RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 021388
(313 letters)
>gnl|CDD|240633 cd12156, HPPR, Hydroxy(phenyl)pyruvate Reductase, D-isomer-specific
2-hydroxyacid-related dehydrogenase.
Hydroxy(phenyl)pyruvate reductase (HPPR) catalyzes the
NADP-dependent reduction of hydroxyphenylpyruvates,
hydroxypyruvate, or pyruvate to its respective lactate.
HPPR acts as a dimer and is related to D-isomer-specific
2-hydroxyacid dehydrogenases, a superfamily that
includes groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-Adenosylhomocysteine Hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 301
Score = 495 bits (1276), Expect = e-178
Identities = 166/300 (55%), Positives = 211/300 (70%)
Query: 4 IGVLMACPMNTYLEQELERRFNLFKFWTVSDKTQFLKAQQNNIRAVVGNATAGADAELID 63
VL P+ L ELE RF + + W +D L IRAVV N G A LI
Sbjct: 1 PDVLQLGPLPPELLAELEARFTVHRLWEAADPAALLAEHGGRIRAVVTNGETGLSAALIA 60
Query: 64 ALPKLEIVSSFSVGLDKVDMVKCKEKGVRVTNTPDVLTDDVADLAIGLMLAVLRRLCESD 123
ALP LE+++SF VG D +D+ + +G+RVTNTP VLTDDVADLA+GL+LAVLRR+ +D
Sbjct: 61 ALPALELIASFGVGYDGIDLDAARARGIRVTNTPGVLTDDVADLAVGLLLAVLRRIPAAD 120
Query: 124 RYVRSGKWKKGDYKLTTKFTGKTVGIIGLGRIGMAVAKRAEAFSCPINYYSRTEKPNLKY 183
R+VR+G+W KG + LT K +GK VGI+GLGRIG A+A+R EAF I Y+ R KP++ Y
Sbjct: 121 RFVRAGRWPKGAFPLTRKVSGKRVGIVGLGRIGRAIARRLEAFGMEIAYHGRRPKPDVPY 180
Query: 184 KYYPSVVELASNCHILVVACPLTEETRHIINREVIDALGPKGVLINIGRGPHVDERELVS 243
+YY S++ELA+ +LVVACP TRH++N EV++ALGP GVL+N+ RG VDE L++
Sbjct: 181 RYYASLLELAAESDVLVVACPGGPATRHLVNAEVLEALGPDGVLVNVARGSVVDEAALIA 240
Query: 244 ALVEGRLGGAGLDVFENEPHVPEELFGLENVVLMPHVGSGTVETRKTMADLVLGNLEAHF 303
AL EGR+ GAGLDVFENEP+VP L L+NVVL PH+ S TVETR+ M DLVL NLEA F
Sbjct: 241 ALQEGRIAGAGLDVFENEPNVPAALLDLDNVVLTPHIASATVETRRAMGDLVLANLEAFF 300
>gnl|CDD|240626 cd05301, GDH, D-glycerate dehydrogenase/hydroxypyruvate reductase
(GDH). D-glycerate dehydrogenase (GDH, also known as
hydroxypyruvate reductase, HPR) catalyzes the reversible
reaction of (R)-glycerate + NAD+ to hydroxypyruvate +
NADH + H+. In humans, HPR deficiency causes primary
hyperoxaluria type 2, characterized by over-excretion of
L-glycerate and oxalate in the urine, possibly due to an
imbalance in competition with L-lactate dehydrogenase,
another formate dehydrogenase (FDH)-like enzyme. GDH,
like FDH and other members of the D-specific hydroxyacid
dehydrogenase family that also includes L-alanine
dehydrogenase and S-adenosylhomocysteine hydrolase,
typically have a characteristic arrangement of 2 similar
subdomains of the alpha/beta Rossmann-fold NAD+ binding
form, despite often low sequence identity. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 309
Score = 335 bits (863), Expect = e-116
Identities = 133/309 (43%), Positives = 183/309 (59%), Gaps = 15/309 (4%)
Query: 6 VLMACPMNTYLEQELERRFNLFKFWTVSDKTQFLKAQQ--NNIR---AVVGNATAGADAE 60
VL+ + L F + V D+ + L ++ + ++ T DAE
Sbjct: 3 VLVTRRLPEEALALLREGFEV----EVWDEDRPLPREELLEAAKGADGLLCTLTDKIDAE 58
Query: 61 LIDALPKLEIVSSFSVGLDKVDMVKCKEKGVRVTNTPDVLTDDVADLAIGLMLAVLRRLC 120
L+DA P L++++++SVG D +D+ K +G+ VTNTPDVLTD ADLA L+LA RR+
Sbjct: 59 LLDAAPPLKVIANYSVGYDHIDVDAAKARGIPVTNTPDVLTDATADLAFALLLAAARRVV 118
Query: 121 ESDRYVRSGKWKKG--DYKLTTKFTGKTVGIIGLGRIGMAVAKRAEAFSCPINYYSRTEK 178
E DR+VR+G+WK L T GKT+GI+G+GRIG AVA+RA+ F I Y++R+ K
Sbjct: 119 EGDRFVRAGEWKGWSPTLLLGTDLHGKTLGIVGMGRIGQAVARRAKGFGMKILYHNRSRK 178
Query: 179 PNLKYK---YYPSVVELASNCHILVVACPLTEETRHIINREVIDALGPKGVLINIGRGPH 235
P + + Y S+ EL + + + CPLT ETRH+IN E + + P +LIN RG
Sbjct: 179 PEAEEELGARYVSLDELLAESDFVSLHCPLTPETRHLINAERLALMKPTAILINTARGGV 238
Query: 236 VDERELVSALVEGRLGGAGLDVFENEPHVPE-ELFGLENVVLMPHVGSGTVETRKTMADL 294
VDE LV AL G++ GAGLDVFE EP + L L NVVL+PH+GS TVETR MA+L
Sbjct: 239 VDEDALVEALKSGKIAGAGLDVFEPEPLPADHPLLTLPNVVLLPHIGSATVETRTAMAEL 298
Query: 295 VLGNLEAHF 303
NL A
Sbjct: 299 AADNLLAVL 307
>gnl|CDD|223980 COG1052, LdhA, Lactate dehydrogenase and related dehydrogenases
[Energy production and conversion / Coenzyme metabolism
/ General function prediction only].
Length = 324
Score = 326 bits (839), Expect = e-112
Identities = 127/320 (39%), Positives = 177/320 (55%), Gaps = 12/320 (3%)
Query: 4 IGVLMACPMNTYLEQELERRFNLFKFWTVSDKTQFLKAQQNNIRAVVGNATAGADAELID 63
I VL + + + L+ +F + ++ L + + AV+ DAE+++
Sbjct: 3 IVVLSTRKLPPEVLERLKEKFEVERYEDDLTPDTELAERLKDADAVITFVNDRIDAEVLE 62
Query: 64 ALPKLEIVSSFSVGLDKVDMVKCKEKGVRVTNTPDVLTDDVADLAIGLMLAVLRRLCESD 123
LP L+++++ S G D VD+ KE+G+ VTN P T+ VA+ A+ L+LA+ RR+ E D
Sbjct: 63 KLPGLKLIATRSAGYDNVDLEAAKERGITVTNVPGYSTEAVAEHAVALILALARRIHEGD 122
Query: 124 RYVRSGKWKK---GDYKLTTKFTGKTVGIIGLGRIGMAVAKRAEAFSCPINYYSRTEKP- 179
R VR G W D L GKT+GIIGLGRIG AVA+R + F + YY R+ P
Sbjct: 123 RRVREGNWSLSGGPDPLLGFDLRGKTLGIIGLGRIGQAVARRLKGFGMKVLYYDRSPNPE 182
Query: 180 ---NLKYKYYPSVVELASNCHILVVACPLTEETRHIINREVIDALGPKGVLINIGRGPHV 236
L +Y + EL + I+ + CPLT ETRH+IN E + + P +L+N RG V
Sbjct: 183 AEKELGARYVD-LDELLAESDIISLHCPLTPETRHLINAEELAKMKPGAILVNTARGGLV 241
Query: 237 DERELVSALVEGRLGGAGLDVFENEPH-VPEELFGLEN---VVLMPHVGSGTVETRKTMA 292
DE+ L+ AL G++ GAGLDVFENEP L L+N VVL PH+ S T E RK MA
Sbjct: 242 DEQALIDALKSGKIAGAGLDVFENEPALFDHPLLRLDNFPNVVLTPHIASATEEARKAMA 301
Query: 293 DLVLGNLEAHFLNKPLLTPV 312
+L L NLEA F V
Sbjct: 302 ELALENLEAFFDGGVPPNEV 321
>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 = 295 bits (758), Expect = e-100
Identities = 113/301 (37%), Positives = 161/301 (53%), Gaps = 6/301 (1%)
Query: 6 VLMACPMN-TYLEQELERRFNLFKFWTVSDKTQFLKAQQNNIRAVVGNATAGADAELIDA 64
VL+ P+ + LE L+A + A++ ++T AE++
Sbjct: 2 VLVLEPLFPPEALEALEATGFEVIVADD-LLADELEALLADADALIVSSTTPVTAEVLAK 60
Query: 65 LPKLEIVSSFSVGLDKVDMVKCKEKGVRVTNTPDVLTDDVADLAIGLMLAVLRRLCESDR 124
PKL+ + G+D +D+ K++G+ VTN P + VA+ A+GL+LA+LRRL +D
Sbjct: 61 APKLKFIQVAGAGVDNIDLDAAKKRGITVTNVPGANAEAVAEHALGLLLALLRRLPRADA 120
Query: 125 YVRSGKWKKGDYKLTTKFTGKTVGIIGLGRIGMAVAKRAEAFSCPINYYSRTEKPN---L 181
VR G + GKTVGI+GLGRIG VAKR +AF + YY RT KP
Sbjct: 121 AVRRGWGWLWAGFPGYELEGKTVGIVGLGRIGQRVAKRLQAFGMKVLYYDRTRKPEPEED 180
Query: 182 KYKYYPSVVELASNCHILVVACPLTEETRHIINREVIDALGPKGVLINIGRGPHVDEREL 241
S+ EL + ++V+ PLT ETRH+IN E + + P VL+N RG VDE L
Sbjct: 181 LGFRVVSLDELLAQSDVVVLHLPLTPETRHLINEEELALMKPGAVLVNTARGGLVDEDAL 240
Query: 242 VSALVEGRLGGAGLDVFENEPHVPEE-LFGLENVVLMPHVGSGTVETRKTMADLVLGNLE 300
+ AL G++ GA LDVFE EP + L L NV+L PH+ T E R+ MA++ + NLE
Sbjct: 241 LRALKSGKIAGAALDVFEPEPLPADHPLLELPNVILTPHIAGYTEEARERMAEIAVENLE 300
Query: 301 A 301
Sbjct: 301 R 301
>gnl|CDD|240655 cd12178, 2-Hacid_dh_13, Putative D-isomer specific 2-hydroxyacid
dehydrogenases, NAD-binding and catalytic domains.
2-Hydroxyacid dehydrogenases catalyze the conversion of
a wide variety of D-2-hydroxy acids to their
corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 317
Score = 271 bits (694), Expect = 4e-90
Identities = 110/261 (42%), Positives = 147/261 (56%), Gaps = 6/261 (2%)
Query: 58 DAELIDALPKLEIVSSFSVGLDKVDMVKCKEKGVRVTNTPDVLTDDVADLAIGLMLAVLR 117
D E+IDA L+I++++ G D +D+ KEKG+ VTNTP V T+ A+L GL+LA+ R
Sbjct: 56 DKEIIDAAKNLKIIANYGAGFDNIDVDYAKEKGIPVTNTPAVSTEPTAELTFGLILALAR 115
Query: 118 RLCESDRYVRSGKWKKGD--YKLTTKFTGKTVGIIGLGRIGMAVAKRAEAFSCPINYYSR 175
R+ E DR +R G + + L + GKT+GIIG+GRIG AVA+RA+AF I YY+R
Sbjct: 116 RIAEGDRLMRRGGFLGWAPLFFLGHELAGKTLGIIGMGRIGQAVARRAKAFGMKILYYNR 175
Query: 176 TEKPNLKYK----YYPSVVELASNCHILVVACPLTEETRHIINREVIDALGPKGVLINIG 231
K Y + EL + + P T ET H+I+ + P LIN
Sbjct: 176 HRLSEETEKELGATYVDLDELLKESDFVSLHAPYTPETHHLIDAAAFKLMKPTAYLINAA 235
Query: 232 RGPHVDERELVSALVEGRLGGAGLDVFENEPHVPEELFGLENVVLMPHVGSGTVETRKTM 291
RGP VDE+ LV AL G + GA LDVFE EP V EL L+NV+L PH+G+ TVE R M
Sbjct: 236 RGPLVDEKALVDALKTGEIAGAALDVFEFEPEVSPELKKLDNVILTPHIGNATVEARDAM 295
Query: 292 ADLVLGNLEAHFLNKPLLTPV 312
A N+ + K V
Sbjct: 296 AKEAADNIISFLEGKRPKNIV 316
>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 = 269 bits (691), Expect = 2e-89
Identities = 111/298 (37%), Positives = 171/298 (57%), Gaps = 16/298 (5%)
Query: 19 ELERRFNLFKFWTVSDKTQFLKA----QQNNIRAVV-GNATAGA----DAELIDALPK-L 68
EL + T + +F++A + + A+ +AG D ELI LP L
Sbjct: 19 ELSSIAEVIYP-TSGTREEFIEALKEGKYGDFVAIYRTFGSAGETGPFDEELISPLPPSL 77
Query: 69 EIVSSFSVGLDKVDMVKCKEKGVRVTNTPDVLTDDVADLAIGLMLAVLRRLCESDRYVRS 128
+I++ G D++D+ ++G++V+NTP + + AD A+ L+L LR ++R R+
Sbjct: 78 KIIAHAGAGYDQIDVDALTKRGIQVSNTPGAVDEATADTALFLILGALRNFSRAERSARA 137
Query: 129 GKWKKG-DYKLTTKFTGKTVGIIGLGRIGMAVAKRAEAFSCPINYYSRTEKP-NLKY--- 183
GKW+ D L GKT+GI+GLG IG A+A++A AF I Y++R+ P L+
Sbjct: 138 GKWRGFLDLTLAHDPRGKTLGILGLGGIGKAIARKAAAFGMKIIYHNRSRLPEELEKALA 197
Query: 184 KYYPSVVELASNCHILVVACPLTEETRHIINREVIDALGPKGVLINIGRGPHVDERELVS 243
YY S+ EL + ++ + CPLT TRH+IN++ + +++N RG +DE LV
Sbjct: 198 TYYVSLDELLAQSDVVSLNCPLTAATRHLINKKEFAKMKDGVIIVNTARGAVIDEDALVD 257
Query: 244 ALVEGRLGGAGLDVFENEPHVPEELFGLENVVLMPHVGSGTVETRKTMADLVLGNLEA 301
AL G++ AGLDVFENEP V L + NV L+PH+G+ TVET++ M +LVL N+EA
Sbjct: 258 ALESGKVASAGLDVFENEPEVNPGLLKMPNVTLLPHMGTLTVETQEKMEELVLENIEA 315
>gnl|CDD|183914 PRK13243, PRK13243, glyoxylate reductase; Reviewed.
