RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 021361
(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 = 451 bits (1162), Expect = e-161
Identities = 161/301 (53%), Positives = 210/301 (69%)
Query: 4 IGVLMTTPMSNYLEQELAARFTLFKLWTQSCKNKFFQENSSAIRAVVGDTKCGADAELID 63
VL P+ L EL ARFT+ +LW + E+ IRAVV + + G A LI
Sbjct: 1 PDVLQLGPLPPELLAELEARFTVHRLWEAADPAALLAEHGGRIRAVVTNGETGLSAALIA 60
Query: 64 SLPTLEIVASYSVGLDKIDLDKCKDKAVRVTNTPDVLTDDVADLAVGLVLAVLRRVCEFD 123
+LP LE++AS+ VG D IDLD + + +RVTNTP VLTDDVADLAVGL+LAVLRR+ D
Sbjct: 61 ALPALELIASFGVGYDGIDLDAARARGIRVTNTPGVLTDDVADLAVGLLLAVLRRIPAAD 120
Query: 124 EFVKSGKWKNGHFELGSKFSGKSVGIVGLGRIGTAIAKRVEAFGCPISYHSRSEKSDANY 183
FV++G+W G F L K SGK VGIVGLGRIG AIA+R+EAFG I+YH R K D Y
Sbjct: 121 RFVRAGRWPKGAFPLTRKVSGKRVGIVGLGRIGRAIARRLEAFGMEIAYHGRRPKPDVPY 180
Query: 184 KYYTNIIDLASNCQILIVACSLTEETHHIVNRKVIDALGPSGILINIGRGAHIDEPELVS 243
+YY ++++LA+ +L+VAC T H+VN +V++ALGP G+L+N+ RG+ +DE L++
Sbjct: 181 RYYASLLELAAESDVLVVACPGGPATRHLVNAEVLEALGPDGVLVNVARGSVVDEAALIA 240
Query: 244 ALLEGRLAGAGLDVYENEPEVPEQMLGLNNVVLLPHVGSDTEETSKAMADLVIENLVAHF 303
AL EGR+AGAGLDV+ENEP VP +L L+NVVL PH+ S T ET +AM DLV+ NL A F
Sbjct: 241 ALQEGRIAGAGLDVFENEPNVPAALLDLDNVVLTPHIASATVETRRAMGDLVLANLEAFF 300
Query: 304 S 304
+
Sbjct: 301 A 301
>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 = 318 bits (817), Expect = e-109
Identities = 122/254 (48%), Positives = 168/254 (66%), Gaps = 6/254 (2%)
Query: 58 DAELIDSLPTLEIVASYSVGLDKIDLDKCKDKAVRVTNTPDVLTDDVADLAVGLVLAVLR 117
DAEL+D+ P L+++A+YSVG D ID+D K + + VTNTPDVLTD ADLA L+LA R
Sbjct: 56 DAELLDAAPPLKVIANYSVGYDHIDVDAAKARGIPVTNTPDVLTDATADLAFALLLAAAR 115
Query: 118 RVCEFDEFVKSGKWKNGH--FELGSKFSGKSVGIVGLGRIGTAIAKRVEAFGCPISYHSR 175
RV E D FV++G+WK LG+ GK++GIVG+GRIG A+A+R + FG I YH+R
Sbjct: 116 RVVEGDRFVRAGEWKGWSPTLLLGTDLHGKTLGIVGMGRIGQAVARRAKGFGMKILYHNR 175
Query: 176 SEKSDANYK---YYTNIIDLASNCQILIVACSLTEETHHIVNRKVIDALGPSGILINIGR 232
S K +A + Y ++ +L + + + C LT ET H++N + + + P+ ILIN R
Sbjct: 176 SRKPEAEEELGARYVSLDELLAESDFVSLHCPLTPETRHLINAERLALMKPTAILINTAR 235
Query: 233 GAHIDEPELVSALLEGRLAGAGLDVYENEPEVPEQ-MLGLNNVVLLPHVGSDTEETSKAM 291
G +DE LV AL G++AGAGLDV+E EP + +L L NVVLLPH+GS T ET AM
Sbjct: 236 GGVVDEDALVEALKSGKIAGAGLDVFEPEPLPADHPLLTLPNVVLLPHIGSATVETRTAM 295
Query: 292 ADLVIENLVAHFSN 305
A+L +NL+A +
Sbjct: 296 AELAADNLLAVLAG 309
>gnl|CDD|223980 COG1052, LdhA, Lactate dehydrogenase and related dehydrogenases
[Energy production and conversion / Coenzyme metabolism
/ General function prediction only].
Length = 324
Score = 303 bits (779), Expect = e-103
Identities = 118/320 (36%), Positives = 180/320 (56%), Gaps = 10/320 (3%)
Query: 3 KIGVLMTTPMSNYLEQELAARFTLFKLWTQSCKNKFFQENSSAIRAVVGDTKCGADAELI 62
KI VL T + + + L +F + + + E AV+ DAE++
Sbjct: 2 KIVVLSTRKLPPEVLERLKEKFEVERYEDDLTPDTELAERLKDADAVITFVNDRIDAEVL 61
Query: 63 DSLPTLEIVASYSVGLDKIDLDKCKDKAVRVTNTPDVLTDDVADLAVGLVLAVLRRVCEF 122
+ LP L+++A+ S G D +DL+ K++ + VTN P T+ VA+ AV L+LA+ RR+ E
Sbjct: 62 EKLPGLKLIATRSAGYDNVDLEAAKERGITVTNVPGYSTEAVAEHAVALILALARRIHEG 121
Query: 123 DEFVKSGKW-KNGHFE--LGSKFSGKSVGIVGLGRIGTAIAKRVEAFGCPISYHSRSEKS 179
D V+ G W +G + LG GK++GI+GLGRIG A+A+R++ FG + Y+ RS
Sbjct: 122 DRRVREGNWSLSGGPDPLLGFDLRGKTLGIIGLGRIGQAVARRLKGFGMKVLYYDRSPNP 181
Query: 180 DANYKY---YTNIIDLASNCQILIVACSLTEETHHIVNRKVIDALGPSGILINIGRGAHI 236
+A + Y ++ +L + I+ + C LT ET H++N + + + P IL+N RG +
Sbjct: 182 EAEKELGARYVDLDELLAESDIISLHCPLTPETRHLINAEELAKMKPGAILVNTARGGLV 241
Query: 237 DEPELVSALLEGRLAGAGLDVYENEPEVPEQ----MLGLNNVVLLPHVGSDTEETSKAMA 292
DE L+ AL G++AGAGLDV+ENEP + + + NVVL PH+ S TEE KAMA
Sbjct: 242 DEQALIDALKSGKIAGAGLDVFENEPALFDHPLLRLDNFPNVVLTPHIASATEEARKAMA 301
Query: 293 DLVIENLVAHFSNKPLLTPV 312
+L +ENL A 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 = 265 bits (680), Expect = 4e-88
Identities = 93/258 (36%), Positives = 147/258 (56%), Gaps = 4/258 (1%)
Query: 48 AVVGDTKCGADAELIDSLPTLEIVASYSVGLDKIDLDKCKDKAVRVTNTPDVLTDDVADL 107
A++ + AE++ P L+ + G+D IDLD K + + VTN P + VA+
Sbjct: 44 ALIVSSTTPVTAEVLAKAPKLKFIQVAGAGVDNIDLDAAKKRGITVTNVPGANAEAVAEH 103
Query: 108 AVGLVLAVLRRVCEFDEFVKSGKWKNGHFELGSKFSGKSVGIVGLGRIGTAIAKRVEAFG 167
A+GL+LA+LRR+ D V+ G G + GK+VGIVGLGRIG +AKR++AFG
Sbjct: 104 ALGLLLALLRRLPRADAAVRRGWGWLWAGFPGYELEGKTVGIVGLGRIGQRVAKRLQAFG 163
Query: 168 CPISYHSRSEKSDA---NYKYYTNIIDLASNCQILIVACSLTEETHHIVNRKVIDALGPS 224
+ Y+ R+ K + ++ +L + ++++ LT ET H++N + + + P
Sbjct: 164 MKVLYYDRTRKPEPEEDLGFRVVSLDELLAQSDVVVLHLPLTPETRHLINEEELALMKPG 223
Query: 225 GILINIGRGAHIDEPELVSALLEGRLAGAGLDVYENEPEVPEQ-MLGLNNVVLLPHVGSD 283
+L+N RG +DE L+ AL G++AGA LDV+E EP + +L L NV+L PH+
Sbjct: 224 AVLVNTARGGLVDEDALLRALKSGKIAGAALDVFEPEPLPADHPLLELPNVILTPHIAGY 283
Query: 284 TEETSKAMADLVIENLVA 301
TEE + MA++ +ENL
Sbjct: 284 TEEARERMAEIAVENLER 301
>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 = 249 bits (639), Expect = 1e-81
Identities = 102/249 (40%), Positives = 151/249 (60%), Gaps = 8/249 (3%)
Query: 58 DAELIDSLP-TLEIVASYSVGLDKIDLDKCKDKAVRVTNTPDVLTDDVADLAVGLVLAVL 116
D ELI LP +L+I+A G D+ID+D + ++V+NTP + + AD A+ L+L L
Sbjct: 66 DEELISPLPPSLKIIAHAGAGYDQIDVDALTKRGIQVSNTPGAVDEATADTALFLILGAL 125
Query: 117 RRVCEFDEFVKSGKWKNGHFELGSKFS--GKSVGIVGLGRIGTAIAKRVEAFGCPISYHS 174
R + ++GKW+ G +L GK++GI+GLG IG AIA++ AFG I YH+
Sbjct: 126 RNFSRAERSARAGKWR-GFLDLTLAHDPRGKTLGILGLGGIGKAIARKAAAFGMKIIYHN 184
Query: 175 RSEKSD----ANYKYYTNIIDLASNCQILIVACSLTEETHHIVNRKVIDALGPSGILINI 230
RS + A YY ++ +L + ++ + C LT T H++N+K + I++N
Sbjct: 185 RSRLPEELEKALATYYVSLDELLAQSDVVSLNCPLTAATRHLINKKEFAKMKDGVIIVNT 244
Query: 231 GRGAHIDEPELVSALLEGRLAGAGLDVYENEPEVPEQMLGLNNVVLLPHVGSDTEETSKA 290
RGA IDE LV AL G++A AGLDV+ENEPEV +L + NV LLPH+G+ T ET +
Sbjct: 245 ARGAVIDEDALVDALESGKVASAGLDVFENEPEVNPGLLKMPNVTLLPHMGTLTVETQEK 304
Query: 291 MADLVIENL 299
M +LV+EN+
Sbjct: 305 MEELVLENI 313
>gnl|CDD|240655 cd12178, 2-Hacid_dh_13, Putative D-isomer specific 2-hydroxyacid
dehydrogenases, NAD-binding and catalytic domains.
2-Hydroxyacid dehydrogenases catalyze the conversion of
a wide variety of D-2-hydroxy acids to their
corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 317
Score = 248 bits (636), Expect = 3e-81
Identities = 102/261 (39%), Positives = 153/261 (58%), Gaps = 6/261 (2%)
Query: 58 DAELIDSLPTLEIVASYSVGLDKIDLDKCKDKAVRVTNTPDVLTDDVADLAVGLVLAVLR 117
D E+ID+ L+I+A+Y G D ID+D K+K + VTNTP V T+ A+L GL+LA+ R
Sbjct: 56 DKEIIDAAKNLKIIANYGAGFDNIDVDYAKEKGIPVTNTPAVSTEPTAELTFGLILALAR 115
Query: 118 RVCEFDEFVKSGKWKNGH--FELGSKFSGKSVGIVGLGRIGTAIAKRVEAFGCPISYHSR 175
R+ E D ++ G + F LG + +GK++GI+G+GRIG A+A+R +AFG I Y++R
Sbjct: 116 RIAEGDRLMRRGGFLGWAPLFFLGHELAGKTLGIIGMGRIGQAVARRAKAFGMKILYYNR 175
Query: 176 SEKSDANYK----YYTNIIDLASNCQILIVACSLTEETHHIVNRKVIDALGPSGILINIG 231
S+ K Y ++ +L + + T ETHH+++ + P+ LIN
Sbjct: 176 HRLSEETEKELGATYVDLDELLKESDFVSLHAPYTPETHHLIDAAAFKLMKPTAYLINAA 235
Query: 232 RGAHIDEPELVSALLEGRLAGAGLDVYENEPEVPEQMLGLNNVVLLPHVGSDTEETSKAM 291
RG +DE LV AL G +AGA LDV+E EPEV ++ L+NV+L PH+G+ T E AM
Sbjct: 236 RGPLVDEKALVDALKTGEIAGAALDVFEFEPEVSPELKKLDNVILTPHIGNATVEARDAM 295
Query: 292 ADLVIENLVAHFSNKPLLTPV 312
A +N+++ K V
Sbjct: 296 AKEAADNIISFLEGKRPKNIV 316
>gnl|CDD|183914 PRK13243, PRK13243, glyoxylate reductase; Reviewed.
Length = 333
Score = 245 bits (628), Expect = 6e-80
Identities = 110/253 (43%), Positives = 157/253 (62%), Gaps = 9/253 (3%)
Query: 58 DAELIDSLPTLEIVASYSVGLDKIDLDKCKDKAVRVTNTPDVLTDDVADLAVGLVLAVLR 117
D E+ ++ P L IVA+Y+VG D ID+++ + + VTNTP VLT+ AD A L+LA R
Sbjct: 58 DCEVFEAAPRLRIVANYAVGYDNIDVEEATRRGIYVTNTPGVLTEATADFAWALLLATAR 117
Query: 118 RVCEFDEFVKSGKWKNGHFE------LGSKFSGKSVGIVGLGRIGTAIAKRVEAFGCPIS 171
R+ E D FV+SG+WK LG GK++GI+G GRIG A+A+R + FG I
Sbjct: 118 RLVEADHFVRSGEWKRRGVAWHPLMFLGYDVYGKTIGIIGFGRIGQAVARRAKGFGMRIL 177
Query: 172 YHSRSEKSDANYKY---YTNIIDLASNCQILIVACSLTEETHHIVNRKVIDALGPSGILI 228
Y+SR+ K +A + Y + +L + + LT+ET+H++N + + + P+ IL+
Sbjct: 178 YYSRTRKPEAEKELGAEYRPLEELLRESDFVSLHVPLTKETYHMINEERLKLMKPTAILV 237
Query: 229 NIGRGAHIDEPELVSALLEGRLAGAGLDVYENEPEVPEQMLGLNNVVLLPHVGSDTEETS 288
N RG +D LV AL EG +AGAGLDV+E EP E++ L NVVL PH+GS T E
Sbjct: 238 NTARGKVVDTKALVKALKEGWIAGAGLDVFEEEPYYNEELFSLKNVVLAPHIGSATFEAR 297
Query: 289 KAMADLVIENLVA 301
+ MA+LV ENL+A
Sbjct: 298 EGMAELVAENLIA 310
>gnl|CDD|223189 COG0111, SerA, Phosphoglycerate dehydrogenase and related
dehydrogenases [Amino acid transport and metabolism].
Length = 324
Score = 229 bits (587), Expect = 6e-74
Identities = 101/312 (32%), Positives = 167/312 (53%), Gaps = 9/312 (2%)
Query: 6 VLMTTPMSNYLEQELAARFTLFKLWTQSCKNKFFQENSSAIRA-VVGDTKCGADAELIDS 64
VL+T P++ +EL A + + + E + A +V T E++ +
Sbjct: 6 VLVTDPLAPDALEELLAAYDVEVPDGPDLDEEELLEALADADALIVSVTP--VTEEVLAA 63
Query: 65 LPTLEIVASYSVGLDKIDLDKCKDKAVRVTNTPDVLTDDVADLAVGLVLAVLRRVCEFDE 124
P L+ + G+D IDL+ + + V N P VA+L + L+LA+ RR+ + D
Sbjct: 64 APNLKAIGRAGAGVDNIDLEAATKRGILVVNAPGGNAISVAELVLALLLALARRIPDADA 123
Query: 125 FVKSGKWKNGHFELGSKFSGKSVGIVGLGRIGTAIAKRVEAFGCPISYHSR-SEKSDAN- 182
+ G+W F G++ +GK+VGI+GLGRIG A+AKR++AFG + + S + A
Sbjct: 124 SQRRGEWDRKAF-RGTELAGKTVGIIGLGRIGRAVAKRLKAFGMKVIGYDPYSPRERAGV 182
Query: 183 --YKYYTNIIDLASNCQILIVACSLTEETHHIVNRKVIDALGPSGILINIGRGAHIDEPE 240
++ +L + IL + LT ET ++N + + + P ILIN RG +DE
Sbjct: 183 DGVVGVDSLDELLAEADILTLHLPLTPETRGLINAEELAKMKPGAILINAARGGVVDEDA 242
Query: 241 LVSALLEGRLAGAGLDVYENEPEVPEQML-GLNNVVLLPHVGSDTEETSKAMADLVIENL 299
L++AL G++AGA LDV+E EP + L L NV+L PH+G T+E + +A++V EN+
Sbjct: 243 LLAALDSGKIAGAALDVFEEEPLPADSPLWDLPNVILTPHIGGSTDEAQERVAEIVAENI 302
Query: 300 VAHFSNKPLLTP 311
V + + P++
Sbjct: 303 VRYLAGGPVVNN 314
>gnl|CDD|240649 cd12172, PGDH_like_2, Putative D-3-Phosphoglycerate Dehydrogenases,
NAD-binding and catalytic domains. Phosphoglycerate
dehydrogenases (PGDHs) catalyze the initial step in the
biosynthesis of L-serine from D-3-phosphoglycerate.
PGDHs come in 3 distinct structural forms, with this
first group being related to 2-hydroxy acid
dehydrogenases, sharing structural similarity to formate
and glycerate dehydrogenases of the D-specific
2-hydroxyacid dehydrogenase superfamily, which also
include groups such as L-alanine dehydrogenase and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. Many, not all, members of this family are
dimeric.
