RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3240
(274 letters)
>gnl|CDD|240626 cd05301, GDH, D-glycerate dehydrogenase/hydroxypyruvate reductase
(GDH). D-glycerate dehydrogenase (GDH, also known as
hydroxypyruvate reductase, HPR) catalyzes the reversible
reaction of (R)-glycerate + NAD+ to hydroxypyruvate +
NADH + H+. In humans, HPR deficiency causes primary
hyperoxaluria type 2, characterized by over-excretion of
L-glycerate and oxalate in the urine, possibly due to an
imbalance in competition with L-lactate dehydrogenase,
another formate dehydrogenase (FDH)-like enzyme. GDH,
like FDH and other members of the D-specific hydroxyacid
dehydrogenase family that also includes L-alanine
dehydrogenase and S-adenosylhomocysteine hydrolase,
typically have a characteristic arrangement of 2 similar
subdomains of the alpha/beta Rossmann-fold NAD+ binding
form, despite often low sequence identity. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 309
Score = 174 bits (445), Expect = 3e-53
Identities = 59/122 (48%), Positives = 84/122 (68%), Gaps = 2/122 (1%)
Query: 24 RGEWKSWAPNFMCGPALQNSTVGIVGCGRIGLSVLEKLIPYKVSKFLYTSRSKKPEADKR 83
GEWK W+P + G L T+GIVG GRIG +V + + + K LY +RS+KPEA++
Sbjct: 126 AGEWKGWSPTLLLGTDLHGKTLGIVGMGRIGQAVARRAKGFGM-KILYHNRSRKPEAEEE 184
Query: 84 -GAEHTNIDDLCKQSDFIIITSALTPDTHHLINRARLESMKPGAILINTSRGQLVDQEAL 142
GA + ++D+L +SDF+ + LTP+T HLIN RL MKP AILINT+RG +VD++AL
Sbjct: 185 LGARYVSLDELLAESDFVSLHCPLTPETRHLINAERLALMKPTAILINTARGGVVDEDAL 244
Query: 143 ID 144
++
Sbjct: 245 VE 246
Score = 113 bits (285), Expect = 1e-29
Identities = 36/64 (56%), Positives = 43/64 (67%)
Query: 202 DVLKAKKIRGAGLDVMYPEPLPLDSPLLQLDNCVILPHIGSAQIETRQEMARITAQNIIN 261
+ LK+ KI GAGLDV PEPLP D PLL L N V+LPHIGSA +ETR MA + A N++
Sbjct: 246 EALKSGKIAGAGLDVFEPEPLPADHPLLTLPNVVLLPHIGSATVETRTAMAELAADNLLA 305
Query: 262 TFHN 265
Sbjct: 306 VLAG 309
>gnl|CDD|223980 COG1052, LdhA, Lactate dehydrogenase and related dehydrogenases
[Energy production and conversion / Coenzyme metabolism
/ General function prediction only].
Length = 324
Score = 172 bits (438), Expect = 4e-52
Identities = 83/254 (32%), Positives = 113/254 (44%), Gaps = 64/254 (25%)
Query: 24 RGEWKSWA-PNFMCGPALQNSTVGIVGCGRIGLSVLEKLIPYKVSKFLYTSRSKKPEADK 82
G W P+ + G L+ T+GI+G GRIG +V +L + + K LY RS PEA+K
Sbjct: 127 EGNWSLSGGPDPLLGFDLRGKTLGIIGLGRIGQAVARRLKGFGM-KVLYYDRSPNPEAEK 185
Query: 83 RG-AEHTNIDDLCKQSDFIIITSALTPDTHHLINRARLESMKPGAILINTSRGQLVDQEA 141
A + ++D+L +SD I + LTP+T HLIN L MKPGAIL+NT+RG LVD++A
Sbjct: 186 ELGARYVDLDELLAESDIISLHCPLTPETRHLINAEELAKMKPGAILVNTARGGLVDEQA 245
Query: 142 LIDFIADIRVISISMVTNEKHLHRVFTLGDSFHKGHVSAFIFIHMIMGDTVGIYFIFSAS 201
LID + G ++
Sbjct: 246 LIDALKS---------------------------GKIAGA------------------GL 260
Query: 202 DVLKAKKIRGAGLDVMYPEPLPLDSPLLQLDNC---VILPHIGSAQIETRQEMARITAQN 258
D V EP D PLL+LDN V+ PHI SA E R+ MA + +N
Sbjct: 261 D-------------VFENEPALFDHPLLRLDNFPNVVLTPHIASATEEARKAMAELALEN 307
Query: 259 IINTFHNKPMIYEV 272
+ F EV
Sbjct: 308 LEAFFDGGVPPNEV 321
>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 = 166 bits (424), Expect = 8e-52
Identities = 72/212 (33%), Positives = 98/212 (46%), Gaps = 59/212 (27%)
Query: 30 WAPNFMCGPALQNSTVGIVGCGRIGLSVLEKLIPYKVSKFLYTSRSKKPEADKRGAEHTN 89
W P+ + G L TVGI+G GRIG +V +L + + K + R K EA+ GA + +
Sbjct: 23 WRPDALLGRELSGKTVGIIGLGRIGRAVARRLKAFGM-KVIAYDRYPKAEAEALGARYVS 81
Query: 90 IDDLCKQSDFIIITSALTPDTHHLINRARLESMKPGAILINTSRGQLVDQEALIDFIADI 149
+D+L +SD + + LTP+T HLIN RL MKPGAILINT+RG LVD++ALI +
Sbjct: 82 LDELLAESDVVSLHLPLTPETRHLINAERLALMKPGAILINTARGGLVDEDALIAALKS- 140
Query: 150 RVISISMVTNEKHLHRVFTLGDSFHKGHVSAFIFIHMIMGDTVGIYFIFSASDVLKAKKI 209
G ++
Sbjct: 141 --------------------------GRIAGA---------------------------- 146
Query: 210 RGAGLDVMYPEPLPLDSPLLQLDNCVILPHIG 241
LDV PEPLP D PLL+L N ++ PHI
Sbjct: 147 ---ALDVFEPEPLPPDHPLLELPNVILTPHIA 175
>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 = 165 bits (421), Expect = 9e-50
Identities = 79/246 (32%), Positives = 106/246 (43%), Gaps = 63/246 (25%)
Query: 24 RGEWKSWAPNFMCGPALQNSTVGIVGCGRIGLSVLEKLIPYKVSKFLYTSRSKKPEA--D 81
G W L TVGIVG G IG +V +L + V + +Y R + PEA
Sbjct: 126 AGRWGRPE--GRPSRELSGKTVGIVGLGNIGRAVARRLRGFGV-EVIYYDRFRDPEAEEK 182
Query: 82 KRGAEHTNIDDLCKQSDFIIITSALTPDTHHLINRARLESMKPGAILINTSRGQLVDQEA 141
G + +D+L +SD + + LTP+T HLI L +MKPGAILINT+RG
Sbjct: 183 DLGVRYVELDELLAESDVVSLHVPLTPETRHLIGAEELAAMKPGAILINTARG------G 236
Query: 142 LIDFIADIRVISISMVTNEKHLHRVFTLGDSFHKGHVSAFIFIHMIMGDTVGIYFIFSAS 201
L+D E+ L
Sbjct: 237 LVD---------------EEALLAA----------------------------------- 246
Query: 202 DVLKAKKIRGAGLDVMYPEPLPLDSPLLQLDNCVILPHIGSAQIETRQEMARITAQNIIN 261
L++ + GAGLDV + EPLP D PLL+LDN ++ PHI E+ Q MA I A+NI
Sbjct: 247 --LRSGHLAGAGLDVFWQEPLPPDDPLLRLDNVILTPHIAGVTDESYQRMAAIVAENIAR 304
Query: 262 TFHNKP 267
+P
Sbjct: 305 LLRGEP 310
>gnl|CDD|223189 COG0111, SerA, Phosphoglycerate dehydrogenase and related
dehydrogenases [Amino acid transport and metabolism].
Length = 324
Score = 154 bits (390), Expect = 5e-45
Identities = 76/251 (30%), Positives = 109/251 (43%), Gaps = 62/251 (24%)
Query: 24 RGEWKSWAPNFMCGPALQNSTVGIVGCGRIGLSVLEKLIPYKVSKFLYTSRSKKPEADKR 83
RGEW F G L TVGI+G GRIG +V ++L + + Y S + A
Sbjct: 127 RGEWDR--KAFR-GTELAGKTVGIIGLGRIGRAVAKRLKAFGMKVIGYDPYSPRERAGVD 183
Query: 84 GAEH-TNIDDLCKQSDFIIITSALTPDTHHLINRARLESMKPGAILINTSRGQLVDQEAL 142
G ++D+L ++D + + LTP+T LIN L MKPGAILIN +RG +VD++AL
Sbjct: 184 GVVGVDSLDELLAEADILTLHLPLTPETRGLINAEELAKMKPGAILINAARGGVVDEDAL 243
Query: 143 IDFIADIRVISISMVTNEKHLHRVFTLGDSFHKGHVSAFIFIHMIMGDTVGIYFIFSASD 202
+ + G ++
Sbjct: 244 LAALDS---------------------------GKIA----------------------- 253
Query: 203 VLKAKKIRGAGLDVMYPEPLPLDSPLLQLDNCVILPHIGSAQIETRQEMARITAQNIINT 262
GA LDV EPLP DSPL L N ++ PHIG + E ++ +A I A+NI+
Sbjct: 254 --------GAALDVFEEEPLPADSPLWDLPNVILTPHIGGSTDEAQERVAEIVAENIVRY 305
Query: 263 FHNKPMIYEVP 273
P++ P
Sbjct: 306 LAGGPVVNNAP 316
>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 = 145 bits (368), Expect = 8e-42
Identities = 66/237 (27%), Positives = 98/237 (41%), Gaps = 59/237 (24%)
Query: 24 RGEWKSWAPNF-MCGPALQNSTVGIVGCGRIGLSVLEKLIPYKVSKFLYTSRSKKPEADK 82
GEW+ N+ GP L+ TVGIVG G IG V ++L + +Y + +
Sbjct: 128 DGEWRKDYYNYDGYGPELRGKTVGIVGFGAIGRRVAKRLKAFGAEVLVYDPYVDPEKIEA 187
Query: 83 RGAEHTNIDDLCKQSDFIIITSALTPDTHHLINRARLESMKPGAILINTSRGQLVDQEAL 142
G + ++++L K+SD + + + LTP+T +I MKP A INT+R LVD++AL
Sbjct: 188 DGVKKVSLEELLKRSDVVSLHARLTPETRGMIGAEEFALMKPTAYFINTARAGLVDEDAL 247
Query: 143 IDFIADIRVISISMVTNEKHLHRVFTLGDSFHKGHVSAFIFIHMIMGDTVGIYFIFSASD 202
I+ + + I G
Sbjct: 248 IEALEE------------------------------------GKIGG------------- 258
Query: 203 VLKAKKIRGAGLDVMYPEPLPLDSPLLQLDNCVILPHIGSAQIETRQEMARITAQNI 259
A LDV EPLP D PLL+LDN + PHI A + + I A+ +
Sbjct: 259 ---------AALDVFPEEPLPADHPLLKLDNVTLTPHIAGATRDVAERSPEIIAEEL 306
>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 = 144 bits (367), Expect = 1e-41
Identities = 61/241 (25%), Positives = 93/241 (38%), Gaps = 61/241 (25%)
Query: 29 SWAPNFMCGPA-LQNSTVGIVGCGRIGLSVLEKLIPYKVSKFLYTSRSKKPEADKR-GAE 86
W L+ T+G+VG GRIG +V ++ + + + G
Sbjct: 128 GWDWTVGGPIRRLRGLTLGLVGFGRIGRAVAKRAKAFGF-RVIAYDPYVPDGVAALGGVR 186
Query: 87 HTNIDDLCKQSDFIIITSALTPDTHHLINRARLESMKPGAILINTSRGQLVDQEALIDFI 146
++D+L +SD + + LTP+T HLI+ L MKPGA L+NT+RG LVD+ AL +
Sbjct: 187 VVSLDELLARSDVVSLHCPLTPETRHLIDAEALALMKPGAFLVNTARGGLVDEAALARAL 246
Query: 147 ADIRVISISMVTNEKHLHRVFTLGDSFHKGHVSAFIFIHMIMGDTVGIYFIFSASDVLKA 206
G ++
Sbjct: 247 KS---------------------------GRIA--------------------------- 252
Query: 207 KKIRGAGLDVMYPEPLPLDSPLLQLDNCVILPHIGSAQIETRQEMARITAQNIINTFHNK 266
GA LDV+ EP P DSPLL N ++ PH E+ E+ R A+ ++ +
Sbjct: 253 ----GAALDVLEEEPPPADSPLLSAPNVILTPHAAWYSEESLAELRRKAAEEVVRVLRGE 308
Query: 267 P 267
P
Sbjct: 309 P 309
>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 = 144 bits (366), Expect = 2e-41
Identities = 64/244 (26%), Positives = 109/244 (44%), Gaps = 67/244 (27%)
Query: 24 RGEWKSWAPNFMCGPA--LQNSTVGIVGCGRIGLSVLEKLIPYKVSKFLYTSRSKKPEAD 81
G+W+ + A + T+GI+G G IG ++ K + + K +Y +RS+ PE
Sbjct: 137 AGKWRGFLD---LTLAHDPRGKTLGILGLGGIGKAIARKAAAFGM-KIIYHNRSRLPEEL 192
Query: 82 KRG--AEHTNIDDLCKQSDFIIITSALTPDTHHLINRARLESMKPGAILINTSRGQLVDQ 139
++ + ++D+L QSD + + LT T HLIN+ MK G I++NT+RG ++D+
Sbjct: 193 EKALATYYVSLDELLAQSDVVSLNCPLTAATRHLINKKEFAKMKDGVIIVNTARGAVIDE 252
Query: 140 EALIDFIADIRVISISMVTNEKHLHRVFTLGDSFHKGHVSAFIFIHMIMGDTVGIYFIFS 199
+AL+D L +S G V++
Sbjct: 253 DALVD-----------------AL-------ES---GKVAS------------------- 266
Query: 200 ASDVLKAKKIRGAGLDVMYPEPLPLDSPLLQLDNCVILPHIGSAQIETRQEMARITAQNI 259
AGLDV EP + LL++ N +LPH+G+ +ET+++M + +NI
Sbjct: 267 ------------AGLDVFENEPEV-NPGLLKMPNVTLLPHMGTLTVETQEKMEELVLENI 313
Query: 260 INTF 263
Sbjct: 314 EAFL 317
>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 = 143 bits (362), Expect = 8e-41
Identities = 69/250 (27%), Positives = 101/250 (40%), Gaps = 60/250 (24%)
Query: 23 CRGEWKSWAPNFMCGPALQNSTVGIVGCGRIGLSVLEKLIPYKVSKFLYTSRSKKPEADK 82
G W G L TVGIVG GRIG +V+E L P+ + +Y EA
Sbjct: 132 RAGRDWGWPTRRG-GRGLYGRTVGIVGFGRIGRAVVELLRPFGLRVLVYDPYLPAAEAAA 190
Query: 83 RGAEHTNIDDLCKQSDFIIITSALTPDTHHLINRARLESMKPGAILINTSRGQLVDQEAL 142
G E ++D+L +SD + + + LTP+T +I+ L M+ GA INT+RG LVD+ AL
Sbjct: 191 LGVELVSLDELLARSDVVSLHAPLTPETRGMIDARLLALMRDGATFINTARGALVDEAAL 250
Query: 143 IDFIADIRVISISMVTNEKHLHRVFTLGDSFHKGHVSAFIFIHMIMGDTVGIYFIFSASD 202
+ + G + A A D
Sbjct: 251 LAELR---------------------------SGRLRA-------------------ALD 264
Query: 203 VLKAKKIRGAGLDVMYPEPLPLDSPLLQLDNCVILPHIGSAQIETRQEMARITAQNIINT 262
V PEPLP DSPL L N ++ PHI + + R+ + +
Sbjct: 265 VT-------------DPEPLPPDSPLRTLPNVLLTPHIAGSTGDERRRLGDYALDELERF 311
Query: 263 FHNKPMIYEV 272
+P+++EV
Sbjct: 312 LAGEPLLHEV 321
>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 = 135 bits (342), Expect = 5e-38
Identities = 69/240 (28%), Positives = 100/240 (41%), Gaps = 54/240 (22%)
Query: 24 RGEWKSWAPNFMCGPALQNSTVGIVGCGRIGLSVLEKLIPYKVSKFLYTSRSKKPEADKR 83
G++ W P F G L TVGI+G G +G ++ +L + LY +A+++
Sbjct: 127 SGKFGGWRPKFY-GTGLDGKTVGILGMGALGRAIARRLSGFGA-TLLYYDPHPLDQAEEQ 184
Query: 84 --GAEHTNIDDLCKQSDFIIITSALTPDTHHLINRARLESMKPGAILINTSRGQLVDQEA 141
+D+L + SDF+++ LTPDT HLIN L MKPGA+L+N RG +VD+ A
Sbjct: 185 ALNLRRVELDELLESSDFLVLALPLTPDTLHLINAEALAKMKPGALLVNPCRGSVVDEAA 244
Query: 142 LIDFIADIRVISISMVTNEKHLHRVFTLGDSFHKGHVSAFIFIHMIMGDTVGIYFIFSAS 201
+ + + HL G Y A+
Sbjct: 245 VAEAL------------KSGHL-----------------------------GGY----AA 259
Query: 202 DVLKAKKIRGAGLDVMYPEPLPLDSPLLQLDNCVILPHIGSAQIETRQEMARITAQNIIN 261
DV + + P+ L L Q D V PHIGSA E R E+ A NI+
Sbjct: 260 DVFEMEDWARPDRPRSIPQEL-----LDQHDRTVFTPHIGSAVDEVRLEIELEAALNILQ 314
>gnl|CDD|240650 cd12173, PGDH_4, Phosphoglycerate dehydrogenases, NAD-binding and
catalytic domains. Phosphoglycerate dehydrogenases
(PGDHs) catalyze the initial step in the biosynthesis of
L-serine from D-3-phosphoglycerate. PGDHs come in 3
distinct structural forms, with this first group being
related to 2-hydroxy acid dehydrogenases, sharing
structural similarity to formate and glycerate
dehydrogenases. PGDH in E. coli and Mycobacterium
tuberculosis form tetramers, with subunits containing a
Rossmann-fold NAD binding domain. Formate/glycerate and
related dehydrogenases of the D-specific 2-hydroxyacid
dehydrogenase superfamily include groups such as formate
dehydrogenase, glycerate dehydrogenase, L-alanine
dehydrogenase, and S-adenosylhomocysteine hydrolase.