Length = 333
Score = 253 bits (647), Expect = 7e-83
Identities = 123/263 (46%), Positives = 164/263 (62%), Gaps = 9/263 (3%)
Query: 48 AVVGNATAGADAELIDALPKLEIVSSFSVGLDKVDMVKCKEKGVRVTNTPDVLTDDVADL 107
A+V + D E+ +A P+L IV++++VG D +D+ + +G+ VTNTP VLT+ AD
Sbjct: 48 ALVTMLSERIDCEVFEAAPRLRIVANYAVGYDNIDVEEATRRGIYVTNTPGVLTEATADF 107
Query: 108 AIGLMLAVLRRLCESDRYVRSGKWKKGDYK------LTTKFTGKTVGIIGLGRIGMAVAK 161
A L+LA RRL E+D +VRSG+WK+ L GKT+GIIG GRIG AVA+
Sbjct: 108 AWALLLATARRLVEADHFVRSGEWKRRGVAWHPLMFLGYDVYGKTIGIIGFGRIGQAVAR 167
Query: 162 RAEAFSCPINYYSRTEKPNLKYKY---YPSVVELASNCHILVVACPLTEETRHIINREVI 218
RA+ F I YYSRT KP + + Y + EL + + PLT+ET H+IN E +
Sbjct: 168 RAKGFGMRILYYSRTRKPEAEKELGAEYRPLEELLRESDFVSLHVPLTKETYHMINEERL 227
Query: 219 DALGPKGVLINIGRGPHVDERELVSALVEGRLGGAGLDVFENEPHVPEELFGLENVVLMP 278
+ P +L+N RG VD + LV AL EG + GAGLDVFE EP+ EELF L+NVVL P
Sbjct: 228 KLMKPTAILVNTARGKVVDTKALVKALKEGWIAGAGLDVFEEEPYYNEELFSLKNVVLAP 287
Query: 279 HVGSGTVETRKTMADLVLGNLEA 301
H+GS T E R+ MA+LV NL A
Sbjct: 288 HIGSATFEAREGMAELVAENLIA 310
>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 = 248 bits (635), Expect = 3e-81
Identities = 105/258 (40%), Positives = 149/258 (57%), Gaps = 5/258 (1%)
Query: 49 VVGNATAGADAELIDALPKLEIVSSFSVGLDKVDMVKCKEKGVRVTNTPDVLTDDVADLA 108
+V DAEL+ A P+L ++ VGLD VD+ +G+ V N P + VA+ A
Sbjct: 47 LVPGMRKVIDAELLAAAPRLRLIQQPGVGLDGVDLEAATARGIPVANIPGGNAESVAEHA 106
Query: 109 IGLMLAVLRRLCESDRYVRSGKWKKGDYKLTTKFTGKTVGIIGLGRIGMAVAKRAEAFSC 168
+ LMLA+LRRL E+DR +R+G+W + + + + + +GKTVGI+GLG IG AVA+R F
Sbjct: 107 VMLMLALLRRLPEADRELRAGRWGRPEGRPSRELSGKTVGIVGLGNIGRAVARRLRGFGV 166
Query: 169 PINYYSRTEKPNLKYKYYPSVV----ELASNCHILVVACPLTEETRHIINREVIDALGPK 224
+ YY R P + K EL + ++ + PLT ETRH+I E + A+ P
Sbjct: 167 EVIYYDRFRDPEAEEKDLGVRYVELDELLAESDVVSLHVPLTPETRHLIGAEELAAMKPG 226
Query: 225 GVLINIGRGPHVDERELVSALVEGRLGGAGLDVFENEPHVPE-ELFGLENVVLMPHVGSG 283
+LIN RG VDE L++AL G L GAGLDVF EP P+ L L+NV+L PH+
Sbjct: 227 AILINTARGGLVDEEALLAALRSGHLAGAGLDVFWQEPLPPDDPLLRLDNVILTPHIAGV 286
Query: 284 TVETRKTMADLVLGNLEA 301
T E+ + MA +V N+
Sbjct: 287 TDESYQRMAAIVAENIAR 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 = 247 bits (633), Expect = 5e-81
Identities = 99/248 (39%), Positives = 139/248 (56%), Gaps = 11/248 (4%)
Query: 58 DAELIDALPKLEIVSSFSVGLDKVDMVKCKEKGVRVTNTPDVLTDDVADLAIGLMLAVLR 117
E++ A P+L+++S + VG D +D+ K++G+ VTNTP ++ VA+L IGLMLA+ R
Sbjct: 59 TEEVLAAAPRLKVISRYGVGYDNIDLEAAKKRGIVVTNTPGANSNSVAELTIGLMLALAR 118
Query: 118 RLCESDRYVRSGKWKK--GDYKLTTKFTGKTVGIIGLGRIGMAVAKRAEAFSCPINYYSR 175
++ ++DR VR+G W + G T+ GKT+GIIGLGRIG AVA+R F + Y
Sbjct: 119 QIPQADREVRAGGWDRPVG-----TELYGKTLGIIGLGRIGKAVARRLSGFGMKVLAYDP 173
Query: 176 TEKPNLKYKYYPSVV---ELASNCHILVVACPLTEETRHIINREVIDALGPKGVLINIGR 232
++ V EL + + PLT ETRH+IN + + P +LIN R
Sbjct: 174 YPDEEFAKEHGVEFVSLEELLKESDFISLHLPLTPETRHLINAAELALMKPGAILINTAR 233
Query: 233 GPHVDERELVSALVEGRLGGAGLDVFENEP-HVPEELFGLENVVLMPHVGSGTVETRKTM 291
G VDE L AL GR+ GA LDVFE EP L L NV+L PH+G+ T E M
Sbjct: 234 GGLVDEEALYEALKSGRIAGAALDVFEEEPPPADSPLLELPNVILTPHIGASTKEAVLRM 293
Query: 292 ADLVLGNL 299
+ N+
Sbjct: 294 GTMAAQNV 301
>gnl|CDD|223189 COG0111, SerA, Phosphoglycerate dehydrogenase and related
dehydrogenases [Amino acid transport and metabolism].
Length = 324
Score = 247 bits (634), Expect = 5e-81
Identities = 103/311 (33%), Positives = 161/311 (51%), Gaps = 7/311 (2%)
Query: 6 VLMACPMNTYLEQELERRFNLFKFWTVSDKTQFLKAQQNNIRAVVGNATAGADAELIDAL 65
VL+ P+ +EL +++ + L + A++ + T E++ A
Sbjct: 6 VLVTDPLAPDALEELLAAYDVEVPDGPDLDEEELLEALADADALIVSVT-PVTEEVLAAA 64
Query: 66 PKLEIVSSFSVGLDKVDMVKCKEKGVRVTNTPDVLTDDVADLAIGLMLAVLRRLCESDRY 125
P L+ + G+D +D+ ++G+ V N P VA+L + L+LA+ RR+ ++D
Sbjct: 65 PNLKAIGRAGAGVDNIDLEAATKRGILVVNAPGGNAISVAELVLALLLALARRIPDADAS 124
Query: 126 VRSGKWKKGDYKLTTKFTGKTVGIIGLGRIGMAVAKRAEAFSCPINYYSRTEKPN----L 181
R G+W + ++ T GKTVGIIGLGRIG AVAKR +AF + Y
Sbjct: 125 QRRGEWDRKAFRGTELA-GKTVGIIGLGRIGRAVAKRLKAFGMKVIGYDPYSPRERAGVD 183
Query: 182 KYKYYPSVVELASNCHILVVACPLTEETRHIINREVIDALGPKGVLINIGRGPHVDEREL 241
S+ EL + IL + PLT ETR +IN E + + P +LIN RG VDE L
Sbjct: 184 GVVGVDSLDELLAEADILTLHLPLTPETRGLINAEELAKMKPGAILINAARGGVVDEDAL 243
Query: 242 VSALVEGRLGGAGLDVFENEPHVPE-ELFGLENVVLMPHVGSGTVETRKTMADLVLGNLE 300
++AL G++ GA LDVFE EP + L+ L NV+L PH+G T E ++ +A++V N+
Sbjct: 244 LAALDSGKIAGAALDVFEEEPLPADSPLWDLPNVILTPHIGGSTDEAQERVAEIVAENIV 303
Query: 301 AHFLNKPLLTP 311
+ P++
Sbjct: 304 RYLAGGPVVNN 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 = 237 bits (607), Expect = 5e-77
Identities = 96/243 (39%), Positives = 133/243 (54%), Gaps = 14/243 (5%)
Query: 53 ATAGADA----------ELIDALPKLEIVSSFSVGLDKVDMVKCKEKGVRVTNTPDVLTD 102
A A ADA E+I+ALP+L+++ + VG+D VD+ E+G+ V N PD T+
Sbjct: 41 AAADADALLVQYAPVTAEVIEALPRLKVIVRYGVGVDNVDVAAATERGIPVCNVPDYCTE 100
Query: 103 DVADLAIGLMLAVLRRLCESDRYVRSGKWKKGDYKLTTKFTGKTVGIIGLGRIGMAVAKR 162
+VAD A+ L+LA+ R+L DR VR+G W + G T+G++G GRIG AVAKR
Sbjct: 101 EVADHALALILALARKLPFLDRAVRAGGWDWTVGGPIRRLRGLTLGLVGFGRIGRAVAKR 160
Query: 163 AEAFSCPINYYSRTEKPNLKYKYYPSVV---ELASNCHILVVACPLTEETRHIINREVID 219
A+AF + Y + VV EL + ++ + CPLT ETRH+I+ E +
Sbjct: 161 AKAFGFRVIAYDPYVPDGVAALGGVRVVSLDELLARSDVVSLHCPLTPETRHLIDAEALA 220
Query: 220 ALGPKGVLINIGRGPHVDERELVSALVEGRLGGAGLDVFENEPHVPE-ELFGLENVVLMP 278
+ P L+N RG VDE L AL GR+ GA LDV E EP + L NV+L P
Sbjct: 221 LMKPGAFLVNTARGGLVDEAALARALKSGRIAGAALDVLEEEPPPADSPLLSAPNVILTP 280
Query: 279 HVG 281
H
Sbjct: 281 HAA 283
>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 = 233 bits (597), Expect = 1e-75
Identities = 91/314 (28%), Positives = 147/314 (46%), Gaps = 10/314 (3%)
Query: 6 VLMACPMNTYLEQELERRFNLFKFWTVSDKTQFLKAQQNNIRAVVGNATAGADAELIDAL 65
VL+ P+ + L+ + + + L+A ++ A++ +T AE+++A
Sbjct: 1 VLITDPLRPEELELLKEGGEV-EVHDELLTEELLEAAKD-ADALIVRSTTPVTAEVLEAA 58
Query: 66 PKLEIVSSFSVGLDKVDMVKCKEKGVRVTNTPDVLTDDVADLAIGLMLAVLRRLCESDRY 125
P L++++ VG+D +D+ E+G+ VTN P T+ VA+L +GL+LA+ RR+ E+D
Sbjct: 59 PGLKVIARRGVGVDNIDLDAATERGILVTNVPGYSTESVAELTVGLILALARRIPEADAS 118
Query: 126 VRSGKWKKGDYKLTTKFTGKTVGIIGLGRIGMAVAKRAEAFSC-PINYYSRTEKPNLKYK 184
VR+G WKKG + + GKT+G+IG G IG A A+A + Y +
Sbjct: 119 VRAGDWKKGGP-IGLELYGKTLGVIGGGGIGGIGAAIAKALGMGVVAYDPYPNPERAEEG 177
Query: 185 YYPSVVEL------ASNCHILVVACPLTEETRHIINREVIDALGPKGVLINIGRGPHVDE 238
++ + ++ +A P T +T HII E L + N G ++E
Sbjct: 178 GVEVLLLDLLLLDLKESDDLINLAPPTTMKTGHIIINEARGMLKDAVAINNARGGGVIEE 237
Query: 239 RELVSALVEGRLGGAGLDVFENEPHVPEELFGLENVVLMPHVGSGTVETRKTMADLVLGN 298
L + L EG A V E P V L L NV+L PH+ T E ++ MA+ N
Sbjct: 238 AALDALLEEGIAAAALDVVEEEPPPVNSPLLDLPNVILTPHIAGATEEAQENMAEEAAEN 297
Query: 299 LEAHFLNKPLLTPV 312
L A V
Sbjct: 298 LLAFLKGGTPPNAV 311
>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 = 228 bits (584), Expect = 9e-74
Identities = 96/268 (35%), Positives = 147/268 (54%), Gaps = 4/268 (1%)
Query: 39 LKAQQNNIRAVVGNATAGADAELIDALPKLEIVSSFSVGLDKVDMVKCKEKGVRVTNTPD 98
L + + ++ + E+IDA L+I++ VGLD +D+ K+KG++V NTP
Sbjct: 35 LLEKIKDYDVLIVRSRTKVTKEVIDAAKNLKIIARAGVGLDNIDVEYAKKKGIKVINTPG 94
Query: 99 VLTDDVADLAIGLMLAVLRRLCESDRYVRSGKWKKGDYKLTTKFTGKTVGIIGLGRIGMA 158
++ VA+L IGLML++ R + ++R ++ GKW K YK + GKT+GIIG GRIG
Sbjct: 95 ASSNSVAELVIGLMLSLARFIHRANREMKLGKWNKKKYK-GIELRGKTLGIIGFGRIGRE 153
Query: 159 VAKRAEAFSCPINYYSRTEKPNLKYKYYPSVV---ELASNCHILVVACPLTEETRHIINR 215
VAK A A + Y K + V EL N + + PLT ET+H+IN+
Sbjct: 154 VAKIARALGMNVIAYDPYPKDEQAVELGVKTVSLEELLKNSDFISLHVPLTPETKHMINK 213
Query: 216 EVIDALGPKGVLINIGRGPHVDERELVSALVEGRLGGAGLDVFENEPHVPEELFGLENVV 275
+ ++ + ++IN RG +DE L+ AL G+L GA LDVFENEP +L L NV
Sbjct: 214 KELELMKDGAIIINTSRGGVIDEEALLEALKSGKLAGAALDVFENEPPPGSKLLELPNVS 273
Query: 276 LMPHVGSGTVETRKTMADLVLGNLEAHF 303
L PH+G+ T E ++ + + + +
Sbjct: 274 LTPHIGASTKEAQERIGEELANKIIEFL 301
>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 = 227 bits (582), Expect = 3e-73
Identities = 96/251 (38%), Positives = 141/251 (56%), Gaps = 6/251 (2%)
Query: 49 VVGNATAGADAELIDALPKLEIVSSFSVGLDKVDMVKCKEKGVRVTNTPDVLTDDVADLA 108
+V +AT AE+I+A P+L+++ VG+D +D+ +G+ V N P T VA+
Sbjct: 45 IVRSATK-VTAEVIEAAPRLKVIGRAGVGVDNIDVEAATARGILVVNAPGANTISVAEHT 103
Query: 109 IGLMLAVLRRLCESDRYVRSGKWKKGDYKLTTKFTGKTVGIIGLGRIGMAVAKRAEAFSC 168
I LMLA+ R + ++D +R+GKW + + + GKT+GI+GLGRIG VA+RA AF
Sbjct: 104 IALMLALARNIPQADASLRAGKWDRKKFM-GVELRGKTLGIVGLGRIGREVARRARAFGM 162
Query: 169 PINYYSRT---EKPNLKYKYYPSVVELASNCHILVVACPLTEETRHIINREVIDALGPKG 225
+ Y E+ S+ EL + + + PLT ETR +IN E + + P
Sbjct: 163 KVLAYDPYISAERAAAGGVELVSLDELLAEADFISLHTPLTPETRGLINAEELAKMKPGA 222
Query: 226 VLINIGRGPHVDERELVSALVEGRLGGAGLDVFENEPHVPE-ELFGLENVVLMPHVGSGT 284
+LIN RG VDE L AL G++ GA LDVFE EP + L GL NV+L PH+G+ T
Sbjct: 223 ILINTARGGIVDEAALADALKSGKIAGAALDVFEQEPPPADSPLLGLPNVILTPHLGAST 282
Query: 285 VETRKTMADLV 295
E ++ +A
Sbjct: 283 EEAQERVAVDA 293
>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 = 220 bits (563), Expect = 2e-70
Identities = 99/253 (39%), Positives = 145/253 (57%), Gaps = 6/253 (2%)
Query: 59 AELIDALPKLEIVSSFSVGLDKVDMVKCKEKGVRVTNTPDVLTDDVADLAIGLMLAVLRR 118
E+I+A L+++S G+D VD+ CKE+G+ V+N T+ VA+L IGL + +LR
Sbjct: 61 GEVIEACKNLKMISVAFTGVDHVDLEACKERGITVSNAAGYSTEAVAELTIGLAIDLLRN 120
Query: 119 LCESDRYVRSGKWKKGDYKLTTKFTGKTVGIIGLGRIGMAVAKRAEAFSCPINYYSRTEK 178
+ D VR+G K G + + GKTVGI+G G IG+ VA+ +AF C + YSR+EK
Sbjct: 121 IVPCDAAVRAGGTKAG--LIGRELAGKTVGIVGTGAIGLRVARLFKAFGCKVLAYSRSEK 178
Query: 179 PNLKYKY--YPSVVELASNCHILVVACPLTEETRHIINREVIDALGPKGVLINIGRGPHV 236
K Y S+ EL + I+ + PL +ET+ +I +E + + +LIN RGP V
Sbjct: 179 EEAKALGIEYVSLDELLAESDIVSLHLPLNDETKGLIGKEKLALMKESAILINTARGPVV 238
Query: 237 DERELVSALVEGRLGGAGLDVFENEPHVPEE--LFGLENVVLMPHVGSGTVETRKTMADL 294
D L AL EG++ GAG+DVF+ EP +P + L N +L PHV T E + A++
Sbjct: 239 DNEALADALNEGKIAGAGIDVFDMEPPLPADYPLLHAPNTILTPHVAFATEEAMEKRAEI 298
Query: 295 VLGNLEAHFLNKP 307
V N+EA KP
Sbjct: 299 VFDNIEAWLAGKP 311
>gnl|CDD|217244 pfam02826, 2-Hacid_dh_C, D-isomer specific 2-hydroxyacid
dehydrogenase, NAD binding domain. This domain is
inserted into the catalytic domain, the large
dehydrogenase and D-lactate dehydrogenase families in
SCOP. N-terminal portion of which is represented by
family pfam00389.
Length = 175
Score = 213 bits (546), Expect = 9e-70
Identities = 80/176 (45%), Positives = 109/176 (61%), Gaps = 4/176 (2%)
Query: 109 IGLMLAVLRRLCESDRYVRSGKWKKGDYKLTTKFTGKTVGIIGLGRIGMAVAKRAEAFSC 168
+ L+LA+ RR+ E+DR VR+G+W+ L + +GKTVGIIGLGRIG AVA+R +AF
Sbjct: 1 LALLLALARRIPEADRQVRAGRWRPDAL-LGRELSGKTVGIIGLGRIGRAVARRLKAFGM 59
Query: 169 PINYYSRTEKPNLK--YKYYPSVVELASNCHILVVACPLTEETRHIINREVIDALGPKGV 226
+ Y R K + Y S+ EL + ++ + PLT ETRH+IN E + + P +
Sbjct: 60 KVIAYDRYPKAEAEALGARYVSLDELLAESDVVSLHLPLTPETRHLINAERLALMKPGAI 119
Query: 227 LINIGRGPHVDERELVSALVEGRLGGAGLDVFENEPHVPE-ELFGLENVVLMPHVG 281
LIN RG VDE L++AL GR+ GA LDVFE EP P+ L L NV+L PH+
Sbjct: 120 LINTARGGLVDEDALIAALKSGRIAGAALDVFEPEPLPPDHPLLELPNVILTPHIA 175
>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 = 211 bits (541), Expect = 4e-67
Identities = 94/254 (37%), Positives = 143/254 (56%), Gaps = 14/254 (5%)
Query: 58 DAELIDALPKLEIVSSFSVGLDKVDMVKCKEKGVRVTNTPDVLTDDVADLAIGLMLAVLR 117
DAE++ LP L+++ + G + VD+ KE+G+ VTN P TD VA L+LA+ R
Sbjct: 56 DAEVLAQLPNLKLIGVLATGYNNVDLAAAKERGITVTNVPGYSTDSVAQHTFALLLALAR 115
Query: 118 RLCESDRYVRSGKWKKG------DYKLTTKFTGKTVGIIGLGRIGMAVAKRAEAFSCPIN 171
+ + V++G+W+K DY + GKT+GIIG G IG AVA+ A AF +
Sbjct: 116 LVAYHNDVVKAGEWQKSPDFCFWDYPIIE-LAGKTLGIIGYGNIGQAVARIARAFGMKVL 174
Query: 172 YYSRTEKPNLKYKYYPSVVELASNCHILVVACPLTEETRHIINREVIDALGPKGVLINIG 231
+ R P L+ Y S+ EL + ++ + CPLT ETR++IN E + + P +LIN
Sbjct: 175 FAERKGAPPLREGY-VSLDELLAQSDVISLHCPLTPETRNLINAEELAKMKPGAILINTA 233
Query: 232 RGPHVDERELVSALVEGRLGGAGLDVFENEPHVPEE----LFGLENVVLMPHVGSGTVET 287
RG VDE+ L AL G++ GAGLDV EP P L N+++ PH+ + E
Sbjct: 234 RGGLVDEQALADALNSGKIAGAGLDVLSQEP--PRADNPLLKAAPNLIITPHIAWASREA 291
Query: 288 RKTMADLVLGNLEA 301
R+ + D+++ N++A
Sbjct: 292 RQRLMDILVDNIKA 305
>gnl|CDD|185307 PRK15409, PRK15409, bifunctional glyoxylate/hydroxypyruvate
reductase B; Provisional.