Length = 306
Score = 224 bits (573), Expect = 5e-72
Identities = 88/258 (34%), Positives = 141/258 (54%), Gaps = 11/258 (4%)
Query: 48 AVVGDTKCGADAELIDSLPTLEIVASYSVGLDKIDLDKCKDKAVRVTNTPDVLTDDVADL 107
+ G E++ + P L++++ Y VG D IDL+ K + + VTNTP ++ VA+L
Sbjct: 51 VIAGLDPI--TEEVLAAAPRLKVISRYGVGYDNIDLEAAKKRGIVVTNTPGANSNSVAEL 108
Query: 108 AVGLVLAVLRRVCEFDEFVKSGKW-KNGHFELGSKFSGKSVGIVGLGRIGTAIAKRVEAF 166
+GL+LA+ R++ + D V++G W + EL GK++GI+GLGRIG A+A+R+ F
Sbjct: 109 TIGLMLALARQIPQADREVRAGGWDRPVGTEL----YGKTLGIIGLGRIGKAVARRLSGF 164
Query: 167 GCPISYHSRSEKSDANYKYYTNIIDLA---SNCQILIVACSLTEETHHIVNRKVIDALGP 223
G + + + ++ + L + + LT ET H++N + + P
Sbjct: 165 GMKVLAYDPYPDEEFAKEHGVEFVSLEELLKESDFISLHLPLTPETRHLINAAELALMKP 224
Query: 224 SGILINIGRGAHIDEPELVSALLEGRLAGAGLDVYENEP-EVPEQMLGLNNVVLLPHVGS 282
ILIN RG +DE L AL GR+AGA LDV+E EP +L L NV+L PH+G+
Sbjct: 225 GAILINTARGGLVDEEALYEALKSGRIAGAALDVFEEEPPPADSPLLELPNVILTPHIGA 284
Query: 283 DTEETSKAMADLVIENLV 300
T+E M + +N++
Sbjct: 285 STKEAVLRMGTMAAQNVI 302
>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 = 223 bits (570), Expect = 2e-71
Identities = 98/265 (36%), Positives = 151/265 (56%), Gaps = 5/265 (1%)
Query: 49 VVGDTKCGADAELIDSLPTLEIVASYSVGLDKIDLDKCKDKAVRVTNTPDVLTDDVADLA 108
+V + DAEL+ + P L ++ VGLD +DL+ + + V N P + VA+ A
Sbjct: 47 LVPGMRKVIDAELLAAAPRLRLIQQPGVGLDGVDLEAATARGIPVANIPGGNAESVAEHA 106
Query: 109 VGLVLAVLRRVCEFDEFVKSGKWKNGHFELGSKFSGKSVGIVGLGRIGTAIAKRVEAFGC 168
V L+LA+LRR+ E D +++G+W + SGK+VGIVGLG IG A+A+R+ FG
Sbjct: 107 VMLMLALLRRLPEADRELRAGRWGRPEGRPSRELSGKTVGIVGLGNIGRAVARRLRGFGV 166
Query: 169 PISYHSRSEKSDANYKY----YTNIIDLASNCQILIVACSLTEETHHIVNRKVIDALGPS 224
+ Y+ R +A K Y + +L + ++ + LT ET H++ + + A+ P
Sbjct: 167 EVIYYDRFRDPEAEEKDLGVRYVELDELLAESDVVSLHVPLTPETRHLIGAEELAAMKPG 226
Query: 225 GILINIGRGAHIDEPELVSALLEGRLAGAGLDVYENEPEVPEQ-MLGLNNVVLLPHVGSD 283
ILIN RG +DE L++AL G LAGAGLDV+ EP P+ +L L+NV+L PH+
Sbjct: 227 AILINTARGGLVDEEALLAALRSGHLAGAGLDVFWQEPLPPDDPLLRLDNVILTPHIAGV 286
Query: 284 TEETSKAMADLVIENLVAHFSNKPL 308
T+E+ + MA +V EN+ +P
Sbjct: 287 TDESYQRMAAIVAENIARLLRGEPP 311
>gnl|CDD|240624 cd05299, CtBP_dh, C-terminal binding protein (CtBP),
D-isomer-specific 2-hydroxyacid dehydrogenases related
repressor. The transcriptional corepressor CtBP is a
dehydrogenase with sequence and structural similarity to
the d2-hydroxyacid dehydrogenase family. CtBP was
initially identified as a protein that bound the PXDLS
sequence at the adenovirus E1A C terminus, causing the
loss of CR-1-mediated transactivation. CtBP binds NAD(H)
within a deep cleft, undergoes a conformational change
upon NAD binding, and has NAD-dependent dehydrogenase
activity.
Length = 312
Score = 223 bits (570), Expect = 2e-71
Identities = 83/258 (32%), Positives = 136/258 (52%), Gaps = 10/258 (3%)
Query: 58 DAELIDSLPTLEIVASYSVGLDKIDLDKCKDKAVRVTNTPDVLTDDVADLAVGLVLAVLR 117
AE+I++LP L+++ Y VG+D +D+ ++ + V N PD T++VAD A+ L+LA+ R
Sbjct: 56 TAEVIEALPRLKVIVRYGVGVDNVDVAAATERGIPVCNVPDYCTEEVADHALALILALAR 115
Query: 118 RVCEFDEFVKSGKWKNGHFELGSK---FSGKSVGIVGLGRIGTAIAKRVEAFGCPISYHS 174
++ D V++G W + +G G ++G+VG GRIG A+AKR +AFG + +
Sbjct: 116 KLPFLDRAVRAGGW---DWTVGGPIRRLRGLTLGLVGFGRIGRAVAKRAKAFGFRVIAYD 172
Query: 175 RSEKSDANYKYYT---NIIDLASNCQILIVACSLTEETHHIVNRKVIDALGPSGILINIG 231
++ +L + ++ + C LT ET H+++ + + + P L+N
Sbjct: 173 PYVPDGVAALGGVRVVSLDELLARSDVVSLHCPLTPETRHLIDAEALALMKPGAFLVNTA 232
Query: 232 RGAHIDEPELVSALLEGRLAGAGLDVYENEPEVPEQML-GLNNVVLLPHVGSDTEETSKA 290
RG +DE L AL GR+AGA LDV E EP + L NV+L PH +EE+
Sbjct: 233 RGGLVDEAALARALKSGRIAGAALDVLEEEPPPADSPLLSAPNVILTPHAAWYSEESLAE 292
Query: 291 MADLVIENLVAHFSNKPL 308
+ E +V +P
Sbjct: 293 LRRKAAEEVVRVLRGEPP 310
>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 = 207 bits (530), Expect = 2e-65
Identities = 87/253 (34%), Positives = 142/253 (56%), Gaps = 5/253 (1%)
Query: 58 DAELIDSLPTLEIVASYSVGLDKIDLDKCKDKAVRVTNTPDVLTDDVADLAVGLVLAVLR 117
AE+I++ P L+++ VG+D ID++ + + V N P T VA+ + L+LA+ R
Sbjct: 53 TAEVIEAAPRLKVIGRAGVGVDNIDVEAATARGILVVNAPGANTISVAEHTIALMLALAR 112
Query: 118 RVCEFDEFVKSGKWKNGHFELGSKFSGKSVGIVGLGRIGTAIAKRVEAFGCPISYHSRS- 176
+ + D +++GKW F G + GK++GIVGLGRIG +A+R AFG + +
Sbjct: 113 NIPQADASLRAGKWDRKKFM-GVELRGKTLGIVGLGRIGREVARRARAFGMKVLAYDPYI 171
Query: 177 --EKSDANYKYYTNIIDLASNCQILIVACSLTEETHHIVNRKVIDALGPSGILINIGRGA 234
E++ A ++ +L + + + LT ET ++N + + + P ILIN RG
Sbjct: 172 SAERAAAGGVELVSLDELLAEADFISLHTPLTPETRGLINAEELAKMKPGAILINTARGG 231
Query: 235 HIDEPELVSALLEGRLAGAGLDVYENEPEVPE-QMLGLNNVVLLPHVGSDTEETSKAMAD 293
+DE L AL G++AGA LDV+E EP + +LGL NV+L PH+G+ TEE + +A
Sbjct: 232 IVDEAALADALKSGKIAGAALDVFEQEPPPADSPLLGLPNVILTPHLGASTEEAQERVAV 291
Query: 294 LVIENLVAHFSNK 306
E ++A + +
Sbjct: 292 DAAEQVLAVLAGE 304
>gnl|CDD|215893 pfam00389, 2-Hacid_dh, D-isomer specific 2-hydroxyacid
dehydrogenase, catalytic domain. This family represents
the largest portion of the catalytic domain of
2-hydroxyacid dehydrogenases as the NAD binding domain
is inserted within the structural domain.
Length = 312
Score = 206 bits (527), Expect = 5e-65
Identities = 86/262 (32%), Positives = 132/262 (50%), Gaps = 8/262 (3%)
Query: 58 DAELIDSLPTLEIVASYSVGLDKIDLDKCKDKAVRVTNTPDVLTDDVADLAVGLVLAVLR 117
AE++++ P L+++A VG+D IDLD ++ + VTN P T+ VA+L VGL+LA+ R
Sbjct: 51 TAEVLEAAPGLKVIARRGVGVDNIDLDAATERGILVTNVPGYSTESVAELTVGLILALAR 110
Query: 118 RVCEFDEFVKSGKWKNGHFELGSKFSGKSVGIVGLGRIGTAIAKRVEAFGC-PISYHSRS 176
R+ E D V++G WK G +G + GK++G++G G IG A +A G ++Y
Sbjct: 111 RIPEADASVRAGDWKKGGP-IGLELYGKTLGVIGGGGIGGIGAAIAKALGMGVVAYDPYP 169
Query: 177 EKSDANYKYYT------NIIDLASNCQILIVACSLTEETHHIVNRKVIDALGPSGILINI 230
A ++DL + ++ +A T +T HI+ + L + + N
Sbjct: 170 NPERAEEGGVEVLLLDLLLLDLKESDDLINLAPPTTMKTGHIIINEARGMLKDAVAINNA 229
Query: 231 GRGAHIDEPELVSALLEGRLAGAGLDVYENEPEVPEQMLGLNNVVLLPHVGSDTEETSKA 290
G I+E L + L EG A A V E P V +L L NV+L PH+ TEE +
Sbjct: 230 RGGGVIEEAALDALLEEGIAAAALDVVEEEPPPVNSPLLDLPNVILTPHIAGATEEAQEN 289
Query: 291 MADLVIENLVAHFSNKPLLTPV 312
MA+ ENL+A V
Sbjct: 290 MAEEAAENLLAFLKGGTPPNAV 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 = 196 bits (502), Expect = 4e-63
Identities = 71/176 (40%), Positives = 112/176 (63%), Gaps = 4/176 (2%)
Query: 109 VGLVLAVLRRVCEFDEFVKSGKWKNGHFELGSKFSGKSVGIVGLGRIGTAIAKRVEAFGC 168
+ L+LA+ RR+ E D V++G+W+ LG + SGK+VGI+GLGRIG A+A+R++AFG
Sbjct: 1 LALLLALARRIPEADRQVRAGRWRPDAL-LGRELSGKTVGIIGLGRIGRAVARRLKAFGM 59
Query: 169 PISYHSRS--EKSDANYKYYTNIIDLASNCQILIVACSLTEETHHIVNRKVIDALGPSGI 226
+ + R +++A Y ++ +L + ++ + LT ET H++N + + + P I
Sbjct: 60 KVIAYDRYPKAEAEALGARYVSLDELLAESDVVSLHLPLTPETRHLINAERLALMKPGAI 119
Query: 227 LINIGRGAHIDEPELVSALLEGRLAGAGLDVYENEPEVPEQ-MLGLNNVVLLPHVG 281
LIN RG +DE L++AL GR+AGA LDV+E EP P+ +L L NV+L PH+
Sbjct: 120 LINTARGGLVDEDALIAALKSGRIAGAALDVFEPEPLPPDHPLLELPNVILTPHIA 175
>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 = 201 bits (514), Expect = 4e-63
Identities = 89/253 (35%), Positives = 149/253 (58%), Gaps = 6/253 (2%)
Query: 59 AELIDSLPTLEIVASYSVGLDKIDLDKCKDKAVRVTNTPDVLTDDVADLAVGLVLAVLRR 118
E+I++ L++++ G+D +DL+ CK++ + V+N T+ VA+L +GL + +LR
Sbjct: 61 GEVIEACKNLKMISVAFTGVDHVDLEACKERGITVSNAAGYSTEAVAELTIGLAIDLLRN 120
Query: 119 VCEFDEFVKSGKWKNGHFELGSKFSGKSVGIVGLGRIGTAIAKRVEAFGCPISYHSRSEK 178
+ D V++G K G +G + +GK+VGIVG G IG +A+ +AFGC + +SRSEK
Sbjct: 121 IVPCDAAVRAGGTKAGL--IGRELAGKTVGIVGTGAIGLRVARLFKAFGCKVLAYSRSEK 178
Query: 179 SDANYKY--YTNIIDLASNCQILIVACSLTEETHHIVNRKVIDALGPSGILINIGRGAHI 236
+A Y ++ +L + I+ + L +ET ++ ++ + + S ILIN RG +
Sbjct: 179 EEAKALGIEYVSLDELLAESDIVSLHLPLNDETKGLIGKEKLALMKESAILINTARGPVV 238
Query: 237 DEPELVSALLEGRLAGAGLDVYENEPEVPEQ--MLGLNNVVLLPHVGSDTEETSKAMADL 294
D L AL EG++AGAG+DV++ EP +P +L N +L PHV TEE + A++
Sbjct: 239 DNEALADALNEGKIAGAGIDVFDMEPPLPADYPLLHAPNTILTPHVAFATEEAMEKRAEI 298
Query: 295 VIENLVAHFSNKP 307
V +N+ A + KP
Sbjct: 299 VFDNIEAWLAGKP 311
>gnl|CDD|185307 PRK15409, PRK15409, bifunctional glyoxylate/hydroxypyruvate
reductase B; Provisional.
Length = 323
Score = 201 bits (512), Expect = 1e-62
Identities = 98/256 (38%), Positives = 144/256 (56%), Gaps = 7/256 (2%)
Query: 58 DAELIDSLPTLEIVASYSVGLDKIDLDKCKDKAVRVTNTPDVLTDDVADLAVGLVLAVLR 117
DA L++ +P L ++ SVG D D+D + + + +TP VLT+ VAD + LVL+ R
Sbjct: 57 DAALLEKMPKLRAASTISVGYDNFDVDALTARKILLMHTPTVLTETVADTLMALVLSTAR 116
Query: 118 RVCEFDEFVKSGKWKN--GHFELGSKFSGKSVGIVGLGRIGTAIAKRVE-AFGCPISYHS 174
RV E E VK+G+W G G+ K++GIVG+GRIG A+A+R F PI Y++
Sbjct: 117 RVVEVAERVKAGEWTASIGPDWFGTDVHHKTLGIVGMGRIGMALAQRAHFGFNMPILYNA 176
Query: 175 RSEKSDANYKY---YTNIIDLASNCQILIVACSLTEETHHIVNRKVIDALGPSGILINIG 231
R +A ++ Y ++ L + + LT+ETHH+ + + S I IN G
Sbjct: 177 RRHHKEAEERFNARYCDLDTLLQESDFVCIILPLTDETHHLFGAEQFAKMKSSAIFINAG 236
Query: 232 RGAHIDEPELVSALLEGRLAGAGLDVYENEP-EVPEQMLGLNNVVLLPHVGSDTEETSKA 290
RG +DE L++AL +G + AGLDV+E EP V +L L NVV +PH+GS T ET
Sbjct: 237 RGPVVDENALIAALQKGEIHAAGLDVFEQEPLSVDSPLLSLPNVVAVPHIGSATHETRYN 296
Query: 291 MADLVIENLVAHFSNK 306
MA ++NL+ K
Sbjct: 297 MAACAVDNLIDALQGK 312
>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 = 199 bits (509), Expect = 2e-62
Identities = 89/258 (34%), Positives = 142/258 (55%), Gaps = 6/258 (2%)
Query: 49 VVGDTKCGADAELIDSLPTLEIVASYSVGLDKIDLDKCKDKAVRVTNTPDVLTDDVADLA 108
V TK E+ID+ L+I+A VGLD ID++ K K ++V NTP ++ VA+L
Sbjct: 47 VRSRTK--VTKEVIDAAKNLKIIARAGVGLDNIDVEYAKKKGIKVINTPGASSNSVAELV 104
Query: 109 VGLVLAVLRRVCEFDEFVKSGKWKNGHFELGSKFSGKSVGIVGLGRIGTAIAKRVEAFGC 168
+GL+L++ R + + +K GKW ++ G + GK++GI+G GRIG +AK A G
Sbjct: 105 IGLMLSLARFIHRANREMKLGKWNKKKYK-GIELRGKTLGIIGFGRIGREVAKIARALGM 163
Query: 169 PISYHSRSEKSDANYKYYTNIIDLA---SNCQILIVACSLTEETHHIVNRKVIDALGPSG 225
+ + K + + + L N + + LT ET H++N+K ++ +
Sbjct: 164 NVIAYDPYPKDEQAVELGVKTVSLEELLKNSDFISLHVPLTPETKHMINKKELELMKDGA 223
Query: 226 ILINIGRGAHIDEPELVSALLEGRLAGAGLDVYENEPEVPEQMLGLNNVVLLPHVGSDTE 285
I+IN RG IDE L+ AL G+LAGA LDV+ENEP ++L L NV L PH+G+ T+
Sbjct: 224 IIINTSRGGVIDEEALLEALKSGKLAGAALDVFENEPPPGSKLLELPNVSLTPHIGASTK 283
Query: 286 ETSKAMADLVIENLVAHF 303
E + + + + ++
Sbjct: 284 EAQERIGEELANKIIEFL 301
>gnl|CDD|240639 cd12162, 2-Hacid_dh_4, Putative D-isomer specific 2-hydroxyacid
dehydrogenases. 2-Hydroxyacid dehydrogenases catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine yydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 307
Score = 184 bits (469), Expect = 2e-56
Identities = 83/257 (32%), Positives = 138/257 (53%), Gaps = 20/257 (7%)
Query: 58 DAELIDSLPTLEIVASYSVGLDKIDLDKCKDKAVRVTNTPDVLTDDVADLAVGLVLAVLR 117
DAE++ LP L+++ + G + +DL K++ + VTN P TD VA L+LA+ R
Sbjct: 56 DAEVLAQLPNLKLIGVLATGYNNVDLAAAKERGITVTNVPGYSTDSVAQHTFALLLALAR 115
Query: 118 RVCEFDEFVKSGKW-KNGHF--------ELGSKFSGKSVGIVGLGRIGTAIAKRVEAFGC 168
V ++ VK+G+W K+ F EL +GK++GI+G G IG A+A+ AFG
Sbjct: 116 LVAYHNDVVKAGEWQKSPDFCFWDYPIIEL----AGKTLGIIGYGNIGQAVARIARAFGM 171
Query: 169 PISYHSRSEKSDANYKYYTNIIDLASNCQILIVACSLTEETHHIVNRKVIDALGPSGILI 228
+ + R Y ++ +L + ++ + C LT ET +++N + + + P ILI
Sbjct: 172 KVLFAERKGAPPLREGY-VSLDELLAQSDVISLHCPLTPETRNLINAEELAKMKPGAILI 230
Query: 229 NIGRGAHIDEPELVSALLEGRLAGAGLDVYENEPEVPEQ----MLGLNNVVLLPHVGSDT 284
N RG +DE L AL G++AGAGLDV EP P + N+++ PH+ +
Sbjct: 231 NTARGGLVDEQALADALNSGKIAGAGLDVLSQEP--PRADNPLLKAAPNLIITPHIAWAS 288
Query: 285 EETSKAMADLVIENLVA 301
