1e-52
Identities = 92/256 (35%), Positives = 137/256 (53%), Gaps = 19/256 (7%)
Query: 1 MAVGYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDG 60
++VGY+N DV+A I + +TP VLTET A+ +L L+ ARR+VE E ++AG +
Sbjct: 73 ISVGYDNFDVDALTARKILLMHTPTVLTETVADTLMALVLSTARRVVEVAERVKAGEWTA 132
Query: 61 WLPNLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQ 120
+ + G + +T+G++G GRIG A A+ GF M ++Y E+ A
Sbjct: 133 SIGPDWFGTDVHHKTLGIVGMGRIGMALAQRAHFGFNMPILYNARRHHKEAEERFNA--- 189
Query: 121 FLKANGEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHLINKERLATMKKEAILVNCS 180
R +D +L+E+D + + L T+HL E+ A MK AI +N
Sbjct: 190 -------------RYCDLDTLLQESDFVCIILPLTDETHHLFGAEQFAKMKSSAIFINAG 236
Query: 181 RGPVIDEVALVEHLKQNPMFRVGLDVFEDEPYMK--PGLSEMKNAIVVPHIASASKWTRE 238
RGPV+DE AL+ L++ + GLDVFE EP P LS + N + VPHI SA+ TR
Sbjct: 237 RGPVVDENALIAALQKGEIHAAGLDVFEQEPLSVDSPLLS-LPNVVAVPHIGSATHETRY 295
Query: 239 GMATLAALNVLGKIKG 254
MA A N++ ++G
Sbjct: 296 NMAACAVDNLIDALQG 311
>gnl|CDD|240638 cd12161, GDH_like_1, Putative glycerate dehydrogenase and related
proteins of the D-specific 2-hydroxy dehydrogenase
family. This group contains a variety of proteins
variously identified as glycerate dehydrogenase (GDH,
aka Hydroxypyruvate Reductase) and other enzymes of the
2-hydroxyacid dehydrogenase family. GDH catalyzes the
reversible reaction of (R)-glycerate + NAD+ to
hydroxypyruvate + NADH + H+. 2-hydroxyacid
dehydrogenases catalyze the conversion of a wide variety
of D-2-hydroxy acids to their corresponding keto acids.
The general mechanism is (R)-lactate + acceptor to
pyruvate + reduced acceptor. Formate/glycerate and
related dehydrogenases of the D-specific 2-hydroxyacid
dehydrogenase superfamily include groups such as formate
dehydrogenase, glycerate dehydrogenase, L-alanine
dehydrogenase, and S-adenosylhomocysteine hydrolase.
Despite often low sequence identity, these proteins
typically have a characteristic arrangement of 2 similar
subdomains of the alpha/beta Rossmann-fold NAD+ binding
form. The NAD+ binding domain is inserted within the
linear sequence of the mostly N-terminal catalytic
domain, which has a similar domain structure to the
internal NAD binding domain. Structurally, these domains
are connected by extended alpha helices and create a
cleft in which NAD is bound, primarily to the C-terminal
portion of the 2nd (internal) domain. Some related
proteins have similar structural subdomain but with a
tandem arrangement of the catalytic and NAD-binding
subdomains in the linear sequence. While many members of
this family are dimeric, alanine DH is hexameric and
phosphoglycerate DH is tetrameric.
Length = 315
Score = 171 bits (435), Expect = 2e-51
Identities = 93/260 (35%), Positives = 133/260 (51%), Gaps = 30/260 (11%)
Query: 3 VGYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDGWL 62
G ++VD+ A + GI V N G TE AEL L++ R IV D +RAG
Sbjct: 78 TGVDHVDLEACKERGITVSNAAGYSTEAVAELTIGLAIDLLRNIVPCDAAVRAG----GT 133
Query: 63 PNLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQFL 122
+G L G+TVG++G G IG AR+ + F ++ Y R EK +
Sbjct: 134 KAGLIGRELAGKTVGIVGTGAIGLRVARL-FKAFGCKVLAYS-----RSEK------EEA 181
Query: 123 KANGEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHLINKERLATMKKEAILVNCSRG 182
KA G + + S+DE+L E+D++SLH L+ T LI KE+LA MK+ AIL+N +RG
Sbjct: 182 KALG---IEYV---SLDELLAESDIVSLHLPLNDETKGLIGKEKLALMKESAILINTARG 235
Query: 183 PVIDEVALVEHLKQNPMFRVGLDVFEDEPYMKPG--LSEMKNAIVVPHIASASKWTREGM 240
PV+D AL + L + + G+DVF+ EP + L N I+ PH+A A T E M
Sbjct: 236 PVVDNEALADALNEGKIAGAGIDVFDMEPPLPADYPLLHAPNTILTPHVAFA---TEEAM 292
Query: 241 ATLAAL---NVLGKIKGYPI 257
A + N+ + G P
Sbjct: 293 EKRAEIVFDNIEAWLAGKPQ 312
>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 = 171 bits (435), Expect = 2e-51
Identities = 97/260 (37%), Positives = 127/260 (48%), Gaps = 26/260 (10%)
Query: 4 GYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDGWLP 63
GY+N DV A GI V P +LTE TAEL L + R I+ D F+R+G + GW P
Sbjct: 76 GYDNFDVEACTARGIWVTIVPDLLTEPTAELTIGLLIGLGRHILAGDRFVRSGKFGGWRP 135
Query: 64 NLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQFLK 123
+ G L G+TVG++G G +G A AR + GF L+YYD A Q L
Sbjct: 136 KFY-GTGLDGKTVGILGMGALGRAIARRLS-GFGATLLYYD------PHPLDQAEEQALN 187
Query: 124 ANGEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHLINKERLATMKKEAILVNCSRGP 183
R +DE+L +D + L L T HLIN E LA MK A+LVN RG
Sbjct: 188 L---------RRVELDELLESSDFLVLALPLTPDTLHLINAEALAKMKPGALLVNPCRGS 238
Query: 184 VIDEVALVEHLKQNPMFRVGLDVFEDEPYMKP--------GLSEMK-NAIVVPHIASASK 234
V+DE A+ E LK + DVFE E + +P L + + PHI SA
Sbjct: 239 VVDEAAVAEALKSGHLGGYAADVFEMEDWARPDRPRSIPQELLDQHDRTVFTPHIGSAVD 298
Query: 235 WTREGMATLAALNVLGKIKG 254
R + AALN+L ++G
Sbjct: 299 EVRLEIELEAALNILQALQG 318
>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 = 168 bits (428), Expect = 3e-50
Identities = 84/207 (40%), Positives = 113/207 (54%), Gaps = 21/207 (10%)
Query: 4 GYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDGWLP 63
G+NNVD+ AA + GI V P AE A +L LA R+I A +R G + L
Sbjct: 78 GFNNVDLKAAKELGITVVRVPAYSPYAVAEHAVALLLALNRKIHRAYNRVREGNFS--LD 135
Query: 64 NLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQFLK 123
L +G L G+TVGVIG G+IG A+AR++ GF ++ YD Y L K Y
Sbjct: 136 GL-LGFDLHGKTVGVIGTGKIGQAFARILK-GFGCRVLAYDPYPNPELAKLGVEYV---- 189
Query: 124 ANGEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHLINKERLATMKKEAILVNCSRGP 183
+DE+L E+D+ISLH L T+HLIN E +A MK +L+N SRG
Sbjct: 190 -------------DLDELLAESDIISLHCPLTPETHHLINAETIAKMKDGVMLINTSRGG 236
Query: 184 VIDEVALVEHLKQNPMFRVGLDVFEDE 210
+ID AL+E LK + +GLDV+E+E
Sbjct: 237 LIDTKALIEALKSGKIGGLGLDVYEEE 263
>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 = 166 bits (423), Expect = 2e-49
Identities = 87/255 (34%), Positives = 124/255 (48%), Gaps = 53/255 (20%)
Query: 3 VGYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADE------FMRAG 56
G++++D+ A + GIAV N P T AE A +L LA +R++ EA E F +AG
Sbjct: 72 TGFDHIDLEACRERGIAVCNVPDYGEATVAEHAFALLLALSRKLREAIERTRRGDFSQAG 131
Query: 57 LYDGWLPNLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVT 116
L G L G+T+GV+G GRIG AR+ GF M ++ YD+ E+
Sbjct: 132 L---------RGFELAGKTLGVVGTGRIGRRVARIAR-GFGMKVLAYDVVPD---EELAE 178
Query: 117 AYGQFLKANGEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHLINKERLATMKKEAIL 176
G R S++E+L+E+D+ISLH T+HLIN+E A MK A+L
Sbjct: 179 RLGF-------------RYVSLEELLQESDIISLHVPYTPQTHHLINRENFALMKPGAVL 225
Query: 177 VNCSRGPVIDEVALVEHLKQNPMFRVGLDVFEDEPYMKPG-------------------- 216
+N +RG V+D ALV LK+ + GLDV E E ++
Sbjct: 226 INTARGAVVDTEALVRALKEGKLAGAGLDVLEQEEVLREEAELFREDVSPEDLKKLLADH 285
Query: 217 -LSEMKNAIVVPHIA 230
L N I+ PH+A
Sbjct: 286 ALLRKPNVIITPHVA 300
>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 = 160 bits (407), Expect = 2e-47
Identities = 89/253 (35%), Positives = 125/253 (49%), Gaps = 23/253 (9%)
Query: 3 VGYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDGWL 62
+ ++D+ AA + GI V T G TAEL +L LA AR + E D +RAG GW
Sbjct: 78 MRNASIDLAAAKERGIVVCGTGGG-PTATAELTWALILALARNLPEEDAALRAG---GWQ 133
Query: 63 PNLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQFL 122
L G L G+T+G++G GRIG+ AR+ + F M V A+ L
Sbjct: 134 TTL--GTGLAGKTLGIVGLGRIGARVARIG-QAFGMR---------------VIAWSSNL 175
Query: 123 KANGEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHLINKERLATMKKEAILVNCSRG 182
A + A S +E+ +DV+SLH VL T L+ E LA MK A+LVN SRG
Sbjct: 176 TAERAAAAGVEAAVSKEELFATSDVVSLHLVLSDRTRGLVGAEDLALMKPTALLVNTSRG 235
Query: 183 PVIDEVALVEHLKQNPMFRVGLDVFEDEP-YMKPGLSEMKNAIVVPHIASASKWTREGMA 241
P++DE AL+ L+ + LDVF+ EP L + N ++ PHI ++ EG
Sbjct: 236 PLVDEGALLAALRAGRIAGAALDVFDVEPLPADHPLRGLPNVLLTPHIGYVTEEAYEGFY 295
Query: 242 TLAALNVLGKIKG 254
A N+ + G
Sbjct: 296 GQAVENIAAWLAG 308
>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 = 158 bits (403), Expect = 8e-47
Identities = 83/233 (35%), Positives = 115/233 (49%), Gaps = 25/233 (10%)
Query: 3 VGYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDG-- 60
G NN+DV+AA+K GI V NTPG AEL ++ LA +R I++A +++ G D
Sbjct: 59 AGVNNIDVDAASKRGIVVFNTPGANANAVAELVIAMMLALSRNIIQAIKWVTNGDGDDIS 118
Query: 61 ----WLPNLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVT 116
FVG L+G+T+GVIG G IG A M +I YD Y + ++
Sbjct: 119 KGVEKGKKQFVGTELRGKTLGVIGLGNIGRLVANA-ALALGMKVIGYDPYLSVEAAWKLS 177
Query: 117 AYGQFLKANGEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHLINKERLATMKKEAIL 176
Q R +S++E+L AD I+LH L T LIN E LA MK AIL
Sbjct: 178 VEVQ-------------RVTSLEELLATADYITLHVPLTDETRGLINAELLAKMKPGAIL 224
Query: 177 VNCSRGPVIDEVALVEHLKQNPMFRVGLDVFEDEPYMKPGLSEMKNAIVVPHI 229
+N +RG ++DE AL+E L + + D E L + N I PH+
Sbjct: 225 LNFARGEIVDEEALLEALDEGKLGGYVTDFPEPA-----LLGHLPNVIATPHL 272
>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 = 153 bits (389), Expect = 1e-44
Identities = 79/247 (31%), Positives = 116/247 (46%), Gaps = 47/247 (19%)
Query: 3 VGYNNVDVNAANKYGIAVGNTP----GVLTETTAELAASLSLAAARRIVEADEFMRAGLY 58
+GY+++D++AA + GI V N V A+ L L A R+ + RA +
Sbjct: 77 IGYDHIDLDAAKELGIKVSNVTYSPNSV-----ADYTVMLMLMALRKYKQI--MKRAEVN 129
Query: 59 DGWLPNLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAY 118
D L L G L+ TVGVIG GRIG A + + GF ++ YD Y ++K+ Y
Sbjct: 130 DYSLGGL-QGRELRNLTVGVIGTGRIGQAVIKNL-SGFGCKILAYDPYPNEEVKKYAE-Y 186
Query: 119 GQFLKANGEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHLINKERLATMKKEAILVN 178
+D + +E+D+I+LH L + TYHLINKE +A MK I++N
Sbjct: 187 -----------------VDLDTLYKESDIITLHTPLTEETYHLINKESIAKMKDGVIIIN 229
Query: 179 CSRGPVIDEVALVEHLKQNPMFRVGLDVFEDE---------------PYMKPGLSEMKNA 223
+RG +ID AL+E L+ + LDV E E + L N
Sbjct: 230 TARGELIDTEALIEGLESGKIGGAALDVIEGEDGIYYNDRKGDILSNRELAI-LRSFPNV 288
Query: 224 IVVPHIA 230
I+ PH+A
Sbjct: 289 ILTPHMA 295
>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 = 152 bits (387), Expect = 2e-44
Identities = 83/264 (31%), Positives = 123/264 (46%), Gaps = 28/264 (10%)
Query: 1 MAVGYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDG 60
+ G +++ + + G+ V N G + AE A +L LA A+RIVE D +R G++ G
Sbjct: 67 PSAGVDHLPLERLPE-GVVVANNHG-NSPAVAEHALALILALAKRIVEYDNDLRRGIWHG 124
Query: 61 WLPNLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQ 120
L+G+TVG++G G IG AR++ + F M V +
Sbjct: 125 RAGEEPESKELRGKTVGILGYGHIGREIARLL-KAFGMR---------------VIGVSR 168
Query: 121 FLKANGEQPVTWKRASSM-DEVLREADVISLHPVLDKTTYHLINKERLATMKKEAILVNC 179
K ++ + S DE L +ADV+ + L K T LI LA MK AILVN
Sbjct: 169 SPKE--DEGADFVGTLSDLDEALEQADVVVVALPLTKQTRGLIGAAELAAMKPGAILVNV 226
Query: 180 SRGPVIDEVALVEHLKQNPMFRVGLDVF----EDEPYMKP---GLSEMKNAIVVPHIASA 232
RGPV+DE AL E LK+ P+ +DV+ + P E+ N I+ PH A
Sbjct: 227 GRGPVVDEEALYEALKERPIAGAAIDVWWRYPSRGDPVAPSRYPFHELPNVIMSPHNAGW 286
Query: 233 SKWTREGMATLAALNVLGKIKGYP 256
++ T AA N+ ++G P
Sbjct: 287 TEETFRRRIDEAAENIRRYLRGEP 310
>gnl|CDD|181414 PRK08410, PRK08410, 2-hydroxyacid dehydrogenase; Provisional.