Length = 323
Score = 205 bits (524), Expect = 2e-64
Identities = 98/249 (39%), Positives = 139/249 (55%), Gaps = 7/249 (2%)
Query: 58 DAELIDALPKLEIVSSFSVGLDKVDMVKCKEKGVRVTNTPDVLTDDVADLAIGLMLAVLR 117
DA L++ +PKL S+ SVG D D+ + + + +TP VLT+ VAD + L+L+ R
Sbjct: 57 DAALLEKMPKLRAASTISVGYDNFDVDALTARKILLMHTPTVLTETVADTLMALVLSTAR 116
Query: 118 RLCESDRYVRSGKWKK--GDYKLTTKFTGKTVGIIGLGRIGMAVAKRAE-AFSCPINYYS 174
R+ E V++G+W G T KT+GI+G+GRIGMA+A+RA F+ PI Y +
Sbjct: 117 RVVEVAERVKAGEWTASIGPDWFGTDVHHKTLGIVGMGRIGMALAQRAHFGFNMPILYNA 176
Query: 175 RTEKPNLKYKY---YPSVVELASNCHILVVACPLTEETRHIINREVIDALGPKGVLINIG 231
R + ++ Y + L + + PLT+ET H+ E + + IN G
Sbjct: 177 RRHHKEAEERFNARYCDLDTLLQESDFVCIILPLTDETHHLFGAEQFAKMKSSAIFINAG 236
Query: 232 RGPHVDERELVSALVEGRLGGAGLDVFENEP-HVPEELFGLENVVLMPHVGSGTVETRKT 290
RGP VDE L++AL +G + AGLDVFE EP V L L NVV +PH+GS T ETR
Sbjct: 237 RGPVVDENALIAALQKGEIHAAGLDVFEQEPLSVDSPLLSLPNVVAVPHIGSATHETRYN 296
Query: 291 MADLVLGNL 299
MA + NL
Sbjct: 297 MAACAVDNL 305
>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 = 193 bits (494), Expect = 5e-60
Identities = 86/261 (32%), Positives = 130/261 (49%), Gaps = 15/261 (5%)
Query: 54 TAGADAELIDALPKLEIVSSFSVGLDKVDMVKCKEKGVRVTNTPDVLTDDVADLAIGLML 113
A ++I+A PKL+++ G + VD+ E+G+ V NTP + VA+ +GLML
Sbjct: 54 FAPVTKKVIEAAPKLKLIGVCRGGPENVDVEAATERGIPVLNTPGRNAEAVAEFTVGLML 113
Query: 114 AVLRRLCESDRYVRSGKWKKG---DYKLTTKFTGKTVGIIGLGRIGMAVAKRAEAFSCPI 170
A R + + ++ G+W+K + GKTVGI+G G IG VAKR +AF +
Sbjct: 114 AETRNIARAHAALKDGEWRKDYYNYDGYGPELRGKTVGIVGFGAIGRRVAKRLKAFGAEV 173
Query: 171 NYY------SRTEKPNLKYKYYPSVVELASNCHILVVACPLTEETRHIINREVIDALGPK 224
Y + E +K S+ EL ++ + LT ETR +I E + P
Sbjct: 174 LVYDPYVDPEKIEADGVKKV---SLEELLKRSDVVSLHARLTPETRGMIGAEEFALMKPT 230
Query: 225 GVLINIGRGPHVDERELVSALVEGRLGGAGLDVFENEPHVPE--ELFGLENVVLMPHVGS 282
IN R VDE L+ AL EG++GGA LDVF EP +P L L+NV L PH+
Sbjct: 231 AYFINTARAGLVDEDALIEALEEGKIGGAALDVFPEEP-LPADHPLLKLDNVTLTPHIAG 289
Query: 283 GTVETRKTMADLVLGNLEAHF 303
T + + +++ L+ +
Sbjct: 290 ATRDVAERSPEIIAEELKRYL 310
>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 = 193 bits (494), Expect = 5e-60
Identities = 99/313 (31%), Positives = 156/313 (49%), Gaps = 14/313 (4%)
Query: 6 VLMACPMNTYLEQELERRFNLFKFWTVSDKTQFLKAQQNNIRAVVGNATAGADAELIDAL 65
+L+ P++ + L + V+ + L + + ++GN EL+ A
Sbjct: 3 ILVLSPLDDEHLERLRAAAPGAELRVVTAEE--LTEELADADVLLGN---PPLPELLPAA 57
Query: 66 PKLEIVSSFSVGLDKVDMVKCKEKGVRVTNTPDVLTDDVADLAIGLMLAVLRRLCESDRY 125
P+L + S S G+D + + E+ V +TN + +A+ +G MLA R+L R
Sbjct: 58 PRLRWIQSTSAGVDALLFPELLERDVVLTNARGIFGPPIAEYVLGYMLAFARKLPRYARN 117
Query: 126 VRSGKWKKGDYKLTTKFTGKTVGIIGLGRIGMAVAKRAEAFSCPINYYSRT--EKPNLKY 183
+W++ + GKTV I+GLG IG +A+RA+AF + R+ P +
Sbjct: 118 QAERRWQRRG--PVRELAGKTVLIVGLGDIGREIARRAKAFGMRVIGVRRSGRPAPPVVD 175
Query: 184 KYYPS--VVELASNCHILVVACPLTEETRHIINREVIDALGPKGVLINIGRGPHVDEREL 241
+ Y + EL +V A PLT ETR + N E A+ P VLIN+GRG VDE L
Sbjct: 176 EVYTPDELDELLPEADYVVNALPLTPETRGLFNAERFAAMKPGAVLINVGRGSVVDEDAL 235
Query: 242 VSALVEGRLGGAGLDVFENEPHVPEE--LFGLENVVLMPHVGSGTVETRKTMADLVLGNL 299
+ AL GR+ GA LDVFE EP +P + L+ L NV++ PH+ + + + ++ L NL
Sbjct: 236 IEALESGRIAGAALDVFEEEP-LPADSPLWDLPNVIITPHISGDSPSYPERVVEIFLENL 294
Query: 300 EAHFLNKPLLTPV 312
+ +PLL V
Sbjct: 295 RRYLAGEPLLNVV 307
>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 = 193 bits (493), Expect = 9e-60
Identities = 90/271 (33%), Positives = 128/271 (47%), Gaps = 30/271 (11%)
Query: 58 DAELIDALPKLEIVSSFSVGLDKVDMVKCKEKGVRVTNTPDVLTDDVADLAIGLMLAVLR 117
DAEL+D P L+ +S + G D +D+ KE G+ VTN P+ + VA+ I L+LA+LR
Sbjct: 58 DAELLDKAPGLKFISLRATGYDNIDLDYAKELGIGVTNVPEYSPNAVAEHTIALILALLR 117
Query: 118 RLCESDRYVRSGKWKKGDYKLTTKFT----GKTVGIIGLGRIGMAVAKRAEAFSCPINYY 173
D K D + +TVG++G G+IG AVA+RA+ F + Y
Sbjct: 118 NRKYIDERD-----KNQDLQDAGVIGRELEDQTVGVVGTGKIGRAVAQRAKGFGMKVIAY 172
Query: 174 SRTEKPNLKYK--YYPSVVELASNCHILVVACPLTEETRHIINREVIDALGPKGVLINIG 231
P L+ K Y S+ EL N I+ + PLT E H+IN E + ++IN
Sbjct: 173 DPFRNPELEDKGVKYVSLEELFKNSDIISLHVPLTPENHHMINEEAFKLMKKGVIIINTA 232
Query: 232 RGPHVDERELVSALVEGRLGGAGLDVFENEPHVP----------------EELFGLENVV 275
RG VD L+ AL G++ GAGLDV E+E P L NV+
Sbjct: 233 RGSLVDTEALIEALDSGKIFGAGLDVLEDE--TPDLLKDLEGEIFKDALNALLGRRPNVI 290
Query: 276 LMPHVGSGTVETRKTMADLVLGNLEAHFLNK 306
+ PH T + K M ++ N+ FL
Sbjct: 291 ITPHTAFYTDDALKNMVEISCENI-VDFLEG 320
>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 = 192 bits (489), Expect = 3e-59
Identities = 91/245 (37%), Positives = 130/245 (53%), Gaps = 14/245 (5%)
Query: 58 DAELIDALPKLEIVSSFSVGLDKVDMVKCKEKGVRVTNTPDVLTDDVADLAIGLMLAVLR 117
DA+ +DA P+L+I++ G D D+ C +G+ VT PD+LT+ A+L IGL++ + R
Sbjct: 57 DADFLDACPRLKIIACALKGYDNFDVEACTARGIWVTIVPDLLTEPTAELTIGLLIGLGR 116
Query: 118 RLCESDRYVRSGKWKKGDYKL-TTKFTGKTVGIIGLGRIGMAVAKRAEAFSCPINYYSRT 176
+ DR+VRSGK+ K T GKTVGI+G+G +G A+A+R F + YY
Sbjct: 117 HILAGDRFVRSGKFGGWRPKFYGTGLDGKTVGILGMGALGRAIARRLSGFGATLLYYDPH 176
Query: 177 EKPNLKYKY----YPSVVELASNCHILVVACPLTEETRHIINREVIDALGPKGVLINIGR 232
+ + + EL + LV+A PLT +T H+IN E + + P +L+N R
Sbjct: 177 PLDQAEEQALNLRRVELDELLESSDFLVLALPLTPDTLHLINAEALAKMKPGALLVNPCR 236
Query: 233 GPHVDERELVSALVEGRLGGAGLDVFENE-------PH-VPEELFGLE-NVVLMPHVGSG 283
G VDE + AL G LGG DVFE E P +P+EL V PH+GS
Sbjct: 237 GSVVDEAAVAEALKSGHLGGYAADVFEMEDWARPDRPRSIPQELLDQHDRTVFTPHIGSA 296
Query: 284 TVETR 288
E R
Sbjct: 297 VDEVR 301
>gnl|CDD|237436 PRK13581, PRK13581, D-3-phosphoglycerate dehydrogenase;
Provisional.
Length = 526
Score = 194 bits (497), Expect = 3e-58
Identities = 89/236 (37%), Positives = 130/236 (55%), Gaps = 12/236 (5%)
Query: 58 DAELIDALPKLEIVSSFSVGLDKVDMVKCKEKGVRVTNTPDVLTDDVADLAIGLMLAVLR 117
AE+++A L+++ VG+D VD+ +G+ V N P T A+ I LMLA+ R
Sbjct: 55 TAEVLEAAKNLKVIGRAGVGVDNVDVPAATRRGIIVVNAPTGNTISAAEHTIALMLALAR 114
Query: 118 RLCESDRYVRSGKWKKGDYKLTTKFTGKTVGIIGLGRIGMAVAKRAEAFSCPINYY---- 173
+ ++ +++GKW++ + + GKT+GIIGLGRIG VAKRA+AF + Y
Sbjct: 115 NIPQAHASLKAGKWERKKFM-GVELYGKTLGIIGLGRIGSEVAKRAKAFGMKVIAYDPYI 173
Query: 174 --SRTEKPNLKYKYYPSVVELASNCHILVVACPLTEETRHIINREVIDALGPKGV-LINI 230
R + ++ S+ EL + + + PLT ETR +I E + A GV +IN
Sbjct: 174 SPERAAQLGVELV---SLDELLARADFITLHTPLTPETRGLIGAEEL-AKMKPGVRIINC 229
Query: 231 GRGPHVDERELVSALVEGRLGGAGLDVFENEPHVPEELFGLENVVLMPHVGSGTVE 286
RG +DE L AL G++ GA LDVFE EP LF L NVV+ PH+G+ T E
Sbjct: 230 ARGGIIDEAALAEALKSGKVAGAALDVFEKEPPTDSPLFELPNVVVTPHLGASTAE 285
>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 = 191 bits (488), Expect = 5e-57
Identities = 91/270 (33%), Positives = 141/270 (52%), Gaps = 17/270 (6%)
Query: 58 DAELIDALPKLEIVSSFSVGLDKVDMVKCKEKGVRVTNTPDVLTDDVADLAIGLMLAVLR 117
E+I A PKL+++ VG+D +D+ +G+ V N P T A+ A+ ++LA R
Sbjct: 53 TEEVIAAAPKLKVIGRAGVGVDNIDIEAATARGILVVNAPTGNTISAAEHALAMLLAAAR 112
Query: 118 RLCESDRYVRSGKWKKGDYKLTTKFTGKTVGIIGLGRIGMAVAKRAEAFSCPINYY---- 173
+ ++D ++ G+W + + T+ GKT+G+IGLGRIG VAKRA+AF + Y
Sbjct: 113 NIPQADASLKEGEWDRKAFM-GTELYGKTLGVIGLGRIGSIVAKRAKAFGMKVLAYDPYI 171
Query: 174 --SRTEKPNLKYKYYPSVVELASNCHILVVACPLTEETRHIINREVIDALGPKGVLINIG 231
R E+ L + + EL + + V PLT ETR +I E + + +++N
Sbjct: 172 SPERAEQ--LGVELVDDLDELLARADFITVHTPLTPETRGLIGAEELAKMKKGVIIVNCA 229
Query: 232 RGPHVDERELVSALVEGRLGGAGLDVFENEPHVPEELFGLENVVLMPHVGSGTVETRKTM 291
RG +DE L AL EG + A LDVFE EP LF L+NV+ PH+G+ T E ++ +
Sbjct: 230 RGGIIDEAALYEALEEGHVRAAALDVFEKEPPTDNPLFDLDNVIATPHLGASTREAQENV 289
Query: 292 A--------DLVLGNLEAHFLNKPLLTPVV 313
A D + G + +N P + V
Sbjct: 290 ATQVAEQVLDALKGLPVPNAVNAPGIDADV 319
>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 = 182 bits (464), Expect = 2e-55
Identities = 92/266 (34%), Positives = 139/266 (52%), Gaps = 6/266 (2%)
Query: 48 AVVGNATAGADAELIDALPKLEIVSSFSVGLDKVDMVKCKEKGVRVTNTPD-VLTDDVAD 106
++ + T D E + L++++ +G D VD+ E GV VT P V D VA+
Sbjct: 50 IIIASVTPNFDKEFFEYNDGLKLIARHGIGYDNVDLKAATEHGVIVTRVPGAVERDAVAE 109
Query: 107 LAIGLMLAVLRRLCESDRYVRSGKWKKGDYKLTTKFTGKTVGIIGLGRIGMAVAKRA-EA 165
A+ L+L VLR++ ++ V+ GKW + + + +GKTVGIIG G IG VA+ E
Sbjct: 110 HAVALILTVLRKINQASEAVKEGKWTERANFVGHELSGKTVGIIGYGNIGSRVAEILKEG 169
Query: 166 FSCPINYYS---RTEKPNLKYKYYPSVVELASNCHILVVACPLTEETRHIINREVIDALG 222
F+ + Y E K S+ EL + I+ + PLTEET H+IN + +
Sbjct: 170 FNAKVLAYDPYVSEEVIKKKGAKPVSLEELLAESDIISLHAPLTEETYHMINEKAFSKMK 229
Query: 223 PKGVLINIGRGPHVDERELVSALVEGRLGGAGLDVFENEPHVPEE-LFGLENVVLMPHVG 281
+L+N RG +DE L+ AL G++ GAGLDV E EP + L ENVV+ PH+G
Sbjct: 230 KGVILVNTARGELIDEEALIEALKSGKIAGAGLDVLEEEPIKADHPLLHYENVVITPHIG 289
Query: 282 SGTVETRKTMADLVLGNLEAHFLNKP 307
+ T E+ M + V+ ++E K
Sbjct: 290 AYTYESLYGMGEKVVDDIEDFLAGKE 315
>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 = 177 bits (451), Expect = 1e-53
Identities = 84/252 (33%), Positives = 131/252 (51%), Gaps = 11/252 (4%)
Query: 58 DAELIDALPKLEIVSSFSVGLDKVDMVKCKEKGVRVTNTPDVLTDDVADLAIGLMLAVLR 117
A L++ LP L+++ + + +D+ KE+G+ V T A+L L+LA+ R
Sbjct: 60 PAALLERLPNLKLLVTTGMRNASIDLAAAKERGIVVCGTGGG-PTATAELTWALILALAR 118
Query: 118 RLCESDRYVRSGKWKKGDYKLTTKFTGKTVGIIGLGRIGMAVAKRAEAFSCPINYYSRTE 177
L E D +R+G W+ L T GKT+GI+GLGRIG VA+ +AF + +S
Sbjct: 119 NLPEEDAALRAGGWQTT---LGTGLAGKTLGIVGLGRIGARVARIGQAFGMRVIAWSSNL 175
Query: 178 KP----NLKYKYYPSVVELASNCHILVVACPLTEETRHIINREVIDALGPKGVLINIGRG 233
+ S EL + ++ + L++ TR ++ E + + P +L+N RG
Sbjct: 176 TAERAAAAGVEAAVSKEELFATSDVVSLHLVLSDRTRGLVGAEDLALMKPTALLVNTSRG 235
Query: 234 PHVDERELVSALVEGRLGGAGLDVFENEPHVPEE--LFGLENVVLMPHVGSGTVETRKTM 291
P VDE L++AL GR+ GA LDVF+ EP +P + L GL NV+L PH+G T E +
Sbjct: 236 PLVDEGALLAALRAGRIAGAALDVFDVEP-LPADHPLRGLPNVLLTPHIGYVTEEAYEGF 294
Query: 292 ADLVLGNLEAHF 303
+ N+ A
Sbjct: 295 YGQAVENIAAWL 306
>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 = 170 bits (434), Expect = 4e-51
Identities = 91/310 (29%), Positives = 144/310 (46%), Gaps = 24/310 (7%)
Query: 16 LEQELERRFNLFKFW--TVSDKT--QFLKAQQNNIRAVVGNATAGADAELIDALPKLEIV 71
L +E E + D+ + L+ + +VG E + AL +L+++
Sbjct: 11 LREEFEAALEGLYAEVPELPDEAAEEALE----DADVLVGGR--LTKEEALAALKRLKLI 64
Query: 72 SSFSVGLDKVDMVKCKEKGVRVTNTPDVLTDDVADLAIGLMLAVLRRLCESDRYVRSGKW 131
S G+D + + + E GV V N + VA+ A+ L+LA+ +R+ E D +R G W
Sbjct: 65 QVPSAGVDHLPLERLPE-GVVVANNHG-NSPAVAEHALALILALAKRIVEYDNDLRRGIW 122
Query: 132 KK--GDYKLTTKFTGKTVGIIGLGRIGMAVAKRAEAFSCPINYYSRTEK---PNLKYKYY 186
G+ + + GKTVGI+G G IG +A+ +AF + SR+ K
Sbjct: 123 HGRAGEEPESKELRGKTVGILGYGHIGREIARLLKAFGMRVIGVSRSPKEDEGADFVGTL 182
Query: 187 PSVVELASNCHILVVACPLTEETRHIINREVIDALGPKGVLINIGRGPHVDERELVSALV 246
+ E ++VVA PLT++TR +I + A+ P +L+N+GRGP VDE L AL
Sbjct: 183 SDLDEALEQADVVVVALPLTKQTRGLIGAAELAAMKPGAILVNVGRGPVVDEEALYEALK 242
Query: 247 EGRLGGAGLDVFENEP-------HVPEELFGLENVVLMPHVGSGTVETRKTMADLVLGNL 299
E + GA +DV+ P L NV++ PH T ET + D N+
Sbjct: 243 ERPIAGAAIDVWWRYPSRGDPVAPSRYPFHELPNVIMSPHNAGWTEETFRRRIDEAAENI 302
Query: 300 EAHFLNKPLL 309
+ +PLL
Sbjct: 303 RRYLRGEPLL 312
>gnl|CDD|181414 PRK08410, PRK08410, 2-hydroxyacid dehydrogenase; Provisional.