E + + D++++N+ A
Sbjct: 289 REARQRLMDILVDNIKA 305
>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 = 177 bits (452), Expect = 9e-54
Identities = 89/257 (34%), Positives = 139/257 (54%), Gaps = 8/257 (3%)
Query: 58 DAELIDSLPTLEIVASYSVGLDKIDLDKCKDKAVRVTNTPD-VLTDDVADLAVGLVLAVL 116
D E + L+++A + +G D +DL + V VT P V D VA+ AV L+L VL
Sbjct: 60 DKEFFEYNDGLKLIARHGIGYDNVDLKAATEHGVIVTRVPGAVERDAVAEHAVALILTVL 119
Query: 117 RRVCEFDEFVKSGKW-KNGHFELGSKFSGKSVGIVGLGRIGTAIAKRV-EAFGCPI---S 171
R++ + E VK GKW + +F G + SGK+VGI+G G IG+ +A+ + E F +
Sbjct: 120 RKINQASEAVKEGKWTERANFV-GHELSGKTVGIIGYGNIGSRVAEILKEGFNAKVLAYD 178
Query: 172 YHSRSEKSDANYKYYTNIIDLASNCQILIVACSLTEETHHIVNRKVIDALGPSGILINIG 231
+ E ++ +L + I+ + LTEET+H++N K + IL+N
Sbjct: 179 PYVSEEVIKKKGAKPVSLEELLAESDIISLHAPLTEETYHMINEKAFSKMKKGVILVNTA 238
Query: 232 RGAHIDEPELVSALLEGRLAGAGLDVYENEPEVPEQ-MLGLNNVVLLPHVGSDTEETSKA 290
RG IDE L+ AL G++AGAGLDV E EP + +L NVV+ PH+G+ T E+
Sbjct: 239 RGELIDEEALIEALKSGKIAGAGLDVLEEEPIKADHPLLHYENVVITPHIGAYTYESLYG 298
Query: 291 MADLVIENLVAHFSNKP 307
M + V++++ + K
Sbjct: 299 MGEKVVDDIEDFLAGKE 315
>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 = 177 bits (452), Expect = 1e-53
Identities = 83/263 (31%), Positives = 137/263 (52%), Gaps = 17/263 (6%)
Query: 55 CGADAELIDSLPTLEIVASYSVGLDKIDLDKCKDKAVRVTNTPDVLTDDVADLAVGLVLA 114
DAEL+D P L+ ++ + G D IDLD K+ + VTN P+ + VA+ + L+LA
Sbjct: 55 DKIDAELLDKAPGLKFISLRATGYDNIDLDYAKELGIGVTNVPEYSPNAVAEHTIALILA 114
Query: 115 VLRRVCEFDEFVKSGKWKNGHFELGSKFSGKSVGIVGLGRIGTAIAKRVEAFGCP-ISYH 173
+LR DE K+ ++ +G + ++VG+VG G+IG A+A+R + FG I+Y
Sbjct: 115 LLRNRKYIDERDKNQDLQDA-GVIGRELEDQTVGVVGTGKIGRAVAQRAKGFGMKVIAYD 173
Query: 174 SRSEKSDANYKY-YTNIIDLASNCQILIVACSLTEETHHIVNRKVIDALGPSGILINIGR 232
+ Y ++ +L N I+ + LT E HH++N + + I+IN R
Sbjct: 174 PFRNPELEDKGVKYVSLEELFKNSDIISLHVPLTPENHHMINEEAFKLMKKGVIIINTAR 233
Query: 233 GAHIDEPELVSALLEGRLAGAGLDVYENE-PEVPEQMLG-------------LNNVVLLP 278
G+ +D L+ AL G++ GAGLDV E+E P++ + + G NV++ P
Sbjct: 234 GSLVDTEALIEALDSGKIFGAGLDVLEDETPDLLKDLEGEIFKDALNALLGRRPNVIITP 293
Query: 279 HVGSDTEETSKAMADLVIENLVA 301
H T++ K M ++ EN+V
Sbjct: 294 HTAFYTDDALKNMVEISCENIVD 316
>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 = 177 bits (451), Expect = 1e-53
Identities = 91/314 (28%), Positives = 156/314 (49%), Gaps = 16/314 (5%)
Query: 6 VLMTTPMSNYLEQELAARFTLFKLWTQSCKNKFFQENSSAIRAVVGDTKCGADAELIDSL 65
+L+ +P+ + + L A + +E + A ++G+ EL+ +
Sbjct: 3 ILVLSPLDDEHLERLRAAAPGA-ELRVVTAEELTEELADA-DVLLGN---PPLPELLPAA 57
Query: 66 PTLEIVASYSVGLDKIDLDKCKDKAVRVTNTPDVLTDDVADLAVGLVLAVLRRVCEFDEF 125
P L + S S G+D + + ++ V +TN + +A+ +G +LA R++ +
Sbjct: 58 PRLRWIQSTSAGVDALLFPELLERDVVLTNARGIFGPPIAEYVLGYMLAFARKLPRYARN 117
Query: 126 VKSGKWKN--GHFELGSKFSGKSVGIVGLGRIGTAIAKRVEAFGCPISYHSRSEKSDANY 183
+W+ EL +GK+V IVGLG IG IA+R +AFG + RS +
Sbjct: 118 QAERRWQRRGPVREL----AGKTVLIVGLGDIGREIARRAKAFGMRVIGVRRSGRPAPPV 173
Query: 184 --KYYT--NIIDLASNCQILIVACSLTEETHHIVNRKVIDALGPSGILINIGRGAHIDEP 239
+ YT + +L ++ A LT ET + N + A+ P +LIN+GRG+ +DE
Sbjct: 174 VDEVYTPDELDELLPEADYVVNALPLTPETRGLFNAERFAAMKPGAVLINVGRGSVVDED 233
Query: 240 ELVSALLEGRLAGAGLDVYENEPEVPEQML-GLNNVVLLPHVGSDTEETSKAMADLVIEN 298
L+ AL GR+AGA LDV+E EP + L L NV++ PH+ D+ + + ++ +EN
Sbjct: 234 ALIEALESGRIAGAALDVFEEEPLPADSPLWDLPNVIITPHISGDSPSYPERVVEIFLEN 293
Query: 299 LVAHFSNKPLLTPV 312
L + + +PLL V
Sbjct: 294 LRRYLAGEPLLNVV 307
>gnl|CDD|240634 cd12157, PTDH, Thermostable Phosphite Dehydrogenase. Phosphite
dehydrogenase (PTDH), a member of the D-specific
2-hydroxyacid dehydrogenase family, catalyzes the
NAD-dependent formation of phosphate from phosphite
(hydrogen phosphonate). PTDH has been suggested as a
potential enzyme for cofactor regeneration systems. The
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD-binding
domain.
Length = 318
Score = 171 bits (435), Expect = 3e-51
Identities = 79/260 (30%), Positives = 135/260 (51%), Gaps = 16/260 (6%)
Query: 58 DAELIDSLPTLEIVASYSVGLDKIDLDKCKDKAVRVTNTPDVLTDDVADLAVGLVLAVLR 117
DA+ +D+ P L+I+A G D D++ C + + VT PD+LT+ A+L +GL++ + R
Sbjct: 57 DADFLDACPRLKIIACALKGYDNFDVEACTARGIWVTIVPDLLTEPTAELTIGLLIGLGR 116
Query: 118 RVCEFDEFVKSGKWKNGH--FELGSKFSGKSVGIVGLGRIGTAIAKRVEAFGCPISYHSR 175
+ D FV+SGK+ G G+ GK+VGI+G+G +G AIA+R+ FG + Y+
Sbjct: 117 HILAGDRFVRSGKFG-GWRPKFYGTGLDGKTVGILGMGALGRAIARRLSGFGATLLYYDP 175
Query: 176 SEKSDANYKY----YTNIIDLASNCQILIVACSLTEETHHIVNRKVIDALGPSGILINIG 231
A + + +L + L++A LT +T H++N + + + P +L+N
Sbjct: 176 HPLDQAEEQALNLRRVELDELLESSDFLVLALPLTPDTLHLINAEALAKMKPGALLVNPC 235
Query: 232 RGAHIDEPELVSALLEGRLAGAGLDVYENEP--------EVPEQMLGL-NNVVLLPHVGS 282
RG+ +DE + AL G L G DV+E E +P+++L + V PH+GS
Sbjct: 236 RGSVVDEAAVAEALKSGHLGGYAADVFEMEDWARPDRPRSIPQELLDQHDRTVFTPHIGS 295
Query: 283 DTEETSKAMADLVIENLVAH 302
+E + N++
Sbjct: 296 AVDEVRLEIELEAALNILQA 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 = 170 bits (434), Expect = 4e-51
Identities = 79/254 (31%), Positives = 137/254 (53%), Gaps = 11/254 (4%)
Query: 58 DAELIDSLPTLEIVASYSVGLDKIDLDKCKDKAVRVTNTPDVLTDDVADLAVGLVLAVLR 117
A L++ LP L+++ + + IDL K++ + V T A+L L+LA+ R
Sbjct: 60 PAALLERLPNLKLLVTTGMRNASIDLAAAKERGIVVCGTGGG-PTATAELTWALILALAR 118
Query: 118 RVCEFDEFVKSGKWKNGHFELGSKFSGKSVGIVGLGRIGTAIAKRVEAFGCPI----SYH 173
+ E D +++G W+ LG+ +GK++GIVGLGRIG +A+ +AFG + S
Sbjct: 119 NLPEEDAALRAGGWQTT---LGTGLAGKTLGIVGLGRIGARVARIGQAFGMRVIAWSSNL 175
Query: 174 SRSEKSDANYKYYTNIIDLASNCQILIVACSLTEETHHIVNRKVIDALGPSGILINIGRG 233
+ + A + + +L + ++ + L++ T +V + + + P+ +L+N RG
Sbjct: 176 TAERAAAAGVEAAVSKEELFATSDVVSLHLVLSDRTRGLVGAEDLALMKPTALLVNTSRG 235
Query: 234 AHIDEPELVSALLEGRLAGAGLDVYENEPEVPEQ--MLGLNNVVLLPHVGSDTEETSKAM 291
+DE L++AL GR+AGA LDV++ EP +P + GL NV+L PH+G TEE +
Sbjct: 236 PLVDEGALLAALRAGRIAGAALDVFDVEP-LPADHPLRGLPNVLLTPHIGYVTEEAYEGF 294
Query: 292 ADLVIENLVAHFSN 305
+EN+ A +
Sbjct: 295 YGQAVENIAAWLAG 308
>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 = 168 bits (428), Expect = 3e-50
Identities = 74/253 (29%), Positives = 131/253 (51%), Gaps = 9/253 (3%)
Query: 55 CGADAELIDSLPTLEIVASYSVGLDKIDLDKCKDKAVRVTNTPDVLTDDVADLAVGLVLA 114
++I++ P L+++ G + +D++ ++ + V NTP + VA+ VGL+LA
Sbjct: 55 APVTKKVIEAAPKLKLIGVCRGGPENVDVEAATERGIPVLNTPGRNAEAVAEFTVGLMLA 114
Query: 115 VLRRVCEFDEFVKSGKWKNG---HFELGSKFSGKSVGIVGLGRIGTAIAKRVEAFGCPIS 171
R + +K G+W+ + G + GK+VGIVG G IG +AKR++AFG +
Sbjct: 115 ETRNIARAHAALKDGEWRKDYYNYDGYGPELRGKTVGIVGFGAIGRRVAKRLKAFGAEVL 174
Query: 172 YHS---RSEKSDANYKYYTNIIDLASNCQILIVACSLTEETHHIVNRKVIDALGPSGILI 228
+ EK +A+ ++ +L ++ + LT ET ++ + + P+ I
Sbjct: 175 VYDPYVDPEKIEADGVKKVSLEELLKRSDVVSLHARLTPETRGMIGAEEFALMKPTAYFI 234
Query: 229 NIGRGAHIDEPELVSALLEGRLAGAGLDVYENEPEVPEQ--MLGLNNVVLLPHVGSDTEE 286
N R +DE L+ AL EG++ GA LDV+ EP +P +L L+NV L PH+ T +
Sbjct: 235 NTARAGLVDEDALIEALEEGKIGGAALDVFPEEP-LPADHPLLKLDNVTLTPHIAGATRD 293
Query: 287 TSKAMADLVIENL 299
++ +++ E L
Sbjct: 294 VAERSPEIIAEEL 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 = 167 bits (424), Expect = 1e-49
Identities = 82/273 (30%), Positives = 136/273 (49%), Gaps = 22/273 (8%)
Query: 53 TKCGADAELIDSLPTLEIVASYSVGLDKIDLDKCKDKAVRVTNTPDVLTDDVADLAVGLV 112
E + +L L+++ S G+D + L++ + V V N + VA+ A+ L+
Sbjct: 46 GGRLTKEEALAALKRLKLIQVPSAGVDHLPLERLPEG-VVVANNHG-NSPAVAEHALALI 103
Query: 113 LAVLRRVCEFDEFVKSGKW------KNGHFELGSKFSGKSVGIVGLGRIGTAIAKRVEAF 166
LA+ +R+ E+D ++ G W + EL GK+VGI+G G IG IA+ ++AF
Sbjct: 104 LALAKRIVEYDNDLRRGIWHGRAGEEPESKEL----RGKTVGILGYGHIGREIARLLKAF 159
Query: 167 GCPISYHSRSEKSDA---NYKYYTNIIDLASNCQILIVACSLTEETHHIVNRKVIDALGP 223
G + SRS K D +++ + +++VA LT++T ++ + A+ P
Sbjct: 160 GMRVIGVSRSPKEDEGADFVGTLSDLDEALEQADVVVVALPLTKQTRGLIGAAELAAMKP 219
Query: 224 SGILINIGRGAHIDEPELVSALLEGRLAGAGLDVYENEPEVPEQMLG-------LNNVVL 276
IL+N+GRG +DE L AL E +AGA +DV+ P + + L NV++
Sbjct: 220 GAILVNVGRGPVVDEEALYEALKERPIAGAAIDVWWRYPSRGDPVAPSRYPFHELPNVIM 279
Query: 277 LPHVGSDTEETSKAMADLVIENLVAHFSNKPLL 309
PH TEET + D EN+ + +PLL
Sbjct: 280 SPHNAGWTEETFRRRIDEAAENIRRYLRGEPLL 312
>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 = 168 bits (428), Expect = 2e-48
Identities = 80/267 (29%), Positives = 133/267 (49%), Gaps = 13/267 (4%)
Query: 58 DAELIDSLPTLEIVASYSVGLDKIDLDKCKDKAVRVTNTPDVLTDDVADLAVGLVLAVLR 117
E+I + P L+++ VG+D ID++ + + V N P T A+ A+ ++LA R
Sbjct: 53 TEEVIAAAPKLKVIGRAGVGVDNIDIEAATARGILVVNAPTGNTISAAEHALAMLLAAAR 112
Query: 118 RVCEFDEFVKSGKWKNGHFELGSKFSGKSVGIVGLGRIGTAIAKRVEAFGCPI----SYH 173
+ + D +K G+W F +G++ GK++G++GLGRIG+ +AKR +AFG + Y
Sbjct: 113 NIPQADASLKEGEWDRKAF-MGTELYGKTLGVIGLGRIGSIVAKRAKAFGMKVLAYDPYI 171
Query: 174 SRSEKSDANYKYYTNIIDLASNCQILIVACSLTEETHHIVNRKVIDALGPSGILINIGRG 233
S + ++ +L + + V LT ET ++ + + + I++N RG
Sbjct: 172 SPERAEQLGVELVDDLDELLARADFITVHTPLTPETRGLIGAEELAKMKKGVIIVNCARG 231
Query: 234 AHIDEPELVSALLEGRLAGAGLDVYENEPEVPEQMLGLNNVVLLPHVGSDTEETSKAMAD 293
IDE L AL EG + A LDV+E EP + L+NV+ PH+G+ T E + +A
Sbjct: 232 GIIDEAALYEALEEGHVRAAALDVFEKEPPTDNPLFDLDNVIATPHLGASTREAQENVAT 291
Query: 294 LVIEN--------LVAHFSNKPLLTPV 312
V E V + N P +
Sbjct: 292 QVAEQVLDALKGLPVPNAVNAPGIDAD 318
>gnl|CDD|237436 PRK13581, PRK13581, D-3-phosphoglycerate dehydrogenase;
Provisional.
Length = 526
Score = 161 bits (410), Expect = 1e-45
Identities = 77/236 (32%), Positives = 127/236 (53%), Gaps = 12/236 (5%)
Query: 58 DAELIDSLPTLEIVASYSVGLDKIDLDKCKDKAVRVTNTPDVLTDDVADLAVGLVLAVLR 117
AE++++ L+++ VG+D +D+ + + V N P T A+ + L+LA+ R
Sbjct: 55 TAEVLEAAKNLKVIGRAGVGVDNVDVPAATRRGIIVVNAPTGNTISAAEHTIALMLALAR 114
Query: 118 RVCEFDEFVKSGKWKNGHFELGSKFSGKSVGIVGLGRIGTAIAKRVEAFGC------P-I 170
+ + +K+GKW+ F +G + GK++GI+GLGRIG+ +AKR +AFG P I
Sbjct: 115 NIPQAHASLKAGKWERKKF-MGVELYGKTLGIIGLGRIGSEVAKRAKAFGMKVIAYDPYI 173
Query: 171 SYHSRSEKSDANYKYYTNIIDLASNCQILIVACSLTEETHHIVNRKVIDALGPSGILINI 230
S R+ + ++ +L + + + LT ET ++ + + + P +IN
Sbjct: 174 S-PERAAQLGVEL---VSLDELLARADFITLHTPLTPETRGLIGAEELAKMKPGVRIINC 229
Query: 231 GRGAHIDEPELVSALLEGRLAGAGLDVYENEPEVPEQMLGLNNVVLLPHVGSDTEE 286
RG IDE L AL G++AGA LDV+E EP + L NVV+ PH+G+ T E
Sbjct: 230 ARGGIIDEAALAEALKSGKVAGAALDVFEKEPPTDSPLFELPNVVVTPHLGASTAE 285
>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 = 153 bits (390), Expect = 2e-44
Identities = 90/277 (32%), Positives = 144/277 (51%), Gaps = 31/277 (11%)
Query: 58 DAELIDSLPTLEIVASYSVGLDKIDLDKCKDKAVRVTNTPDVLTDDVADLAVGLVLAVLR 117
DAE+++ LP L+++A+ S G D IDL+ C+++ + V N PD VA+ A L+LA+ R
Sbjct: 54 DAEVLEKLPRLKLIATRSTGFDHIDLEACRERGIAVCNVPDYGEATVAEHAFALLLALSR 113
Query: 118 RVCEFDEFVKSGKWK---NGHFELGSKFSGKSVGIVGLGRIGTAIAKRVEAFGCPISYHS 174
++ E E + G + FEL +GK++G+VG GRIG +A+ FG + +
Sbjct: 114 KLREAIERTRRGDFSQAGLRGFEL----AGKTLGVVGTGRIGRRVARIARGFGMKVLAYD 169
Query: 175 RSEKSDANYKY---YTNIIDLASNCQILIVACSLTEETHHIVNRKVIDALGPSGILINIG 231
+ + Y ++ +L I+ + T +THH++NR+ + P +LIN
Sbjct: 170 VVPDEELAERLGFRYVSLEELLQESDIISLHVPYTPQTHHLINRENFALMKPGAVLINTA 229
Query: 232 RGAHIDEPELVSALLEGRLAGAGLDVYENEPEVPE---------------------QMLG 270
RGA +D LV AL EG+LAGAGLDV E E + E +L
Sbjct: 230 RGAVVDTEALVRALKEGKLAGAGLDVLEQEEVLREEAELFREDVSPEDLKKLLADHALLR 289
Query: 271 LNNVVLLPHVGSDTEETSKAMADLVIENLVAHFSNKP 307
NV++ PHV +T+E + + D +EN+ A + +P
Sbjct: 290 KPNVIITPHVAYNTKEALERILDTTVENIKAFAAGQP 326
>gnl|CDD|181414 PRK08410, PRK08410, 2-hydroxyacid dehydrogenase; Provisional.