Despite often low sequence identity, these proteins
typically have a characteristic arrangement of 2 similar
subdomains of the alpha/beta Rossmann fold NAD+ binding
form. The NAD+ binding domain is inserted within the
linear sequence of the mostly N-terminal catalytic
domain, which has a similar domain structure to the
internal NAD binding domain. Structurally, these domains
are connected by extended alpha helices and create a
cleft in which NAD is bound, primarily to the C-terminal
portion of the 2nd (internal) domain. Some related
proteins have similar structural subdomain but with a
tandem arrangement of the catalytic and NAD-binding
subdomains in the linear sequence.
Length = 304
Score = 134 bits (339), Expect = 1e-37
Identities = 73/246 (29%), Positives = 106/246 (43%), Gaps = 67/246 (27%)
Query: 24 RGEWKSWAPNFMCGPALQNSTVGIVGCGRIGLSVLEKLIPY--KVSKFLYTSRSKKPE-A 80
G+W FM G L+ T+GIVG GRIG V + + KV L E A
Sbjct: 123 AGKWDRKK--FM-GVELRGKTLGIVGLGRIGREVARRARAFGMKV---LAYDPYISAERA 176
Query: 81 DKRGAEHTNIDDLCKQSDFIIITSALTPDTHHLINRARLESMKPGAILINTSRGQLVDQE 140
G E ++D+L ++DFI + + LTP+T LIN L MKPGAILINT+RG +VD+
Sbjct: 177 AAGGVELVSLDELLAEADFISLHTPLTPETRGLINAEELAKMKPGAILINTARGGIVDEA 236
Query: 141 ALIDFIADIRVISISMVTNEKHLHRVFTLGDSFHKGHVSAFIFIHMIMGDTVGIYFIFSA 200
AL D + G ++ +A
Sbjct: 237 ALADALKS---------------------------GKIAG------------------AA 251
Query: 201 SDVLKAKKIRGAGLDVMYPEPLPLDSPLLQLDNCVILPHIGSAQIETRQEMARITAQNII 260
DV + EP P DSPLL L N ++ PH+G++ E ++ +A A+ ++
Sbjct: 252 LDVFE-------------QEPPPADSPLLGLPNVILTPHLGASTEEAQERVAVDAAEQVL 298
Query: 261 NTFHNK 266
+
Sbjct: 299 AVLAGE 304
>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 = 131 bits (331), Expect = 2e-36
Identities = 72/223 (32%), Positives = 95/223 (42%), Gaps = 67/223 (30%)
Query: 40 LQNSTVGIVGCGRIGLSV--LEKLIPYKVSKFLYTSRSKKPEADKRGAEHTNIDDLCKQS 97
L T+GI+G G IG +V + + KV L+ R P + ++D+L QS
Sbjct: 145 LAGKTLGIIGYGNIGQAVARIARAFGMKV---LFAERKGAPP---LREGYVSLDELLAQS 198
Query: 98 DFIIITSALTPDTHHLINRARLESMKPGAILINTSRGQLVDQEALIDFIADIRVISISMV 157
D I + LTP+T +LIN L MKPGAILINT+RG L+D
Sbjct: 199 DVISLHCPLTPETRNLINAEELAKMKPGAILINTARG------GLVD------------- 239
Query: 158 TNEKHLHRVFTLGDSFHKGHVSAFIFIHMIMGDTVGIYFIFSASDVLKAKKIRGAGLDVM 217
E+ L +D L + KI GAGLDV+
Sbjct: 240 --EQAL-------------------------------------ADALNSGKIAGAGLDVL 260
Query: 218 YPEPLPLDSPLLQ-LDNCVILPHIGSAQIETRQEMARITAQNI 259
EP D+PLL+ N +I PHI A E RQ + I NI
Sbjct: 261 SQEPPRADNPLLKAAPNLIITPHIAWASREARQRLMDILVDNI 303
>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 = 129 bits (327), Expect = 7e-36
Identities = 52/116 (44%), Positives = 74/116 (63%), Gaps = 2/116 (1%)
Query: 30 WAPNFMCGPALQNSTVGIVGCGRIGLSVLEKLIPYKVSKFLYTSRSKKPEADKR-GAEHT 88
W G L+ TVGIVG GRIG V ++L + + K LY R++KPE ++ G
Sbjct: 128 WLWAGFPGYELEGKTVGIVGLGRIGQRVAKRLQAFGM-KVLYYDRTRKPEPEEDLGFRVV 186
Query: 89 NIDDLCKQSDFIIITSALTPDTHHLINRARLESMKPGAILINTSRGQLVDQEALID 144
++D+L QSD +++ LTP+T HLIN L MKPGA+L+NT+RG LVD++AL+
Sbjct: 187 SLDELLAQSDVVVLHLPLTPETRHLINEEELALMKPGAVLVNTARGGLVDEDALLR 242
Score = 83.8 bits (208), Expect = 8e-19
Identities = 29/57 (50%), Positives = 36/57 (63%)
Query: 204 LKAKKIRGAGLDVMYPEPLPLDSPLLQLDNCVILPHIGSAQIETRQEMARITAQNII 260
LK+ KI GA LDV PEPLP D PLL+L N ++ PHI E R+ MA I +N+
Sbjct: 244 LKSGKIAGAALDVFEPEPLPADHPLLELPNVILTPHIAGYTEEARERMAEIAVENLE 300
>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 = 128 bits (324), Expect = 2e-35
Identities = 52/121 (42%), Positives = 71/121 (58%), Gaps = 5/121 (4%)
Query: 24 RGEWKSWAPNFMCGPALQNSTVGIVGCGRIGLSVLEKLIPYKVSKFLYTSRSKKPEADKR 83
G W + G L T+GI+G GRIG +V +L + + Y + A +
Sbjct: 129 AGGW-----DRPVGTELYGKTLGIIGLGRIGKAVARRLSGFGMKVLAYDPYPDEEFAKEH 183
Query: 84 GAEHTNIDDLCKQSDFIIITSALTPDTHHLINRARLESMKPGAILINTSRGQLVDQEALI 143
G E ++++L K+SDFI + LTP+T HLIN A L MKPGAILINT+RG LVD+EAL
Sbjct: 184 GVEFVSLEELLKESDFISLHLPLTPETRHLINAAELALMKPGAILINTARGGLVDEEALY 243
Query: 144 D 144
+
Sbjct: 244 E 244
Score = 81.8 bits (203), Expect = 4e-18
Identities = 28/62 (45%), Positives = 39/62 (62%)
Query: 202 DVLKAKKIRGAGLDVMYPEPLPLDSPLLQLDNCVILPHIGSAQIETRQEMARITAQNIIN 261
+ LK+ +I GA LDV EP P DSPLL+L N ++ PHIG++ E M + AQN+I+
Sbjct: 244 EALKSGRIAGAALDVFEEEPPPADSPLLELPNVILTPHIGASTKEAVLRMGTMAAQNVID 303
Query: 262 TF 263
Sbjct: 304 VL 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 = 127 bits (321), Expect = 7e-35
Identities = 71/265 (26%), Positives = 109/265 (41%), Gaps = 63/265 (23%)
Query: 11 IDVIKYVSTPVSC--RGEWKSWAPNFMCGPALQNSTVGIVGCGRIGLSVLEKLIPYKVSK 68
+ V++ ++ G+W A NF+ G L TVGI+G G IG V E L +K
Sbjct: 116 LTVLRKINQASEAVKEGKWTERA-NFV-GHELSGKTVGIIGYGNIGSRVAEILKEGFNAK 173
Query: 69 FLYTSRSKKPEA-DKRGAEHTNIDDLCKQSDFIIITSALTPDTHHLINRARLESMKPGAI 127
L E K+GA+ ++++L +SD I + + LT +T+H+IN MK G I
Sbjct: 174 VLAYDPYVSEEVIKKKGAKPVSLEELLAESDIISLHAPLTEETYHMINEKAFSKMKKGVI 233
Query: 128 LINTSRGQLVDQEALIDFIADIRVISISMVTNEKHLHRVFTLGDSFHKGHVSAFIFIHMI 187
L+NT+RG+L+D+EALI+ + G ++
Sbjct: 234 LVNTARGELIDEEALIEALK---------------------------SGKIAGA------ 260
Query: 188 MGDTVGIYFIFSASDVLKAKKIRGAGLDVMYPEPLPLDSPLLQLDNCVILPHIGSAQIET 247
DVL+ EP+ D PLL +N VI PHIG+ E+
Sbjct: 261 ------------GLDVLEE-------------EPIKADHPLLHYENVVITPHIGAYTYES 295
Query: 248 RQEMARITAQNIINTFHNKPMIYEV 272
M +I + K +
Sbjct: 296 LYGMGEKVVDDIEDFLAGKEPKGIL 320
>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 = 123 bits (311), Expect = 2e-33
Identities = 53/127 (41%), Positives = 80/127 (62%), Gaps = 3/127 (2%)
Query: 24 RGEWKSWAPNFMCGPALQNSTVGIVGCGRIGLSVLEKLIPYKVSKFLYTSRSKKPEADKR 83
RG + WAP F G L T+GI+G GRIG +V + + + K LY +R + E ++
Sbjct: 126 RGGFLGWAPLFFLGHELAGKTLGIIGMGRIGQAVARRAKAFGM-KILYYNRHRLSEETEK 184
Query: 84 --GAEHTNIDDLCKQSDFIIITSALTPDTHHLINRARLESMKPGAILINTSRGQLVDQEA 141
GA + ++D+L K+SDF+ + + TP+THHLI+ A + MKP A LIN +RG LVD++A
Sbjct: 185 ELGATYVDLDELLKESDFVSLHAPYTPETHHLIDAAAFKLMKPTAYLINAARGPLVDEKA 244
Query: 142 LIDFIAD 148
L+D +
Sbjct: 245 LVDALKT 251
Score = 77.3 bits (191), Expect = 2e-16
Identities = 30/71 (42%), Positives = 38/71 (53%), Gaps = 1/71 (1%)
Query: 202 DVLKAKKIRGAGLDVMYPEPLPLDSPLLQLDNCVILPHIGSAQIETRQEMARITAQNIIN 261
D LK +I GA LDV EP L +LDN ++ PHIG+A +E R MA+ A NII+
Sbjct: 247 DALKTGEIAGAALDVFEFEPEVSPE-LKKLDNVILTPHIGNATVEARDAMAKEAADNIIS 305
Query: 262 TFHNKPMIYEV 272
K V
Sbjct: 306 FLEGKRPKNIV 316
>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 = 122 bits (309), Expect = 3e-33
Identities = 63/236 (26%), Positives = 97/236 (41%), Gaps = 64/236 (27%)
Query: 24 RGEWKSWAPNFMCGPALQNSTVGIVGCGRIGLSVLEKLIPYKVSKFLYTSRSKKPEADKR 83
G W F + VGIVG GRIG ++ +L + + + Y R KP+ R
Sbjct: 125 AGRWP--KGAFPLTRKVSGKRVGIVGLGRIGRAIARRLEAFGM-EIAYHGRRPKPDVPYR 181
Query: 84 GAEHTNIDDLCKQSDFIIITSALTPDTHHLINRARLESMKPGAILINTSRGQLVDQEALI 143
+ ++ +L +SD +++ P T HL+N LE++ P +L+N +RG ++
Sbjct: 182 --YYASLLELAAESDVLVVACPGGPATRHLVNAEVLEALGPDGVLVNVARGS------VV 233
Query: 144 DFIADIRVISISMVTNEKHLHRVFTLGDSFHKGHVSAFIFIHMIMGDTVGIYFIFSASDV 203
D E L ++A
Sbjct: 234 D---------------EAAL--------------IAA----------------------- 241
Query: 204 LKAKKIRGAGLDVMYPEPLPLDSPLLQLDNCVILPHIGSAQIETRQEMARITAQNI 259
L+ +I GAGLDV EP + LL LDN V+ PHI SA +ETR+ M + N+
Sbjct: 242 LQEGRIAGAGLDVFENEPNV-PAALLDLDNVVLTPHIASATVETRRAMGDLVLANL 296
>gnl|CDD|183914 PRK13243, PRK13243, glyoxylate reductase; Reviewed.
Length = 333
Score = 123 bits (310), Expect = 3e-33
Identities = 73/241 (30%), Positives = 109/241 (45%), Gaps = 65/241 (26%)
Query: 25 GEWK----SWAPNFMCGPALQNSTVGIVGCGRIGLSVLEKLIPYKVSKFLYTSRSKKPEA 80
GEWK +W P G + T+GI+G GRIG +V + + + + LY SR++KPEA
Sbjct: 129 GEWKRRGVAWHPLMFLGYDVYGKTIGIIGFGRIGQAVARRAKGFGM-RILYYSRTRKPEA 187
Query: 81 DKR-GAEHTNIDDLCKQSDFIIITSALTPDTHHLINRARLESMKPGAILINTSRGQLVDQ 139
+K GAE+ +++L ++SDF+ + LT +T+H+I N R +L+
Sbjct: 188 EKELGAEYRPLEELLRESDFVSLHVPLTKETYHMI---------------NEERLKLMKP 232
Query: 140 EALIDFIADIRVISISMVTNEKHLHRVFTLGDSFHKGHVSAFIFIHMIMGDTVGIYFIFS 199
A++ A +V+ DT +
Sbjct: 233 TAILVNTARGKVV-------------------------------------DTKALV---- 251
Query: 200 ASDVLKAKKIRGAGLDVMYPEPLPLDSPLLQLDNCVILPHIGSAQIETRQEMARITAQNI 259
LK I GAGLDV EP + L L N V+ PHIGSA E R+ MA + A+N+
Sbjct: 252 --KALKEGWIAGAGLDVFEEEPYY-NEELFSLKNVVLAPHIGSATFEAREGMAELVAENL 308
Query: 260 I 260
I
Sbjct: 309 I 309
>gnl|CDD|237436 PRK13581, PRK13581, D-3-phosphoglycerate dehydrogenase;
Provisional.