Length = 311
Score = 167 bits (424), Expect = 1e-49
Identities = 90/265 (33%), Positives = 136/265 (51%), Gaps = 25/265 (9%)
Query: 58 DAELIDALPKLEIVSSFSVGLDKVDMVKCKEKGVRVTNTPDVLTDDVADLAIGLMLAVLR 117
D E++ LP L+++ + G + VD+ K+KG+ V N T+ VA ++L++L
Sbjct: 54 DKEVLSQLPNLKLICITATGTNNVDIEYAKKKGIAVKNVAGYSTESVAQHTFAMLLSLLG 113
Query: 118 RLCESDRYVRSGKWKKGDYKLTTKFT----------GKTVGIIGLGRIGMAVAKRAEAFS 167
R+ DRYV+SG++ + FT GK GIIGLG IG VAK A+AF
Sbjct: 114 RINYYDRYVKSGEYSESPI-----FTHISRPLGEIKGKKWGIIGLGTIGKRVAKIAQAFG 168
Query: 168 CPINYYSRTEKPNLKYKYYPSVV--ELASNCHILVVACPLTEETRHIINREVIDALGPKG 225
+ YYS T N + Y V EL I+ + PL E+T+++I + + L
Sbjct: 169 AKVVYYS-TSGKNKNEE-YERVSLEELLKTSDIISIHAPLNEKTKNLIAYKELKLLKDGA 226
Query: 226 VLINIGRGPHVDERELVSALVEGRLGGAGLDVFENEPHVPEELF----GLENVVLMPHVG 281
+LIN+GRG V+E++L AL E + AGLDV E EP E +++ PH+
Sbjct: 227 ILINVGRGGIVNEKDLAKALDEKDI-YAGLDVLEKEPMEKNHPLLSIKNKEKLLITPHIA 285
Query: 282 SGTVETRKTMADLVLGNLEAHFLNK 306
+ E RKT+ + V N++ FL
Sbjct: 286 WASKEARKTLIEKVKENIKD-FLEG 309
>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 = 161 bits (410), Expect = 2e-47
Identities = 95/272 (34%), Positives = 139/272 (51%), Gaps = 33/272 (12%)
Query: 58 DAELIDALPKLEIVSSFSVGLDKVDMVKCKEKGVRVTNTPDVLTDDVADLAIGLMLAVLR 117
DAE+++ LP+L+++++ S G D +D+ C+E+G+ V N PD VA+ A L+LA+ R
Sbjct: 54 DAEVLEKLPRLKLIATRSTGFDHIDLEACRERGIAVCNVPDYGEATVAEHAFALLLALSR 113
Query: 118 RLCESDRYVRSGKWKKGDYKLT--TKF--TGKTVGIIGLGRIGMAVAKRAEAFSCPINYY 173
+L E+ R+ ++GD+ F GKT+G++G GRIG VA+ A F + Y
Sbjct: 114 KLREA--IERT---RRGDFSQAGLRGFELAGKTLGVVGTGRIGRRVARIARGFGMKVLAY 168
Query: 174 SRTEKPNLKYKY---YPSVVELASNCHILVVACPLTEETRHIINREVIDALGPKGVLINI 230
L + Y S+ EL I+ + P T +T H+INRE + P VLIN
Sbjct: 169 DVVPDEELAERLGFRYVSLEELLQESDIISLHVPYTPQTHHLINRENFALMKPGAVLINT 228
Query: 231 GRGPHVDERELVSALVEGRLGGAGLDVFENEPHVPEE---------------------LF 269
RG VD LV AL EG+L GAGLDV E E + EE L
Sbjct: 229 ARGAVVDTEALVRALKEGKLAGAGLDVLEQEEVLREEAELFREDVSPEDLKKLLADHALL 288
Query: 270 GLENVVLMPHVGSGTVETRKTMADLVLGNLEA 301
NV++ PHV T E + + D + N++A
Sbjct: 289 RKPNVIITPHVAYNTKEALERILDTTVENIKA 320
>gnl|CDD|180588 PRK06487, PRK06487, glycerate dehydrogenase; Provisional.
Length = 317
Score = 157 bits (400), Expect = 4e-46
Identities = 93/304 (30%), Positives = 146/304 (48%), Gaps = 22/304 (7%)
Query: 18 QELERRFNLFKFWTVSDKTQFLKAQQNNIRAVVGNATAGADAELIDALPKLEIVSSFSVG 77
LE+ F+ + + Q + + + + N A DA + A P+L+++ + G
Sbjct: 19 SPLEQAFDELQLHDATTPEQVAERLRG-AQVAISNKVA-LDAAALAAAPQLKLILVAATG 76
Query: 78 LDKVDMVKCKEKGVRVTNTPDVLTDDVADLAIGLMLAVLRRLCESDRYVRSGKWKKG--- 134
+ VD+ +E+G+ V N T VA + L+LA+ RL + + V +G+W++
Sbjct: 77 TNNVDLAAARERGITVCNCQGYGTPSVAQHTLALLLALATRLPDYQQAVAAGRWQQSSQF 136
Query: 135 ---DYKLTTKFTGKTVGIIGLGRIGMAVAKRAEAFSCPI---NYYSRTEKPN-LKYKYYP 187
D+ + + GKT+G++G G +G AVA+ AEAF + R +P+ L
Sbjct: 137 CLLDFPIV-ELEGKTLGLLGHGELGGAVARLAEAFGMRVLIGQLPGRPARPDRLPLD--- 192
Query: 188 SVVELASNCHILVVACPLTEETRHIINREVIDALGPKGVLINIGRGPHVDERELVSALVE 247
EL L + CPLTE TRH+I + + P +LIN RG VDE+ L AL
Sbjct: 193 ---ELLPQVDALTLHCPLTEHTRHLIGARELALMKPGALLINTARGGLVDEQALADALRS 249
Query: 248 GRLGGAGLDVFENEPHV---PEELFGLENVVLMPHVGSGTVETRKTMADLVLGNLEAHFL 304
G LGGA DV EP V P + +++ PH G+ E R+ + + N A F
Sbjct: 250 GHLGGAATDVLSVEPPVNGNPLLAPDIPRLIVTPHSAWGSREARQRIVGQLAENARAFFA 309
Query: 305 NKPL 308
KPL
Sbjct: 310 GKPL 313
>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 = 158 bits (401), Expect = 4e-46
Identities = 84/270 (31%), Positives = 124/270 (45%), Gaps = 26/270 (9%)
Query: 58 DAELIDALPKLEIV--SSFSVGLDKVDMVKCKEKGVRVTNTPDVLTDDVADLAIGLMLAV 115
DAEL+ P+L V ++ SV V E+G+ VT+ D + VA+ + +L
Sbjct: 63 DAELLARAPRLRAVVHAAGSV-RGLVT-DAVWERGILVTSAADANAEPVAEFTLAAILLA 120
Query: 116 LRRLCESDRYVRSGKWKKGDYKLTTK-FTGKTVGIIGLGRIGMAVAKRAEAFSCPINYYS 174
LRR+ R+G+ + + G+TVGI+G GRIG AV + F + Y
Sbjct: 121 LRRIPRFAAAYRAGRDWGWPTRRGGRGLYGRTVGIVGFGRIGRAVVELLRPFGLRVLVYD 180
Query: 175 R-----------TEKPNLKYKYYPSVVELASNCHILVVACPLTEETRHIINREVIDALGP 223
E +L EL + ++ + PLT ETR +I+ ++ +
Sbjct: 181 PYLPAAEAAALGVELVSLD--------ELLARSDVVSLHAPLTPETRGMIDARLLALMRD 232
Query: 224 KGVLINIGRGPHVDERELVSALVEGRLGGAGLDVFENEPHVPE-ELFGLENVVLMPHVGS 282
IN RG VDE L++ L GRL A LDV + EP P+ L L NV+L PH+
Sbjct: 233 GATFINTARGALVDEAALLAELRSGRL-RAALDVTDPEPLPPDSPLRTLPNVLLTPHIAG 291
Query: 283 GTVETRKTMADLVLGNLEAHFLNKPLLTPV 312
T + R+ + D L LE +PLL V
Sbjct: 292 STGDERRRLGDYALDELERFLAGEPLLHEV 321
>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 = 157 bits (399), Expect = 4e-46
Identities = 84/249 (33%), Positives = 124/249 (49%), Gaps = 19/249 (7%)
Query: 58 DAELIDALPKLEIVSSFSVGLDKVDMVKCKEKGVRVTNTPDVLTDDVADLAIGLMLAVLR 117
D E I+ L+ ++ GL+ +D+ KEKG+ + N P+ D V + A+G++LA+
Sbjct: 53 DKEFIEKATNLKFIARAGAGLENIDLEYAKEKGIELFNAPEGNRDAVGEHALGMLLALFN 112
Query: 118 RLCESDRYVRSGKWKK----GDYKLTTKFTGKTVGIIGLGRIGMAVAKRAEAFSCPINYY 173
+L +D+ VR+G W + G + GKTVGIIG G +G A AKR F C + Y
Sbjct: 113 KLNRADQEVRNGIWDREGNRGV-----ELMGKTVGIIGYGNMGKAFAKRLSGFGCKVIAY 167
Query: 174 SRTEKPNLKYKYYPSVVELASNCHILVVACPLTEETRHIINREVIDALGPKGVLINIGRG 233
+ + Y S+ L IL + PLT ETR ++N+E I + IN RG
Sbjct: 168 DKYKNFGDAYAEQVSLETLFKEADILSLHIPLTPETRGMVNKEFISSFKKPFYFINTARG 227
Query: 234 PHVDERELVSALVEGRLGGAGLDVFENE----------PHVPEELFGLENVVLMPHVGSG 283
V ++LV AL G++ GA LDV E E P E L V+L PH+
Sbjct: 228 KVVVTKDLVKALKSGKILGACLDVLEYEKASFESIFNQPEAFEYLIKSPKVILTPHIAGW 287
Query: 284 TVETRKTMA 292
T E+ + +A
Sbjct: 288 TFESYEKIA 296
>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 = 156 bits (397), Expect = 1e-45
Identities = 81/261 (31%), Positives = 125/261 (47%), Gaps = 27/261 (10%)
Query: 48 AVVGNATAGADA--------ELIDALPKLEIVSSFSVGLDKVDMVKCKEKGVRVTNTPDV 99
V +A DA +D P L+ ++ G++ +D+ ++G+ V NTP
Sbjct: 23 EVKEDALEDPDALIVRSDKLHDMDFAPSLKAIARAGAGVNNIDVDAASKRGIVVFNTPGA 82
Query: 100 LTDDVADLAIGLMLAVLRRLCESDRYV--------RSGKWKKGDYKLTTKFTGKTVGIIG 151
+ VA+L I +MLA+ R + ++ ++V G K + T+ GKT+G+IG
Sbjct: 83 NANAVAELVIAMMLALSRNIIQAIKWVTNGDGDDISKGVEKGKKQFVGTELRGKTLGVIG 142
Query: 152 LGRIGMAVAKRAEAFSCPINYYSRTEKPNLKYK------YYPSVVELASNCHILVVACPL 205
LG IG VA A A + Y +K S+ EL + + + PL
Sbjct: 143 LGNIGRLVANAALALGMKVIGYDPYLSVEAAWKLSVEVQRVTSLEELLATADYITLHVPL 202
Query: 206 TEETRHIINREVIDALGPKGVLINIGRGPHVDERELVSALVEGRLGGAGLDVFENEPHVP 265
T+ETR +IN E++ + P +L+N RG VDE L+ AL EG+LGG + F P
Sbjct: 203 TDETRGLINAELLAKMKPGAILLNFARGEIVDEEALLEALDEGKLGGY-VTDFPE----P 257
Query: 266 EELFGLENVVLMPHVGSGTVE 286
L L NV+ PH+G+ T E
Sbjct: 258 ALLGHLPNVIATPHLGASTEE 278
>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 = 151 bits (383), Expect = 2e-43
Identities = 78/267 (29%), Positives = 134/267 (50%), Gaps = 26/267 (9%)
Query: 61 LIDALPKLEIVSSFSVGLDKVDMVKCKEKGVRVTNTPDVLTDDVADLAIGLMLAVLRRLC 120
+ + L+ + +S G+D + + K+KG+ +TN + + +A+ +G +L + + L
Sbjct: 54 DLAKMKNLKWIQLYSAGVDYLPLEYIKKKGILLTNNSGIHSIPIAEWIVGYILEIYKGLK 113
Query: 121 ESDRYVRSGKWKKGDYKLTTKFTGKTVGIIGLGRIGMAVAKRAEAFSC----------PI 170
++ + + KWK + GKT+ +G G IG +AKR +AF +
Sbjct: 114 KAYKNQKEKKWKM--DSSLLELYGKTILFLGTGSIGQEIAKRLKAFGMKVIGVNTSGRDV 171
Query: 171 NYYSRT-EKPNLKYKYYPSVVELASNCHILVVACPLTEETRHIINREVIDALGPKGVLIN 229
Y+ + L E+ I+V PLTEET H+ + + + + IN
Sbjct: 172 EYFDKCYPLEELD--------EVLKEADIVVNVLPLTEETHHLFDEAFFEQMKKGALFIN 223
Query: 230 IGRGPHVDERELVSALVEGRLGGAGLDVFENEPHVPEE--LFGLENVVLMPHVGSGTVET 287
+GRGP VDE L+ AL ++ GA LDVFE EP +P++ L+ L+NV++ PH+ SG E
Sbjct: 224 VGRGPSVDEDALIEALKNKQIRGAALDVFEEEP-LPKDSPLWDLDNVLITPHI-SGVSEH 281
Query: 288 R-KTMADLVLGNLEAHFLNKPLLTPVV 313
+ + D+ NL++ + LL VV
Sbjct: 282 FNERLFDIFYENLKSFLEDGELLKNVV 308
>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 = 150 bits (381), Expect = 2e-43
Identities = 83/238 (34%), Positives = 121/238 (50%), Gaps = 13/238 (5%)
Query: 58 DAELIDALPKLEIVSSFSVGLDKVDMVKCKEKGVRVTNTPDVLTDDVADLAIGLMLAVLR 117
E+++A PKL + F +G ++VD+ ++G+ V N P T VA+L IG ++ + R
Sbjct: 55 TEEVLEAAPKLLAIGCFCIGTNQVDLDAAAKRGIPVFNAPFSNTRSVAELVIGEIIMLAR 114
Query: 118 RLCESDRYVRSGKWKK---GDYKLTTKFTGKTVGIIGLGRIGMAVAKRAEAFSCPINYYS 174
RL + + G W K G +++ GKT+GIIG G IG ++ AEA + +Y
Sbjct: 115 RLPDRNAAAHRGIWNKSATGSHEVR----GKTLGIIGYGHIGSQLSVLAEALGMRVIFYD 170
Query: 175 RTEKPNL-KYKYYPSVVELASNCHILVVACPLTEETRHIINREVIDALGPKGVLINIGRG 233
EK L + S+ EL + + + P T T+++I E I + +LIN RG
Sbjct: 171 IAEKLPLGNARQVSSLEELLAEADFVTLHVPATPSTKNMIGAEEIAQMKKGAILINASRG 230
Query: 234 PHVDERELVSALVEGRLGGAGLDVFENEPHVPEELF-----GLENVVLMPHVGSGTVE 286
VD L AL G L GA +DVF EP E F GL NV+L PH+G T E
Sbjct: 231 TVVDIDALAEALRSGHLAGAAVDVFPEEPASNGEPFSSPLQGLPNVILTPHIGGSTEE 288
>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 = 149 bits (379), Expect = 8e-43
Identities = 79/254 (31%), Positives = 113/254 (44%), Gaps = 27/254 (10%)
Query: 47 RAVVGNATAGADAELIDALPKLEI--VSSFSVGLDKVDMVKCKEKGVRVTNTPDVLTDDV 104
+ + AEL++ L + + +S+ S+G D +D+ KE G++V+N + V
Sbjct: 46 DGISILGKSKISAELLEKLKEAGVKYISTRSIGYDHIDLDAAKELGIKVSNVT-YSPNSV 104
Query: 105 ADLAIGLMLAVLRRLCESDRYVRSGKWKKGDYKLTTK----FTGKTVGIIGLGRIGMAVA 160
AD + LML LR+ + + DY L TVG+IG GRIG AV
Sbjct: 105 ADYTVMLMLMALRKYKQIMKRAEVN-----DYSLGGLQGRELRNLTVGVIGTGRIGQAVI 159
Query: 161 KRAEAFSCPINYYSRTEKPNLK-YKYYPSVVELASNCHILVVACPLTEETRHIINREVID 219
K F C I Y +K Y Y + L I+ + PLTEET H+IN+E I