Length = 311
Score = 150 bits (380), Expect = 4e-43
Identities = 77/259 (29%), Positives = 130/259 (50%), Gaps = 12/259 (4%)
Query: 58 DAELIDSLPTLEIVASYSVGLDKIDLDKCKDKAVRVTNTPDVLTDDVADLAVGLVLAVLR 117
D E++ LP L+++ + G + +D++ K K + V N T+ VA ++L++L
Sbjct: 54 DKEVLSQLPNLKLICITATGTNNVDIEYAKKKGIAVKNVAGYSTESVAQHTFAMLLSLLG 113
Query: 118 RVCEFDEFVKSGKWKNG----HFELG-SKFSGKSVGIVGLGRIGTAIAKRVEAFGCPISY 172
R+ +D +VKSG++ H + GK GI+GLG IG +AK +AFG + Y
Sbjct: 114 RINYYDRYVKSGEYSESPIFTHISRPLGEIKGKKWGIIGLGTIGKRVAKIAQAFGAKVVY 173
Query: 173 HSRSEK-SDANYKYYTNIIDLASNCQILIVACSLTEETHHIVNRKVIDALGPSGILINIG 231
+S S K + Y+ + + +L I+ + L E+T +++ K + L ILIN+G
Sbjct: 174 YSTSGKNKNEEYERVS-LEELLKTSDIISIHAPLNEKTKNLIAYKELKLLKDGAILINVG 232
Query: 232 RGAHIDEPELVSALLEGRLAGAGLDVYENEPEVPEQML----GLNNVVLLPHVGSDTEET 287
RG ++E +L AL E + AGLDV E EP L +++ PH+ ++E
Sbjct: 233 RGGIVNEKDLAKALDE-KDIYAGLDVLEKEPMEKNHPLLSIKNKEKLLITPHIAWASKEA 291
Query: 288 SKAMADLVIENLVAHFSNK 306
K + + V EN+
Sbjct: 292 RKTLIEKVKENIKDFLEGG 310
>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 = 146 bits (371), Expect = 1e-41
Identities = 73/270 (27%), Positives = 122/270 (45%), Gaps = 26/270 (9%)
Query: 58 DAELIDSLPTLEIVASYSVG--LDKIDLDKCKDKAVRVTNTPDVLTDDVADLAVGLVLAV 115
DAEL+ P L V ++ G + ++ + VT+ D + VA+ + +L
Sbjct: 63 DAELLARAPRLRAVV-HAAGSVRGLVTDA-VWERGILVTSAADANAEPVAEFTLAAILLA 120
Query: 116 LRRVCEFDEFVKSG-KWKNGHFELGSKFSGKSVGIVGLGRIGTAIAKRVEAFGCPISYHS 174
LRR+ F ++G W G G++VGIVG GRIG A+ + + FG + +
Sbjct: 121 LRRIPRFAAAYRAGRDWGWPTRRGGRGLYGRTVGIVGFGRIGRAVVELLRPFGLRVLVYD 180
Query: 175 R-----------SEKSDANYKYYTNIIDLASNCQILIVACSLTEETHHIVNRKVIDALGP 223
E + +L + ++ + LT ET +++ +++ +
Sbjct: 181 PYLPAAEAAALGVELVSLD--------ELLARSDVVSLHAPLTPETRGMIDARLLALMRD 232
Query: 224 SGILINIGRGAHIDEPELVSALLEGRLAGAGLDVYENEPEVPEQML-GLNNVVLLPHVGS 282
IN RGA +DE L++ L GRL A LDV + EP P+ L L NV+L PH+
Sbjct: 233 GATFINTARGALVDEAALLAELRSGRL-RAALDVTDPEPLPPDSPLRTLPNVLLTPHIAG 291
Query: 283 DTEETSKAMADLVIENLVAHFSNKPLLTPV 312
T + + + D ++ L + +PLL V
Sbjct: 292 STGDERRRLGDYALDELERFLAGEPLLHEV 321
>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 = 145 bits (369), Expect = 1e-41
Identities = 73/280 (26%), Positives = 129/280 (46%), Gaps = 27/280 (9%)
Query: 48 AVVGDTKCGADA--------ELIDSLPTLEIVASYSVGLDKIDLDKCKDKAVRVTNTPDV 99
V D DA +D P+L+ +A G++ ID+D + + V NTP
Sbjct: 23 EVKEDALEDPDALIVRSDKLHDMDFAPSLKAIARAGAGVNNIDVDAASKRGIVVFNTPGA 82
Query: 100 LTDDVADLAVGLVLAVLRRVCEFDEFVKS--------GKWKNGHFELGSKFSGKSVGIVG 151
+ VA+L + ++LA+ R + + ++V + G K +G++ GK++G++G
Sbjct: 83 NANAVAELVIAMMLALSRNIIQAIKWVTNGDGDDISKGVEKGKKQFVGTELRGKTLGVIG 142
Query: 152 LGRIGTAIAKRVEAFGCPISYHSRS------EKSDANYKYYTNIIDLASNCQILIVACSL 205
LG IG +A A G + + K + T++ +L + + + L
Sbjct: 143 LGNIGRLVANAALALGMKVIGYDPYLSVEAAWKLSVEVQRVTSLEELLATADYITLHVPL 202
Query: 206 TEETHHIVNRKVIDALGPSGILINIGRGAHIDEPELVSALLEGRLAGAGLDVYENEPEVP 265
T+ET ++N +++ + P IL+N RG +DE L+ AL EG+L G D E P
Sbjct: 203 TDETRGLINAELLAKMKPGAILLNFARGEIVDEEALLEALDEGKLGGYVTDFPE-----P 257
Query: 266 EQMLGLNNVVLLPHVGSDTEETSKAMADLVIENLVAHFSN 305
+ L NV+ PH+G+ TEE + A + ++
Sbjct: 258 ALLGHLPNVIATPHLGASTEEAEENCAVMAARQIMDFLET 297
>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 = 142 bits (361), Expect = 4e-40
Identities = 85/290 (29%), Positives = 136/290 (46%), Gaps = 30/290 (10%)
Query: 41 ENSSAIRAVVGDTKCGADAELIDSLPTLEI--VASYSVGLDKIDLDKCKDKAVRVTNTPD 98
+ A+ V D DA +++ L L + +A G + +DL K+ + V P
Sbjct: 43 KGFDAVCVFVNDD---LDAPVLEKLAELGVKLIALRCAGFNNVDLKAAKELGITVVRVPA 99
Query: 99 VLTDDVADLAVGLVLAVLRRVCEFDEFVKSGKWKNGHFEL----GSKFSGKSVGIVGLGR 154
VA+ AV L+LA+ R++ V+ G+F L G GK+VG++G G+
Sbjct: 100 YSPYAVAEHAVALLLALNRKIHRAYNRVR-----EGNFSLDGLLGFDLHGKTVGVIGTGK 154
Query: 155 IGTAIAKRVEAFGCPISYHSRSEKSDANYKY--YTNIIDLASNCQILIVACSLTEETHHI 212
IG A A+ ++ FGC + + + Y ++ +L + I+ + C LT ETHH+
Sbjct: 155 IGQAFARILKGFGCRVLAYDPYPNPELAKLGVEYVDLDELLAESDIISLHCPLTPETHHL 214
Query: 213 VNRKVIDALGPSGILINIGRGAHIDEPELVSALLEGRLAGAGLDVYENEPE--------- 263
+N + I + +LIN RG ID L+ AL G++ G GLDVYE E
Sbjct: 215 INAETIAKMKDGVMLINTSRGGLIDTKALIEALKSGKIGGLGLDVYEEEAGLFFEDHSDE 274
Query: 264 -----VPEQMLGLNNVVLLPHVGSDTEETSKAMADLVIENLVAHFSNKPL 308
V ++L NV++ H T+E +A+ +ENL + KPL
Sbjct: 275 IIQDDVLARLLSFPNVLITGHQAFFTKEALTNIAETTLENLDDFEAGKPL 324
>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 = 140 bits (354), Expect = 2e-39
Identities = 83/259 (32%), Positives = 132/259 (50%), Gaps = 19/259 (7%)
Query: 58 DAELIDSLPTLEIVASYSVGLDKIDLDKCKDKAVRVTNTPDVLTDDVADLAVGLVLAVLR 117
D E I+ L+ +A GL+ IDL+ K+K + + N P+ D V + A+G++LA+
Sbjct: 53 DKEFIEKATNLKFIARAGAGLENIDLEYAKEKGIELFNAPEGNRDAVGEHALGMLLALFN 112
Query: 118 RVCEFDEFVKSGKWK---NGHFELGSKFSGKSVGIVGLGRIGTAIAKRVEAFGCP-ISYH 173
++ D+ V++G W N EL GK+VGI+G G +G A AKR+ FGC I+Y
Sbjct: 113 KLNRADQEVRNGIWDREGNRGVEL----MGKTVGIIGYGNMGKAFAKRLSGFGCKVIAYD 168
Query: 174 SRSEKSDANYKYYTNIIDLASNCQILIVACSLTEETHHIVNRKVIDALGPSGILINIGRG 233
DA + ++ L IL + LT ET +VN++ I + IN RG
Sbjct: 169 KYKNFGDAYAE-QVSLETLFKEADILSLHIPLTPETRGMVNKEFISSFKKPFYFINTARG 227
Query: 234 AHIDEPELVSALLEGRLAGAGLDVYENE----------PEVPEQMLGLNNVVLLPHVGSD 283
+ +LV AL G++ GA LDV E E PE E ++ V+L PH+
Sbjct: 228 KVVVTKDLVKALKSGKILGACLDVLEYEKASFESIFNQPEAFEYLIKSPKVILTPHIAGW 287
Query: 284 TEETSKAMADLVIENLVAH 302
T E+ + +A+++++ + A
Sbjct: 288 TFESYEKIAEVLVDKIKAL 306
>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 = 139 bits (353), Expect = 3e-39
Identities = 76/261 (29%), Positives = 125/261 (47%), Gaps = 13/261 (4%)
Query: 60 ELIDSLPTLEIVASYSVGLDK-IDLDKCKDKAVRVTNTPDVLTDDVADLAVGLVLAVLRR 118
E + + P + V G++ ++ D R TN + VA+ A+ L+LA LR+
Sbjct: 42 ERLPASPGVRWVQLPFAGVEAFVEAGVITDPGRRWTNAAGAYAETVAEHALALLLAGLRQ 101
Query: 119 VCEFDEFVKSGKW-KNGHFELGSKFSGKSVGIVGLGRIGTAIAKRVEAFGCPISYHSRS- 176
++ W +L + G +V IVG G IG A+ + FG + +RS
Sbjct: 102 ---LPARARATTWDPAEEDDLVTLLRGSTVAIVGAGGIGRALIPLLAPFGAKVIAVNRSG 158
Query: 177 ---EKSDANYKYYTNIIDLASNCQILIVACSLTEETHHIVNRKVIDALGPSGILINIGRG 233
E +D + ++ + +++A LT ET H+V+ + A+ P L+N+ RG
Sbjct: 159 RPVEGADETVPAD-RLDEVWPDADHVVLAAPLTPETRHLVDAAALAAMKPHAWLVNVARG 217
Query: 234 AHIDEPELVSALLEGRLAGAGLDVYENEPEVPE--QMLGLNNVVLLPHVGSDTEETSKAM 291
+D LV AL G +AGA LDV + EP +P+ + L N ++ PHV + E +
Sbjct: 218 PLVDTDALVDALRSGEIAGAALDVTDPEP-LPDGHPLWSLPNALITPHVANTPEVIRPLL 276
Query: 292 ADLVIENLVAHFSNKPLLTPV 312
A+ V EN+ A + +PLL V
Sbjct: 277 AERVAENVRAFAAGEPLLGVV 297
>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 = 138 bits (351), Expect = 6e-39
Identities = 79/261 (30%), Positives = 124/261 (47%), Gaps = 19/261 (7%)
Query: 58 DAELIDSLPTLEIVASYSVGLDKIDLDK-CKD-KAVRVTNTPDVLTDDVADLAVGLVLAV 115
L+ LP L+ + S G+D + D D VR+ P L +A+ + VL +
Sbjct: 49 PPGLLARLPNLKAIFSLGAGVDHLLADPDLPDVPIVRLV-DPG-LAQGMAEYVLAAVLRL 106
Query: 116 LRRVCEFDEFV---KSGKWKNGHFELGSKFSGKSVGIVGLGRIGTAIAKRVEAFGCPISY 172
R D + + G WK ++ VG++GLG +G A+A+R+ A G P+S
Sbjct: 107 HRD---MDRYAAQQRRGVWKPLPQRPAAERR---VGVLGLGELGAAVARRLAALGFPVSG 160
Query: 173 HSRSEKSDANYKYYT---NIIDLASNCQILIVACSLTEETHHIVNRKVIDALGPSGILIN 229
SRS K + + + IL+ LT ET I+N +++ L LIN
Sbjct: 161 WSRSPKDIEGVTCFHGEEGLDAFLAQTDILVCLLPLTPETRGILNAELLARLPRGAALIN 220
Query: 230 IGRGAHIDEPELVSALLEGRLAGAGLDVYENEPEVPEQML-GLNNVVLLPHVGSDTEETS 288
+GRG H+ E +L++AL G L+GA LDV+E EP + L V + PH+ + T+
Sbjct: 221 VGRGPHLVEADLLAALDSGHLSGAVLDVFEQEPLPADHPLWRHPRVTVTPHIAAITD--P 278
Query: 289 KAMADLVIENLVAHFSNKPLL 309
+ A V EN+ + +PL
Sbjct: 279 DSAAAQVAENIRRLEAGEPLP 299
>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 = 138 bits (349), Expect = 2e-38
Identities = 81/284 (28%), Positives = 130/284 (45%), Gaps = 31/284 (10%)
Query: 47 RAVVGDTKCGADAELIDSLPTLEI--VASYSVGLDKIDLDKCKDKAVRVTNTPDVLTDDV 104
+ K AEL++ L + +++ S+G D IDLD K+ ++V+N + V
Sbjct: 46 DGISILGKSKISAELLEKLKEAGVKYISTRSIGYDHIDLDAAKELGIKVSNVT-YSPNSV 104
Query: 105 ADLAVGLVLAVLRRVCEFDEFVKSGKWK-NGH-FEL----GSKFSGKSVGIVGLGRIGTA 158
AD V L+L LR+ K + + + L G + +VG++G GRIG A
Sbjct: 105 ADYTVMLMLMALRKY-------KQIMKRAEVNDYSLGGLQGRELRNLTVGVIGTGRIGQA 157
Query: 159 IAKRVEAFGCPISYHSRSEKSD-ANYKYYTNIIDLASNCQILIVACSLTEETHHIVNRKV 217
+ K + FGC I + + Y Y ++ L I+ + LTEET+H++N++
Sbjct: 158 VIKNLSGFGCKILAYDPYPNEEVKKYAEYVDLDTLYKESDIITLHTPLTEETYHLINKES 217
Query: 218 IDALGPSGILINIGRGAHIDEPELVSALLEGRLAGAGLDVYENEPEV-----------PE 266
I + I+IN RG ID L+ L G++ GA LDV E E +
Sbjct: 218 IAKMKDGVIIINTARGELIDTEALIEGLESGKIGGAALDVIEGEDGIYYNDRKGDILSNR 277
Query: 267 QMLGLN---NVVLLPHVGSDTEETSKAMADLVIENLVAHFSNKP 307
++ L NV+L PH+ T++ M + IE+LVA
Sbjct: 278 ELAILRSFPNVILTPHMAFYTDQAVSDMVENSIESLVAFEKGGE 321
>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 = 136 bits (345), Expect = 5e-38
Identities = 76/261 (29%), Positives = 132/261 (50%), Gaps = 14/261 (5%)
Query: 61 LIDSLPTLEIVASYSVGLDKIDLDKCKDKAVRVTNTPDVLTDDVADLAVGLVLAVLRRVC 120
+ + L+ + YS G+D + L+ K K + +TN + + +A+ VG +L + + +
Sbjct: 54 DLAKMKNLKWIQLYSAGVDYLPLEYIKKKGILLTNNSGIHSIPIAEWIVGYILEIYKGLK 113
Query: 121 EFDEFVKSGKWKNGHFELGSKFSGKSVGIVGLGRIGTAIAKRVEAFGCP---ISYHSRSE 177
+ + K KWK + GK++ +G G IG IAKR++AFG ++ R
Sbjct: 114 KAYKNQKEKKWK--MDSSLLELYGKTILFLGTGSIGQEIAKRLKAFGMKVIGVNTSGR-- 169
Query: 178 KSDANY--KYYT--NIIDLASNCQILIVACSLTEETHHIVNRKVIDALGPSGILINIGRG 233
D Y K Y + ++ I++ LTEETHH+ + + + + IN+GRG
Sbjct: 170 --DVEYFDKCYPLEELDEVLKEADIVVNVLPLTEETHHLFDEAFFEQMKKGALFINVGRG 227
Query: 234 AHIDEPELVSALLEGRLAGAGLDVYENEPEVPEQML-GLNNVVLLPHVGSDTEETSKAMA 292
+DE L+ AL ++ GA LDV+E EP + L L+NV++ PH+ +E ++ +
Sbjct: 228 PSVDEDALIEALKNKQIRGAALDVFEEEPLPKDSPLWDLDNVLITPHISGVSEHFNERLF 287
Query: 293 DLVIENLVAHFSNKPLLTPVI 313
D+ ENL + + LL V+
Sbjct: 288 DIFYENLKSFLEDGELLKNVV 308
>gnl|CDD|215501 PLN02928, PLN02928, oxidoreductase family protein.