Length = 311
Score = 142 bits (361), Expect = 1e-40
Identities = 81/258 (31%), Positives = 128/258 (49%), Gaps = 34/258 (13%)
Query: 1 MAVGYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDG 60
A G NNVD+ A K GIAV N G TE+ A+ ++ L+ RI D ++++G Y
Sbjct: 70 TATGTNNVDIEYAKKKGIAVKNVAGYSTESVAQHTFAMLLSLLGRINYYDRYVKSGEYSE 129
Query: 61 WLPNLFVG-----NLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFV 115
+F +KG+ G+IG G IG A++ + F ++YY + E++
Sbjct: 130 --SPIFTHISRPLGEIKGKKWGIIGLGTIGKRVAKI-AQAFGAKVVYYSTSGKNKNEEY- 185
Query: 116 TAYGQFLKANGEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHLINKERLATMKKEAI 175
S++E+L+ +D+IS+H L++ T +LI + L +K AI
Sbjct: 186 ------------------ERVSLEELLKTSDIISIHAPLNEKTKNLIAYKELKLLKDGAI 227
Query: 176 LVNCSRGPVIDEVALVEHLKQNPMFRVGLDVFEDEPYMK--PGLSEMKNA---IVVPHIA 230
L+N RG +++E L + L + + GLDV E EP K P LS +KN ++ PHIA
Sbjct: 228 LINVGRGGIVNEKDLAKALDEKDI-YAGLDVLEKEPMEKNHPLLS-IKNKEKLLITPHIA 285
Query: 231 SASKWTREGMATLAALNV 248
ASK R+ + N+
Sbjct: 286 WASKEARKTLIEKVKENI 303
>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 = 142 bits (360), Expect = 3e-40
Identities = 73/231 (31%), Positives = 108/231 (46%), Gaps = 24/231 (10%)
Query: 17 GIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDGWLPNLFVGNLLKGQTV 76
GI V + E AE + L A RRI RAG D P G L G+TV
Sbjct: 95 GILVTSAADANAEPVAEFTLAAILLALRRIPRFAAAYRAG-RDWGWPTRRGGRGLYGRTV 153
Query: 77 GVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQFLKANGEQPVTWKRAS 136
G++G GRIG A + + F + ++ YD ++ A A G
Sbjct: 154 GIVGFGRIGRAVVEL-LRPFGLRVLVYD--------PYLPA--AEAAALGV------ELV 196
Query: 137 SMDEVLREADVISLH-PVLDKTTYHLINKERLATMKKEAILVNCSRGPVIDEVALVEHLK 195
S+DE+L +DV+SLH P+ +T +I+ LA M+ A +N +RG ++DE AL+ L+
Sbjct: 197 SLDELLARSDVVSLHAPLTPETR-GMIDARLLALMRDGATFINTARGALVDEAALLAELR 255
Query: 196 QNPMFRVGLDVFEDEPYMKPG--LSEMKNAIVVPHIASASKWTREGMATLA 244
R LDV + EP + P L + N ++ PHIA ++ R + A
Sbjct: 256 SG-RLRAALDVTDPEP-LPPDSPLRTLPNVLLTPHIAGSTGDERRRLGDYA 304
>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 = 138 bits (350), Expect = 5e-39
Identities = 79/233 (33%), Positives = 119/233 (51%), Gaps = 29/233 (12%)
Query: 3 VGYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDGWL 62
+G N VD++AA K GI V N P T + AEL + ARR+ + + G W
Sbjct: 73 IGTNQVDLDAAAKRGIPVFNAPFSNTRSVAELVIGEIIMLARRLPDRNAAAHRG---IWN 129
Query: 63 PNLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQFL 122
+ + ++G+T+G+IG G IGS + + E M +I+YD+ A +L G
Sbjct: 130 KSATGSHEVRGKTLGIIGYGHIGSQLSVL-AEALGMRVIFYDI--AEKL-----PLG--- 178
Query: 123 KANGEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHLINKERLATMKKEAILVNCSRG 182
++ SS++E+L EAD ++LH +T ++I E +A MKK AIL+N SRG
Sbjct: 179 --------NARQVSSLEELLAEADFVTLHVPATPSTKNMIGAEEIAQMKKGAILINASRG 230
Query: 183 PVIDEVALVEHLKQNPMFRVGLDVF------EDEPYMKPGLSEMKNAIVVPHI 229
V+D AL E L+ + +DVF EP+ P L + N I+ PHI
Sbjct: 231 TVVDIDALAEALRSGHLAGAAVDVFPEEPASNGEPFSSP-LQGLPNVILTPHI 282
>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 = 135 bits (342), Expect = 2e-37
Identities = 74/232 (31%), Positives = 112/232 (48%), Gaps = 48/232 (20%)
Query: 4 GYNNVDVNAANKYGIAVGNTPGVLTETTAE-LAASLSLAAARRIVEADEFMRAGLYDGWL 62
G +++D + + GI N PG + AE + ++L + A R+
Sbjct: 67 GTDHIDTDYLKERGIGFANAPGCNANSVAEYVLSALLVLAQRQ----------------- 109
Query: 63 PNLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQFL 122
G LKG+TVG++G G +GS AR +E MN++ D +A
Sbjct: 110 -----GFSLKGKTVGIVGVGNVGSRLARR-LEALGMNVLLCDPPRAEAEGDPGFV----- 158
Query: 123 KANGEQPVTWKRASSMDEVLREADVISLHPVLDKT----TYHLINKERLATMKKEAILVN 178
S++E+L EAD+I+LH L + TYHL++++ LA +K IL+N
Sbjct: 159 --------------SLEELLAEADIITLHVPLTRDGEHPTYHLLDEDFLAALKPGQILIN 204
Query: 179 CSRGPVIDEVALVEHLKQNPMFRVGLDVFEDEPYMKPGLSEMKNAIVVPHIA 230
SRG VID AL+ L++ RV LDV+E+EP + L + K I PHIA
Sbjct: 205 ASRGAVIDNQALLALLQRGKDLRVVLDVWENEPEIDLELLD-KVDIATPHIA 255
>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 = 127 bits (321), Expect = 1e-34
Identities = 66/211 (31%), Positives = 105/211 (49%), Gaps = 26/211 (12%)
Query: 3 VGYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLY--DG 60
VG+N++D+ AA + G + P AELA +L++ +R + D
Sbjct: 77 VGFNHIDLEAAKELGFKMARVPSYSPNAIAELAFTLAMTLSRHTAYTASRTANKNFKVD- 135
Query: 61 WLPNLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQ 120
P +F ++ TVG+IG GRIG A++ +G +I YD+Y + + VT
Sbjct: 136 --PFMF-SKEIRNSTVGIIGTGRIGLTAAKLF-KGLGAKVIGYDIYPSDAAKDVVTFV-- 189
Query: 121 FLKANGEQPVTWKRASSMDEVLREADVISLH-PVLDKTTYHLINKERLATMKKEAILVNC 179
S+DE+L+++D+ISLH P + LINKE ++ MK AIL+N
Sbjct: 190 ----------------SLDELLKKSDIISLHVPYIKGKNDKLINKEFISKMKDGAILINT 233
Query: 180 SRGPVIDEVALVEHLKQNPMFRVGLDVFEDE 210
+RG + DE A++E L+ + G DV +E
Sbjct: 234 ARGELQDEEAILEALESGKLAGFGTDVLNNE 264
>gnl|CDD|236985 PRK11790, PRK11790, D-3-phosphoglycerate dehydrogenase;
Provisional.
Length = 409
Score = 122 bits (310), Expect = 2e-32
Identities = 76/233 (32%), Positives = 115/233 (49%), Gaps = 29/233 (12%)
Query: 3 VGYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDGWL 62
+G N VD++AA K GI V N P T + AEL + R I E + G GW
Sbjct: 84 IGTNQVDLDAAAKRGIPVFNAPFSNTRSVAELVIGEIILLLRGIPEKNAKAHRG---GWN 140
Query: 63 PNLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQFL 122
+ ++G+T+G++G G IG+ + ++ E M + +YD+ +L G
Sbjct: 141 KSAAGSFEVRGKTLGIVGYGHIGTQLS-VLAESLGMRVYFYDI--EDKL-----PLG--- 189
Query: 123 KANGEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHLINKERLATMKKEAILVNCSRG 182
N Q S++E+L ++DV+SLH +T ++I E LA MK AIL+N SRG
Sbjct: 190 --NARQ------VGSLEELLAQSDVVSLHVPETPSTKNMIGAEELALMKPGAILINASRG 241
Query: 183 PVIDEVALVEHLKQNPMFRVGLDVF------EDEPYMKPGLSEMKNAIVVPHI 229
V+D AL + LK + +DVF +P+ P L + N I+ PHI
Sbjct: 242 TVVDIDALADALKSGHLAGAAIDVFPVEPKSNGDPFESP-LRGLDNVILTPHI 293
>gnl|CDD|180588 PRK06487, PRK06487, glycerate dehydrogenase; Provisional.
