RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 006758
(632 letters)
>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 = 267 bits (684), Expect = 2e-84
Identities = 112/325 (34%), Positives = 162/325 (49%), Gaps = 23/325 (7%)
Query: 20 PSVVALNCIE-DCVLEQDSL--AGVALVEHVPLGRLADGKIEA--AAAVLLHSLAYLPRA 74
P VV + D +E++ L AGV LV+ + A A A+L+ A +
Sbjct: 1 PKVVITDYDFPDLDIEREVLEEAGVELVD-AQSRTEDELIEAAADADALLVQY-APVTAE 58
Query: 75 AQRRLRPYQLILCLGSSDRTVDSALAADLGLRLIHVDTSRAEEIADTVMALLLGLLRRTH 134
L ++I+ G VD A A + G+ + +V EE+AD +AL+L L R+
Sbjct: 59 VIEALPRLKVIVRYGVGVDNVDVAAATERGIPVCNVPDYCTEEVADHALALILALARKLP 118
Query: 135 LLARHALSASGWLGSVQPLCRGMRRCRGLVLGIVGRSASARALATRSLSFKMSVLYFD-- 192
L R + +RR RGL LG+VG RA+A R+ +F V+ +D
Sbjct: 119 FLDRAVRAGGWDWTV----GGPIRRLRGLTLGLVGFGRIGRAVAKRAKAFGFRVIAYDPY 174
Query: 193 VPEGKGKVTFPSAARRMDTLNDLLAASDVISLHCAVTDETIQIINAECLQHIKPGAFLVN 252
VP+G R+ +L++LLA SDV+SLHC +T ET +I+AE L +KPGAFLVN
Sbjct: 175 VPDGV----AALGGVRVVSLDELLARSDVVSLHCPLTPETRHLIDAEALALMKPGAFLVN 230
Query: 253 TGSSQLLDDCAVKQLLIDGTLAGCALDGA--EGPQWMEAWVREMPNVLILPRSADYSEEV 310
T L+D+ A+ + L G +AG ALD E P PNV++ P +A YSEE
Sbjct: 231 TARGGLVDEAALARALKSGRIAGAALDVLEEEPPPADSPL-LSAPNVILTPHAAWYSEES 289
Query: 311 WMEIRDKAIS-VLQTFFFDGVIPKN 334
E+R KA V++ G P+N
Sbjct: 290 LAELRRKAAEEVVR--VLRGEPPRN 312
>gnl|CDD|223980 COG1052, LdhA, Lactate dehydrogenase and related dehydrogenases
[Energy production and conversion / Coenzyme metabolism
/ General function prediction only].
Length = 324
Score = 141 bits (358), Expect = 2e-37
Identities = 89/249 (35%), Positives = 124/249 (49%), Gaps = 12/249 (4%)
Query: 94 TVDSALAADLGLRLIHVDTSRAEEIADTVMALLLGLLRRTHLLARHALSA--SGWLGSVQ 151
VD A + G+ + +V E +A+ +AL+L L RR H R S G
Sbjct: 79 NVDLEAAKERGITVTNVPGYSTEAVAEHAVALILALARRIHEGDRRVREGNWSLSGGPDP 138
Query: 152 PLCRGMRRCRGLVLGIVGRSASARALATRSLSFKMSVLYFDVPEGKGKVTFPSAARRMDT 211
L RG LGI+G +A+A R F M VLY+D + AR +D
Sbjct: 139 LL---GFDLRGKTLGIIGLGRIGQAVARRLKGFGMKVLYYD-RSPNPEAEKELGARYVD- 193
Query: 212 LNDLLAASDVISLHCAVTDETIQIINAECLQHIKPGAFLVNTGSSQLLDDCAVKQLLIDG 271
L++LLA SD+ISLHC +T ET +INAE L +KPGA LVNT L+D+ A+ L G
Sbjct: 194 LDELLAESDIISLHCPLTPETRHLINAEELAKMKPGAILVNTARGGLVDEQALIDALKSG 253
Query: 272 TLAGCALD--GAEGPQWMEAWVR--EMPNVLILPRSADYSEEVWMEIRDKAISVLQTFFF 327
+AG LD E + +R PNV++ P A +EE + + A+ L+ FF
Sbjct: 254 KIAGAGLDVFENEPALFDHPLLRLDNFPNVVLTPHIASATEEARKAMAELALENLEA-FF 312
Query: 328 DGVIPKNAI 336
DG +P N +
Sbjct: 313 DGGVPPNEV 321
>gnl|CDD|240622 cd05198, formate_dh_like, Formate/glycerate and related
dehydrogenases of the D-specific 2-hydroxy acid
dehydrogenase family. Formate dehydrogenase, D-specific
2-hydroxy acid dehydrogenase, Phosphoglycerate
Dehydrogenase, Lactate dehydrogenase, Thermostable
Phosphite Dehydrogenase, and Hydroxy(phenyl)pyruvate
reductase, among others, share a characteristic
arrangement of 2 similar subdomains of the alpha/beta
Rossmann fold NAD+ binding form. 2-hydroxyacid
dehydrogenases are enzymes that catalyze the conversion
of a wide variety of D-2-hydroxy acids to their
corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
The NAD+ binding domain is inserted within the linear
sequence of the mostly N-terminal catalytic domain,
which has a similar domain structure to the internal NAD
binding domain. Structurally, these domains are
connected by extended alpha helices and create a cleft
in which NAD is bound, primarily to the C-terminal
portion of the 2nd (internal) domain. Some related
proteins have similar structural subdomain but with a
tandem arrangement of the catalytic and NAD-binding
subdomains in the linear sequence. Formate dehydrogenase
(FDH) catalyzes the NAD+-dependent oxidation of formate
ion to carbon dioxide with the concomitant reduction of
NAD+ to NADH. FDHs of this family contain no metal ions
or prosthetic groups. Catalysis occurs though direct
transfer of hydride ion to NAD+ without the stages of
acid-base catalysis typically found in related
dehydrogenases. FDHs are found in all methylotrophic
microorganisms in energy production and in the stress
responses of plants. Formate/glycerate and related
dehydrogenases of the D-specific 2-hydroxyacid
dehydrogenase superfamily include groups such as formate
dehydrogenase, glycerate dehydrogenase, L-alanine
dehydrogenase, and S-Adenosylhomocysteine Hydrolase,
among others. While many members of this family are
dimeric, alanine DH is hexameric and phosphoglycerate DH
is tetrameric.
Length = 302
Score = 140 bits (356), Expect = 2e-37
Identities = 83/243 (34%), Positives = 121/243 (49%), Gaps = 7/243 (2%)
Query: 84 LILCLGSSDRTVDSALAADLGLRLIHVDTSRAEEIADTVMALLLGLLRRTHLLARHALSA 143
I G+ +D A G+ + +V + AE +A+ + LLL LLRR
Sbjct: 66 FIQVAGAGVDNIDLDAAKKRGITVTNVPGANAEAVAEHALGLLLALLRRLPRADAAVRRG 125
Query: 144 SGWLGSVQPLCRGMRRCRGLVLGIVGRSASARALATRSLSFKMSVLYFDVPEGKGKVTFP 203
GWL + P G +GIVG + +A R +F M VLY+D K +
Sbjct: 126 WGWLWAGFPG----YELEGKTVGIVGLGRIGQRVAKRLQAFGMKVLYYD-RTRKPEPEED 180
Query: 204 SAARRMDTLNDLLAASDVISLHCAVTDETIQIINAECLQHIKPGAFLVNTGSSQLLDDCA 263
R +L++LLA SDV+ LH +T ET +IN E L +KPGA LVNT L+D+ A
Sbjct: 181 LGFRV-VSLDELLAQSDVVVLHLPLTPETRHLINEEELALMKPGAVLVNTARGGLVDEDA 239
Query: 264 VKQLLIDGTLAGCALDGAEG-PQWMEAWVREMPNVLILPRSADYSEEVWMEIRDKAISVL 322
+ + L G +AG ALD E P + + E+PNV++ P A Y+EE + + A+ L
Sbjct: 240 LLRALKSGKIAGAALDVFEPEPLPADHPLLELPNVILTPHIAGYTEEARERMAEIAVENL 299
Query: 323 QTF 325
+ F
Sbjct: 300 ERF 302
>gnl|CDD|223189 COG0111, SerA, Phosphoglycerate dehydrogenase and related
dehydrogenases [Amino acid transport and metabolism].