Length = 347
Score = 137 bits (347), Expect = 6e-38
Identities = 76/260 (29%), Positives = 130/260 (50%), Gaps = 23/260 (8%)
Query: 58 DAELIDSLPTLEIVASYSVGLDKIDLDKCKDKAVRVTNTPDVLT---DDVADLAVGLVLA 114
DA++I ++++ + VGL+ +D+D ++V P T A++A+ L+L
Sbjct: 73 DADIIARASQMKLIMQFGVGLEGVDVDAATKHGIKVARIPSEGTGNAASCAEMAIYLMLG 132
Query: 115 VLRRVCEFDEFVKSGKWKNGHFELGSKFSGKSVGIVGLGRIGTAIAKRVEAFGCPISYHS 174
+LR+ +E S K + +G GK+V I+G G IG +AKR+ FG +
Sbjct: 133 LLRKQ---NEMQISLKARRLGEPIGDTLFGKTVFILGYGAIGIELAKRLRPFGVKLLATR 189
Query: 175 RS---EKSDANYKYYTNIIDL-------------ASNCQILIVACSLTEETHHIVNRKVI 218
RS E D ++ DL A I+++ C+LT+ET IVN + +
Sbjct: 190 RSWTSEPEDGLLIPNGDVDDLVDEKGGHEDIYEFAGEADIVVLCCTLTKETAGIVNDEFL 249
Query: 219 DALGPSGILINIGRGAHIDEPELVSALLEGRLAGAGLDVYENEPEVPE-QMLGLNNVVLL 277
++ +L+NI RG +D +++AL G L G +DV +EP P+ +L NV++
Sbjct: 250 SSMKKGALLVNIARGGLLDYDAVLAALESGHLGGLAIDVAWSEPFDPDDPILKHPNVIIT 309
Query: 278 PHVGSDTEETSKAMADLVIE 297
PHV TE + ++M +V +
Sbjct: 310 PHVAGVTEYSYRSMGKIVGD 329
>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 = 134 bits (340), Expect = 4e-37
Identities = 83/264 (31%), Positives = 134/264 (50%), Gaps = 22/264 (8%)
Query: 58 DAELIDSLPTLEI--VASYSVGLDKIDLDKCKDKAVRVTNTPDVLTDDVADLAVGLVLAV 115
D E+ + L I +A S G+D IDLD K+ +++TN P +A+ AV L +
Sbjct: 57 DEEVYEKLAEYGIKQIALRSAGVDMIDLDLAKENGLKITNVPAYSPRAIAEFAVTQALNL 116
Query: 116 LRRVCEFDEFVKSG--KWKNGHFELGSKFSGKSVGIVGLGRIGTAIAKRVEAFGCP-ISY 172
LR E D V G +W G +G + +VGI+G GRIG+A AK + FG I+Y
Sbjct: 117 LRNTPEIDRRVAKGDFRWAPGL--IGREIRDLTVGIIGTGRIGSAAAKIFKGFGAKVIAY 174
Query: 173 H-SRSEKSDANYKYYTNIIDLASNCQILIVACSLTEETHHIVNRKVIDALGPSGILINIG 231
+ + + YY ++ DL I+ + LT+E HH++N + + IL+N
Sbjct: 175 DPYPNPELEKFLLYYDSLEDLLKQADIISLHVPLTKENHHLINAEAFAKMKDGAILVNAA 234
Query: 232 RGAHIDEPELVSALLEGRLAGAGLDVYENE--------------PEVPEQMLGLNNVVLL 277
RG +D L+ AL G++AGA LD YENE EV ++++ + NV++
Sbjct: 235 RGGLVDTKALIDALDSGKIAGAALDTYENETGYFNKDWSGKEIEDEVLKELIAMPNVLIT 294
Query: 278 PHVGSDTEETSKAMADLVIENLVA 301
PH+ T+ K M ++ +++ +
Sbjct: 295 PHIAFYTDTAVKNMVEISLDDALE 318
>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 = 131 bits (332), Expect = 4e-36
Identities = 73/254 (28%), Positives = 116/254 (45%), Gaps = 7/254 (2%)
Query: 57 ADAELIDSLPTLEIVASYSVGLDKIDLDKCKDKAVRVTNTPDVLTDDVADLAVGLVLAVL 116
E + +LP L +V + S G D + L + V + N V A+LAV L+LA L
Sbjct: 50 PVLEALRALPRLRVVQTLSAGYDGV-LPLLPE-GVTLCNARGVHDASTAELAVALILASL 107
Query: 117 RRVCEFDEFVKSGKWKNGHFELGSKFSGKSVGIVGLGRIGTAIAKRVEAFGCPISYHSRS 176
R + F G+W+ S + + V IVG G IG AI +R+ F ++ +R+
Sbjct: 108 RGLPRFVRAQARGRWE--PRRTPS-LADRRVLIVGYGSIGRAIERRLAPFEVRVTRVART 164
Query: 177 EKSDANYKYYTNIIDLASNCQILIVACSLTEETHHIVNRKVIDALGPSGILINIGRGAHI 236
+ + L ++++ LT+ET +V+ + + + +L+N+ RG +
Sbjct: 165 ARPGEQVHGIDELPALLPEADVVVLIVPLTDETRGLVDAEFLARMPDGALLVNVARGPVV 224
Query: 237 DEPELVSALLEGRLAGAGLDVYENEPEVPEQML-GLNNVVLLPHVGSDTEETSKAMADLV 295
D LV+ L GRL A LDV + EP P L V++ PHVG T LV
Sbjct: 225 DTDALVAELASGRLR-AALDVTDPEPLPPGHPLWSAPGVLITPHVGGATPAFLPRAYALV 283
Query: 296 IENLVAHFSNKPLL 309
L + + +PL
Sbjct: 284 RRQLRRYAAGEPLE 297
>gnl|CDD|177941 PLN02306, PLN02306, hydroxypyruvate reductase.
Length = 386
Score = 132 bits (333), Expect = 9e-36
Identities = 76/259 (29%), Positives = 136/259 (52%), Gaps = 22/259 (8%)
Query: 72 ASYSVGLDKIDLDKCKDKAVRVTNTPDVLTDDVADLAVGLVLAVLRRVCEFDEFVKSGKW 131
++ +VG + +D++ + V NTP VLT+ A+LA L LA RR+ E DEF+++G +
Sbjct: 91 SNMAVGYNNVDVEAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRAGLY 150
Query: 132 KN--GHFELGSKFSGKSVGIVGLGRIGTAIAKR-VEAFGCPISYH-----SRSEKSDANY 183
+ H +G+ G++VG++G GRIG+A A+ VE F + Y+ +R EK Y
Sbjct: 151 EGWLPHLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQSTRLEKFVTAY 210
Query: 184 --------------KYYTNIIDLASNCQILIVACSLTEETHHIVNRKVIDALGPSGILIN 229
K +++ ++ ++ + L + T+H++N++ + + +L+N
Sbjct: 211 GQFLKANGEQPVTWKRASSMEEVLREADVISLHPVLDKTTYHLINKERLALMKKEAVLVN 270
Query: 230 IGRGAHIDEPELVSALLEGRLAGAGLDVYENEPEVPEQMLGLNNVVLLPHVGSDTEETSK 289
RG IDE LV L + GLDV+E+EP + + + N V++PH+ S ++ T +
Sbjct: 271 ASRGPVIDEVALVEHLKANPMFRVGLDVFEDEPYMKPGLADMKNAVVVPHIASASKWTRE 330
Query: 290 AMADLVIENLVAHFSNKPL 308
MA L N++ P+
Sbjct: 331 GMATLAALNVLGKLKGYPV 349
>gnl|CDD|180588 PRK06487, PRK06487, glycerate dehydrogenase; Provisional.
Length = 317
Score = 127 bits (322), Expect = 1e-34
Identities = 75/266 (28%), Positives = 126/266 (47%), Gaps = 24/266 (9%)
Query: 58 DAELIDSLPTLEIVASYSVGLDKIDLDKCKDKAVRVTNTPDVLTDDVADLAVGLVLAVLR 117
DA + + P L+++ + G + +DL +++ + V N T VA + L+LA+
Sbjct: 57 DAAALAAAPQLKLILVAATGTNNVDLAAARERGITVCNCQGYGTPSVAQHTLALLLALAT 116
Query: 118 RVCEFDEFVKSGKW-KNGHF--------ELGSKFSGKSVGIVGLGRIGTAIAKRVEAFGC 168
R+ ++ + V +G+W ++ F EL GK++G++G G +G A+A+ EAFG
Sbjct: 117 RLPDYQQAVAAGRWQQSSQFCLLDFPIVEL----EGKTLGLLGHGELGGAVARLAEAFGM 172
Query: 169 PI---SYHSRSEKSDANYKYYTNIIDLASNCQILIVACSLTEETHHIVNRKVIDALGPSG 225
+ R + D + +L L + C LTE T H++ + + + P
Sbjct: 173 RVLIGQLPGRPARPDR-----LPLDELLPQVDALTLHCPLTEHTRHLIGARELALMKPGA 227
Query: 226 ILINIGRGAHIDEPELVSALLEGRLAGAGLDVYENEPEVPEQML---GLNNVVLLPHVGS 282
+LIN RG +DE L AL G L GA DV EP V L + +++ PH
Sbjct: 228 LLINTARGGLVDEQALADALRSGHLGGAATDVLSVEPPVNGNPLLAPDIPRLIVTPHSAW 287
Query: 283 DTEETSKAMADLVIENLVAHFSNKPL 308
+ E + + + EN A F+ KPL
Sbjct: 288 GSREARQRIVGQLAENARAFFAGKPL 313
>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 = 125 bits (316), Expect = 9e-34
Identities = 72/252 (28%), Positives = 125/252 (49%), Gaps = 13/252 (5%)
Query: 58 DAELIDSLPTLEIVASYSVGLDKIDLDKCKDKAVRVTNTPDVLTDDVADLAVGLVLAVLR 117
E++++ P L + + +G +++DLD + + V N P T VA+L +G ++ + R
Sbjct: 55 TEEVLEAAPKLLAIGCFCIGTNQVDLDAAAKRGIPVFNAPFSNTRSVAELVIGEIIMLAR 114
Query: 118 RVCEFDEFVKSGKWK---NGHFELGSKFSGKSVGIVGLGRIGTAIAKRVEAFGCPISYHS 174
R+ + + G W G E+ GK++GI+G G IG+ ++ EA G + ++
Sbjct: 115 RLPDRNAAAHRGIWNKSATGSHEV----RGKTLGIIGYGHIGSQLSVLAEALGMRVIFYD 170
Query: 175 RSEK-SDANYKYYTNIIDLASNCQILIVACSLTEETHHIVNRKVIDALGPSGILINIGRG 233
+EK N + +++ +L + + + T T +++ + I + ILIN RG
Sbjct: 171 IAEKLPLGNARQVSSLEELLAEADFVTLHVPATPSTKNMIGAEEIAQMKKGAILINASRG 230
Query: 234 AHIDEPELVSALLEGRLAGAGLDVYENEPEVPEQ-----MLGLNNVVLLPHVGSDTEETS 288
+D L AL G LAGA +DV+ EP + + GL NV+L PH+G TEE
Sbjct: 231 TVVDIDALAEALRSGHLAGAAVDVFPEEPASNGEPFSSPLQGLPNVILTPHIGGSTEEAQ 290
Query: 289 KAMADLVIENLV 300
+ + V LV
Sbjct: 291 ENIGLEVAGKLV 302
>gnl|CDD|235800 PRK06436, PRK06436, glycerate dehydrogenase; Provisional.
Length = 303
Score = 115 bits (289), Expect = 4e-30
Identities = 73/256 (28%), Positives = 123/256 (48%), Gaps = 11/256 (4%)
Query: 57 ADAELIDSLPTL----EIVASYSVGLDKIDLDKCKDKAVRVTNTPDVLTDDVADLAVGLV 112
A+A LI +++ S S G+D ID+ + V +N + VA+ A L+
Sbjct: 35 AEAILIKGRYVPGKKTKMIQSLSAGVDHIDVSGIPENVVLCSNA-GAYSISVAEHAFALL 93
Query: 113 LAVLRRVCEFDEFVKSGKWKNGHFELGSKFSGKSVGIVGLGRIGTAIAKRVEAFGCPISY 172
LA + +CE + +K+G +K +L KS+GI+G G IG +A +AFG I
Sbjct: 94 LAWAKNICENNYNMKNGNFKQSPTKL---LYNKSLGILGYGGIGRRVALLAKAFGMNIYA 150
Query: 173 HSRSEKSDANYKYYTNIIDLASNCQILIVACSLTEETHHIVNRKVIDALGPSGILINIGR 232
++RS +D Y D+ ++++ LT+ET ++N K++ +IN+ R
Sbjct: 151 YTRSYVNDGISSIYMEPEDIMKKSDFVLISLPLTDETRGMINSKMLSLFRKGLAIINVAR 210
Query: 233 GAHIDEPELVSALLEGRLAGAGLDVYENEPEVPEQMLGLNNVVLLPHV-GSDTEETSKAM 291
+D+ ++++ L DV+ NEP + E +NV+L PHV G + E +
Sbjct: 211 ADVVDKNDMLNFLRNHNDKYYLSDVWWNEPIITETN--PDNVILSPHVAGGMSGEIMQPA 268
Query: 292 ADLVIENLVAHFSNKP 307
L EN+ F KP
Sbjct: 269 VALAFENIKNFFEGKP 284
>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 = 112 bits (282), Expect = 6e-29
Identities = 72/228 (31%), Positives = 115/228 (50%), Gaps = 11/228 (4%)
Query: 90 AVRVTNTPDVLTDDVADLAVGLVLAVLRRVCEFDEFVKS-GKWKNGHFELGSKFSGKSVG 148
VT V + +A+ + +LA +R+ E +VK +W+ LGS +G ++G
Sbjct: 85 GPVVTCARGVAAEAIAEFVLAAILAAAKRLPE--IWVKGAEQWR--REPLGS-LAGSTLG 139
Query: 149 IVGLGRIGTAIAKRVEAFGCPISYHSRSEKSD--ANYKYYTNIIDLASNCQILIVACSLT 206
IVG G IG A+A+R A G + RS + + ++ +L + L++A LT
Sbjct: 140 IVGFGAIGQALARRALALGMRVLALRRSGRPSDVPGVEAAADLAELFARSDHLVLAAPLT 199
Query: 207 EETHHIVNRKVIDALGPSGILINIGRGAHIDEPELVSALLEGRLAGAGLDVYENEPEVPE 266
ET H++N V+ P LINI RG +D+ L+ AL GR++ A LDV + EP +PE
Sbjct: 200 PETRHLINADVLAQAKPGLHLINIARGGLVDQEALLEALDSGRISLASLDVTDPEP-LPE 258
Query: 267 QMLGLNN--VVLLPHVGSDTEETSKAMADLVIENLVAHFSNKPLLTPV 312
+ V L PH + + + +AD +ENL + + +PL V
Sbjct: 259 GHPLYTHPRVRLSPHTSAIAPDGRRNLADRFLENLARYRAGQPLHDLV 306
>gnl|CDD|181041 PRK07574, PRK07574, formate dehydrogenase; Provisional.
Length = 385
Score = 112 bits (283), Expect = 1e-28
Identities = 67/261 (25%), Positives = 110/261 (42%), Gaps = 15/261 (5%)
Query: 59 AELIDSLPTLEIVASYSVGLDKIDLDKCKDKAVRVTNTPDVLTDDVADLAVGLVLAVLRR 118
AE I P L++ + +G D +DL + + V + VA+ V ++LA++R
Sbjct: 106 AERIAKAPNLKLAITAGIGSDHVDLQAASEHGITVAEVTGSNSISVAEHVVMMILALVRN 165
Query: 119 VCEFDEFVKSGKWK-----NGHFELGSKFSGKSVGIVGLGRIGTAIAKRVEAFGCPISYH 173
G W + ++L G +VGIVG GRIG A+ +R++ F + Y
Sbjct: 166 YEPSHRQAVEGGWNIADCVSRSYDL----EGMTVGIVGAGRIGLAVLRRLKPFDVKLHYT 221
Query: 174 SRSEKSDA-----NYKYYTNIIDLASNCQILIVACSLTEETHHIVNRKVIDALGPSGILI 228
R + Y+ + L S C ++ + C L ET H+ + V+ + L+
Sbjct: 222 DRHRLPEEVEQELGLTYHVSFDSLVSVCDVVTIHCPLHPETEHLFDADVLSRMKRGSYLV 281
Query: 229 NIGRGAHIDEPELVSALLEGRLAGAGLDVYENEPEVPEQ-MLGLNNVVLLPHVGSDTEET 287
N RG +D +V AL G LAG DV+ +P + + + PH+ T
Sbjct: 282 NTARGKIVDRDAVVRALESGHLAGYAGDVWFPQPAPADHPWRTMPRNGMTPHISGTTLSA 341
Query: 288 SKAMADLVIENLVAHFSNKPL 308
A E L F +P+
Sbjct: 342 QARYAAGTREILECFFEGRPI 362
>gnl|CDD|236985 PRK11790, PRK11790, D-3-phosphoglycerate dehydrogenase;
Provisional.