Length = 526
Score = 124 bits (315), Expect = 1e-32
Identities = 70/251 (27%), Positives = 103/251 (41%), Gaps = 78/251 (31%)
Query: 25 GEW-KSWAPNFMCGPALQNSTVGIVGCGRIGLSV------LE-KLIPYKVSKFLYTSRSK 76
G+W + FM G L T+GI+G GRIG V K+I Y Y S +
Sbjct: 126 GKWERK---KFM-GVELYGKTLGIIGLGRIGSEVAKRAKAFGMKVIAYDP----YISPER 177
Query: 77 KPEADKRGAEHTNIDDLCKQSDFIIITSALTPDTHHLINRARLESMKPGAILINTSRGQL 136
A + G E ++D+L ++DFI + + LTP+T LI L MKPG +IN +RG +
Sbjct: 178 ---AAQLGVELVSLDELLARADFITLHTPLTPETRGLIGAEELAKMKPGVRIINCARGGI 234
Query: 137 VDQEALIDFIADIRVISISMVTNEKHLHRVFTLGDSFHKGHVSAFIFIHMIMGDTVGIYF 196
+D+ AL + + G V
Sbjct: 235 IDEAALAEALKS---------------------------GKV------------------ 249
Query: 197 IFSASDVLKAKKIRGAGLDVMYPEPLPLDSPLLQLDNCVILPHIGSAQIETRQEMARITA 256
GA LDV EP DSPL +L N V+ PH+G++ E ++ +A A
Sbjct: 250 -------------AGAALDVFEKEPPT-DSPLFELPNVVVTPHLGASTAEAQENVAIQVA 295
Query: 257 QNIINTFHNKP 267
+ +I+ P
Sbjct: 296 EQVIDALRGGP 306
>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 = 113 bits (286), Expect = 7e-30
Identities = 62/225 (27%), Positives = 96/225 (42%), Gaps = 61/225 (27%)
Query: 40 LQNSTVGIVGCGRIGLSVLEKLIPYKVSKFLYTSRSKKPE-ADKRGAEHTNIDDLCKQSD 98
L+ T+GI+G GRIG V + + + K E A + G + ++++L K SD
Sbjct: 137 LRGKTLGIIGFGRIGREVAKIARALGM-NVIAYDPYPKDEQAVELGVKTVSLEELLKNSD 195
Query: 99 FIIITSALTPDTHHLINRARLESMKPGAILINTSRGQLVDQEALIDFIADIRVISISMVT 158
FI + LTP+T H+IN+ LE MK GAI+INTSRG ++D+EAL++ +
Sbjct: 196 FISLHVPLTPETKHMINKKELELMKDGAIIINTSRGGVIDEEALLEALKS---------- 245
Query: 159 NEKHLHRVFTLGDSFHKGHVSAFIFIHMIMGDTVGIYFIFSASDVLKAKKIRGAGLDVMY 218
G ++ +A DV +
Sbjct: 246 -----------------GKLA------------------GAALDV--------------F 256
Query: 219 PEPLPLDSPLLQLDNCVILPHIGSAQIETRQEMARITAQNIINTF 263
P S LL+L N + PHIG++ E ++ + A II
Sbjct: 257 ENEPPPGSKLLELPNVSLTPHIGASTKEAQERIGEELANKIIEFL 301
>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 = 113 bits (285), Expect = 1e-28
Identities = 67/250 (26%), Positives = 106/250 (42%), Gaps = 63/250 (25%)
Query: 24 RGEWKSWAPNFMCGPALQNSTVGIVGCGRIGLSVLEKLIPYKVSKFLYTSRSKKPEADKR 83
GEW A FM G L T+G++G GRIG V ++ + + Y A++
Sbjct: 123 EGEWDRKA--FM-GTELYGKTLGVIGLGRIGSIVAKRAKAFGMKVLAYDPYISPERAEQL 179
Query: 84 GAEHT-NIDDLCKQSDFIIITSALTPDTHHLINRARLESMKPGAILINTSRGQLVDQEAL 142
G E ++D+L ++DFI + + LTP+T LI L MK G I++N +RG ++D+ AL
Sbjct: 180 GVELVDDLDELLARADFITVHTPLTPETRGLIGAEELAKMKKGVIIVNCARGGIIDEAAL 239
Query: 143 IDFIADIRVISISMVTNEKHLHRVFTLGDSFHKGHVSAFIFIHMIMGDTVGIYFIFSASD 202
+ + +GHV
Sbjct: 240 YEAL---------------------------EEGHV------------------------ 248
Query: 203 VLKAKKIRGAGLDVMYPEPLPLDSPLLQLDNCVILPHIGSAQIETRQEMARITAQNIINT 262
R A LDV EP P D+PL LDN + PH+G++ E ++ +A A+ +++
Sbjct: 249 -------RAAALDVFEKEP-PTDNPLFDLDNVIATPHLGASTREAQENVATQVAEQVLDA 300
Query: 263 FHNKPMIYEV 272
P+ V
Sbjct: 301 LKGLPVPNAV 310
>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 = 108 bits (273), Expect = 8e-28
Identities = 47/123 (38%), Positives = 68/123 (55%), Gaps = 19/123 (15%)
Query: 33 NF----MCGPALQNSTVGIVGCGRIGLSVLE-------KLIPYKVSKFLYTSRSKKPEAD 81
NF + G L TVG++G G+IG + +++ Y Y + PE
Sbjct: 131 NFSLDGLLGFDLHGKTVGVIGTGKIGQAFARILKGFGCRVLAYDP----YPN----PELA 182
Query: 82 KRGAEHTNIDDLCKQSDFIIITSALTPDTHHLINRARLESMKPGAILINTSRGQLVDQEA 141
K G E+ ++D+L +SD I + LTP+THHLIN + MK G +LINTSRG L+D +A
Sbjct: 183 KLGVEYVDLDELLAESDIISLHCPLTPETHHLINAETIAKMKDGVMLINTSRGGLIDTKA 242
Query: 142 LID 144
LI+
Sbjct: 243 LIE 245
Score = 29.7 bits (68), Expect = 1.7
Identities = 26/85 (30%), Positives = 35/85 (41%), Gaps = 15/85 (17%)
Query: 202 DVLKAKKIRGAGLDVMYPEPLPL---D-----------SPLLQLDNCVILPHIGSAQIET 247
+ LK+ KI G GLDV Y E L D + LL N +I H E
Sbjct: 245 EALKSGKIGGLGLDV-YEEEAGLFFEDHSDEIIQDDVLARLLSFPNVLITGHQAFFTKEA 303
Query: 248 RQEMARITAQNIINTFHNKPMIYEV 272
+A T +N+ + KP+ EV
Sbjct: 304 LTNIAETTLENLDDFEAGKPLKNEV 328
>gnl|CDD|185307 PRK15409, PRK15409, bifunctional glyoxylate/hydroxypyruvate
reductase B; Provisional.
Length = 323
Score = 107 bits (270), Expect = 2e-27
Identities = 47/121 (38%), Positives = 70/121 (57%), Gaps = 3/121 (2%)
Query: 25 GEW-KSWAPNFMCGPALQNSTVGIVGCGRIGLSVLEKLIPYKVSKFLYTSRSKKPEADKR 83
GEW S P++ G + + T+GIVG GRIG+++ ++ LY +R EA++R
Sbjct: 128 GEWTASIGPDWF-GTDVHHKTLGIVGMGRIGMALAQRAHFGFNMPILYNARRHHKEAEER 186
Query: 84 -GAEHTNIDDLCKQSDFIIITSALTPDTHHLINRARLESMKPGAILINTSRGQLVDQEAL 142
A + ++D L ++SDF+ I LT +THHL + MK AI IN RG +VD+ AL
Sbjct: 187 FNARYCDLDTLLQESDFVCIILPLTDETHHLFGAEQFAKMKSSAIFINAGRGPVVDENAL 246
Query: 143 I 143
I
Sbjct: 247 I 247
>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 = 107 bits (269), Expect = 3e-27
Identities = 62/241 (25%), Positives = 99/241 (41%), Gaps = 62/241 (25%)
Query: 28 KSWAPNFMCGPALQNSTVGIVGCGRIGLSVLE-------KLIPYKVSKFLYTSRSKKPEA 80
A G L++ TVG+VG G+IG +V + K+I Y + PE
Sbjct: 131 LQDAGVI--GRELEDQTVGVVGTGKIGRAVAQRAKGFGMKVIAYDPFR--------NPEL 180
Query: 81 DKRGAEHTNIDDLCKQSDFIIITSALTPDTHHLINRARLESMKPGAILINTSRGQLVDQE 140
+ +G ++ ++++L K SD I + LTP+ HH+IN + MK G I+INT+RG LVD E
Sbjct: 181 EDKGVKYVSLEELFKNSDIISLHVPLTPENHHMINEEAFKLMKKGVIIINTARGSLVDTE 240
Query: 141 ALIDFIADIRVISISMVTNEKHLHRVFTLGDSFHKGHVSAFIFIHMIMGDTVGIYFIFSA 200
ALI+ + DS G +
Sbjct: 241 ALIEAL------------------------DS---GKIFGA------------------G 255
Query: 201 SDVLKAKKIRGAGLDVMYPEPLPLDSPLLQLDNCVILPHIGSAQIETRQEMARITAQNII 260
DVL+ + L++ L + N +I PH + + M I+ +NI+
Sbjct: 256 LDVLEDETPDLLKDLEGEIFKDALNALLGRRPNVIITPHTAFYTDDALKNMVEISCENIV 315
Query: 261 N 261
+
Sbjct: 316 D 316
>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 = 107 bits (269), Expect = 3e-27
Identities = 50/127 (39%), Positives = 75/127 (59%), Gaps = 10/127 (7%)
Query: 24 RGEWKSWAPNFMCGPALQNSTVGIVGCGRIGLSVLEKLIPYKVSKF----LYTSRSKKPE 79
R E ++ + G L+N TVG++G GRIG +V++ L S F L E
Sbjct: 125 RAEVNDYSLGGLQGRELRNLTVGVIGTGRIGQAVIKNL-----SGFGCKILAYDPYPNEE 179
Query: 80 ADKRGAEHTNIDDLCKQSDFIIITSALTPDTHHLINRARLESMKPGAILINTSRGQLVDQ 139
K AE+ ++D L K+SD I + + LT +T+HLIN+ + MK G I+INT+RG+L+D
Sbjct: 180 VKK-YAEYVDLDTLYKESDIITLHTPLTEETYHLINKESIAKMKDGVIIINTARGELIDT 238
Query: 140 EALIDFI 146
EALI+ +
Sbjct: 239 EALIEGL 245
>gnl|CDD|181041 PRK07574, PRK07574, formate dehydrogenase; Provisional.
Length = 385
Score = 107 bits (268), Expect = 9e-27
Identities = 45/107 (42%), Positives = 65/107 (60%), Gaps = 4/107 (3%)
Query: 40 LQNSTVGIVGCGRIGLSVLEKLIPYKVSKFLYTSRSKKPEADKRGAE---HTNIDDLCKQ 96
L+ TVGIVG GRIGL+VL +L P+ V K YT R + PE ++ H + D L
Sbjct: 190 LEGMTVGIVGAGRIGLAVLRRLKPFDV-KLHYTDRHRLPEEVEQELGLTYHVSFDSLVSV 248
Query: 97 SDFIIITSALTPDTHHLINRARLESMKPGAILINTSRGQLVDQEALI 143
D + I L P+T HL + L MK G+ L+NT+RG++VD++A++
Sbjct: 249 CDVVTIHCPLHPETEHLFDADVLSRMKRGSYLVNTARGKIVDRDAVV 295
Score = 33.1 bits (76), Expect = 0.13
Identities = 16/64 (25%), Positives = 28/64 (43%)
Query: 204 LKAKKIRGAGLDVMYPEPLPLDSPLLQLDNCVILPHIGSAQIETRQEMARITAQNIINTF 263
L++ + G DV +P+P P D P + + PHI + + A T + + F
Sbjct: 298 LESGHLAGYAGDVWFPQPAPADHPWRTMPRNGMTPHISGTTLSAQARYAAGTREILECFF 357
Query: 264 HNKP 267
+P
Sbjct: 358 EGRP 361
>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 = 103 bits (258), Expect = 6e-26
Identities = 55/231 (23%), Positives = 86/231 (37%), Gaps = 67/231 (29%)
Query: 29 SWAPNFMCGPALQNSTVGIVGCGRIGLSVLEKLIPYKVSKFLYTSRSKKPEADKRGAEHT 88
W P P+L + V IVG G IG ++ +L P++V +R+ +P G +
Sbjct: 121 RWEPRRT--PSLADRRVLIVGYGSIGRAIERRLAPFEVR-VTRVARTARPGEQVHGIDE- 176
Query: 89 NIDDLCKQSDFIIITSALTPDTHHLINRARLESMKPGAILINTSRGQLVDQEALIDFIAD 148
+ L ++D +++ LT +T L++ L M GA+L+N +RG +VD +AL+
Sbjct: 177 -LPALLPEADVVVLIVPLTDETRGLVDAEFLARMPDGALLVNVARGPVVDTDALV----- 230
Query: 149 IRVISISMVTNEKHLHRVFTLGDSFHKGHVSAFIFIHMIMGDTVGIYFIFSASDVLKAKK 208
L G + A
Sbjct: 231 ------------AELAS----------GRLRA---------------------------- 240
Query: 209 IRGAGLDVMYPEPLPLDSPLLQLDNCVILPHIG--SAQIETRQEMARITAQ 257
LDV PEPLP PL +I PH+G + R A + Q
Sbjct: 241 ----ALDVTDPEPLPPGHPLWSAPGVLITPHVGGATPAFLPRAY-ALVRRQ 286
>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 = 102 bits (257), Expect = 1e-25
Identities = 48/118 (40%), Positives = 68/118 (57%), Gaps = 2/118 (1%)
Query: 29 SWAPNFMCGPALQNSTVGIVGCGRIGLSVLEKLIPYKVSKFLYTSRSKKPEADKRGAEHT 88
WAP + G +++ TVGI+G GRIG S K+ +K + PE +K +
Sbjct: 133 RWAPGLI-GREIRDLTVGIIGTGRIG-SAAAKIFKGFGAKVIAYDPYPNPELEKFLLYYD 190
Query: 89 NIDDLCKQSDFIIITSALTPDTHHLINRARLESMKPGAILINTSRGQLVDQEALIDFI 146
+++DL KQ+D I + LT + HHLIN MK GAIL+N +RG LVD +ALID +
Sbjct: 191 SLEDLLKQADIISLHVPLTKENHHLINAEAFAKMKDGAILVNAARGGLVDTKALIDAL 248
>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 = 101 bits (255), Expect = 2e-25
Identities = 48/115 (41%), Positives = 63/115 (54%), Gaps = 15/115 (13%)
Query: 37 GPALQNSTVGIVGCGRIGLSVLE-------KLIPYKVSKFLYTSRSKKPEADKRGAEHTN 89
G L TVGIVG G IGL V K++ Y SRS+K EA G E+ +
Sbjct: 139 GRELAGKTVGIVGTGAIGLRVARLFKAFGCKVLAY--------SRSEKEEAKALGIEYVS 190
Query: 90 IDDLCKQSDFIIITSALTPDTHHLINRARLESMKPGAILINTSRGQLVDQEALID 144
+D+L +SD + + L +T LI + +L MK AILINT+RG +VD EAL D
Sbjct: 191 LDELLAESDIVSLHLPLNDETKGLIGKEKLALMKESAILINTARGPVVDNEALAD 245
Score = 56.8 bits (138), Expect = 2e-09
Identities = 29/69 (42%), Positives = 36/69 (52%), Gaps = 3/69 (4%)
Query: 201 SDVLKAKKIRGAGLDV--MYPEPLPLDSPLLQLDNCVILPHIGSAQIETRQEMARITAQN 258
+D L KI GAG+DV M P PLP D PLL N ++ PH+ A E ++ A I N
Sbjct: 244 ADALNEGKIAGAGIDVFDMEP-PLPADYPLLHAPNTILTPHVAFATEEAMEKRAEIVFDN 302
Query: 259 IINTFHNKP 267
I KP
Sbjct: 303 IEAWLAGKP 311
>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 = 102 bits (256), Expect = 3e-25
Identities = 43/108 (39%), Positives = 64/108 (59%), Gaps = 4/108 (3%)
Query: 40 LQNSTVGIVGCGRIGLSVLEKLIPYKVSKFLYTSRSKKPEADKRGAE---HTNIDDLCKQ 96
L+ TVG VG GRIGL VL +L P+ V LY R + PE ++ H +++D+ +
Sbjct: 160 LEGKTVGTVGAGRIGLRVLRRLKPFDV-HLLYYDRHRLPEEVEKELGLTRHADLEDMVSK 218
Query: 97 SDFIIITSALTPDTHHLINRARLESMKPGAILINTSRGQLVDQEALID 144
D + I L P+T L N+ L MK GA L+NT+RG++ D+EA+ +
Sbjct: 219 CDVVTINCPLHPETEGLFNKELLSKMKKGAYLVNTARGKICDREAVAE 266
Score = 36.1 bits (84), Expect = 0.015
Identities = 17/64 (26%), Positives = 30/64 (46%)
Query: 204 LKAKKIRGAGLDVMYPEPLPLDSPLLQLDNCVILPHIGSAQIETRQEMARITAQNIINTF 263
L++ + G DV +P+P P D P + N + PHI ++ + A T + + F
Sbjct: 268 LESGHLAGYAGDVWFPQPAPKDHPWRTMPNNAMTPHISGTTLDAQARYAAGTKEILERFF 327
Query: 264 HNKP 267
+P
Sbjct: 328 EGEP 331
>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 = 101 bits (253), Expect = 4e-25
Identities = 41/122 (33%), Positives = 62/122 (50%)
Query: 24 RGEWKSWAPNFMCGPALQNSTVGIVGCGRIGLSVLEKLIPYKVSKFLYTSRSKKPEADKR 83
RG W A L+ TVGI+G G IG + L + + + K+ E
Sbjct: 119 RGIWHGRAGEEPESKELRGKTVGILGYGHIGREIARLLKAFGMRVIGVSRSPKEDEGADF 178
Query: 84 GAEHTNIDDLCKQSDFIIITSALTPDTHHLINRARLESMKPGAILINTSRGQLVDQEALI 143
+++D+ +Q+D +++ LT T LI A L +MKPGAIL+N RG +VD+EAL
Sbjct: 179 VGTLSDLDEALEQADVVVVALPLTKQTRGLIGAAELAAMKPGAILVNVGRGPVVDEEALY 238
Query: 144 DF 145
+
Sbjct: 239 EA 240
Score = 58.4 bits (142), Expect = 6e-10
Identities = 20/76 (26%), Positives = 32/76 (42%), Gaps = 6/76 (7%)
Query: 202 DVLKAKKIRGAGLDVMYPEP------LPLDSPLLQLDNCVILPHIGSAQIETRQEMARIT 255