Length = 324
Score = 130 bits (330), Expect = 1e-33
Identities = 77/289 (26%), Positives = 127/289 (43%), Gaps = 11/289 (3%)
Query: 29 EDCVLEQDSLAGVALVEHVPLGRLADGKIEAAAAVLLHSLAYLPRAAQRRLRPYQLILCL 88
D + E + V + + L + A A L+ S+ + + I
Sbjct: 14 PDALEELLAAYDVEVPDGPDLDEEELLEALADADALIVSVTPVTEEVLAAAPNLKAIGRA 73
Query: 89 GSSDRTVDSALAADLGLRLIHVDTSRAEEIADTVMALLLGLLRRTHLLARHALSASGWLG 148
G+ +D A G+ +++ A +A+ V+ALLL L RR A + W
Sbjct: 74 GAGVDNIDLEAATKRGILVVNAPGGNAISVAELVLALLLALARR-IPDADASQRRGEW-- 130
Query: 149 SVQPLCRGMRRCRGLVLGIVGRSASARALATRSLSFKMSVLYFDVPEGKGKVTFPSAARR 208
G +GI+G RA+A R +F M V+ +D P +
Sbjct: 131 --DRKAFRGTELAGKTVGIIGLGRIGRAVAKRLKAFGMKVIGYD-PYSPRERAGVDGVVG 187
Query: 209 MDTLNDLLAASDVISLHCAVTDETIQIINAECLQHIKPGAFLVNTGSSQLLDDCAVKQLL 268
+D+L++LLA +D+++LH +T ET +INAE L +KPGA L+N ++D+ A+ L
Sbjct: 188 VDSLDELLAEADILTLHLPLTPETRGLINAEELAKMKPGAILINAARGGVVDEDALLAAL 247
Query: 269 IDGTLAGCALDGAEG---PQWMEAWVREMPNVLILPRSADYSEEVWMEI 314
G +AG ALD E P W ++PNV++ P ++E +
Sbjct: 248 DSGKIAGAALDVFEEEPLPADSPLW--DLPNVILTPHIGGSTDEAQERV 294
>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 = 126 bits (320), Expect = 2e-32
Identities = 88/271 (32%), Positives = 125/271 (46%), Gaps = 27/271 (9%)
Query: 61 AAVLLHSLAYLPR----AAQRRLRPYQLILCLGSSDRTVDSALAADLGLRLIHVDTSRAE 116
A VL+ + + AA RLR LI G VD A G+ + ++ AE
Sbjct: 44 ADVLVPGMRKVIDAELLAAAPRLR---LIQQPGVGLDGVDLEAATARGIPVANIPGGNAE 100
Query: 117 EIADTVMALLLGLLRRTHLLARHALSASGWLGSVQPLCRGMRRCRGLVLGIVGRSASARA 176
+A+ + L+L LLRR R + G G +P R R G +GIVG RA
Sbjct: 101 SVAEHAVMLMLALLRRLPEADRELRA--GRWG--RPEGRPSRELSGKTVGIVGLGNIGRA 156
Query: 177 LATRSLSFKMSVLYFDV---PEGKGKVTFPSAARRMDTLNDLLAASDVISLHCAVTDETI 233
+A R F + V+Y+D PE + K R L++LLA SDV+SLH +T ET
Sbjct: 157 VARRLRGFGVEVIYYDRFRDPEAEEKDLGV----RYVELDELLAESDVVSLHVPLTPETR 212
Query: 234 QIINAECLQHIKPGAFLVNTGSSQLLDDCAVKQLLIDGTLAGCALDGAEGPQWMEAW--- 290
+I AE L +KPGA L+NT L+D+ A+ L G LAG LD W E
Sbjct: 213 HLIGAEELAAMKPGAILINTARGGLVDEEALLAALRSGHLAGAGLDVF----WQEPLPPD 268
Query: 291 --VREMPNVLILPRSADYSEEVWMEIRDKAI 319
+ + NV++ P A ++E + +
Sbjct: 269 DPLLRLDNVILTPHIAGVTDESYQRMAAIVA 299
>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 = 122 bits (309), Expect = 6e-31
Identities = 65/205 (31%), Positives = 95/205 (46%), Gaps = 28/205 (13%)
Query: 115 AEEIADTVMALLLGLLRRTHLLARHALSASGWLGSVQPLCRGMRRCRGLVLGIVGRSASA 174
+ +A+ + L+L L R+ R + A GW V G LGI+G
Sbjct: 102 SNSVAELTIGLMLALARQIPQADR-EVRAGGWDRPV------GTELYGKTLGIIGLGRIG 154
Query: 175 RALATRSLSFKMSVLYFDV---PEGKGKVTFPSAARRMDTLNDLLAASDVISLHCAVTDE 231
+A+A R F M VL +D E + +L +LL SD ISLH +T E
Sbjct: 155 KAVARRLSGFGMKVLAYDPYPDEEFAKEHGV-----EFVSLEELLKESDFISLHLPLTPE 209
Query: 232 TIQIINAECLQHIKPGAFLVNTGSSQLLDDCAVKQLLIDGTLAGCALD-------GAEGP 284
T +INA L +KPGA L+NT L+D+ A+ + L G +AG ALD A+ P
Sbjct: 210 TRHLINAAELALMKPGAILINTARGGLVDEEALYEALKSGRIAGAALDVFEEEPPPADSP 269
Query: 285 QWMEAWVREMPNVLILPRSADYSEE 309
+ E+PNV++ P ++E
Sbjct: 270 ------LLELPNVILTPHIGASTKE 288
>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 = 118 bits (299), Expect = 6e-31
Identities = 68/180 (37%), Positives = 95/180 (52%), Gaps = 9/180 (5%)
Query: 123 MALLLGLLRRTHLLARHALSASGWLGSVQPLCRGMRRCRGLVLGIVGRSASARALATRSL 182
+ALLL L RR A + A W +P R G +GI+G RA+A R
Sbjct: 1 LALLLALARRIPE-ADRQVRAGRW----RPDALLGRELSGKTVGIIGLGRIGRAVARRLK 55
Query: 183 SFKMSVLYFDVPEGKGKVTFPSAARRMDTLNDLLAASDVISLHCAVTDETIQIINAECLQ 242
+F M V+ +D K + R +L++LLA SDV+SLH +T ET +INAE L
Sbjct: 56 AFGMKVIAYDR---YPKAEAEALGARYVSLDELLAESDVVSLHLPLTPETRHLINAERLA 112
Query: 243 HIKPGAFLVNTGSSQLLDDCAVKQLLIDGTLAGCALDGAEG-PQWMEAWVREMPNVLILP 301
+KPGA L+NT L+D+ A+ L G +AG ALD E P + + E+PNV++ P
Sbjct: 113 LMKPGAILINTARGGLVDEDALIAALKSGRIAGAALDVFEPEPLPPDHPLLELPNVILTP 172
>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 = 121 bits (307), Expect = 1e-30
Identities = 66/243 (27%), Positives = 107/243 (44%), Gaps = 20/243 (8%)
Query: 95 VDSALAADLGLRLIHVDTSRAEEIADTVMALLLGLLRRTHLLARHALSASGWLGSVQPLC 154
+D G+++ + + E ADT + L+LG LR A + A W G
Sbjct: 90 IDVDALTKRGIQVSNTPGAVDEATADTALFLILGALRNFSR-AERSARAGKWRG--FLDL 146
Query: 155 RGMRRCRGLVLGIVGRSASARALATRSLSFKMSVLYFDV------PEGKGKVTFPSAARR 208
RG LGI+G +A+A ++ +F M ++Y + E + S
Sbjct: 147 TLAHDPRGKTLGILGLGGIGKAIARKAAAFGMKIIYHNRSRLPEELEKALATYYVS---- 202
Query: 209 MDTLNDLLAASDVISLHCAVTDETIQIINAECLQHIKPGAFLVNTGSSQLLDDCAVKQLL 268
L++LLA SDV+SL+C +T T +IN + +K G +VNT ++D+ A+ L
Sbjct: 203 ---LDELLAQSDVVSLNCPLTAATRHLINKKEFAKMKDGVIIVNTARGAVIDEDALVDAL 259
Query: 269 IDGTLAGCALDGAEGPQWMEAWVREMPNVLILPRSADYSEEVW--MEIRDKAISVLQTFF 326
G +A LD E + + +MPNV +LP + E ME + ++ F
Sbjct: 260 ESGKVASAGLDVFENEPEVNPGLLKMPNVTLLPHMGTLTVETQEKMEEL--VLENIEAFL 317
Query: 327 FDG 329
G
Sbjct: 318 ETG 320
>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 = 113 bits (285), Expect = 1e-27
Identities = 66/231 (28%), Positives = 102/231 (44%), Gaps = 20/231 (8%)
Query: 83 QLILCLGSSDRTVDSALAADLGLRLIHVDTSRAEEIADTVMALLLGLLRRTHLLARHALS 142
+LI VD A + G+ +++ AE +A+ + L+L R A AL
Sbjct: 69 KLIGVCRGGPENVDVEAATERGIPVLNTPGRNAEAVAEFTVGLMLAETRNI-ARAHAALK 127
Query: 143 ASGWLGSVQPLCRGMRRCRGLVLGIVGRSASARALATRSLSFKMSVLYFD--VPEGKGKV 200
W RG +GIVG A R +A R +F VL +D V
Sbjct: 128 DGEWRKDYYNYDGYGPELRGKTVGIVGFGAIGRRVAKRLKAFGAEVLVYDPYVDP----E 183
Query: 201 TFPSAARRMDTLNDLLAASDVISLHCAVTDETIQIINAECLQHIKPGAFLVNTGSSQLLD 260
+ + +L +LL SDV+SLH +T ET +I AE +KP A+ +NT + L+D
Sbjct: 184 KIEADGVKKVSLEELLKRSDVVSLHARLTPETRGMIGAEEFALMKPTAYFINTARAGLVD 243
Query: 261 DCAVKQLLIDGTLAGCALD-------GAEGPQWMEAWVREMPNVLILPRSA 304
+ A+ + L +G + G ALD A+ P + ++ NV + P A
Sbjct: 244 EDALIEALEEGKIGGAALDVFPEEPLPADHP------LLKLDNVTLTPHIA 288
>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 = 112 bits (282), Expect = 3e-27