Length = 409
Score = 112 bits (282), Expect = 3e-28
Identities = 77/262 (29%), Positives = 129/262 (49%), Gaps = 25/262 (9%)
Query: 59 AELIDSLPTLEIVASYSVGLDKIDLDKCKDKAVRVTNTPDVLTDDVADLAVGLVLAVLRR 118
E++ + L + + +G +++DLD + + V N P T VA+L +G ++ +LR
Sbjct: 67 EEVLAAAEKLVAIGCFCIGTNQVDLDAAAKRGIPVFNAPFSNTRSVAELVIGEIILLLRG 126
Query: 119 VCEFDEFVKSGKWK---NGHFELGSKFSGKSVGIVGLGRIGTAIAKRVEAFGCPISYHSR 175
+ E + G W G FE+ GK++GIVG G IGT ++ E+ G + ++
Sbjct: 127 IPEKNAKAHRGGWNKSAAGSFEV----RGKTLGIVGYGHIGTQLSVLAESLGMRVYFYDI 182
Query: 176 SEK-SDANYKYYTNIIDLASNCQILIVACSL----TEETHHIVNRKVIDALGPSGILINI 230
+K N + ++ +L + ++ SL T T +++ + + + P ILIN
Sbjct: 183 EDKLPLGNARQVGSLEELLAQSDVV----SLHVPETPSTKNMIGAEELALMKPGAILINA 238
Query: 231 GRGAHIDEPELVSALLEGRLAGAGLDVYENEP-------EVPEQMLGLNNVVLLPHVGSD 283
RG +D L AL G LAGA +DV+ EP E P + GL+NV+L PH+G
Sbjct: 239 SRGTVVDIDALADALKSGHLAGAAIDVFPVEPKSNGDPFESPLR--GLDNVILTPHIGGS 296
Query: 284 TEETSKAMADLVIENLVAHFSN 305
T+E + + V LV + N
Sbjct: 297 TQEAQENIGLEVAGKLVKYSDN 318
>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 = 108 bits (271), Expect = 4e-27
Identities = 70/247 (28%), Positives = 118/247 (47%), Gaps = 46/247 (18%)
Query: 46 IRAVVGDTKCGADAELIDSLPTLEIVASYSVGLDKIDLDKCKDKAVRVTNTPDVLTDDVA 105
+R+V TK + L++ ++ V + ++G D ID D K++ + N P + VA
Sbjct: 42 VRSV---TKV--NEALLEGSK-VKFVGTATIGTDHIDTDYLKERGIGFANAPGCNANSVA 95
Query: 106 DLAVGLVLAVLRRVCEFDEFVKSGKWKNGHFELGSKFSGKSVGIVGLGRIGTAIAKRVEA 165
+ VL+ L + G GK+VGIVG+G +G+ +A+R+EA
Sbjct: 96 EY----VLSAL---LVLAQ------------RQGFSLKGKTVGIVGVGNVGSRLARRLEA 136
Query: 166 FGC------PISYHSRSEKSDANYKYYTNIIDLASNCQILIVACSLTEE----THHIVNR 215
G P R+E + ++ +L + I+ + LT + T+H+++
Sbjct: 137 LGMNVLLCDPP----RAEAEGDPG--FVSLEELLAEADIITLHVPLTRDGEHPTYHLLDE 190
Query: 216 KVIDALGPSGILINIGRGAHIDEPELVSALLEGRLAGAGLDVYENEPEVPEQMLGLNNVV 275
+ AL P ILIN RGA ID L++ L G+ LDV+ENEPE+ ++L + V
Sbjct: 191 DFLAALKPGQILINASRGAVIDNQALLALLQRGKDLRVVLDVWENEPEIDLELL---DKV 247
Query: 276 LL--PHV 280
+ PH+
Sbjct: 248 DIATPHI 254
>gnl|CDD|235890 PRK06932, PRK06932, glycerate dehydrogenase; Provisional.
Length = 314
Score = 106 bits (267), Expect = 8e-27
Identities = 65/254 (25%), Positives = 121/254 (47%), Gaps = 15/254 (5%)
Query: 58 DAELIDSLPTLEIVASYSVGLDKIDLDKCKDKAVRVTNTPDVLTDDVADLAVGLVLAVLR 117
E + LP L+++A + G + +DL K+ + V N + V + +G++ A+
Sbjct: 56 TRETLAQLPKLKLIAITATGTNNVDLVAAKELGIAVKNVTGYSSTTVPEHVLGMIFALKH 115
Query: 118 RVCEFDEFVKSGKWKN-GHFELG----SKFSGKSVGIVGLGRIGTAIAKRVEAFGCPISY 172
+ + S +W F + G ++G+ G G +GT + + +A G + Y
Sbjct: 116 SLMGWYRDQLSDRWATCKQFCYFDYPITDVRGSTLGVFGKGCLGTEVGRLAQALGMKVLY 175
Query: 173 HSRSEKSDANY--KYYTNIIDLASNCQILIVACSLTEETHHIVNRKVIDALGPSGILINI 230
+E A+ + YT ++ I+ + C LTE T +++N + + + P+ LIN
Sbjct: 176 ---AEHKGASVCREGYTPFEEVLKQADIVTLHCPLTETTQNLINAETLALMKPTAFLINT 232
Query: 231 GRGAHIDEPELVSALLEGRLAGAGLDVYENEPEVPEQML-----GLNNVVLLPHVGSDTE 285
GRG +DE L+ AL G++AGA LDV EP + L L N+++ PH+ ++
Sbjct: 233 GRGPLVDEQALLDALENGKIAGAALDVLVKEPPEKDNPLIQAAKRLPNLLITPHIAWASD 292
Query: 286 ETSKAMADLVIENL 299
+ + V +N+
Sbjct: 293 SAVTTLVNKVAQNI 306
>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 = 107 bits (268), Expect = 1e-26
Identities = 65/262 (24%), Positives = 111/262 (42%), Gaps = 19/262 (7%)
Query: 59 AELIDSLPTLEIVASYSVGLDKIDLDKCKDKAVRVTNTPDVLTDDVADLAVGLVLAVLRR 118
AE I L++ + +G D +DL D+ + V VA+ V ++L ++R
Sbjct: 76 AERIAKAKNLKLALTAGIGSDHVDLQAANDRGITVAEVTGSNVVSVAEHVVMMILILVRN 135
Query: 119 VCEFDEFVKSGKWK-----NGHFELGSKFSGKSVGIVGLGRIGTAIAKRVEAFGCPISYH 173
E G W ++L GK+VG VG GRIG + +R++ F + Y+
Sbjct: 136 YVPGHEQAIEGGWNVADVVKRAYDL----EGKTVGTVGAGRIGLRVLRRLKPFDVHLLYY 191
Query: 174 SRSEKSDA-----NYKYYTNIIDLASNCQILIVACSLTEETHHIVNRKVIDALGPSGILI 228
R + + ++ D+ S C ++ + C L ET + N++++ + L+
Sbjct: 192 DRHRLPEEVEKELGLTRHADLEDMVSKCDVVTINCPLHPETEGLFNKELLSKMKKGAYLV 251
Query: 229 NIGRGAHIDEPELVSALLEGRLAGAGLDVYENEP---EVPEQMLGLNNVVLLPHVGSDTE 285
N RG D + AL G LAG DV+ +P + P + + N + PH+ T
Sbjct: 252 NTARGKICDREAVAEALESGHLAGYAGDVWFPQPAPKDHPWRTMP--NNAMTPHISGTTL 309
Query: 286 ETSKAMADLVIENLVAHFSNKP 307
+ A E L F +P
Sbjct: 310 DAQARYAAGTKEILERFFEGEP 331
>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 = 105 bits (264), Expect = 3e-26
Identities = 75/271 (27%), Positives = 120/271 (44%), Gaps = 19/271 (7%)
Query: 48 AVVGDTKCGADAELIDSLPTLEI--VASYSVGLDKIDLDKCKDKAVRVTNTPDVLTDDVA 105
AV+ C AD E ++ I V + +VG + IDL+ K+ ++ P + +A
Sbjct: 47 AVIVRGNCFADKENLEIYKEYGIKYVFTRTVGFNHIDLEAAKELGFKMARVPSYSPNAIA 106
Query: 106 DLAVGLVLAVLRRVCEFDEFVKSGKWKNGHFELGSKFSGKSVGIVGLGRIGTAIAKRVEA 165
+LA L + + R + +K F + +VGI+G GRIG AK +
Sbjct: 107 ELAFTLAMTLSRHTAYTASRTANKNFKVDPFMFSKEIRNSTVGIIGTGRIGLTAAKLFKG 166
Query: 166 FGCP-ISYHSRSEKSDANYKYYTNIIDLASNCQILIVACS-LTEETHHIVNRKVIDALGP 223
G I Y + + + ++ +L I+ + + + ++N++ I +
Sbjct: 167 LGAKVIGYDIYPSDAAKDVVTFVSLDELLKKSDIISLHVPYIKGKNDKLINKEFISKMKD 226
Query: 224 SGILINIGRGAHIDEPELVSALLEGRLAGAGLDVYENEPEV--------------PEQML 269
ILIN RG DE ++ AL G+LAG G DV NE E+ E++L
Sbjct: 227 GAILINTARGELQDEEAILEALESGKLAGFGTDVLNNEKEIFFKDFDGDKIEDPVVEKLL 286
Query: 270 GLNNVVLL-PHVGSDTEETSKAMADLVIENL 299
L VLL PH+GS T+E M + ENL
Sbjct: 287 DLYPRVLLTPHIGSYTDEALSNMIETSYENL 317
>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 = 105 bits (264), Expect = 3e-26
Identities = 71/288 (24%), Positives = 118/288 (40%), Gaps = 46/288 (15%)
Query: 63 DSLPTLEIVASYSVGLDK-IDLDKCKDKAVRVTNTPDVLTDDVADLAVGLVLAVLRRVCE 121
+ +P L +V +S G D + KD V + + +A+ +G L + +
Sbjct: 50 EDVPNLRLVQLFSAGADHWLGHPLYKDPEVPLCTASGIHGPQIAEWVIGTWLVLSHHFLQ 109
Query: 122 FDEFVKSGKWKNGHFELGSKFS-GKSVGIVGLGRIGTAIAKRVEAFGC------------ 168
+ E K W + S GK VGI+G G IG A+ +A G
Sbjct: 110 YIELQKEQTWGRRQEAYSVEDSVGKRVGILGYGSIGRQTARLAQALGMEVYAYTRSPRPT 169
Query: 169 ---------------------PISYHSRSEKSDANYKYYTNIIDLASNCQILIVACSLTE 207
P ++ S ++K+ + L + +L+V+ LT
Sbjct: 170 PESRKDDGYIVPGTGDPDGSIPSAWFSGTDKASLHEF-------LRQDLDLLVVSLPLTP 222
Query: 208 ETHHIVNRKVIDALGPSG-ILINIGRGAHIDEPELVSALLEGRLAGAGLDVYENEPEVPE 266
T H++ + + L + NI RG+ +D LV+AL G++ GA LDV + EP +P
Sbjct: 223 ATKHLLGAEEFEILAKRKTFVSNIARGSLVDTDALVAALESGQIRGAALDVTDPEP-LPA 281
Query: 267 Q--MLGLNNVVLLPHVGSDTEETSKAMADLVIENLVAHFSNKPLLTPV 312
+ NV++ PHV T+E D++ ENL +PL+ V
Sbjct: 282 DHPLWSAPNVIITPHVSWQTQEYFDRALDVLEENLERLRKGEPLINLV 329
>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 = 99.8 bits (249), Expect = 3e-24
Identities = 67/220 (30%), Positives = 104/220 (47%), Gaps = 22/220 (10%)
Query: 104 VADLAVGLVLAVLRRVCEFDEFVKSGKWKNGHFELG-----------SKFSGKSVGIVGL 152
VA+ + L+LA +RR+ E E + +W ELG + G V I G
Sbjct: 95 VAEHTLALILAAVRRLDEMREAQREHRWAG---ELGGLQPLRPAGRLTTLLGARVLIWGF 151
Query: 153 GRIGTAIAKRVEAFGCPISYHSRSEKSDANYKYYT--NIIDLASNCQILIVACSLTEETH 210
G IG +A + A G ++ +RS A + + +L +L++ T T
Sbjct: 152 GSIGQRLAPLLTALGARVTGVARSAGERAGFPVVAEDELPELLPETDVLVMILPATPSTA 211
Query: 211 HIVNRKVIDALGPSGILINIGRGAHIDEPELVSALLEGRLAGAGLDVYENEPEVPEQ--M 268
H ++ +V+ AL ++N+GRGA +DE LV+AL GRL GA LDV EP +P +
Sbjct: 212 HALDAEVLAALPKHAWVVNVGRGATVDEDALVAALESGRLGGAALDVTATEP-LPASSPL 270
Query: 269 LGLNNVVLLPHVGSDTEETSKAMADLVIENLVAHFSNKPL 308
N++L PH + + +L+ ENL A + PL
Sbjct: 271 WDAPNLILTPHAAGGRPQGA---EELIAENLRAFLAGGPL 307
>gnl|CDD|183550 PRK12480, PRK12480, D-lactate dehydrogenase; Provisional.
Length = 330
Score = 92.3 bits (229), Expect = 2e-21
Identities = 54/192 (28%), Positives = 98/192 (51%), Gaps = 1/192 (0%)
Query: 71 VASYSVGLDKIDLDKCKDKAVRVTNTPDVLTDDVADLAVGLVLAVLRRVCEFDEFVKSGK 130
+A + G D DLD K + ++N P + +A+ +V + L ++RR + + V++
Sbjct: 73 IAQRTAGFDMYDLDLAKKHNIVISNVPSYSPETIAEYSVSIALQLVRRFPDIERRVQAHD 132
Query: 131 WKNGHFELGSKFSGKSVGIVGLGRIGTAIAKRVEAFGCPI-SYHSRSEKSDANYKYYTNI 189
+ + +V I+G GRIG A AK FG I +Y + K Y ++
Sbjct: 133 FTWQAEIMSKPVKNMTVAIIGTGRIGAATAKIYAGFGATITAYDAYPNKDLDFLTYKDSV 192
Query: 190 IDLASNCQILIVACSLTEETHHIVNRKVIDALGPSGILINIGRGAHIDEPELVSALLEGR 249
+ + I+ + +E++H+ ++ + D + IL+N RGA I+ P+L++A+ +G
Sbjct: 193 KEAIKDADIISLHVPANKESYHLFDKAMFDHVKKGAILVNAARGAVINTPDLIAAVNDGT 252
Query: 250 LAGAGLDVYENE 261
L GA +D YENE
Sbjct: 253 LLGAAIDTYENE 264
>gnl|CDD|185366 PRK15469, ghrA, bifunctional glyoxylate/hydroxypyruvate reductase
A; Provisional.
Length = 312
Score = 83.7 bits (207), Expect = 2e-18
Identities = 57/181 (31%), Positives = 95/181 (52%), Gaps = 7/181 (3%)
Query: 108 AVGLVLAVLRRVCEFDEFVKSGKWKNGHFELGSKFSGKSVGIVGLGRIGTAIAKRVEAFG 167
AV VL RR ++ S W+ F+ +GI+G G +G+ +A+ ++ +G
Sbjct: 103 AVSQVLHWFRRFDDYQALQNSSHWQPLPEYHREDFT---IGILGAGVLGSKVAQSLQTWG 159
Query: 168 CPISYHSRSEKSDANYKYYTNIIDLA---SNCQILIVACSLTEETHHIVNRKVIDALGPS 224
P+ SRS KS + + +L+ S ++LI T ET I+N+++++ L
Sbjct: 160 FPLRCWSRSRKSWPGVQSFAGREELSAFLSQTRVLINLLPNTPETVGIINQQLLEQLPDG 219
Query: 225 GILINIGRGAHIDEPELVSALLEGRLAGAGLDVYENEPEVPEQMLGLN-NVVLLPHVGSD 283
L+N+ RG H+ E +L++AL G++ GA LDV+ EP PE L + V + PHV +
Sbjct: 220 AYLLNLARGVHVVEDDLLAALDSGKVKGAMLDVFSREPLPPESPLWQHPRVAITPHVAAV 279
Query: 284 T 284
T
Sbjct: 280 T 280
>gnl|CDD|181499 PRK08605, PRK08605, D-lactate dehydrogenase; Validated.
Length = 332
Score = 83.6 bits (207), Expect = 3e-18
Identities = 60/248 (24%), Positives = 107/248 (43%), Gaps = 20/248 (8%)
Query: 71 VASYSVGLDKIDLDKCKDKAVRVTNTPDVLTDDVADLAVGLVLAVLRRVCEFDEFVKSGK 130
+A S G D DL+ + ++N P + +A+ V + ++R + V+
Sbjct: 73 IAQRSAGFDTYDLELATKYNLIISNVPSYSPESIAEFTVTQAINLVRHFNQIQTKVREHD 132
Query: 131 WKNGHFELGSKFSGKSVGIVGLGRIGTAIAK-RVEAFGCP-ISYHSRSEKSDANYKYYTN 188
++ L V ++G GRIG A+AK + +G ++Y A Y Y +
Sbjct: 133 FRWEPPILSRSIKDLKVAVIGTGRIGLAVAKIFAKGYGSDVVAYDPFPNAKAATYVDYKD 192
Query: 189 IIDLA-SNCQILIVACSLTEETHHIVNRKVIDALGPSGILINIGRGAHIDEPELVSALLE 247
I+ A I+ + T+ H++ N + + +N RG+ +D L+ AL
Sbjct: 193 TIEEAVEGADIVTLHMPATKYNHYLFNADLFKHFKKGAVFVNCARGSLVDTKALLDALDN 252
Query: 248 GRLAGAGLDVYENE-PEVP-------------EQMLGLNNVVLLPHVGSDTEETSKAMAD 293
G + GA LD YE E P P E ++ +V+L PH+ T+ A+ +
Sbjct: 253 GLIKGAALDTYEFERPLFPSDQRGQTINDPLLESLINREDVILTPHIAFYTDA---AVKN 309
Query: 294 LVIENLVA 301
L+++ L A
Sbjct: 310 LIVDALDA 317
>gnl|CDD|178684 PLN03139, PLN03139, formate dehydrogenase; Provisional.
Length = 386
Score = 83.4 bits (206), Expect = 4e-18
Identities = 57/210 (27%), Positives = 97/210 (46%), Gaps = 6/210 (2%)
Query: 59 AELIDSLPTLEIVASYSVGLDKIDLDKCKDKAVRVTNTPDVLTDDVADLAVGLVLAVLRR 118
AE I LE++ + +G D IDL + V VA+ + +L +LR
Sbjct: 113 AERIKKAKNLELLLTAGIGSDHIDLPAAAAAGLTVAEVTGSNVVSVAEDELMRILILLRN 172
Query: 119 VCEFDEFVKSGKWK-NGHFELGSKFSGKSVGIVGLGRIGTAIAKRVEAFGCPISYHSRSE 177
V SG+W G GK+VG VG GRIG + +R++ F C + YH R +
Sbjct: 173 FLPGYHQVVSGEWNVAGIAYRAYDLEGKTVGTVGAGRIGRLLLQRLKPFNCNLLYHDRLK 232
Query: 178 -----KSDANYKYYTNIIDLASNCQILIVACSLTEETHHIVNRKVIDALGPSGILINIGR 232
+ + K+ ++ + C ++++ LTE+T + N++ I + +++N R
Sbjct: 233 MDPELEKETGAKFEEDLDAMLPKCDVVVINTPLTEKTRGMFNKERIAKMKKGVLIVNNAR 292
Query: 233 GAHIDEPELVSALLEGRLAGAGLDVYENEP 262
GA +D + A G + G G DV+ +P
Sbjct: 293 GAIMDTQAVADACSSGHIGGYGGDVWYPQP 322
>gnl|CDD|166874 PRK00257, PRK00257, erythronate-4-phosphate dehydrogenase;
Validated.
