RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 019328
(342 letters)
>gnl|CDD|177941 PLN02306, PLN02306, hydroxypyruvate reductase.
Length = 386
Score = 727 bits (1877), Expect = 0.0
Identities = 323/341 (94%), Positives = 337/341 (98%)
Query: 1 MAKPVSIEVWNPNGKYRVVSTKPMPGTRWINLLIEQDCRVEICTQKKTILSVEDIIALIG 60
MAKPVSIEV+NPNGKYRVVSTKPMPGTRWINLL++QDCRVEICT+KKTILSVEDIIALIG
Sbjct: 1 MAKPVSIEVYNPNGKYRVVSTKPMPGTRWINLLVDQDCRVEICTEKKTILSVEDIIALIG 60
Query: 61 DKCDGVIGQLTEDWGETLFAALSRAGGKAFSNMAVGYNNVDVNAANKYGIAVGNTPGVLT 120
DKCDGVIGQLTEDWGETLF+ALS+AGGKAFSNMAVGYNNVDV AANKYGIAVGNTPGVLT
Sbjct: 61 DKCDGVIGQLTEDWGETLFSALSKAGGKAFSNMAVGYNNVDVEAANKYGIAVGNTPGVLT 120
Query: 121 ETTAELAASLSLAAARRIVEADEFMRAGLYDGWLPNLFVGNLLKGQTVGVIGAGRIGSAY 180
ETTAELAASLSLAAARRIVEADEFMRAGLY+GWLP+LFVGNLLKGQTVGVIGAGRIGSAY
Sbjct: 121 ETTAELAASLSLAAARRIVEADEFMRAGLYEGWLPHLFVGNLLKGQTVGVIGAGRIGSAY 180
Query: 181 ARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQFLKANGEQPVTWKRASSMDEVLREADVI 240
ARMMVEGFKMNLIYYDLYQ+TRLEKFVTAYGQFLKANGEQPVTWKRASSM+EVLREADVI
Sbjct: 181 ARMMVEGFKMNLIYYDLYQSTRLEKFVTAYGQFLKANGEQPVTWKRASSMEEVLREADVI 240
Query: 241 SLHPVLDKTTYHLINKERLATMKKEAILVNCSRGPVIDEVALVEHLKQNPMFRVGLDVFE 300
SLHPVLDKTTYHLINKERLA MKKEA+LVN SRGPVIDEVALVEHLK NPMFRVGLDVFE
Sbjct: 241 SLHPVLDKTTYHLINKERLALMKKEAVLVNASRGPVIDEVALVEHLKANPMFRVGLDVFE 300
Query: 301 DEPYMKPGLSEMKNAIVVPHIASASKWTREGMATLAALNVL 341
DEPYMKPGL++MKNA+VVPHIASASKWTREGMATLAALNVL
Sbjct: 301 DEPYMKPGLADMKNAVVVPHIASASKWTREGMATLAALNVL 341
>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 = 378 bits (973), Expect = e-132
Identities = 134/327 (40%), Positives = 186/327 (56%), Gaps = 24/327 (7%)
Query: 16 YRVVSTKPMPGTRWINLLIEQDCRVEICTQKKTILSVEDIIALIGDKCDGVIGQLTEDWG 75
+V+ T+ +P + LL + VE+ + L E+++ DG++ LT+
Sbjct: 1 PKVLVTRRLPE-EALALL-REGFEVEVW-DEDRPLPREELLEAAKG-ADGLLCTLTDKID 56
Query: 76 ETLFAALSRAGGKAFSNMAVGYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAA 135
L A K +N +VGY+++DV+AA GI V NTP VLT+ TA+LA +L LAAA
Sbjct: 57 AELLDAAPPL--KVIANYSVGYDHIDVDAAKARGIPVTNTPDVLTDATADLAFALLLAAA 114
Query: 136 RRIVEADEFMRAGLYDGWLPNLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYY 195
RR+VE D F+RAG + GW P L +G L G+T+G++G GRIG A AR GF M ++Y+
Sbjct: 115 RRVVEGDRFVRAGEWKGWSPTLLLGTDLHGKTLGIVGMGRIGQAVARRAK-GFGMKILYH 173
Query: 196 DLYQATRLEKFVTAYGQFLKANGEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHLIN 255
+ + E+ + A S+DE+L E+D +SLH L T HLIN
Sbjct: 174 NRSRKPEAEEELGAR----------------YVSLDELLAESDFVSLHCPLTPETRHLIN 217
Query: 256 KERLATMKKEAILVNCSRGPVIDEVALVEHLKQNPMFRVGLDVFEDEPYMK-PGLSEMKN 314
ERLA MK AIL+N +RG V+DE ALVE LK + GLDVFE EP L + N
Sbjct: 218 AERLALMKPTAILINTARGGVVDEDALVEALKSGKIAGAGLDVFEPEPLPADHPLLTLPN 277
Query: 315 AIVVPHIASASKWTREGMATLAALNVL 341
+++PHI SA+ TR MA LAA N+L
Sbjct: 278 VVLLPHIGSATVETRTAMAELAADNLL 304
>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 = 255 bits (653), Expect = 2e-83
Identities = 115/315 (36%), Positives = 169/315 (53%), Gaps = 34/315 (10%)
Query: 34 IEQDCRVEICTQKKTILSVEDIIALIGDKCDGVIGQLTE-------DWGETLFAALSRAG 86
+E++ V ++S E+++ I D D +I L+ D + L
Sbjct: 17 LEENFEV-TYYDGLGLISKEELLERIAD-YDALITPLSTPVDKEIIDAAKNL-------- 66
Query: 87 GKAFSNMAVGYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMR 146
K +N G++N+DV+ A + GI V NTP V TE TAEL L LA ARRI E D MR
Sbjct: 67 -KIIANYGAGFDNIDVDYAKEKGIPVTNTPAVSTEPTAELTFGLILALARRIAEGDRLMR 125
Query: 147 AGLYDGWLPNLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKF 206
G + GW P F+G+ L G+T+G+IG GRIG A AR + F M ++YY+ ++ + +
Sbjct: 126 RGGFLGWAPLFFLGHELAGKTLGIIGMGRIGQAVARR-AKAFGMKILYYNRHRLSEETE- 183
Query: 207 VTAYGQFLKANGEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHLINKERLATMKKEA 266
G T+ +DE+L+E+D +SLH T+HLI+ MK A
Sbjct: 184 -KELG----------ATYV---DLDELLKESDFVSLHAPYTPETHHLIDAAAFKLMKPTA 229
Query: 267 ILVNCSRGPVIDEVALVEHLKQNPMFRVGLDVFEDEPYMKPGLSEMKNAIVVPHIASASK 326
L+N +RGP++DE ALV+ LK + LDVFE EP + P L ++ N I+ PHI +A+
Sbjct: 230 YLINAARGPLVDEKALVDALKTGEIAGAALDVFEFEPEVSPELKKLDNVILTPHIGNATV 289
Query: 327 WTREGMATLAALNVL 341
R+ MA AA N++
Sbjct: 290 EARDAMAKEAADNII 304
>gnl|CDD|240649 cd12172, PGDH_like_2, Putative D-3-Phosphoglycerate Dehydrogenases,
NAD-binding and catalytic domains. Phosphoglycerate
dehydrogenases (PGDHs) catalyze the initial step in the
biosynthesis of L-serine from D-3-phosphoglycerate.
PGDHs come in 3 distinct structural forms, with this
first group being related to 2-hydroxy acid
dehydrogenases, sharing structural similarity to formate
and glycerate dehydrogenases of the D-specific
2-hydroxyacid dehydrogenase superfamily, which also
include groups such as L-alanine dehydrogenase and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. Many, not all, members of this family are
dimeric.
Length = 306
Score = 254 bits (652), Expect = 2e-83
Identities = 128/312 (41%), Positives = 171/312 (54%), Gaps = 30/312 (9%)
Query: 32 LLIEQDCRVEICTQKKTILSVEDIIALIGDKCDGVI-GQLTEDWGETLFAALSRAGGKAF 90
LL V + + L+ E++I L+ D DGVI G + E + AA R K
Sbjct: 19 LLEAAGFEVVLNPLGR-PLTEEELIELLKD-ADGVIAG--LDPITEEVLAAAPRL--KVI 72
Query: 91 SNMAVGYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLY 150
S VGY+N+D+ AA K GI V NTPG + + AEL L LA AR+I +AD +RAG
Sbjct: 73 SRYGVGYDNIDLEAAKKRGIVVTNTPGANSNSVAELTIGLMLALARQIPQADREVRAG-- 130
Query: 151 DGWLPNLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAY 210
GW VG L G+T+G+IG GRIG A AR + GF M ++ YD Y
Sbjct: 131 -GWDR--PVGTELYGKTLGIIGLGRIGKAVARRLS-GFGMKVLAYDPYPDE--------- 177
Query: 211 GQFLKANGEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHLINKERLATMKKEAILVN 270
+F K +G + V S++E+L+E+D ISLH L T HLIN LA MK AIL+N
Sbjct: 178 -EFAKEHGVEFV------SLEELLKESDFISLHLPLTPETRHLINAAELALMKPGAILIN 230
Query: 271 CSRGPVIDEVALVEHLKQNPMFRVGLDVFEDEPYMKPG-LSEMKNAIVVPHIASASKWTR 329
+RG ++DE AL E LK + LDVFE+EP L E+ N I+ PHI +++K
Sbjct: 231 TARGGLVDEEALYEALKSGRIAGAALDVFEEEPPPADSPLLELPNVILTPHIGASTKEAV 290
Query: 330 EGMATLAALNVL 341
M T+AA NV+
Sbjct: 291 LRMGTMAAQNVI 302
>gnl|CDD|223980 COG1052, LdhA, Lactate dehydrogenase and related dehydrogenases
[Energy production and conversion / Coenzyme metabolism
/ General function prediction only].
Length = 324
Score = 245 bits (629), Expect = 9e-80
Identities = 121/333 (36%), Positives = 173/333 (51%), Gaps = 29/333 (8%)
Query: 14 GKYRVVSTKPMPGTRWINLLIEQDCRVEICTQKKTILSVEDIIALIGDKCDGVIGQLTED 73
K V+ST+ +P + +++ VE L+ + +A D VI + +
Sbjct: 1 MKIVVLSTRKLP--PEVLERLKEKFEVERYEDD---LTPDTELAERLKDADAVITFVNDR 55
Query: 74 WGETLFAALSRAGGKAFSNMAVGYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLA 133
+ L K + + GY+NVD+ AA + GI V N PG TE AE A +L LA
Sbjct: 56 IDAEVLEKLPGL--KLIATRSAGYDNVDLEAAKERGITVTNVPGYSTEAVAEHAVALILA 113
Query: 134 AARRIVEADEFMRAGLYDGW-LPNLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNL 192
ARRI E D +R G + P+ +G L+G+T+G+IG GRIG A AR + +GF M +
Sbjct: 114 LARRIHEGDRRVREGNWSLSGGPDPLLGFDLRGKTLGIIGLGRIGQAVARRL-KGFGMKV 172
Query: 193 IYYDLYQATRLEKFVTAYGQFLKANGEQPVTWKRASSMDEVLREADVISLHPVLDKTTYH 252
+YYD EK +++ +DE+L E+D+ISLH L T H
Sbjct: 173 LYYDRSPNPEAEK--ELGARYV--------------DLDELLAESDIISLHCPLTPETRH 216
Query: 253 LINKERLATMKKEAILVNCSRGPVIDEVALVEHLKQNPMFRVGLDVFEDEPYMKP----G 308
LIN E LA MK AILVN +RG ++DE AL++ LK + GLDVFE+EP +
Sbjct: 217 LINAEELAKMKPGAILVNTARGGLVDEQALIDALKSGKIAGAGLDVFENEPALFDHPLLR 276
Query: 309 LSEMKNAIVVPHIASASKWTREGMATLAALNVL 341
L N ++ PHIASA++ R+ MA LA N+
Sbjct: 277 LDNFPNVVLTPHIASATEEARKAMAELALENLE 309
>gnl|CDD|183914 PRK13243, PRK13243, glyoxylate reductase; Reviewed.
Length = 333
Score = 242 bits (619), Expect = 3e-78
Identities = 137/331 (41%), Positives = 193/331 (58%), Gaps = 27/331 (8%)
Query: 15 KYRVVSTKPMPGTRWINLLIEQDCRVEICTQKKTILSVEDIIALIGDKCDGVIGQLTEDW 74
K +V T+ +P I +L E+ VE+ ++ I E ++ + D D ++ L+E
Sbjct: 2 KPKVFITREIP-ENGIEML-EEHFEVEVWEDEREI-PREVLLEKVRD-VDALVTMLSERI 57
Query: 75 GETLFAALSRAGGKAFSNMAVGYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAA 134
+F A R + +N AVGY+N+DV A + GI V NTPGVLTE TA+ A +L LA
Sbjct: 58 DCEVFEAAPRL--RIVANYAVGYDNIDVEEATRRGIYVTNTPGVLTEATADFAWALLLAT 115
Query: 135 ARRIVEADEFMRAGLYD----GWLPNLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKM 190
ARR+VEAD F+R+G + W P +F+G + G+T+G+IG GRIG A AR +GF M
Sbjct: 116 ARRLVEADHFVRSGEWKRRGVAWHPLMFLGYDVYGKTIGIIGFGRIGQAVARR-AKGFGM 174
Query: 191 NLIYYDLYQATRLEKFVTAYGQFLKANGEQPVTWKRASSMDEVLREADVISLHPVLDKTT 250
++YY + EK + A ++E+LRE+D +SLH L K T
Sbjct: 175 RILYYSRTRKPEAEKELGA----------------EYRPLEELLRESDFVSLHVPLTKET 218
Query: 251 YHLINKERLATMKKEAILVNCSRGPVIDEVALVEHLKQNPMFRVGLDVFEDEPYMKPGLS 310
YH+IN+ERL MK AILVN +RG V+D ALV+ LK+ + GLDVFE+EPY L
Sbjct: 219 YHMINEERLKLMKPTAILVNTARGKVVDTKALVKALKEGWIAGAGLDVFEEEPYYNEELF 278
Query: 311 EMKNAIVVPHIASASKWTREGMATLAALNVL 341
+KN ++ PHI SA+ REGMA L A N++
Sbjct: 279 SLKNVVLAPHIGSATFEAREGMAELVAENLI 309
>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 = 240 bits (614), Expect = 8e-78
Identities = 116/325 (35%), Positives = 160/325 (49%), Gaps = 52/325 (16%)
Query: 30 INLLIEQDCRVEICTQKKTILSVEDIIALIGDKCDGVI----GQLTEDWGETLFAA---- 81
+ LL E V++ LS E+++A+I D D +I ++T + + A
Sbjct: 13 LELLREAGIEVDV----APGLSEEELLAIIAD-ADALIVRSATKVTAE----VIEAAPRL 63
Query: 82 --LSRAGGKAFSNMAVGYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIV 139
+ RAG VG +N+DV AA GI V N PG T + AE +L LA AR I
Sbjct: 64 KVIGRAG--------VGVDNIDVEAATARGILVVNAPGANTISVAEHTIALMLALARNIP 115
Query: 140 EADEFMRAGLYDGWLPNLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLY- 198
+AD +RAG W F+G L+G+T+G++G GRIG AR F M ++ YD Y
Sbjct: 116 QADASLRAG---KWDRKKFMGVELRGKTLGIVGLGRIGREVARRAR-AFGMKVLAYDPYI 171
Query: 199 QATRLEKFVTAYGQFLKANGEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHLINKER 258
A R S+DE+L EAD ISLH L T LIN E
Sbjct: 172 SAERAAAGGV-----------------ELVSLDELLAEADFISLHTPLTPETRGLINAEE 214
Query: 259 LATMKKEAILVNCSRGPVIDEVALVEHLKQNPMFRVGLDVFEDEPYMKPG--LSEMKNAI 316
LA MK AIL+N +RG ++DE AL + LK + LDVFE EP L + N I
Sbjct: 215 LAKMKPGAILINTARGGIVDEAALADALKSGKIAGAALDVFEQEP-PPADSPLLGLPNVI 273
Query: 317 VVPHIASASKWTREGMATLAALNVL 341
+ PH+ ++++ +E +A AA VL
Sbjct: 274 LTPHLGASTEEAQERVAVDAAEQVL 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 = 235 bits (601), Expect = 7e-76
Identities = 107/295 (36%), Positives = 149/295 (50%), Gaps = 23/295 (7%)
Query: 48 TILSVEDIIALIGDKCDGVIGQLTEDWGETLFAALSRAGGKAFSNMAVGYNNVDVNAANK 107
L +++ AL+ D D +I T + A + K G +N+D++AA K
Sbjct: 28 DDLLADELEALLAD-ADALIVSSTTPVTAEVLAKAPKL--KFIQVAGAGVDNIDLDAAKK 84
Query: 108 YGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDGWLPNLFVGNLLKGQT 167
GI V N PG E AE A L LA RR+ AD +R G W F G L+G+T
Sbjct: 85 RGITVTNVPGANAEAVAEHALGLLLALLRRLPRADAAVRRGWGWLWAG--FPGYELEGKT 142
Query: 168 VGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQFLKANGEQPVTWKRA 227
VG++G GRIG A+ + + F M ++YYD + E+ R
Sbjct: 143 VGIVGLGRIGQRVAKRL-QAFGMKVLYYDRTRKPEPEED----------------LGFRV 185
Query: 228 SSMDEVLREADVISLHPVLDKTTYHLINKERLATMKKEAILVNCSRGPVIDEVALVEHLK 287
S+DE+L ++DV+ LH L T HLIN+E LA MK A+LVN +RG ++DE AL+ LK
Sbjct: 186 VSLDELLAQSDVVVLHLPLTPETRHLINEEELALMKPGAVLVNTARGGLVDEDALLRALK 245
Query: 288 QNPMFRVGLDVFEDEPYMKPG-LSEMKNAIVVPHIASASKWTREGMATLAALNVL 341
+ LDVFE EP L E+ N I+ PHIA ++ RE MA +A N+
Sbjct: 246 SGKIAGAALDVFEPEPLPADHPLLELPNVILTPHIAGYTEEARERMAEIAVENLE 300
>gnl|CDD|223189 COG0111, SerA, Phosphoglycerate dehydrogenase and related
dehydrogenases [Amino acid transport and metabolism].