Identities = 62/247 (25%), Positives = 104/247 (42%), Gaps = 30/247 (12%)
Query: 94 TVDSALAADLGLRLIHVDTSRAEEIADTVMALLLGLLRRT----HLLARHALSASGWLGS 149
+D A +LG+ + +V +A+ +AL+L LLR L +G +G
Sbjct: 80 NIDLDYAKELGIGVTNVPEYSPNAVAEHTIALILALLRNRKYIDERDKNQDLQDAGVIG- 138
Query: 150 VQPLCRGMRRCRGLVLGIVGRSASARALATRSLSFKMSVLYFDVPEGKGKVTFPSAARRM 209
R +G+VG RA+A R+ F M V+ +D +
Sbjct: 139 --------RELEDQTVGVVGTGKIGRAVAQRAKGFGMKVIAYDPFRNPE---LEDKGVKY 187
Query: 210 DTLNDLLAASDVISLHCAVTDETIQIINAECLQHIKPGAFLVNTGSSQLLDDCAVKQLLI 269
+L +L SD+ISLH +T E +IN E + +K G ++NT L+D A+ + L
Sbjct: 188 VSLEELFKNSDIISLHVPLTPENHHMINEEAFKLMKKGVIIINTARGSLVDTEALIEALD 247
Query: 270 DGTLAGCALD--GAEGPQWMEAWVRE------------MPNVLILPRSADYSEEVWMEIR 315
G + G LD E P ++ E PNV+I P +A Y+++ +
Sbjct: 248 SGKIFGAGLDVLEDETPDLLKDLEGEIFKDALNALLGRRPNVIITPHTAFYTDDALKNMV 307
Query: 316 DKAISVL 322
+ + +
Sbjct: 308 EISCENI 314
>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 = 108 bits (273), Expect = 4e-26
Identities = 80/257 (31%), Positives = 117/257 (45%), Gaps = 32/257 (12%)
Query: 71 LPRAA-QRRLRPYQLILCLGSSDRTVDSALAADLG-LRLI--------HVD----TSRA- 115
LPR + +LC + D+ +D+ L L++I H+D +R
Sbjct: 32 LPREELLEAAKGADGLLCTLT-DK-IDAELLDAAPPLKVIANYSVGYDHIDVDAAKARGI 89
Query: 116 ----------EEIADTVMALLLGLLRRTHLLARHALSASGWLGSVQPLCRGMRRCRGLVL 165
+ AD ALLL RR R + A W P G L
Sbjct: 90 PVTNTPDVLTDATADLAFALLLAAARRVVEGDRF-VRAGEW-KGWSPTLLLGTDLHGKTL 147
Query: 166 GIVGRSASARALATRSLSFKMSVLYFDVPEGKGKVTFPSAARRMDTLNDLLAASDVISLH 225
GIVG +A+A R+ F M +LY + K + AR + L++LLA SD +SLH
Sbjct: 148 GIVGMGRIGQAVARRAKGFGMKILYHN-RSRKPEAEEELGARYVS-LDELLAESDFVSLH 205
Query: 226 CAVTDETIQIINAECLQHIKPGAFLVNTGSSQLLDDCAVKQLLIDGTLAGCALDGAEG-P 284
C +T ET +INAE L +KP A L+NT ++D+ A+ + L G +AG LD E P
Sbjct: 206 CPLTPETRHLINAERLALMKPTAILINTARGGVVDEDALVEALKSGKIAGAGLDVFEPEP 265
Query: 285 QWMEAWVREMPNVLILP 301
+ + +PNV++LP
Sbjct: 266 LPADHPLLTLPNVVLLP 282
>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 = 105 bits (265), Expect = 4e-25
Identities = 73/250 (29%), Positives = 114/250 (45%), Gaps = 24/250 (9%)
Query: 95 VDSALAADLGLRLIHVDTSRAEEIADTVMALLLGLLRRTHLLARHALSASGWLGSVQPLC 154
+D A + G+ + + E A+ L+L L RR R + G+LG PL
Sbjct: 79 IDVDYAKEKGIPVTNTPAVSTEPTAELTFGLILALARRIAEGDRL-MRRGGFLG-WAPLF 136
Query: 155 RGMRRCRGLVLGIVGRSASARALATRSLSFKMSVLYFDV------PEGKGKVTFPSAARR 208
G LGI+G +A+A R+ +F M +LY++ E + T+
Sbjct: 137 FLGHELAGKTLGIIGMGRIGQAVARRAKAFGMKILYYNRHRLSEETEKELGATYVD---- 192
Query: 209 MDTLNDLLAASDVISLHCAVTDETIQIINAECLQHIKPGAFLVNTGSSQLLDDCAVKQLL 268
L++LL SD +SLH T ET +I+A + +KP A+L+N L+D+ A+ L
Sbjct: 193 ---LDELLKESDFVSLHAPYTPETHHLIDAAAFKLMKPTAYLINAARGPLVDEKALVDAL 249
Query: 269 IDGTLAGCALDGAEGPQWMEAWVREMPNVLILPR--SADYSEEVWM--EIRDKAISVLQT 324
G +AG ALD E + ++++ NV++ P +A M E D IS L+
Sbjct: 250 KTGEIAGAALDVFEFEPEVSPELKKLDNVILTPHIGNATVEARDAMAKEAADNIISFLE- 308
Query: 325 FFFDGVIPKN 334
G PKN
Sbjct: 309 ----GKRPKN 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 = 101 bits (255), Expect = 9e-24
Identities = 66/201 (32%), Positives = 98/201 (48%), Gaps = 26/201 (12%)
Query: 119 ADTVMALLLGLLRRTHLLARHALSASGWLGSVQPLCRGMRR-CRGLVLGIVGRSASARAL 177
A+ +AL+L L R +L A W + M RG LGIVG R +
Sbjct: 100 AEHTIALMLALARNIPQADA-SLRAGKWDRK-----KFMGVELRGKTLGIVGLGRIGREV 153
Query: 178 ATRSLSFKMSVLYFD--VPEGKGKVTFPSAARRMDTLNDLLAASDVISLHCAVTDETIQI 235
A R+ +F M VL +D + + + + +L++LLA +D ISLH +T ET +
Sbjct: 154 ARRARAFGMKVLAYDPYISAER----AAAGGVELVSLDELLAEADFISLHTPLTPETRGL 209
Query: 236 INAECLQHIKPGAFLVNTGSSQLLDDCAVKQLLIDGTLAGCALD-------GAEGPQWME 288
INAE L +KPGA L+NT ++D+ A+ L G +AG ALD A+ P
Sbjct: 210 INAEELAKMKPGAILINTARGGIVDEAALADALKSGKIAGAALDVFEQEPPPADSP---- 265
Query: 289 AWVREMPNVLILPRSADYSEE 309
+ +PNV++ P +EE
Sbjct: 266 --LLGLPNVILTPHLGASTEE 284
>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 = 101 bits (253), Expect = 2e-23
Identities = 79/289 (27%), Positives = 122/289 (42%), Gaps = 15/289 (5%)
Query: 41 VALVEHVPLGRLADGKIEAAAAVLLHSLAYLPRAAQRRLRPYQLILCLGSSDRTVDSALA 100
L E L AV+ + L A L +LI G +D A
Sbjct: 24 HRLWEAADPAALLAEHGGRIRAVVTNGETGLSAALIAALPALELIASFGVGYDGIDLDAA 83
Query: 101 ADLGLRLIHVDTSRAEEIADTVMALLLGLLRRTHLLAR--HALSASGWLGSVQPLCRGMR 158
G+R+ + +++AD + LLL +LRR + + A W PL R +
Sbjct: 84 RARGIRVTNTPGVLTDDVADLAVGLLLAVLRR---IPAADRFVRAGRWPKGAFPLTRKVS 140
Query: 159 RCRGLVLGIVGRSASARALATRSLSFKMSVLYFDVPEGKGKVTFPSAARRMDTLNDLLAA 218
R +GIVG RA+A R +F M + Y K V + R +L +L A
Sbjct: 141 GKR---VGIVGLGRIGRAIARRLEAFGMEIAYHG-RRPKPDVPY----RYYASLLELAAE 192
Query: 219 SDVISLHCAVTDETIQIINAECLQHIKPGAFLVNTGSSQLLDDCAVKQLLIDGTLAGCAL 278
SDV+ + C T ++NAE L+ + P LVN ++D+ A+ L +G +AG L
Sbjct: 193 SDVLVVACPGGPATRHLVNAEVLEALGPDGVLVNVARGSVVDEAALIAALQEGRIAGAGL 252
Query: 279 DGAEG-PQWMEAWVREMPNVLILPRSADYSEEVWMEIRDKAISVLQTFF 326
D E P A ++ NV++ P A + E + D ++ L+ FF
Sbjct: 253 DVFENEPNVPAAL-LDLDNVVLTPHIASATVETRRAMGDLVLANLEAFF 300
>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 = 100 bits (252), Expect = 3e-23
Identities = 66/193 (34%), Positives = 92/193 (47%), Gaps = 21/193 (10%)
Query: 95 VDSALAADLGLRLIHVDTSRAEEIADTVMALLLGLLRRTHLLARHALSAS--GWLGSVQ- 151
VD A A + G+ + +V + +A ALLL L L+A H W S
Sbjct: 79 VDLAAAKERGITVTNVPGYSTDSVAQHTFALLLAL---ARLVAYHNDVVKAGEWQKSPDF 135
Query: 152 -----PLCRGMRRCRGLVLGIVGRSASARALATRSLSFKMSVLYFDVPEGKGKVTFPSAA 206
P+ G LGI+G +A+A + +F M VL+ + P
Sbjct: 136 CFWDYPI----IELAGKTLGIIGYGNIGQAVARIARAFGMKVLFAERKGAP-----PLRE 186
Query: 207 RRMDTLNDLLAASDVISLHCAVTDETIQIINAECLQHIKPGAFLVNTGSSQLLDDCAVKQ 266
+ L++LLA SDVISLHC +T ET +INAE L +KPGA L+NT L+D+ A+
Sbjct: 187 GYVS-LDELLAQSDVISLHCPLTPETRNLINAEELAKMKPGAILINTARGGLVDEQALAD 245
Query: 267 LLIDGTLAGCALD 279
L G +AG LD
Sbjct: 246 ALNSGKIAGAGLD 258
>gnl|CDD|235890 PRK06932, PRK06932, glycerate dehydrogenase; Provisional.