Length = 317
Score = 121 bits (305), Expect = 2e-32
Identities = 83/268 (30%), Positives = 124/268 (46%), Gaps = 40/268 (14%)
Query: 2 AVGYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDGW 61
A G NNVD+ AA + GI V N G T + A+ +L LA A R+ + + + AG W
Sbjct: 74 ATGTNNVDLAAARERGITVCNCQGYGTPSVAQHTLALLLALATRLPDYQQAVAAG---RW 130
Query: 62 -------LPNLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKF 114
L + F L+G+T+G++G G +G A AR+ E F M ++
Sbjct: 131 QQSSQFCLLD-FPIVELEGKTLGLLGHGELGGAVARL-AEAFGMRVLI------------ 176
Query: 115 VTAYGQFLKANGEQPVTWKRASSM--DEVLREADVISLHPVLDKTTYHLINKERLATMKK 172
G+ P R + DE+L + D ++LH L + T HLI LA MK
Sbjct: 177 -----------GQLPGRPARPDRLPLDELLPQVDALTLHCPLTEHTRHLIGARELALMKP 225
Query: 173 EAILVNCSRGPVIDEVALVEHLKQNPMFRVGLDVFEDEPYMK--PGLSE-MKNAIVVPHI 229
A+L+N +RG ++DE AL + L+ + DV EP + P L+ + IV PH
Sbjct: 226 GALLINTARGGLVDEQALADALRSGHLGGAATDVLSVEPPVNGNPLLAPDIPRLIVTPHS 285
Query: 230 ASASKWTREGMATLAALNVLGKIKGYPI 257
A S+ R+ + A N G P+
Sbjct: 286 AWGSREARQRIVGQLAENARAFFAGKPL 313
>gnl|CDD|235890 PRK06932, PRK06932, glycerate dehydrogenase; Provisional.
Length = 314
Score = 120 bits (302), Expect = 6e-32
Identities = 75/246 (30%), Positives = 113/246 (45%), Gaps = 41/246 (16%)
Query: 2 AVGYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDGW 61
A G NNVD+ AA + GIAV N G + T E + A ++ + R L D W
Sbjct: 73 ATGTNNVDLVAAKELGIAVKNVTGYSSTTVPEHVLGMIFALKHSLMG---WYRDQLSDRW 129
Query: 62 LPNLFVGNL---------LKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLE 112
++G T+GV G G +G+ R+ + M ++Y + A+
Sbjct: 130 ATC---KQFCYFDYPITDVRGSTLGVFGKGCLGTEVGRL-AQALGMKVLYAEHKGASVCR 185
Query: 113 KFVTAYGQFLKANGEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHLINKERLATMKK 172
+ T + +EVL++AD+++LH L +TT +LIN E LA MK
Sbjct: 186 EGYTPF--------------------EEVLKQADIVTLHCPLTETTQNLINAETLALMKP 225
Query: 173 EAILVNCSRGPVIDEVALVEHLKQNPMFRVGLDVFEDEPYMKP-----GLSEMKNAIVVP 227
A L+N RGP++DE AL++ L+ + LDV EP K + N ++ P
Sbjct: 226 TAFLINTGRGPLVDEQALLDALENGKIAGAALDVLVKEPPEKDNPLIQAAKRLPNLLITP 285
Query: 228 HIASAS 233
HIA AS
Sbjct: 286 HIAWAS 291
>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 = 117 bits (294), Expect = 8e-31
Identities = 76/245 (31%), Positives = 115/245 (46%), Gaps = 36/245 (14%)
Query: 4 GYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDGWLP 63
G N+D+ A + GI + N P + E A + LA ++ AD+ +R G+ W
Sbjct: 72 GLENIDLEYAKEKGIELFNAPEGNRDAVGEHALGMLLALFNKLNRADQEVRNGI---WDR 128
Query: 64 NLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQFLK 123
G L G+TVG+IG G +G A+A+ + GF +I YD Y+ F
Sbjct: 129 EGNRGVELMGKTVGIIGYGNMGKAFAKRL-SGFGCKVIAYDKYK------------NFGD 175
Query: 124 ANGEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHLINKERLATMKKEAILVNCSRGP 183
A EQ S++ + +EAD++SLH L T ++NKE +++ KK +N +RG
Sbjct: 176 AYAEQ-------VSLETLFKEADILSLHIPLTPETRGMVNKEFISSFKKPFYFINTARGK 228
Query: 184 VIDEVALVEHLKQNPMFRVGLDVFEDE------PYMKPG----LSEMKNAIVVPHIASAS 233
V+ LV+ LK + LDV E E + +P L + I+ PHIA
Sbjct: 229 VVVTKDLVKALKSGKILGACLDVLEYEKASFESIFNQPEAFEYLIKSPKVILTPHIAG-- 286
Query: 234 KWTRE 238
WT E
Sbjct: 287 -WTFE 290
>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 = 115 bits (291), Expect = 2e-30
Identities = 71/258 (27%), Positives = 104/258 (40%), Gaps = 39/258 (15%)
Query: 1 MAVGYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDG 60
+ G + + + + + N G+ AE LA AR++
Sbjct: 66 TSAGVDALLFPELLERDVVLTNARGIFGPPIAEYVLGYMLAFARKLPRYARNQAERR--- 122
Query: 61 WLPNLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAY-- 118
W V L G+TV ++G G IG AR + F M V
Sbjct: 123 WQRRGPVR-ELAGKTVLIVGLGDIGREIARRA-KAFGMR---------------VIGVRR 165
Query: 119 -GQFLKANGEQPVTWKRASSMDEVLREAD-VISLHPVLDKTTYHLINKERLATMKKEAIL 176
G+ ++ T +DE+L EAD V++ P L T L N ER A MK A+L
Sbjct: 166 SGRPAPPVVDEVYT---PDELDELLPEADYVVNALP-LTPETRGLFNAERFAAMKPGAVL 221
Query: 177 VNCSRGPVIDEVALVEHLKQNPMFRVGLDVFEDEPYMKPGLSE------MKNAIVVPHIA 230
+N RG V+DE AL+E L+ + LDVFE+EP L + N I+ PHI+
Sbjct: 222 INVGRGSVVDEDALIEALESGRIAGAALDVFEEEP-----LPADSPLWDLPNVIITPHIS 276
Query: 231 SASKWTREGMATLAALNV 248
S E + + N+
Sbjct: 277 GDSPSYPERVVEIFLENL 294
>gnl|CDD|181499 PRK08605, PRK08605, D-lactate dehydrogenase; Validated.
Length = 332
Score = 110 bits (277), Expect = 3e-28
Identities = 61/242 (25%), Positives = 108/242 (44%), Gaps = 35/242 (14%)
Query: 4 GYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYD-GWL 62
G++ D+ A KY + + N P E+ AE + ++ R + +R +D W
Sbjct: 79 GFDTYDLELATKYNLIISNVPSYSPESIAEFTVTQAINLVRHFNQIQTKVR--EHDFRWE 136
Query: 63 PNLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQFL 122
P + + +K V VIG GRIG A A++ +G+ +++ YD + + +V
Sbjct: 137 PPI-LSRSIKDLKVAVIGTGRIGLAVAKIFAKGYGSDVVAYDPFPNAKAATYVD------ 189
Query: 123 KANGEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHLINKERLATMKKEAILVNCSRG 182
+++E + AD+++LH K ++L N + KK A+ VNC+RG
Sbjct: 190 -----------YKDTIEEAVEGADIVTLHMPATKYNHYLFNADLFKHFKKGAVFVNCARG 238
Query: 183 PVIDEVALVEHLKQNPMFRVGLDVFEDEPYMKPG--------------LSEMKNAIVVPH 228
++D AL++ L + LD +E E + P L ++ I+ PH
Sbjct: 239 SLVDTKALLDALDNGLIKGAALDTYEFERPLFPSDQRGQTINDPLLESLINREDVILTPH 298
Query: 229 IA 230
IA
Sbjct: 299 IA 300
>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 = 107 bits (270), Expect = 2e-27
Identities = 74/230 (32%), Positives = 105/230 (45%), Gaps = 26/230 (11%)
Query: 22 NTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDGWLPNLFVGNLLKGQTVGVIGA 81
N G ET AE A +L LA R++ RA +D + LL+G TV ++GA
Sbjct: 78 NAAGAYAETVAEHALALLLAGLRQLPA---RARATTWDPAEE-DDLVTLLRGSTVAIVGA 133
Query: 82 GRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQFLKANGEQPVTWKRASSMDEV 141
G IG A ++ F +I V G+ G A +DEV
Sbjct: 134 GGIGRALIPLLA-PFGAKVIA------------VNRSGR--PVEGADETV--PADRLDEV 176
Query: 142 LREADVISLHPVLDKTTYHLINKERLATMKKEAILVNCSRGPVIDEVALVEHLKQNPMFR 201
+AD + L L T HL++ LA MK A LVN +RGP++D ALV+ L+ +
Sbjct: 177 WPDADHVVLAAPLTPETRHLVDAAALAAMKPHAWLVNVARGPLVDTDALVDALRSGEIAG 236
Query: 202 VGLDVFEDEPYMKPG---LSEMKNAIVVPHIASASKWTREGMATLAALNV 248
LDV + EP P L + NA++ PH+A+ + R +A A NV
Sbjct: 237 AALDVTDPEPL--PDGHPLWSLPNALITPHVANTPEVIRPLLAERVAENV 284
>gnl|CDD|183550 PRK12480, PRK12480, D-lactate dehydrogenase; Provisional.
Length = 330
Score = 105 bits (264), Expect = 2e-26
Identities = 73/241 (30%), Positives = 116/241 (48%), Gaps = 35/241 (14%)
Query: 4 GYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDGWLP 63
G++ D++ A K+ I + N P ET AE + S++L RR + + ++A +
Sbjct: 79 GFDMYDLDLAKKHNIVISNVPSYSPETIAEYSVSIALQLVRRFPDIERRVQAHDFTWQAE 138
Query: 64 NLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQFLK 123
+ +K TV +IG GRIG+A A++ GF + YD Y L+ FL
Sbjct: 139 --IMSKPVKNMTVAIIGTGRIGAATAKIYA-GFGATITAYDAYPNKDLD--------FL- 186
Query: 124 ANGEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHLINKERLATMKKEAILVNCSRGP 183
T+K S+ E +++AD+ISLH +K +YHL +K +KK AILVN +RG
Sbjct: 187 -------TYK--DSVKEAIKDADIISLHVPANKESYHLFDKAMFDHVKKGAILVNAARGA 237
Query: 184 VIDEVALVEHLKQNPMFRVGLDVFEDE-PYM----------KPGLSEM---KNAIVVPHI 229
VI+ L+ + + +D +E+E Y L E+ + +V PHI
Sbjct: 238 VINTPDLIAAVNDGTLLGAAIDTYENEAAYFTNDWTNKDIDDKTLLELIEHERILVTPHI 297
Query: 230 A 230
A
Sbjct: 298 A 298
>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 = 104 bits (263), Expect = 2e-26
Identities = 67/242 (27%), Positives = 110/242 (45%), Gaps = 46/242 (19%)
Query: 1 MAVGYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDG 60
+ G + + + K GI + N G+ + AE L + + +A + +
Sbjct: 67 YSAGVDYLPLEYIKKKGILLTNNSGIHSIPIAEWIVGYILEIYKGLKKAYKNQKEKK--- 123
Query: 61 WLPNLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLI----------YYDLYQATR 110
W + + L G+T+ +G G IG A+ + + F M +I Y+D
Sbjct: 124 WKMDSSLLEL-YGKTILFLGTGSIGQEIAKRL-KAFGMKVIGVNTSGRDVEYFD------ 175
Query: 111 LEKFVTAYGQFLKANGEQPVTWKRASSMDEVLREAD-VISLHPVLDKTTYHLINKERLAT 169
+ + E +DEVL+EAD V+++ P L + T+HL ++
Sbjct: 176 -KCY---------PLEE----------LDEVLKEADIVVNVLP-LTEETHHLFDEAFFEQ 214
Query: 170 MKKEAILVNCSRGPVIDEVALVEHLKQNPMFRVGLDVFEDEPYMK--PGLSEMKNAIVVP 227
MKK A+ +N RGP +DE AL+E LK + LDVFE+EP K P L ++ N ++ P
Sbjct: 215 MKKGALFINVGRGPSVDEDALIEALKNKQIRGAALDVFEEEPLPKDSP-LWDLDNVLITP 273
Query: 228 HI 229
HI
Sbjct: 274 HI 275
>gnl|CDD|166874 PRK00257, PRK00257, erythronate-4-phosphate dehydrogenase;
Validated.