Length = 324
Score = 218 bits (558), Expect = 4e-69
Identities = 106/292 (36%), Positives = 145/292 (49%), Gaps = 25/292 (8%)
Query: 52 VEDIIALIGDKCDGVIGQLTEDWGETLFAALSRAGGKAFSNMAVGYNNVDVNAANKYGIA 111
E+ + D +I +T E + AA KA G +N+D+ AA K GI
Sbjct: 35 DEEELLEALADADALIVSVTP-VTEEVLAAAPN--LKAIGRAGAGVDNIDLEAATKRGIL 91
Query: 112 VGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDGWLPNLFVGNLLKGQTVGVI 171
V N PG + AEL +L LA ARRI +AD R G W F G L G+TVG+I
Sbjct: 92 VVNAPGGNAISVAELVLALLLALARRIPDADASQRRG---EWDRKAFRGTELAGKTVGII 148
Query: 172 GAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQFLKANGEQPVTWKRASSMD 231
G GRIG A A+ + + F M +I YD Y G S+D
Sbjct: 149 GLGRIGRAVAKRL-KAFGMKVIGYDPYSPRERAGVDGVVG---------------VDSLD 192
Query: 232 EVLREADVISLHPVLDKTTYHLINKERLATMKKEAILVNCSRGPVIDEVALVEHLKQNPM 291
E+L EAD+++LH L T LIN E LA MK AIL+N +RG V+DE AL+ L +
Sbjct: 193 ELLAEADILTLHLPLTPETRGLINAEELAKMKPGAILINAARGGVVDEDALLAALDSGKI 252
Query: 292 FRVGLDVFEDEPYMKPG--LSEMKNAIVVPHIASASKWTREGMATLAALNVL 341
LDVFE+EP + L ++ N I+ PHI ++ +E +A + A N++
Sbjct: 253 AGAALDVFEEEP-LPADSPLWDLPNVILTPHIGGSTDEAQERVAEIVAENIV 303
>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 = 205 bits (523), Expect = 4e-64
Identities = 92/247 (37%), Positives = 130/247 (52%), Gaps = 20/247 (8%)
Query: 95 VGYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDGWL 154
VG +N+DV A K GI V NTPG + + AEL L L+ AR I A+ M+ G W
Sbjct: 72 VGLDNIDVEYAKKKGIKVINTPGASSNSVAELVIGLMLSLARFIHRANREMKLG---KWN 128
Query: 155 PNLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQFL 214
+ G L+G+T+G+IG GRIG A++ MN+I YD Y +
Sbjct: 129 KKKYKGIELRGKTLGIIGFGRIGREVAKI-ARALGMNVIAYDPYPKDEQAVELGV----- 182
Query: 215 KANGEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHLINKERLATMKKEAILVNCSRG 274
+ S++E+L+ +D ISLH L T H+INK+ L MK AI++N SRG
Sbjct: 183 -----------KTVSLEELLKNSDFISLHVPLTPETKHMINKKELELMKDGAIIINTSRG 231
Query: 275 PVIDEVALVEHLKQNPMFRVGLDVFEDEPYMKPGLSEMKNAIVVPHIASASKWTREGMAT 334
VIDE AL+E LK + LDVFE+EP L E+ N + PHI +++K +E +
Sbjct: 232 GVIDEEALLEALKSGKLAGAALDVFENEPPPGSKLLELPNVSLTPHIGASTKEAQERIGE 291
Query: 335 LAALNVL 341
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 = 205 bits (524), Expect = 4e-64
Identities = 99/277 (35%), Positives = 144/277 (51%), Gaps = 22/277 (7%)
Query: 65 GVIGQLTEDWGETLFAALSRAGGKAFSNMAVGYNNVDVNAANKYGIAVGNTPGVLTETTA 124
G G E+ L + L K ++ GY+ +DV+A K GI V NTPG + E TA
Sbjct: 60 GETGPFDEE----LISPLP-PSLKIIAHAGAGYDQIDVDALTKRGIQVSNTPGAVDEATA 114
Query: 125 ELAASLSLAAARRIVEADEFMRAGLYDGWLPNLFVGNLLKGQTVGVIGAGRIGSAYARMM 184
+ A L L A R A+ RAG + G+L + +G+T+G++G G IG A AR
Sbjct: 115 DTALFLILGALRNFSRAERSARAGKWRGFLDLTLAHDP-RGKTLGILGLGGIGKAIARKA 173
Query: 185 VEGFKMNLIYYDLYQATRLEKFVTAYGQFLKANGEQPVTWKRASSMDEVLREADVISLHP 244
F M +IY++ + + A S+DE+L ++DV+SL+
Sbjct: 174 A-AFGMKIIYHNRSRLPEELEKALA---------------TYYVSLDELLAQSDVVSLNC 217
Query: 245 VLDKTTYHLINKERLATMKKEAILVNCSRGPVIDEVALVEHLKQNPMFRVGLDVFEDEPY 304
L T HLINK+ A MK I+VN +RG VIDE ALV+ L+ + GLDVFE+EP
Sbjct: 218 PLTAATRHLINKKEFAKMKDGVIIVNTARGAVIDEDALVDALESGKVASAGLDVFENEPE 277
Query: 305 MKPGLSEMKNAIVVPHIASASKWTREGMATLAALNVL 341
+ PGL +M N ++PH+ + + T+E M L N+
Sbjct: 278 VNPGLLKMPNVTLLPHMGTLTVETQEKMEELVLENIE 314
>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 = 198 bits (507), Expect = 1e-61
Identities = 99/279 (35%), Positives = 137/279 (49%), Gaps = 34/279 (12%)
Query: 53 EDIIALIGDKCDGVIGQ---LTEDWGETLFAALSRAGGKAFSNMAVGYNNVDVNAANKYG 109
+++I D D ++ Q +T + + AL R K VG +NVDV AA + G
Sbjct: 36 DELIEAAAD-ADALLVQYAPVTAE----VIEALPR--LKVIVRYGVGVDNVDVAAATERG 88
Query: 110 IAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDGWLPNLFVGNL--LKGQT 167
I V N P TE A+ A +L LA AR++ D +RAG +D + G + L+G T
Sbjct: 89 IPVCNVPDYCTEEVADHALALILALARKLPFLDRAVRAGGWDWTV----GGPIRRLRGLT 144
Query: 168 VGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQFLKANGEQPVTWKRA 227
+G++G GRIG A A+ + F +I YD Y +G + R
Sbjct: 145 LGLVGFGRIGRAVAKRA-KAFGFRVIAYDPY----------------VPDGVAALGGVRV 187
Query: 228 SSMDEVLREADVISLHPVLDKTTYHLINKERLATMKKEAILVNCSRGPVIDEVALVEHLK 287
S+DE+L +DV+SLH L T HLI+ E LA MK A LVN +RG ++DE AL LK
Sbjct: 188 VSLDELLARSDVVSLHCPLTPETRHLIDAEALALMKPGAFLVNTARGGLVDEAALARALK 247
Query: 288 QNPMFRVGLDVFEDEPYMKPG-LSEMKNAIVVPHIASAS 325
+ LDV E+EP L N I+ PH A S
Sbjct: 248 SGRIAGAALDVLEEEPPPADSPLLSAPNVILTPHAAWYS 286
>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 = 197 bits (503), Expect = 5e-61
Identities = 113/329 (34%), Positives = 159/329 (48%), Gaps = 32/329 (9%)
Query: 17 RVVSTKPMPGTRW--INLLIEQDCRVEICTQKKTILSVEDIIALIGDKCDGVIGQLTEDW 74
+V+ P + L+ VE+ T +++ AL+ D D ++ + +
Sbjct: 1 KVLFLGPEFPDAEELLRALLPPAPGVEV----VTAAELDEEAALLAD-ADVLVPGMRKVI 55
Query: 75 GETLFAALSRAGGKAFSNMAVGYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAA 134
L AA R + VG + VD+ AA GI V N PG E+ AE A L LA
Sbjct: 56 DAELLAAAPRL--RLIQQPGVGLDGVDLEAATARGIPVANIPGGNAESVAEHAVMLMLAL 113
Query: 135 ARRIVEADEFMRAGLYDGW-LPNLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLI 193
RR+ EAD +RAG W P L G+TVG++G G IG A AR + GF + +I
Sbjct: 114 LRRLPEADRELRAG---RWGRPEGRPSRELSGKTVGIVGLGNIGRAVARRLR-GFGVEVI 169
Query: 194 YYDLYQATRLEKFVTAYGQFLKANGEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHL 253
YYD +F E+ R +DE+L E+DV+SLH L T HL
Sbjct: 170 YYD---------------RFRDPEAEEKDLGVRYVELDELLAESDVVSLHVPLTPETRHL 214
Query: 254 INKERLATMKKEAILVNCSRGPVIDEVALVEHLKQNPMFRVGLDVFEDEPYMKPG--LSE 311
I E LA MK AIL+N +RG ++DE AL+ L+ + GLDVF EP + P L
Sbjct: 215 IGAEELAAMKPGAILINTARGGLVDEEALLAALRSGHLAGAGLDVFWQEP-LPPDDPLLR 273
Query: 312 MKNAIVVPHIASASKWTREGMATLAALNV 340
+ N I+ PHIA + + + MA + A N+
Sbjct: 274 LDNVILTPHIAGVTDESYQRMAAIVAENI 302
>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 (484), Expect = 5e-60
Identities = 88/196 (44%), Positives = 109/196 (55%), Gaps = 24/196 (12%)
Query: 129 SLSLAAARRIVEADEFMRAGLYDGWLPNLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGF 188
+L LA ARRI EAD +RAG W P+ +G L G+TVG+IG GRIG A AR + + F
Sbjct: 2 ALLLALARRIPEADRQVRAG---RWRPDALLGRELSGKTVGIIGLGRIGRAVARRL-KAF 57
Query: 189 KMNLIYYDLYQATRLEKFVTAYGQFLKANGEQPVTWKRASSMDEVLREADVISLHPVLDK 248
M +I YD Y E Y S+DE+L E+DV+SLH L
Sbjct: 58 GMKVIAYDRYPKAEAEALGARY-----------------VSLDELLAESDVVSLHLPLTP 100
Query: 249 TTYHLINKERLATMKKEAILVNCSRGPVIDEVALVEHLKQNPMFRVGLDVFEDEPYMKPG 308
T HLIN ERLA MK AIL+N +RG ++DE AL+ LK + LDVFE EP P
Sbjct: 101 ETRHLINAERLALMKPGAILINTARGGLVDEDALIAALKSGRIAGAALDVFEPEPL-PPD 159
Query: 309 --LSEMKNAIVVPHIA 322
L E+ N I+ PHIA
Sbjct: 160 HPLLELPNVILTPHIA 175
>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 = 191 bits (487), Expect = 2e-58
Identities = 91/274 (33%), Positives = 136/274 (49%), Gaps = 34/274 (12%)
Query: 63 CDGVIGQLTEDWGETLFAALSRAGGKAFSNMAVGYNNVDVNAANKYGIAVGNTPGVLTET 122
DGV+ Q T + E ++ L+ G K + + G + +D++ A + G+ + N P
Sbjct: 45 YDGVVVQQTLPYDEEVYEKLAEYGIKQIALRSAGVDMIDLDLAKENGLKITNVPAYSPRA 104
Query: 123 TAELAASLSLAAARRIVEADEFMRAGLYDGWLPNLFVGNLLKGQTVGVIGAGRIGSAYAR 182
AE A + +L R E D + G + W P L +G ++ TVG+IG GRIGSA A+
Sbjct: 105 IAEFAVTQALNLLRNTPEIDRRVAKGDFR-WAPGL-IGREIRDLTVGIIGTGRIGSAAAK 162
Query: 183 MMVEGFKMNLIYYDLYQATRLEKFVTAYGQFLKANGEQPVTWKRASSMDEVLREADVISL 242
+ +GF +I YD Y LEKF+ Y S++++L++AD+ISL
Sbjct: 163 IF-KGFGAKVIAYDPYPNPELEKFLLYY-----------------DSLEDLLKQADIISL 204
Query: 243 HPVLDKTTYHLINKERLATMKKEAILVNCSRGPVIDEVALVEHLKQNPMFRVGLDVFEDE 302
H L K +HLIN E A MK AILVN +RG ++D AL++ L + LD +E+E
Sbjct: 205 HVPLTKENHHLINAEAFAKMKDGAILVNAARGGLVDTKALIDALDSGKIAGAALDTYENE 264
Query: 303 -PYMKPGLS-------------EMKNAIVVPHIA 322
Y S M N ++ PHIA
Sbjct: 265 TGYFNKDWSGKEIEDEVLKELIAMPNVLITPHIA 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 = 189 bits (482), Expect = 7e-58
Identities = 93/309 (30%), Positives = 140/309 (45%), Gaps = 23/309 (7%)
Query: 33 LIEQDCRVEICTQKKTILSVEDIIALIGDKCDGVIGQLTEDWGETLFAALSRAGGKAFSN 92
L+++ VE+ + L E+++ D D +I + T + A K +
Sbjct: 14 LLKEGGEVEVHDE----LLTEELLEAAKD-ADALIVRSTTPVTAEVLEAAPGL--KVIAR 66
Query: 93 MAVGYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDG 152
VG +N+D++AA + GI V N PG TE+ AEL L LA ARRI EAD +RAG +
Sbjct: 67 RGVGVDNIDLDAATERGILVTNVPGYSTESVAELTVGLILALARRIPEADASVRAGDWKK 126
Query: 153 WLPNLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQ 212
P L G+T+GVIG G IG A + + M ++ YD Y +
Sbjct: 127 GGPIGL---ELYGKTLGVIGGGGIGGIGAAIA-KALGMGVVAYDPYPNPERAEEGGVEVL 182
Query: 213 FLKANGEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHLINKERLATMKKEAILVNCS 272
L + ++ D+I+L P T H+I E +K + N
Sbjct: 183 LLDLL------------LLDLKESDDLINLAPPTTMKTGHIIINEARGMLKDAVAINNAR 230
Query: 273 RGPVIDEVALVEHLKQNPMFRVGLDVFEDEPYMKPGLSEMKNAIVVPHIASASKWTREGM 332
G VI+E AL L++ V E+ P + L ++ N I+ PHIA A++ +E M
Sbjct: 231 GGGVIEEAALDALLEEGIAAAALDVVEEEPPPVNSPLLDLPNVILTPHIAGATEEAQENM 290
Query: 333 ATLAALNVL 341
A AA N+L
Sbjct: 291 AEEAAENLL 299
>gnl|CDD|237436 PRK13581, PRK13581, D-3-phosphoglycerate dehydrogenase;
Provisional.