Length = 314
Score = 99.5 bits (248), Expect = 6e-23
Identities = 81/286 (28%), Positives = 131/286 (45%), Gaps = 22/286 (7%)
Query: 52 LADGKIEAA--AAVLLHSLAYLPRAAQRRLRPYQLILCLGSSDRTVDSALAADLGLRLIH 109
A+ IE A A +++ S R +L +LI + VD A +LG+ + +
Sbjct: 34 SAEQTIERAKDADIVITSKVLFTRETLAQLPKLKLIAITATGTNNVDLVAAKELGIAVKN 93
Query: 110 VDTSRAEEIADTVMALLLGLLRRTHLLARHALSASGWLGSVQPLC---RGMRRCRGLVLG 166
V + + + V+ ++ L R LS W Q C + RG LG
Sbjct: 94 VTGYSSTTVPEHVLGMIFALKHSLMGWYRDQLSDR-WATCKQ-FCYFDYPITDVRGSTLG 151
Query: 167 IVGRSASARALATRSLSFKMSVLYFDVPEGKGKVTFPSAARRMDT-LNDLLAASDVISLH 225
+ G+ + + + M VLY E KG S R T ++L +D+++LH
Sbjct: 152 VFGKGCLGTEVGRLAQALGMKVLY---AEHKGA----SVCREGYTPFEEVLKQADIVTLH 204
Query: 226 CAVTDETIQIINAECLQHIKPGAFLVNTGSSQLLDDCAVKQLLIDGTLAGCALD--GAEG 283
C +T+ T +INAE L +KP AFL+NTG L+D+ A+ L +G +AG ALD E
Sbjct: 205 CPLTETTQNLINAETLALMKPTAFLINTGRGPLVDEQALLDALENGKIAGAALDVLVKEP 264
Query: 284 PQ----WMEAWVREMPNVLILPRSADYSEEVWMEIRDKAISVLQTF 325
P+ ++A + +PN+LI P A S+ + +K ++ F
Sbjct: 265 PEKDNPLIQA-AKRLPNLLITPHIAWASDSAVTTLVNKVAQNIEEF 309
>gnl|CDD|240663 cd12187, LDH_like_1, D-Lactate and related Dehydrogenase like
proteins, NAD-binding and catalytic domains. D-Lactate
dehydrogenase (LDH) catalyzes the interconversion of
pyruvate and lactate, and is a member of the
2-hydroxyacid dehydrogenase family. LDH is homologous to
D-2-Hydroxyisocaproic acid dehydrogenase(D-HicDH) and
shares the 2 domain structure of formate dehydrogenase.
D-2-hydroxyisocaproate dehydrogenase-like (HicDH)
proteins are NAD-dependent members of the
hydroxycarboxylate dehydrogenase family, and share the
Rossmann fold typical of many NAD binding proteins.
HicDH from Lactobacillus casei forms a monomer and
catalyzes the reaction R-CO-COO(-) + NADH + H+ to
R-COH-COO(-) + NAD+. D-HicDH, like the structurally
distinct L-HicDH, exhibits low side-chain R specificity,
accepting a wide range of 2-oxocarboxylic acid side
chains. Formate/glycerate and related dehydrogenases of
the D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-Adenosylhomocysteine Hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain.
Length = 329
Score = 99.3 bits (248), Expect = 1e-22
Identities = 70/246 (28%), Positives = 99/246 (40%), Gaps = 44/246 (17%)
Query: 109 HVDTSRAEEIADTVMALLLGLLRR---THLLARH-ALSASGWLGSVQPLCRGMRRCRGLV 164
+V +A+ ALLL L R+ R S +G G G
Sbjct: 91 NVPDYGEATVAEHAFALLLALSRKLREAIERTRRGDFSQAGLRG---------FELAGKT 141
Query: 165 LGIVGRSASARALATRSLSFKMSVLYFDVPEGKGKVTFPSAARRMD----TLNDLLAASD 220
LG+VG R +A + F M VL +DV V A R+ +L +LL SD
Sbjct: 142 LGVVGTGRIGRRVARIARGFGMKVLAYDV------VPDEELAERLGFRYVSLEELLQESD 195
Query: 221 VISLHCAVTDETIQIINAECLQHIKPGAFLVNTGSSQLLDDCAVKQLLIDGTLAGCALDG 280
+ISLH T +T +IN E +KPGA L+NT ++D A+ + L +G LAG LD
Sbjct: 196 IISLHVPYTPQTHHLINRENFALMKPGAVLINTARGAVVDTEALVRALKEGKLAGAGLDV 255
Query: 281 AEG-PQWME---------------AWVR-----EMPNVLILPRSADYSEEVWMEIRDKAI 319
E E + PNV+I P A ++E I D +
Sbjct: 256 LEQEEVLREEAELFREDVSPEDLKKLLADHALLRKPNVIITPHVAYNTKEALERILDTTV 315
Query: 320 SVLQTF 325
++ F
Sbjct: 316 ENIKAF 321
>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 = 95.2 bits (238), Expect = 2e-21
Identities = 77/271 (28%), Positives = 112/271 (41%), Gaps = 53/271 (19%)
Query: 95 VDSALAADLGLRLIHVDTSRAEEIADTVMALLLGLLRRTHLLARHA--------LSASGW 146
VD A +LG+ ++ V +A+ +ALLL L R+ H A S G
Sbjct: 82 VDLKAAKELGITVVRVPAYSPYAVAEHAVALLLALNRKIH----RAYNRVREGNFSLDGL 137
Query: 147 LGSVQPLCRGMRRCRGLVLGIVGRSASARALATRSLSFKMSVLYFDVPEGKGKVTFPSAA 206
LG + G +G++G +A A F VL +D +P+
Sbjct: 138 LG------FDLH---GKTVGVIGTGKIGQAFARILKGFGCRVLAYDP--------YPNPE 180
Query: 207 R-----RMDTLNDLLAASDVISLHCAVTDETIQIINAECLQHIKPGAFLVNTGSSQLLDD 261
L++LLA SD+ISLHC +T ET +INAE + +K G L+NT L+D
Sbjct: 181 LAKLGVEYVDLDELLAESDIISLHCPLTPETHHLINAETIAKMKDGVMLINTSRGGLIDT 240
Query: 262 CAVKQLLIDGTLAGCALD--GAEGPQWMEAWVRE------------MPNVLILPRSADYS 307
A+ + L G + G LD E + E E PNVLI A ++
Sbjct: 241 KALIEALKSGKIGGLGLDVYEEEAGLFFEDHSDEIIQDDVLARLLSFPNVLITGHQAFFT 300
Query: 308 EEVWMEIRDKAISVLQ--TFFFDGVIPKNAI 336
+E I A + L+ F G KN +
Sbjct: 301 KEALTNI---AETTLENLDDFEAGKPLKNEV 328
>gnl|CDD|180588 PRK06487, PRK06487, glycerate dehydrogenase; Provisional.