Length = 381
Score = 105 bits (265), Expect = 3e-26
Identities = 54/167 (32%), Positives = 78/167 (46%), Gaps = 25/167 (14%)
Query: 71 LKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQFLKANGEQPV 130
L +T GV+GAG +G R++ G ++ D + G F+
Sbjct: 114 LAERTYGVVGAGHVGGRLVRVL-RGLGWKVLVCDPPRQEAEGD-----GDFV-------- 159
Query: 131 TWKRASSMDEVLREADVISLHPVLDKT----TYHLINKERLATMKKEAILVNCSRGPVID 186
S++ +L E DVISLH L K T HL+++ LA+++ A L+N SRG V+D
Sbjct: 160 ------SLERILEECDVISLHTPLTKEGEHPTRHLLDEAFLASLRPGAWLINASRGAVVD 213
Query: 187 EVALVEHLKQNPMFRVGLDVFEDEPYMKPGLSEMKNAIVVPHIASAS 233
AL E L LDV+E EP + L++ I PHIA S
Sbjct: 214 NQALREALLSGEDLDAVLDVWEGEPQIDLELAD-LCTIATPHIAGYS 259
>gnl|CDD|215501 PLN02928, PLN02928, oxidoreductase family protein.
Length = 347
Score = 103 bits (258), Expect = 2e-25
Identities = 70/236 (29%), Positives = 110/236 (46%), Gaps = 21/236 (8%)
Query: 3 VGYNNVDVNAANKYGIAVGNTPGVLT---ETTAELAASLSLAAARRIVEADEFMRAGLYD 59
VG VDV+AA K+GI V P T + AE+A L L R+ E ++A
Sbjct: 91 VGLEGVDVDAATKHGIKVARIPSEGTGNAASCAEMAIYLMLGLLRKQNEMQISLKARRLG 150
Query: 60 GWLPNLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATR---LEKFVT 116
P +G+ L G+TV ++G G IG A+ + F + L+ ATR +
Sbjct: 151 E--P---IGDTLFGKTVFILGYGAIGIELAKRL-RPFGVKLL------ATRRSWTSEPED 198
Query: 117 AYGQFLKANGEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHLINKERLATMKKEAIL 176
+ + E EAD++ L L K T ++N E L++MKK A+L
Sbjct: 199 GLLIPNGDVDDLVDEKGGHEDIYEFAGEADIVVLCCTLTKETAGIVNDEFLSSMKKGALL 258
Query: 177 VNCSRGPVIDEVALVEHLKQNPMFRVGLDVFEDEPYMKPG--LSEMKNAIVVPHIA 230
VN +RG ++D A++ L+ + + +DV EP+ P + + N I+ PH+A
Sbjct: 259 VNIARGGLLDYDAVLAALESGHLGGLAIDVAWSEPF-DPDDPILKHPNVIITPHVA 313
>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 = 100 bits (251), Expect = 2e-24
Identities = 72/235 (30%), Positives = 112/235 (47%), Gaps = 23/235 (9%)
Query: 3 VGYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDGWL 62
+G ++VD+ AAN GI V G + AE + L R V E G GW
Sbjct: 93 IGSDHVDLQAANDRGITVAEVTGSNVVSVAEHVVMMILILVRNYVPGHEQAIEG---GWN 149
Query: 63 PNLFVGNL--LKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQ 120
V L+G+TVG +GAGRIG R + + F ++L+YYD ++
Sbjct: 150 VADVVKRAYDLEGKTVGTVGAGRIGLRVLRRL-KPFDVHLLYYDRHR------------- 195
Query: 121 FLKANGEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHLINKERLATMKKEAILVNCS 180
L E+ + R + +++++ + DV++++ L T L NKE L+ MKK A LVN +
Sbjct: 196 -LPEEVEKELGLTRHADLEDMVSKCDVVTINCPLHPETEGLFNKELLSKMKKGAYLVNTA 254
Query: 181 RGPVIDEVALVEHLKQNPMFRVGLDVFEDEPYMK--PGLSEMKNAIVVPHIASAS 233
RG + D A+ E L+ + DV+ +P K P M N + PHI+ +
Sbjct: 255 RGKICDREAVAEALESGHLAGYAGDVWFPQPAPKDHP-WRTMPNNAMTPHISGTT 308
>gnl|CDD|181041 PRK07574, PRK07574, formate dehydrogenase; Provisional.
Length = 385
Score = 99.0 bits (247), Expect = 1e-23
Identities = 67/241 (27%), Positives = 110/241 (45%), Gaps = 35/241 (14%)
Query: 3 VGYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDGWL 62
+G ++VD+ AA+++GI V G + + AE + LA R + G GW
Sbjct: 123 IGSDHVDLQAASEHGITVAEVTGSNSISVAEHVVMMILALVRNYEPSHRQAVEG---GW- 178
Query: 63 PNLF-VGNL---LKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAY 118
N+ + L+G TVG++GAGRIG A R + + F + L Y D ++
Sbjct: 179 -NIADCVSRSYDLEGMTVGIVGAGRIGLAVLRRL-KPFDVKLHYTDRHR----------- 225
Query: 119 GQFLKANGEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHLINKERLATMKKEAILVN 178
L EQ + S D ++ DV+++H L T HL + + L+ MK+ + LVN
Sbjct: 226 ---LPEEVEQELGLTYHVSFDSLVSVCDVVTIHCPLHPETEHLFDADVLSRMKRGSYLVN 282
Query: 179 CSRGPVIDEVALVEHLKQNPMFRVGLDVF------EDEPYMKPGLSEMKNAIVVPHIASA 232
+RG ++D A+V L+ + DV+ D P+ M + PHI+
Sbjct: 283 TARGKIVDRDAVVRALESGHLAGYAGDVWFPQPAPADHPWRT-----MPRNGMTPHISGT 337
Query: 233 S 233
+
Sbjct: 338 T 338
>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 = 93.4 bits (233), Expect = 4e-22
Identities = 70/235 (29%), Positives = 99/235 (42%), Gaps = 37/235 (15%)
Query: 17 GIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDG-WLPNLFVGNLLKGQT 75
G+ + N GV +TAELA +L LA+ R + G ++ P+L +
Sbjct: 81 GVTLCNARGVHDASTAELAVALILASLRGLPRFVRAQARGRWEPRRTPSL------ADRR 134
Query: 76 VGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKF---VTAYGQFLKANGEQPVTW 132
V ++G G IG A R RL F VT + + GEQ
Sbjct: 135 VLIVGYGSIGRAIER-------------------RLAPFEVRVTRVARTARP-GEQVHGI 174
Query: 133 KRASSMDEVLREADVISLHPVLDKTTYHLINKERLATMKKEAILVNCSRGPVIDEVALVE 192
+ +L EADV+ L L T L++ E LA M A+LVN +RGPV+D ALV
Sbjct: 175 ---DELPALLPEADVVVLIVPLTDETRGLVDAEFLARMPDGALLVNVARGPVVDTDALVA 231
Query: 193 HLKQNPMFRVGLDVFEDEPYMKPG--LSEMKNAIVVPHIASASKWTREGMATLAA 245
L + R LDV + EP + PG L ++ PH+ A+ L
Sbjct: 232 ELASGRL-RAALDVTDPEP-LPPGHPLWSAPGVLITPHVGGATPAFLPRAYALVR 284
>gnl|CDD|235800 PRK06436, PRK06436, glycerate dehydrogenase; Provisional.
Length = 303
Score = 81.9 bits (202), Expect = 5e-18
Identities = 58/257 (22%), Positives = 119/257 (46%), Gaps = 29/257 (11%)
Query: 1 MAVGYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDG 60
++ G +++DV+ + + + + G + + AE A +L LA A+ I E + M+ G +
Sbjct: 56 LSAGVDHIDVSGIPE-NVVLCSNAGAYSISVAEHAFALLLAWAKNICENNYNMKNGNFKQ 114
Query: 61 WLPNLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQ 120
P LL +++G++G G IG A ++ + F MN+ Y TR +
Sbjct: 115 -SPT----KLLYNKSLGILGYGGIGRRVA-LLAKAFGMNIYAY-----TR-----SYVND 158
Query: 121 FLKANGEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHLINKERLATMKKEAILVNCS 180
+ + +P +++++++D + + L T +IN + L+ +K ++N +
Sbjct: 159 GISSIYMEP---------EDIMKKSDFVLISLPLTDETRGMINSKMLSLFRKGLAIINVA 209
Query: 181 RGPVIDEVALVEHLKQNPMFRVGLDVFEDEPYMKPGLSEMKNAIVVPHIASA-SKWTREG 239
R V+D+ ++ L+ + DV+ +EP + + N I+ PH+A S +
Sbjct: 210 RADVVDKNDMLNFLRNHNDKYYLSDVWWNEPIITE--TNPDNVILSPHVAGGMSGEIMQP 267
Query: 240 MATLAALNVLGKIKGYP 256
LA N+ +G P
Sbjct: 268 AVALAFENIKNFFEGKP 284
>gnl|CDD|178684 PLN03139, PLN03139, formate dehydrogenase; Provisional.
Length = 386
Score = 79.9 bits (197), Expect = 6e-17
Identities = 70/241 (29%), Positives = 109/241 (45%), Gaps = 41/241 (17%)
Query: 3 VGYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRI------VEADEFMRAG 56
+G +++D+ AA G+ V G + AE L R V + E+ AG
Sbjct: 130 IGSDHIDLPAAAAAGLTVAEVTGSNVVSVAEDELMRILILLRNFLPGYHQVVSGEWNVAG 189
Query: 57 L----YDGWLPNLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYD-LYQATRL 111
+ YD L+G+TVG +GAGRIG + + + F NL+Y+D L L
Sbjct: 190 IAYRAYD-----------LEGKTVGTVGAGRIGRLLLQRL-KPFNCNLLYHDRLKMDPEL 237
Query: 112 EKFVTAYGQFLKANGEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHLINKERLATMK 171
EK A K +D +L + DV+ ++ L + T + NKER+A MK
Sbjct: 238 EKETGA---------------KFEEDLDAMLPKCDVVVINTPLTEKTRGMFNKERIAKMK 282
Query: 172 KEAILVNCSRGPVIDEVALVEHLKQNPMFRVGLDVFEDEPYMK--PGLSEMKNAIVVPHI 229
K ++VN +RG ++D A+ + + G DV+ +P K P M N + PHI
Sbjct: 283 KGVLIVNNARGAIMDTQAVADACSSGHIGGYGGDVWYPQPAPKDHPWRY-MPNHAMTPHI 341
Query: 230 A 230
+
Sbjct: 342 S 342
>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 = 74.1 bits (183), Expect = 3e-15
Identities = 55/215 (25%), Positives = 85/215 (39%), Gaps = 37/215 (17%)
Query: 27 LTETTAELAASLSLAAARRIVEADEFMRAGLYDGWLPNLFVGNLLKGQTVGVIGAGRIGS 86
L + AE + L R + R G+ W P + VGV+G G +G+
Sbjct: 91 LAQGMAEYVLAAVLRLHRDMDRYAAQQRRGV---WKPLPQR--PAAERRVGVLGLGELGA 145
Query: 87 AYARMMVE-GFKMNLIYYDLYQATRLEKFVTAYGQFLKANGEQPVTWKRASSMDEVLREA 145
A AR + GF V+ + + K + E + +D L +
Sbjct: 146 AVARRLAALGFP-----------------VSGWSRSPK-DIEGVTCFHGEEGLDAFLAQT 187
Query: 146 DV-ISLHPVLDKTTYHLINKERLATMKKEAILVNCSRGPVIDEVALVEHLKQNPMFRVGL 204
D+ + L P+ +T ++N E LA + + A L+N RGP + E L+ L + L
Sbjct: 188 DILVCLLPLTPETR-GILNAELLARLPRGAALINVGRGPHLVEADLLAALDSGHLSGAVL 246
Query: 205 DVFEDEPYMKPGLSE------MKNAIVVPHIASAS 233
DVFE EP L V PHIA+ +
Sbjct: 247 DVFEQEP-----LPADHPLWRHPRVTVTPHIAAIT 276
>gnl|CDD|185335 PRK15438, PRK15438, erythronate-4-phosphate dehydrogenase PdxB;
Provisional.