Length = 526
Score = 194 bits (495), Expect = 1e-57
Identities = 111/316 (35%), Positives = 153/316 (48%), Gaps = 64/316 (20%)
Query: 33 LIEQDCRVEICTQKKTILSVEDIIALIGDKCDGVIG----QLTEDWGETLFAALS----- 83
+++ VE+ KT L E+++ +IGD D +I ++T + + A
Sbjct: 16 ILKDAPGVEVDV--KTGLDKEELLEIIGD-YDALIVRSATKVTAE----VLEAAKNLKVI 68
Query: 84 -RAGGKAFSNMAVGYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEAD 142
RAG VG +NVDV AA + GI V N P T + AE +L LA AR I +A
Sbjct: 69 GRAG--------VGVDNVDVPAATRRGIIVVNAPTGNTISAAEHTIALMLALARNIPQAH 120
Query: 143 EFMRAGLYDGWLPNLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATR 202
++AG W F+G L G+T+G+IG GRIGS A+ + F M +I YD Y
Sbjct: 121 ASLKAGK---WERKKFMGVELYGKTLGIIGLGRIGSEVAKRA-KAFGMKVIAYDPY---- 172
Query: 203 LEKFVTAYGQFLKANGEQPVTWKRASSM-------DEVLREADVISLHPVLDKTTYHLIN 255
++ +RA+ + DE+L AD I+LH L T LI
Sbjct: 173 -------------------ISPERAAQLGVELVSLDELLARADFITLHTPLTPETRGLIG 213
Query: 256 KERLATMKKEAILVNCSRGPVIDEVALVEHLKQNPMFRVGLDVFEDEP-YMKPGLSEMKN 314
E LA MK ++NC+RG +IDE AL E LK + LDVFE EP P L E+ N
Sbjct: 214 AEELAKMKPGVRIINCARGGIIDEAALAEALKSGKVAGAALDVFEKEPPTDSP-LFELPN 272
Query: 315 AIVVPHIASASKWTRE 330
+V PH+ AS T E
Sbjct: 273 VVVTPHLG-AS--TAE 285
>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 = 186 bits (474), Expect = 1e-56
Identities = 94/251 (37%), Positives = 137/251 (54%), Gaps = 24/251 (9%)
Query: 91 SNMAVGYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLY 150
++ VGY+ +D++AA GI V NTPGVLT+ A+LA L LA RRI AD F+RAG
Sbjct: 69 ASFGVGYDGIDLDAARARGIRVTNTPGVLTDDVADLAVGLLLAVLRRIPAADRFVRAG-- 126
Query: 151 DGWLPNLF-VGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTA 209
W F + + G+ VG++G GRIG A AR +E F M + Y+ R K
Sbjct: 127 -RWPKGAFPLTRKVSGKRVGIVGLGRIGRAIAR-RLEAFGMEIAYHG-----RRPK---- 175
Query: 210 YGQFLKANGEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHLINKERLATMKKEAILV 269
V ++ +S+ E+ E+DV+ + T HL+N E L + + +LV
Sbjct: 176 ----------PDVPYRYYASLLELAAESDVLVVACPGGPATRHLVNAEVLEALGPDGVLV 225
Query: 270 NCSRGPVIDEVALVEHLKQNPMFRVGLDVFEDEPYMKPGLSEMKNAIVVPHIASASKWTR 329
N +RG V+DE AL+ L++ + GLDVFE+EP + L ++ N ++ PHIASA+ TR
Sbjct: 226 NVARGSVVDEAALIAALQEGRIAGAGLDVFENEPNVPAALLDLDNVVLTPHIASATVETR 285
Query: 330 EGMATLAALNV 340
M L N+
Sbjct: 286 RAMGDLVLANL 296
>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 (472), Expect = 3e-56
Identities = 98/279 (35%), Positives = 152/279 (54%), Gaps = 24/279 (8%)
Query: 66 VIGQLTEDWGETLFAALSRAGGKAFSNMAVGYNNVDVNAANKYGIAVGNTPG-VLTETTA 124
+I +T ++ + F K + +GY+NVD+ AA ++G+ V PG V + A
Sbjct: 51 IIASVTPNFDKEFFEYNDGL--KLIARHGIGYDNVDLKAATEHGVIVTRVPGAVERDAVA 108
Query: 125 ELAASLSLAAARRIVEADEFMRAGLYDGWLPNLFVGNLLKGQTVGVIGAGRIGSAYARMM 184
E A +L L R+I +A E ++ G + FVG+ L G+TVG+IG G IGS A ++
Sbjct: 109 EHAVALILTVLRKINQASEAVKEGKWT--ERANFVGHELSGKTVGIIGYGNIGSRVAEIL 166
Query: 185 VEGFKMNLIYYDLYQATRLEKFVTAYGQFLKANGEQPVTWKRASSMDEVLREADVISLHP 244
EGF ++ YD Y + + +K G +PV S++E+L E+D+ISLH
Sbjct: 167 KEGFNAKVLAYDPYVSE----------EVIKKKGAKPV------SLEELLAESDIISLHA 210
Query: 245 VLDKTTYHLINKERLATMKKEAILVNCSRGPVIDEVALVEHLKQNPMFRVGLDVFEDEPY 304
L + TYH+IN++ + MKK ILVN +RG +IDE AL+E LK + GLDV E+EP
Sbjct: 211 PLTEETYHMINEKAFSKMKKGVILVNTARGELIDEEALIEALKSGKIAGAGLDVLEEEP- 269
Query: 305 MKPG--LSEMKNAIVVPHIASASKWTREGMATLAALNVL 341
+K L +N ++ PHI + + + GM ++
Sbjct: 270 IKADHPLLHYENVVITPHIGAYTYESLYGMGEKVVDDIE 308
>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 = 184 bits (469), Expect = 5e-56
Identities = 90/255 (35%), Positives = 132/255 (51%), Gaps = 30/255 (11%)
Query: 93 MAVGYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLY-- 150
+A GYNNVD+ AA + GI V N PG T++ A+ +L LA AR + ++ ++AG +
Sbjct: 72 LATGYNNVDLAAAKERGITVTNVPGYSTDSVAQHTFALLLALARLVAYHNDVVKAGEWQK 131
Query: 151 -DGWLPNLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRL-EKFVT 208
+ + L G+T+G+IG G IG A AR+ F M +++ + A L E +V
Sbjct: 132 SPDFCFWDYPIIELAGKTLGIIGYGNIGQAVARI-ARAFGMKVLFAERKGAPPLREGYV- 189
Query: 209 AYGQFLKANGEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHLINKERLATMKKEAIL 268
S+DE+L ++DVISLH L T +LIN E LA MK AIL
Sbjct: 190 --------------------SLDELLAQSDVISLHCPLTPETRNLINAEELAKMKPGAIL 229
Query: 269 VNCSRGPVIDEVALVEHLKQNPMFRVGLDVFEDEPYMKPG---LSEMKNAIVVPHIASAS 325
+N +RG ++DE AL + L + GLDV EP + L N I+ PHIA AS
Sbjct: 230 INTARGGLVDEQALADALNSGKIAGAGLDVLSQEP-PRADNPLLKAAPNLIITPHIAWAS 288
Query: 326 KWTREGMATLAALNV 340
+ R+ + + N+
Sbjct: 289 REARQRLMDILVDNI 303
>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 = 181 bits (461), Expect = 1e-54
Identities = 94/326 (28%), Positives = 141/326 (43%), Gaps = 41/326 (12%)
Query: 30 INLLIEQDCRVEICTQKKTILSVEDIIALIGDKCDGVIGQLTEDWGETLFAALSRAGGKA 89
+L VEI T +L+ ++ L D ++ T+ L G K
Sbjct: 17 KEILKAGGVDVEIVT---YLLNDDETAELAKG-ADAILTAFTDKIDAELLDKA--PGLKF 70
Query: 90 FSNMAVGYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGL 149
S A GY+N+D++ A + GI V N P AE +L LA R DE +
Sbjct: 71 ISLRATGYDNIDLDYAKELGIGVTNVPEYSPNAVAEHTIALILALLRNRKYIDERDKNQD 130
Query: 150 YDGWLPNLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTA 209
+ G L+ QTVGV+G G+IG A A+ +GF M +I YD ++ LE
Sbjct: 131 LQ-DAGVI--GRELEDQTVGVVGTGKIGRAVAQRA-KGFGMKVIAYDPFRNPELEDKGVK 186
Query: 210 YGQFLKANGEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHLINKERLATMKKEAILV 269
Y S++E+ + +D+ISLH L +H+IN+E MKK I++
Sbjct: 187 Y-----------------VSLEELFKNSDIISLHVPLTPENHHMINEEAFKLMKKGVIII 229
Query: 270 NCSRGPVIDEVALVEHLKQNPMFRVGLDVFEDEPYM--------------KPGLSEMKNA 315
N +RG ++D AL+E L +F GLDV EDE L N
Sbjct: 230 NTARGSLVDTEALIEALDSGKIFGAGLDVLEDETPDLLKDLEGEIFKDALNALLGRRPNV 289
Query: 316 IVVPHIASASKWTREGMATLAALNVL 341
I+ PH A + + M ++ N++
Sbjct: 290 IITPHTAFYTDDALKNMVEISCENIV 315
>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 = 9e-54
Identities = 80/233 (34%), Positives = 120/233 (51%), Gaps = 21/233 (9%)
Query: 96 GYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDGWLP 155
G NVDV AA + GI V NTPG E AE L LA R I A ++ G +
Sbjct: 77 GPENVDVEAATERGIPVLNTPGRNAEAVAEFTVGLMLAETRNIARAHAALKDGEWRKDYY 136
Query: 156 NL-FVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQFL 214
N G L+G+TVG++G G IG A+ + + F ++ YD +V + +
Sbjct: 137 NYDGYGPELRGKTVGIVGFGAIGRRVAKRL-KAFGAEVLVYD--------PYVDP--EKI 185
Query: 215 KANGEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHLINKERLATMKKEAILVNCSRG 274
+A+G + V S++E+L+ +DV+SLH L T +I E A MK A +N +R
Sbjct: 186 EADGVKKV------SLEELLKRSDVVSLHARLTPETRGMIGAEEFALMKPTAYFINTARA 239
Query: 275 PVIDEVALVEHLKQNPMFRVGLDVFEDEPYMKPG--LSEMKNAIVVPHIASAS 325
++DE AL+E L++ + LDVF +EP + L ++ N + PHIA A+
Sbjct: 240 GLVDEDALIEALEEGKIGGAALDVFPEEP-LPADHPLLKLDNVTLTPHIAGAT 291
>gnl|CDD|185307 PRK15409, PRK15409, bifunctional glyoxylate/hydroxypyruvate
reductase B; Provisional.
Length = 323
Score = 178 bits (452), Expect = 2e-53
Identities = 101/282 (35%), Positives = 148/282 (52%), Gaps = 26/282 (9%)
Query: 64 DGVIGQLTEDWGETLFAALSRAGGK--AFSNMAVGYNNVDVNAANKYGIAVGNTPGVLTE 121
+G++G GE + AAL K A S ++VGY+N DV+A I + +TP VLTE
Sbjct: 47 EGLLGS-----GEKVDAALLEKMPKLRAASTISVGYDNFDVDALTARKILLMHTPTVLTE 101
Query: 122 TTAELAASLSLAAARRIVEADEFMRAGLYDGWLPNLFVGNLLKGQTVGVIGAGRIGSAYA 181
T A+ +L L+ ARR+VE E ++AG + + + G + +T+G++G GRIG A A
Sbjct: 102 TVADTLMALVLSTARRVVEVAERVKAGEWTASIGPDWFGTDVHHKTLGIVGMGRIGMALA 161
Query: 182 RMMVEGFKMNLIYYDLYQATRLEKFVTAYGQFLKANGEQPVTWKRASSMDEVLREADVIS 241
+ GF M ++Y E+ A R +D +L+E+D +
Sbjct: 162 QRAHFGFNMPILYNARRHHKEAEERFNA----------------RYCDLDTLLQESDFVC 205
Query: 242 LHPVLDKTTYHLINKERLATMKKEAILVNCSRGPVIDEVALVEHLKQNPMFRVGLDVFED 301
+ L T+HL E+ A MK AI +N RGPV+DE AL+ L++ + GLDVFE
Sbjct: 206 IILPLTDETHHLFGAEQFAKMKSSAIFINAGRGPVVDENALIAALQKGEIHAAGLDVFEQ 265
Query: 302 EPYMK--PGLSEMKNAIVVPHIASASKWTREGMATLAALNVL 341
EP P LS + N + VPHI SA+ TR MA A N++
Sbjct: 266 EPLSVDSPLLS-LPNVVAVPHIGSATHETRYNMAACAVDNLI 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 = 181 bits (461), Expect = 1e-52
Identities = 116/340 (34%), Positives = 172/340 (50%), Gaps = 57/340 (16%)
Query: 17 RVVSTKPM-PGTRWINLLIEQDCRVEICTQKKTILSVEDIIALIGDKCDGVI----GQLT 71
+V+ P+ P I++L + V++ +T LS E+++ +I D D +I ++T
Sbjct: 1 KVLIADPISPDG--IDILEDVGVEVDV----QTGLSREELLEIIPDY-DALIVRSATKVT 53
Query: 72 EDWGETLFAALS------RAGGKAFSNMAVGYNNVDVNAANKYGIAVGNTPGVLTETTAE 125
E+ + AA RAG VG +N+D+ AA GI V N P T + AE
Sbjct: 54 EE----VIAAAPKLKVIGRAG--------VGVDNIDIEAATARGILVVNAPTGNTISAAE 101
Query: 126 LAASLSLAAARRIVEADEFMRAGLYDGWLPNLFVGNLLKGQTVGVIGAGRIGSAYARMMV 185
A ++ LAAAR I +AD ++ G W F+G L G+T+GVIG GRIGS A+
Sbjct: 102 HALAMLLAAARNIPQADASLKEG---EWDRKAFMGTELYGKTLGVIGLGRIGSIVAKR-A 157
Query: 186 EGFKMNLIYYDLY----QATRLEKFVTAYGQFLKANGEQPVTWKRASSMDEVLREADVIS 241
+ F M ++ YD Y +A +L + +DE+L AD I+
Sbjct: 158 KAFGMKVLAYDPYISPERAEQL-------------------GVELVDDLDELLARADFIT 198
Query: 242 LHPVLDKTTYHLINKERLATMKKEAILVNCSRGPVIDEVALVEHLKQNPMFRVGLDVFED 301
+H L T LI E LA MKK I+VNC+RG +IDE AL E L++ + LDVFE
Sbjct: 199 VHTPLTPETRGLIGAEELAKMKKGVIIVNCARGGIIDEAALYEALEEGHVRAAALDVFEK 258
Query: 302 EPYMKPGLSEMKNAIVVPHIASASKWTREGMATLAALNVL 341
EP L ++ N I PH+ ++++ +E +AT A VL
Sbjct: 259 EPPTDNPLFDLDNVIATPHLGASTREAQENVATQVAEQVL 298
>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 = 175 bits (447), Expect = 1e-52
Identities = 112/334 (33%), Positives = 153/334 (45%), Gaps = 32/334 (9%)
Query: 17 RVVSTKPMPGTRWINLLIEQDCRVEICTQKKTILSVEDIIALIGDKCDGVIGQLTEDWGE 76
+VV T + + LL + C V + LS E+++ D DG++ + +
Sbjct: 3 KVVITHKVH-PEVLELL-KPHCEVISNQTDEP-LSREELLRRCKD-ADGLMAFMPDRIDA 58
Query: 77 TLFAALSRAGGKAFSNMAVGYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAAR 136
A R K + GY+N DV A GI V P +LTE TAEL L + R
Sbjct: 59 DFLDACPRL--KIIACALKGYDNFDVEACTARGIWVTIVPDLLTEPTAELTIGLLIGLGR 116
Query: 137 RIVEADEFMRAGLYDGWLPNLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYD 196
I+ D F+R+G + GW P + G L G+TVG++G G +G A AR + GF L+YYD
Sbjct: 117 HILAGDRFVRSGKFGGWRPKFY-GTGLDGKTVGILGMGALGRAIARRLS-GFGATLLYYD 174
Query: 197 LYQATRLEKFVTAYGQFLKANGEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHLINK 256
A Q L R +DE+L +D + L L T HLIN
Sbjct: 175 ------PHPLDQAEEQALNL---------RRVELDELLESSDFLVLALPLTPDTLHLINA 219
Query: 257 ERLATMKKEAILVNCSRGPVIDEVALVEHLKQNPMFRVGLDVFEDEPYMKP--------G 308
E LA MK A+LVN RG V+DE A+ E LK + DVFE E + +P
Sbjct: 220 EALAKMKPGALLVNPCRGSVVDEAAVAEALKSGHLGGYAADVFEMEDWARPDRPRSIPQE 279
Query: 309 LSEMK-NAIVVPHIASASKWTREGMATLAALNVL 341
L + + PHI SA R + AALN+L
Sbjct: 280 LLDQHDRTVFTPHIGSAVDEVRLEIELEAALNIL 313
>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 = 170 bits (432), Expect = 2e-50
Identities = 90/244 (36%), Positives = 127/244 (52%), Gaps = 27/244 (11%)
Query: 95 VGYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDGWL 154
G ++VD+ A + GI V N G TE AEL L++ R IV D +RAG
Sbjct: 78 TGVDHVDLEACKERGITVSNAAGYSTEAVAELTIGLAIDLLRNIVPCDAAVRAG----GT 133
Query: 155 PNLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQFL 214
+G L G+TVG++G G IG AR+ + F ++ Y R EK +
Sbjct: 134 KAGLIGRELAGKTVGIVGTGAIGLRVARL-FKAFGCKVLAYS-----RSEK------EEA 181
Query: 215 KANGEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHLINKERLATMKKEAILVNCSRG 274
KA G + + S+DE+L E+D++SLH L+ T LI KE+LA MK+ AIL+N +RG