Length = 317
Score = 94.4 bits (235), Expect = 3e-21
Identities = 71/233 (30%), Positives = 108/233 (46%), Gaps = 15/233 (6%)
Query: 83 QLILCLGSSDRTVDSALAADLGLRLIHVDTSRAEEIADTVMALLLGLLRRTHLLA-RHAL 141
+LIL + VD A A + G+ + + +A +ALLL L R L + A+
Sbjct: 68 KLILVAATGTNNVDLAAARERGITVCNCQGYGTPSVAQHTLALLLALATR--LPDYQQAV 125
Query: 142 SASGWLGSVQ--PLCRGMRRCRGLVLGIVGRSASARALATRSLSFKMSVLYFDVPEGKGK 199
+A W S Q L + G LG++G A+A + +F M VL +P
Sbjct: 126 AAGRWQQSSQFCLLDFPIVELEGKTLGLLGHGELGGAVARLAEAFGMRVLIGQLPGR--- 182
Query: 200 VTFPSAARRMDTLNDLLAASDVISLHCAVTDETIQIINAECLQHIKPGAFLVNTGSSQLL 259
P+ R+ L++LL D ++LHC +T+ T +I A L +KPGA L+NT L+
Sbjct: 183 ---PARPDRLP-LDELLPQVDALTLHCPLTEHTRHLIGARELALMKPGALLINTARGGLV 238
Query: 260 DDCAVKQLLIDGTLAGCALD--GAEGP-QWMEAWVREMPNVLILPRSADYSEE 309
D+ A+ L G L G A D E P ++P +++ P SA S E
Sbjct: 239 DEQALADALRSGHLGGAATDVLSVEPPVNGNPLLAPDIPRLIVTPHSAWGSRE 291
>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 = 93.9 bits (234), Expect = 5e-21
Identities = 66/182 (36%), Positives = 93/182 (51%), Gaps = 16/182 (8%)
Query: 115 AEEIADTVMALLLGLLRRTHLLARHALSASGWLGSVQPLCRGMRRCRGL---VLGIVGRS 171
E A+ + LL+GL R H+LA SG G +P G GL +GI+G
Sbjct: 100 TEPTAELTIGLLIGLGR--HILAGDRFVRSGKFGGWRPKFYGT----GLDGKTVGILGMG 153
Query: 172 ASARALATRSLSFKMSVLYFDVPEGKGKVTF-PSAARRMDTLNDLLAASDVISLHCAVTD 230
A RA+A R F ++LY+D P + RR++ L++LL +SD + L +T
Sbjct: 154 ALGRAIARRLSGFGATLLYYD-PHPLDQAEEQALNLRRVE-LDELLESSDFLVLALPLTP 211
Query: 231 ETIQIINAECLQHIKPGAFLVNTGSSQLLDDCAVKQLLIDGTLAGCALDGAEGPQWMEAW 290
+T+ +INAE L +KPGA LVN ++D+ AV + L G L G A D E ME W
Sbjct: 212 DTLHLINAEALAKMKPGALLVNPCRGSVVDEAAVAEALKSGHLGGYAADVFE----MEDW 267
Query: 291 VR 292
R
Sbjct: 268 AR 269
>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 = 93.4 bits (233), Expect = 6e-21
Identities = 56/188 (29%), Positives = 93/188 (49%), Gaps = 13/188 (6%)
Query: 95 VDSALAADLGLRLIHVDTSRAEEIADTVMALLLGLLRRTHLLARHALSASGWLGSVQPLC 154
+D A G+++I+ + + +A+ V+ L+L L R H R + W
Sbjct: 77 IDVEYAKKKGIKVINTPGASSNSVAELVIGLMLSLARFIHRANRE-MKLGKWNKK---KY 132
Query: 155 RGMRRCRGLVLGIVGRSASARALATRSLSFKMSVLYFDV---PEGKGKVTFPSAARRMDT 211
+G RG LGI+G R +A + + M+V+ +D E ++ + +
Sbjct: 133 KG-IELRGKTLGIIGFGRIGREVAKIARALGMNVIAYDPYPKDEQAVELGVKTV-----S 186
Query: 212 LNDLLAASDVISLHCAVTDETIQIINAECLQHIKPGAFLVNTGSSQLLDDCAVKQLLIDG 271
L +LL SD ISLH +T ET +IN + L+ +K GA ++NT ++D+ A+ + L G
Sbjct: 187 LEELLKNSDFISLHVPLTPETKHMINKKELELMKDGAIIINTSRGGVIDEEALLEALKSG 246
Query: 272 TLAGCALD 279
LAG ALD
Sbjct: 247 KLAGAALD 254
>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 = 91.1 bits (227), Expect = 4e-20
Identities = 64/226 (28%), Positives = 105/226 (46%), Gaps = 28/226 (12%)
Query: 87 CLGSSDRTVDSALAADLGLRLIHVDTSRAEEIADTVMALLLGLLRRTHLLAR-HALSASG 145
C+G VD AA G+ + + S +A+ V+ ++ L RR L R A
Sbjct: 72 CIG--TNQVDLDAAAKRGIPVFNAPFSNTRSVAELVIGEIIMLARR--LPDRNAAAHRGI 127
Query: 146 WLGSVQPLCRGMRRCRGLVLGIVGRSASARALATRSLSFKMSVLYFDV----PEGKGKVT 201
W S G RG LGI+G L+ + + M V+++D+ P G
Sbjct: 128 WNKS----ATGSHEVRGKTLGIIGYGHIGSQLSVLAEALGMRVIFYDIAEKLPLGN---- 179
Query: 202 FPSAARRMDTLNDLLAASDVISLHCAVTDETIQIINAECLQHIKPGAFLVNTGSSQLLDD 261
AR++ +L +LLA +D ++LH T T +I AE + +K GA L+N ++D
Sbjct: 180 ----ARQVSSLEELLAEADFVTLHVPATPSTKNMIGAEEIAQMKKGAILINASRGTVVDI 235
Query: 262 CAVKQLLIDGTLAGCALD------GAEGPQWMEAWVREMPNVLILP 301
A+ + L G LAG A+D + G + + ++ +PNV++ P
Sbjct: 236 DALAEALRSGHLAGAAVDVFPEEPASNGEPF-SSPLQGLPNVILTP 280
>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 = 90.3 bits (225), Expect = 9e-20
Identities = 73/243 (30%), Positives = 104/243 (42%), Gaps = 47/243 (19%)
Query: 94 TVDSALAADLGLRLIHVDTSRAEEIADTVMALLLGLLRRT----HLLARHALSASGWLGS 149
+D LA + GL++ +V IA+ + L LLR T +A+ W
Sbjct: 81 MIDLDLAKENGLKITNVPAYSPRAIAEFAVTQALNLLRNTPEIDRRVAKGDFR---WAPG 137
Query: 150 VQPLCRGMRRCRGLVLGIVG--R--SASARALATRSLSFKMSVLYFDV---PEGKGKVTF 202
+ R R L +GI+G R SA+A+ F V+ +D PE + + +
Sbjct: 138 LIG-----REIRDLTVGIIGTGRIGSAAAKIFK----GFGAKVIAYDPYPNPELEKFLLY 188
Query: 203 PSAARRMDTLNDLLAASDVISLHCAVTDETIQIINAECLQHIKPGAFLVNTGSSQLLDDC 262
D+L DLL +D+ISLH +T E +INAE +K GA LVN L+D
Sbjct: 189 ------YDSLEDLLKQADIISLHVPLTKENHHLINAEAFAKMKDGAILVNAARGGLVDTK 242
Query: 263 AVKQLLIDGTLAGCALDGAEG----------------PQWMEAWVREMPNVLILPRSADY 306
A+ L G +AG ALD E E + MPNVLI P A Y
Sbjct: 243 ALIDALDSGKIAGAALDTYENETGYFNKDWSGKEIEDEVLKE--LIAMPNVLITPHIAFY 300
Query: 307 SEE 309
++
Sbjct: 301 TDT 303
>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 = 90.3 bits (225), Expect = 1e-19
Identities = 72/252 (28%), Positives = 121/252 (48%), Gaps = 36/252 (14%)
Query: 95 VDSALAADLGLRLIHVDTSRAEEIAD-TVMALLLGLLRRTHLLARHALSASGWLGSVQPL 153
+D A +LG+++ +V S +AD TVM L+L LR+ + + A LG +Q
Sbjct: 82 IDLDAAKELGIKVSNVTYS-PNSVADYTVM-LMLMALRKYKQIMKRAEVNDYSLGGLQ-- 137
Query: 154 CRGMRRCRGLVLGIVGRSASARALATRSLS-FKMSVLYFDV---PEGKGKVTFPSAARRM 209
G R R L +G++G +A+ ++LS F +L +D E K +
Sbjct: 138 --G-RELRNLTVGVIGTGRIGQAVI-KNLSGFGCKILAYDPYPNEEVKKYAEYVD----- 188
Query: 210 DTLNDLLAASDVISLHCAVTDETIQIINAECLQHIKPGAFLVNTGSSQLLDDCAVKQLLI 269