Sbjct: 160 KNLSGFGCKILAYDPYPNEEVKKYAEYVDLDTLYKESDIITLHTPLTEETYHLINKESIA 219
Query: 220 ALGPKGVLINIGRGPHVDERELVSALVEGRLGGAGLDVFENE--------------PHVP 265
+ ++IN RG +D L+ L G++GGA LDV E E
Sbjct: 220 KMKDGVIIINTARGELIDTEALIEGLESGKIGGAALDVIEGEDGIYYNDRKGDILSNREL 279
Query: 266 EELFGLENVVLMPH 279
L NV+L PH
Sbjct: 280 AILRSFPNVILTPH 293
>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 = 147 bits (374), Expect = 3e-42
Identities = 84/280 (30%), Positives = 124/280 (44%), Gaps = 47/280 (16%)
Query: 53 ATAGADAELIDALPKLEIVSSFSVGLDKVDMVKCKEKGVRVTNTPDV---------LTDD 103
L+ LP L+ + S G+D + + PDV L
Sbjct: 44 LVWKPPPGLLARLPNLKAIFSLGAGVDHLL---------ADPDLPDVPIVRLVDPGLAQG 94
Query: 104 VADLAIGLMLAVLRRLCESDRYV---RSGKWKKGDYKLTTKFTGKTVGIIGLGRIGMAVA 160
+A+ + +L + R + DRY R G WK + + VG++GLG +G AVA
Sbjct: 95 MAEYVLAAVLRLHRDM---DRYAAQQRRGVWKPLPQRPAAERR---VGVLGLGELGAAVA 148
Query: 161 KRAEAFSCPINYYSRTEKPNLKYKYYPSVVELA---------SNCHILVVACPLTEETRH 211
+R A P++ +SR+ K V + ILV PLT ETR
Sbjct: 149 RRLAALGFPVSGWSRSPKD------IEGVTCFHGEEGLDAFLAQTDILVCLLPLTPETRG 202
Query: 212 IINREVIDALGPKGVLINIGRGPHVDERELVSALVEGRLGGAGLDVFENEPHVPEE--LF 269
I+N E++ L LIN+GRGPH+ E +L++AL G L GA LDVFE EP +P + L+
Sbjct: 203 ILNAELLARLPRGAALINVGRGPHLVEADLLAALDSGHLSGAVLDVFEQEP-LPADHPLW 261
Query: 270 GLENVVLMPHVGSGTVETRKTMADLVLGNLEAHFLNKPLL 309
V + PH+ + T + A V N+ +PL
Sbjct: 262 RHPRVTVTPHIAAIT--DPDSAAAQVAENIRRLEAGEPLP 299
>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 = 147 bits (374), Expect = 5e-42
Identities = 91/275 (33%), Positives = 132/275 (48%), Gaps = 29/275 (10%)
Query: 57 ADAELIDALPKLEI--VSSFSVGLDKVDMVKCKEKGVRVTNTPDVLTDDVADLAIGLMLA 114
DA +++ L +L + ++ G + VD+ KE G+ V P VA+ A+ L+LA
Sbjct: 56 LDAPVLEKLAELGVKLIALRCAGFNNVDLKAAKELGITVVRVPAYSPYAVAEHAVALLLA 115
Query: 115 VLRRLCESDRYVRSGKWKKGDYKLT--TKFT--GKTVGIIGLGRIGMAVAKRAEAFSCPI 170
+ R++ + VR +G++ L F GKTVG+IG G+IG A A+ + F C +
Sbjct: 116 LNRKIHRAYNRVR-----EGNFSLDGLLGFDLHGKTVGVIGTGKIGQAFARILKGFGCRV 170
Query: 171 NYYSRTEKPNLKYKY--YPSVVELASNCHILVVACPLTEETRHIINREVIDALGPKGV-L 227
Y P L Y + EL + I+ + CPLT ET H+IN E I A GV L
Sbjct: 171 LAYDPYPNPELAKLGVEYVDLDELLAESDIISLHCPLTPETHHLINAETI-AKMKDGVML 229
Query: 228 INIGRGPHVDERELVSALVEGRLGGAGLDVFENEPH--------------VPEELFGLEN 273
IN RG +D + L+ AL G++GG GLDV+E E V L N
Sbjct: 230 INTSRGGLIDTKALIEALKSGKIGGLGLDVYEEEAGLFFEDHSDEIIQDDVLARLLSFPN 289
Query: 274 VVLMPHVGSGTVETRKTMADLVLGNLEAHFLNKPL 308
V++ H T E +A+ L NL+ KPL
Sbjct: 290 VLITGHQAFFTKEALTNIAETTLENLDDFEAGKPL 324
>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 = 145 bits (368), Expect = 2e-41
Identities = 85/273 (31%), Positives = 133/273 (48%), Gaps = 12/273 (4%)
Query: 47 RAVVGNATAGADAELIDALPKLEIVSSFSVGLDK-VDMVKCKEKGVRVTNTPDVLTDDVA 105
A+V + + E + A P + V G++ V+ + G R TN + VA
Sbjct: 30 DALV-WTGSAREPERLPASPGVRWVQLPFAGVEAFVEAGVITDPGRRWTNAAGAYAETVA 88
Query: 106 DLAIGLMLAVLRRLCESDRYVRSGKW-KKGDYKLTTKFTGKTVGIIGLGRIGMAVAKRAE 164
+ A+ L+LA LR+L R+ W + L T G TV I+G G IG A+
Sbjct: 89 EHALALLLAGLRQL---PARARATTWDPAEEDDLVTLLRGSTVAIVGAGGIGRALIPLLA 145
Query: 165 AFSCPINYYSRTEKP-NLKYKYYPS--VVELASNCHILVVACPLTEETRHIINREVIDAL 221
F + +R+ +P + P+ + E+ + +V+A PLT ETRH+++ + A+
Sbjct: 146 PFGAKVIAVNRSGRPVEGADETVPADRLDEVWPDADHVVLAAPLTPETRHLVDAAALAAM 205
Query: 222 GPKGVLINIGRGPHVDERELVSALVEGRLGGAGLDVFENEPHVPEE--LFGLENVVLMPH 279
P L+N+ RGP VD LV AL G + GA LDV + EP +P+ L+ L N ++ PH
Sbjct: 206 KPHAWLVNVARGPLVDTDALVDALRSGEIAGAALDVTDPEP-LPDGHPLWSLPNALITPH 264
Query: 280 VGSGTVETRKTMADLVLGNLEAHFLNKPLLTPV 312
V + R +A+ V N+ A +PLL V
Sbjct: 265 VANTPEVIRPLLAERVAENVRAFAAGEPLLGVV 297
>gnl|CDD|240643 cd12166, 2-Hacid_dh_7, Putative D-isomer specific 2-hydroxyacid
dehydrogenases. 2-Hydroxyacid dehydrogenases catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 300
Score = 141 bits (358), Expect = 5e-40
Identities = 82/264 (31%), Positives = 123/264 (46%), Gaps = 23/264 (8%)
Query: 55 AGADAELIDALPKLEIVSSFSVGLDKV-DMVKCKEKGVRVTNTPDVLTDDVADLAIGLML 113
A E + ALP+L +V + S G D V ++ +GV + N V A+LA+ L+L
Sbjct: 48 APPVLEALRALPRLRVVQTLSAGYDGVLPLLP---EGVTLCNARGVHDASTAELAVALIL 104
Query: 114 AVLRRLCESDRYVRSGKWKKGDYKLTTKFTGKTVGIIGLGRIGMAVAKRAEAFSCPINYY 173
A LR L R G+W+ + T + V I+G G IG A+ +R F +
Sbjct: 105 ASLRGLPRFVRAQARGRWE---PRRTPSLADRRVLIVGYGSIGRAIERRLAPFEVRVTRV 161
Query: 174 SRTEKPNLKYKYYPSVV------ELASNCHILVVACPLTEETRHIINREVIDALGPKGVL 227
+RT +P V L ++V+ PLT+ETR +++ E + + +L
Sbjct: 162 ARTARPG------EQVHGIDELPALLPEADVVVLIVPLTDETRGLVDAEFLARMPDGALL 215
Query: 228 INIGRGPHVDERELVSALVEGRLGGAGLDVFENEPHVPEE--LFGLENVVLMPHVGSGTV 285
+N+ RGP VD LV+ L GRL A LDV + EP +P L+ V++ PHVG T
Sbjct: 216 VNVARGPVVDTDALVAELASGRL-RAALDVTDPEP-LPPGHPLWSAPGVLITPHVGGATP 273
Query: 286 ETRKTMADLVLGNLEAHFLNKPLL 309
LV L + +PL
Sbjct: 274 AFLPRAYALVRRQLRRYAAGEPLE 297
>gnl|CDD|177941 PLN02306, PLN02306, hydroxypyruvate reductase.
Length = 386
Score = 143 bits (361), Expect = 8e-40
Identities = 93/278 (33%), Positives = 142/278 (51%), Gaps = 30/278 (10%)
Query: 49 VVGNATAGADAELIDALPKL--EIVSSFSVGLDKVDMVKCKEKGVRVTNTPDVLTDDVAD 106
V+G T L AL K + S+ +VG + VD+ + G+ V NTP VLT+ A+
Sbjct: 66 VIGQLTEDWGETLFSALSKAGGKAFSNMAVGYNNVDVEAANKYGIAVGNTPGVLTETTAE 125
Query: 107 LAIGLMLAVLRRLCESDRYVRSGKWKKGDYKLTTKFTG-----KTVGIIGLGRIGMAVAK 161
LA L LA RR+ E+D ++R+G + + L F G +TVG+IG GRIG A A+
Sbjct: 126 LAASLSLAAARRIVEADEFMRAGLY---EGWLPHLFVGNLLKGQTVGVIGAGRIGSAYAR 182
Query: 162 R-AEAFSCPINYY-----SRTEK--------------PNLKYKYYPSVVELASNCHILVV 201
E F + YY +R EK + +K S+ E+ ++ +
Sbjct: 183 MMVEGFKMNLIYYDLYQSTRLEKFVTAYGQFLKANGEQPVTWKRASSMEEVLREADVISL 242
Query: 202 ACPLTEETRHIINREVIDALGPKGVLINIGRGPHVDERELVSALVEGRLGGAGLDVFENE 261
L + T H+IN+E + + + VL+N RGP +DE LV L + GLDVFE+E
Sbjct: 243 HPVLDKTTYHLINKERLALMKKEAVLVNASRGPVIDEVALVEHLKANPMFRVGLDVFEDE 302
Query: 262 PHVPEELFGLENVVLMPHVGSGTVETRKTMADLVLGNL 299
P++ L ++N V++PH+ S + TR+ MA L N+
Sbjct: 303 PYMKPGLADMKNAVVVPHIASASKWTREGMATLAALNV 340
>gnl|CDD|215501 PLN02928, PLN02928, oxidoreductase family protein.
Length = 347
Score = 139 bits (351), Expect = 1e-38
Identities = 75/258 (29%), Positives = 127/258 (49%), Gaps = 23/258 (8%)
Query: 58 DAELIDALPKLEIVSSFSVGLDKVDMVKCKEKGVRVTNTPDVLT---DDVADLAIGLMLA 114
DA++I +++++ F VGL+ VD+ + G++V P T A++AI LML
Sbjct: 73 DADIIARASQMKLIMQFGVGLEGVDVDAATKHGIKVARIPSEGTGNAASCAEMAIYLMLG 132
Query: 115 VLRRLCESDRYVRSGKWKKGDYKLTTKFTGKTVGIIGLGRIGMAVAKRAEAFSCPINYYS 174
+LR+ E +++ ++ + GKTV I+G G IG+ +AKR F +
Sbjct: 133 LLRKQNEMQISLKA---RRLGEPIGDTLFGKTVFILGYGAIGIELAKRLRPFGVKLLATR 189
Query: 175 R--TEKPNLKYKYYP--------------SVVELASNCHILVVACPLTEETRHIINREVI 218
R T +P + E A I+V+ C LT+ET I+N E +
Sbjct: 190 RSWTSEPEDGLLIPNGDVDDLVDEKGGHEDIYEFAGEADIVVLCCTLTKETAGIVNDEFL 249
Query: 219 DALGPKGVLINIGRGPHVDERELVSALVEGRLGGAGLDVFENEPHVPEE-LFGLENVVLM 277
++ +L+NI RG +D +++AL G LGG +DV +EP P++ + NV++
Sbjct: 250 SSMKKGALLVNIARGGLLDYDAVLAALESGHLGGLAIDVAWSEPFDPDDPILKHPNVIIT 309
Query: 278 PHVGSGTVETRKTMADLV 295
PHV T + ++M +V
Sbjct: 310 PHVAGVTEYSYRSMGKIV 327
>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 = 135 bits (342), Expect = 2e-37
Identities = 87/269 (32%), Positives = 128/269 (47%), Gaps = 28/269 (10%)
Query: 48 AVVGNATAGADAELIDALPKLEI--VSSFSVGLDKVDMVKCKEKGVRVTNTPDVLTDDVA 105
VV T D E+ + L + I ++ S G+D +D+ KE G+++TN P +A
Sbjct: 47 GVVVQQTLPYDEEVYEKLAEYGIKQIALRSAGVDMIDLDLAKENGLKITNVPAYSPRAIA 106
Query: 106 DLAIGLMLAVLRRLCESDRYVRSGKWKKGDYKLTTKFTGK-----TVGIIGLGRIGMAVA 160
+ A+ L +LR E DR V KGD++ G+ TVGIIG GRIG A A
Sbjct: 107 EFAVTQALNLLRNTPEIDRRVA-----KGDFRWAPGLIGREIRDLTVGIIGTGRIGSAAA 161
Query: 161 KRAEAFSCPINYYSRTEKPNLK--YKYYPSVVELASNCHILVVACPLTEETRHIINREVI 218
K + F + Y P L+ YY S+ +L I+ + PLT+E H+IN E
Sbjct: 162 KIFKGFGAKVIAYDPYPNPELEKFLLYYDSLEDLLKQADIISLHVPLTKENHHLINAEAF 221
Query: 219 DALGPKGVLINIGRGPHVDERELVSALVEGRLGGAGLDVFENE--------------PHV 264
+ +L+N RG VD + L+ AL G++ GA LD +ENE V
Sbjct: 222 AKMKDGAILVNAARGGLVDTKALIDALDSGKIAGAALDTYENETGYFNKDWSGKEIEDEV 281
Query: 265 PEELFGLENVVLMPHVGSGTVETRKTMAD 293
+EL + NV++ PH+ T K M +
Sbjct: 282 LKELIAMPNVLITPHIAFYTDTAVKNMVE 310
>gnl|CDD|235890 PRK06932, PRK06932, glycerate dehydrogenase; Provisional.
Length = 314
Score = 131 bits (330), Expect = 6e-36
Identities = 80/258 (31%), Positives = 128/258 (49%), Gaps = 21/258 (8%)
Query: 58 DAELIDALPKLEIVSSFSVGLDKVDMVKCKEKGVRVTNTPDVLTDDVADLAIGLMLAVLR 117
E + LPKL++++ + G + VD+V KE G+ V N + V + +G++ A+
Sbjct: 56 TRETLAQLPKLKLIAITATGTNNVDLVAAKELGIAVKNVTGYSSTTVPEHVLGMIFALKH 115
Query: 118 RLCE------SDRYVRSGKWKKGDYKLTTKFTGKTVGIIGLGRIGMAVAKRAEAFSCPIN 171
L SDR+ ++ DY +T G T+G+ G G +G V + A+A +
Sbjct: 116 SLMGWYRDQLSDRWATCKQFCYFDYPIT-DVRGSTLGVFGKGCLGTEVGRLAQALGMKVL 174
Query: 172 YYSRTEKPNLKYKYYP--SVVELASNCHILVVACPLTEETRHIINREVIDALGPKGVLIN 229
Y + Y P V++ A I+ + CPLTE T+++IN E + + P LIN
Sbjct: 175 YAEHKGASVCREGYTPFEEVLKQAD---IVTLHCPLTETTQNLINAETLALMKPTAFLIN 231
Query: 230 IGRGPHVDERELVSALVEGRLGGAGLDVFENEPHVPEE-------LFGLENVVLMPHVGS 282
GRGP VDE+ L+ AL G++ GA LDV EP PE+ L N+++ PH+
Sbjct: 232 TGRGPLVDEQALLDALENGKIAGAALDVLVKEP--PEKDNPLIQAAKRLPNLLITPHIAW 289
Query: 283 GTVETRKTMADLVLGNLE 300
+ T+ + V N+E
Sbjct: 290 ASDSAVTTLVNKVAQNIE 307
>gnl|CDD|236985 PRK11790, PRK11790, D-3-phosphoglycerate dehydrogenase;
Provisional.