Sbjct: 182 KALG---IEYV---SLDELLAESDIVSLHLPLNDETKGLIGKEKLALMKESAILINTARG 235
Query: 275 PVIDEVALVEHLKQNPMFRVGLDVFEDEPYMKPG--LSEMKNAIVVPHIASASKWTREGM 332
PV+D AL + L + + G+DVF+ EP + L N I+ PH+A A T E M
Sbjct: 236 PVVDNEALADALNEGKIAGAGIDVFDMEPPLPADYPLLHAPNTILTPHVAFA---TEEAM 292
Query: 333 ATLA 336
A
Sbjct: 293 EKRA 296
>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 = 167 bits (426), Expect = 2e-49
Identities = 84/207 (40%), Positives = 113/207 (54%), Gaps = 21/207 (10%)
Query: 96 GYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDGWLP 155
G+NNVD+ AA + GI V P AE A +L LA R+I A +R G + L
Sbjct: 78 GFNNVDLKAAKELGITVVRVPAYSPYAVAEHAVALLLALNRKIHRAYNRVREGNFS--LD 135
Query: 156 NLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQFLK 215
L +G L G+TVGVIG G+IG A+AR++ GF ++ YD Y L K Y
Sbjct: 136 GL-LGFDLHGKTVGVIGTGKIGQAFARILK-GFGCRVLAYDPYPNPELAKLGVEYV---- 189
Query: 216 ANGEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHLINKERLATMKKEAILVNCSRGP 275
+DE+L E+D+ISLH L T+HLIN E +A MK +L+N SRG
Sbjct: 190 -------------DLDELLAESDIISLHCPLTPETHHLINAETIAKMKDGVMLINTSRGG 236
Query: 276 VIDEVALVEHLKQNPMFRVGLDVFEDE 302
+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 = 165 bits (421), Expect = 1e-48
Identities = 87/255 (34%), Positives = 124/255 (48%), Gaps = 53/255 (20%)
Query: 95 VGYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADE------FMRAG 148
G++++D+ A + GIAV N P T AE A +L LA +R++ EA E F +AG
Sbjct: 72 TGFDHIDLEACRERGIAVCNVPDYGEATVAEHAFALLLALSRKLREAIERTRRGDFSQAG 131
Query: 149 LYDGWLPNLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVT 208
L G L G+T+GV+G GRIG AR+ GF M ++ YD+ E+
Sbjct: 132 L---------RGFELAGKTLGVVGTGRIGRRVARIAR-GFGMKVLAYDVVPD---EELAE 178
Query: 209 AYGQFLKANGEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHLINKERLATMKKEAIL 268
G R S++E+L+E+D+ISLH T+HLIN+E A MK A+L
Sbjct: 179 RLGF-------------RYVSLEELLQESDIISLHVPYTPQTHHLINRENFALMKPGAVL 225
Query: 269 VNCSRGPVIDEVALVEHLKQNPMFRVGLDVFEDEPYMKPG-------------------- 308
+N +RG V+D ALV LK+ + GLDV E E ++
Sbjct: 226 INTARGAVVDTEALVRALKEGKLAGAGLDVLEQEEVLREEAELFREDVSPEDLKKLLADH 285
Query: 309 -LSEMKNAIVVPHIA 322
L N I+ PH+A
Sbjct: 286 ALLRKPNVIITPHVA 300
>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 = 161 bits (409), Expect = 4e-47
Identities = 87/247 (35%), Positives = 121/247 (48%), Gaps = 33/247 (13%)
Query: 81 ALSRAGGKAFSNMAVGYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVE 140
A++RAG G NN+DV+AA+K GI V NTPG AEL ++ LA +R I++
Sbjct: 53 AIARAG--------AGVNNIDVDAASKRGIVVFNTPGANANAVAELVIAMMLALSRNIIQ 104
Query: 141 ADEFMRAGLYDG------WLPNLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIY 194
A +++ G D FVG L+G+T+GVIG G IG A M +I
Sbjct: 105 AIKWVTNGDGDDISKGVEKGKKQFVGTELRGKTLGVIGLGNIGRLVANA-ALALGMKVIG 163
Query: 195 YDLYQATRLEKFVTAYGQFLKANGEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHLI 254
YD Y + ++ Q R +S++E+L AD I+LH L T LI
Sbjct: 164 YDPYLSVEAAWKLSVEVQ-------------RVTSLEELLATADYITLHVPLTDETRGLI 210
Query: 255 NKERLATMKKEAILVNCSRGPVIDEVALVEHLKQNPMFRVGLDVFEDEPYMKPGLSEMKN 314
N E LA MK AIL+N +RG ++DE AL+E L + + D E L + N
Sbjct: 211 NAELLAKMKPGAILLNFARGEIVDEEALLEALDEGKLGGYVTDFPEPA-----LLGHLPN 265
Query: 315 AIVVPHI 321
I PH+
Sbjct: 266 VIATPHL 272
>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 = 9e-47
Identities = 85/236 (36%), Positives = 117/236 (49%), Gaps = 23/236 (9%)
Query: 88 KAFSNMAVGYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRA 147
K + ++D+ AA + GI V T G TAEL +L LA AR + E D +RA
Sbjct: 71 KLLVTTGMRNASIDLAAAKERGIVVCGTGGG-PTATAELTWALILALARNLPEEDAALRA 129
Query: 148 GLYDGWLPNLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFV 207
G GW L G L G+T+G++G GRIG+ AR+ + F M V
Sbjct: 130 G---GWQTTL--GTGLAGKTLGIVGLGRIGARVARIG-QAFGMR---------------V 168
Query: 208 TAYGQFLKANGEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHLINKERLATMKKEAI 267
A+ L A + A S +E+ +DV+SLH VL T L+ E LA MK A+
Sbjct: 169 IAWSSNLTAERAAAAGVEAAVSKEELFATSDVVSLHLVLSDRTRGLVGAEDLALMKPTAL 228
Query: 268 LVNCSRGPVIDEVALVEHLKQNPMFRVGLDVFEDEP-YMKPGLSEMKNAIVVPHIA 322
LVN SRGP++DE AL+ L+ + LDVF+ EP L + N ++ PHI
Sbjct: 229 LVNTSRGPLVDEGALLAALRAGRIAGAALDVFDVEPLPADHPLRGLPNVLLTPHIG 284
>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 = 156 bits (398), Expect = 2e-45
Identities = 91/298 (30%), Positives = 134/298 (44%), Gaps = 49/298 (16%)
Query: 44 TQKKTILSVEDIIALIGDKCDGVIGQLTEDWGETLFAALSRAGGKAFSNMAVGYNNVDVN 103
T K L++E+ G ++G L L AG K S ++GY+++D++
Sbjct: 28 TLTKEPLTLENAHLAEGYDGISILG--KSKISAELLEKLKEAGVKYISTRSIGYDHIDLD 85
Query: 104 AANKYGIAVGNTP----GVLTETTAELAASLSLAAARRIVEADEFMRAGLYDGWLPNLFV 159
AA + GI V N V A+ L L A R+ + RA + D L L
Sbjct: 86 AAKELGIKVSNVTYSPNSV-----ADYTVMLMLMALRKYKQI--MKRAEVNDYSLGGL-Q 137
Query: 160 GNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQFLKANGE 219
G L+ TVGVIG GRIG A + + GF ++ YD Y ++K+ Y
Sbjct: 138 GRELRNLTVGVIGTGRIGQAVIKNL-SGFGCKILAYDPYPNEEVKKYAE-Y--------- 186
Query: 220 QPVTWKRASSMDEVLREADVISLHPVLDKTTYHLINKERLATMKKEAILVNCSRGPVIDE 279
+D + +E+D+I+LH L + TYHLINKE +A MK I++N +RG +ID
Sbjct: 187 --------VDLDTLYKESDIITLHTPLTEETYHLINKESIAKMKDGVIIINTARGELIDT 238
Query: 280 VALVEHLKQNPMFRVGLDVFEDE---------------PYMKPGLSEMKNAIVVPHIA 322
AL+E L+ + LDV E E + L N I+ PH+A
Sbjct: 239 EALIEGLESGKIGGAALDVIEGEDGIYYNDRKGDILSNRELAI-LRSFPNVILTPHMA 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 = 7e-44
Identities = 81/256 (31%), Positives = 119/256 (46%), Gaps = 28/256 (10%)
Query: 93 MAVGYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDG 152
+ G +++ + + G+ V N G + AE A +L LA A+RIVE D +R G++ G
Sbjct: 67 PSAGVDHLPLERLPE-GVVVANNHG-NSPAVAEHALALILALAKRIVEYDNDLRRGIWHG 124
Query: 153 WLPNLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQ 212
L+G+TVG++G G IG AR++ + F M V +
Sbjct: 125 RAGEEPESKELRGKTVGILGYGHIGREIARLL-KAFGMR---------------VIGVSR 168
Query: 213 FLKANGEQPVTWKRASSM-DEVLREADVISLHPVLDKTTYHLINKERLATMKKEAILVNC 271
K ++ + S DE L +ADV+ + L K T LI LA MK AILVN
Sbjct: 169 SPKE--DEGADFVGTLSDLDEALEQADVVVVALPLTKQTRGLIGAAELAAMKPGAILVNV 226
Query: 272 SRGPVIDEVALVEHLKQNPMFRVGLDVF----EDEPYMKP---GLSEMKNAIVVPHIASA 324
RGPV+DE AL E LK+ P+ +DV+ + P E+ N I+ PH A
Sbjct: 227 GRGPVVDEEALYEALKERPIAGAAIDVWWRYPSRGDPVAPSRYPFHELPNVIMSPHNAGW 286
Query: 325 SKWTREGMATLAALNV 340
++ T AA N+
Sbjct: 287 TEETFRRRIDEAAENI 302
>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 = 144 bits (366), Expect = 1e-40
Identities = 73/231 (31%), Positives = 108/231 (46%), Gaps = 24/231 (10%)
Query: 109 GIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDGWLPNLFVGNLLKGQTV 168
GI V + E AE + L A RRI RAG D P G L G+TV
Sbjct: 95 GILVTSAADANAEPVAEFTLAAILLALRRIPRFAAAYRAG-RDWGWPTRRGGRGLYGRTV 153
Query: 169 GVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQFLKANGEQPVTWKRAS 228
G++G GRIG A + + F + ++ YD ++ A A G
Sbjct: 154 GIVGFGRIGRAVVEL-LRPFGLRVLVYD--------PYLPA--AEAAALGV------ELV 196
Query: 229 SMDEVLREADVISLH-PVLDKTTYHLINKERLATMKKEAILVNCSRGPVIDEVALVEHLK 287
S+DE+L +DV+SLH P+ +T +I+ LA M+ A +N +RG ++DE AL+ L+
Sbjct: 197 SLDELLARSDVVSLHAPLTPETR-GMIDARLLALMRDGATFINTARGALVDEAALLAELR 255
Query: 288 QNPMFRVGLDVFEDEPYMKPG--LSEMKNAIVVPHIASASKWTREGMATLA 336
R LDV + EP + P L + N ++ PHIA ++ R + A
Sbjct: 256 SG-RLRAALDVTDPEP-LPPDSPLRTLPNVLLTPHIAGSTGDERRRLGDYA 304
>gnl|CDD|181414 PRK08410, PRK08410, 2-hydroxyacid dehydrogenase; Provisional.
Length = 311
Score = 142 bits (360), Expect = 7e-40
Identities = 81/258 (31%), Positives = 128/258 (49%), Gaps = 34/258 (13%)
Query: 93 MAVGYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDG 152
A G NNVD+ A K GIAV N G TE+ A+ ++ L+ RI D ++++G Y
Sbjct: 70 TATGTNNVDIEYAKKKGIAVKNVAGYSTESVAQHTFAMLLSLLGRINYYDRYVKSGEYSE 129
Query: 153 WLPNLFVG-----NLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFV 207
+F +KG+ G+IG G IG A++ + F ++YY + E++
Sbjct: 130 --SPIFTHISRPLGEIKGKKWGIIGLGTIGKRVAKI-AQAFGAKVVYYSTSGKNKNEEY- 185
Query: 208 TAYGQFLKANGEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHLINKERLATMKKEAI 267
S++E+L+ +D+IS+H L++ T +LI + L +K AI
Sbjct: 186 ------------------ERVSLEELLKTSDIISIHAPLNEKTKNLIAYKELKLLKDGAI 227
Query: 268 LVNCSRGPVIDEVALVEHLKQNPMFRVGLDVFEDEPYMK--PGLSEMKNA---IVVPHIA 322
L+N RG +++E L + L + + GLDV E EP K P LS +KN ++ PHIA
Sbjct: 228 LINVGRGGIVNEKDLAKALDEKDI-YAGLDVLEKEPMEKNHPLLS-IKNKEKLLITPHIA 285
Query: 323 SASKWTREGMATLAALNV 340
ASK R+ + N+
Sbjct: 286 WASKEARKTLIEKVKENI 303
>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 (351), Expect = 1e-38
Identities = 79/233 (33%), Positives = 119/233 (51%), Gaps = 29/233 (12%)
Query: 95 VGYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDGWL 154
+G N VD++AA K GI V N P T + AEL + ARR+ + + G W
Sbjct: 73 IGTNQVDLDAAAKRGIPVFNAPFSNTRSVAELVIGEIIMLARRLPDRNAAAHRG---IWN 129
Query: 155 PNLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQFL 214
+ + ++G+T+G+IG G IGS + + E M +I+YD+ A +L G
Sbjct: 130 KSATGSHEVRGKTLGIIGYGHIGSQLSVL-AEALGMRVIFYDI--AEKL-----PLG--- 178
Query: 215 KANGEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHLINKERLATMKKEAILVNCSRG 274
++ SS++E+L EAD ++LH +T ++I E +A MKK AIL+N SRG
Sbjct: 179 --------NARQVSSLEELLAEADFVTLHVPATPSTKNMIGAEEIAQMKKGAILINASRG 230
Query: 275 PVIDEVALVEHLKQNPMFRVGLDVF------EDEPYMKPGLSEMKNAIVVPHI 321
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 = 5e-37
Identities = 74/232 (31%), Positives = 112/232 (48%), Gaps = 48/232 (20%)
Query: 96 GYNNVDVNAANKYGIAVGNTPGVLTETTAE-LAASLSLAAARRIVEADEFMRAGLYDGWL 154
G +++D + + GI N PG + AE + ++L + A R+
Sbjct: 67 GTDHIDTDYLKERGIGFANAPGCNANSVAEYVLSALLVLAQRQ----------------- 109
Query: 155 PNLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQFL 214
G LKG+TVG++G G +GS AR +E MN++ D +A
Sbjct: 110 -----GFSLKGKTVGIVGVGNVGSRLARR-LEALGMNVLLCDPPRAEAEGDPGFV----- 158
Query: 215 KANGEQPVTWKRASSMDEVLREADVISLHPVLDKT----TYHLINKERLATMKKEAILVN 270
S++E+L EAD+I+LH L + TYHL++++ LA +K IL+N
Sbjct: 159 --------------SLEELLAEADIITLHVPLTRDGEHPTYHLLDEDFLAALKPGQILIN 204
Query: 271 CSRGPVIDEVALVEHLKQNPMFRVGLDVFEDEPYMKPGLSEMKNAIVVPHIA 322
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 = 4e-34
Identities = 74/256 (28%), Positives = 118/256 (46%), Gaps = 28/256 (10%)
Query: 50 LSVEDIIALIGDKCDGVIGQLTEDWGETLFAALSRAGGKAFSNMAVGYNNVDVNAANKYG 109
L+ E++ G D VI + + G K VG+N++D+ AA + G
Sbjct: 34 LNDENVHLAKG--HDAVIVRGNCFADKENLEIYKEYGIKYVFTRTVGFNHIDLEAAKELG 91
Query: 110 IAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLY--DGWLPNLFVGNLLKGQT 167
+ P AELA +L++ +R + D P +F ++ T
Sbjct: 92 FKMARVPSYSPNAIAELAFTLAMTLSRHTAYTASRTANKNFKVD---PFMF-SKEIRNST 147
Query: 168 VGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQFLKANGEQPVTWKRA 227
VG+IG GRIG A++ +G +I YD+Y + + VT
Sbjct: 148 VGIIGTGRIGLTAAKLF-KGLGAKVIGYDIYPSDAAKDVVTFV----------------- 189
Query: 228 SSMDEVLREADVISLH-PVLDKTTYHLINKERLATMKKEAILVNCSRGPVIDEVALVEHL 286
S+DE+L+++D+ISLH P + LINKE ++ MK AIL+N +RG + DE A++E L
Sbjct: 190 -SLDELLKKSDIISLHVPYIKGKNDKLINKEFISKMKDGAILINTARGELQDEEAILEAL 248
Query: 287 KQNPMFRVGLDVFEDE 302
+ + G DV +E
Sbjct: 249 ESGKLAGFGTDVLNNE 264
>gnl|CDD|236985 PRK11790, PRK11790, D-3-phosphoglycerate dehydrogenase;
Provisional.