Length = 381
Score = 82.4 bits (204), Expect = 1e-17
Identities = 57/245 (23%), Positives = 102/245 (41%), Gaps = 42/245 (17%)
Query: 46 IRAVVGDTKCGADAELIDSLPTLEIVASYSVGLDKIDLDKCKDKAVRVTNTPDVLTDDVA 105
+R+V T+ D L++ + V + ++G D +DLD + + ++ P V
Sbjct: 43 VRSV---TRV--DRALLEGSR-VRFVGTCTIGTDHLDLDYFAEAGITWSSAPGCNARGVV 96
Query: 106 DLAVGLVLAVLRRVCEFDEFVKSGKWKNGHFELGSKFSGKSVGIVGLGRIGTAIAKRVEA 165
D VL L + E + G + ++ G+VG G +G + + +
Sbjct: 97 DY----VLGSLLTLAERE---------------GVDLAERTYGVVGAGHVGGRLVRVLRG 137
Query: 166 FG-----CPISYHSRSEKSDANYKYYTNIIDLASNCQILIVACSLTEE----THHIVNRK 216
G C D + ++ + C ++ + LT+E T H+++
Sbjct: 138 LGWKVLVCDPPRQEAEGDGD-----FVSLERILEECDVISLHTPLTKEGEHPTRHLLDEA 192
Query: 217 VIDALGPSGILINIGRGAHIDEPELVSALLEGRLAGAGLDVYENEPEVPEQMLGLNNVVL 276
+ +L P LIN RGA +D L ALL G A LDV+E EP++ ++ L +
Sbjct: 193 FLASLRPGAWLINASRGAVVDNQALREALLSGEDLDAVLDVWEGEPQIDLELADL--CTI 250
Query: 277 -LPHV 280
PH+
Sbjct: 251 ATPHI 255
>gnl|CDD|185335 PRK15438, PRK15438, erythronate-4-phosphate dehydrogenase PdxB;
Provisional.
Length = 378
Score = 65.7 bits (160), Expect = 5e-12
Identities = 49/157 (31%), Positives = 78/157 (49%), Gaps = 15/157 (9%)
Query: 139 GSKFSGKSVGIVGLGRIGTAIAKRVEAFG-----CPISYHSRSEKSDANYKYYTNIIDLA 193
G ++VGIVG+G +G + R+EA G C R ++ D + ++ +L
Sbjct: 111 GFSLHDRTVGIVGVGNVGRRLQARLEALGIKTLLCDPPRADRGDEGD-----FRSLDELV 165
Query: 194 SNCQILIVACSLTEE----THHIVNRKVIDALGPSGILINIGRGAHIDEPELVSALLEGR 249
IL L ++ T H+ + K+I +L P ILIN RGA +D L++ L EG+
Sbjct: 166 QEADILTFHTPLFKDGPYKTLHLADEKLIRSLKPGAILINACRGAVVDNTALLTCLNEGQ 225
Query: 250 LAGAGLDVYENEPEVPEQMLGLNNVVLLPHVGSDTEE 286
LDV+E EPE+ ++L ++ PH+ T E
Sbjct: 226 KLSVVLDVWEGEPELNVELLKKVDIG-TPHIAGYTLE 261
>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 = 55.4 bits (134), Expect = 7e-09
Identities = 41/175 (23%), Positives = 73/175 (41%), Gaps = 19/175 (10%)
Query: 131 WKNGHFELGSKFSGKSVGIVGLGRIGTAIAKRVEAFGCPISYHSRSEKSD---ANYKYYT 187
WK EL +G VGI+GLG G IA + FG + Y+SR+ K D +Y
Sbjct: 129 WKEEPREL----TGLKVGIIGLGTTGQMIADALSFFGADVYYYSRTRKPDAEAKGIRYLP 184
Query: 188 NIIDLASNCQILIVACSLTEETHHIVNRKVIDALGPSGILINIGRGAHIDEPELVSALLE 247
+L ++ C+ + ++ + + LG IL N G + L+
Sbjct: 185 L-NELLKTVDVI---CTCLPKNVILLGEEEFELLGDGKILFNTSLGPSFEVEA-----LK 235
Query: 248 GRLAGAGLDVYENEPE---VPEQMLGLNNVVLLPHVGSDTEETSKAMADLVIENL 299
L +G ++++ + E++L NV+ T + + ++ V+ NL
Sbjct: 236 KWLKASGYNIFDCDTAGALGDEELLRYPNVICTNKSAGWTRQAFERLSQKVLANL 290
>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 = 54.5 bits (131), Expect = 2e-08
Identities = 39/226 (17%), Positives = 84/226 (37%), Gaps = 19/226 (8%)
Query: 49 VVGDTKCGADAELIDSLPTLEIVASYSVGLDKIDLDKCKDKA-VRVTNTPDVLTDDVADL 107
V + A+ LI L ++ +Y++G D DL + +A + V +
Sbjct: 70 KVKEPLTNAEYALIQKLG-DRLLFTYTIGADHRDLTEALARAGLTAIAVEGVELPLLTSN 128
Query: 108 AVGLV-LAVLRRVCEFDEFVKSGKWKNGHFELGSKFSGKSVGIVGLGRIGTAIAKRVEAF 166
++G L+V + GK+V +VG G +G A+ +
Sbjct: 129 SIGAGELSVQFIARFLEVQQPGRLGGAPDVA------GKTVVVVGAGVVGKEAAQMLRGL 182
Query: 167 GCPISYH-----SRSEKSDANYKYYTNIIDLASNCQILIVACSLTEETHHIVNRK-VIDA 220
G + + + + K + + + +++ L + I+ + +++
Sbjct: 183 GAQVLITDINVEALEQLEELGGKNVEELEEALAEADVIVTTTLLPGKRAGILVPEELVEQ 242
Query: 221 LGPSGILINIGRGAHIDEPELVSALLEGRLAGAGLDVYENEPEVPE 266
+ P +++N+ GA L + LLE G G+ Y + +P
Sbjct: 243 MKPGSVIVNVAVGAVGCVQALHTQLLEE---GHGVVHY-GDVNMPG 284
>gnl|CDD|215144 PLN02256, PLN02256, arogenate dehydrogenase.
Length = 304
Score = 35.8 bits (83), Expect = 0.018
Identities = 15/50 (30%), Positives = 22/50 (44%), Gaps = 4/50 (8%)
Query: 147 VGIVGLGRIGTAIAKRVEAFGCPISYHSRSEKSDA----NYKYYTNIIDL 192
+GIVG G G +AK G + SRS+ SD ++ + D
Sbjct: 39 IGIVGFGNFGQFLAKTFVKQGHTVLATSRSDYSDIAAELGVSFFRDPDDF 88
>gnl|CDD|215382 PLN02712, PLN02712, arogenate dehydrogenase.
Length = 667
Score = 32.6 bits (74), Expect = 0.31
Identities = 22/88 (25%), Positives = 40/88 (45%), Gaps = 4/88 (4%)
Query: 147 VGIVGLGRIGTAIAKRVEAFGCPISYHSRSEKSDANYK----YYTNIIDLASNCQILIVA 202
+ IVG G G +AK + G + +SRS+ SD K Y+++ DL +I+
Sbjct: 372 IAIVGFGNFGQFLAKTMVKQGHTVLAYSRSDYSDEAQKLGVSYFSDADDLCEEHPEVILL 431
Query: 203 CSLTEETHHIVNRKVIDALGPSGILINI 230
C+ T ++ L S + +++
Sbjct: 432 CTSILSTEKVLKSLPFQRLKRSTLFVDV 459
Score = 28.8 bits (64), Expect = 4.7
Identities = 17/62 (27%), Positives = 30/62 (48%), Gaps = 4/62 (6%)
Query: 147 VGIVGLGRIGTAIAKRVEAFGCPISYHSRSEKSDANYK----YYTNIIDLASNCQILIVA 202
+ I+G G G +AK + + G + HSRS+ S A ++ + DL +I+
Sbjct: 55 IAIIGFGNYGQFLAKTLISQGHTVLAHSRSDHSLAARSLGVSFFLDPHDLCERHPDVILL 114
Query: 203 CS 204
C+
Sbjct: 115 CT 116
>gnl|CDD|173621 PTZ00431, PTZ00431, pyrroline carboxylate reductase; Provisional.
Length = 260
Score = 30.7 bits (69), Expect = 0.83
Identities = 27/98 (27%), Positives = 50/98 (51%), Gaps = 8/98 (8%)
Query: 147 VGIVGLGRIGTAIAKRVEAFGC----PISYHSRSEKSDANYKYYTNIIDLASNCQILIVA 202
VG +GLG++G+A+A +E I YH+ S+K + + Y + +LA C I++
Sbjct: 6 VGFIGLGKMGSALAYGIENSNIIGKENIYYHTPSKK-NTPFVYLQSNEELAKTCDIIV-- 62
Query: 203 CSLTEETHHIVNRKVIDALGPSGILINIGRGAHIDEPE 240
++ + V ++ LG +LI+I G ++ E
Sbjct: 63 LAVKPDLAGKVLLEIKPYLGSK-LLISICGGLNLKTLE 99
>gnl|CDD|187594 cd05333, BKR_SDR_c, beta-Keto acyl carrier protein reductase (BKR),
involved in Type II FAS, classical (c) SDRs. This
subgroup includes the Escherichai coli K12 BKR, FabG.
BKR catalyzes the NADPH-dependent reduction of ACP in
the first reductive step of de novo fatty acid synthesis
(FAS). FAS consists of four elongation steps, which are
repeated to extend the fatty acid chain through the
addition of two-carbo units from malonyl acyl-carrier
protein (ACP): condensation, reduction, dehydration, and
a final reduction. Type II FAS, typical of plants and
many bacteria, maintains these activities on discrete
polypeptides, while type I FAS utilizes one or two
multifunctional polypeptides. BKR resembles enoyl
reductase, which catalyzes the second reduction step in
FAS. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with
structurally conserved Rossmann fold (alpha/beta folding
pattern with a central beta-sheet) NAD(P)(H) binding
region and a structurally diverse C-terminal region.
Classical SDRs are typically about 250 residues long,
while extended SDRS are approximately 350 residues.
Sequence identity between different SDR enzymes are
typically in the 15-30% range, but the enzymes share the
Rossmann fold NAD binding motif and characteristic
NAD-binding and catalytic sequence patterns. These
enzymes have a 3-glycine N-terminal NAD(P)(H) binding
pattern: TGxxxGxG in classical SDRs. Extended SDRs have
additional elements in the C-terminal region, and
typically have a TGXXGXXG cofactor binding motif.
Complex (multidomain) SDRs such as ketoreductase domains
of fatty acid synthase have a GGXGXXG NAD(P) binding
motif and an altered active site motif (YXXXN). Fungal
type type ketoacyl reductases have a TGXXXGX(1-2)G
NAD(P)-binding motif. Some atypical SDRs have lost
catalytic activity and/or have an unusual NAD(P) binding
motif and missing or unusual active site residues.
Reactions catalyzed within the SDR family include
isomerization, decarboxylation, epimerization, C=N bond
reduction, dehydratase activity, dehalogenation,
Enoyl-CoA reduction, and carbonyl-alcohol
oxidoreduction. A critical catalytic Tyr residue
(Tyr-151, human 15-hydroxyprostaglandin dehydrogenase
(15-PGDH) numbering), is often found in a conserved
YXXXK pattern. In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) or additional
Ser, contributing to the active site. Substrates for
these enzymes include sugars, steroids, alcohols, and
aromatic compounds. The standard reaction mechanism is a
proton relay involving the conserved Tyr-151 and
Lys-155, and well as Asn-111 (or Ser). Some SDR family
members, including 17 beta-hydroxysteroid dehydrogenase
contain an additional helix-turn-helix motif that is not
generally found among SDRs.
Length = 240
Score = 30.2 bits (69), Expect = 1.2
Identities = 29/86 (33%), Positives = 37/86 (43%), Gaps = 4/86 (4%)
Query: 145 KSVGIVGLGR-IGTAIAKRVEAFGCPISYHSRSEKSDANYKYYTNIIDLASNCQILIVAC 203
K + G R IG AIA R+ A G ++ RSE++ A I L N L
Sbjct: 1 KVALVTGASRGIGRAIALRLAAEGAKVAVTDRSEEAAAETV--EEIKALGGNAAALEADV 58
Query: 204 SLTEETHHIVNRKVIDALGPSGILIN 229
S E +V KV GP IL+N
Sbjct: 59 SDREAVEALVE-KVEAEFGPVDILVN 83
>gnl|CDD|177834 PLN02178, PLN02178, cinnamyl-alcohol dehydrogenase.
Length = 375
Score = 30.4 bits (68), Expect = 1.2
Identities = 33/126 (26%), Positives = 51/126 (40%), Gaps = 22/126 (17%)
Query: 140 SKFSGKSVGIVGLGRIGTAIAKRVEAFGCPISYHSRSEKSDANYKYYTNIIDLASNCQIL 199
+K SGK +G+ GLG +G K +AFG ++ SRS + + ID L
Sbjct: 175 TKESGKRLGVNGLGGLGHIAVKIGKAFGLRVTVISRSSEKE------REAIDRLGADSFL 228
Query: 200 IVACSLTEETHHIVNRKVIDALGPSGILINIGRGAHIDEPELVSALLEGRLAGAGLDVYE 259
+ S +K+ +A+G +I+ H P + G+L GL
Sbjct: 229 VTTDS----------QKMKEAVGTMDFIIDTVSAEHALLPLFSLLKVSGKLVALGL---- 274
Query: 260 NEPEVP 265
PE P
Sbjct: 275 --PEKP 278
>gnl|CDD|215351 PLN02649, PLN02649, glucose-6-phosphate isomerase.
Length = 560
Score = 30.4 bits (69), Expect = 1.3
Identities = 12/24 (50%), Positives = 15/24 (62%)
Query: 109 VGLVLAVLRRVCEFDEFVKSGKWK 132
V V VL ++ F E V+SGKWK
Sbjct: 117 VPEVWEVLDKIKAFSEDVRSGKWK 140
>gnl|CDD|224996 COG2085, COG2085, Predicted dinucleotide-binding enzymes [General
function prediction only].
Length = 211
Score = 29.6 bits (67), Expect = 1.4
Identities = 13/38 (34%), Positives = 20/38 (52%), Gaps = 1/38 (2%)
Query: 145 KSVGIVGLGRIGTAIAKRVEAFGCPISY-HSRSEKSDA 181
+ I+G G IG+A+A R+ G + SR K+ A
Sbjct: 2 MIIAIIGTGNIGSALALRLAKAGHEVIIGSSRGPKALA 39
>gnl|CDD|224995 COG2084, MmsB, 3-hydroxyisobutyrate dehydrogenase and related
beta-hydroxyacid dehydrogenases [Lipid metabolism].
Length = 286
Score = 29.9 bits (68), Expect = 1.8
Identities = 26/126 (20%), Positives = 50/126 (39%), Gaps = 19/126 (15%)
Query: 145 KSVGIVGLGRIGTAIAKRVEAFGCPISYHSRS-EKS-----DANYKYYTNIIDLASNCQI 198
+ +GLG +G+ +A + G ++ ++R+ EK+ A + + A+ +
Sbjct: 1 MKIAFIGLGIMGSPMAANLLKAGHEVTVYNRTPEKAAELLAAAGATVAASPAEAAAEADV 60
Query: 199 LIVACSLTEETHHIVNRKVIDALGPSGILINIGRGA-HID----EPELVSALLEGRLAGA 253
+I ++ G +G+L + GA ID PE L LA
Sbjct: 61 VITMLPDDAAVRAVL-------FGENGLLEGLKPGAIVIDMSTISPETARELAA-ALAAK 112
Query: 254 GLDVYE 259
GL+ +
Sbjct: 113 GLEFLD 118
>gnl|CDD|131900 TIGR02853, spore_dpaA, dipicolinic acid synthetase, A subunit.
This predicted Rossman fold-containing protein is the A
subunit of dipicolinic acid synthetase as found in most,
though not all, endospore-forming low-GC Gram-positive
bacteria; it is absent in Clostridium. The B subunit is
represented by TIGR02852. This protein is also known as
SpoVFA [Cellular processes, Sporulation and
germination].
Length = 287
Score = 29.7 bits (67), Expect = 2.0
Identities = 13/38 (34%), Positives = 19/38 (50%)
Query: 144 GKSVGIVGLGRIGTAIAKRVEAFGCPISYHSRSEKSDA 181
G +V ++G GR G IA+ A G + +RS A
Sbjct: 151 GSNVMVLGFGRTGMTIARTFSALGARVFVGARSSADLA 188
>gnl|CDD|223364 COG0287, TyrA, Prephenate dehydrogenase [Amino acid transport and
metabolism].
Length = 279
Score = 29.2 bits (66), Expect = 2.3
Identities = 23/97 (23%), Positives = 41/97 (42%), Gaps = 16/97 (16%)
Query: 147 VGIVGLGRIGTAIAK-------RVEAFGCPISYHS--RSEKSDANYKYYTNI-IDLASNC 196
VGIVGLG +G ++A+ V G S + + + + + A+
Sbjct: 6 VGIVGLGLMGGSLARALKEAGLVVRIIGRDRSAATLKAALELGVIDELTVAGLAEAAAEA 65
Query: 197 QILIVAC--SLTEETHHIVNRKVIDALGPSGILINIG 231
++IVA TEE V +++ L I+ ++G
Sbjct: 66 DLVIVAVPIEATEE----VLKELAPHLKKGAIVTDVG 98
>gnl|CDD|153033 pfam12599, DUF3768, Protein of unknown function (DUF3768). This
family of proteins is found in bacteria. Proteins in
this family are typically between 108 and 129 amino
acids in length. There are two conserved sequence
motifs: NDP and RVLT.
Length = 84
Score = 27.5 bits (62), Expect = 2.6
Identities = 11/27 (40%), Positives = 14/27 (51%)
Query: 99 VLTDDVADLAVGLVLAVLRRVCEFDEF 125
V+T VA L +LR V FD+F
Sbjct: 1 VITQGVAALGEDDQQELLRAVRAFDDF 27
>gnl|CDD|188169 TIGR01829, AcAcCoA_reduct, acetoacetyl-CoA reductase. This model
represent acetoacetyl-CoA reductase, a member of the
family short-chain-alcohol dehydrogenases. Note that,
despite the precision implied by the enzyme name, the
reaction of EC 1.1.1.36 is defined more generally as
(R)-3-hydroxyacyl-CoA + NADP+ = 3-oxoacyl-CoA + NADPH.
Members of this family may act in the biosynthesis of
poly-beta-hydroxybutyrate (e.g. Rhizobium meliloti) and
related poly-beta-hydroxyalkanoates. Note that the
member of this family from Azospirillum brasilense,
designated NodG, appears to lack acetoacetyl-CoA
reductase activity and to act instead in the production
of nodulation factor. This family is downgraded to
subfamily for this NodG. Other proteins designated NodG,
as from Rhizobium, belong to related but distinct
protein families.