Length = 409
Score = 129 bits (327), Expect = 1e-34
Identities = 78/237 (32%), Positives = 122/237 (51%), Gaps = 13/237 (5%)
Query: 59 AELIDALPKLEIVSSFSVGLDKVDMVKCKEKGVRVTNTPDVLTDDVADLAIGLMLAVLRR 118
E++ A KL + F +G ++VD+ ++G+ V N P T VA+L IG ++ +LR
Sbjct: 67 EEVLAAAEKLVAIGCFCIGTNQVDLDAAAKRGIPVFNAPFSNTRSVAELVIGEIILLLRG 126
Query: 119 LCESDRYVRSGKWKK---GDYKLTTKFTGKTVGIIGLGRIGMAVAKRAEAFSCPINYYSR 175
+ E + G W K G +++ GKT+GI+G G IG ++ AE+ + +Y
Sbjct: 127 IPEKNAKAHRGGWNKSAAGSFEVR----GKTLGIVGYGHIGTQLSVLAESLGMRVYFYDI 182
Query: 176 TEKPNL-KYKYYPSVVELASNCHILVVACPLTEETRHIINREVIDALGPKGVLINIGRGP 234
+K L + S+ EL + ++ + P T T+++I E + + P +LIN RG
Sbjct: 183 EDKLPLGNARQVGSLEELLAQSDVVSLHVPETPSTKNMIGAEELALMKPGAILINASRGT 242
Query: 235 HVDERELVSALVEGRLGGAGLDVFENEPHVPEELF-----GLENVVLMPHVGSGTVE 286
VD L AL G L GA +DVF EP + F GL+NV+L PH+G T E
Sbjct: 243 VVDIDALADALKSGHLAGAAIDVFPVEPKSNGDPFESPLRGLDNVILTPHIGGSTQE 299
>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 = 126 bits (319), Expect = 3e-34
Identities = 77/227 (33%), Positives = 114/227 (50%), Gaps = 9/227 (3%)
Query: 90 GVRVTNTPDVLTDDVADLAIGLMLAVLRRLCESDRYVRSGKWKKGDYKLTTKFTGKTVGI 149
G VT V + +A+ + +LA +RL E + +W+ + G T+GI
Sbjct: 85 GPVVTCARGVAAEAIAEFVLAAILAAAKRLPEI-WVKGAEQWR---REPLGSLAGSTLGI 140
Query: 150 IGLGRIGMAVAKRAEAFSCPINYYSRTEKPN--LKYKYYPSVVELASNCHILVVACPLTE 207
+G G IG A+A+RA A + R+ +P+ + + EL + LV+A PLT
Sbjct: 141 VGFGAIGQALARRALALGMRVLALRRSGRPSDVPGVEAAADLAELFARSDHLVLAAPLTP 200
Query: 208 ETRHIINREVIDALGPKGVLINIGRGPHVDERELVSALVEGRLGGAGLDVFENEPHVPEE 267
ETRH+IN +V+ P LINI RG VD+ L+ AL GR+ A LDV + EP +PE
Sbjct: 201 ETRHLINADVLAQAKPGLHLINIARGGLVDQEALLEALDSGRISLASLDVTDPEP-LPEG 259
Query: 268 --LFGLENVVLMPHVGSGTVETRKTMADLVLGNLEAHFLNKPLLTPV 312
L+ V L PH + + R+ +AD L NL + +PL V
Sbjct: 260 HPLYTHPRVRLSPHTSAIAPDGRRNLADRFLENLARYRAGQPLHDLV 306
>gnl|CDD|181041 PRK07574, PRK07574, formate dehydrogenase; Provisional.
Length = 385
Score = 127 bits (322), Expect = 4e-34
Identities = 77/261 (29%), Positives = 118/261 (45%), Gaps = 15/261 (5%)
Query: 59 AELIDALPKLEIVSSFSVGLDKVDMVKCKEKGVRVTNTPDVLTDDVADLAIGLMLAVLRR 118
AE I P L++ + +G D VD+ E G+ V + VA+ + ++LA++R
Sbjct: 106 AERIAKAPNLKLAITAGIGSDHVDLQAASEHGITVAEVTGSNSISVAEHVVMMILALVRN 165
Query: 119 LCESDRYVRSGKWKKGD-----YKLTTKFTGKTVGIIGLGRIGMAVAKRAEAFSCPINYY 173
S R G W D Y L G TVGI+G GRIG+AV +R + F ++Y
Sbjct: 166 YEPSHRQAVEGGWNIADCVSRSYDLE----GMTVGIVGAGRIGLAVLRRLKPFDVKLHYT 221
Query: 174 SRTEKP-----NLKYKYYPSVVELASNCHILVVACPLTEETRHIINREVIDALGPKGVLI 228
R P L Y+ S L S C ++ + CPL ET H+ + +V+ + L+
Sbjct: 222 DRHRLPEEVEQELGLTYHVSFDSLVSVCDVVTIHCPLHPETEHLFDADVLSRMKRGSYLV 281
Query: 229 NIGRGPHVDERELVSALVEGRLGGAGLDVFENEPHVPEELF-GLENVVLMPHVGSGTVET 287
N RG VD +V AL G L G DV+ +P + + + + PH+ T+
Sbjct: 282 NTARGKIVDRDAVVRALESGHLAGYAGDVWFPQPAPADHPWRTMPRNGMTPHISGTTLSA 341
Query: 288 RKTMADLVLGNLEAHFLNKPL 308
+ A LE F +P+
Sbjct: 342 QARYAAGTREILECFFEGRPI 362
>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 = 125 bits (316), Expect = 2e-33
Identities = 69/267 (25%), Positives = 111/267 (41%), Gaps = 29/267 (10%)
Query: 59 AELIDALPKLEIVSSFSVGLDKVDMVKCKEKGVRVTNTPDVLTDDVADLAIGLMLAVLRR 118
AE I L++ + +G D VD+ ++G+ V VA+ + ++L ++R
Sbjct: 76 AERIAKAKNLKLALTAGIGSDHVDLQAANDRGITVAEVTGSNVVSVAEHVVMMILILVRN 135
Query: 119 LCESDRYVRSGKWKKGD-----YKLTTKFTGKTVGIIGLGRIGMAVAKRAEAFSCPINYY 173
G W D Y L GKTVG +G GRIG+ V +R + F + YY
Sbjct: 136 YVPGHEQAIEGGWNVADVVKRAYDLE----GKTVGTVGAGRIGLRVLRRLKPFDVHLLYY 191
Query: 174 SRTEKPNLKYK-----YYPSVVELASNCHILVVACPLTEETRHIINREVIDALGPKGVLI 228
R P K + + ++ S C ++ + CPL ET + N+E++ + L+
Sbjct: 192 DRHRLPEEVEKELGLTRHADLEDMVSKCDVVTINCPLHPETEGLFNKELLSKMKKGAYLV 251
Query: 229 NIGRGPHVDERELVSALVEGRLGGAGLDVFENEP--------HVPEELFGLENVVLMPHV 280
N RG D + AL G L G DV+ +P +P N + PH+
Sbjct: 252 NTARGKICDREAVAEALESGHLAGYAGDVWFPQPAPKDHPWRTMP-------NNAMTPHI 304
Query: 281 GSGTVETRKTMADLVLGNLEAHFLNKP 307
T++ + A LE F +P
Sbjct: 305 SGTTLDAQARYAAGTKEILERFFEGEP 331
>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 = 124 bits (313), Expect = 4e-33
Identities = 81/293 (27%), Positives = 128/293 (43%), Gaps = 41/293 (13%)
Query: 54 TAGADAELIDALPKLEIVSSFSVGLDK-VDMVKCKEKGVRVTNTPDVLTDDVADLAIGLM 112
DAE + P L +V FS G D + K+ V + + +A+ IG
Sbjct: 44 HPHPDAEDV---PNLRLVQLFSAGADHWLGHPLYKDPEVPLCTASGIHGPQIAEWVIGTW 100
Query: 113 LAVLRRLCESDRYV---RSGKWKKGDYKLTTK-FTGKTVGIIGLGRIGMAVAKRAEAFSC 168
L + +Y+ + W + + + GK VGI+G G IG A+ A+A
Sbjct: 101 LVLSHHF---LQYIELQKEQTWGRRQEAYSVEDSVGKRVGILGYGSIGRQTARLAQALGM 157
Query: 169 PINYYSRTEKPNLK------Y--------------KYY-----PSVVE-LASNCHILVVA 202
+ Y+R+ +P + Y ++ S+ E L + +LVV+
Sbjct: 158 EVYAYTRSPRPTPESRKDDGYIVPGTGDPDGSIPSAWFSGTDKASLHEFLRQDLDLLVVS 217
Query: 203 CPLTEETRHIINREVIDALGPKG-VLINIGRGPHVDERELVSALVEGRLGGAGLDVFENE 261
PLT T+H++ E + L + + NI RG VD LV+AL G++ GA LDV + E
Sbjct: 218 LPLTPATKHLLGAEEFEILAKRKTFVSNIARGSLVDTDALVAALESGQIRGAALDVTDPE 277
Query: 262 PHVPE--ELFGLENVVLMPHVGSGTVETRKTMADLVLGNLEAHFLNKPLLTPV 312
P +P L+ NV++ PHV T E D++ NLE +PL+ V
Sbjct: 278 P-LPADHPLWSAPNVIITPHVSWQTQEYFDRALDVLEENLERLRKGEPLINLV 329
>gnl|CDD|235800 PRK06436, PRK06436, glycerate dehydrogenase; Provisional.
Length = 303
Score = 117 bits (294), Expect = 8e-31
Identities = 74/256 (28%), Positives = 127/256 (49%), Gaps = 11/256 (4%)
Query: 57 ADAELIDALP----KLEIVSSFSVGLDKVDMVKCKEKGVRVTNTPDVLTDDVADLAIGLM 112
A+A LI K +++ S S G+D +D+ E V +N + VA+ A L+
Sbjct: 35 AEAILIKGRYVPGKKTKMIQSLSAGVDHIDVSGIPENVVLCSNA-GAYSISVAEHAFALL 93
Query: 113 LAVLRRLCESDRYVRSGKWKKGDYKLTTKFTGKTVGIIGLGRIGMAVAKRAEAFSCPINY 172
LA + +CE++ +++G +K+ KL K++GI+G G IG VA A+AF I
Sbjct: 94 LAWAKNICENNYNMKNGNFKQSPTKL---LYNKSLGILGYGGIGRRVALLAKAFGMNIYA 150
Query: 173 YSRTEKPNLKYKYYPSVVELASNCHILVVACPLTEETRHIINREVIDALGPKGVLINIGR 232
Y+R+ + Y ++ ++++ PLT+ETR +IN +++ +IN+ R
Sbjct: 151 YTRSYVNDGISSIYMEPEDIMKKSDFVLISLPLTDETRGMINSKMLSLFRKGLAIINVAR 210
Query: 233 GPHVDERELVSALVEGRLGGAGLDVFENEPHVPEELFGLENVVLMPHVGSG-TVETRKTM 291
VD+ ++++ L DV+ NEP + E +NV+L PHV G + E +
Sbjct: 211 ADVVDKNDMLNFLRNHNDKYYLSDVWWNEPIITETN--PDNVILSPHVAGGMSGEIMQPA 268
Query: 292 ADLVLGNLEAHFLNKP 307
L N++ F KP
Sbjct: 269 VALAFENIKNFFEGKP 284
>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 = 111 bits (280), Expect = 3e-28
Identities = 65/230 (28%), Positives = 111/230 (48%), Gaps = 31/230 (13%)
Query: 58 DAELIDALPKLEIVSSFSVGLDKVDMVKCKEKGVRVTNTPDVLTDDVADLAIGLMLAVLR 117
+ L++ K++ V + ++G D +D KE+G+ N P + VA+ + +L + +
Sbjct: 49 NEALLEG-SKVKFVGTATIGTDHIDTDYLKERGIGFANAPGCNANSVAEYVLSALLVLAQ 107
Query: 118 RLCESDRYVRSGKWKKGDYKLTTKFTGKTVGIIGLGRIGMAVAKRAEAFSCPINYYS--R 175
R S + GKTVGI+G+G +G +A+R EA + R
Sbjct: 108 RQGFSLK-------------------GKTVGIVGVGNVGSRLARRLEALGMNVLLCDPPR 148
Query: 176 TEKPNLKYKYYPSVVELASNCHILVVACPLTEE----TRHIINREVIDALGPKGVLINIG 231
E + S+ EL + I+ + PLT + T H+++ + + AL P +LIN
Sbjct: 149 AEAEGDPG--FVSLEELLAEADIITLHVPLTRDGEHPTYHLLDEDFLAALKPGQILINAS 206
Query: 232 RGPHVDERELVSALVEGRLGGAGLDVFENEPHVPEELFGLENVVL-MPHV 280
RG +D + L++ L G+ LDV+ENEP + EL L+ V + PH+
Sbjct: 207 RGAVIDNQALLALLQRGKDLRVVLDVWENEPEIDLEL--LDKVDIATPHI 254
>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 = 108 bits (273), Expect = 2e-27
Identities = 74/275 (26%), Positives = 119/275 (43%), Gaps = 27/275 (9%)
Query: 48 AVVGNATAGADAELIDALPKLEI--VSSFSVGLDKVDMVKCKEKGVRVTNTPDVLTDDVA 105
AV+ AD E ++ + I V + +VG + +D+ KE G ++ P + +A
Sbjct: 47 AVIVRGNCFADKENLEIYKEYGIKYVFTRTVGFNHIDLEAAKELGFKMARVPSYSPNAIA 106
Query: 106 DLAIGLMLAVLRRLCESDRYVRSGKWKKGDYKLTTKFTGKTVGIIGLGRIGMAVAKRAEA 165
+LA L + + R + + +K + + + TVGIIG GRIG+ AK +
Sbjct: 107 ELAFTLAMTLSRHTAYTASRTANKNFKVDPFMFSKEIRNSTVGIIGTGRIGLTAAKLFKG 166
Query: 166 FSCPINYYSRTEKPNLK-YKYYPSVVELASNCHILVVACP-LTEETRHIINREVIDALGP 223
+ Y K + S+ EL I+ + P + + +IN+E I +
Sbjct: 167 LGAKVIGYDIYPSDAAKDVVTFVSLDELLKKSDIISLHVPYIKGKNDKLINKEFISKMKD 226
Query: 224 KGVLINIGRGPHVDERELVSALVEGRLGGAGLDVFENEPHVPEELFG-------LEN--- 273
+LIN RG DE ++ AL G+L G G DV NE +E+F +E+
Sbjct: 227 GAILINTARGELQDEEAILEALESGKLAGFGTDVLNNE----KEIFFKDFDGDKIEDPVV 282
Query: 274 ---------VVLMPHVGSGTVETRKTMADLVLGNL 299
V+L PH+GS T E M + NL
Sbjct: 283 EKLLDLYPRVLLTPHIGSYTDEALSNMIETSYENL 317
Score = 27.6 bits (62), Expect = 9.5
Identities = 17/63 (26%), Positives = 27/63 (42%), Gaps = 6/63 (9%)
Query: 87 KEKGVRVTNTPDVLTDDVADLAIGLMLAVLRRLCESDRYVRSGKWKKG-DYKLTTKFTGK 145
K+ G +T + L D+ LA G ++R C +D+ + G Y T +
Sbjct: 21 KKFGYDLTLVEEYLNDENVHLAKGHDAVIVRGNCFADKENLEIYKEYGIKYVFT-----R 75
Query: 146 TVG 148
TVG
Sbjct: 76 TVG 78
>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 = 106 bits (267), Expect = 8e-27
Identities = 75/247 (30%), Positives = 108/247 (43%), Gaps = 14/247 (5%)
Query: 49 VVGNATAGADAELIDALPKLEIVSSFSVGLDKVDMVKCKEKGVRVTNTPDVLTDDVADLA 108
VV ++ A+ L +L V + + G D V + V VT+ + VA+
Sbjct: 41 VVWGNSSDNLADAARRLTRLRWVQALAAGPDAVLAAGFAPE-VAVTSGRGLHDGTVAEHT 99
Query: 109 IGLMLAVLRRLCESDRYVRSGKWKK--------GDYKLTTKFTGKTVGIIGLGRIGMAVA 160
+ L+LA +RRL E R +W T G V I G G IG +A
Sbjct: 100 LALILAAVRRLDEMREAQREHRWAGELGGLQPLRPAGRLTTLLGARVLIWGFGSIGQRLA 159
Query: 161 KRAEAFSCPINYYSRTEKPNLKYKYYP--SVVELASNCHILVVACPLTEETRHIINREVI 218
A + +R+ + + EL +LV+ P T T H ++ EV+
Sbjct: 160 PLLTALGARVTGVARSAGERAGFPVVAEDELPELLPETDVLVMILPATPSTAHALDAEVL 219
Query: 219 DALGPKGVLINIGRGPHVDERELVSALVEGRLGGAGLDVFENEPHVPEE--LFGLENVVL 276
AL ++N+GRG VDE LV+AL GRLGGA LDV EP +P L+ N++L
Sbjct: 220 AALPKHAWVVNVGRGATVDEDALVAALESGRLGGAALDVTATEP-LPASSPLWDAPNLIL 278
Query: 277 MPHVGSG 283
PH G
Sbjct: 279 TPHAAGG 285
>gnl|CDD|183550 PRK12480, PRK12480, D-lactate dehydrogenase; Provisional.
Length = 330
Score = 93.4 bits (232), Expect = 7e-22
Identities = 67/259 (25%), Positives = 120/259 (46%), Gaps = 23/259 (8%)
Query: 63 DALPKLE-----IVSSFSVGLDKVDMVKCKEKGVRVTNTPDVLTDDVADLAIGLMLAVLR 117
D PKLE ++ + G D D+ K+ + ++N P + +A+ ++ + L ++R
Sbjct: 60 DVYPKLESYGIKQIAQRTAGFDMYDLDLAKKHNIVISNVPSYSPETIAEYSVSIALQLVR 119
Query: 118 RLCESDRYVRSGKWKKGDYKLTTKFTGKTVGIIGLGRIGMAVAKRAEAFSCPINYYSRTE 177
R + +R V++ + ++ TV IIG GRIG A AK F I Y
Sbjct: 120 RFPDIERRVQAHDFTWQAEIMSKPVKNMTVAIIGTGRIGAATAKIYAGFGATITAYDAYP 179
Query: 178 KPNLKY-KYYPSVVELASNCHILVVACPLTEETRHIINREVIDALGPKGVLINIGRGPHV 236
+L + Y SV E + I+ + P +E+ H+ ++ + D + +L+N RG +
Sbjct: 180 NKDLDFLTYKDSVKEAIKDADIISLHVPANKESYHLFDKAMFDHVKKGAILVNAARGAVI 239
Query: 237 DERELVSALVEGRLGGAGLDVFENEPH--------------VPEELFGLENVVLMPHVGS 282
+ +L++A+ +G L GA +D +ENE EL E +++ PH+
Sbjct: 240 NTPDLIAAVNDGTLLGAAIDTYENEAAYFTNDWTNKDIDDKTLLELIEHERILVTPHIAF 299
Query: 283 GTVETRKTMADLVLGNLEA 301
+ E + +LV G L A
Sbjct: 300 FSDE---AVQNLVEGGLNA 315
>gnl|CDD|178684 PLN03139, PLN03139, formate dehydrogenase; Provisional.