Length = 409
Score = 124 bits (315), Expect = 1e-32
Identities = 93/288 (32%), Positives = 137/288 (47%), Gaps = 46/288 (15%)
Query: 47 KTILSVEDIIALIGDKCDGVIG-----QLTEDWGETLFAALSR--AGGKAFSNMAVGYNN 99
K L E++I I D IG QLTE+ + AA + A G F +G N
Sbjct: 39 KGALDEEELIEAIKDA--HFIGIRSRTQLTEE----VLAAAEKLVAIG-CFC---IGTNQ 88
Query: 100 VDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDGWLPNLFV 159
VD++AA K GI V N P T + AEL + R I E + G GW +
Sbjct: 89 VDLDAAAKRGIPVFNAPFSNTRSVAELVIGEIILLLRGIPEKNAKAHRG---GWNKSAAG 145
Query: 160 GNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQFLKANGE 219
++G+T+G++G G IG+ + ++ E M + +YD+ +L G N
Sbjct: 146 SFEVRGKTLGIVGYGHIGTQLS-VLAESLGMRVYFYDI--EDKL-----PLG-----NAR 192
Query: 220 QPVTWKRASSMDEVLREADVISLHPVLDKTTYHLINKERLATMKKEAILVNCSRGPVIDE 279
Q S++E+L ++DV+SLH +T ++I E LA MK AIL+N SRG V+D
Sbjct: 193 Q------VGSLEELLAQSDVVSLHVPETPSTKNMIGAEELALMKPGAILINASRGTVVDI 246
Query: 280 VALVEHLKQNPMFRVGLDVF------EDEPYMKPGLSEMKNAIVVPHI 321
AL + LK + +DVF +P+ P L + N I+ PHI
Sbjct: 247 DALADALKSGHLAGAAIDVFPVEPKSNGDPFESP-LRGLDNVILTPHI 293
>gnl|CDD|180588 PRK06487, PRK06487, glycerate dehydrogenase; Provisional.
Length = 317
Score = 120 bits (304), Expect = 8e-32
Identities = 81/259 (31%), Positives = 121/259 (46%), Gaps = 40/259 (15%)
Query: 94 AVGYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDGW 153
A G NNVD+ AA + GI V N G T + A+ +L LA A R+ + + + AG W
Sbjct: 74 ATGTNNVDLAAARERGITVCNCQGYGTPSVAQHTLALLLALATRLPDYQQAVAAG---RW 130
Query: 154 -------LPNLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKF 206
L + F L+G+T+G++G G +G A AR+ E F M ++
Sbjct: 131 QQSSQFCLLD-FPIVELEGKTLGLLGHGELGGAVARL-AEAFGMRVLI------------ 176
Query: 207 VTAYGQFLKANGEQPVTWKRASSM--DEVLREADVISLHPVLDKTTYHLINKERLATMKK 264
G+ P R + DE+L + D ++LH L + T HLI LA MK
Sbjct: 177 -----------GQLPGRPARPDRLPLDELLPQVDALTLHCPLTEHTRHLIGARELALMKP 225
Query: 265 EAILVNCSRGPVIDEVALVEHLKQNPMFRVGLDVFEDEPYMK--PGLSE-MKNAIVVPHI 321
A+L+N +RG ++DE AL + L+ + DV EP + P L+ + IV PH
Sbjct: 226 GALLINTARGGLVDEQALADALRSGHLGGAATDVLSVEPPVNGNPLLAPDIPRLIVTPHS 285
Query: 322 ASASKWTREGMATLAALNV 340
A S+ R+ + A N
Sbjct: 286 AWGSREARQRIVGQLAENA 304
>gnl|CDD|235890 PRK06932, PRK06932, glycerate dehydrogenase; Provisional.
Length = 314
Score = 120 bits (302), Expect = 1e-31
Identities = 75/246 (30%), Positives = 113/246 (45%), Gaps = 41/246 (16%)
Query: 94 AVGYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDGW 153
A G NNVD+ AA + GIAV N G + T E + A ++ + R L D W
Sbjct: 73 ATGTNNVDLVAAKELGIAVKNVTGYSSTTVPEHVLGMIFALKHSLMG---WYRDQLSDRW 129
Query: 154 LPNLFVGNL---------LKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLE 204
++G T+GV G G +G+ R+ + M ++Y + A+
Sbjct: 130 ATC---KQFCYFDYPITDVRGSTLGVFGKGCLGTEVGRL-AQALGMKVLYAEHKGASVCR 185
Query: 205 KFVTAYGQFLKANGEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHLINKERLATMKK 264
+ T + +EVL++AD+++LH L +TT +LIN E LA MK
Sbjct: 186 EGYTPF--------------------EEVLKQADIVTLHCPLTETTQNLINAETLALMKP 225
Query: 265 EAILVNCSRGPVIDEVALVEHLKQNPMFRVGLDVFEDEPYMKP-----GLSEMKNAIVVP 319
A L+N RGP++DE AL++ L+ + LDV EP K + N ++ P
Sbjct: 226 TAFLINTGRGPLVDEQALLDALENGKIAGAALDVLVKEPPEKDNPLIQAAKRLPNLLITP 285
Query: 320 HIASAS 325
HIA AS
Sbjct: 286 HIAWAS 291
>gnl|CDD|181499 PRK08605, PRK08605, D-lactate dehydrogenase; Validated.
Length = 332
Score = 117 bits (295), Expect = 2e-30
Identities = 67/274 (24%), Positives = 120/274 (43%), Gaps = 35/274 (12%)
Query: 64 DGVIGQLTEDWGETLFAALSRAGGKAFSNMAVGYNNVDVNAANKYGIAVGNTPGVLTETT 123
DG+ E ++ L+ G K + + G++ D+ A KY + + N P E+
Sbjct: 47 DGLSLSQQIPLSEAIYKLLNELGIKQIAQRSAGFDTYDLELATKYNLIISNVPSYSPESI 106
Query: 124 AELAASLSLAAARRIVEADEFMRAGLYD-GWLPNLFVGNLLKGQTVGVIGAGRIGSAYAR 182
AE + ++ R + +R +D W P + + +K V VIG GRIG A A+
Sbjct: 107 AEFTVTQAINLVRHFNQIQTKVR--EHDFRWEPPI-LSRSIKDLKVAVIGTGRIGLAVAK 163
Query: 183 MMVEGFKMNLIYYDLYQATRLEKFVTAYGQFLKANGEQPVTWKRASSMDEVLREADVISL 242
+ +G+ +++ YD + + +V +++E + AD+++L
Sbjct: 164 IFAKGYGSDVVAYDPFPNAKAATYVD-----------------YKDTIEEAVEGADIVTL 206
Query: 243 HPVLDKTTYHLINKERLATMKKEAILVNCSRGPVIDEVALVEHLKQNPMFRVGLDVFEDE 302
H K ++L N + KK A+ VNC+RG ++D AL++ L + LD +E E
Sbjct: 207 HMPATKYNHYLFNADLFKHFKKGAVFVNCARGSLVDTKALLDALDNGLIKGAALDTYEFE 266
Query: 303 PYMKPG--------------LSEMKNAIVVPHIA 322
+ P L ++ I+ PHIA
Sbjct: 267 RPLFPSDQRGQTINDPLLESLINREDVILTPHIA 300
>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 = 116 bits (292), Expect = 4e-30
Identities = 76/245 (31%), Positives = 115/245 (46%), Gaps = 36/245 (14%)
Query: 96 GYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDGWLP 155
G N+D+ A + GI + N P + E A + LA ++ AD+ +R G+ W
Sbjct: 72 GLENIDLEYAKEKGIELFNAPEGNRDAVGEHALGMLLALFNKLNRADQEVRNGI---WDR 128
Query: 156 NLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQFLK 215
G L G+TVG+IG G +G A+A+ + GF +I YD Y+ F
Sbjct: 129 EGNRGVELMGKTVGIIGYGNMGKAFAKRL-SGFGCKVIAYDKYK------------NFGD 175
Query: 216 ANGEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHLINKERLATMKKEAILVNCSRGP 275
A EQ S++ + +EAD++SLH L T ++NKE +++ KK +N +RG
Sbjct: 176 AYAEQ-------VSLETLFKEADILSLHIPLTPETRGMVNKEFISSFKKPFYFINTARGK 228
Query: 276 VIDEVALVEHLKQNPMFRVGLDVFEDE------PYMKPG----LSEMKNAIVVPHIASAS 325
V+ LV+ LK + LDV E E + +P L + I+ PHIA
Sbjct: 229 VVVTKDLVKALKSGKILGACLDVLEYEKASFESIFNQPEAFEYLIKSPKVILTPHIAG-- 286
Query: 326 KWTRE 330
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 = 116 bits (293), Expect = 4e-30
Identities = 71/258 (27%), Positives = 104/258 (40%), Gaps = 39/258 (15%)
Query: 93 MAVGYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDG 152
+ G + + + + + N G+ AE LA AR++
Sbjct: 66 TSAGVDALLFPELLERDVVLTNARGIFGPPIAEYVLGYMLAFARKLPRYARNQAERR--- 122
Query: 153 WLPNLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAY-- 210
W V L G+TV ++G G IG AR + F M V
Sbjct: 123 WQRRGPVR-ELAGKTVLIVGLGDIGREIARRA-KAFGMR---------------VIGVRR 165
Query: 211 -GQFLKANGEQPVTWKRASSMDEVLREAD-VISLHPVLDKTTYHLINKERLATMKKEAIL 268
G+ ++ T +DE+L EAD V++ P L T L N ER A MK A+L
Sbjct: 166 SGRPAPPVVDEVYT---PDELDELLPEADYVVNALP-LTPETRGLFNAERFAAMKPGAVL 221
Query: 269 VNCSRGPVIDEVALVEHLKQNPMFRVGLDVFEDEPYMKPGLSE------MKNAIVVPHIA 322
+N RG V+DE AL+E L+ + LDVFE+EP L + N I+ PHI+
Sbjct: 222 INVGRGSVVDEDALIEALESGRIAGAALDVFEEEP-----LPADSPLWDLPNVIITPHIS 276
Query: 323 SASKWTREGMATLAALNV 340
S E + + N+
Sbjct: 277 GDSPSYPERVVEIFLENL 294
>gnl|CDD|183550 PRK12480, PRK12480, D-lactate dehydrogenase; Provisional.
Length = 330
Score = 111 bits (279), Expect = 4e-28
Identities = 86/300 (28%), Positives = 139/300 (46%), Gaps = 44/300 (14%)
Query: 40 VEICTQKKTILSVEDIIALIGDKCDGVIGQLTEDWGE---TLFAALSRAGGKAFSNMAVG 96
VE+ T K+ +LS + D+ G T +G+ ++ L G K + G
Sbjct: 26 VEVTTSKE-LLSSATV-----DQLKDYDGVTTMQFGKLENDVYPKLESYGIKQIAQRTAG 79
Query: 97 YNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDGWLPN 156
++ D++ A K+ I + N P ET AE + S++L RR + + ++A +
Sbjct: 80 FDMYDLDLAKKHNIVISNVPSYSPETIAEYSVSIALQLVRRFPDIERRVQAHDFTWQAE- 138
Query: 157 LFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQFLKA 216
+ +K TV +IG GRIG+A A++ GF + YD Y L+ FL
Sbjct: 139 -IMSKPVKNMTVAIIGTGRIGAATAKIYA-GFGATITAYDAYPNKDLD--------FL-- 186
Query: 217 NGEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHLINKERLATMKKEAILVNCSRGPV 276
T+K S+ E +++AD+ISLH +K +YHL +K +KK AILVN +RG V
Sbjct: 187 ------TYK--DSVKEAIKDADIISLHVPANKESYHLFDKAMFDHVKKGAILVNAARGAV 238
Query: 277 IDEVALVEHLKQNPMFRVGLDVFEDE-PYM----------KPGLSEM---KNAIVVPHIA 322
I+ L+ + + +D +E+E Y L E+ + +V PHIA
Sbjct: 239 INTPDLIAAVNDGTLLGAAIDTYENEAAYFTNDWTNKDIDDKTLLELIEHERILVTPHIA 298
>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 = 108 bits (273), Expect = 2e-27
Identities = 74/230 (32%), Positives = 105/230 (45%), Gaps = 26/230 (11%)
Query: 114 NTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDGWLPNLFVGNLLKGQTVGVIGA 173
N G ET AE A +L LA R++ RA +D + LL+G TV ++GA
Sbjct: 78 NAAGAYAETVAEHALALLLAGLRQLPA---RARATTWDPAEE-DDLVTLLRGSTVAIVGA 133
Query: 174 GRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQFLKANGEQPVTWKRASSMDEV 233
G IG A ++ F +I V G+ G A +DEV
Sbjct: 134 GGIGRALIPLLA-PFGAKVIA------------VNRSGR--PVEGADETV--PADRLDEV 176
Query: 234 LREADVISLHPVLDKTTYHLINKERLATMKKEAILVNCSRGPVIDEVALVEHLKQNPMFR 293
+AD + L L T HL++ LA MK A LVN +RGP++D ALV+ L+ +
Sbjct: 177 WPDADHVVLAAPLTPETRHLVDAAALAAMKPHAWLVNVARGPLVDTDALVDALRSGEIAG 236
Query: 294 VGLDVFEDEPYMKPG---LSEMKNAIVVPHIASASKWTREGMATLAALNV 340
LDV + EP P L + NA++ PH+A+ + R +A A NV
Sbjct: 237 AALDVTDPEPL--PDGHPLWSLPNALITPHVANTPEVIRPLLAERVAENV 284
>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 (262), Expect = 8e-26
Identities = 67/242 (27%), Positives = 110/242 (45%), Gaps = 46/242 (19%)
Query: 93 MAVGYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDG 152
+ G + + + K GI + N G+ + AE L + + +A + +
Sbjct: 67 YSAGVDYLPLEYIKKKGILLTNNSGIHSIPIAEWIVGYILEIYKGLKKAYKNQKEKK--- 123
Query: 153 WLPNLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLI----------YYDLYQATR 202
W + + L G+T+ +G G IG A+ + + F M +I Y+D
Sbjct: 124 WKMDSSLLEL-YGKTILFLGTGSIGQEIAKRL-KAFGMKVIGVNTSGRDVEYFD------ 175
Query: 203 LEKFVTAYGQFLKANGEQPVTWKRASSMDEVLREAD-VISLHPVLDKTTYHLINKERLAT 261
+ + E +DEVL+EAD V+++ P L + T+HL ++
Sbjct: 176 -KCY---------PLEE----------LDEVLKEADIVVNVLP-LTEETHHLFDEAFFEQ 214
Query: 262 MKKEAILVNCSRGPVIDEVALVEHLKQNPMFRVGLDVFEDEPYMK--PGLSEMKNAIVVP 319
MKK A+ +N RGP +DE AL+E LK + LDVFE+EP K P L ++ N ++ P
Sbjct: 215 MKKGALFINVGRGPSVDEDALIEALKNKQIRGAALDVFEEEPLPKDSP-LWDLDNVLITP 273
Query: 320 HI 321
HI
Sbjct: 274 HI 275
>gnl|CDD|166874 PRK00257, PRK00257, erythronate-4-phosphate dehydrogenase;
Validated.