+ LK + I GA +DV + P P P +L N ++ PH ET +
Sbjct: 239 EALKERPIAGAAIDVWWRYPSRGDPVAPSRYPFHELPNVIMSPHNAGWTEETFRRRIDEA 298
Query: 256 AQNIINTFHNKPMIYE 271
A+NI +P++
Sbjct: 299 AENIRRYLRGEPLLNL 314
>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 = 99.3 bits (248), Expect = 2e-24
Identities = 45/113 (39%), Positives = 67/113 (59%), Gaps = 3/113 (2%)
Query: 40 LQNSTVGIVGCGRIGLSVLEKLIPYKVSKFLYTSRSKKPEADKRGAEHT-NIDDLCKQSD 98
L ST+GIVG G IG ++ + + + + L RS +P D G E ++ +L +SD
Sbjct: 133 LAGSTLGIVGFGAIGQALARRALALGM-RVLALRRSGRPS-DVPGVEAAADLAELFARSD 190
Query: 99 FIIITSALTPDTHHLINRARLESMKPGAILINTSRGQLVDQEALIDFIADIRV 151
+++ + LTP+T HLIN L KPG LIN +RG LVDQEAL++ + R+
Sbjct: 191 HLVLAAPLTPETRHLINADVLAQAKPGLHLINIARGGLVDQEALLEALDSGRI 243
Score = 40.0 bits (94), Expect = 6e-04
Identities = 17/51 (33%), Positives = 24/51 (47%)
Query: 209 IRGAGLDVMYPEPLPLDSPLLQLDNCVILPHIGSAQIETRQEMARITAQNI 259
I A LDV PEPLP PL + PH + + R+ +A +N+
Sbjct: 243 ISLASLDVTDPEPLPEGHPLYTHPRVRLSPHTSAIAPDGRRNLADRFLENL 293
>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 = 98.9 bits (247), Expect = 3e-24
Identities = 60/249 (24%), Positives = 89/249 (35%), Gaps = 58/249 (23%)
Query: 24 RGEWKSWAPNFMCGPALQNSTVGIVGCGRIGLSVLEKLIPYKVSKFLYTSRSKKPEADKR 83
G+WK P G L T+G++G G IG + + + PE +
Sbjct: 121 AGDWKKGGPI---GLELYGKTLGVIGGGGIG-GIGAAIAKALGMGVVAYDPYPNPERAEE 176
Query: 84 GAEHTNIDDLCKQSDFIIITSALTPDTHHLINRARLESMKPGAILINTSRGQLVDQEALI 143
G + DL ++ LIN A +MK G I+IN +RG L D A+
Sbjct: 177 GGVEVLLLDLLLLDL---------KESDDLINLAPPTTMKTGHIIINEARGMLKDAVAIN 227
Query: 144 DFIADIRVISISMVTNEKHLHRVFTLGDSFHKGHVSAFIFIHMIMGDTVGIYFIFSASDV 203
+ VI + + D
Sbjct: 228 N-ARGGGVI-------------------------------------EEAAL-------DA 242
Query: 204 LKAKKIRGAGLDVMYPEPLPLDSPLLQLDNCVILPHIGSAQIETRQEMARITAQNIINTF 263
L + I A LDV+ EP P++SPLL L N ++ PHI A E ++ MA A+N++
Sbjct: 243 LLEEGIAAAALDVVEEEPPPVNSPLLDLPNVILTPHIAGATEEAQENMAEEAAENLLAFL 302
Query: 264 HNKPMIYEV 272
V
Sbjct: 303 KGGTPPNAV 311
>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 = 98.0 bits (245), Expect = 6e-24
Identities = 40/121 (33%), Positives = 61/121 (50%), Gaps = 8/121 (6%)
Query: 28 KSWAPNFMCGPALQNSTVGIVGCGRIGLSVLEKLIPY--KVSKFLYTSRSKKPEADKRGA 85
+ W L TV IVG G IG + + + +V RS +P
Sbjct: 121 RRWQRRGPVRE-LAGKTVLIVGLGDIGREIARRAKAFGMRVIG---VRRSGRPAPPVVDE 176
Query: 86 EHT--NIDDLCKQSDFIIITSALTPDTHHLINRARLESMKPGAILINTSRGQLVDQEALI 143
+T +D+L ++D+++ LTP+T L N R +MKPGA+LIN RG +VD++ALI
Sbjct: 177 VYTPDELDELLPEADYVVNALPLTPETRGLFNAERFAAMKPGAVLINVGRGSVVDEDALI 236
Query: 144 D 144
+
Sbjct: 237 E 237
Score = 76.8 bits (190), Expect = 3e-16
Identities = 25/71 (35%), Positives = 37/71 (52%)
Query: 202 DVLKAKKIRGAGLDVMYPEPLPLDSPLLQLDNCVILPHIGSAQIETRQEMARITAQNIIN 261
+ L++ +I GA LDV EPLP DSPL L N +I PHI + + I +N+
Sbjct: 237 EALESGRIAGAALDVFEEEPLPADSPLWDLPNVIITPHISGDSPSYPERVVEIFLENLRR 296
Query: 262 TFHNKPMIYEV 272
+P++ V
Sbjct: 297 YLAGEPLLNVV 307
>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 = 97.6 bits (244), Expect = 6e-24
Identities = 56/222 (25%), Positives = 82/222 (36%), Gaps = 72/222 (32%)
Query: 44 TVGIVGCGRIGLSVLEKLIP--YKVSKFLYTSRSKKPEADKR---GAEHTNIDDLCKQSD 98
VG++G G +G +V +L + VS + SRS K G E +D Q+D
Sbjct: 134 RVGVLGLGELGAAVARRLAALGFPVSGW---SRSPKDIEGVTCFHGEEG--LDAFLAQTD 188
Query: 99 FIIITSALTPDTHHLINRARLESMKPGAILINTSRGQLVDQEALIDFIADIRVISISMVT 158
++ LTP+T ++N L + GA LIN RG + + L+ +
Sbjct: 189 ILVCLLPLTPETRGILNAELLARLPRGAALINVGRGPHLVEADLLAAL------------ 236
Query: 159 NEKHLHRVFTLGDSFHKGHVSAFIFIHMIMGDTVGIYFIFSASDVLKAKKIRGAGLDVMY 218
DS GH+S GA LDV
Sbjct: 237 ------------DS---GHLS-------------------------------GAVLDVFE 250
Query: 219 PEPLPLDSPLLQLDNCVILPHIGS-AQIETRQEMARITAQNI 259
EPLP D PL + + PHI + ++ A A+NI
Sbjct: 251 QEPLPADHPLWRHPRVTVTPHIAAITDPDSA---AAQVAENI 289
>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 = 98.1 bits (245), Expect = 7e-24
Identities = 56/220 (25%), Positives = 92/220 (41%), Gaps = 38/220 (17%)
Query: 40 LQNSTVGIVGCGRIGLSVLEKLIPYKVSKFLYTSRSKKPEADKRGAEHTNIDDLCKQSDF 99
L T+G+VG GRIG V + + Y + A++ G + ++++L ++SD
Sbjct: 137 LAGKTLGVVGTGRIGRRVARIARGFGMKVLAYDVVPDEELAERLGFRYVSLEELLQESDI 196
Query: 100 IIITSALTPDTHHLINRARLESMKPGAILINTSRGQLVDQEALIDFIADIRVISISMVTN 159
I + TP THHLINR MKPGA+LINT+RG +VD EAL+
Sbjct: 197 ISLHVPYTPQTHHLINRENFALMKPGAVLINTARGAVVDTEALVRA-------------- 242
Query: 160 EKHLHRVFTLGDSFHKGHVSAFIFIHMIMGDTVGIYFIFSASDVLKAKKIRGAGLDVMYP 219
+G ++ G+ + + + ++ +
Sbjct: 243 -------------LKEGKLAG-----------AGLDVLEQEEVLREEAELFREDVSPEDL 278
Query: 220 EPLPLDSPLLQLDNCVILPHIGSAQIETRQEMARITAQNI 259
+ L D LL+ N +I PH+ E + + T +NI
Sbjct: 279 KKLLADHALLRKPNVIITPHVAYNTKEALERILDTTVENI 318
>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 = 96.1 bits (240), Expect = 3e-23
Identities = 61/212 (28%), Positives = 83/212 (39%), Gaps = 61/212 (28%)
Query: 40 LQNSTVGIVGCGRIGLSVLEKLIPYKVSKF-LYTSRSKKPEADKRGAEHTNIDDLCKQSD 98
L T+ +G G IG + ++L + + + TS DK +D++ K++D
Sbjct: 133 LYGKTILFLGTGSIGQEIAKRLKAFGMKVIGVNTSGRDVEYFDKCYPL-EELDEVLKEAD 191
Query: 99 FIIITSALTPDTHHLINRARLESMKPGAILINTSRGQLVDQEALIDFIADIRVISISMVT 158
++ LT +THHL + A E MK GA+ IN RG V
Sbjct: 192 IVVNVLPLTEETHHLFDEAFFEQMKKGALFINVGRGPSV--------------------- 230
Query: 159 NEKHLHRVFTLGDSFHKGHVSAFIFIHMIMGDTVGIYFIFSASDVLKAKKIRGAGLDVMY 218
+E L + LK K+IRGA LDV
Sbjct: 231 DEDALI-------------------------------------EALKNKQIRGAALDVFE 253
Query: 219 PEPLPLDSPLLQLDNCVILPHIGSAQIETRQE 250
EPLP DSPL LDN +I PHI S E E
Sbjct: 254 EEPLPKDSPLWDLDNVLITPHI-SGVSEHFNE 284
>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 = 95.3 bits (238), Expect = 5e-23
Identities = 39/117 (33%), Positives = 63/117 (53%), Gaps = 9/117 (7%)
Query: 37 GPALQNSTVGIVGCGRIGLSVLEKLIPY--KVSKFLYTSRSKKPEADKRGAEH----TNI 90
G L+ T+G++G G IG V + KV + EA + + T++
Sbjct: 130 GTELRGKTLGVIGLGNIGRLVANAALALGMKVIGY---DPYLSVEAAWKLSVEVQRVTSL 186
Query: 91 DDLCKQSDFIIITSALTPDTHHLINRARLESMKPGAILINTSRGQLVDQEALIDFIA 147
++L +D+I + LT +T LIN L MKPGAIL+N +RG++VD+EAL++ +
Sbjct: 187 EELLATADYITLHVPLTDETRGLINAELLAKMKPGAILLNFARGEIVDEEALLEALD 243
Score = 36.0 bits (84), Expect = 0.014
Identities = 15/59 (25%), Positives = 25/59 (42%), Gaps = 6/59 (10%)
Query: 203 VLKAKKIRGAGLDVMYPEPLPLDSPLLQLDNCVILPHIGSAQIETRQEMARITAQNIIN 261
L K+ G D P L L N + PH+G++ E + A + A+ I++
Sbjct: 241 ALDEGKLGGYVTDFPEPALLG------HLPNVIATPHLGASTEEAEENCAVMAARQIMD 293
>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 = 91.9 bits (229), Expect = 8e-22
Identities = 44/109 (40%), Positives = 67/109 (61%), Gaps = 8/109 (7%)
Query: 40 LQNSTVGIVGCGRIGLSVLEKLIPYKVSKFLYTSRSKKPEADKRGAEHT-NIDDLCK--- 95
L+ STV IVG G IG +++ L P+ K + +RS +P GA+ T D L +
Sbjct: 123 LRGSTVAIVGAGGIGRALIPLLAPFGA-KVIAVNRSGRP---VEGADETVPADRLDEVWP 178
Query: 96 QSDFIIITSALTPDTHHLINRARLESMKPGAILINTSRGQLVDQEALID 144
+D +++ + LTP+T HL++ A L +MKP A L+N +RG LVD +AL+D
Sbjct: 179 DADHVVLAAPLTPETRHLVDAAALAAMKPHAWLVNVARGPLVDTDALVD 227
Score = 66.5 bits (163), Expect = 1e-12
Identities = 24/58 (41%), Positives = 33/58 (56%)
Query: 202 DVLKAKKIRGAGLDVMYPEPLPLDSPLLQLDNCVILPHIGSAQIETRQEMARITAQNI 259
D L++ +I GA LDV PEPLP PL L N +I PH+ + R +A A+N+
Sbjct: 227 DALRSGEIAGAALDVTDPEPLPDGHPLWSLPNALITPHVANTPEVIRPLLAERVAENV 284
>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 = 90.3 bits (225), Expect = 3e-21
Identities = 59/225 (26%), Positives = 89/225 (39%), Gaps = 70/225 (31%)
Query: 44 TVGIVGCGRIG--LSVLEKLIPYKVSKFLYTSRSKKPEADKRGAEHTNIDDLCKQSDFII 101
T+GI+G G IG LSVL + + +V Y K P + R +++L ++DF+
Sbjct: 142 TLGIIGYGHIGSQLSVLAEALGMRV--IFYDIAEKLPLGNARQVSS--LEELLAEADFVT 197
Query: 102 ITSALTPDTHHLINRARLESMKPGAILINTSRGQLVDQEALIDFIADIRVISISMVTNEK 161
+ TP T ++I + MK GAILIN SRG +VD +AL + +
Sbjct: 198 LHVPATPSTKNMIGAEEIAQMKKGAILINASRGTVVDIDALAEAL------------RSG 245
Query: 162 HLHRVFTLGDSFHKGHVSAFIFIHMIMGDTVGIYFIFSASDVLKAKKIRGAGLDVMYP-E 220
HL GA +DV +P E
Sbjct: 246 HLA----------------------------------------------GAAVDV-FPEE 258
Query: 221 PL----PLDSPLLQLDNCVILPHIGSAQIETRQEMARITAQNIIN 261
P P SPL L N ++ PHIG + E ++ + A ++
Sbjct: 259 PASNGEPFSSPLQGLPNVILTPHIGGSTEEAQENIGLEVAGKLVK 303
>gnl|CDD|180588 PRK06487, PRK06487, glycerate dehydrogenase; Provisional.
Length = 317
Score = 89.4 bits (222), Expect = 1e-20
Identities = 66/253 (26%), Positives = 94/253 (37%), Gaps = 76/253 (30%)
Query: 24 RGEWKSWAPNFMCGP-----ALQNSTVGIVGCGRIGLSV--LEKLIPYKVSKFLYTSRSK 76
G W+ + F C L+ T+G++G G +G +V L + +V L
Sbjct: 127 AGRWQQ-SSQF-CLLDFPIVELEGKTLGLLGHGELGGAVARLAEAFGMRV---LIGQLPG 181
Query: 77 KPEADKRGAEHTNIDDLCKQSDFIIITSALTPDTHHLINRARLESMKPGAILINTSRGQL 136
+P R +D+L Q D + + LT T HLI L MKPGA+LINT+RG L
Sbjct: 182 RPARPDR----LPLDELLPQVDALTLHCPLTEHTRHLIGARELALMKPGALLINTARGGL 237
Query: 137 VDQEALIDFIADIRVISISMVTNEKHLHRVFTLGDSFHKGHVSAFIFIHMIMGDTVGIYF 196
VD++AL D+ GH+
Sbjct: 238 VDEQALA---------------------------DALRSGHLGG---------------- 254
Query: 197 IFSASDVLKAKKIRGAGLDVMYPEPLPLDSPLLQLD--NCVILPHIGSAQIETRQEMARI 254
+A+DVL EP +PLL D ++ PH E RQ +
Sbjct: 255 --AATDVLSV-------------EPPVNGNPLLAPDIPRLIVTPHSAWGSREARQRIVGQ 299
Query: 255 TAQNIINTFHNKP 267
A+N F KP
Sbjct: 300 LAENARAFFAGKP 312
>gnl|CDD|181414 PRK08410, PRK08410, 2-hydroxyacid dehydrogenase; Provisional.
Length = 311
Score = 87.7 bits (218), Expect = 3e-20
Identities = 61/223 (27%), Positives = 86/223 (38%), Gaps = 65/223 (29%)
Query: 40 LQNSTVGIVGCGRIGLSVLEKLIPYKVSKFLYTSRSKKPEADKRGAEHTNIDDLCKQSDF 99
++ GI+G G IG V K+ +K +Y S S K E ++++L K SD
Sbjct: 143 IKGKKWGIIGLGTIGKRV-AKIAQAFGAKVVYYSTSGK--NKNEEYERVSLEELLKTSDI 199
Query: 100 IIITSALTPDTHHLINRARLESMKPGAILINTSRGQLVDQEALIDFIADIRVISISMVTN 159
I I + L T +LI L+ +K GAILIN RG +V N
Sbjct: 200 ISIHAPLNEKTKNLIAYKELKLLKDGAILINVGRGGIV---------------------N 238
Query: 160 EKHLHRVFTLGDSFHKGHVSAFIFIHMIMGDTVGIYFIFSASDVLKAKKIRGAGLDVMYP 219
EK L + L K I AGLDV+
Sbjct: 239 EKDLAKA-------------------------------------LDEKDI-YAGLDVLEK 260
Query: 220 EPLPLDSPLLQL---DNCVILPHIGSAQIETRQEMARITAQNI 259
EP+ + PLL + + +I PHI A E R+ + +NI
Sbjct: 261 EPMEKNHPLLSIKNKEKLLITPHIAWASKEARKTLIEKVKENI 303
>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 = 81.8 bits (203), Expect = 5e-18
Identities = 40/117 (34%), Positives = 55/117 (47%), Gaps = 17/117 (14%)
Query: 37 GPALQNSTVGIVGCGRIGLSVLE-------KLIPYKVSKFLYTSRSKKPE-ADKRGAEHT 88
G L T+GIVG GRIG V ++I + S + E A G E
Sbjct: 137 GTGLAGKTLGIVGLGRIGARVARIGQAFGMRVIAW--------SSNLTAERAAAAGVEAA 188
Query: 89 N-IDDLCKQSDFIIITSALTPDTHHLINRARLESMKPGAILINTSRGQLVDQEALID 144
++L SD + + L+ T L+ L MKP A+L+NTSRG LVD+ AL+
Sbjct: 189 VSKEELFATSDVVSLHLVLSDRTRGLVGAEDLALMKPTALLVNTSRGPLVDEGALLA 245
Score = 62.1 bits (152), Expect = 3e-11
Identities = 24/58 (41%), Positives = 30/58 (51%)
Query: 202 DVLKAKKIRGAGLDVMYPEPLPLDSPLLQLDNCVILPHIGSAQIETRQEMARITAQNI 259
L+A +I GA LDV EPLP D PL L N ++ PHIG E + +NI
Sbjct: 245 AALRAGRIAGAALDVFDVEPLPADHPLRGLPNVLLTPHIGYVTEEAYEGFYGQAVENI 302
>gnl|CDD|235890 PRK06932, PRK06932, glycerate dehydrogenase; Provisional.