Length = 386
Score = 92.2 bits (229), Expect = 4e-21
Identities = 72/256 (28%), Positives = 119/256 (46%), Gaps = 9/256 (3%)
Query: 59 AELIDALPKLEIVSSFSVGLDKVDMVKCKEKGVRVTNTPDVLTDDVADLAIGLMLAVLRR 118
AE I LE++ + +G D +D+ G+ V VA+ + +L +LR
Sbjct: 113 AERIKKAKNLELLLTAGIGSDHIDLPAAAAAGLTVAEVTGSNVVSVAEDELMRILILLRN 172
Query: 119 LCESDRYVRSGKWK-KGDYKLTTKFTGKTVGIIGLGRIGMAVAKRAEAFSCPINYYSRTE 177
V SG+W G GKTVG +G GRIG + +R + F+C + Y+ R +
Sbjct: 173 FLPGYHQVVSGEWNVAGIAYRAYDLEGKTVGTVGAGRIGRLLLQRLKPFNCNLLYHDRLK 232
Query: 178 KP-----NLKYKYYPSVVELASNCHILVVACPLTEETRHIINREVIDALGPKGVLI-NIG 231
K+ + + C ++V+ PLTE+TR + N+E I + KGVLI N
Sbjct: 233 MDPELEKETGAKFEEDLDAMLPKCDVVVINTPLTEKTRGMFNKERIAKM-KKGVLIVNNA 291
Query: 232 RGPHVDERELVSALVEGRLGGAGLDVFENEPHVPEELFG-LENVVLMPHVGSGTVETRKT 290
RG +D + + A G +GG G DV+ +P + + + N + PH+ T++ +
Sbjct: 292 RGAIMDTQAVADACSSGHIGGYGGDVWYPQPAPKDHPWRYMPNHAMTPHISGTTIDAQLR 351
Query: 291 MADLVLGNLEAHFLNK 306
A V L+ +F +
Sbjct: 352 YAAGVKDMLDRYFKGE 367
>gnl|CDD|181499 PRK08605, PRK08605, D-lactate dehydrogenase; Validated.
Length = 332
Score = 89.8 bits (223), Expect = 1e-20
Identities = 63/246 (25%), Positives = 105/246 (42%), Gaps = 24/246 (9%)
Query: 75 SVGLDKVDMVKCKEKGVRVTNTPDVLTDDVADLAIGLMLAVLRRLCESDRYVRSGKWKKG 134
S G D D+ + + ++N P + +A+ + + ++R + VR ++
Sbjct: 77 SAGFDTYDLELATKYNLIISNVPSYSPESIAEFTVTQAINLVRHFNQIQTKVREHDFRWE 136
Query: 135 DYKLTTKFTGKTVGIIGLGRIGMAVAK-RAEAFSCPINYYSRTEKPNLKYK----YYPSV 189
L+ V +IG GRIG+AVAK A+ + + Y PN K Y ++
Sbjct: 137 PPILSRSIKDLKVAVIGTGRIGLAVAKIFAKGYGSDVVAYDPF--PNAKAATYVDYKDTI 194
Query: 190 VELASNCHILVVACPLTEETRHIINREVIDALGPKGVLINIGRGPHVDERELVSALVEGR 249
E I+ + P T+ ++ N ++ V +N RG VD + L+ AL G
Sbjct: 195 EEAVEGADIVTLHMPATKYNHYLFNADLFKHFKKGAVFVNCARGSLVDTKALLDALDNGL 254
Query: 250 LGGAGLDVFENE-PHVP-------------EELFGLENVVLMPHVGSGTVETRKTMADLV 295
+ GA LD +E E P P E L E+V+L PH+ T K +L+
Sbjct: 255 IKGAALDTYEFERPLFPSDQRGQTINDPLLESLINREDVILTPHIAFYTDAAVK---NLI 311
Query: 296 LGNLEA 301
+ L+A
Sbjct: 312 VDALDA 317
>gnl|CDD|185366 PRK15469, ghrA, bifunctional glyoxylate/hydroxypyruvate reductase
A; Provisional.
Length = 312
Score = 84.8 bits (210), Expect = 7e-19
Identities = 51/144 (35%), Positives = 81/144 (56%), Gaps = 6/144 (4%)
Query: 146 TVGIIGLGRIGMAVAKRAEAFSCPINYYSRTEKPNLKYKYYPSVVELA---SNCHILVVA 202
T+GI+G G +G VA+ + + P+ +SR+ K + + EL+ S +L+
Sbjct: 138 TIGILGAGVLGSKVAQSLQTWGFPLRCWSRSRKSWPGVQSFAGREELSAFLSQTRVLINL 197
Query: 203 CPLTEETRHIINREVIDALGPKGVLINIGRGPHVDERELVSALVEGRLGGAGLDVFENEP 262
P T ET IIN+++++ L L+N+ RG HV E +L++AL G++ GA LDVF EP
Sbjct: 198 LPNTPETVGIINQQLLEQLPDGAYLLNLARGVHVVEDDLLAALDSGKVKGAMLDVFSREP 257
Query: 263 HVPEE--LFGLENVVLMPHVGSGT 284
+P E L+ V + PHV + T
Sbjct: 258 -LPPESPLWQHPRVAITPHVAAVT 280
>gnl|CDD|166874 PRK00257, PRK00257, erythronate-4-phosphate dehydrogenase;
Validated.
Length = 381
Score = 81.6 bits (202), Expect = 2e-17
Identities = 53/221 (23%), Positives = 93/221 (42%), Gaps = 30/221 (13%)
Query: 67 KLEIVSSFSVGLDKVDMVKCKEKGVRVTNTPDVLTDDVADLAIGLMLAVLRRLCESDRYV 126
++ V + ++G D +D+ E G+ ++ P V D +G +L + R
Sbjct: 58 RVRFVGTCTIGTDHLDLDYFAEAGITWSSAPGCNARGVVDYVLGSLLTLAER-------- 109
Query: 127 RSGKWKKGDYKLTTKFTGKTVGIIGLGRIGMAVAKRAEAF--SCPINYYSRTEKPNLKYK 184
+G +T G++G G +G + + + R E
Sbjct: 110 ------EG-----VDLAERTYGVVGAGHVGGRLVRVLRGLGWKVLVCDPPRQEAEG--DG 156
Query: 185 YYPSVVELASNCHILVVACPLTEE----TRHIINREVIDALGPKGVLINIGRGPHVDERE 240
+ S+ + C ++ + PLT+E TRH+++ + +L P LIN RG VD +
Sbjct: 157 DFVSLERILEECDVISLHTPLTKEGEHPTRHLLDEAFLASLRPGAWLINASRGAVVDNQA 216
Query: 241 LVSALVEGRLGGAGLDVFENEPHVPEELFGLENVVL-MPHV 280
L AL+ G A LDV+E EP + EL + + PH+
Sbjct: 217 LREALLSGEDLDAVLDVWEGEPQIDLEL--ADLCTIATPHI 255
>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 = 67.7 bits (166), Expect = 6e-13
Identities = 65/250 (26%), Positives = 101/250 (40%), Gaps = 24/250 (9%)
Query: 58 DAELIDALPKLEIV----SSFSVGLDKVDMVKCKEKGVRVTNTPDVLTDDVADLAIGLML 113
D E+++A P ++ + S +S VD+ +E G+ VT D + V + I ++
Sbjct: 59 DEEVLEACPNIKYIGMCCSLYSEESANVDIAAARENGITVTGIRDYGDEGVVEYVISELI 118
Query: 114 AVLRRLCESDRYVRSGKWKKGDYKLTTKFTGKTVGIIGLGRIGMAVAKRAEAFSCPINYY 173
+L +WK+ +LT G VGIIGLG G +A F + YY
Sbjct: 119 RLLHGFGGK-------QWKEEPRELT----GLKVGIIGLGTTGQMIADALSFFGADVYYY 167
Query: 174 SRTEKPNLK---YKYYPSVVELASNCHILVVACPLTEETRHIINREVIDALGPKGVLINI 230
SRT KP+ + +Y P + EL ++ P ++ E + LG +L N
Sbjct: 168 SRTRKPDAEAKGIRYLP-LNELLKTVDVICTCLPKNVI---LLGEEEFELLGDGKILFNT 223
Query: 231 GRGPHVDERELVSALVEGRLGGAGLDVFENEPHVPEELFGLENVVLMPHVGSGTVETRKT 290
GP + L L G D EEL NV+ T + +
Sbjct: 224 SLGPSFEVEALKKWL--KASGYNIFDCDTAGALGDEELLRYPNVICTNKSAGWTRQAFER 281
Query: 291 MADLVLGNLE 300
++ VL NLE
Sbjct: 282 LSQKVLANLE 291
>gnl|CDD|185335 PRK15438, PRK15438, erythronate-4-phosphate dehydrogenase PdxB;
Provisional.
Length = 378
Score = 63.8 bits (155), Expect = 2e-11
Identities = 70/267 (26%), Positives = 113/267 (42%), Gaps = 51/267 (19%)
Query: 45 NIRAVVG-----NATAGADAELIDALPK----------LEIVSSFSVGLDKVDMVKCKEK 89
++AV G A ADA ++ ++ K ++ V + + G D VD K+
Sbjct: 21 EVKAVPGRPIPVAQLADADALMVRSVTKVNESLLAGKPIKFVGTATAGTDHVDEAWLKQA 80
Query: 90 GVRVTNTPDVLTDDVADLAIGLMLAVLRRLCESDRYVRSGKWKKGDYKLTTKFTGKTVGI 149
G+ + P V + +L L E D + +TVGI
Sbjct: 81 GIGFSAAPGCNAIAVVEYVFSSLLM----LAERDGFS---------------LHDRTVGI 121
Query: 150 IGLGRIGMAVAKRAEAFS-----CPINYYSRTEKPNLKYKYYPSVVELASNCHILVVACP 204
+G+G +G + R EA C R ++ + + S+ EL IL P
Sbjct: 122 VGVGNVGRRLQARLEALGIKTLLCDPPRADRGDEGDFR-----SLDELVQEADILTFHTP 176
Query: 205 LTEE----TRHIINREVIDALGPKGVLINIGRGPHVDERELVSALVEGRLGGAGLDVFEN 260
L ++ T H+ + ++I +L P +LIN RG VD L++ L EG+ LDV+E
Sbjct: 177 LFKDGPYKTLHLADEKLIRSLKPGAILINACRGAVVDNTALLTCLNEGQKLSVVLDVWEG 236
Query: 261 EPHVPEELFGLENV-VLMPHVGSGTVE 286
EP + EL L+ V + PH+ T+E
Sbjct: 237 EPELNVEL--LKKVDIGTPHIAGYTLE 261
>gnl|CDD|240631 cd12154, FDH_GDH_like, Formate/glycerate dehydrogenases, D-specific
2-hydroxy acid dehydrogenases and related
dehydrogenases. The formate/glycerate dehydrogenase
like family contains a diverse group of enzymes such as
formate dehydrogenase (FDH), glycerate dehydrogenase
(GDH), D-lactate dehydrogenase, L-alanine dehydrogenase,
and S-Adenosylhomocysteine hydrolase, that share a
common 2-domain structure. Despite often low sequence
identity, these proteins typically have a characteristic
arrangement of 2 similar domains of the alpha/beta
Rossmann fold NAD+ binding form. The NAD(P) binding
domain is inserted within the linear sequence of the
mostly N-terminal catalytic domain. Structurally, these
domains are connected by extended alpha helices and
create a cleft in which NAD(P) is bound, primarily to
the C-terminal portion of the 2nd (internal) domain.
While many members of this family are dimeric, alanine
DH is hexameric and phosphoglycerate DH is tetrameric.
2-hydroxyacid dehydrogenases are enzymes that catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate dehydrogenase (FDH) catalyzes the NAD+-dependent
oxidation of formate ion to carbon dioxide with the
concomitant reduction of NAD+ to NADH. FDHs of this
family contain no metal ions or prosthetic groups.
Catalysis occurs though direct transfer of a hydride ion
to NAD+ without the stages of acid-base catalysis
typically found in related dehydrogenases.
Length = 310
Score = 51.1 bits (122), Expect = 2e-07
Identities = 40/221 (18%), Positives = 78/221 (35%), Gaps = 15/221 (6%)
Query: 40 KAQQNNIRAVVGNATAGADAELIDALPKLEIVSSFSVGLDKVDMVKC-KEKGVRVTNTPD 98
++ V A+ LI L ++ ++++G D D+ + G+
Sbjct: 61 ALWSLDVVLKVKEPLTNAEYALIQKLG-DRLLFTYTIGADHRDLTEALARAGLTAIAVEG 119
Query: 99 VLTDDVADLAIGLM-LAVLRRLCESDRYVRSGKWKKGDYKLTTKFTGKTVGIIGLGRIGM 157
V + +IG L+V + D GKTV ++G G +G
Sbjct: 120 VELPLLTSNSIGAGELSVQFIARFLEVQQPGRLGGAPDVA------GKTVVVVGAGVVGK 173
Query: 158 AVAKRAEAFS-----CPINYYSRTEKPNLKYKYYPSVVELASNCHILVVACPLTEETRHI 212
A+ IN + + L K + E + ++V L + I
Sbjct: 174 EAAQMLRGLGAQVLITDINVEALEQLEELGGKNVEELEEALAEADVIVTTTLLPGKRAGI 233
Query: 213 IN-REVIDALGPKGVLINIGRGPHVDERELVSALVEGRLGG 252
+ E+++ + P V++N+ G + L + L+E G
Sbjct: 234 LVPEELVEQMKPGSVIVNVAVGAVGCVQALHTQLLEEGHGV 274
>gnl|CDD|173621 PTZ00431, PTZ00431, pyrroline carboxylate reductase; Provisional.
Length = 260
Score = 34.5 bits (79), Expect = 0.045
Identities = 29/90 (32%), Positives = 42/90 (46%), Gaps = 6/90 (6%)
Query: 147 VGIIGLGRIGMAVA---KRAEAFSCPINYYSRTEKPNLKYKYYPSVVELASNCHILVVAC 203
VG IGLG++G A+A + + YY K N + Y S ELA C I+V
Sbjct: 6 VGFIGLGKMGSALAYGIENSNIIGKENIYYHTPSKKNTPFVYLQSNEELAKTCDIIV--L 63
Query: 204 PLTEETRHIINREVIDALGPKGVLINIGRG 233
+ + + E+ LG K +LI+I G
Sbjct: 64 AVKPDLAGKVLLEIKPYLGSK-LLISICGG 92
>gnl|CDD|236573 PRK09567, nirA, ferredoxin-nitrite reductase; Reviewed.
Length = 593
Score = 32.3 bits (74), Expect = 0.36
Identities = 13/23 (56%), Positives = 15/23 (65%), Gaps = 1/23 (4%)
Query: 45 NIRAVVGNATAGADA-ELIDALP 66
NIR V G+ TAG D EL+D P
Sbjct: 187 NIRNVTGSPTAGIDPQELLDTRP 209
>gnl|CDD|224995 COG2084, MmsB, 3-hydroxyisobutyrate dehydrogenase and related
beta-hydroxyacid dehydrogenases [Lipid metabolism].
Length = 286
Score = 31.4 bits (72), Expect = 0.47
Identities = 26/120 (21%), Positives = 47/120 (39%), Gaps = 10/120 (8%)
Query: 145 KTVGIIGLGRIGMAVAKRAEAFSCPINYYSRTEKPNLKY------KYYPSVVELASNCHI 198
+ IGLG +G +A + Y+RT + + S E A+ +
Sbjct: 1 MKIAFIGLGIMGSPMAANLLKAGHEVTVYNRTPEKAAELLAAAGATVAASPAEAAAEADV 60
Query: 199 LVVACPLTEETRHIINRE--VIDALGPKGVLINIGRGPHVDERELVSALVEGRLGGAGLD 256
++ P R ++ E +++ L P ++I++ REL +AL G LD
Sbjct: 61 VITMLPDDAAVRAVLFGENGLLEGLKPGAIVIDMSTISPETARELAAALAAK--GLEFLD 118
>gnl|CDD|223842 COG0771, MurD, UDP-N-acetylmuramoylalanine-D-glutamate ligase [Cell
envelope biogenesis, outer membrane].
Length = 448
Score = 30.7 bits (70), Expect = 1.1
Identities = 10/22 (45%), Positives = 15/22 (68%)
Query: 140 TKFTGKTVGIIGLGRIGMAVAK 161
F GK V ++GLG+ G+A A+
Sbjct: 3 EDFQGKKVLVLGLGKSGLAAAR 24
>gnl|CDD|176261 cd08301, alcohol_DH_plants, Plant alcohol dehydrogenase.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and aldehydes
or ketones. Alcohol dehydrogenase in the liver converts
ethanol and NAD+ to acetaldehyde and NADH, while in
yeast and some other microorganisms ADH catalyzes the
conversion acetaldehyde to ethanol in alcoholic
fermentation. There are 7 vertebrate ADH 7 classes, 6
of which have been identified in humans. Class III,
glutathione-dependent formaldehyde dehydrogenase, has
been identified as the primordial form and exists in
diverse species, including plants, micro-organisms,
vertebrates, and invertebrates. Class I, typified by
liver dehydrogenase, is an evolving form. Gene
duplication and functional specialization of ADH into
ADH classes and subclasses created numerous forms in
vertebrates. For example, the A, B and C (formerly
alpha, beta, gamma) human class I subunits have high
overall structural similarity, but differ in the
substrate binding pocket and therefore in substrate
specificity. In human ADH catalysis, the zinc ion helps
coordinate the alcohol, followed by deprotonation of a
histidine (His-51), the ribose of NAD, a serine
(Ser-48) , then the alcohol, which allows the transfer
of a hydride to NAD+, creating NADH and a zinc-bound
aldehyde or ketone. In yeast and some bacteria, the
active site zinc binds an aldehyde, polarizing it, and
leading to the reverse reaction. ADH is a member of the
medium chain alcohol dehydrogenase family (MDR), which
has a NAD(P)(H)-binding domain in a Rossmann fold of an
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES.