Length = 381
Score = 105 bits (264), Expect = 1e-25
Identities = 54/167 (32%), Positives = 78/167 (46%), Gaps = 25/167 (14%)
Query: 163 LKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQFLKANGEQPV 222
L +T GV+GAG +G R++ G ++ D + G F+
Sbjct: 114 LAERTYGVVGAGHVGGRLVRVL-RGLGWKVLVCDPPRQEAEGD-----GDFV-------- 159
Query: 223 TWKRASSMDEVLREADVISLHPVLDKT----TYHLINKERLATMKKEAILVNCSRGPVID 278
S++ +L E DVISLH L K T HL+++ LA+++ A L+N SRG V+D
Sbjct: 160 ------SLERILEECDVISLHTPLTKEGEHPTRHLLDEAFLASLRPGAWLINASRGAVVD 213
Query: 279 EVALVEHLKQNPMFRVGLDVFEDEPYMKPGLSEMKNAIVVPHIASAS 325
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 = 102 bits (257), Expect = 7e-25
Identities = 70/236 (29%), Positives = 110/236 (46%), Gaps = 21/236 (8%)
Query: 95 VGYNNVDVNAANKYGIAVGNTPGVLT---ETTAELAASLSLAAARRIVEADEFMRAGLYD 151
VG VDV+AA K+GI V P T + AE+A L L R+ E ++A
Sbjct: 91 VGLEGVDVDAATKHGIKVARIPSEGTGNAASCAEMAIYLMLGLLRKQNEMQISLKARRLG 150
Query: 152 GWLPNLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATR---LEKFVT 208
P +G+ L G+TV ++G G IG A+ + F + L+ ATR +
Sbjct: 151 E--P---IGDTLFGKTVFILGYGAIGIELAKRL-RPFGVKLL------ATRRSWTSEPED 198
Query: 209 AYGQFLKANGEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHLINKERLATMKKEAIL 268
+ + E EAD++ L L K T ++N E L++MKK A+L
Sbjct: 199 GLLIPNGDVDDLVDEKGGHEDIYEFAGEADIVVLCCTLTKETAGIVNDEFLSSMKKGALL 258
Query: 269 VNCSRGPVIDEVALVEHLKQNPMFRVGLDVFEDEPYMKPG--LSEMKNAIVVPHIA 322
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 = 4e-24
Identities = 72/235 (30%), Positives = 112/235 (47%), Gaps = 23/235 (9%)
Query: 95 VGYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDGWL 154
+G ++VD+ AAN GI V G + AE + L R V E G GW
Sbjct: 93 IGSDHVDLQAANDRGITVAEVTGSNVVSVAEHVVMMILILVRNYVPGHEQAIEG---GWN 149
Query: 155 PNLFVGNL--LKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQ 212
V L+G+TVG +GAGRIG R + + F ++L+YYD ++
Sbjct: 150 VADVVKRAYDLEGKTVGTVGAGRIGLRVLRRL-KPFDVHLLYYDRHR------------- 195
Query: 213 FLKANGEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHLINKERLATMKKEAILVNCS 272
L E+ + R + +++++ + DV++++ L T L NKE L+ MKK A LVN +
Sbjct: 196 -LPEEVEKELGLTRHADLEDMVSKCDVVTINCPLHPETEGLFNKELLSKMKKGAYLVNTA 254
Query: 273 RGPVIDEVALVEHLKQNPMFRVGLDVFEDEPYMK--PGLSEMKNAIVVPHIASAS 325
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 = 99.7 bits (249), Expect = 1e-23
Identities = 67/241 (27%), Positives = 110/241 (45%), Gaps = 35/241 (14%)
Query: 95 VGYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDGWL 154
+G ++VD+ AA+++GI V G + + AE + LA R + G GW
Sbjct: 123 IGSDHVDLQAASEHGITVAEVTGSNSISVAEHVVMMILALVRNYEPSHRQAVEG---GW- 178
Query: 155 PNLF-VGNL---LKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAY 210
N+ + L+G TVG++GAGRIG A R + + F + L Y D ++
Sbjct: 179 -NIADCVSRSYDLEGMTVGIVGAGRIGLAVLRRL-KPFDVKLHYTDRHR----------- 225
Query: 211 GQFLKANGEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHLINKERLATMKKEAILVN 270
L EQ + S D ++ DV+++H L T HL + + L+ MK+ + LVN
Sbjct: 226 ---LPEEVEQELGLTYHVSFDSLVSVCDVVTIHCPLHPETEHLFDADVLSRMKRGSYLVN 282
Query: 271 CSRGPVIDEVALVEHLKQNPMFRVGLDVF------EDEPYMKPGLSEMKNAIVVPHIASA 324
+RG ++D A+V L+ + DV+ D P+ M + PHI+
Sbjct: 283 TARGKIVDRDAVVRALESGHLAGYAGDVWFPQPAPADHPWRT-----MPRNGMTPHISGT 337
Query: 325 S 325
+
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 = 95.3 bits (238), Expect = 2e-22
Identities = 70/235 (29%), Positives = 99/235 (42%), Gaps = 37/235 (15%)
Query: 109 GIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDG-WLPNLFVGNLLKGQT 167
G+ + N GV +TAELA +L LA+ R + G ++ P+L +
Sbjct: 81 GVTLCNARGVHDASTAELAVALILASLRGLPRFVRAQARGRWEPRRTPSL------ADRR 134
Query: 168 VGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKF---VTAYGQFLKANGEQPVTW 224
V ++G G IG A R RL F VT + + GEQ
Sbjct: 135 VLIVGYGSIGRAIER-------------------RLAPFEVRVTRVARTARP-GEQVHGI 174
Query: 225 KRASSMDEVLREADVISLHPVLDKTTYHLINKERLATMKKEAILVNCSRGPVIDEVALVE 284
+ +L EADV+ L L T L++ E LA M A+LVN +RGPV+D ALV
Sbjct: 175 ---DELPALLPEADVVVLIVPLTDETRGLVDAEFLARMPDGALLVNVARGPVVDTDALVA 231
Query: 285 HLKQNPMFRVGLDVFEDEPYMKPG--LSEMKNAIVVPHIASASKWTREGMATLAA 337
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 = 83.4 bits (206), Expect = 3e-18
Identities = 53/235 (22%), Positives = 112/235 (47%), Gaps = 28/235 (11%)
Query: 88 KAFSNMAVGYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRA 147
K +++ G +++DV+ + + + + G + + AE A +L LA A+ I E + M+
Sbjct: 51 KMIQSLSAGVDHIDVSGIPE-NVVLCSNAGAYSISVAEHAFALLLAWAKNICENNYNMKN 109
Query: 148 GLYDGWLPNLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFV 207
G + P LL +++G++G G IG A ++ + F MN+ Y TR
Sbjct: 110 GNFKQ-SPT----KLLYNKSLGILGYGGIGRRVA-LLAKAFGMNIYAY-----TR----- 153
Query: 208 TAYGQFLKANGEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHLINKERLATMKKEAI 267
+ + + +P +++++++D + + L T +IN + L+ +K
Sbjct: 154 SYVNDGISSIYMEP---------EDIMKKSDFVLISLPLTDETRGMINSKMLSLFRKGLA 204
Query: 268 LVNCSRGPVIDEVALVEHLKQNPMFRVGLDVFEDEPYMKPGLSEMKNAIVVPHIA 322
++N +R V+D+ ++ L+ + DV+ +EP + + N I+ PH+A
Sbjct: 205 IINVARADVVDKNDMLNFLRNHNDKYYLSDVWWNEPIITE--TNPDNVILSPHVA 257
>gnl|CDD|178684 PLN03139, PLN03139, formate dehydrogenase; Provisional.
Length = 386
Score = 80.7 bits (199), Expect = 7e-17
Identities = 70/241 (29%), Positives = 109/241 (45%), Gaps = 41/241 (17%)
Query: 95 VGYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRI------VEADEFMRAG 148
+G +++D+ AA G+ V G + AE L R V + E+ AG
Sbjct: 130 IGSDHIDLPAAAAAGLTVAEVTGSNVVSVAEDELMRILILLRNFLPGYHQVVSGEWNVAG 189
Query: 149 L----YDGWLPNLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYD-LYQATRL 203
+ YD L+G+TVG +GAGRIG + + + F NL+Y+D L L
Sbjct: 190 IAYRAYD-----------LEGKTVGTVGAGRIGRLLLQRL-KPFNCNLLYHDRLKMDPEL 237
Query: 204 EKFVTAYGQFLKANGEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHLINKERLATMK 263
EK A K +D +L + DV+ ++ L + T + NKER+A MK
Sbjct: 238 EKETGA---------------KFEEDLDAMLPKCDVVVINTPLTEKTRGMFNKERIAKMK 282
Query: 264 KEAILVNCSRGPVIDEVALVEHLKQNPMFRVGLDVFEDEPYMK--PGLSEMKNAIVVPHI 321
K ++VN +RG ++D A+ + + G DV+ +P K P M N + PHI
Sbjct: 283 KGVLIVNNARGAIMDTQAVADACSSGHIGGYGGDVWYPQPAPKDHPWRY-MPNHAMTPHI 341
Query: 322 A 322
+
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 = 74.8 bits (185), Expect = 3e-15
Identities = 55/215 (25%), Positives = 85/215 (39%), Gaps = 37/215 (17%)
Query: 119 LTETTAELAASLSLAAARRIVEADEFMRAGLYDGWLPNLFVGNLLKGQTVGVIGAGRIGS 178
L + AE + L R + R G+ W P + VGV+G G +G+
Sbjct: 91 LAQGMAEYVLAAVLRLHRDMDRYAAQQRRGV---WKPLPQR--PAAERRVGVLGLGELGA 145
Query: 179 AYARMMVE-GFKMNLIYYDLYQATRLEKFVTAYGQFLKANGEQPVTWKRASSMDEVLREA 237
A AR + GF V+ + + K + E + +D L +
Sbjct: 146 AVARRLAALGFP-----------------VSGWSRSPK-DIEGVTCFHGEEGLDAFLAQT 187
Query: 238 DV-ISLHPVLDKTTYHLINKERLATMKKEAILVNCSRGPVIDEVALVEHLKQNPMFRVGL 296
D+ + L P+ +T ++N E LA + + A L+N RGP + E L+ L + L
Sbjct: 188 DILVCLLPLTPETR-GILNAELLARLPRGAALINVGRGPHLVEADLLAALDSGHLSGAVL 246
Query: 297 DVFEDEPYMKPGLSE------MKNAIVVPHIASAS 325
DVFE EP L V PHIA+ +
Sbjct: 247 DVFEQEP-----LPADHPLWRHPRVTVTPHIAAIT 276
>gnl|CDD|185335 PRK15438, PRK15438, erythronate-4-phosphate dehydrogenase PdxB;
Provisional.