Length = 314
Score = 80.2 bits (198), Expect = 2e-17
Identities = 64/228 (28%), Positives = 89/228 (39%), Gaps = 80/228 (35%)
Query: 43 STVGIVGCGRIGLSV--LEKLIPYKVSKFLYTSRSKKPEADKRGAEH-----TNIDDLCK 95
ST+G+ G G +G V L + + KV LY A+ +GA T +++ K
Sbjct: 148 STLGVFGKGCLGTEVGRLAQALGMKV---LY--------AEHKGASVCREGYTPFEEVLK 196
Query: 96 QSDFIIITSALTPDTHHLINRARLESMKPGAILINTSRGQLVDQEALIDFIADIRVISIS 155
Q+D + + LT T +LIN L MKP A LINT RG LVD++AL+
Sbjct: 197 QADIVTLHCPLTETTQNLINAETLALMKPTAFLINTGRGPLVDEQALL------------ 244
Query: 156 MVTNEKHLHRVFTLGDSFHKGHVSAFIFIHMIMGDTVGIYFIFSASDVLKAKKIRGAGLD 215
D+ G ++ A LD
Sbjct: 245 ---------------DALENGKIAG-------------------------------AALD 258
Query: 216 VMYPEPLPLDSPLLQ----LDNCVILPHIGSAQIETRQEMARITAQNI 259
V+ EP D+PL+Q L N +I PHI A + AQNI
Sbjct: 259 VLVKEPPEKDNPLIQAAKRLPNLLITPHIAWASDSAVTTLVNKVAQNI 306
>gnl|CDD|177941 PLN02306, PLN02306, hydroxypyruvate reductase.
Length = 386
Score = 79.5 bits (196), Expect = 5e-17
Identities = 40/140 (28%), Positives = 73/140 (52%), Gaps = 23/140 (16%)
Query: 25 GEWKSWAPNFMCGPALQNSTVGIVGCGRIGLSVLEKLI-----------PY---KVSKF- 69
G ++ W P+ G L+ TVG++G GRIG + ++ Y ++ KF
Sbjct: 148 GLYEGWLPHLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQSTRLEKFV 207
Query: 70 -----LYTSRSKKPEADKRGAEHTNIDDLCKQSDFIIITSALTPDTHHLINRARLESMKP 124
+ ++P KR + +++++ +++D I + L T+HLIN+ RL MK
Sbjct: 208 TAYGQFLKANGEQPVTWKRAS---SMEEVLREADVISLHPVLDKTTYHLINKERLALMKK 264
Query: 125 GAILINTSRGQLVDQEALID 144
A+L+N SRG ++D+ AL++
Sbjct: 265 EAVLVNASRGPVIDEVALVE 284
Score = 45.6 bits (108), Expect = 1e-05
Identities = 24/65 (36%), Positives = 34/65 (52%), Gaps = 1/65 (1%)
Query: 204 LKAKKIRGAGLDVMYPEPLPLDSPLLQLDNCVILPHIGSAQIETRQEMARITAQNIINTF 263
LKA + GLDV EP + L + N V++PHI SA TR+ MA + A N++
Sbjct: 286 LKANPMFRVGLDVFEDEPY-MKPGLADMKNAVVVPHIASASKWTREGMATLAALNVLGKL 344
Query: 264 HNKPM 268
P+
Sbjct: 345 KGYPV 349
>gnl|CDD|236985 PRK11790, PRK11790, D-3-phosphoglycerate dehydrogenase;
Provisional.
Length = 409
Score = 79.1 bits (196), Expect = 8e-17
Identities = 66/206 (32%), Positives = 87/206 (42%), Gaps = 72/206 (34%)
Query: 44 TVGIVGCGRIG--LSVLEKLIPYKVSKFLYTSRSKKPEADKRGAEHTNIDDLCKQSDFII 101
T+GIVG G IG LSVL + + +V + Y K P + R +++L QSD +
Sbjct: 153 TLGIVGYGHIGTQLSVLAESLGMRV--YFYDIEDKLPLGNARQVGS--LEELLAQSDVVS 208
Query: 102 ITSALTPDTHHLINRARLESMKPGAILINTSRGQLVDQEALIDFIADIRVISISMVTNEK 161
+ TP T ++I L MKPGAILIN SRG +VD +AL D +
Sbjct: 209 LHVPETPSTKNMIGAEELALMKPGAILINASRGTVVDIDALADALKS------------- 255
Query: 162 HLHRVFTLGDSFHKGHVSAFIFIHMIMGDTVGIYFIFSASDVLKAKKIRGAGLDVMYP-E 220
GH++ GA +DV +P E
Sbjct: 256 --------------GHLA-------------------------------GAAIDV-FPVE 269
Query: 221 PL----PLDSPLLQLDNCVIL-PHIG 241
P P +SPL LDN VIL PHIG
Sbjct: 270 PKSNGDPFESPLRGLDN-VILTPHIG 294
>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 = 78.1 bits (193), Expect = 1e-16
Identities = 68/233 (29%), Positives = 100/233 (42%), Gaps = 57/233 (24%)
Query: 33 NFMCGPALQNSTVGIVGCGRIGL--SVLEKLIPYKVSKF-LYTSRSKKPEADKRGAEHTN 89
FM ++NSTVGI+G GRIGL + L K + KV + +Y S +A K +
Sbjct: 136 PFMFSKEIRNSTVGIIGTGRIGLTAAKLFKGLGAKVIGYDIYPS-----DAAKDVVTFVS 190
Query: 90 IDDLCKQSDFIIITSALTPDTH-HLINRARLESMKPGAILINTSRGQLVDQEALIDFIAD 148
+D+L K+SD I + + LIN+ + MK GAILINT+RG+L D+EA+++ +
Sbjct: 191 LDELLKKSDIISLHVPYIKGKNDKLINKEFISKMKDGAILINTARGELQDEEAILEALES 250
Query: 149 IRVISISMVTNEKHLHRVFTLGDSFHKGHVSAFIFIHMIMGDTVGIYFIFSASDVLK-AK 207
G ++ F +DVL K
Sbjct: 251 ---------------------------GKLAGF------------------GTDVLNNEK 265
Query: 208 KIRGAGLDVMYPEPLPLDSPLLQLDNCVIL-PHIGSAQIETRQEMARITAQNI 259
+I D P+ LL L V+L PHIGS E M + +N+
Sbjct: 266 EIFFKDFDG-DKIEDPVVEKLLDLYPRVLLTPHIGSYTDEALSNMIETSYENL 317
>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 = 77.6 bits (192), Expect = 2e-16
Identities = 38/123 (30%), Positives = 65/123 (52%), Gaps = 14/123 (11%)
Query: 39 ALQNSTVGIVGCGRIGLSVLEKLIPYKVSKFLYTSRSKKPEADKRG--AEHTNIDDLCKQ 96
+L+ TVGIVG G +G + +L ++ L P + ++++L +
Sbjct: 112 SLKGKTVGIVGVGNVGSRLARRLEALGMNVLLC-----DPPRAEAEGDPGFVSLEELLAE 166
Query: 97 SDFIIITSALTPD----THHLINRARLESMKPGAILINTSRGQLVDQEALIDFIA---DI 149
+D I + LT D T+HL++ L ++KPG ILIN SRG ++D +AL+ + D+
Sbjct: 167 ADIITLHVPLTRDGEHPTYHLLDEDFLAALKPGQILINASRGAVIDNQALLALLQRGKDL 226
Query: 150 RVI 152
RV+
Sbjct: 227 RVV 229
>gnl|CDD|178684 PLN03139, PLN03139, formate dehydrogenase; Provisional.
Length = 386
Score = 76.0 bits (187), Expect = 8e-16
Identities = 56/216 (25%), Positives = 89/216 (41%), Gaps = 62/216 (28%)
Query: 40 LQNSTVGIVGCGRIGLSVLEKLIPYKVSKFLYTSRSK-KPEADKR-GAEH-TNIDDLCKQ 96
L+ TVG VG GRIG +L++L P+ LY R K PE +K GA+ ++D + +
Sbjct: 197 LEGKTVGTVGAGRIGRLLLQRLKPFNC-NLLYHDRLKMDPELEKETGAKFEEDLDAMLPK 255
Query: 97 SDFIIITSALTPDTHHLINRARLESMKPGAILINTSRGQLVDQEALIDFIADIRVISISM 156
D ++I + LT T + N+ R+ MK G +++N +RG ++D +A+ D +
Sbjct: 256 CDVVVINTPLTEKTRGMFNKERIAKMKKGVLIVNNARGAIMDTQAVADACS--------- 306
Query: 157 VTNEKHLHRVFTLGDSFHKGHVSAFIFIHMIMGDTVGIYFIFSASDVLKAKKIRGAGLDV 216
GH+ + G DV
Sbjct: 307 ------------------SGHIGGY-------------------------------GGDV 317
Query: 217 MYPEPLPLDSPLLQLDNCVILPHIGSAQIETRQEMA 252
YP+P P D P + N + PHI I+ + A
Sbjct: 318 WYPQPAPKDHPWRYMPNHAMTPHISGTTIDAQLRYA 353
>gnl|CDD|215501 PLN02928, PLN02928, oxidoreductase family protein.
Length = 347
Score = 70.1 bits (172), Expect = 7e-14
Identities = 57/234 (24%), Positives = 91/234 (38%), Gaps = 73/234 (31%)
Query: 37 GPALQNSTVGIVGCGRIGLSVLEKLIPYKVSKFLYTSRS-KKPEADKRGAEHTNIDDLC- 94
G L TV I+G G IG+ + ++L P+ V K L T RS D + ++DDL
Sbjct: 154 GDTLFGKTVFILGYGAIGIELAKRLRPFGV-KLLATRRSWTSEPEDGLLIPNGDVDDLVD 212
Query: 95 ------------KQSDFIIITSALTPDTHHLINRARLESMKPGAILINTSRGQLVDQEAL 142
++D +++ LT +T ++N L SMK GA+L+N +RG L+D +A+
Sbjct: 213 EKGGHEDIYEFAGEADIVVLCCTLTKETAGIVNDEFLSSMKKGALLVNIARGGLLDYDAV 272
Query: 143 IDFIADIRVISISMVTNEKHLHRVFTLGDSFHKGHVSAFIFIHMIMGDTVGIYFIFSASD 202
+ L +S H G
Sbjct: 273 LA-----------------AL-------ESGHLG-------------------------- 282
Query: 203 VLKAKKIRGAGLDVMYPEPLPLDSPLLQLDNCVILPHIGSAQIETRQEMARITA 256
G +DV + EP D P+L+ N +I PH+ + + M +I
Sbjct: 283 --------GLAIDVAWSEPFDPDDPILKHPNVIITPHVAGVTEYSYRSMGKIVG 328
>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 = 67.3 bits (165), Expect = 6e-13
Identities = 54/235 (22%), Positives = 82/235 (34%), Gaps = 87/235 (37%)
Query: 44 TVGIVGCGRIGLSV--LEKLIPYKVSKFLYTSRSKK-PEADK------------------ 82
VGI+G G IG L + + +V + YT + PE+ K
Sbjct: 135 RVGILGYGSIGRQTARLAQALGMEV--YAYTRSPRPTPESRKDDGYIVPGTGDPDGSIPS 192
Query: 83 ---RGAEHTNIDD-LCKQSDFIIITSALTPDTHHLINRARLESM-KPGAILINTSRGQLV 137
G + ++ + L + D ++++ LTP T HL+ E + K + N +RG LV
Sbjct: 193 AWFSGTDKASLHEFLRQDLDLLVVSLPLTPATKHLLGAEEFEILAKRKTFVSNIARGSLV 252
Query: 138 DQEALIDFIADIRVISISMVTNEKHLHRVFTLGDSFHKGHVSAFIFIHMIMGDTVGIYFI 197
D +AL+ + G +
Sbjct: 253 DTDALV---------------------------AALESGQIR------------------ 267
Query: 198 FSASDVLKAKKIRGAGLDVMYPEPLPLDSPLLQLDNCVILPHIGSAQIETRQEMA 252
GA LDV PEPLP D PL N +I PH+ S Q + + A
Sbjct: 268 -------------GAALDVTDPEPLPADHPLWSAPNVIITPHV-SWQTQEYFDRA 308
>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 = 64.6 bits (157), Expect = 5e-12
Identities = 25/109 (22%), Positives = 50/109 (45%), Gaps = 5/109 (4%)
Query: 38 PALQNSTVGIVGCGRIGLSVLEKLIPYKVSKFLYTSR---SKKPEADKRGAEHTNIDDLC 94
P + TV +VG G +G + L ++ L T + + + G +++
Sbjct: 156 PDVAGKTVVVVGAGVVGKEAAQMLRGLG-AQVLITDINVEALEQLEELGGKNVEELEEAL 214
Query: 95 KQSDFIIITSALTPDTHH-LINRARLESMKPGAILINTSRGQLVDQEAL 142
++D I+ T+ L L+ +E MKPG++++N + G + +AL
Sbjct: 215 AEADVIVTTTLLPGKRAGILVPEELVEQMKPGSVIVNVAVGAVGCVQAL 263
>gnl|CDD|166874 PRK00257, PRK00257, erythronate-4-phosphate dehydrogenase;
Validated.
Length = 381
Score = 63.5 bits (155), Expect = 1e-11
Identities = 36/117 (30%), Positives = 59/117 (50%), Gaps = 9/117 (7%)
Query: 37 GPALQNSTVGIVGCGRIGLSVLEKLIPYKVSKFLYTSRSKKPEADKRGA-EHTNIDDLCK 95
G L T G+VG G +G ++ L K L P + G + +++ + +
Sbjct: 111 GVDLAERTYGVVGAGHVGGRLVRVLRGLGW-KVL---VCDPPRQEAEGDGDFVSLERILE 166
Query: 96 QSDFIIITSALTPD----THHLINRARLESMKPGAILINTSRGQLVDQEALIDFIAD 148
+ D I + + LT + T HL++ A L S++PGA LIN SRG +VD +AL + +
Sbjct: 167 ECDVISLHTPLTKEGEHPTRHLLDEAFLASLRPGAWLINASRGAVVDNQALREALLS 223
>gnl|CDD|185335 PRK15438, PRK15438, erythronate-4-phosphate dehydrogenase PdxB;
Provisional.
Length = 378
Score = 63.0 bits (153), Expect = 2e-11
Identities = 41/113 (36%), Positives = 60/113 (53%), Gaps = 11/113 (9%)
Query: 37 GPALQNSTVGIVGCGRIGLSVLEKLIPYKVSKFLYTSRSKKPEADKRGAE--HTNIDDLC 94
G +L + TVGIVG G +G + +L + L P AD RG E ++D+L
Sbjct: 111 GFSLHDRTVGIVGVGNVGRRLQARLEALGIKTLL----CDPPRAD-RGDEGDFRSLDELV 165
Query: 95 KQSDFIIITSALTPD----THHLINRARLESMKPGAILINTSRGQLVDQEALI 143
+++D + + L D T HL + + S+KPGAILIN RG +VD AL+
Sbjct: 166 QEADILTFHTPLFKDGPYKTLHLADEKLIRSLKPGAILINACRGAVVDNTALL 218
>gnl|CDD|235800 PRK06436, PRK06436, glycerate dehydrogenase; Provisional.
Length = 303
Score = 61.1 bits (148), Expect = 8e-11
Identities = 31/107 (28%), Positives = 55/107 (51%), Gaps = 3/107 (2%)
Query: 40 LQNSTVGIVGCGRIGLSVLEKLIPYKVSKFLYTSRSKKPEADKRGAEHTNIDDLCKQSDF 99
L N ++GI+G G IG V + ++ + YT E +D+ K+SDF
Sbjct: 120 LYNKSLGILGYGGIGRRVALLAKAFGMNIYAYTRSYVNDGISSIYMEP---EDIMKKSDF 176
Query: 100 IIITSALTPDTHHLINRARLESMKPGAILINTSRGQLVDQEALIDFI 146
++I+ LT +T +IN L + G +IN +R +VD+ +++F+
Sbjct: 177 VLISLPLTDETRGMINSKMLSLFRKGLAIINVARADVVDKNDMLNFL 223
>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 = 58.1 bits (141), Expect = 7e-10
Identities = 31/112 (27%), Positives = 55/112 (49%), Gaps = 3/112 (2%)
Query: 37 GPALQNSTVGIVGCGRIGLSVLEKLIPYKVSKFLYTSRSKKPEADKRGAEHTNIDDLCKQ 96
G L TVGI+G G +G + ++L + Y K AE +++ L K+
Sbjct: 133 GVELMGKTVGIIGYGNMGKAFAKRLSGFGCKVIAY---DKYKNFGDAYAEQVSLETLFKE 189
Query: 97 SDFIIITSALTPDTHHLINRARLESMKPGAILINTSRGQLVDQEALIDFIAD 148
+D + + LTP+T ++N+ + S K INT+RG++V + L+ +
Sbjct: 190 ADILSLHIPLTPETRGMVNKEFISSFKKPFYFINTARGKVVVTKDLVKALKS 241
>gnl|CDD|183550 PRK12480, PRK12480, D-lactate dehydrogenase; Provisional.