Length = 378
Score = 74.6 bits (183), Expect = 4e-15
Identities = 56/178 (31%), Positives = 87/178 (48%), Gaps = 28/178 (15%)
Query: 68 GNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQFLKANGE 127
G L +TVG++G G +G + E + + D +A R ++ G F
Sbjct: 111 GFSLHDRTVGIVGVGNVGRRLQARL-EALGIKTLLCDPPRADRGDE-----GDF------ 158
Query: 128 QPVTWKRASSMDEVLREADVISLHPVLDK----TTYHLINKERLATMKKEAILVNCSRGP 183
S+DE+++EAD+++ H L K T HL +++ + ++K AIL+N RG
Sbjct: 159 --------RSLDELVQEADILTFHTPLFKDGPYKTLHLADEKLIRSLKPGAILINACRGA 210
Query: 184 VIDEVALVEHLKQNPMFRVGLDVFEDEPYMKPGLSEMKNAIVVPHIASASKWTREGMA 241
V+D AL+ L + V LDV+E EP + L + K I PHIA +T EG A
Sbjct: 211 VVDNTALLTCLNEGQKLSVVLDVWEGEPELNVELLK-KVDIGTPHIAG---YTLEGKA 264
>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 = 70.1 bits (172), Expect = 7e-14
Identities = 66/213 (30%), Positives = 89/213 (41%), Gaps = 35/213 (16%)
Query: 30 TTAELAASLSLAAARRIVEADEFMRAGLYDGWL-------PNLFVGNLLKGQTVGVIGAG 82
T AE +L LAA RR+ E E R + G L P + LL G V + G G
Sbjct: 94 TVAEHTLALILAAVRRLDEMREAQREHRWAGELGGLQPLRPAGRLTTLL-GARVLIWGFG 152
Query: 83 RIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQFLKANGEQ---PVTWKRASSMD 139
IG A ++ T L VT + + GE+ PV +
Sbjct: 153 SIGQRLAPLL----------------TALGARVTGVAR---SAGERAGFPVV--AEDELP 191
Query: 140 EVLREADV-ISLHPVLDKTTYHLINKERLATMKKEAILVNCSRGPVIDEVALVEHLKQNP 198
E+L E DV + + P T H ++ E LA + K A +VN RG +DE ALV L+
Sbjct: 192 ELLPETDVLVMILPATPSTA-HALDAEVLAALPKHAWVVNVGRGATVDEDALVAALESGR 250
Query: 199 MFRVGLDVFEDEPYMKPG-LSEMKNAIVVPHIA 230
+ LDV EP L + N I+ PH A
Sbjct: 251 LGGAALDVTATEPLPASSPLWDAPNLILTPHAA 283
>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 = 69.6 bits (171), Expect = 1e-13
Identities = 55/232 (23%), Positives = 93/232 (40%), Gaps = 23/232 (9%)
Query: 18 IAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDGWLPNLFVGNLLKGQTVG 77
+ + G+ AE L + ++ E + + V + + G+ VG
Sbjct: 79 VPLCTASGIHGPQIAEWVIGTWLVLSHHFLQYIELQKEQTWGRRQEAYSVEDSV-GKRVG 137
Query: 78 VIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEK------FVTAYGQFLKANGEQPVT 131
++G G IG AR+ M + Y E V G +G P
Sbjct: 138 ILGYGSIGRQTARLAQ-ALGMEVYAYTRSPRPTPESRKDDGYIVPGTGD---PDGSIPSA 193
Query: 132 W---KRASSMDEVLREA-D--VISLHPVLDKTTYHLINKERLATM-KKEAILVNCSRGPV 184
W +S+ E LR+ D V+SL P+ T HL+ E + K++ + N +RG +
Sbjct: 194 WFSGTDKASLHEFLRQDLDLLVVSL-PLTPATK-HLLGAEEFEILAKRKTFVSNIARGSL 251
Query: 185 IDEVALVEHLKQNPMFRVGLDVFEDEPYMKPG--LSEMKNAIVVPHIASASK 234
+D ALV L+ + LDV + EP + L N I+ PH++ ++
Sbjct: 252 VDTDALVAALESGQIRGAALDVTDPEP-LPADHPLWSAPNVIITPHVSWQTQ 302
>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 = 67.0 bits (164), Expect = 1e-12
Identities = 65/246 (26%), Positives = 99/246 (40%), Gaps = 45/246 (18%)
Query: 25 GVLTETTAELAASLSLAAARRI----VEADEFMRAGLYDGWLPNLFVGNLLKGQTVGVIG 80
GV E AE + LAAA+R+ V+ E W L G T+G++G
Sbjct: 93 GVAAEAIAEFVLAAILAAAKRLPEIWVKGAEQ--------WRRE--PLGSLAGSTLGIVG 142
Query: 81 AGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQFLKANGEQPVTWKRASSMDE 140
G IG A AR + M ++ A R G+ G + A+ + E
Sbjct: 143 FGAIGQALARRAL-ALGMRVL------ALRRS------GRPSDVPGVE-----AAADLAE 184
Query: 141 VLREADVISLHPVLDKTTYHLINKERLATMKKEAILVNCSRGPVIDEVALVEHLKQNPMF 200
+ +D + L L T HLIN + LA K L+N +RG ++D+ AL+E L +
Sbjct: 185 LFARSDHLVLAAPLTPETRHLINADVLAQAKPGLHLINIARGGLVDQEALLEALDSGRIS 244
Query: 201 RVGLDVFEDEP-------YMKPGLSEMKNAIVVPHIASASKWTREGMATLAALNVLGKIK 253
LDV + EP Y P + + PH ++ + R +A N+
Sbjct: 245 LASLDVTDPEPLPEGHPLYTHPRVR------LSPHTSAIAPDGRRNLADRFLENLARYRA 298
Query: 254 GYPIWG 259
G P+
Sbjct: 299 GQPLHD 304
>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 = 63.8 bits (155), Expect = 1e-11
Identities = 43/189 (22%), Positives = 71/189 (37%), Gaps = 29/189 (15%)
Query: 10 VNAANKYGIAVGNTPGVLTETT---AELAASLSLAAARRIVEADEFMRAGLYDGWLPNLF 66
A + G+ GV + A LS+ R +E + R G
Sbjct: 104 TEALARAGLTAIAVEGVELPLLTSNSIGAGELSVQFIARFLEVQQPGRLGGAPD------ 157
Query: 67 VGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQFLKANG 126
+ G+TV V+GAG +G A+M+ G ++ D+ +
Sbjct: 158 ----VAGKTVVVVGAGVVGKEAAQMLR-GLGAQVLITDINVEALEQ-------------- 198
Query: 127 EQPVTWKRASSMDEVLREADVISLH-PVLDKTTYHLINKERLATMKKEAILVNCSRGPVI 185
+ + K ++E L EADVI + K L+ +E + MK +++VN + G V
Sbjct: 199 LEELGGKNVEELEEALAEADVIVTTTLLPGKRAGILVPEELVEQMKPGSVIVNVAVGAVG 258
Query: 186 DEVALVEHL 194
AL L
Sbjct: 259 CVQALHTQL 267
>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 = 50.8 bits (122), Expect = 2e-07
Identities = 61/257 (23%), Positives = 84/257 (32%), Gaps = 56/257 (21%)
Query: 7 NVDVNAANKYGIAVGNT-----PGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDGW 61
NVD+ AA + GI V GV+ +EL R + W
Sbjct: 85 NVDIAAARENGITVTGIRDYGDEGVVEYVISELI--------RLLHGFGGKQ-------W 129
Query: 62 LPNLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQF 121
L G VG+IG G G A + F ++ YY + E Y
Sbjct: 130 KE---EPRELTGLKVGIIGLGTTGQMIADAL-SFFGADVYYYSRTRKPDAEAKGIRY--- 182
Query: 122 LKANGEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHLINKERLATMKKEAILVNCSR 181
P ++E+L+ DVI L K L+ +E + IL N S
Sbjct: 183 ------LP--------LNELLKTVDVICTC--LPKNVI-LLGEEEFELLGDGKILFNTSL 225
Query: 182 GPVIDEVALVEHL---KQNPMFRVGLDVFEDEPYMKPGLSEMKNAIVVPHIASASKWTRE 238
GP + AL + L N DE L N I A WTR+
Sbjct: 226 GPSFEVEALKKWLKASGYNIFDCDTAGALGDEE-----LLRYPNVICTNKSAG---WTRQ 277
Query: 239 GMATLAALNVLGKIKGY 255
L+ VL ++ Y
Sbjct: 278 AFERLSQ-KVLANLEEY 293
>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 = 45.5 bits (108), Expect = 1e-05
Identities = 21/112 (18%), Positives = 49/112 (43%), Gaps = 15/112 (13%)
Query: 72 KGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQFLKANGEQPVT 131
V +IGAG +G A++ N++ YD+ + + ++ G +
Sbjct: 161 PPAKVLIIGAGVVGLGAAKIAK-KLGANVLVYDIKEEKL---------KGVETLGGSRLR 210
Query: 132 WKRASSMDEVLREADVI---SLHPVLDKTTYHLINKERLATMKKEAILVNCS 180
+ + +++ L++ D++ L LI +E + MK+ A++V+ +
Sbjct: 211 YSQKEELEKELKQTDILINAILVD--GPRAPILIMEELVGPMKRGAVIVDLA 260
>gnl|CDD|188459 TIGR03944, dehyd_SbnB_fam, 2,3-diaminopropionate biosynthesis
protein SbnB. Members of this protein family are
probable NAD-dependent dehydrogenases related to the
alanine dehydrogenase of Archaeoglobus fulgidus (see
TIGR02371, PDB structure 1OMO and PMID:15313611) and
more distantly to ornithine cyclodeaminase. Members
include the staphylobactin biosynthesis protein SbnB and
tend to occur in contexts suggesting non-ribosomal
peptide synthesis, always adjacent to (occasionally
fused with) a pyridoxal phosphate-dependent enzyme,
SbnA. The pair appears to provide 2,3-diaminopropionate
for biosynthesis of siderophores or other secondary
metabolites [Cellular processes, Biosynthesis of natural
products].
Length = 327
Score = 37.2 bits (87), Expect = 0.006
Identities = 24/81 (29%), Positives = 35/81 (43%), Gaps = 13/81 (16%)
Query: 74 QTVGVIGAGRIGSAYARMMVEGF----KMNLIYYDLYQATRLEKFVTAYGQFLKANGEQP 129
VG+IG G I R ++ ++ L YDL A R E F + G
Sbjct: 133 TRVGIIGCGPIAREILRFLLALGPEIRRVVL--YDLDPA-RAEAFA----ARCQELGPGK 185
Query: 130 VTWKRASSMDEVLREADVISL 150
VT A+S + LR+AD++
Sbjct: 186 VT--VAASAEAALRQADLVVT 204
>gnl|CDD|234592 PRK00045, hemA, glutamyl-tRNA reductase; Reviewed.
Length = 423
Score = 36.7 bits (86), Expect = 0.011
Identities = 28/103 (27%), Positives = 44/103 (42%), Gaps = 20/103 (19%)
Query: 71 LKGQTVGVIGAGRIGSAYARMMVE-GFKMNLIYYDLYQATR-LEKFVTAYGQFLKANGEQ 128
L G+ V VIGAG +G A+ + E G + + A R LE+ +F G +
Sbjct: 180 LSGKKVLVIGAGEMGELVAKHLAEKGVR------KITVANRTLERAEELAEEF----GGE 229
Query: 129 PVTWKRASSMDEVLREADVI-----SLHPVLDKTTYHLINKER 166
+ + E L EAD++ + HP++ K K R
Sbjct: 230 AIPL---DELPEALAEADIVISSTGAPHPIIGKGMVERALKAR 269
>gnl|CDD|215776 pfam00185, OTCace, Aspartate/ornithine carbamoyltransferase,
Asp/Orn binding domain.
Length = 156
Score = 34.5 bits (80), Expect = 0.022
Identities = 32/138 (23%), Positives = 53/138 (38%), Gaps = 27/138 (19%)
Query: 72 KGQTVGVIGAGRIGS-------AYARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQFLKA 124
G V ++G G+ A A+ G ++ L+ E A + LK+
Sbjct: 1 DGLKVAIVGDGKHNRVAHSLILALAKF---GMEVVLVAPKGLYPPDPELLDKAKKEALKS 57
Query: 125 NGEQPVTWKRASSMDEVLREADVI-------SLHPVLD--KTTYHLINKERLATMKKEAI 175
G +T ++E L+ ADV+ L+ K Y + +E L K +AI
Sbjct: 58 GG---ITITVTDDLEEALKGADVVYTDRWQKEREERLEKFKPRYQ-VTEELLKKAKPDAI 113
Query: 176 LVNC---SRGPVI-DEVA 189
++ RG I D+V
Sbjct: 114 FMHPLPAHRGEEITDDVD 131
>gnl|CDD|223364 COG0287, TyrA, Prephenate dehydrogenase [Amino acid transport and
metabolism].