Length = 378
Score = 75.3 bits (185), Expect = 4e-15
Identities = 56/178 (31%), Positives = 87/178 (48%), Gaps = 28/178 (15%)
Query: 160 GNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQFLKANGE 219
G L +TVG++G G +G + E + + D +A R ++ G F
Sbjct: 111 GFSLHDRTVGIVGVGNVGRRLQARL-EALGIKTLLCDPPRADRGDE-----GDF------ 158
Query: 220 QPVTWKRASSMDEVLREADVISLHPVLDK----TTYHLINKERLATMKKEAILVNCSRGP 275
S+DE+++EAD+++ H L K T HL +++ + ++K AIL+N RG
Sbjct: 159 --------RSLDELVQEADILTFHTPLFKDGPYKTLHLADEKLIRSLKPGAILINACRGA 210
Query: 276 VIDEVALVEHLKQNPMFRVGLDVFEDEPYMKPGLSEMKNAIVVPHIASASKWTREGMA 333
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 = 72.4 bits (178), Expect = 2e-14
Identities = 66/213 (30%), Positives = 89/213 (41%), Gaps = 35/213 (16%)
Query: 122 TTAELAASLSLAAARRIVEADEFMRAGLYDGWL-------PNLFVGNLLKGQTVGVIGAG 174
T AE +L LAA RR+ E E R + G L P + LL G V + G G
Sbjct: 94 TVAEHTLALILAAVRRLDEMREAQREHRWAGELGGLQPLRPAGRLTTLL-GARVLIWGFG 152
Query: 175 RIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQFLKANGEQ---PVTWKRASSMD 231
IG A ++ T L VT + + GE+ PV +
Sbjct: 153 SIGQRLAPLL----------------TALGARVTGVAR---SAGERAGFPVV--AEDELP 191
Query: 232 EVLREADV-ISLHPVLDKTTYHLINKERLATMKKEAILVNCSRGPVIDEVALVEHLKQNP 290
E+L E DV + + P T H ++ E LA + K A +VN RG +DE ALV L+
Sbjct: 192 ELLPETDVLVMILPATPSTA-HALDAEVLAALPKHAWVVNVGRGATVDEDALVAALESGR 250
Query: 291 MFRVGLDVFEDEPYMKPG-LSEMKNAIVVPHIA 322
+ 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 = 70.8 bits (174), Expect = 8e-14
Identities = 55/232 (23%), Positives = 93/232 (40%), Gaps = 23/232 (9%)
Query: 110 IAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDGWLPNLFVGNLLKGQTVG 169
+ + G+ AE L + ++ E + + V + + G+ VG
Sbjct: 79 VPLCTASGIHGPQIAEWVIGTWLVLSHHFLQYIELQKEQTWGRRQEAYSVEDSV-GKRVG 137
Query: 170 VIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEK------FVTAYGQFLKANGEQPVT 223
++G G IG AR+ M + Y E V G +G P
Sbjct: 138 ILGYGSIGRQTARLAQ-ALGMEVYAYTRSPRPTPESRKDDGYIVPGTGD---PDGSIPSA 193
Query: 224 W---KRASSMDEVLREA-D--VISLHPVLDKTTYHLINKERLATM-KKEAILVNCSRGPV 276
W +S+ E LR+ D V+SL P+ T HL+ E + K++ + N +RG +
Sbjct: 194 WFSGTDKASLHEFLRQDLDLLVVSL-PLTPATK-HLLGAEEFEILAKRKTFVSNIARGSL 251
Query: 277 IDEVALVEHLKQNPMFRVGLDVFEDEPYMKPG--LSEMKNAIVVPHIASASK 326
+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 = 68.1 bits (167), Expect = 6e-13
Identities = 63/234 (26%), Positives = 95/234 (40%), Gaps = 45/234 (19%)
Query: 117 GVLTETTAELAASLSLAAARRI----VEADEFMRAGLYDGWLPNLFVGNLLKGQTVGVIG 172
GV E AE + LAAA+R+ V+ E W L G T+G++G
Sbjct: 93 GVAAEAIAEFVLAAILAAAKRLPEIWVKGAEQ--------WRRE--PLGSLAGSTLGIVG 142
Query: 173 AGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQFLKANGEQPVTWKRASSMDE 232
G IG A AR + M ++ A R G+ G + A+ + E
Sbjct: 143 FGAIGQALARRAL-ALGMRVL------ALRRS------GRPSDVPGVE-----AAADLAE 184
Query: 233 VLREADVISLHPVLDKTTYHLINKERLATMKKEAILVNCSRGPVIDEVALVEHLKQNPMF 292
+ +D + L L T HLIN + LA K L+N +RG ++D+ AL+E L +
Sbjct: 185 LFARSDHLVLAAPLTPETRHLINADVLAQAKPGLHLINIARGGLVDQEALLEALDSGRIS 244
Query: 293 RVGLDVFEDEP-------YMKPGLSEMKNAIVVPHIASASKWTREGMATLAALN 339
LDV + EP Y P + + PH ++ + R +A N
Sbjct: 245 LASLDVTDPEPLPEGHPLYTHPRVR------LSPHTSAIAPDGRRNLADRFLEN 292
>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 = 65.7 bits (160), Expect = 4e-12
Identities = 47/212 (22%), Positives = 82/212 (38%), Gaps = 30/212 (14%)
Query: 80 AALSRAGGKAFSNMAVGYNNVDVNAAN-KYGIAVGNTPGVLTETT---AELAASLSLAAA 135
A + + G + +G ++ D+ A + G+ GV + A LS+
Sbjct: 81 ALIQKLGDRLLFTYTIGADHRDLTEALARAGLTAIAVEGVELPLLTSNSIGAGELSVQFI 140
Query: 136 RRIVEADEFMRAGLYDGWLPNLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYY 195
R +E + R G + G+TV V+GAG +G A+M+ G ++
Sbjct: 141 ARFLEVQQPGRLGGAPD----------VAGKTVVVVGAGVVGKEAAQMLR-GLGAQVLIT 189
Query: 196 DLYQATRLEKFVTAYGQFLKANGEQPVTWKRASSMDEVLREADVISLH-PVLDKTTYHLI 254
D+ + + + K ++E L EADVI + K L+
Sbjct: 190 DINVEALEQ--------------LEELGGKNVEELEEALAEADVIVTTTLLPGKRAGILV 235
Query: 255 NKERLATMKKEAILVNCSRGPVIDEVALVEHL 286
+E + MK +++VN + G V AL L
Sbjct: 236 PEELVEQMKPGSVIVNVAVGAVGCVQALHTQL 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 = 48.8 bits (117), Expect = 1e-06
Identities = 48/196 (24%), Positives = 68/196 (34%), Gaps = 44/196 (22%)
Query: 99 NVDVNAANKYGIAVGNT-----PGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDGW 153
NVD+ AA + GI V GV+ +EL R + W
Sbjct: 85 NVDIAAARENGITVTGIRDYGDEGVVEYVISELI--------RLLHGFGGKQ-------W 129
Query: 154 LPNLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQF 213
L G VG+IG G G A + F ++ YY + E Y
Sbjct: 130 KE---EPRELTGLKVGIIGLGTTGQMIADAL-SFFGADVYYYSRTRKPDAEAKGIRY--- 182
Query: 214 LKANGEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHLINKERLATMKKEAILVNCSR 273
P ++E+L+ DVI L K L+ +E + IL N S
Sbjct: 183 ------LP--------LNELLKTVDVICTC--LPKNVI-LLGEEEFELLGDGKILFNTSL 225
Query: 274 GPVIDEVALVEHLKQN 289
GP + AL + LK +
Sbjct: 226 GPSFEVEALKKWLKAS 241
>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 = 45.9 bits (109), Expect = 2e-05
Identities = 21/112 (18%), Positives = 49/112 (43%), Gaps = 15/112 (13%)
Query: 164 KGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQFLKANGEQPVT 223
V +IGAG +G A++ N++ YD+ + + ++ G +
Sbjct: 161 PPAKVLIIGAGVVGLGAAKIAK-KLGANVLVYDIKEEKL---------KGVETLGGSRLR 210
Query: 224 WKRASSMDEVLREADVI---SLHPVLDKTTYHLINKERLATMKKEAILVNCS 272
+ + +++ 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 = 37.6 bits (88), Expect = 0.007
Identities = 24/81 (29%), Positives = 35/81 (43%), Gaps = 13/81 (16%)
Query: 166 QTVGVIGAGRIGSAYARMMVEGF----KMNLIYYDLYQATRLEKFVTAYGQFLKANGEQP 221
VG+IG G I R ++ ++ L YDL A R E F + G
Sbjct: 133 TRVGIIGCGPIAREILRFLLALGPEIRRVVL--YDLDPA-RAEAFA----ARCQELGPGK 185
Query: 222 VTWKRASSMDEVLREADVISL 242
VT A+S + LR+AD++
Sbjct: 186 VT--VAASAEAALRQADLVVT 204
>gnl|CDD|234592 PRK00045, hemA, glutamyl-tRNA reductase; Reviewed.
Length = 423
Score = 36.3 bits (85), Expect = 0.019
Identities = 28/103 (27%), Positives = 44/103 (42%), Gaps = 20/103 (19%)
Query: 163 LKGQTVGVIGAGRIGSAYARMMVE-GFKMNLIYYDLYQATR-LEKFVTAYGQFLKANGEQ 220
L G+ V VIGAG +G A+ + E G + + A R LE+ +F G +
Sbjct: 180 LSGKKVLVIGAGEMGELVAKHLAEKGVR------KITVANRTLERAEELAEEF----GGE 229
Query: 221 PVTWKRASSMDEVLREADVI-----SLHPVLDKTTYHLINKER 258
+ + 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 = 0.030
Identities = 32/138 (23%), Positives = 53/138 (38%), Gaps = 27/138 (19%)
Query: 164 KGQTVGVIGAGRIGS-------AYARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQFLKA 216
G V ++G G+ A A+ G ++ L+ E A + LK+
Sbjct: 1 DGLKVAIVGDGKHNRVAHSLILALAKF---GMEVVLVAPKGLYPPDPELLDKAKKEALKS 57
Query: 217 NGEQPVTWKRASSMDEVLREADVI-------SLHPVLD--KTTYHLINKERLATMKKEAI 267
G +T ++E L+ ADV+ L+ K Y + +E L K +AI
Sbjct: 58 GG---ITITVTDDLEEALKGADVVYTDRWQKEREERLEKFKPRYQ-VTEELLKKAKPDAI 113
Query: 268 LVNC---SRGPVI-DEVA 281
++ RG I D+V
Sbjct: 114 FMHPLPAHRGEEITDDVD 131
>gnl|CDD|223364 COG0287, TyrA, Prephenate dehydrogenase [Amino acid transport and
metabolism].
Length = 279
Score = 33.5 bits (77), Expect = 0.11
Identities = 26/112 (23%), Positives = 41/112 (36%), Gaps = 28/112 (25%)
Query: 166 QTVGVIGAGRIGSAYARMMVE-GFKMNLIYYDLYQATRLEKFVTAYGQFLKANGEQPVTW 224
VG++G G +G + AR + E G + +I D AT A +
Sbjct: 4 MKVGIVGLGLMGGSLARALKEAGLVVRIIGRDRSAATLKA-----------ALELGVIDE 52
Query: 225 KRASSMDEVLREADVI-------SLHPVLDKTTYHLINKERLATMKKEAILV 269
+ + E EAD++ + VL + HL KK AI+
Sbjct: 53 LTVAGLAEAAAEADLVIVAVPIEATEEVLKELAPHL---------KKGAIVT 95
>gnl|CDD|185366 PRK15469, ghrA, bifunctional glyoxylate/hydroxypyruvate reductase
A; Provisional.
Length = 312
Score = 33.6 bits (77), Expect = 0.12
Identities = 22/78 (28%), Positives = 37/78 (47%), Gaps = 1/78 (1%)
Query: 250 TYHLINKERLATMKKEAILVNCSRGPVIDEVALVEHLKQNPMFRVGLDVFEDEPYMKPG- 308
T +IN++ L + A L+N +RG + E L+ L + LDVF EP
Sbjct: 204 TVGIINQQLLEQLPDGAYLLNLARGVHVVEDDLLAALDSGKVKGAMLDVFSREPLPPESP 263
Query: 309 LSEMKNAIVVPHIASASK 326
L + + PH+A+ ++
Sbjct: 264 LWQHPRVAITPHVAAVTR 281
>gnl|CDD|223117 COG0039, Mdh, Malate/lactate dehydrogenases [Energy production and
conversion].
Length = 313
Score = 33.7 bits (78), Expect = 0.13
Identities = 12/33 (36%), Positives = 21/33 (63%), Gaps = 1/33 (3%)
Query: 168 VGVIGAGRIGSAYA-RMMVEGFKMNLIYYDLYQ 199
V VIGAG +GS+ A ++++G L+ D+ +
Sbjct: 3 VAVIGAGNVGSSLAFLLLLQGLGSELVLIDINE 35
>gnl|CDD|234849 PRK00856, pyrB, aspartate carbamoyltransferase catalytic subunit;
Provisional.
Length = 305
Score = 33.1 bits (77), Expect = 0.19
Identities = 16/54 (29%), Positives = 24/54 (44%), Gaps = 17/54 (31%)
Query: 229 SMDEVLREADVI------------SLHPVLDKTTYHL---INKERLATMKKEAI 267
+DEV+ +ADV+ L P ++ Y + ERLA K +AI
Sbjct: 206 DLDEVIEDADVVMMLRVQKERMDGGLLPSYEE--YKRSYGLTAERLALAKPDAI 257
>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 = 31.7 bits (73), Expect = 0.22
Identities = 24/113 (21%), Positives = 39/113 (34%), Gaps = 27/113 (23%)
Query: 167 TVGVIGAGRIGSAYARM------MVEGFKMNLIYYDLYQATRLEKFVTAYGQFLKANGEQ 220
V VIGAG +G A V + RL + + G
Sbjct: 22 KVVVIGAGVVGLGAAATAKGLGAEVTVLDVRP--------ARLRQLESLLGARFT----- 68
Query: 221 PVTWKRASSMD---EVLREAD-VISLHPVLDKTTYHLINKERLATMKKEAILV 269
S + E ++EAD VI + L+ +E + +MK +++V
Sbjct: 69 ----TLYSQAELLEEAVKEADLVIGAVLIPGAKAPKLVTREMVKSMKPGSVIV 117
>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 = 0.24
Identities = 15/87 (17%), Positives = 29/87 (33%), Gaps = 12/87 (13%)
Query: 206 FVTAYGQFLKANGEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHLINKERLATMKKE 265
F A G G S + ++L ++ + I+ E + +
Sbjct: 144 FGYADGGGYVVFGSG-------SYIGDLLDALGGENIAAETKGSESAPISFENILAADPD 196
Query: 266 AILVNCSRGPVIDEVALVEHLKQNPMF 292
I+V+ V+ LK NP++
Sbjct: 197 VIIVSGRETKTG-----VDELKANPLW 218
>gnl|CDD|225280 COG2423, COG2423, Predicted ornithine cyclodeaminase, mu-crystallin
homolog [Amino acid transport and metabolism].
Length = 330
Score = 32.7 bits (75), Expect = 0.27
Identities = 22/90 (24%), Positives = 33/90 (36%), Gaps = 19/90 (21%)
Query: 167 TVGVIGAGRIGSAYARMMVEGFK--MNLIYYDLYQAT--RLEKFVTAYGQFLKANGEQPV 222
T+ +IGAG A AR +E K ++ +Y E F +
Sbjct: 132 TLAIIGAG----AQARTQLEALKAVRDIREIRVYSRDPEAAEAFAARLRKRG------GE 181
Query: 223 TWKRASSMDEVLREADVI-----SLHPVLD 247
A S +E + AD++ S PVL
Sbjct: 182 AVGAADSAEEAVEGADIVVTATPSTEPVLK 211
>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: 131 SLAAARRIVEADEFMRAGLYD 151
S AAA AD F +AGLY+
Sbjct: 60 SRAAAEAFAAADPFAKAGLYE 80
>gnl|CDD|223450 COG0373, HemA, Glutamyl-tRNA reductase [Coenzyme metabolism].
Length = 414
Score = 31.4 bits (72), Expect = 0.65
Identities = 27/93 (29%), Positives = 41/93 (44%), Gaps = 20/93 (21%)
Query: 163 LKGQTVGVIGAGRIGSAYARMMVE-GFKMNLIYYDLYQATR-LEKFVTAYGQFLKANGEQ 220
LK + V VIGAG +G A+ + E G K + A R LE+ + G +
Sbjct: 176 LKDKKVLVIGAGEMGELVAKHLAEKGVK------KITIANRTLERAEELAKKL----GAE 225
Query: 221 PVTWKRASSMDEVLREADVI-----SLHPVLDK 248
V + E L EADV+ + HP++ +
Sbjct: 226 AVA---LEELLEALAEADVVISSTSAPHPIITR 255
>gnl|CDD|215300 PLN02545, PLN02545, 3-hydroxybutyryl-CoA dehydrogenase.
Length = 295
Score = 31.2 bits (71), Expect = 0.67
Identities = 36/149 (24%), Positives = 59/149 (39%), Gaps = 15/149 (10%)
Query: 168 VGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQA----------TRLEKFVTAYGQFLKAN 217
VGV+GAG++GS A++ M++ D A + L + V G+ +
Sbjct: 7 VGVVGAGQMGSGIAQLAAAA-GMDVWLLDSDPAALSRGLDSISSSLARLV-KKGKMSQEE 64
Query: 218 GEQPVTWKRASSMDEVLREADVISLHPVLDKTTYHLINKERLATMKKEAILVNCSRGPVI 277
+ + R ++ E LR+AD I V + + E K AIL + + I
Sbjct: 65 ADATLGRIRCTTNLEELRDADFIIEAIVESEDLKKKLFSELDRICKPSAILASNTSSISI 124
Query: 278 DEVALVEHLKQNPMFRVGLDVFEDEPYMK 306
+A Q P +G+ P MK
Sbjct: 125 TRLASA---TQRPQQVIGMHFMNPPPIMK 150
>gnl|CDD|214959 smart00990, VRR_NUC, This model contains proteins with the VRR-NUC
domain. It is associated with members of the PD-(D/E)XK
nuclease superfamily, which include the type III
restriction modification enzymes, for example StyLTI.
Length = 108
Score = 29.8 bits (67), Expect = 0.74
Identities = 17/47 (36%), Positives = 21/47 (44%), Gaps = 8/47 (17%)
Query: 4 PVSIEVWNPNGKYRVVSTKPMPGTR-------WINLLIEQDCRVEIC 43
P I +G+YR V K PG R WI+ L RVE+C
Sbjct: 59 PDLILFLPQDGRYRFVEVK-GPGDRLSPLQKRWIDRLAGLGFRVEVC 104
>gnl|CDD|235488 PRK05476, PRK05476, S-adenosyl-L-homocysteine hydrolase;
Provisional.