Length = 330
Score = 58.4 bits (141), Expect = 8e-10
Identities = 32/121 (26%), Positives = 60/121 (49%), Gaps = 5/121 (4%)
Query: 29 SWAPNFMCGPALQNSTVGIVGCGRIGLSVLEKLIPYKVSKFLYTSRSKKPEADKRGAEHT 88
+W M P ++N TV I+G GRIG + + + + Y + P D +
Sbjct: 134 TWQAEIMSKP-VKNMTVAIIGTGRIGAATAKIYAGFGATITAYDAY---PNKDLDFLTYK 189
Query: 89 N-IDDLCKQSDFIIITSALTPDTHHLINRARLESMKPGAILINTSRGQLVDQEALIDFIA 147
+ + + K +D I + +++HL ++A + +K GAIL+N +RG +++ LI +
Sbjct: 190 DSVKEAIKDADIISLHVPANKESYHLFDKAMFDHVKKGAILVNAARGAVINTPDLIAAVN 249
Query: 148 D 148
D
Sbjct: 250 D 250
>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 = 57.3 bits (139), Expect = 1e-09
Identities = 32/108 (29%), Positives = 54/108 (50%), Gaps = 4/108 (3%)
Query: 40 LQNSTVGIVGCGRIGLSVLEKLIPYKVSKFLYTSRSKKPEADKRGAEHTNIDDLCKQSDF 99
L VGI+G G G + + L + + Y SR++KP+A+ +G + +++L K D
Sbjct: 136 LTGLKVGIIGLGTTGQMIADALSFFG-ADVYYYSRTRKPDAEAKGIRYLPLNELLKTVD- 193
Query: 100 IIITSALTPDTHHLINRARLESMKPGAILINTSRGQLVDQEALIDFIA 147
+I + L + L+ E + G IL NTS G + EAL ++
Sbjct: 194 -VICTCLPKNV-ILLGEEEFELLGDGKILFNTSLGPSFEVEALKKWLK 239
>gnl|CDD|181499 PRK08605, PRK08605, D-lactate dehydrogenase; Validated.
Length = 332
Score = 56.7 bits (137), Expect = 3e-09
Identities = 32/120 (26%), Positives = 59/120 (49%), Gaps = 5/120 (4%)
Query: 29 SWAPNFMCGPALQNSTVGIVGCGRIGLSVLEKLIPYKVSKFLYTSRSKKPEADKRG-AEH 87
W P + ++++ V ++G GRIGL+V + I K + P A ++
Sbjct: 134 RWEPPIL-SRSIKDLKVAVIGTGRIGLAVAK--IFAKGYGSDVVAYDPFPNAKAATYVDY 190
Query: 88 TN-IDDLCKQSDFIIITSALTPDTHHLINRARLESMKPGAILINTSRGQLVDQEALIDFI 146
+ I++ + +D + + T H+L N + K GA+ +N +RG LVD +AL+D +
Sbjct: 191 KDTIEEAVEGADIVTLHMPATKYNHYLFNADLFKHFKKGAVFVNCARGSLVDTKALLDAL 250
>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 = 49.3 bits (118), Expect = 7e-07
Identities = 27/133 (20%), Positives = 41/133 (30%), Gaps = 58/133 (43%)
Query: 107 TPDTHHLINRARLESMKPGAILINTSRGQLVDQEALIDFIADIRVISISMVTNEKHLHRV 166
TP T H ++ L ++ A ++N RG VD++AL+
Sbjct: 207 TPSTAHALDAEVLAALPKHAWVVNVGRGATVDEDALV----------------------- 243
Query: 167 FTLGDSFHKGHVSAFIFIHMIMGDTVGIYFIFSASDVLKAKKIRGAGLDVMYPEPLPLDS 226
+ G + +A DV EPLP S
Sbjct: 244 ----AALESGRLGG------------------AALDVTA-------------TEPLPASS 268
Query: 227 PLLQLDNCVILPH 239
PL N ++ PH
Sbjct: 269 PLWDAPNLILTPH 281
>gnl|CDD|185366 PRK15469, ghrA, bifunctional glyoxylate/hydroxypyruvate reductase
A; Provisional.
Length = 312
Score = 40.9 bits (96), Expect = 4e-04
Identities = 21/49 (42%), Positives = 27/49 (55%), Gaps = 3/49 (6%)
Query: 204 LKAKKIRGAGLDVMYPEPLPLDSPLLQLDNCVILPHIGSAQIETRQEMA 252
L + K++GA LDV EPLP +SPL Q I PH+ + TR A
Sbjct: 240 LDSGKVKGAMLDVFSREPLPPESPLWQHPRVAITPHVAAV---TRPAEA 285
Score = 39.0 bits (91), Expect = 0.001
Identities = 32/104 (30%), Positives = 51/104 (49%), Gaps = 6/104 (5%)
Query: 44 TVGIVGCGRIGLSVLEKLIPYKVSKFLYTSRSKK--PEADK-RGAEHTNIDDLCKQSDFI 100
T+GI+G G +G V + L + + SRS+K P G E + Q+ +
Sbjct: 138 TIGILGAGVLGSKVAQSLQTWGFPLRCW-SRSRKSWPGVQSFAGREE--LSAFLSQTRVL 194
Query: 101 IITSALTPDTHHLINRARLESMKPGAILINTSRGQLVDQEALID 144
I TP+T +IN+ LE + GA L+N +RG V ++ L+
Sbjct: 195 INLLPNTPETVGIINQQLLEQLPDGAYLLNLARGVHVVEDDLLA 238
>gnl|CDD|214966 smart01002, AlaDh_PNT_C, Alanine dehydrogenase/PNT, C-terminal
domain. Alanine dehydrogenase catalyzes the
NAD-dependent reversible reductive amination of pyruvate
into alanine.
Length = 149
Score = 37.9 bits (89), Expect = 0.001
Identities = 12/43 (27%), Positives = 27/43 (62%), Gaps = 3/43 (6%)
Query: 89 NIDDLCKQSDFIIITSALTPD--THHLINRARLESMKPGAILI 129
+++ K++D ++I + L P L+ R ++SMKPG++++
Sbjct: 76 LLEEAVKEAD-LVIGAVLIPGAKAPKLVTREMVKSMKPGSVIV 117
>gnl|CDD|240629 cd05304, Rubrum_tdh, Rubrum transdehydrogenase NAD-binding and
catalytic domains. Transhydrogenases found in bacterial
and inner mitochondrial membranes link
NAD(P)(H)-dependent redox reactions to proton
translocation. The energy of the proton electrochemical
gradient (delta-p), generated by the respiratory
electron transport chain, is consumed by
transhydrogenase in NAD(P)+ reduction. Transhydrogenase
is likely involved in the regulation of the citric acid
cycle. Rubrum transhydrogenase has 3 components, dI,
dII, and dIII. dII spans the membrane while dI and dIII
protrude on the cytoplasmic/matrix side. DI contains 2
domains in Rossmann-like folds, linked by a long alpha
helix, and contains a NAD binding site. Two dI
polypeptides (represented in this sub-family)
spontaneously form a heterotrimer with dIII in the
absence of dII. In the heterotrimer, both dI chains may
bind NAD, but only one is well-ordered. dIII also binds
a well-ordered NADP, but in a different orientation than
a classical Rossmann domain.
Length = 363
Score = 37.8 bits (89), Expect = 0.005
Identities = 15/52 (28%), Positives = 28/52 (53%), Gaps = 3/52 (5%)
Query: 80 ADKRGAEHTNIDDLCKQSDFIIITSALTP--DTHHLINRARLESMKPGAILI 129
+ + + ++D I+IT+AL P LI + +ESMKPG++++
Sbjct: 233 EEFLAKQRELLAKHIAEAD-IVITTALIPGRKAPKLITKEMVESMKPGSVIV 283
Score = 27.8 bits (63), Expect = 7.4
Identities = 16/73 (21%), Positives = 28/73 (38%), Gaps = 10/73 (13%)
Query: 84 GAEHTNIDDLCKQSDFIIITSALTPDTHHLINRARLESMKPGAILINTSRGQLVDQEALI 143
GAE + + Q+D I+ P + +K GA+LI L+
Sbjct: 54 GAEIVSDAEELAQAD--IVLKVRPPSEEEV------ALLKEGAVLI--GFLDPAQNPELV 103
Query: 144 DFIADIRVISISM 156
+ +A V + +M
Sbjct: 104 EALAKKGVTAFAM 116
>gnl|CDD|224626 COG1712, COG1712, Predicted dinucleotide-utilizing enzyme [General
function prediction only].
Length = 255
Score = 36.6 bits (85), Expect = 0.007
Identities = 25/103 (24%), Positives = 46/103 (44%), Gaps = 11/103 (10%)
Query: 44 TVGIVGCGRIGLSVLEKL----IPYKVSKFLYTSRSKKPEADK--RGAEHTNIDDLCKQS 97
VGIVGCG IG +LE + + +++ K E + ++ID+L +
Sbjct: 2 KVGIVGCGAIGKFLLELVRDGRVDFELVAVYDRDEEKAKELEASVGRRCVSDIDELIAEV 61
Query: 98 DFIIITSALTPDTHHLINRARLESMKPGAILINTSRGQLVDQE 140
D +++ +A + + + +K G +I S G L D+
Sbjct: 62 D-LVVEAA----SPEAVREYVPKILKAGIDVIVMSVGALADEG 99
>gnl|CDD|225826 COG3288, PntA, NAD/NADP transhydrogenase alpha subunit [Energy
production and conversion].
Length = 356
Score = 36.6 bits (85), Expect = 0.010
Identities = 15/44 (34%), Positives = 25/44 (56%), Gaps = 5/44 (11%)
Query: 95 KQSDFIIITSALTP--DTHHLINRARLESMKPGAILIN--TSRG 134
K+ D I+IT+AL P L+ + SMKPG+++++ G
Sbjct: 243 KEVD-IVITTALIPGRPAPKLVTAEMVASMKPGSVIVDLAAETG 285
>gnl|CDD|188459 TIGR03944, dehyd_SbnB_fam, 2,3-diaminopropionate biosynthesis
protein SbnB. Members of this protein family are
probable NAD-dependent dehydrogenases related to the
alanine dehydrogenase of Archaeoglobus fulgidus (see
TIGR02371, PDB structure 1OMO and PMID:15313611) and
more distantly to ornithine cyclodeaminase. Members
include the staphylobactin biosynthesis protein SbnB and
tend to occur in contexts suggesting non-ribosomal
peptide synthesis, always adjacent to (occasionally
fused with) a pyridoxal phosphate-dependent enzyme,
SbnA. The pair appears to provide 2,3-diaminopropionate
for biosynthesis of siderophores or other secondary
metabolites [Cellular processes, Biosynthesis of natural
products].
Length = 327
Score = 36.0 bits (84), Expect = 0.014
Identities = 28/109 (25%), Positives = 46/109 (42%), Gaps = 19/109 (17%)
Query: 37 GPALQNSTVGIVGCGRIGLSVLEKLI---PYKVSKFLYTSRSKKPEA-DKRGAEH----- 87
+ VGI+GCG I +L L+ P LY + EA R E
Sbjct: 127 AAGRGFTRVGIIGCGPIAREILRFLLALGPEIRRVVLYDLDPARAEAFAARCQELGPGKV 186
Query: 88 ---TNIDDLCKQSDFIII-TSALTPDTHHLINRARLESMKPGAILINTS 132
+ + +Q+D ++ T A TP ++ + A +PGA+++N S
Sbjct: 187 TVAASAEAALRQADLVVTATVAGTP---YIDDPAWF---QPGALVLNIS 229
>gnl|CDD|240630 cd05305, L-AlaDH, Alanine dehydrogenase NAD-binding and catalytic
domains. Alanine dehydrogenase (L-AlaDH) catalyzes the
NAD-dependent conversion of pyruvate to L-alanine via
reductive amination. Like formate dehydrogenase and
related enzymes, L-AlaDH is comprised of 2 domains
connected by a long alpha helical stretch, each
resembling a Rossmann fold NAD-binding domain. The
NAD-binding domain is inserted within the linear
sequence of the more divergent catalytic domain. Ligand
binding and active site residues are found in the cleft
between the subdomains. L-AlaDH is typically hexameric
and is critical in carbon and nitrogen metabolism in
micro-organisms.
Length = 359
Score = 35.5 bits (83), Expect = 0.020
Identities = 14/55 (25%), Positives = 31/55 (56%), Gaps = 11/55 (20%)
Query: 89 NIDDLCKQSDFII----ITSALTPDTHHLINRARLESMKPGAILINTSRGQLVDQ 139
N+++ K++D +I I A P L+ +++MKPG+++++ + +DQ
Sbjct: 224 NLEEALKEADLVIGAVLIPGAKAP---KLVTEEMVKTMKPGSVIVDVA----IDQ 271
>gnl|CDD|129609 TIGR00518, alaDH, alanine dehydrogenase. The family of known
L-alanine dehydrogenases includes representatives from
the Proteobacteria, Firmicutes, and Cyanobacteria, all
with about 50 % identity or better. An outlier to this
group in both sequence and gap pattern is the homolog
from Helicobacter pylori, an epsilon division
Proteobacteria, which must be considered a putative
alanine dehydrogenase. Related proteins include
saccharopine dehydrogenase and the N-terminal half of
the NAD(P) transhydrogenase alpha subunit. All of these
related proteins bind NAD and/or NADP [Energy
metabolism, Amino acids and amines].
Length = 370
Score = 34.5 bits (79), Expect = 0.048
Identities = 20/86 (23%), Positives = 38/86 (44%), Gaps = 14/86 (16%)
Query: 81 DKRGAEHTNIDDLCKQSDFII----ITSALTPDTHHLINRARLESMKPGAILINTSRGQL 136
R + I+D K++D +I I A P L++ + + MKPGA++++ +
Sbjct: 215 HTRYSNAYEIEDAVKRADLLIGAVLIPGAKAPK---LVSNSLVAQMKPGAVIVDVA---- 267
Query: 137 VDQEALIDFIADIRVISISMVTNEKH 162
+DQ ++ R + T H
Sbjct: 268 IDQGGCVE---TSRPTTHDQPTYAVH 290
>gnl|CDD|223758 COG0686, Ald, Alanine dehydrogenase [Amino acid transport and
metabolism].
Length = 371
Score = 34.2 bits (79), Expect = 0.059
Identities = 18/78 (23%), Positives = 35/78 (44%), Gaps = 14/78 (17%)
Query: 89 NIDDLCKQSDFII----ITSALTPDTHHLINRARLESMKPGAILINTSRGQLVDQEALID 144
NI++ K++D +I I A P L+ R ++ MKPG+++++ + +DQ +
Sbjct: 224 NIEEAVKKADLVIGAVLIPGAKAP---KLVTREMVKQMKPGSVIVDVA----IDQGGCFE 276
Query: 145 FIADIRVISISMVTNEKH 162
+ T E
Sbjct: 277 ---TSHPTTHDDPTYEVD 291
>gnl|CDD|216396 pfam01262, AlaDh_PNT_C, Alanine dehydrogenase/PNT, C-terminal
domain. This family now also contains the lysine
2-oxoglutarate reductases.
Length = 150
Score = 33.3 bits (77), Expect = 0.060
Identities = 9/42 (21%), Positives = 23/42 (54%), Gaps = 1/42 (2%)
Query: 89 NIDDLCKQSDFIIITSALTPD-THHLINRARLESMKPGAILI 129
+ + ++D +I T + L+ R +++MKPG++++
Sbjct: 77 YLAEAIAEADLVIGTVLIPGARAPKLVTREMVKTMKPGSVIV 118
>gnl|CDD|223137 COG0059, IlvC, Ketol-acid reductoisomerase [Amino acid transport
and metabolism / Coenzyme metabolism].
Length = 338
Score = 34.1 bits (79), Expect = 0.064
Identities = 23/100 (23%), Positives = 39/100 (39%), Gaps = 19/100 (19%)
Query: 39 ALQNSTVGIVGCGRIGL--------SVLEKLIPYKVSKFLYTSRSKKPEADKRGAEHTNI 90
L+ V I+G G G S L V L S +A + G + +
Sbjct: 15 LLKGKKVAIIGYGSQGHAQALNLRDSGL------NVIIGLRKGSSSWKKAKEDGFKVYTV 68
Query: 91 DDLCKQSDFIIITSALTPDTHH--LINRARLESMKPGAIL 128
++ K++D ++I L PD + + ++K GA L
Sbjct: 69 EEAAKRADVVMI---LLPDEQQKEVYEKEIAPNLKEGAAL 105
>gnl|CDD|116601 pfam07991, IlvN, Acetohydroxy acid isomeroreductase, catalytic
domain. Acetohydroxy acid isomeroreductase catalyzes
the conversion of acetohydroxy acids into dihydroxy
valerates. This reaction is the second in the synthetic
pathway of the essential branched side chain amino acids
valine and isoleucine.
Length = 165
Score = 31.7 bits (73), Expect = 0.19
Identities = 21/97 (21%), Positives = 38/97 (39%), Gaps = 13/97 (13%)
Query: 39 ALQNSTVGIVGCGRIGLSVLEKLIPYKVSKF-----LYTSRSKKPEADKRGAEHTNIDDL 93
L+ + ++G G G + L + S L +A K G E + +
Sbjct: 1 ILKGKKIAVIGYGSQGHAHALNL---RDSGVNVIVGLRPGSKSWEKAKKDGFEVYTVAEA 57
Query: 94 CKQSDFIIITSALTPDTHH--LINRARLESMKPGAIL 128
K++D ++I L PD + + ++K GA L
Sbjct: 58 VKKADVVMI---LLPDEVQAEVYEKEIAPNLKEGAAL 91
>gnl|CDD|224995 COG2084, MmsB, 3-hydroxyisobutyrate dehydrogenase and related
beta-hydroxyacid dehydrogenases [Lipid metabolism].