L+ L SD+I+LH +T+ET +IN E + +K G ++NT +L+D A+ + L
Sbjct: 189 --LDTLYKESDIITLHTPLTEETYHLINKESIAKMKDGVIIINTARGELIDTEALIEGLE 246
Query: 270 DGTLAGCALDGAEGP---------------QWMEAWVREMPNVLILPRSADYSEEVWMEI 314
G + G ALD EG + + A +R PNV++ P A Y+++ ++
Sbjct: 247 SGKIGGAALDVIEGEDGIYYNDRKGDILSNREL-AILRSFPNVILTPHMAFYTDQAVSDM 305
Query: 315 RDKAISVLQTFF 326
+ +I L F
Sbjct: 306 VENSIESLVAFE 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 = 90.3 bits (225), Expect = 1e-19
Identities = 69/243 (28%), Positives = 111/243 (45%), Gaps = 25/243 (10%)
Query: 68 LAYLPRAAQRRLRPYQLILCLGSSDRTVDSALAADLGLRLIHVDTSRAEEIADTVMALLL 127
LA PR LR ++ S R + + + G+ + + AE +A+ +A +L
Sbjct: 67 LARAPR-----LR---AVVHAAGSVRGLVTDAVWERGILVTSAADANAEPVAEFTLAAIL 118
Query: 128 GLLRRTHLLARHALSASGWLGSVQPLCRGMRRCRGLVLGIVGRSASARALATRSLSFKMS 187
LRR A + W + RG+ G +GIVG RA+ F +
Sbjct: 119 LALRRIPRFAAAYRAGRDWGWPTRRGGRGLY---GRTVGIVGFGRIGRAVVELLRPFGLR 175
Query: 188 VLYFD--VPEGKGKVTFPSAARRMDTLNDLLAASDVISLHCAVTDETIQIINAECLQHIK 245
VL +D +P + + + +L++LLA SDV+SLH +T ET +I+A L ++
Sbjct: 176 VLVYDPYLPAAEAA----ALGVELVSLDELLARSDVVSLHAPLTPETRGMIDARLLALMR 231
Query: 246 PGAFLVNTGSSQLLDDCAVKQLLIDGTLAG---CALD-GAEGPQWMEAWVREMPNVLILP 301
GA +NT L+D+ A L+ +G ALD P ++ +R +PNVL+ P
Sbjct: 232 DGATFINTARGALVDEAA----LLAELRSGRLRAALDVTDPEPLPPDSPLRTLPNVLLTP 287
Query: 302 RSA 304
A
Sbjct: 288 HIA 290
>gnl|CDD|240625 cd05300, 2-Hacid_dh_1, Putative D-isomer specific 2-hydroxyacid
dehydrogenase. 2-Hydroxyacid dehydrogenases catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomains but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric. Formate dehydrogenase (FDH) catalyzes the
NAD+-dependent oxidation of formate ion to carbon
dioxide with the concomitant reduction of NAD+ to NADH.
FDHs of this family contain no metal ions or prosthetic
groups. Catalysis occurs though direct transfer of the
hydride ion to NAD+ without the stages of acid-base
catalysis typically found in related dehydrogenases.
FDHs are found in all methylotrophic microorganisms in
energy production and in the stress responses of plants.
Length = 313
Score = 89.1 bits (222), Expect = 2e-19
Identities = 64/235 (27%), Positives = 101/235 (42%), Gaps = 33/235 (14%)
Query: 95 VDSALAADLGLRLIHVDTSR---AEEIADTVMALLLGLLRRTHLLARHALSASGWLGSVQ 151
VD+ L +L R + + +R IA+ V+ +L R+ AR+ W Q
Sbjct: 70 VDALLFPELLERDVVLTNARGIFGPPIAEYVLGYMLAFARKLPRYARNQAERR-W----Q 124
Query: 152 PLCRGMRRCRGLVLGIVGRSASARALATRSLSFKMSVL-----YFDVPEGKGKVTFPSAA 206
+R G + IVG R +A R+ +F M V+ P +V
Sbjct: 125 RR-GPVRELAGKTVLIVGLGDIGREIARRAKAFGMRVIGVRRSGRPAPPVVDEV------ 177
Query: 207 RRMDTLNDLLAASDVISLHCAVTDETIQIINAECLQHIKPGAFLVNTGSSQLLDDCAVKQ 266
D L++LL +D + +T ET + NAE +KPGA L+N G ++D+ A+ +
Sbjct: 178 YTPDELDELLPEADYVVNALPLTPETRGLFNAERFAAMKPGAVLINVGRGSVVDEDALIE 237
Query: 267 LLIDGTLAGCALD-------GAEGPQWMEAWVREMPNVLILPRSADYSEEVWMEI 314
L G +AG ALD A+ P W ++PNV+I P + S +
Sbjct: 238 ALESGRIAGAALDVFEEEPLPADSPLW------DLPNVIITPHISGDSPSYPERV 286
>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 = 88.4 bits (220), Expect = 3e-19
Identities = 67/241 (27%), Positives = 109/241 (45%), Gaps = 46/241 (19%)
Query: 115 AEEIADTVMALLLGLLRRTHLLARHALSASGW--LGSVQPLCRGMRR---------CRGL 163
A +A+ V+A++L L+R+ + A W G + +G+ + RG
Sbjct: 84 ANAVAELVIAMML-------ALSRNIIQAIKWVTNGDGDDISKGVEKGKKQFVGTELRGK 136
Query: 164 VLGIVGRSASARALATRSLSFKMSVLYFDVPEGKGKVTFPSAAR---------RMDTLND 214
LG++G R +A +L+ M V+ +D + S R+ +L +
Sbjct: 137 TLGVIGLGNIGRLVANAALALGMKVIGYD--------PYLSVEAAWKLSVEVQRVTSLEE 188
Query: 215 LLAASDVISLHCAVTDETIQIINAECLQHIKPGAFLVNTGSSQLLDDCAVKQLLIDGTLA 274
LLA +D I+LH +TDET +INAE L +KPGA L+N +++D+ A+ + L +G L
Sbjct: 189 LLATADYITLHVPLTDETRGLINAELLAKMKPGAILLNFARGEIVDEEALLEALDEGKLG 248
Query: 275 GCALDGAEGPQWMEAWVREMPNVLILPR---SADYSEEVWMEIRDKAISVLQTFFFDGVI 331
G D E A + +PNV+ P S + +EE A + F G I
Sbjct: 249 GYVTDFPE-----PALLGHLPNVIATPHLGASTEEAEE---NCAVMAARQIMDFLETGNI 300
Query: 332 P 332
Sbjct: 301 T 301
>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 = 86.6 bits (215), Expect = 2e-18
Identities = 58/248 (23%), Positives = 98/248 (39%), Gaps = 16/248 (6%)
Query: 95 VDSALAADLGLRLIHVDTSRAEEIADTVMALLLGLLRRTHLLARHALSASGWLGSVQPLC 154
+D A + G+ + +V E +A+ + L+L L RR ++ A W P+
Sbjct: 74 IDLDAATERGILVTNVPGYSTESVAELTVGLILALARRIPEADA-SVRAGDW-KKGGPIG 131
Query: 155 RGMRRCRGLVLGIVGRSASARALATRSLSFKMSVLYFDV-----PEGKGKVTFPSAARRM 209
+ V+G G A+A M V+ +D +G V
Sbjct: 132 LELYGKTLGVIGGGGIGGIGAAIAKA---LGMGVVAYDPYPNPERAEEGGVEVLLLD--- 185
Query: 210 DTLNDLLAASDVISLHCAVTDETIQIINAECLQHIKPGAFLVNTGSSQLLDDCAVKQLLI 269
L DL + D+I+L T +T II E +K + N ++++ A+ LL
Sbjct: 186 LLLLDLKESDDLINLAPPTTMKTGHIIINEARGMLKDAVAINNARGGGVIEEAALDALLE 245
Query: 270 DGTLAGCALDGA-EGPQWMEAWVREMPNVLILPRSADYSEEVWMEIRDKAISVLQTFFFD 328
+G A E P + ++PNV++ P A +EE + ++A L F
Sbjct: 246 EGIAAAALDVVEEEPPPVNSPLL-DLPNVILTPHIAGATEEAQENMAEEAAENLLA-FLK 303
Query: 329 GVIPKNAI 336
G P NA+
Sbjct: 304 GGTPPNAV 311
>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 = 86.4 bits (215), Expect = 2e-18