Length = 425
Score = 30.9 bits (71), Expect = 1.0
Identities = 14/48 (29%), Positives = 19/48 (39%), Gaps = 10/48 (20%)
Query: 226 RASSMDEVLREADVISLHPVLDKTT---YHLINKERLATMKKEAILVN 270
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 = 30.8 bits (70), Expect = 1.2
Identities = 25/103 (24%), Positives = 45/103 (43%), Gaps = 20/103 (19%)
Query: 163 LKGQTVGVIGAGRIGSAYARMMVE--GFKMNLIYYDLYQATRLEKFVTAYGQFLKANGEQ 220
LKG+ +IGAG +G A+ ++ K+ + +A L K + G +
Sbjct: 178 LKGKKALLIGAGEMGELVAKHLLRKGVGKILIANRTYERAEDLAKEL----------GGE 227
Query: 221 PVTWKRASSMDEVLREADVI-----SLHPVLDKTTYHLINKER 258
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 = 1.8
Identities = 14/45 (31%), Positives = 22/45 (48%), Gaps = 10/45 (22%)
Query: 229 SMDEVLREADVISLHPVLDKTT---YHLINKERLATMKKEAILVN 270
+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 = 2.3
Identities = 25/110 (22%), Positives = 44/110 (40%), Gaps = 19/110 (17%)
Query: 166 QTVGVIGAGRIGSAYARMMVE-GFKMNLIYYDLYQATRLEKFVTAYGQFLKANGEQPVTW 224
+G IG G +GS A +++ G+ + Y+ ++E+ V A G
Sbjct: 1 AKIGFIGLGVMGSPMALNLLKAGYT--VTVYNRTPE-KVEELV--------AEGAVG--- 46
Query: 225 KRASSMDEVLREADVISLHPVLDKTTYHLINKER--LATMKKEAILVNCS 272
A+S E + ADV+ +I E L +K I+++ S
Sbjct: 47 --AASPAEFVASADVVITMVPAGAAVDAVILGEDGLLPGLKPGDIIIDGS 94
>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 = 2.6
Identities = 19/88 (21%), Positives = 33/88 (37%), Gaps = 22/88 (25%)
Query: 192 LIYYDLYQATRLEKFVTAYGQFLKANGEQPVTW---KRASSMDEVLREADVISLHPVLDK 248
LIY + + E + A FLK + Q +T + + ++
Sbjct: 231 LIYLLFFAQPKQEAILAANTAFLKDDYSQVITTLEDYSPEKLPKSVK------------- 277
Query: 249 TTYHL----INKERLATMKKEAILVNCS 272
Y L + E+L+ +KE IL N +
Sbjct: 278 --YELAYSYVQTEKLSEDQKENILNNVT 303
>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 = 2.7
Identities = 24/80 (30%), Positives = 38/80 (47%), Gaps = 18/80 (22%)
Query: 214 LKANGEQPVTWKRASSMDEVLREADVISL-------HPVLD-----KTTYHLINKERLAT 261
LKA G + + S++EV+ EADV+ + P + K +Y I ERL
Sbjct: 197 LKAKG---IKVRETESLEEVIDEADVLYVTRIQKERFPDPEEYEKVKGSYG-ITLERLEA 252
Query: 262 MKKEAILVNCSRGPVIDEVA 281
KK I+++ P +DE+
Sbjct: 253 AKKGVIIMH--PLPRVDEID 270
>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 = 3.6
Identities = 26/108 (24%), Positives = 50/108 (46%), Gaps = 17/108 (15%)
Query: 167 TVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQ---FLKANGEQPVT 223
V ++GAG +G AR+ + G + D+ RL +G L +N
Sbjct: 170 KVVILGAGVVGENAARVAL-GLGAEVTVLDI-NLERLRYLDDIFGGRVTTLYSN------ 221
Query: 224 WKRASSMDEVLREADVI--SLHPVLDKTTYHLINKERLATMKKEAILV 269
++++E L+EAD++ ++ K L+ +E + TMK +++V
Sbjct: 222 ---PANLEEALKEADLVIGAVLIPGAKAP-KLVTEEMVKTMKPGSVIV 265
>gnl|CDD|188405 TIGR03890, nif11_cupin, nif11 domain/cupin domain protein. Members
of this protein family occur exclusively in the
Cyanobacteria and contain both a nif11 and a cupin
domain. The function is unknown.
Length = 171
Score = 28.6 bits (64), Expect = 3.7
Identities = 10/21 (47%), Positives = 14/21 (66%)
Query: 12 PNGKYRVVSTKPMPGTRWINL 32
P+ ++RV T P PGT W+ L
Sbjct: 149 PHRRHRVERTDPHPGTLWLAL 169
>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 = 3.8
Identities = 22/84 (26%), Positives = 36/84 (42%), Gaps = 13/84 (15%)
Query: 159 VGNLLKGQTVGVIGAGRIGSAYARMMVE-GFKMNLIYYDLYQATR-LEKFVTAYGQFLKA 216
+ LKG+ V +IGAG + A+ ++ G K + A R LEK +F
Sbjct: 6 IFGDLKGKKVLLIGAGEMARLAAKHLLSKGAK------KITIANRTLEKAKELAEEF--- 56
Query: 217 NGEQPVTWKRASSMDEVLREADVI 240
++E+L EAD++
Sbjct: 57 --PVGGEALPLDELEELLAEADIV 78
>gnl|CDD|234950 PRK01390, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
synthetase; Provisional.
Length = 460
Score = 29.0 bits (66), Expect = 4.0
Identities = 12/26 (46%), Positives = 14/26 (53%)
Query: 162 LLKGQTVGVIGAGRIGSAYARMMVEG 187
G+TV V G G G A AR +V G
Sbjct: 6 GFAGKTVAVFGLGGSGLATARALVAG 31
>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 = 4.2
Identities = 11/27 (40%), Positives = 16/27 (59%)
Query: 169 GVIGAGRIGSAYARMMVEGFKMNLIYY 195
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 = 4.2
Identities = 22/82 (26%), Positives = 35/82 (42%), Gaps = 8/82 (9%)
Query: 163 LKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQFLKANGEQPV 222
LKG+ V V+GAG G A A+ + + +I D EK + L+ GE +
Sbjct: 3 LKGKKVLVVGAGVSGLALAKFLKK-LGAKVILTD-------EKEEDQLKEALEELGELGI 54
Query: 223 TWKRASSMDEVLREADVISLHP 244
+E L D++ + P
Sbjct: 55 ELVLGEYPEEFLEGVDLVVVSP 76
>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 = 4.3
Identities = 22/65 (33%), Positives = 25/65 (38%), Gaps = 10/65 (15%)
Query: 115 TPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDGWLPNLFVGNLLKGQ---TVGVI 171
T L AE A L L V G DG L NL VG + G T+G
Sbjct: 207 TTEQLRGLKAERAPKLGLPEDTPFV-------LGASDGALSNLGVGAVDPGVAAITIGTS 259
Query: 172 GAGRI 176
GA R+
Sbjct: 260 GAIRV 264
>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 = 5.3
Identities = 17/76 (22%), Positives = 28/76 (36%), Gaps = 4/76 (5%)
Query: 168 VGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQFLKANGEQPVTWKRA 227
V +IGAG +G A ++ + + D G A V
Sbjct: 1 VLIIGAGGVGQGVAPLLARHGDLEITVADRSLEKAQALAAPKLGLRFIA---IAVDADNY 57
Query: 228 SSMDEVLREAD-VISL 242
++ +L+E D VI+L
Sbjct: 58 EALVALLKEGDLVINL 73
>gnl|CDD|223318 COG0240, GpsA, Glycerol-3-phosphate dehydrogenase [Energy
production and conversion].
Length = 329
Score = 28.3 bits (64), Expect = 5.4
Identities = 27/123 (21%), Positives = 48/123 (39%), Gaps = 31/123 (25%)
Query: 166 QTVGVIGAGRIGSAYARMMVEGFKMNLIY-------YDLYQATRLEKFVTAYGQFLKANG 218
+ VIGAG G+A A+++ ++ ++ TR ++L
Sbjct: 2 MKIAVIGAGSWGTALAKVLARNGHEVRLWGRDEEIVAEI-NETRENP------KYLP-GI 53
Query: 219 EQPVTWKRASSMDEVLREADVI-------SLHPVLDKTTYHLINKERLATMKKEAILVNC 271
P K + + E L AD+I +L VL + L K+AI+V+
Sbjct: 54 LLPPNLKATTDLAEALDGADIIVIAVPSQALREVLRQLKPLL---------LKDAIIVSA 104
Query: 272 SRG 274
++G
Sbjct: 105 TKG 107
>gnl|CDD|181018 PRK07530, PRK07530, 3-hydroxybutyryl-CoA dehydrogenase; Validated.
Length = 292
Score = 28.4 bits (64), Expect = 5.5
Identities = 15/41 (36%), Positives = 24/41 (58%), Gaps = 4/41 (9%)
Query: 166 QTVGVIGAGRIGSAYARMM-VEGFKMNLIYYDLYQATRLEK 205
+ VGVIGAG++G+ A + + G+ + L D+ RLE
Sbjct: 5 KKVGVIGAGQMGNGIAHVCALAGYDVLL--NDVSAD-RLEA 42
>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 = 28.2 bits (64), Expect = 5.6
Identities = 9/19 (47%), Positives = 14/19 (73%), Gaps = 2/19 (10%)
Query: 168 VGVIGAGRIGS--AYARMM 184
V ++GAG +GS AYA ++
Sbjct: 3 VAIVGAGFVGSTTAYALLL 21
>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 = 27.1 bits (61), Expect = 5.8
Identities = 14/71 (19%), Positives = 27/71 (38%), Gaps = 7/71 (9%)
Query: 170 VIGAGRIGSAYARMMVEGFKMNLIYYDLYQATRLEKFVTAYGQFLKANGEQPVTWKRASS 229
+IG GR+G + A + EG ++ R+E+ + + + A
Sbjct: 3 IIGYGRVGRSLAEELREGGPDVVVIDK--DPERVEELREEGVPVVVGDATDEEVLEEAG- 59
Query: 230 MDEVLREADVI 240
+ EAD +
Sbjct: 60 ----IEEADAV 66
>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 = 5.9
Identities = 18/55 (32%), Positives = 23/55 (41%), Gaps = 3/55 (5%)
Query: 105 ANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDGWLPNLFV 159
A +G+ V P E LAASL LAAA + E++ L D L
Sbjct: 42 AEAFGVPV--APHG-MEGGIGLAASLHLAAALPNFDILEYVPYLLPDDLLTGPPP 93
>gnl|CDD|139376 PRK13150, PRK13150, cytochrome c-type biogenesis protein CcmE;
Reviewed.
Length = 159
Score = 27.6 bits (61), Expect = 5.9
Identities = 18/62 (29%), Positives = 25/62 (40%), Gaps = 13/62 (20%)
Query: 116 PGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDGWLPNLFVGNLLKGQTVGVIGAGR 175
PG + L + SL A V Y+G LP+LF +GQ GV+ G
Sbjct: 68 PGSVRRDPDSLKVNFSLYDAEGSVTVS-------YEGILPDLF----REGQ--GVVVQGT 114
Query: 176 IG 177
+
Sbjct: 115 LE 116
>gnl|CDD|215289 PLN02528, PLN02528, 2-oxoisovalerate dehydrogenase E2 component.
Length = 416
Score = 28.5 bits (64), Expect = 5.9
Identities = 17/51 (33%), Positives = 25/51 (49%), Gaps = 4/51 (7%)
Query: 96 GYNNVDVNAANKYGIAVGNTPGV----LTETTAELAASLSLAAARRIVEAD 142
G +N+ V A ++G+ V N V L E T EL+ LAA ++ D
Sbjct: 274 GSHNIGVAMATEHGLVVPNIKNVQSLSLLEITKELSRLQHLAAENKLNPED 324
>gnl|CDD|236190 PRK08220, PRK08220, 2,3-dihydroxybenzoate-2,3-dehydrogenase;
Validated.
Length = 252
Score = 27.9 bits (63), Expect = 6.2
Identities = 12/25 (48%), Positives = 14/25 (56%), Gaps = 1/25 (4%)
Query: 163 LKGQTVGVIGAGR-IGSAYARMMVE 186
G+TV V GA + IG A A VE
Sbjct: 6 FSGKTVWVTGAAQGIGYAVALAFVE 30
>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 = 28.4 bits (64), Expect = 6.5
Identities = 18/88 (20%), Positives = 33/88 (37%), Gaps = 22/88 (25%)
Query: 192 LIYYDLYQATRLEKFVTAYGQFLKANGEQPVTW---KRASSMDEVLREADVISLHPVLDK 248
LIY + + E + A FL + + +T S+ + ++
Sbjct: 212 LIYLLFFAQPKQEAILEANTAFLNVDYSKVITTLEKYDPESLPKSVK------------- 258
Query: 249 TTYHL----INKERLATMKKEAILVNCS 272
Y L + E+L+ +KE IL N +
Sbjct: 259 --YELAYSYVQVEKLSDDQKENILNNVT 284
>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 = 28.0 bits (63), Expect = 6.5
Identities = 11/33 (33%), Positives = 16/33 (48%)
Query: 161 NLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLI 193
LKG+ V VIGAG +G A+ + +
Sbjct: 174 GNLKGKKVLVIGAGEMGELAAKHLAAKGVAEIT 206
>gnl|CDD|224996 COG2085, COG2085, Predicted dinucleotide-binding enzymes [General
function prediction only].
Length = 211
Score = 27.7 bits (62), Expect = 6.9
Identities = 8/16 (50%), Positives = 10/16 (62%)
Query: 167 TVGVIGAGRIGSAYAR 182
+ +IG G IGSA A
Sbjct: 3 IIAIIGTGNIGSALAL 18
>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 = 27.9 bits (63), Expect = 7.6
Identities = 8/19 (42%), Positives = 9/19 (47%)
Query: 159 VGNLLKGQTVGVIGAGRIG 177
G T V+GAG IG
Sbjct: 167 RSGFKPGDTALVLGAGPIG 185
>gnl|CDD|224995 COG2084, MmsB, 3-hydroxyisobutyrate dehydrogenase and related
beta-hydroxyacid dehydrogenases [Lipid metabolism].
Length = 286
Score = 27.9 bits (63), Expect = 7.8
Identities = 27/109 (24%), Positives = 45/109 (41%), Gaps = 18/109 (16%)
Query: 167 TVGVIGAGRIGSAYARMMVE-GFKMNLIYYDLYQATRLEKFVTAYGQFLKANGEQPVTWK 225
+ IG G +GS A +++ G ++ + Y+ EK + L A G
Sbjct: 2 KIAFIGLGIMGSPMAANLLKAGHEVTV--YNR----TPEKAA----ELLAAAGATV---- 47
Query: 226 RASSMDEVLREADVISLHPVLDKTTYHLINKE--RLATMKKEAILVNCS 272
A+S E EADV+ D ++ E L +K AI+++ S
Sbjct: 48 -AASPAEAAAEADVVITMLPDDAAVRAVLFGENGLLEGLKPGAIVIDMS 95
>gnl|CDD|198065 smart00997, AdoHcyase_NAD, S-adenosyl-L-homocysteine hydrolase, NAD
binding domain.
Length = 162
Score = 27.4 bits (62), Expect = 8.0
Identities = 13/45 (28%), Positives = 18/45 (40%), Gaps = 10/45 (22%)
Query: 229 SMDEVLREADVISLHPVLDKTT---YHLINKERLATMKKEAILVN 270
M+E + AD+ T +I +E MK AIL N
Sbjct: 71 KMEEAAKRADIFV-------TATGNKDVITREHFRAMKDGAILAN 108
>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 = 9.4
Identities = 10/31 (32%), Positives = 19/31 (61%), Gaps = 1/31 (3%)
Query: 168 VGVIGAGRIGSAYA-RMMVEGFKMNLIYYDL 197
+ +IGAG +G+A A ++ +G L+ D+
Sbjct: 1 ITIIGAGNVGAAVAFALIAKGLASELVLVDV 31
>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 = 26.8 bits (60), Expect = 9.4
Identities = 8/15 (53%), Positives = 12/15 (80%)
Query: 168 VGVIGAGRIGSAYAR 182
VG++GAG+IG + R
Sbjct: 3 VGIVGAGKIGRRHLR 17
>gnl|CDD|223422 COG0345, ProC, Pyrroline-5-carboxylate reductase [Amino acid
transport and metabolism].
Length = 266
Score = 27.5 bits (62), Expect = 9.5
Identities = 17/80 (21%), Positives = 29/80 (36%), Gaps = 16/80 (20%)
Query: 166 QTVGVIGAGRIGSAYARMMVEGFKM---NLIYYDLYQATRLEKFVTAYGQFLKANGEQPV 222
+G IGAG +G A +++ + +I + + R YG
Sbjct: 2 MKIGFIGAGNMGEAILSGLLKSGALPPEEIIVTNRSEEKRA-ALAAEYGV---------- 50
Query: 223 TWKRASSMDEVLREADVISL 242
+ E + EADV+ L
Sbjct: 51 --VTTTDNQEAVEEADVVFL 68
>gnl|CDD|227736 COG5449, COG5449, Uncharacterized conserved protein [Function
unknown].
Length = 225
Score = 27.6 bits (61), Expect = 9.8
Identities = 24/95 (25%), Positives = 34/95 (35%), Gaps = 26/95 (27%)
Query: 94 AVGYNNVDVNAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLYDGW 153
G++ ++A G G GVL+ I AD + AG YDG
Sbjct: 46 GGGWSPSAADSAVGLGPGQGEVLGVLSSA--------------GIAPAD--LAAGRYDGA 89
Query: 154 LPNLFVGN--------LLKGQTVGVIGAGRIGSAY 180
F+ N LL T+G + R G A+
Sbjct: 90 RVEAFLVNWSAPDRHVLLWTATIGSV--TREGEAF 122
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.319 0.135 0.395
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: 17,706,863
Number of extensions: 1743629
Number of successful extensions: 2272
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2068
Number of HSP's successfully gapped: 155
Length of query: 342
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 244
Effective length of database: 6,590,910
Effective search space: 1608182040
Effective search space used: 1608182040
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 59 (26.3 bits)