Length = 242
Score = 28.9 bits (65), Expect = 3.1
Identities = 22/89 (24%), Positives = 36/89 (40%), Gaps = 22/89 (24%)
Query: 151 GLGRIGTAIAKRVEAFGCPI--SYHSRSEKSDA--------NYKYYTNIIDLASNCQILI 200
G+G IGTAI +R+ G + + E+++A + + D++S
Sbjct: 8 GMGGIGTAICQRLAKDGYRVAANCGPNEERAEAWLQEQGALGFDFRVVEGDVSS------ 61
Query: 201 VACSLTEETHHIVNRKVIDALGPSGILIN 229
E V KV LGP +L+N
Sbjct: 62 -----FESCKAAV-AKVEAELGPIDVLVN 84
>gnl|CDD|217563 pfam03446, NAD_binding_2, NAD binding domain of 6-phosphogluconate
dehydrogenase. The NAD binding domain of
6-phosphogluconate dehydrogenase adopts a Rossmann fold.
Length = 163
Score = 28.6 bits (65), Expect = 3.1
Identities = 11/62 (17%), Positives = 29/62 (46%), Gaps = 5/62 (8%)
Query: 145 KSVGIVGLGRIGTAIAKRVEAFGCPISYHSRS-EKSD----ANYKYYTNIIDLASNCQIL 199
+G +GLG +G+ +A + G ++ ++R+ EK + + + ++ ++
Sbjct: 1 AKIGFIGLGVMGSPMALNLLKAGYTVTVYNRTPEKVEELVAEGAVGAASPAEFVASADVV 60
Query: 200 IV 201
I
Sbjct: 61 IT 62
>gnl|CDD|233590 TIGR01830, 3oxo_ACP_reduc, 3-oxoacyl-(acyl-carrier-protein)
reductase. This model represents 3-oxoacyl-[ACP]
reductase, also called 3-ketoacyl-acyl carrier protein
reductase, an enzyme of fatty acid biosynthesis [Fatty
acid and phospholipid metabolism, Biosynthesis].
Length = 239
Score = 28.7 bits (65), Expect = 3.2
Identities = 21/84 (25%), Positives = 37/84 (44%), Gaps = 7/84 (8%)
Query: 149 IVGLGR-IGTAIAKRVEAFGCP--ISYHSRSEKSDANYKYYTNIIDLASNCQILIVACSL 205
+ G R IG AIA ++ G I+Y S E ++ + + ++ S
Sbjct: 3 VTGASRGIGRAIALKLAKEGAKVIITYRSSEEGAEEVVEE---LKAYGVKALGVVCDVSD 59
Query: 206 TEETHHIVNRKVIDALGPSGILIN 229
E+ +V ++ + LGP IL+N
Sbjct: 60 REDVKAVVE-EIEEELGPIDILVN 82
>gnl|CDD|176186 cd05283, CAD1, Cinnamyl alcohol dehydrogenases (CAD). Cinnamyl
alcohol dehydrogenases (CAD), members of the medium
chain dehydrogenase/reductase family, reduce
cinnamaldehydes to cinnamyl alcohols in the last step of
monolignal metabolism in plant cells walls. CAD binds 2
zinc ions and is NADPH- dependent. CAD family members
are also found in non-plant species, e.g. in yeast where
they have an aldehyde reductase activity. The medium
chain dehydrogenases/reductase (MDR)/zinc-dependent
alcohol dehydrogenase-like family, which contains the
zinc-dependent alcohol dehydrogenase (ADH-Zn) and
related proteins, is a diverse group of proteins related
to the first identified member, class I mammalian ADH.
MDRs display a broad range of activities and are
distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases
(ADHs) catalyze the NAD(P)(H)-dependent interconversion
of alcohols to aldehydes or ketones. Active site zinc
has a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 337
Score = 29.0 bits (66), Expect = 3.4
Identities = 18/44 (40%), Positives = 21/44 (47%), Gaps = 10/44 (22%)
Query: 144 GKSVGIV---GLGRIGTAIAKRVEAFGCP---ISYHSRSEKSDA 181
GK VG+V GLG + AK A G S S S+K DA
Sbjct: 170 GKRVGVVGIGGLGHLAVKFAK---ALGAEVTAFS-RSPSKKEDA 209
>gnl|CDD|236595 PRK09621, PRK09621, V-type ATP synthase subunit K; Provisional.
Length = 141
Score = 27.8 bits (62), Expect = 3.9
Identities = 15/55 (27%), Positives = 27/55 (49%), Gaps = 6/55 (10%)
Query: 212 IVNRKVIDA-LGP-SGILINIGRGAHIDEPELVSALLEGRLAGAGLDVYENEPEV 264
++N + D L SGI I I G + L+SA+++G+ + + Y E+
Sbjct: 65 LLNDAIKDGKLSALSGIAIGISVGIAL----LLSAIMQGKCCASAIQAYARSSEI 115
>gnl|CDD|216381 pfam01237, Oxysterol_BP, Oxysterol-binding protein.
Length = 335
Score = 28.7 bits (65), Expect = 4.0
Identities = 10/32 (31%), Positives = 13/32 (40%), Gaps = 1/32 (3%)
Query: 125 FVKSGKWK-NGHFELGSKFSGKSVGIVGLGRI 155
+S W G SKF GKS+ + G
Sbjct: 94 HAESKGWTLWGSSAPKSKFWGKSIEVKPEGHA 125
>gnl|CDD|223842 COG0771, MurD, UDP-N-acetylmuramoylalanine-D-glutamate ligase [Cell
envelope biogenesis, outer membrane].
Length = 448
Score = 28.8 bits (65), Expect = 4.0
Identities = 11/31 (35%), Positives = 17/31 (54%)
Query: 140 SKFSGKSVGIVGLGRIGTAIAKRVEAFGCPI 170
F GK V ++GLG+ G A A+ + G +
Sbjct: 3 EDFQGKKVLVLGLGKSGLAAARFLLKLGAEV 33
>gnl|CDD|202773 pfam03807, F420_oxidored, NADP oxidoreductase coenzyme
F420-dependent.
Length = 93
Score = 27.2 bits (61), Expect = 4.1
Identities = 17/93 (18%), Positives = 35/93 (37%), Gaps = 17/93 (18%)
Query: 147 VGIVGLGRIGTAIAKRVEAFGCPISY-HSRSEKSDANY---KYYTNII-----DLASNCQ 197
+GI+G G +G A+A+ + A G + +SR+ + A + +
Sbjct: 2 IGIIGAGNMGEALARGLAAAGHEVVIANSRNPEK-AAALAEELGVKATAVSNEEAVEEAD 60
Query: 198 ILIVAC------SLTEETHHIVNRK-VIDALGP 223
++ +A + E ++ K VI
Sbjct: 61 VVFLAVKPEDAPEVLAELADLLKGKLVISITNG 93
>gnl|CDD|137204 PRK09310, aroDE, bifunctional 3-dehydroquinate
dehydratase/shikimate dehydrogenase protein; Reviewed.
Length = 477
Score = 28.6 bits (64), Expect = 4.2
Identities = 22/82 (26%), Positives = 31/82 (37%), Gaps = 11/82 (13%)
Query: 143 SGKSVGIVGLGRIGTAIAKRVEAFGCPISYHSRSEKSDANYKYYTNIIDLASNCQILIVA 202
+ + V IVG G AIA + G + +R++ LAS CQ
Sbjct: 331 NNQHVAIVGAGGAAKAIATTLARAGAELLIFNRTKAHAE---------ALASRCQGKAFP 381
Query: 203 CSLTEETHHIVNRKVIDALGPS 224
E H I +I+ L PS
Sbjct: 382 LESLPELHRI--DIIINCLPPS 401
>gnl|CDD|130530 TIGR01463, mtaA_cmuA, methyltransferase, MtaA/CmuA family. This
subfamily is closely related to, yet is distinct from,
uroporphyrinogen decarboxylase (EC 4.1.1.37). It
includes two isozymes from Methanosarcina barkeri of
methylcobalamin--coenzyme M methyltransferase. It also
includes a chloromethane utilization protein, CmuA,
which transfers the methyl group of chloromethane to a
corrinoid protein.
Length = 340
Score = 28.3 bits (63), Expect = 5.1
Identities = 13/66 (19%), Positives = 22/66 (33%), Gaps = 4/66 (6%)
Query: 131 WKNGHF--ELGSKFSGKSVGIVGLG--RIGTAIAKRVEAFGCPISYHSRSEKSDANYKYY 186
W H E + + + G R + E GC + Y ++ S +
Sbjct: 42 WPEAHRDGEAMAHLAIAAYEKFGGEAVRPPFDLTTEAECVGCELDYGPYAQPSVTKHPTP 101
Query: 187 TNIIDL 192
TN+ D
Sbjct: 102 TNLADY 107
>gnl|CDD|217077 pfam02514, CobN-Mg_chel, CobN/Magnesium Chelatase. This family
contains a domain common to the cobN protein and to
magnesium protoporphyrin chelatase. CobN is implicated
in the conversion of hydrogenobyrinic acid a,c-diamide
to cobyrinic acid. Magnesium protoporphyrin chelatase is
involved in chlorophyll biosynthesis.
Length = 1079
Score = 28.7 bits (65), Expect = 5.5
Identities = 14/39 (35%), Positives = 18/39 (46%), Gaps = 3/39 (7%)
Query: 229 NIGRGAHIDEPELVSALLEGRLAGAGLDVYENEPEVPEQ 267
NIG A +D P + LL L G DV PE ++
Sbjct: 265 NIGTAAGLDVPASLVNLLR-ALKAEGYDV--GLPESGDE 300
>gnl|CDD|234950 PRK01390, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
synthetase; Provisional.
Length = 460
Score = 28.3 bits (64), Expect = 6.7
Identities = 12/26 (46%), Positives = 17/26 (65%)
Query: 142 FSGKSVGIVGLGRIGTAIAKRVEAFG 167
F+GK+V + GLG G A A+ + A G
Sbjct: 7 FAGKTVAVFGLGGSGLATARALVAGG 32
>gnl|CDD|237612 PRK14108, PRK14108, bifunctional glutamine-synthetase
adenylyltransferase/deadenyltransferase; Provisional.
Length = 986
Score = 28.0 bits (63), Expect = 7.4
Identities = 15/52 (28%), Positives = 22/52 (42%), Gaps = 12/52 (23%)
Query: 105 ADLAVGLVLAVLRRVCEFDEFVKSGKWKNGHFELGSKFSGKSVGIVGLGRIG 156
ADLA ++ A L V E EF + G V I+ +G++G
Sbjct: 672 ADLAELIIGAALDAVEE--EFA----------RAHGRIKGGRVAILAMGKLG 711
>gnl|CDD|215300 PLN02545, PLN02545, 3-hydroxybutyryl-CoA dehydrogenase.
Length = 295
Score = 27.8 bits (62), Expect = 7.6
Identities = 11/26 (42%), Positives = 17/26 (65%)
Query: 145 KSVGIVGLGRIGTAIAKRVEAFGCPI 170
K VG+VG G++G+ IA+ A G +
Sbjct: 5 KKVGVVGAGQMGSGIAQLAAAAGMDV 30
>gnl|CDD|235959 PRK07198, PRK07198, hypothetical protein; Validated.
Length = 418
Score = 27.7 bits (62), Expect = 8.3
Identities = 11/27 (40%), Positives = 15/27 (55%)
Query: 234 AHIDEPELVSALLEGRLAGAGLDVYEN 260
AHI+ PE+ A+ GRL G + N
Sbjct: 135 AHINLPEIHDAIAAGRLKPDGKILLAN 161
>gnl|CDD|184511 PRK14106, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
synthetase; Provisional.
Length = 450
Score = 27.6 bits (62), Expect = 8.7
Identities = 11/26 (42%), Positives = 15/26 (57%)
Query: 142 FSGKSVGIVGLGRIGTAIAKRVEAFG 167
GK V +VG G G A+AK ++ G
Sbjct: 3 LKGKKVLVVGAGVSGLALAKFLKKLG 28
>gnl|CDD|238760 cd01483, E1_enzyme_family, Superfamily of activating enzymes (E1)
of the ubiquitin-like proteins. This family includes
classical ubiquitin-activating enzymes E1,
ubiquitin-like (ubl) activating enzymes and other
mechanistic homologes, like MoeB, Thif1 and others. The
common reaction mechanism catalyzed by MoeB, ThiF and
the E1 enzymes begins with a nucleophilic attack of the
C-terminal carboxylate of MoaD, ThiS and ubiquitin,
respectively, on the alpha-phosphate of an ATP molecule
bound at the active site of the activating enzymes,
leading to the formation of a high-energy acyladenylate
intermediate and subsequently to the formation of a
thiocarboxylate at the C termini of MoaD and ThiS.
Length = 143
Score = 26.8 bits (60), Expect = 8.7
Identities = 8/15 (53%), Positives = 11/15 (73%)
Query: 147 VGIVGLGRIGTAIAK 161
V +VGLG +G+ IA
Sbjct: 2 VLLVGLGGLGSEIAL 16
>gnl|CDD|222736 pfam14399, BtrH, A predicted NlpC/p60-like peptidase. Members of
this family are often found in the gene neighborhood, or
fused to, non-ribosomal peptide synthetases. They are
predicted to function as trans-peptidases in peptide
metabolite biosynthesis.
Length = 329
Score = 27.7 bits (62), Expect = 8.9
Identities = 11/37 (29%), Positives = 15/37 (40%), Gaps = 2/37 (5%)
Query: 225 GILINIGRGAHIDE--PELVSALLEGRLAGAGLDVYE 259
GI + + +E EL L GR LD+Y
Sbjct: 75 GIKLKERETSSPEEAWEELKELLDAGRPVILQLDMYY 111
>gnl|CDD|182479 PRK10463, PRK10463, hydrogenase nickel incorporation protein HypB;
Provisional.
Length = 290
Score = 27.5 bits (61), Expect = 9.0
Identities = 14/43 (32%), Positives = 19/43 (44%)
Query: 218 IDALGPSGILINIGRGAHIDEPELVSALLEGRLAGAGLDVYEN 260
I A G I +N G+G H+D + A L G+ EN
Sbjct: 150 IRATGTPAIQVNTGKGCHLDAQMIADAAPRLPLDDNGILFIEN 192
>gnl|CDD|180970 PRK07417, PRK07417, arogenate dehydrogenase; Reviewed.
Length = 279
Score = 27.5 bits (62), Expect = 9.3
Identities = 24/94 (25%), Positives = 45/94 (47%), Gaps = 14/94 (14%)
Query: 147 VGIVGLGRIGTAIAKRVEAFGCPISYHSRSEKSDANYKYYTNIIDLAS-------NCQIL 199
+GIVGLG IG ++ + + G + SR E + ++D AS +C ++
Sbjct: 3 IGIVGLGLIGGSLGLDLRSLGHTVYGVSRRESTCERAI-ERGLVDEASTDLSLLKDCDLV 61
Query: 200 IVACSLTEETHHIVN--RKVIDALGPSGILINIG 231
I+A + ++ ++I AL P I+ ++G
Sbjct: 62 ILALPI----GLLLPPSEQLIPALPPEAIVTDVG 91
>gnl|CDD|237771 PRK14619, PRK14619, NAD(P)H-dependent glycerol-3-phosphate
dehydrogenase; Provisional.
Length = 308
Score = 27.3 bits (61), Expect = 9.8
Identities = 10/32 (31%), Positives = 16/32 (50%)
Query: 145 KSVGIVGLGRIGTAIAKRVEAFGCPISYHSRS 176
K++ I+G G G+ +A A G + SR
Sbjct: 5 KTIAILGAGAWGSTLAGLASANGHRVRVWSRR 36
>gnl|CDD|200493 cd11356, AmyAc_Sucrose_phosphorylase-like_1, Alpha amylase
catalytic domain found in sucrose phosphorylase-like
proteins (also called sucrose glucosyltransferase,
disaccharide glucosyltransferase, and sucrose-phosphate
alpha-D glucosyltransferase). Sucrose phosphorylase is
a bacterial enzyme that catalyzes the phosphorolysis of
sucrose to yield glucose-1-phosphate and fructose. These
enzymes do not have the conserved calcium ion present in
other alpha amylase family enzymes. The Alpha-amylase
family comprises the largest family of glycoside
hydrolases (GH), with the majority of enzymes acting on
starch, glycogen, and related oligo- and
polysaccharides. These proteins catalyze the
transformation of alpha-1,4 and alpha-1,6 glucosidic
linkages with retention of the anomeric center. The
protein is described as having 3 domains: A, B, C. A is
a (beta/alpha) 8-barrel; B is a loop between the beta 3
strand and alpha 3 helix of A; C is the C-terminal
extension characterized by a Greek key. The majority of
the enzymes have an active site cleft found between
domains A and B where a triad of catalytic residues
(Asp, Glu and Asp) performs catalysis. Other members of
this family have lost the catalytic activity as in the
case of the human 4F2hc or only have 2 residues that
serve as the catalytic nucleophile and the acid/base,
such as Thermus A4 beta-galactosidase with 2 Glu
residues (GH42) and human alpha-galactosidase with 2 Asp
residues (GH31). The family members are quite extensive
and include: alpha amylase, maltosyltransferase,
cyclodextrin glycotransferase, maltogenic amylase,
neopullulanase, isoamylase, 1,4-alpha-D-glucan
maltotetrahydrolase, 4-alpha-glucotransferase,
oligo-1,6-glucosidase, amylosucrase, sucrose
phosphorylase, and amylomaltase.
Length = 458
Score = 27.5 bits (62), Expect = 9.8
Identities = 10/24 (41%), Positives = 15/24 (62%), Gaps = 2/24 (8%)
Query: 207 EETHHIVN--RKVIDALGPSGILI 228
+TH IV R ++DA+ P +LI
Sbjct: 202 PQTHEIVKLLRALLDAVAPGVVLI 225
>gnl|CDD|183719 PRK12747, PRK12747, short chain dehydrogenase; Provisional.
Length = 252
Score = 27.3 bits (60), Expect = 9.9
Identities = 32/105 (30%), Positives = 47/105 (44%), Gaps = 8/105 (7%)
Query: 142 FSGKSVGIVGLGR-IGTAIAKRVEAFGCPISYHSRSEKSDANYKYYTNIIDLASNCQILI 200
GK + G R IG AIAKR+ G ++ H + K +A Y + S I
Sbjct: 2 LKGKVALVTGASRGIGRAIAKRLANDGALVAIHYGNRKEEAEETVYEIQSNGGSAFSIGA 61
Query: 201 VACSL--TEETHHIVNRKVIDALGPS--GILIN---IGRGAHIDE 238
SL E + ++ ++ + G + ILIN IG GA I+E
Sbjct: 62 NLESLHGVEALYSSLDNELQNRTGSTKFDILINNAGIGPGAFIEE 106
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
0.318 0.136 0.390
Gapped
Lambda K H
0.267 0.0694 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 16,126,721
Number of extensions: 1574302
Number of successful extensions: 1794
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1620
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 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 59 (26.6 bits)