Length = 286
Score = 32.2 bits (74), Expect = 0.24
Identities = 19/95 (20%), Positives = 38/95 (40%), Gaps = 5/95 (5%)
Query: 43 STVGIVGCGRIGLSVLEKLIP--YKVSKFLYTSRSKKPEADKRGAE-HTNIDDLCKQSDF 99
+ +G G +G + L+ ++V+ + T GA + + ++D
Sbjct: 1 MKIAFIGLGIMGSPMAANLLKAGHEVTVYNRTPEKAAELLAAAGATVAASPAEAAAEADV 60
Query: 100 IIITSALTPDTHHLINRA--RLESMKPGAILINTS 132
+I ++ LE +KPGAI+I+ S
Sbjct: 61 VITMLPDDAAVRAVLFGENGLLEGLKPGAIVIDMS 95
>gnl|CDD|223422 COG0345, ProC, Pyrroline-5-carboxylate reductase [Amino acid
transport and metabolism].
Length = 266
Score = 31.8 bits (73), Expect = 0.27
Identities = 23/120 (19%), Positives = 54/120 (45%), Gaps = 14/120 (11%)
Query: 43 STVGIVGCGRIGLSVLEKLI---PYKVSKFLYTSRSKKPEADKRGAE-----HTNIDDLC 94
+G +G G +G ++L L+ + + T+RS + + AE T+ +
Sbjct: 2 MKIGFIGAGNMGEAILSGLLKSGALPPEEIIVTNRS-EEKRAALAAEYGVVTTTDNQEAV 60
Query: 95 KQSDFIIITSALTPDTHHLINRARLESMKPGAILINTSRGQLVDQEALIDFIADIRVISI 154
+++D + + A+ P + +L+ + ++I+ + G V E L + +RV+ +
Sbjct: 61 EEADVVFL--AVKPQDLEEVLS-KLKPLTKDKLVISIAAG--VSIETLERLLGGLRVVRV 115
>gnl|CDD|213572 TIGR00936, ahcY, adenosylhomocysteinase. This enzyme hydrolyzes
adenosylhomocysteine as part of a cycle for the
regeneration of the methyl donor S-adenosylmethionine.
Species that lack this enzyme are likely to have
adenosylhomocysteine nucleosidase (EC 3.2.2.9), an
enzyme which also acts as 5'-methyladenosine
nucleosidase (see TIGR01704) [Energy metabolism, Amino
acids and amines].
Length = 407
Score = 32.0 bits (73), Expect = 0.31
Identities = 14/52 (26%), Positives = 21/52 (40%), Gaps = 4/52 (7%)
Query: 79 EADKRGAEHTNIDDLCKQSDFIIITSALTPDTHHLINRARLESMKPGAILIN 130
EA G +++ K D I + +I E+MK GAI+ N
Sbjct: 234 EAAMDGFRVMTMEEAAKIGDIFITATGNK----DVIRGEHFENMKDGAIVAN 281
>gnl|CDD|200436 cd11280, gelsolin_like, Tandemly repeated domains found in
gelsolin, severin, villin, and related proteins.
Gelsolin repeats occur in gelsolin, severin, villin,
advillin, villidin, supervillin, flightless, quail,
fragmin, and other proteins, usually in several copies.
They co-occur with villin headpiece domains,
leucine-rich repeats, and several other domains. These
gelsolin-related actin binding proteins (GRABPs) play
regulatory roles in the assembly and disassembly of
actin filaments; they are involved in F-actin capping,
uncapping, severing, or the nucleation of actin
filaments. Severing of actin filaments is Ca2+
dependent. Villins are also linked to generating bundles
of F-actin with uniform filament polarity, which is most
likely mediated by their extra villin headpiece domain.
Many family members have also adopted functions in the
nucleus, including the regulation of transcription.
Supervillin, gelsolin, and flightless I are involved in
intracellular signaling via nuclear hormone receptors.
The gelsolin-like domain is distantly related to the
actin depolymerizing domains found in cofilin and
similar proteins.
Length = 88
Score = 29.6 bits (67), Expect = 0.39
Identities = 15/67 (22%), Positives = 24/67 (35%), Gaps = 7/67 (10%)
Query: 213 GLDVMYPEPLPLDSPLLQLDNCVILPH-------IGSAQIETRQEMARITAQNIINTFHN 265
G + E +PL S L D+ +L G A + A + A+ +
Sbjct: 9 GSKAIEIEEVPLASSSLDSDDVFVLDTGSEIYIWQGRASSQAELAAAALLAKELDEERKG 68
Query: 266 KPMIYEV 272
KP I +
Sbjct: 69 KPEIVRI 75
>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 = 31.3 bits (72), Expect = 0.44
Identities = 31/120 (25%), Positives = 48/120 (40%), Gaps = 38/120 (31%)
Query: 30 WAP--NFMCGPALQNSTVGIVGCGRIG-LSVLEKLIPYKVSKF----------LYTSRSK 76
++P GP VG+VG G +G L+V KF S SK
Sbjct: 159 YSPLKRNGVGP---GKRVGVVGIGGLGHLAV----------KFAKALGAEVTAFSRSPSK 205
Query: 77 KPEADKRGAEH----TNIDDLCKQS---DFIIITSALTPDTHHLINRARLESMKPGAILI 129
K +A K GA+ + + + K + D II T + + D ++ +KPG L+
Sbjct: 206 KEDALKLGADEFIATKDPEAMKKAAGSLDLIIDTVSASHDLDPYLS-----LLKPGGTLV 260
>gnl|CDD|234849 PRK00856, pyrB, aspartate carbamoyltransferase catalytic subunit;
Provisional.
Length = 305
Score = 30.8 bits (71), Expect = 0.68
Identities = 14/64 (21%), Positives = 24/64 (37%), Gaps = 13/64 (20%)
Query: 77 KPEADKRGAEHTNIDDLCKQSDFII--------ITSALTPDTHHL-----INRARLESMK 123
PE HT++D++ + +D ++ + L P + RL K
Sbjct: 194 LPEGMPEYGVHTDLDEVIEDADVVMMLRVQKERMDGGLLPSYEEYKRSYGLTAERLALAK 253
Query: 124 PGAI 127
P AI
Sbjct: 254 PDAI 257
>gnl|CDD|237343 PRK13304, PRK13304, L-aspartate dehydrogenase; Reviewed.
Length = 265
Score = 30.7 bits (70), Expect = 0.75
Identities = 19/63 (30%), Positives = 31/63 (49%), Gaps = 6/63 (9%)
Query: 45 VGIVGCGRIGL----SVLEKLIPYKVSKFLYTSRSKKPE-ADKRGAEHT-NIDDLCKQSD 98
+GIVGCG I ++L I ++ F + K A K GA+ +ID+L + D
Sbjct: 4 IGIVGCGAIASLITKAILSGRINAELYAFYDRNLEKAENLASKTGAKACLSIDELVEDVD 63
Query: 99 FII 101
++
Sbjct: 64 LVV 66
>gnl|CDD|236071 PRK07638, PRK07638, acyl-CoA synthetase; Validated.
Length = 487
Score = 30.9 bits (70), Expect = 0.82
Identities = 20/71 (28%), Positives = 29/71 (40%), Gaps = 9/71 (12%)
Query: 161 KHLHRVFTLGDSFHKGHVSAFIF--IH-MIMGDTVGIYFIFSASDVLKAKKIRGAGLDVM 217
K V G H S F++ I + +G TV + F + VL K+ + VM
Sbjct: 182 KREDSVLIAGTLVH----SLFLYGAISTLYVGQTVHLMRKFIPNQVLD--KLETENISVM 235
Query: 218 YPEPLPLDSPL 228
Y P L+S
Sbjct: 236 YTVPTMLESLY 246
>gnl|CDD|129557 TIGR00465, ilvC, ketol-acid reductoisomerase. This is the second
enzyme in the parallel isoleucine-valine biosynthetic
pathway [Amino acid biosynthesis, Pyruvate family].
Length = 314
Score = 30.4 bits (69), Expect = 0.87
Identities = 24/99 (24%), Positives = 39/99 (39%), Gaps = 19/99 (19%)
Query: 40 LQNSTVGIVGCGRIGL--------SVLEKLIPYKVSKFLYTSRSKKPEADKRGAEHTNID 91
L+ TV I+G G G S L V L + +A + G + ++
Sbjct: 1 LKGKTVAIIGYGSQGHAQALNLRDSGL------NVIVGLRKGGASWKKATEDGFKVGTVE 54
Query: 92 DLCKQSDFIIITSALTPD-THHLINRARLES-MKPGAIL 128
+ Q+D I+ L PD H + A ++ +K G L
Sbjct: 55 EAIPQADLIMN---LLPDEVQHEVYEAEIQPLLKEGKTL 90
>gnl|CDD|236507 PRK09424, pntA, NAD(P) transhydrogenase subunit alpha; Provisional.
Length = 509
Score = 30.6 bits (70), Expect = 0.96
Identities = 16/39 (41%), Positives = 23/39 (58%), Gaps = 3/39 (7%)
Query: 93 LCKQSDFIIITSALTP--DTHHLINRARLESMKPGAILI 129
K+ D IIIT+AL P LI + SMKPG++++
Sbjct: 245 QAKEVD-IIITTALIPGKPAPKLITAEMVASMKPGSVIV 282
>gnl|CDD|176246 cd08286, FDH_like_ADH2, formaldehyde dehydrogenase (FDH)-like.
This group is related to formaldehyde dehydrogenase
(FDH), which is a member of the zinc-dependent/medium
chain alcohol dehydrogenase family. This family uses
NAD(H) as a cofactor in the interconversion of alcohols
and aldehydes, or ketones. Another member is identified
as a dihydroxyacetone reductase. Like the zinc-dependent
alcohol dehydrogenases (ADH) of the medium chain alcohol
dehydrogenase/reductase family (MDR), tetrameric FDHs
have a catalytic zinc that resides between the catalytic
and NAD(H)binding domains and a structural zinc in a
lobe of the catalytic domain. Unlike ADH, where
NAD(P)(H) acts as a cofactor, NADH in FDH is a tightly
bound redox cofactor (similar to nicotinamide proteins).
The medium chain alcohol dehydrogenase family (MDR) has
a NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The N-terminal region typically has an
all-beta catalytic domain. These proteins typically form
dimers (typically higher plants, mammals) or tetramers
(yeast, bacteria), and have 2 tightly bound zinc atoms
per subunit.
Length = 345
Score = 30.3 bits (69), Expect = 0.98
Identities = 18/48 (37%), Positives = 23/48 (47%), Gaps = 2/48 (4%)
Query: 43 STVGIVGCGRIGLSVLEKLIPYKVSKF--LYTSRSKKPEADKRGAEHT 88
TV IVG G +GL+ L Y SK + ++ A K GA HT
Sbjct: 168 DTVAIVGAGPVGLAALLTAQLYSPSKIIMVDLDDNRLEVAKKLGATHT 215
>gnl|CDD|129652 TIGR00561, pntA, NAD(P) transhydrogenase, alpha subunit. This
integral membrane protein is the alpha subunit of alpha
2 beta 2 tetramer that couples the proton transport
across the membrane to the reversible transfer of
hydride ion equivalents between NAD and NADP. An
alternate name is pyridine nucleotide transhydrogenase
alpha subunit. The N-terminal region is homologous to
alanine dehydrogenase. In some species, such as
Rhodospirillum rubrum, the alpha chain is replaced by
two shorter chains, both with some homology to the
full-length alpha chain modeled here. These score below
the trusted cutoff [Energy metabolism, Electron
transport].
Length = 511
Score = 30.3 bits (68), Expect = 1.3
Identities = 13/33 (39%), Positives = 21/33 (63%), Gaps = 2/33 (6%)
Query: 100 IIITSALTPD--THHLINRARLESMKPGAILIN 130
IIIT+AL P LI ++SMK G+++++
Sbjct: 250 IIITTALIPGKPAPKLITEEMVDSMKAGSVIVD 282
>gnl|CDD|217556 pfam03435, Saccharop_dh, Saccharopine dehydrogenase. This family
comprised of three structural domains that can not be
separated in the linear sequence. In some organisms this
enzyme is found as a bifunctional polypeptide with
lysine ketoglutarate reductase. The saccharopine
dehydrogenase can also function as a saccharopine
reductase.
Length = 380
Score = 30.0 bits (68), Expect = 1.5
Identities = 23/102 (22%), Positives = 37/102 (36%), Gaps = 19/102 (18%)
Query: 45 VGIVGCGRIGLSVLEKLIPYKVSKFLYTSRSKKP----EADKRGAEHTNI---------- 90
V I+G G +G V L + + RS + A K G I
Sbjct: 1 VLIIGAGGVGQGVAPLLARHGDLEITVADRSLEKAQALAAPKLGLRFIAIAVDADNYEAL 60
Query: 91 DDLCKQSDFIIITSALTPDTHHLINRARLESMKPGAILINTS 132
L K+ D +I + P + +A +E+ G ++TS
Sbjct: 61 VALLKEGDLVI--NLAPPFLSLTVLKACIET---GVHYVDTS 97
>gnl|CDD|202773 pfam03807, F420_oxidored, NADP oxidoreductase coenzyme
F420-dependent.
Length = 93
Score = 27.9 bits (63), Expect = 1.6
Identities = 12/65 (18%), Positives = 28/65 (43%), Gaps = 5/65 (7%)
Query: 44 TVGIVGCGRIGLSVLEKLIPYKVSKFLYTSRS-KKPEADKR----GAEHTNIDDLCKQSD 98
+GI+G G +G ++ L + SR+ +K A A + ++ +++D
Sbjct: 1 KIGIIGAGNMGEALARGLAAAGHEVVIANSRNPEKAAALAEELGVKATAVSNEEAVEEAD 60
Query: 99 FIIIT 103
+ +
Sbjct: 61 VVFLA 65
>gnl|CDD|214963 smart00996, AdoHcyase, S-adenosyl-L-homocysteine hydrolase.
Length = 426
Score = 29.8 bits (68), Expect = 1.7
Identities = 15/47 (31%), Positives = 25/47 (53%), Gaps = 4/47 (8%)
Query: 84 GAEHTNIDDLCKQSDFIIITSALTPDTHHLINRARLESMKPGAILIN 130
G E ++++ Q+D I +T T +I R + +MK GAI+ N
Sbjct: 250 GFEVVTMEEVAPQAD-IFVT---TTGNKDVITREHMRAMKDGAIVCN 292
>gnl|CDD|198065 smart00997, AdoHcyase_NAD, S-adenosyl-L-homocysteine hydrolase, NAD
binding domain.
Length = 162
Score = 29.0 bits (66), Expect = 1.7
Identities = 18/52 (34%), Positives = 28/52 (53%), Gaps = 4/52 (7%)
Query: 79 EADKRGAEHTNIDDLCKQSDFIIITSALTPDTHHLINRARLESMKPGAILIN 130
EA G E +++ K++D I +T+ T + +I R +MK GAIL N
Sbjct: 61 EAAMDGFEVMKMEEAAKRAD-IFVTA--TGNKD-VITREHFRAMKDGAILAN 108
>gnl|CDD|240621 cd01620, Ala_dh_like, Alanine dehydrogenase and related
dehydrogenases. Alanine dehydrogenase/Transhydrogenase,
such as the hexameric L-alanine dehydrogenase of
Phormidium lapideum, contain 2 Rossmann fold-like
domains linked by an alpha helical region. Related
proteins include Saccharopine Dehydrogenase (SDH),
bifunctional lysine ketoglutarate reductase
/saccharopine dehydrogenase enzyme,
N(5)-(carboxyethyl)ornithine synthase, and Rubrum
transdehydrogenase. Alanine dehydrogenase (L-AlaDH)
catalyzes the NAD-dependent conversion of pyrucate to
L-alanine via reductive amination. Transhydrogenases
found in bacterial and inner mitochondrial membranes
link NAD(P)(H)-dependent redox reactions to proton
translocation. The energy of the proton electrochemical
gradient (delta-p), generated by the respiratory
electron transport chain, is consumed by
transhydrogenase in NAD(P)+ reduction. Transhydrogenase
is likely involved in the regulation of the citric acid
cycle. Rubrum transhydrogenase has 3 components, dI,
dII, and dIII. dII spans the membrane while dI and dIII
protrude on the cytoplasmic/matirx side. DI contains 2
domains with Rossmann folds, linked by a long alpha
helix, and contains a NAD binding site. Two dI
polypeptides (represented in this sub-family)
spontaneously form a heterotrimer with one dIII in the
absence of dII. In the heterotrimer, both dI chains may
bind NAD, but only one is well-ordered. dIII also binds
a well-ordered NADP, but in a different orientation than
classical Rossmann domains.
Length = 317
Score = 29.3 bits (66), Expect = 1.9
Identities = 21/103 (20%), Positives = 37/103 (35%), Gaps = 20/103 (19%)
Query: 44 TVGIVGCGRIGLSVLEKLIPYKVSKFLYTSRSKKPEADKRGAEHTN------------ID 91
V I+G G +GL + K + +K T ++
Sbjct: 164 KVLIIGAGVVGLGAAKIA-----KKLGANVLVYDIKEEKLKGVETLGGSRLRYSQKEELE 218
Query: 92 DLCKQSDFIIITSALTPD--THHLINRARLESMKPGAILINTS 132
KQ+D I+I + L LI + MK GA++++ +
Sbjct: 219 KELKQTD-ILINAILVDGPRAPILIMEELVGPMKRGAVIVDLA 260
>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 = 2.1
Identities = 20/97 (20%), Positives = 40/97 (41%), Gaps = 10/97 (10%)
Query: 43 STVGIVGCGRIGLSVLEKLI--PYKVSKFLYTSRSKKPEAD--KRGAE-HTNIDDLCKQS 97
+ +G +G G +G + L+ Y V+ + +R+ + + GA + + +
Sbjct: 1 AKIGFIGLGVMGSPMALNLLKAGYTVTVY---NRTPEKVEELVAEGAVGAASPAEFVASA 57
Query: 98 DFIIITSALTPDTHHLINRAR--LESMKPGAILINTS 132
D +I +I L +KPG I+I+ S
Sbjct: 58 DVVITMVPAGAAVDAVILGEDGLLPGLKPGDIIIDGS 94
>gnl|CDD|234094 TIGR03026, NDP-sugDHase, nucleotide sugar dehydrogenase. Enzymes
in this family catalyze the NAD-dependent
alcohol-to-acid oxidation of nucleotide-linked sugars.