Identities = 71/240 (29%), Positives = 107/240 (44%), Gaps = 11/240 (4%)
Query: 71 LPRAAQRRLRPYQLILCLGSSDRTVDSALAADLGLRLIHVDTSRAEEIADTVMALLLGLL 130
P A RL +L++ G + ++D A A + G+ + A+ AL+L L
Sbjct: 59 FPAALLERLPNLKLLVTTGMRNASIDLAAAKERGIVVCGTGGG-PTATAELTWALILALA 117
Query: 131 RRTHLLARHALSASGWLGSVQPLCRGMRRCRGLVLGIVGRSASARALATRSLSFKMSVLY 190
R AL A GW ++ G G LGIVG +A +F M V+
Sbjct: 118 RNLPEEDA-ALRAGGWQTTL-----GTG-LAGKTLGIVGLGRIGARVARIGQAFGMRVIA 170
Query: 191 FDVPEGKGKVTFPSAARRMDTLNDLLAASDVISLHCAVTDETIQIINAECLQHIKPGAFL 250
+ + + + +L A SDV+SLH ++D T ++ AE L +KP A L
Sbjct: 171 WS-SNLTAERAAAAGVEAAVSKEELFATSDVVSLHLVLSDRTRGLVGAEDLALMKPTALL 229
Query: 251 VNTGSSQLLDDCAVKQLLIDGTLAGCALDGAE-GPQWMEAWVREMPNVLILPRSADYSEE 309
VNT L+D+ A+ L G +AG ALD + P + +R +PNVL+ P Y E
Sbjct: 230 VNTSRGPLVDEGALLAALRAGRIAGAALDVFDVEPLPADHPLRGLPNVLLTPHIG-YVTE 288
>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 = 85.5 bits (212), Expect = 4e-18
Identities = 65/226 (28%), Positives = 104/226 (46%), Gaps = 13/226 (5%)
Query: 115 AEEIADTVMALLLGLLRRTHLLARHALSASGWLGSVQPLCRGMRRCRGLVLGIVGRSASA 174
+ +A+ +AL+L +LR+ A A+ W + + G G +GI+G
Sbjct: 104 RDAVAEHAVALILTVLRKI-NQASEAVKEGKW--TERANFVG-HELSGKTVGIIGYGNIG 159
Query: 175 RALA-TRSLSFKMSVLYFD--VPEGKGKVTFPSAARRMDTLNDLLAASDVISLHCAVTDE 231
+A F VL +D V E K + +L +LLA SD+ISLH +T+E
Sbjct: 160 SRVAEILKEGFNAKVLAYDPYVSEEVIK----KKGAKPVSLEELLAESDIISLHAPLTEE 215
Query: 232 TIQIINAECLQHIKPGAFLVNTGSSQLLDDCAVKQLLIDGTLAGCALDGAEG-PQWMEAW 290
T +IN + +K G LVNT +L+D+ A+ + L G +AG LD E P +
Sbjct: 216 TYHMINEKAFSKMKKGVILVNTARGELIDEEALIEALKSGKIAGAGLDVLEEEPIKADHP 275
Query: 291 VREMPNVLILPRSADYSEEVWMEIRDKAISVLQTFFFDGVIPKNAI 336
+ NV+I P Y+ E + +K + ++ F G PK +
Sbjct: 276 LLHYENVVITPHIGAYTYESLYGMGEKVVDDIED-FLAGKEPKGIL 320
>gnl|CDD|185307 PRK15409, PRK15409, bifunctional glyoxylate/hydroxypyruvate
reductase B; Provisional.
Length = 323
Score = 84.4 bits (209), Expect = 8e-18
Identities = 62/214 (28%), Positives = 93/214 (43%), Gaps = 14/214 (6%)
Query: 94 TVDSALAADLGLRLIHVDTSRAEEIADTVMALLLGLLRRTHLLARHALSASGWLGSVQPL 153
D + L+H T E +ADT+MAL+L RR +A + A W S+ P
Sbjct: 79 NFDVDALTARKILLMHTPTVLTETVADTLMALVLSTARRVVEVAER-VKAGEWTASIGPD 137
Query: 154 CRGMRRCRGLVLGIVGRSASARALATRS-LSFKMSVLYFDVPEGKGKVTFPSAARRMDT- 211
G LGIVG ALA R+ F M +LY + A R +
Sbjct: 138 WFGTD-VHHKTLGIVGMGRIGMALAQRAHFGFNMPILY------NARRHHKEAEERFNAR 190
Query: 212 ---LNDLLAASDVISLHCAVTDETIQIINAECLQHIKPGAFLVNTGSSQLLDDCAVKQLL 268
L+ LL SD + + +TDET + AE +K A +N G ++D+ A+ L
Sbjct: 191 YCDLDTLLQESDFVCIILPLTDETHHLFGAEQFAKMKSSAIFINAGRGPVVDENALIAAL 250
Query: 269 IDGTLAGCALDGAEG-PQWMEAWVREMPNVLILP 301
G + LD E P +++ + +PNV+ +P
Sbjct: 251 QKGEIHAAGLDVFEQEPLSVDSPLLSLPNVVAVP 284
>gnl|CDD|236985 PRK11790, PRK11790, D-3-phosphoglycerate dehydrogenase;
Provisional.
Length = 409
Score = 81.8 bits (203), Expect = 2e-16
Identities = 63/196 (32%), Positives = 94/196 (47%), Gaps = 28/196 (14%)
Query: 118 IADTVMALLLGLLRRTHLLARHALSASG-WLGSVQPLCRGMRRCRGLVLGIVGRSASARA 176
+A+ V+ ++ LLR + ++A + G W S G RG LGIVG
Sbjct: 112 VAELVIGEIILLLRG--IPEKNAKAHRGGWNKSAA----GSFEVRGKTLGIVGYGHIGTQ 165
Query: 177 LATRSLSFKMSVLYFDV----PEGKGKVTFPSAARRMDTLNDLLAASDVISLHCAVTDET 232
L+ + S M V ++D+ P G AR++ +L +LLA SDV+SLH T T
Sbjct: 166 LSVLAESLGMRVYFYDIEDKLPLGN--------ARQVGSLEELLAQSDVVSLHVPETPST 217
Query: 233 IQIINAECLQHIKPGAFLVNTGSSQLLDDCAVKQLLIDGTLAGCALD-------GAEGPQ 285
+I AE L +KPGA L+N ++D A+ L G LAG A+D P
Sbjct: 218 KNMIGAEELALMKPGAILINASRGTVVDIDALADALKSGHLAGAAIDVFPVEPKSNGDP- 276
Query: 286 WMEAWVREMPNVLILP 301
E+ +R + NV++ P
Sbjct: 277 -FESPLRGLDNVILTP 291
>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 = 79.6 bits (197), Expect = 3e-16
Identities = 67/276 (24%), Positives = 115/276 (41%), Gaps = 39/276 (14%)
Query: 90 SSDRTVDSALAADLGLRLIHV--------DTSR-------------AEEIADTVMALLLG 128
T + ALAA L+LI V R + +A+ +AL+L
Sbjct: 46 GGRLTKEEALAALKRLKLIQVPSAGVDHLPLERLPEGVVVANNHGNSPAVAEHALALILA 105
Query: 129 LLRRTHLLARHALSASG-WLGSVQPLCRGMRRCRGLVLGIVGRSASARALATRSLSFKMS 187
L +R ++ G W G + RG +GI+G R +A +F M
Sbjct: 106 LAKR--IVEYDNDLRRGIWHGRAGEE-PESKELRGKTVGILGYGHIGREIARLLKAFGMR 162
Query: 188 VLYFDVPEGKGKVTFPSAARR-MDTLNDLLAASDVISLHCAVTDETIQIINAECLQHIKP 246
V+ K + + L++ L +DV+ + +T +T +I A L +KP
Sbjct: 163 VIGVS---RSPKEDEGADFVGTLSDLDEALEQADVVVVALPLTKQTRGLIGAAELAAMKP 219
Query: 247 GAFLVNTGSSQLLDDCAVKQLLIDGTLAGCALD------GAEGPQWMEAW-VREMPNVLI 299
GA LVN G ++D+ A+ + L + +AG A+D P + E+PNV++
Sbjct: 220 GAILVNVGRGPVVDEEALYEALKERPIAGAAIDVWWRYPSRGDPVAPSRYPFHELPNVIM 279
Query: 300 LPRSADYSEEVWME-IRDKAISVLQTFFFDGVIPKN 334
P +A ++EE + I + A ++ + + G N
Sbjct: 280 SPHNAGWTEETFRRRIDEAAENIRR--YLRGEPLLN 313
>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 = 79.7 bits (197), Expect = 3e-16
Identities = 61/222 (27%), Positives = 93/222 (41%), Gaps = 28/222 (12%)
Query: 113 SRAEEIADTVMALLLGLLRRTHLLARHALSASGWLGSVQPLCRGMRRCRGLVLGIVGRSA 172
AE IA+ V+A +L L A W +PL G LGIVG A
Sbjct: 94 VAAEAIAEFVLAAILA--AAKRLPEIWVKGAEQW--RREPL----GSLAGSTLGIVGFGA 145