These proteins typically form dimers (typically higher
plants, mammals) or tetramers (yeast, bacteria), and
have 2 tightly bound zinc atoms per subunit, a catalytic
zinc at the active site and a structural zinc in a lobe
of the catalytic domain. NAD(H) binding occurs in the
cleft between the catalytic and coenzyme-binding
domains at the active site, and coenzyme binding induces
a conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
Length = 369
Score = 30.3 bits (69), Expect = 1.3
Identities = 12/20 (60%), Positives = 15/20 (75%)
Query: 144 GKTVGIIGLGRIGMAVAKRA 163
G TV I GLG +G+AVA+ A
Sbjct: 188 GSTVAIFGLGAVGLAVAEGA 207
>gnl|CDD|176186 cd05283, CAD1, Cinnamyl alcohol dehydrogenases (CAD). Cinnamyl
alcohol dehydrogenases (CAD), members of the medium
chain dehydrogenase/reductase family, reduce
cinnamaldehydes to cinnamyl alcohols in the last step of
monolignal metabolism in plant cells walls. CAD binds 2
zinc ions and is NADPH- dependent. CAD family members
are also found in non-plant species, e.g. in yeast where
they have an aldehyde reductase activity. The medium
chain dehydrogenases/reductase (MDR)/zinc-dependent
alcohol dehydrogenase-like family, which contains the
zinc-dependent alcohol dehydrogenase (ADH-Zn) and
related proteins, is a diverse group of proteins related
to the first identified member, class I mammalian ADH.
MDRs display a broad range of activities and are
distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases
(ADHs) catalyze the NAD(P)(H)-dependent interconversion
of alcohols to aldehydes or ketones. Active site zinc
has a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 337
Score = 30.2 bits (69), Expect = 1.3
Identities = 14/36 (38%), Positives = 23/36 (63%), Gaps = 2/36 (5%)
Query: 144 GKTVGIIGLGRIG-MAVAKRAEAFSCPINYYSRTEK 178
GK VG++G+G +G +AV K A+A + +SR+
Sbjct: 170 GKRVGVVGIGGLGHLAV-KFAKALGAEVTAFSRSPS 204
>gnl|CDD|176184 cd05281, TDH, Threonine dehydrogenase. L-threonine dehydrogenase
(TDH) catalyzes the zinc-dependent formation of
2-amino-3-ketobutyrate from L-threonine via NAD(H)-
dependent oxidation. THD is a member of the
zinc-requiring, medium chain NAD(H)-dependent alcohol
dehydrogenase family (MDR). MDRs have a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. NAD(P)(H)-dependent oxidoreductases are
the major enzymes in the interconversion of alcohols and
aldehydes, or ketones. 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.
Length = 341
Score = 30.3 bits (69), Expect = 1.4
Identities = 15/31 (48%), Positives = 18/31 (58%), Gaps = 3/31 (9%)
Query: 138 LTTKFTGKTVGIIGLGRIGM---AVAKRAEA 165
L +GK+V I G G IG+ AVAK A A
Sbjct: 158 LAGDVSGKSVLITGCGPIGLMAIAVAKAAGA 188
>gnl|CDD|234950 PRK01390, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
synthetase; Provisional.
Length = 460
Score = 30.2 bits (69), Expect = 1.5
Identities = 12/22 (54%), Positives = 15/22 (68%)
Query: 140 TKFTGKTVGIIGLGRIGMAVAK 161
T F GKTV + GLG G+A A+
Sbjct: 5 TGFAGKTVAVFGLGGSGLATAR 26
>gnl|CDD|161783 TIGR00237, xseA, exodeoxyribonuclease VII, large subunit. This
family consist of exodeoxyribonuclease VII, large
subunit XseA which catalyses exonucleolytic cleavage in
either the 5'->3' or 3'->5' direction to yield
5'-phosphomononucleotides. Exonuclease VII consists of
one large subunit and four small subunits [DNA
metabolism, Degradation of DNA].
Length = 432
Score = 29.8 bits (67), Expect = 2.0
Identities = 17/60 (28%), Positives = 30/60 (50%), Gaps = 5/60 (8%)
Query: 237 DERELVSALVEGRLGGAGLDVFE-NEPHVPEELFGLENVVLMPHVGSGTVETRKTMADLV 295
+ + L+ GR GG+ D++ N+ V +F L + ++ VG ET T++D V
Sbjct: 183 NTKNECDVLIVGRGGGSLEDLWSFNDEKVARAIF-LSKIPIISAVGH---ETDFTISDFV 238
>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 = 28.8 bits (65), Expect = 2.0
Identities = 19/83 (22%), Positives = 29/83 (34%), Gaps = 10/83 (12%)
Query: 137 KLTTKFTGKTVGIIGLGRIGMAVAKRAEAFSC-PINYYSRTEKPNLKYKYYPSVVELASN 195
K+ GK V +IG G + AK + I +RT ELA
Sbjct: 5 KIFGDLKGKKVLLIGAGEMARLAAKHLLSKGAKKITIANRT---------LEKAKELAEE 55
Query: 196 CHILVVACPLTEETRHIINREVI 218
+ A PL E + +++
Sbjct: 56 FPVGGEALPLDELEELLAEADIV 78
>gnl|CDD|223207 COG0129, IlvD, Dihydroxyacid dehydratase/phosphogluconate
dehydratase [Amino acid transport and metabolism /
Carbohydrate transport and metabolism].
Length = 575
Score = 29.8 bits (68), Expect = 2.1
Identities = 11/42 (26%), Positives = 16/42 (38%), Gaps = 2/42 (4%)
Query: 128 SGKWKKGDYKLTTKFTGKTVGIIGLGRIGMAVAKRAEAFSCP 169
+GK T+ F + VG G+I E +CP
Sbjct: 158 AGKVNGEKAGGTSVF--EAVGAYAAGKISREELLEIERSACP 197
>gnl|CDD|178341 PLN02740, PLN02740, Alcohol dehydrogenase-like.
Length = 381
Score = 29.8 bits (67), Expect = 2.2
Identities = 12/22 (54%), Positives = 16/22 (72%)
Query: 144 GKTVGIIGLGRIGMAVAKRAEA 165
G +V I GLG +G+AVA+ A A
Sbjct: 199 GSSVAIFGLGAVGLAVAEGARA 220
>gnl|CDD|223643 COG0569, TrkA, K+ transport systems, NAD-binding component
[Inorganic ion transport and metabolism].
Length = 225
Score = 29.2 bits (66), Expect = 2.2
Identities = 8/18 (44%), Positives = 12/18 (66%)
Query: 145 KTVGIIGLGRIGMAVAKR 162
+ IIG GR+G +VA+
Sbjct: 1 MKIIIIGAGRVGRSVARE 18
>gnl|CDD|224996 COG2085, COG2085, Predicted dinucleotide-binding enzymes [General
function prediction only].
Length = 211
Score = 28.8 bits (65), Expect = 2.5
Identities = 24/96 (25%), Positives = 37/96 (38%), Gaps = 15/96 (15%)
Query: 145 KTVGIIGLGRIGMAVAKRAEAFSCPINYYSRTEKPNLK--YKYYPSVVELASN------C 196
+ IIG G IG A+A R + S L ++ SN
Sbjct: 2 MIIAIIGTGNIGSALALRLAKAGHEVIIGSSRGPKALAAAAAALGPLITGGSNEDAAALA 61
Query: 197 HILVVACPLTEETRHI--INREVIDALGPKGVLINI 230
++V+A P I + E+ DALG K ++I+
Sbjct: 62 DVVVLAVPF----EAIPDVLAELRDALGGK-IVIDA 92
>gnl|CDD|223954 COG1023, Gnd, Predicted 6-phosphogluconate dehydrogenase
[Carbohydrate transport and metabolism].
Length = 300
Score = 28.5 bits (64), Expect = 4.5
Identities = 8/19 (42%), Positives = 13/19 (68%)
Query: 145 KTVGIIGLGRIGMAVAKRA 163
+G+IGLGR+G + +R
Sbjct: 1 MQIGMIGLGRMGANLVRRL 19
>gnl|CDD|234142 TIGR03187, DGQHR, DGQHR domain. This highly divergent,
uncharacterized domain has several absolutely conserved
residues, including a QR pair and FxxxN motif. Its most
striking feature, however, is a near invariant
pentapeptide motif DGQHR. Several different subfamilies
occur specifically as a part of DNA phosphorothioation
systems, previously called DND (DNA instability during
electrophoresis), while others (e.g. CPS_2936) occur in
other contexts suggestive of lateral gene transfer
(sporadic distribution of helicase-containing
cassettes). The region described by this model is about
280 amino acids in length; additional sequences show
local sequence similarity.
Length = 271
Score = 28.4 bits (64), Expect = 5.0
Identities = 17/76 (22%), Positives = 26/76 (34%), Gaps = 11/76 (14%)
Query: 81 VDMVKCKEKGVRVTNTPDVLTDDVADLAIGLMLAVLRRLCESDRYVRSGKWKKGDYKLTT 140
VD V R+ P + D+ + ++ + E W K K +
Sbjct: 203 VDAVL------RLLGKPPGVKDENDEEIAQILNNFWTAVAEVFPE----AWLKVPRKGDS 252
Query: 141 KFTGKTVGIIGLGRIG 156
T VGI LG +G
Sbjct: 253 ILT-HGVGIQALGLLG 267
>gnl|CDD|202773 pfam03807, F420_oxidored, NADP oxidoreductase coenzyme
F420-dependent.
Length = 93
Score = 26.8 bits (60), Expect = 5.1
Identities = 14/67 (20%), Positives = 24/67 (35%), Gaps = 8/67 (11%)
Query: 146 TVGIIGLGRIGMAVAKRAEAFSCPINY-YSRTEK--PNLKYKYYPSVV-----ELASNCH 197
+GIIG G +G A+A+ A + SR + L + E
Sbjct: 1 KIGIIGAGNMGEALARGLAAAGHEVVIANSRNPEKAAALAEELGVKATAVSNEEAVEEAD 60
Query: 198 ILVVACP 204
++ +A
Sbjct: 61 VVFLAVK 67
>gnl|CDD|181371 PRK08306, PRK08306, dipicolinate synthase subunit A; Reviewed.
Length = 296
Score = 28.3 bits (64), Expect = 5.1
Identities = 10/24 (41%), Positives = 14/24 (58%), Gaps = 2/24 (8%)
Query: 140 TKFT--GKTVGIIGLGRIGMAVAK 161
T T G V ++G GR GM +A+
Sbjct: 146 TPITIHGSNVLVLGFGRTGMTLAR 169
>gnl|CDD|181359 PRK08293, PRK08293, 3-hydroxybutyryl-CoA dehydrogenase; Validated.
Length = 287
Score = 28.4 bits (64), Expect = 5.3
Identities = 24/74 (32%), Positives = 32/74 (43%), Gaps = 6/74 (8%)
Query: 35 KTQFLKAQQNNIRAVVGNATAGADAEL-IDALP-KLEIVSSFSVGLDKVDMVKCKEKGVR 92
K +A N I A A DA+L I+A+P EI F L KV EK +
Sbjct: 61 KEAPAEAALNRITLTTDLAEAVKDADLVIEAVPEDPEIKGDFYEELAKV----APEKTIF 116
Query: 93 VTNTPDVLTDDVAD 106
TN+ +L A+
Sbjct: 117 ATNSSTLLPSQFAE 130
>gnl|CDD|205865 pfam13689, DUF4154, Domain of unknown function (DUF4154). This
family of proteins is found in bacteria. Proteins in
this family are typically between 172 and 207 amino
acids in length. Many members are annotated as
valyl-tRNA synthetase but this could not be confirmed.
Length = 145
Score = 27.6 bits (62), Expect = 5.4
Identities = 11/59 (18%), Positives = 25/59 (42%), Gaps = 7/59 (11%)
Query: 171 NYYSRTEKP-NLKYKYYPSVVELASNCHILVVACPLTEETRHIINREVIDALGPKGVLI 228
+T ++ + S + A+ CH+L + + E + ++++ L K VL
Sbjct: 44 RLAGKTVGGRPIRVRRLSSA-DEAAGCHVLYIG---SSEPAQL--QQLLRKLAGKPVLT 96
>gnl|CDD|236582 PRK09599, PRK09599, 6-phosphogluconate dehydrogenase-like protein;
Reviewed.
Length = 301
Score = 28.2 bits (64), Expect = 5.4
Identities = 9/16 (56%), Positives = 14/16 (87%)
Query: 147 VGIIGLGRIGMAVAKR 162
+G+IGLGR+G +A+R
Sbjct: 3 LGMIGLGRMGGNMARR 18
>gnl|CDD|176246 cd08286, FDH_like_ADH2, formaldehyde dehydrogenase (FDH)-like.
This group is related to formaldehyde dehydrogenase
(FDH), which is a member of the zinc-dependent/medium
chain alcohol dehydrogenase family. This family uses
NAD(H) as a cofactor in the interconversion of alcohols
and aldehydes, or ketones. Another member is identified
as a dihydroxyacetone reductase. Like the zinc-dependent
alcohol dehydrogenases (ADH) of the medium chain alcohol
dehydrogenase/reductase family (MDR), tetrameric FDHs
have a catalytic zinc that resides between the catalytic
and NAD(H)binding domains and a structural zinc in a
lobe of the catalytic domain. Unlike ADH, where
NAD(P)(H) acts as a cofactor, NADH in FDH is a tightly
bound redox cofactor (similar to nicotinamide proteins).
The medium chain alcohol dehydrogenase family (MDR) has
a NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The N-terminal region typically has an
all-beta catalytic domain. These proteins typically form
dimers (typically higher plants, mammals) or tetramers
(yeast, bacteria), and have 2 tightly bound zinc atoms
per subunit.
Length = 345
Score = 28.0 bits (63), Expect = 6.0
Identities = 10/24 (41%), Positives = 15/24 (62%)
Query: 144 GKTVGIIGLGRIGMAVAKRAEAFS 167
G TV I+G G +G+A A+ +S
Sbjct: 167 GDTVAIVGAGPVGLAALLTAQLYS 190
>gnl|CDD|146585 pfam04026, SpoVG, SpoVG. Stage V sporulation protein G. Essential
for sporulation and specific to stage V sporulation in
Bacillus megaterium and subtilis. In B. subtilis,
expression decreases after 30-60 minutes of cold shock.
Length = 83
Score = 26.0 bits (58), Expect = 7.4
Identities = 7/20 (35%), Positives = 11/20 (55%)
Query: 201 VACPLTEETRHIINREVIDA 220
+A P+ E R I V++A
Sbjct: 59 IAHPINSEFREKIQDAVLEA 78
>gnl|CDD|109787 pfam00743, FMO-like, Flavin-binding monooxygenase-like. This
family includes FMO proteins, cyclohexanone
mono-oxygenase and a number of different
mono-oxygenases.
Length = 532
Score = 27.8 bits (62), Expect = 8.7
Identities = 13/26 (50%), Positives = 15/26 (57%)
Query: 135 DYKLTTKFTGKTVGIIGLGRIGMAVA 160
DYK F GK V +IGLG G +A
Sbjct: 174 DYKHPEGFQGKRVLVIGLGNSGGDIA 199
>gnl|CDD|173942 cd08183, Fe-ADH2, Iron-containing alcohol dehydrogenases-like.
Iron-containing alcohol dehydrogenases (Fe-ADH). Alcohol
dehydrogenase catalyzes the reduction of acetaldehyde to
alcohol with NADP as cofactor. Its activity requires
iron ions. The protein structure represents a
dehydroquinate synthase-like fold and is a member of the
iron-activated alcohol dehydrogenase-like family. They
are distinct from other alcohol dehydrogenases which
contains different protein domain. Proteins of this
family have not been characterized. Their specific
function is unknown. They are mainly found in bacteria.
Length = 374
Score = 27.5 bits (62), Expect = 9.7
Identities = 20/74 (27%), Positives = 28/74 (37%), Gaps = 9/74 (12%)
Query: 58 DAELIDALPKLEIVSSFSVGLDKVDMVKCKEKGVRVTNTPDVLTDDVADLAIGLMLAVLR 117
D EL + P+ +S GLD + + E + P LTD + + LR
Sbjct: 167 DPELTLSCPRSVTAAS---GLDAL--TQLLEPYLSPRANP--LTDALCRSGLPRGARALR 219
Query: 118 RLCE--SDRYVRSG 129
R CE D R
Sbjct: 220 RACENGEDAAARDD 233
>gnl|CDD|235041 PRK02472, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
synthetase; Provisional.
Length = 447
Score = 27.5 bits (62), Expect = 9.7
Identities = 9/22 (40%), Positives = 14/22 (63%)
Query: 140 TKFTGKTVGIIGLGRIGMAVAK 161
T++ K V ++GL + G A AK
Sbjct: 1 TEYQNKKVLVLGLAKSGYAAAK 22
>gnl|CDD|221536 pfam12335, SBF2, Myotubularin protein. This domain family is found
in eukaryotes, and is approximately 220 amino acids in
length. The family is found in association with
pfam02141, pfam03456, pfam03455. This family is the
middle region of SBF2, a member of the myotubularin
family. Myotubularin-related proteins have been
suggested to work in phosphoinositide-mediated
signalling events that may also convey control of
myelination. Mutations of SBF2 are implicated in
Charcot-Marie-Tooth disease.
Length = 224
Score = 27.4 bits (61), Expect = 9.9
Identities = 12/40 (30%), Positives = 16/40 (40%)
Query: 86 CKEKGVRVTNTPDVLTDDVADLAIGLMLAVLRRLCESDRY 125
C+E + V VL DL + LM L+ D Y
Sbjct: 63 CRELNLHVQQNRVVLDHQQFDLVVRLMNCALQDCSSLDEY 102
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 0.138 0.401
Gapped
Lambda K H
0.267 0.0781 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 16,232,333
Number of extensions: 1601248
Number of successful extensions: 1833
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1662
Number of HSP's successfully gapped: 123
Length of query: 313
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 216
Effective length of database: 6,635,264
Effective search space: 1433217024
Effective search space used: 1433217024
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 59 (26.4 bits)