Length = 279
Score = 33.8 bits (78), Expect = 0.077
Identities = 26/112 (23%), Positives = 41/112 (36%), Gaps = 28/112 (25%)
Query: 74 QTVGVIGAGRIGSAYARMMVE-GFKMNLIYYDLYQATRLEKFVTAYGQFLKANGEQPVTW 132
VG++G G +G + AR + E G + +I D AT A +
Sbjct: 4 MKVGIVGLGLMGGSLARALKEAGLVVRIIGRDRSAATLKA-----------ALELGVIDE 52
Query: 133 KRASSMDEVLREADVI-------SLHPVLDKTTYHLINKERLATMKKEAILV 177
+ + E EAD++ + VL + HL KK AI+
Sbjct: 53 LTVAGLAEAAAEADLVIVAVPIEATEEVLKELAPHL---------KKGAIVT 95
>gnl|CDD|223117 COG0039, Mdh, Malate/lactate dehydrogenases [Energy production and
conversion].
Length = 313
Score = 33.7 bits (78), Expect = 0.092
Identities = 12/33 (36%), Positives = 21/33 (63%), Gaps = 1/33 (3%)
Query: 76 VGVIGAGRIGSAYA-RMMVEGFKMNLIYYDLYQ 107
V VIGAG +GS+ A ++++G L+ D+ +
Sbjct: 3 VAVIGAGNVGSSLAFLLLLQGLGSELVLIDINE 35
>gnl|CDD|185366 PRK15469, ghrA, bifunctional glyoxylate/hydroxypyruvate reductase
A; Provisional.
Length = 312
Score = 33.2 bits (76), Expect = 0.14
Identities = 22/78 (28%), Positives = 37/78 (47%), Gaps = 1/78 (1%)
Query: 158 TYHLINKERLATMKKEAILVNCSRGPVIDEVALVEHLKQNPMFRVGLDVFEDEPYMKPG- 216
T +IN++ L + A L+N +RG + E L+ L + LDVF EP
Sbjct: 204 TVGIINQQLLEQLPDGAYLLNLARGVHVVEDDLLAALDSGKVKGAMLDVFSREPLPPESP 263
Query: 217 LSEMKNAIVVPHIASASK 234
L + + PH+A+ ++
Sbjct: 264 LWQHPRVAITPHVAAVTR 281
>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 = 32.1 bits (74), Expect = 0.15
Identities = 24/113 (21%), Positives = 39/113 (34%), Gaps = 27/113 (23%)
Query: 75 TVGVIGAGRIGSAYARM------MVEGFKMNLIYYDLYQATRLEKFVTAYGQFLKANGEQ 128
V VIGAG +G A V + RL + + G
Sbjct: 22 KVVVIGAGVVGLGAAATAKGLGAEVTVLDVRP--------ARLRQLESLLGARFT----- 68
Query: 129 PVTWKRASSMD---EVLREAD-VISLHPVLDKTTYHLINKERLATMKKEAILV 177
S + E ++EAD VI + L+ +E + +MK +++V
Sbjct: 69 ----TLYSQAELLEEAVKEADLVIGAVLIPGAKAPKLVTREMVKSMKPGSVIV 117
>gnl|CDD|234849 PRK00856, pyrB, aspartate carbamoyltransferase catalytic subunit;
Provisional.
Length = 305
Score = 32.7 bits (76), Expect = 0.16
Identities = 16/54 (29%), Positives = 24/54 (44%), Gaps = 17/54 (31%)
Query: 137 SMDEVLREADVI------------SLHPVLDKTTYHL---INKERLATMKKEAI 175
+DEV+ +ADV+ L P ++ Y + ERLA K +AI
Sbjct: 206 DLDEVIEDADVVMMLRVQKERMDGGLLPSYEE--YKRSYGLTAERLALAKPDAI 257
>gnl|CDD|225280 COG2423, COG2423, Predicted ornithine cyclodeaminase, mu-crystallin
homolog [Amino acid transport and metabolism].
Length = 330
Score = 32.7 bits (75), Expect = 0.20
Identities = 22/90 (24%), Positives = 33/90 (36%), Gaps = 19/90 (21%)
Query: 75 TVGVIGAGRIGSAYARMMVEGFK--MNLIYYDLYQAT--RLEKFVTAYGQFLKANGEQPV 130
T+ +IGAG A AR +E K ++ +Y E F +
Sbjct: 132 TLAIIGAG----AQARTQLEALKAVRDIREIRVYSRDPEAAEAFAARLRKRG------GE 181
Query: 131 TWKRASSMDEVLREADVI-----SLHPVLD 155
A S +E + AD++ S PVL
Sbjct: 182 AVGAADSAEEAVEGADIVVTATPSTEPVLK 211
>gnl|CDD|216532 pfam01497, Peripla_BP_2, Periplasmic binding protein. This family
includes bacterial periplasmic binding proteins. Several
of which are involved in iron transport.
Length = 236
Score = 32.3 bits (74), Expect = 0.21
Identities = 15/87 (17%), Positives = 29/87 (33%), Gaps = 12/87 (13%)
Query: 114 FVTAYGQFLKANGEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHLINKERLATMKKE 173
F A G G S + ++L ++ + I+ E + +
Sbjct: 144 FGYADGGGYVVFGSG-------SYIGDLLDALGGENIAAETKGSESAPISFENILAADPD 196
Query: 174 AILVNCSRGPVIDEVALVEHLKQNPMF 200
I+V+ V+ LK NP++
Sbjct: 197 VIIVSGRETKTG-----VDELKANPLW 218
>gnl|CDD|223450 COG0373, HemA, Glutamyl-tRNA reductase [Coenzyme metabolism].
Length = 414
Score = 31.8 bits (73), Expect = 0.42
Identities = 27/93 (29%), Positives = 41/93 (44%), Gaps = 20/93 (21%)
Query: 71 LKGQTVGVIGAGRIGSAYARMMVE-GFKMNLIYYDLYQATR-LEKFVTAYGQFLKANGEQ 128
LK + V VIGAG +G A+ + E G K + A R LE+ + G +
Sbjct: 176 LKDKKVLVIGAGEMGELVAKHLAEKGVK------KITIANRTLERAEELAKKL----GAE 225
Query: 129 PVTWKRASSMDEVLREADVI-----SLHPVLDK 156
V + E L EADV+ + HP++ +
Sbjct: 226 AVA---LEELLEALAEADVVISSTSAPHPIITR 255
>gnl|CDD|183800 PRK12863, PRK12863, YciI-like protein; Reviewed.
Length = 94
Score = 29.9 bits (68), Expect = 0.48
Identities = 11/21 (52%), Positives = 13/21 (61%)
Query: 39 SLAAARRIVEADEFMRAGLYD 59
S AAA AD F +AGLY+
Sbjct: 60 SRAAAEAFAAADPFAKAGLYE 80
>gnl|CDD|215300 PLN02545, PLN02545, 3-hydroxybutyryl-CoA dehydrogenase.
Length = 295
Score = 31.2 bits (71), Expect = 0.49
Identities = 36/149 (24%), Positives = 59/149 (39%), Gaps = 15/149 (10%)
Query: 76 VGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQA----------TRLEKFVTAYGQFLKAN 125
VGV+GAG++GS A++ M++ D A + L + V G+ +
Sbjct: 7 VGVVGAGQMGSGIAQLAAAA-GMDVWLLDSDPAALSRGLDSISSSLARLV-KKGKMSQEE 64
Query: 126 GEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHLINKERLATMKKEAILVNCSRGPVI 185
+ + R ++ E LR+AD I V + + E K AIL + + I
Sbjct: 65 ADATLGRIRCTTNLEELRDADFIIEAIVESEDLKKKLFSELDRICKPSAILASNTSSISI 124
Query: 186 DEVALVEHLKQNPMFRVGLDVFEDEPYMK 214
+A Q P +G+ P MK
Sbjct: 125 TRLASA---TQRPQQVIGMHFMNPPPIMK 150
>gnl|CDD|235488 PRK05476, PRK05476, S-adenosyl-L-homocysteine hydrolase;
Provisional.
Length = 425
Score = 31.2 bits (72), Expect = 0.66
Identities = 14/48 (29%), Positives = 19/48 (39%), Gaps = 10/48 (20%)
Query: 134 RASSMDEVLREADVISLHPVLDKTT---YHLINKERLATMKKEAILVN 178
R +M+E D+ V T +I E + MK AIL N
Sbjct: 257 RVMTMEEAAELGDIF----V---TATGNKDVITAEHMEAMKDGAILAN 297
>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 = 31.2 bits (71), Expect = 0.71
Identities = 25/103 (24%), Positives = 45/103 (43%), Gaps = 20/103 (19%)
Query: 71 LKGQTVGVIGAGRIGSAYARMMVE--GFKMNLIYYDLYQATRLEKFVTAYGQFLKANGEQ 128
LKG+ +IGAG +G A+ ++ K+ + +A L K + G +
Sbjct: 178 LKGKKALLIGAGEMGELVAKHLLRKGVGKILIANRTYERAEDLAKEL----------GGE 227
Query: 129 PVTWKRASSMDEVLREADVI-----SLHPVLDKTTYHLINKER 166
V + ++E L EAD++ + HP++ K +ER
Sbjct: 228 AV---KFEDLEEYLAEADIVISSTGAPHPIVSKEDVERALRER 267
>gnl|CDD|214963 smart00996, AdoHcyase, S-adenosyl-L-homocysteine hydrolase.
Length = 426
Score = 30.2 bits (69), Expect = 1.1
Identities = 14/45 (31%), Positives = 22/45 (48%), Gaps = 10/45 (22%)
Query: 137 SMDEVLREADVISLHPVLDKTT---YHLINKERLATMKKEAILVN 178
+M+EV +AD+ TT +I +E + MK AI+ N
Sbjct: 255 TMEEVAPQADIFV-------TTTGNKDVITREHMRAMKDGAIVCN 292
>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 = 29.0 bits (66), Expect = 2.0
Identities = 25/110 (22%), Positives = 44/110 (40%), Gaps = 19/110 (17%)
Query: 74 QTVGVIGAGRIGSAYARMMVE-GFKMNLIYYDLYQATRLEKFVTAYGQFLKANGEQPVTW 132
+G IG G +GS A +++ G+ + Y+ ++E+ V A G
Sbjct: 1 AKIGFIGLGVMGSPMALNLLKAGYT--VTVYNRTPE-KVEELV--------AEGAVG--- 46
Query: 133 KRASSMDEVLREADVISLHPVLDKTTYHLINKER--LATMKKEAILVNCS 180
A+S E + ADV+ +I E L +K I+++ S
Sbjct: 47 --AASPAEFVASADVVITMVPAGAAVDAVILGEDGLLPGLKPGDIIIDGS 94
>gnl|CDD|233083 TIGR00670, asp_carb_tr, aspartate carbamoyltransferase. Aspartate
transcarbamylase (ATCase) is an alternate name.PyrB
encodes the catalytic chain of aspartate
carbamoyltransferase, an enzyme of pyrimidine
biosynthesis, which organizes into trimers. In some
species, including E. coli and the Archaea but excluding
Bacillus subtilis, a regulatory subunit PyrI is also
present in an allosterically regulated hexameric
holoenzyme. Several molecular weight classes of ATCase
are described in MEDLINE:96303527 and often vary within
taxa. PyrB and PyrI are fused in Thermotoga
maritima.Ornithine carbamoyltransferases are in the same
superfamily and form an outgroup [Purines, pyrimidines,
nucleosides, and nucleotides, Pyrimidine ribonucleotide
biosynthesis].
Length = 301
Score = 29.2 bits (66), Expect = 2.2
Identities = 24/80 (30%), Positives = 38/80 (47%), Gaps = 18/80 (22%)
Query: 122 LKANGEQPVTWKRASSMDEVLREADVISL-------HPVLD-----KTTYHLINKERLAT 169
LKA G + + S++EV+ EADV+ + P + K +Y I ERL
Sbjct: 197 LKAKG---IKVRETESLEEVIDEADVLYVTRIQKERFPDPEEYEKVKGSYG-ITLERLEA 252
Query: 170 MKKEAILVNCSRGPVIDEVA 189
KK I+++ P +DE+
Sbjct: 253 AKKGVIIMH--PLPRVDEID 270
>gnl|CDD|188441 TIGR03926, T7_EssB, type VII secretion protein EssB. Members of
this family are associated with type VII secretion of
WXG100 family targets in the Firmicutes, but not in the
Actinobacteria. This protein is designated YukC in
Bacillus subtilis and EssB is Staphylococcus aureus
[Protein fate, Protein and peptide secretion and
trafficking].