Examples include UDP-glucose 6-dehydrogenase (1.1.1.22)
, GDP-mannose 6-dehydrogenase (1.1.1.132) ,
UDP-N-acetylglucosamine 6-dehydrogenase (1.1.1.136),
UDP-N-acetyl-D-galactosaminuronic acid dehydrogenase and
UDP-N-acetyl-D-mannosaminuronic acid dehydrogenase.
These enzymes are most often involved in the
biosynthesis of polysaccharides and are often found in
operons devoted to that purpose. All of these enzymes
contain three Pfam domains, pfam03721, pfam00984, and
pfam03720 for the N-terminal, central, and C-terminal
regions respectively.
Length = 409
Score = 29.5 bits (67), Expect = 2.1
Identities = 12/54 (22%), Positives = 25/54 (46%), Gaps = 10/54 (18%)
Query: 88 TNIDDLCKQSDFIIITSALTP-------DTHHLINRAR--LESMKPGAILINTS 132
T+ ++ + +D III TP D ++ + A + ++ GA ++ S
Sbjct: 68 TDYEEAIRDADVIIICVP-TPLKEDGSPDLSYVESAAETIAKHLRKGATVVLES 120
>gnl|CDD|201778 pfam01408, GFO_IDH_MocA, Oxidoreductase family, NAD-binding
Rossmann fold. This family of enzymes utilise NADP or
NAD. This family is called the GFO/IDH/MOCA family in
swiss-prot.
Length = 120
Score = 28.3 bits (64), Expect = 2.2
Identities = 19/82 (23%), Positives = 36/82 (43%), Gaps = 6/82 (7%)
Query: 45 VGIVGCGRIG----LSVLEKLIPYKVSKFL--YTSRSKKPEADKRGAEHTNIDDLCKQSD 98
VGIVG G+IG ++ E ++ L +R++ ++++++L D
Sbjct: 3 VGIVGAGKIGRRHLRALNESQDGAELVGILDPDPARAEAVAESFGVPAYSDLEELLADPD 62
Query: 99 FIIITSALTPDTHHLINRARLE 120
++ A P H + A LE
Sbjct: 63 IDAVSVATPPGLHFELALAALE 84
>gnl|CDD|181958 PRK09564, PRK09564, coenzyme A disulfide reductase; Reviewed.
Length = 444
Score = 29.2 bits (66), Expect = 2.3
Identities = 10/35 (28%), Positives = 24/35 (68%), Gaps = 1/35 (2%)
Query: 96 QSDFIIITSALTPDTHHLINRARLESMKPGAILIN 130
++D +I+ + + P+T L + L+++K GAI+++
Sbjct: 234 EADVVIVATGVKPNTEFLED-TGLKTLKNGAIIVD 267
>gnl|CDD|219410 pfam07433, DUF1513, Protein of unknown function (DUF1513). This
family consists of several bacterial proteins of around
360 residues in length. The function of this family is
unknown.
Length = 304
Score = 28.7 bits (65), Expect = 3.0
Identities = 11/35 (31%), Positives = 20/35 (57%), Gaps = 2/35 (5%)
Query: 110 THHLINRAR--LESMKPGAILINTSRGQLVDQEAL 142
TH RA+ L++M+P + ++ G L++Q L
Sbjct: 122 THPDSGRAKLNLDTMQPSLVYLDRRTGALLEQVEL 156
>gnl|CDD|239724 cd03755, proteasome_alpha_type_7, proteasome_alpha_type_7. The 20S
proteasome, multisubunit proteolytic complex, is the
central enzyme of nonlysosomal protein degradation in
both the cytosol and nucleus. It is composed of 28
subunits arranged as four homoheptameric rings that
stack on top of one another forming an elongated
alpha-beta-beta-alpha cylinder with a central cavity.
The proteasome alpha and beta subunits are members of
the N-terminal nucleophile (Ntn)-hydrolase superfamily.
Their N-terminal threonine residues are exposed as a
nucleophile in peptide bond hydrolysis. Mammals have 7
alpha and 7 beta proteasome subunits while archaea have
one of each.
Length = 207
Score = 28.5 bits (64), Expect = 3.2
Identities = 14/29 (48%), Positives = 17/29 (58%), Gaps = 1/29 (3%)
Query: 93 LCKQSDFIIITSA-LTPDTHHLINRARLE 120
+C D + + A LT D LINRARLE
Sbjct: 60 ICMLDDHVCLAFAGLTADARVLINRARLE 88
>gnl|CDD|187576 cd05266, SDR_a4, atypical (a) SDRs, subgroup 4. Atypical SDRs in
this subgroup are poorly defined, one member is
identified as a putative NAD-dependent
epimerase/dehydratase. Atypical SDRs are distinct from
classical SDRs. Members of this subgroup have a
glycine-rich NAD(P)-binding motif that is related to,
but is different from, the archetypical SDRs, GXGXXG.
This subgroup also lacks most of the characteristic
active site residues of the SDRs; however, the upstream
Ser is present at the usual place, and some potential
catalytic residues are present in place of the usual
YXXXK active site motif. Atypical SDRs generally lack
the catalytic residues characteristic of the SDRs, and
their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Atypical SDRs include biliverdin IX beta
reductase (BVR-B,aka flavin reductase), NMRa (a
negative transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane
reductase, isoflavone reductases, and others. SDRs are
a functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. In addition to the Rossmann fold
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids, and typically have a TGXXGXXG cofactor
binding motif. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 251
Score = 28.1 bits (63), Expect = 4.9
Identities = 14/43 (32%), Positives = 24/43 (55%), Gaps = 5/43 (11%)
Query: 45 VGIVGCGRIGLSVLEKLIP--YKVSKFLYTSRSKKPEADKRGA 85
V I+GCG +G + +L+ ++V+ T+RS + A R A
Sbjct: 1 VLILGCGYLGQRLARQLLAQGWQVTG---TTRSPEKLAADRPA 40
>gnl|CDD|176260 cd08300, alcohol_DH_class_III, class III alcohol dehydrogenases.
Members identified as glutathione-dependent formaldehyde
dehydrogenase(FDH), a member of the zinc
dependent/medium chain alcohol dehydrogenase family.
FDH converts formaldehyde and NAD(P) to formate and
NAD(P)H. The initial step in this process the
spontaneous formation of a S-(hydroxymethyl)glutathione
adduct from formaldehyde and glutathione, followed by
FDH-mediated oxidation (and detoxification) of the
adduct to S-formylglutathione. MDH family uses NAD(H)
as a cofactor in the interconversion of alcohols and
aldehydes or ketones. Like many zinc-dependent alcohol
dehydrogenases (ADH) of the medium chain alcohol
dehydrogenase/reductase family (MDR), these FDHs form
dimers, with 4 zinc ions per dimer. The medium chain
alcohol dehydrogenase family (MDR) have a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The N-terminal region typically has an
all-beta catalytic domain. These proteins typically form
dimers (typically higher plants, mammals) or tetramers
(yeast, bacteria), and have 2 tightly bound zinc atoms
per subunit. Alcohol dehydrogenase in the liver
converts ethanol and NAD+ to acetaldehyde and NADH,
while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which have a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES.
These proteins typically form dimers (typically higher
plants, mammals) or tetramers (yeast, bacteria), and
have 2 tightly bound zinc atoms per subunit, a catalytic
zinc at the active site and a structural zinc in a lobe
of the catalytic domain. NAD(H) binding occurs in the
cleft between the catalytic and coenzyme-binding
domains at the active site, and coenzyme binding induces
a conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
Length = 368
Score = 28.0 bits (63), Expect = 5.1
Identities = 14/47 (29%), Positives = 22/47 (46%), Gaps = 2/47 (4%)
Query: 43 STVGIVGCGRIGLSVLEKLIPYKVSKFLY--TSRSKKPEADKRGAEH 87
STV + G G +GL+V++ S+ + + K A K GA
Sbjct: 188 STVAVFGLGAVGLAVIQGAKAAGASRIIGIDINPDKFELAKKFGATD 234
>gnl|CDD|222002 pfam13241, NAD_binding_7, Putative NAD(P)-binding. This domain is
found in fungi, plants, archaea and bacteria.
Length = 104
Score = 26.6 bits (60), Expect = 5.4
Identities = 26/112 (23%), Positives = 41/112 (36%), Gaps = 20/112 (17%)
Query: 40 LQNSTVGIVGCGRIGLSVLEKLIPYK-----VSKFLYTSRSKKPEADKRGAEHTNIDDLC 94
L+ V +VG G + L + L+ VS + + +R E ++D
Sbjct: 5 LKGKRVLVVGGGEVALRKIRALLEAGAKVTVVSPEILEA-EGLVRLIQREFEPGDLDG-- 61
Query: 95 KQSDFIIITSALTPDTHHLINRARLESMKPGAILINTSRGQLVDQEALIDFI 146
+D +I A T D +N + IL+N D L DFI
Sbjct: 62 --ADLVI---AATDDPE--LNERIAALARARGILVNV-----ADDPELCDFI 101
>gnl|CDD|226021 COG3490, COG3490, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 366
Score = 28.2 bits (63), Expect = 5.5
Identities = 11/36 (30%), Positives = 21/36 (58%), Gaps = 2/36 (5%)
Query: 109 DTHHLINRARL--ESMKPGAILINTSRGQLVDQEAL 142
+TH R L +SM+P +L++ + G L+++ L
Sbjct: 184 ETHPDFGRTELNLDSMEPSLVLLDAATGNLIEKHTL 219
>gnl|CDD|223990 COG1062, AdhC, Zn-dependent alcohol dehydrogenases, class III
[Energy production and conversion].
Length = 366
Score = 28.0 bits (63), Expect = 5.5
Identities = 12/48 (25%), Positives = 20/48 (41%), Gaps = 2/48 (4%)
Query: 43 STVGIVGCGRIGLSVLEKLIPYKVSKFLY--TSRSKKPEADKRGAEHT 88
TV + G G +GL+ ++ + + + K A K GA H
Sbjct: 187 DTVAVFGLGGVGLAAIQGAKAAGAGRIIAVDINPEKLELAKKFGATHF 234
>gnl|CDD|187628 cd05370, SDR_c2, classical (c) SDR, subgroup 2. Short-chain
dehydrogenases/reductases (SDRs, aka Tyrosine-dependent
oxidoreductases) are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold (alpha/beta folding
pattern with a central beta-sheet), an NAD(P)(H)-binding
region, and a structurally diverse C-terminal region.
Classical SDRs are typically about 250 residues long,
while extended SDRs are approximately 350 residues.
Sequence identity between different SDR enzymes are
typically in the 15-30% range, but the enzymes share the
Rossmann fold NAD-binding motif and characteristic
NAD-binding and catalytic sequence patterns. These
enzymes catalyze a wide range of activities including
the metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 228
Score = 27.7 bits (62), Expect = 6.4
Identities = 32/123 (26%), Positives = 49/123 (39%), Gaps = 10/123 (8%)
Query: 39 ALQNSTVGIVG-CGRIGLSVLEKLIPYKVSKFLYTSRSKK--PEADKR-GAEHTNIDDLC 94
L +TV I G IGL++ K + + + T R ++ EA K HT + D+
Sbjct: 2 KLTGNTVLITGGTSGIGLALARKFLE-AGNTVIITGRREERLAEAKKELPNIHTIVLDVG 60
Query: 95 KQSDFIIITSALT---PDTHHLINRARLESMKPGAILINTSRGQLVDQEALIDFIADIRV 151
+ AL P+ LIN A + +P + S D E + I IR+
Sbjct: 61 DAESVEALAEALLSEYPNLDILINNAGI--QRPIDLRDPASDLDKADTEIDTNLIGPIRL 118
Query: 152 ISI 154
I
Sbjct: 119 IKA 121
>gnl|CDD|239720 cd03751, proteasome_alpha_type_3, proteasome_alpha_type_3. The 20S
proteasome, multisubunit proteolytic complex, is the
central enzyme of nonlysosomal protein degradation in
both the cytosol and nucleus. It is composed of 28
subunits arranged as four homoheptameric rings that
stack on top of one another forming an elongated
alpha-beta-beta-alpha cylinder with a central cavity.
The proteasome alpha and beta subunits are members of
the N-terminal nucleophile (Ntn)-hydrolase superfamily.
Their N-terminal threonine residues are exposed as a
nucleophile in peptide bond hydrolysis. Mammals have 7
alpha and 7 beta proteasome subunits while archaea have
one of each.
Length = 212
Score = 27.6 bits (62), Expect = 6.4
Identities = 26/87 (29%), Positives = 41/87 (47%), Gaps = 20/87 (22%)
Query: 39 ALQNS--TVGIVGCGRIGLSVLEKLIPYKVSKFLYTSRSKKPEADKRGAEHTNIDDLCKQ 96
A++NS +GI + L+V EKL+ TS+ +P ++KR N+D
Sbjct: 26 AVENSGTAIGIRCKDGVVLAV-EKLV---------TSKLYEPGSNKRIF---NVDRHIG- 71
Query: 97 SDFIIITSALTPDTHHLINRARLESMK 123
I + L D HL++RAR E+
Sbjct: 72 ----IAVAGLLADGRHLVSRAREEAEN 94
>gnl|CDD|217564 pfam03447, NAD_binding_3, Homoserine dehydrogenase, NAD binding
domain. This domain adopts a Rossmann NAD binding
fold. The C-terminal domain of homoserine dehydrogenase
contributes a single helix to this structural domain,
which is not included in the Pfam model.
Length = 116
Score = 26.5 bits (59), Expect = 7.2
Identities = 17/53 (32%), Positives = 22/53 (41%), Gaps = 8/53 (15%)
Query: 49 GCGRIGLSVLEKL------IPYKVSKFLYTSRSKKPEADKRGAE--HTNIDDL 93
GCG IG +LE L IP ++ K A G E ++DDL
Sbjct: 1 GCGAIGSGLLELLLRQQEEIPLELVAVADRDLLSKARAALLGDEPVTLDLDDL 53
>gnl|CDD|221343 pfam11962, Peptidase_G2, Peptidase_G2, IMC autoproteolytic cleavage
domain. This domain is found at the very C-terminus of
bacteriophage parallel beta-helical tailspike proteins.
It carries the enzymic residues that induce
autoproteolytic cleavage to bring about maturation of
the folding process of the helix in a chaperone-like
manner. The domain thus mediates the assembly of a large
tailspike protein and then releases itself after
maturation. These C-terminal regions that
autoproteolytically release themselves after maturation
are exchangeable between functionally unrelated
N-terminal proteins and have been identified in a number
of bacteriophage tailspike proteins.
Length = 222
Score = 27.3 bits (61), Expect = 7.6
Identities = 10/33 (30%), Positives = 15/33 (45%), Gaps = 3/33 (9%)
Query: 71 YTSRSKKPEADK---RGAEHTNIDDLCKQSDFI 100
Y R ++PE + G + ID K D+I
Sbjct: 152 YIPREERPEWNPVGLIGQIYVRIDGTVKPGDYI 184
>gnl|CDD|215144 PLN02256, PLN02256, arogenate dehydrogenase.
Length = 304
Score = 27.3 bits (61), Expect = 8.1
Identities = 20/67 (29%), Positives = 32/67 (47%), Gaps = 5/67 (7%)
Query: 44 TVGIVGCGRIGLSVLEKLIPYKVSKFLYTSRSKKPE-ADKRGAE-HTNIDDLCKQS-DFI 100
+GIVG G G + + + L TSRS + A + G + DD C++ D +
Sbjct: 38 KIGIVGFGNFGQFLAKTFVKQG-HTVLATSRSDYSDIAAELGVSFFRDPDDFCEEHPDVV 96
Query: 101 II-TSAL 106
++ TS L
Sbjct: 97 LLCTSIL 103
>gnl|CDD|223745 COG0673, MviM, Predicted dehydrogenases and related proteins
[General function prediction only].
Length = 342
Score = 27.5 bits (61), Expect = 9.2
Identities = 14/76 (18%), Positives = 26/76 (34%), Gaps = 8/76 (10%)
Query: 45 VGIVGCGRIGLSVLEKLIPYKVSKF----LYTSRSKKPE--ADKRGAEH--TNIDDLCKQ 96
VGI+G G I + + ++ E A++ G T++++L
Sbjct: 6 VGIIGAGGIAGKAHLPALAALGGGLELVAVVDRDPERAEAFAEEFGIAKAYTDLEELLAD 65
Query: 97 SDFIIITSALTPDTHH 112
D + A H
Sbjct: 66 PDIDAVYIATPNALHA 81
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
0.324 0.139 0.417
Gapped
Lambda K H
0.267 0.0831 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,053,516
Number of extensions: 1332294
Number of successful extensions: 1411
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1314
Number of HSP's successfully gapped: 182
Length of query: 274
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 179
Effective length of database: 6,723,972
Effective search space: 1203590988
Effective search space used: 1203590988
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 58 (25.9 bits)