Length = 377
Score = 29.6 bits (67), Expect = 2.3
Identities = 19/88 (21%), Positives = 33/88 (37%), Gaps = 22/88 (25%)
Query: 100 LIYYDLYQATRLEKFVTAYGQFLKANGEQPVTW---KRASSMDEVLREADVISLHPVLDK 156
LIY + + E + A FLK + Q +T + + ++
Sbjct: 231 LIYLLFFAQPKQEAILAANTAFLKDDYSQVITTLEDYSPEKLPKSVK------------- 277
Query: 157 TTYHL----INKERLATMKKEAILVNCS 180
Y L + E+L+ +KE IL N +
Sbjct: 278 --YELAYSYVQTEKLSEDQKENILNNVT 303
>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 = 28.0 bits (63), Expect = 3.2
Identities = 22/84 (26%), Positives = 36/84 (42%), Gaps = 13/84 (15%)
Query: 67 VGNLLKGQTVGVIGAGRIGSAYARMMVE-GFKMNLIYYDLYQATR-LEKFVTAYGQFLKA 124
+ LKG+ V +IGAG + A+ ++ G K + A R LEK +F
Sbjct: 6 IFGDLKGKKVLLIGAGEMARLAAKHLLSKGAK------KITIANRTLEKAKELAEEF--- 56
Query: 125 NGEQPVTWKRASSMDEVLREADVI 148
++E+L EAD++
Sbjct: 57 --PVGGEALPLDELEELLAEADIV 78
>gnl|CDD|216949 pfam02254, TrkA_N, TrkA-N domain. This domain is found in a wide
variety of proteins. These protein include potassium
channels, phosphoesterases, and various other
transporters. This domain binds to NAD.
Length = 116
Score = 27.9 bits (63), Expect = 3.2
Identities = 14/71 (19%), Positives = 27/71 (38%), Gaps = 7/71 (9%)
Query: 78 VIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQFLKANGEQPVTWKRASS 137
+IG GR+G + A + EG ++ R+E+ + + + A
Sbjct: 3 IIGYGRVGRSLAEELREGGPDVVVIDK--DPERVEELREEGVPVVVGDATDEEVLEEAG- 59
Query: 138 MDEVLREADVI 148
+ EAD +
Sbjct: 60 ----IEEADAV 66
>gnl|CDD|233303 TIGR01177, TIGR01177, TIGR01177 family protein. This family is
found exclusively in the Archaea [Hypothetical proteins,
Conserved].
Length = 329
Score = 28.9 bits (65), Expect = 3.2
Identities = 11/27 (40%), Positives = 16/27 (59%)
Query: 77 GVIGAGRIGSAYARMMVEGFKMNLIYY 103
G++GA IG MV G ++NL +Y
Sbjct: 201 GLMGAKVIGCDIDWKMVAGARINLEHY 227
>gnl|CDD|184511 PRK14106, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
synthetase; Provisional.
Length = 450
Score = 28.8 bits (65), Expect = 3.3
Identities = 22/82 (26%), Positives = 35/82 (42%), Gaps = 8/82 (9%)
Query: 71 LKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQFLKANGEQPV 130
LKG+ V V+GAG G A A+ + + +I D EK + L+ GE +
Sbjct: 3 LKGKKVLVVGAGVSGLALAKFLKK-LGAKVILTD-------EKEEDQLKEALEELGELGI 54
Query: 131 TWKRASSMDEVLREADVISLHP 152
+E L D++ + P
Sbjct: 55 ELVLGEYPEEFLEGVDLVVVSP 76
>gnl|CDD|240630 cd05305, L-AlaDH, Alanine dehydrogenase NAD-binding and catalytic
domains. Alanine dehydrogenase (L-AlaDH) catalyzes the
NAD-dependent conversion of pyruvate to L-alanine via
reductive amination. Like formate dehydrogenase and
related enzymes, L-AlaDH is comprised of 2 domains
connected by a long alpha helical stretch, each
resembling a Rossmann fold NAD-binding domain. The
NAD-binding domain is inserted within the linear
sequence of the more divergent catalytic domain. Ligand
binding and active site residues are found in the cleft
between the subdomains. L-AlaDH is typically hexameric
and is critical in carbon and nitrogen metabolism in
micro-organisms.
Length = 359
Score = 28.9 bits (66), Expect = 3.3
Identities = 26/108 (24%), Positives = 50/108 (46%), Gaps = 17/108 (15%)
Query: 75 TVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQ---FLKANGEQPVT 131
V ++GAG +G AR+ + G + D+ RL +G L +N
Sbjct: 170 KVVILGAGVVGENAARVAL-GLGAEVTVLDI-NLERLRYLDDIFGGRVTTLYSN------ 221
Query: 132 WKRASSMDEVLREADVI--SLHPVLDKTTYHLINKERLATMKKEAILV 177
++++E L+EAD++ ++ K L+ +E + TMK +++V
Sbjct: 222 ---PANLEEALKEADLVIGAVLIPGAKAP-KLVTEEMVKTMKPGSVIV 265
>gnl|CDD|212659 cd07770, FGGY_GntK, Gluconate kinases; a subfamily of the FGGY
family of carbohydrate kinases. This subfamily is
composed of a group of gluconate kinases (GntK, also
known as gluconokinase; EC 2.7.1.12) encoded by the gntK
gene, which catalyzes the ATP-dependent phosphorylation
of D-gluconate and produce 6-phospho-D-gluconate and
ADP. The presence of Mg2+ might be required for
catalytic activity. The prototypical member of this
subfamily is GntK from Lactobacillus acidophilus. Unlike
Escherichia coli GntK, which belongs to the superfamily
of P-loop containing nucleoside triphosphate hydrolases,
members in this subfamily are homologous to glycerol
kinase, xylulose kinase, and rhamnulokinase from
Escherichia coli. They have been classified as members
of the FGGY family of carbohydrate kinases, which
contain two large domains separated by a deep cleft that
forms the active site. This model spans both the
N-terminal domain, which adopts a ribonuclease H-like
fold, and the structurally related C-terminal domain.
Some uncharacterized homologous sequences are also
included in this subfamily. The Lactobacillus gnt operon
contains a single gntK gene. The gnt operons of some
bacteria, such as Corynebacterium glutamicum, have two
gntK genes. For example, the C. glutamicum gnt operon
has both a gluconate kinase gntV gene (also known as
gntK) and a second hypothetical gntK gene (also known as
gntK2). Both gluconate kinases encoded by these genes
belong to this family, however the protein encoded by C.
glutamicum gntV is not included in this model as it is
truncated in the C-terminal domain.
Length = 440
Score = 28.7 bits (65), Expect = 3.5
Identities = 22/65 (33%), Positives = 25/65 (38%), Gaps = 10/65 (15%)
Query: 23 TPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDGWLPNLFVGNLLKGQ---TVGVI 79
T L AE A L L V G DG L NL VG + G T+G
Sbjct: 207 TTEQLRGLKAERAPKLGLPEDTPFV-------LGASDGALSNLGVGAVDPGVAAITIGTS 259
Query: 80 GAGRI 84
GA R+
Sbjct: 260 GAIRV 264
>gnl|CDD|234950 PRK01390, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
synthetase; Provisional.
Length = 460
Score = 28.7 bits (65), Expect = 3.8
Identities = 12/26 (46%), Positives = 14/26 (53%)
Query: 70 LLKGQTVGVIGAGRIGSAYARMMVEG 95
G+TV V G G G A AR +V G
Sbjct: 6 GFAGKTVAVFGLGGSGLATARALVAG 31
>gnl|CDD|217556 pfam03435, Saccharop_dh, Saccharopine dehydrogenase. This family
comprised of three structural domains that can not be
separated in the linear sequence. In some organisms this
enzyme is found as a bifunctional polypeptide with
lysine ketoglutarate reductase. The saccharopine
dehydrogenase can also function as a saccharopine
reductase.
Length = 380
Score = 28.4 bits (64), Expect = 4.2
Identities = 17/76 (22%), Positives = 28/76 (36%), Gaps = 4/76 (5%)
Query: 76 VGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQFLKANGEQPVTWKRA 135
V +IGAG +G A ++ + + D G A V
Sbjct: 1 VLIIGAGGVGQGVAPLLARHGDLEITVADRSLEKAQALAAPKLGLRFIA---IAVDADNY 57
Query: 136 SSMDEVLREAD-VISL 150
++ +L+E D VI+L
Sbjct: 58 EALVALLKEGDLVINL 73
>gnl|CDD|133428 cd05292, LDH_2, A subgroup of L-lactate dehydrogenases.
L-lactate dehydrogenases (LDH) are tetrameric enzymes
catalyzing the last step of glycolysis in which
pyruvate is converted to L-lactate. This subgroup is
composed predominantly of bacterial LDHs and a few
fungal LDHs. Bacterial LDHs may be non-allosteric or
may be activated by an allosteric effector such as
fructose-1,6-bisphosphate. LDHs are part of the
NAD(P)-binding Rossmann fold superfamily, which
includes a wide variety of protein families including
the NAD(P)-binding domains of alcohol dehydrogenases,
tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate dehydrogenases,
formate/glycerate dehydrogenases, siroheme synthases,
6-phosphogluconate dehydrogenases, aminoacid
dehydrogenases, repressor rex, and NAD-binding
potassium channel domains, among others.
Length = 308
Score = 28.6 bits (65), Expect = 4.2
Identities = 9/19 (47%), Positives = 14/19 (73%), Gaps = 2/19 (10%)
Query: 76 VGVIGAGRIGS--AYARMM 92
V ++GAG +GS AYA ++
Sbjct: 3 VAIVGAGFVGSTTAYALLL 21
>gnl|CDD|181018 PRK07530, PRK07530, 3-hydroxybutyryl-CoA dehydrogenase; Validated.
Length = 292
Score = 28.4 bits (64), Expect = 4.4
Identities = 15/41 (36%), Positives = 24/41 (58%), Gaps = 4/41 (9%)
Query: 74 QTVGVIGAGRIGSAYARMM-VEGFKMNLIYYDLYQATRLEK 113
+ VGVIGAG++G+ A + + G+ + L D+ RLE
Sbjct: 5 KKVGVIGAGQMGNGIAHVCALAGYDVLL--NDVSAD-RLEA 42
>gnl|CDD|223318 COG0240, GpsA, Glycerol-3-phosphate dehydrogenase [Energy
production and conversion].
Length = 329
Score = 28.3 bits (64), Expect = 4.4
Identities = 27/123 (21%), Positives = 48/123 (39%), Gaps = 31/123 (25%)
Query: 74 QTVGVIGAGRIGSAYARMMVEGFKMNLIY-------YDLYQATRLEKFVTAYGQFLKANG 126
+ VIGAG G+A A+++ ++ ++ TR ++L
Sbjct: 2 MKIAVIGAGSWGTALAKVLARNGHEVRLWGRDEEIVAEI-NETRENP------KYLP-GI 53
Query: 127 EQPVTWKRASSMDEVLREADVI-------SLHPVLDKTTYHLINKERLATMKKEAILVNC 179
P K + + E L AD+I +L VL + L K+AI+V+
Sbjct: 54 LLPPNLKATTDLAEALDGADIIVIAVPSQALREVLRQLKPLL---------LKDAIIVSA 104
Query: 180 SRG 182
++G
Sbjct: 105 TKG 107
>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 = 28.4 bits (64), Expect = 4.7
Identities = 11/33 (33%), Positives = 16/33 (48%)
Query: 69 NLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLI 101
LKG+ V VIGAG +G A+ + +
Sbjct: 174 GNLKGKKVLVIGAGEMGELAAKHLAAKGVAEIT 206
>gnl|CDD|215289 PLN02528, PLN02528, 2-oxoisovalerate dehydrogenase E2 component.
Length = 416
Score = 28.5 bits (64), Expect = 4.8
Identities = 17/51 (33%), Positives = 25/51 (49%), Gaps = 4/51 (7%)
Query: 4 GYNNVDVNAANKYGIAVGNTPGV----LTETTAELAASLSLAAARRIVEAD 50
G +N+ V A ++G+ V N V L E T EL+ LAA ++ D
Sbjct: 274 GSHNIGVAMATEHGLVVPNIKNVQSLSLLEITKELSRLQHLAAENKLNPED 324
>gnl|CDD|198065 smart00997, AdoHcyase_NAD, S-adenosyl-L-homocysteine hydrolase, NAD
binding domain.
Length = 162
Score = 27.8 bits (63), Expect = 4.9
Identities = 13/45 (28%), Positives = 18/45 (40%), Gaps = 10/45 (22%)
Query: 137 SMDEVLREADVISLHPVLDKTT---YHLINKERLATMKKEAILVN 178
M+E + AD+ T +I +E MK AIL N
Sbjct: 71 KMEEAAKRADIFV-------TATGNKDVITREHFRAMKDGAILAN 108
>gnl|CDD|236190 PRK08220, PRK08220, 2,3-dihydroxybenzoate-2,3-dehydrogenase;
Validated.
Length = 252
Score = 27.9 bits (63), Expect = 5.2
Identities = 12/25 (48%), Positives = 14/25 (56%), Gaps = 1/25 (4%)
Query: 71 LKGQTVGVIGAGR-IGSAYARMMVE 94
G+TV V GA + IG A A VE
Sbjct: 6 FSGKTVWVTGAAQGIGYAVALAFVE 30
>gnl|CDD|222086 pfam13378, MR_MLE_C, Enolase C-terminal domain-like. This domain
appears at the C-terminus of many of the proteins that
carry the MR_MLE, pfam01188 and MR_MLE_N pfam02746
domains. EC:4.2.1.40.
Length = 111
Score = 27.2 bits (61), Expect = 5.2
Identities = 18/55 (32%), Positives = 23/55 (41%), Gaps = 3/55 (5%)
Query: 13 ANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDGWLPNLFV 67
A +G+ V P E LAASL LAAA + E++ L D L
Sbjct: 42 AEAFGVPV--APHG-MEGGIGLAASLHLAAALPNFDILEYVPYLLPDDLLTGPPP 93
>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 = 28.3 bits (64), Expect = 5.5
Identities = 8/19 (42%), Positives = 9/19 (47%)
Query: 67 VGNLLKGQTVGVIGAGRIG 85
G T V+GAG IG
Sbjct: 167 RSGFKPGDTALVLGAGPIG 185
>gnl|CDD|118668 pfam10140, YukC, WXG100 protein secretion system (Wss), protein
YukC. Members of this family of proteins include
predicted membrane proteins homologous to YukC in B.
subtilis. The YukC protein family would participate to
the formation of a translocon required for the secretion
of WXG100 proteins (pfam06013) in monoderm bacteria, the
WXG100 protein secretion system (Wss). This family
includes EssB in Staphylococcus aureus.
Length = 359
Score = 28.0 bits (63), Expect = 5.9
Identities = 18/88 (20%), Positives = 33/88 (37%), Gaps = 22/88 (25%)
Query: 100 LIYYDLYQATRLEKFVTAYGQFLKANGEQPVTW---KRASSMDEVLREADVISLHPVLDK 156
LIY + + E + A FL + + +T S+ + ++
Sbjct: 212 LIYLLFFAQPKQEAILEANTAFLNVDYSKVITTLEKYDPESLPKSVK------------- 258
Query: 157 TTYHL----INKERLATMKKEAILVNCS 180
Y L + E+L+ +KE IL N +
Sbjct: 259 --YELAYSYVQVEKLSDDQKENILNNVT 284
>gnl|CDD|227736 COG5449, COG5449, Uncharacterized conserved protein [Function
unknown].
Length = 225
Score = 27.6 bits (61), Expect = 6.4
Identities = 24/95 (25%), Positives = 34/95 (35%), Gaps = 26/95 (27%)
Query: 2 AVGYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDGW 61
G++ ++A G G GVL+ I AD + AG YDG
Sbjct: 46 GGGWSPSAADSAVGLGPGQGEVLGVLSSA--------------GIAPAD--LAAGRYDGA 89
Query: 62 LPNLFVGN--------LLKGQTVGVIGAGRIGSAY 88
F+ N LL T+G + R G A+
Sbjct: 90 RVEAFLVNWSAPDRHVLLWTATIGSV--TREGEAF 122
>gnl|CDD|224996 COG2085, COG2085, Predicted dinucleotide-binding enzymes [General
function prediction only].
Length = 211
Score = 27.7 bits (62), Expect = 6.5
Identities = 8/16 (50%), Positives = 10/16 (62%)
Query: 75 TVGVIGAGRIGSAYAR 90
+ +IG G IGSA A
Sbjct: 3 IIAIIGTGNIGSALAL 18
>gnl|CDD|133418 cd00300, LDH_like, L-lactate dehydrogenase-like enzymes. Members
of this subfamily are tetrameric NAD-dependent
2-hydroxycarboxylate dehydrogenases including LDHs,
L-2-hydroxyisocaproate dehydrogenases (L-HicDH), and
LDH-like malate dehydrogenases (MDH). Dehydrogenases
catalyze the conversion of carbonyl compounds to
alcohols or amino acids. LDHs catalyze the last step of
glycolysis in which pyruvate is converted to L-lactate.
Vertebrate LDHs are non-allosteric, but some bacterial
LDHs are activated by an allosteric effector such as
fructose-1,6-bisphosphate. L-HicDH catalyzes the
conversion of a variety of 2-oxo carboxylic acids with
medium-sized aliphatic or aromatic side chains. MDH is
one of the key enzymes in the citric acid cycle,
facilitating both the conversion of malate to
oxaloacetate and replenishing levels of oxalacetate by
reductive carboxylation of pyruvate. The LDH-like
subfamily is part of the NAD(P)-binding Rossmann fold
superfamily, which includes a wide variety of protein
families including the NAD(P)-binding domains of alcohol
dehydrogenases, tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate dehydrogenases,
formate/glycerate dehydrogenases, siroheme synthases,
6-phosphogluconate dehydrogenases, aminoacid
dehydrogenases, repressor rex, and NAD-binding potassium
channel domains, among others.
Length = 300
Score = 27.6 bits (62), Expect = 7.0
Identities = 10/31 (32%), Positives = 19/31 (61%), Gaps = 1/31 (3%)
Query: 76 VGVIGAGRIGSAYA-RMMVEGFKMNLIYYDL 105
+ +IGAG +G+A A ++ +G L+ D+
Sbjct: 1 ITIIGAGNVGAAVAFALIAKGLASELVLVDV 31
>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 = 27.6 bits (62), Expect = 7.6
Identities = 10/17 (58%), Positives = 11/17 (64%)
Query: 69 NLLKGQTVGVIGAGRIG 85
+ G TV VIGAG IG
Sbjct: 156 GITLGDTVVVIGAGTIG 172
>gnl|CDD|223422 COG0345, ProC, Pyrroline-5-carboxylate reductase [Amino acid
transport and metabolism].
Length = 266
Score = 27.5 bits (62), Expect = 8.1
Identities = 17/80 (21%), Positives = 29/80 (36%), Gaps = 16/80 (20%)
Query: 74 QTVGVIGAGRIGSAYARMMVEGFKM---NLIYYDLYQATRLEKFVTAYGQFLKANGEQPV 130
+G IGAG +G A +++ + +I + + R YG
Sbjct: 2 MKIGFIGAGNMGEAILSGLLKSGALPPEEIIVTNRSEEKRA-ALAAEYGV---------- 50
Query: 131 TWKRASSMDEVLREADVISL 150
+ E + EADV+ L
Sbjct: 51 --VTTTDNQEAVEEADVVFL 68
>gnl|CDD|139376 PRK13150, PRK13150, cytochrome c-type biogenesis protein CcmE;
Reviewed.
Length = 159
Score = 27.3 bits (60), Expect = 8.2
Identities = 18/62 (29%), Positives = 25/62 (40%), Gaps = 13/62 (20%)
Query: 24 PGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDGWLPNLFVGNLLKGQTVGVIGAGR 83
PG + L + SL A V Y+G LP+LF +GQ GV+ G
Sbjct: 68 PGSVRRDPDSLKVNFSLYDAEGSVTVS-------YEGILPDLF----REGQ--GVVVQGT 114
Query: 84 IG 85
+
Sbjct: 115 LE 116
>gnl|CDD|201778 pfam01408, GFO_IDH_MocA, Oxidoreductase family, NAD-binding
Rossmann fold. This family of enzymes utilise NADP or
NAD. This family is called the GFO/IDH/MOCA family in
swiss-prot.
Length = 120
Score = 26.4 bits (59), Expect = 8.5
Identities = 8/15 (53%), Positives = 12/15 (80%)
Query: 76 VGVIGAGRIGSAYAR 90
VG++GAG+IG + R
Sbjct: 3 VGIVGAGKIGRRHLR 17
>gnl|CDD|181084 PRK07688, PRK07688, thiamine/molybdopterin biosynthesis
ThiF/MoeB-like protein; Validated.
Length = 339
Score = 27.3 bits (61), Expect = 9.2
Identities = 11/23 (47%), Positives = 17/23 (73%)
Query: 71 LKGQTVGVIGAGRIGSAYARMMV 93
L+ + V +IGAG +G+A A M+V
Sbjct: 22 LREKHVLIIGAGALGTANAEMLV 44
>gnl|CDD|241244 cd01208, PTB_X11, X11-like Phosphotyrosine-binding (PTB) domain.
The function of the neuronal protein X11 is unknown to
date. X11 has a PTB domain followed by two PDZ domains.
PTB domains have a common PH-like fold and are found in
various eukaryotic signaling molecules. This domain was
initially shown to binds peptides with a NPXY motif with
differing requirements for phosphorylation of the
tyrosine, although more recent studies have found that
some types of PTB domains can bind to peptides lack
tyrosine residues altogether. In contrast to SH2
domains, which recognize phosphotyrosine and adjacent
carboxy-terminal residues, PTB-domain binding
specificity is conferred by residues amino-terminal to
the phosphotyrosine. PTB domains are classified into
three groups: phosphotyrosine-dependent Shc-like,
phosphotyrosine-dependent IRS-like, and
phosphotyrosine-independent Dab-like PTB domains. This
cd is part of the Dab-like subgroup.
Length = 161
Score = 26.8 bits (60), Expect = 9.3
Identities = 8/13 (61%), Positives = 10/13 (76%)
Query: 114 FVTAYGQFLKANG 126
F AY +FL+ANG
Sbjct: 146 FSVAYQEFLRANG 158
>gnl|CDD|224995 COG2084, MmsB, 3-hydroxyisobutyrate dehydrogenase and related
beta-hydroxyacid dehydrogenases [Lipid metabolism].
Length = 286
Score = 27.2 bits (61), Expect = 9.3
Identities = 27/109 (24%), Positives = 45/109 (41%), Gaps = 18/109 (16%)
Query: 75 TVGVIGAGRIGSAYARMMVE-GFKMNLIYYDLYQATRLEKFVTAYGQFLKANGEQPVTWK 133
+ IG G +GS A +++ G ++ + Y+ EK + L A G
Sbjct: 2 KIAFIGLGIMGSPMAANLLKAGHEVTV--YNR----TPEKAA----ELLAAAGATV---- 47
Query: 134 RASSMDEVLREADVISLHPVLDKTTYHLINKE--RLATMKKEAILVNCS 180
A+S E EADV+ D ++ E L +K AI+++ S
Sbjct: 48 -AASPAEAAAEADVVITMLPDDAAVRAVLFGENGLLEGLKPGAIVIDMS 95
>gnl|CDD|217732 pfam03795, YCII, YCII-related domain. The majority of proteins
in this family consist of a single copy of this domain,
though it is also found as a repeat. A strongly
conserved histidine and a aspartate suggest that the
domain has an enzymatic function. This family also now
includes the family formerly known as the DGPF domain
(COG3795). Although its function is unknown it is found
fused to a sigma-70 factor family domain in CC_1329.
Suggesting that this domain plays a role in
transcription initiation (Bateman A per. obs.). This
domain is named after the most conserved motif in the
alignment.
Length = 94
Score = 26.2 bits (58), Expect = 9.4
Identities = 9/20 (45%), Positives = 10/20 (50%)
Query: 39 SLAAARRIVEADEFMRAGLY 58
L A I D F+ AGLY
Sbjct: 66 DLDEAIAIAAGDPFVAAGLY 85
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.317 0.134 0.389
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: 15,278,888
Number of extensions: 1495019
Number of successful extensions: 1948
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1746
Number of HSP's successfully gapped: 152
Length of query: 294
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 198
Effective length of database: 6,679,618
Effective search space: 1322564364
Effective search space used: 1322564364
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 59 (26.3 bits)