Query: 173 SARALATRSLSFKMSVL-------YFDVPEGKGKVTFPSAARRMDTLNDLLAASDVISLH 225
+ALA R+L+ M VL DVP L +L A SD + L
Sbjct: 146 IGQALARRALALGMRVLALRRSGRPSDVP----------GVEAAADLAELFARSDHLVLA 195
Query: 226 CAVTDETIQIINAECLQHIKPGAFLVNTGSSQLLDDCAVKQLLIDGTLAGCALDGAEGPQ 285
+T ET +INA+ L KPG L+N L+D A+ + L G ++ +LD + P+
Sbjct: 196 APLTPETRHLINADVLAQAKPGLHLINIARGGLVDQEALLEALDSGRISLASLDVTD-PE 254
Query: 286 WMEA--WVREMPNVLILPRSADYSEEVWMEIRDKAISVLQTF 325
+ + P V + P ++ + + + D+ + L +
Sbjct: 255 PLPEGHPLYTHPRVRLSPHTSAIAPDGRRNLADRFLENLARY 296
>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 = 79.3 bits (196), Expect = 6e-16
Identities = 61/214 (28%), Positives = 97/214 (45%), Gaps = 9/214 (4%)
Query: 69 AYLPRAAQRRLRPYQLILCLGSSDRTVDSALAADLGLRLIHVDTSRAEEIADTVMALLLG 128
AY+ + + +L L G VD A D G+ + V S +A+ V+ ++L
Sbjct: 72 AYMTAERIAKAKNLKLALTAGIGSDHVDLQAANDRGITVAEVTGSNVVSVAEHVVMMILI 131
Query: 129 LLRRTHLLARHALSASGWLGSVQPLCRGMRRCRGLVLGIVGRSASARALATRSLSFKMSV 188
L+R A+ GW +V + + G +G VG + R F + +
Sbjct: 132 LVRNYVPGHEQAI-EGGW--NVADVVKRAYDLEGKTVGTVGAGRIGLRVLRRLKPFDVHL 188
Query: 189 LYFD---VPEGKGKVTFPSAARRMDTLNDLLAASDVISLHCAVTDETIQIINAECLQHIK 245
LY+D +PE K R L D+++ DV++++C + ET + N E L +K
Sbjct: 189 LYYDRHRLPEEVEKEL---GLTRHADLEDMVSKCDVVTINCPLHPETEGLFNKELLSKMK 245
Query: 246 PGAFLVNTGSSQLLDDCAVKQLLIDGTLAGCALD 279
GA+LVNT ++ D AV + L G LAG A D
Sbjct: 246 KGAYLVNTARGKICDREAVAEALESGHLAGYAGD 279
>gnl|CDD|183914 PRK13243, PRK13243, glyoxylate reductase; Reviewed.
Length = 333
Score = 76.8 bits (189), Expect = 3e-15
Identities = 64/221 (28%), Positives = 97/221 (43%), Gaps = 12/221 (5%)
Query: 95 VDSALAADLGLRLIHVDTSRAEEIADTVMALLLGLLRRTHLLARHALSASGWLGSV--QP 152
+D A G+ + + E AD ALLL RR S V P
Sbjct: 81 IDVEEATRRGIYVTNTPGVLTEATADFAWALLLATARRLVEADHFVRSGEWKRRGVAWHP 140
Query: 153 LCRGMRRCRGLVLGIVGRSASARALATRSLSFKMSVLYFDVPEGKGKVTFPSAARRMD-- 210
L G +GI+G +A+A R+ F M +LY+ + P A + +
Sbjct: 141 LMFLGYDVYGKTIGIIGFGRIGQAVARRAKGFGMRILYYS------RTRKPEAEKELGAE 194
Query: 211 --TLNDLLAASDVISLHCAVTDETIQIINAECLQHIKPGAFLVNTGSSQLLDDCAVKQLL 268
L +LL SD +SLH +T ET +IN E L+ +KP A LVNT +++D A+ + L
Sbjct: 195 YRPLEELLRESDFVSLHVPLTKETYHMINEERLKLMKPTAILVNTARGKVVDTKALVKAL 254
Query: 269 IDGTLAGCALDGAEGPQWMEAWVREMPNVLILPRSADYSEE 309
+G +AG LD E + + + NV++ P + E
Sbjct: 255 KEGWIAGAGLDVFEEEPYYNEELFSLKNVVLAPHIGSATFE 295
>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 = 77.4 bits (191), Expect = 7e-15
Identities = 42/146 (28%), Positives = 73/146 (50%), Gaps = 11/146 (7%)
Query: 161 RGLVLGIVGRSASARALATRSLSFKMSVLYFD--VPEGKGK---VTFPSAARRMDTLNDL 215
G LG++G +A R+ +F M VL +D + + + V +D L++L
Sbjct: 137 YGKTLGVIGLGRIGSIVAKRAKAFGMKVLAYDPYISPERAEQLGVE------LVDDLDEL 190
Query: 216 LAASDVISLHCAVTDETIQIINAECLQHIKPGAFLVNTGSSQLLDDCAVKQLLIDGTLAG 275
LA +D I++H +T ET +I AE L +K G +VN ++D+ A+ + L +G +
Sbjct: 191 LARADFITVHTPLTPETRGLIGAEELAKMKKGVIIVNCARGGIIDEAALYEALEEGHVRA 250
Query: 276 CALDGAEGPQWMEAWVREMPNVLILP 301
ALD E + + ++ NV+ P
Sbjct: 251 AALDVFEKEPPTDNPLFDLDNVIATP 276
>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 = 74.2 bits (183), Expect = 2e-14
Identities = 38/107 (35%), Positives = 59/107 (55%), Gaps = 3/107 (2%)
Query: 211 TLNDLLAASDVISLHCAVTDETIQIINAECLQHIKPGAFLVNTGSSQLLDDCAVKQLLID 270
+L++LLA SD++SLH + DET +I E L +K A L+NT ++D+ A+ L +
Sbjct: 190 SLDELLAESDIVSLHLPLNDETKGLIGKEKLALMKESAILINTARGPVVDNEALADALNE 249
Query: 271 GTLAGCALD--GAEGPQWMEAWVREMPNVLILPRSADYSEEVWMEIR 315
G +AG +D E P + + PN ++ P A +EE ME R
Sbjct: 250 GKIAGAGIDVFDMEPPLPADYPLLHAPNTILTPHVAFATEEA-MEKR 295
>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 = 72.3 bits (178), Expect = 7e-14
Identities = 60/202 (29%), Positives = 86/202 (42%), Gaps = 29/202 (14%)
Query: 115 AEEIADTVMALLLGLLRRTHLLARHALSASGWLGSVQPLCRGMRRCRGLVLGIVGRSASA 174
AE +A+ +ALLL LR+ AR A+ W + RG + IVG
Sbjct: 84 AETVAEHALALLLAGLRQLPARAR----ATTW--DPAEEDDLVTLLRGSTVAIVGAGGIG 137
Query: 175 RALATRSLSFKMSVLYFD----VPEGKGKVTFPSAARRMDTLNDLLAASDVISLHCAVTD 230
RAL F V+ + EG + T P D L+++ +D + L +T
Sbjct: 138 RALIPLLAPFGAKVIAVNRSGRPVEGADE-TVP-----ADRLDEVWPDADHVVLAAPLTP 191
Query: 231 ETIQIINAECLQHIKPGAFLVNTGSSQLLDDCAVKQLLIDGTLAGCALD-------GAEG 283
ET +++A L +KP A+LVN L+D A+ L G +AG ALD
Sbjct: 192 ETRHLVDAAALAAMKPHAWLVNVARGPLVDTDALVDALRSGEIAGAALDVTDPEPLPDGH 251
Query: 284 PQWMEAWVREMPNVLILPRSAD 305
P W +PN LI P A+
Sbjct: 252 PLWS------LPNALITPHVAN 267
>gnl|CDD|177941 PLN02306, PLN02306, hydroxypyruvate reductase.
Length = 386
Score = 72.6 bits (178), Expect = 1e-13
Identities = 44/165 (26%), Positives = 77/165 (46%), Gaps = 21/165 (12%)
Query: 161 RGLVLGIVGR----SASARALATRSLSFKMSVLYFDVPEGKGKVTF-------------- 202
+G +G++G SA AR + FKM+++Y+D+ + F
Sbjct: 164 KGQTVGVIGAGRIGSAYARMMVE---GFKMNLIYYDLYQSTRLEKFVTAYGQFLKANGEQ 220
Query: 203 PSAARRMDTLNDLLAASDVISLHCAVTDETIQIINAECLQHIKPGAFLVNTGSSQLLDDC 262
P +R ++ ++L +DVISLH + T +IN E L +K A LVN ++D+
Sbjct: 221 PVTWKRASSMEEVLREADVISLHPVLDKTTYHLINKERLALMKKEAVLVNASRGPVIDEV 280
Query: 263 AVKQLLIDGTLAGCALDGAEGPQWMEAWVREMPNVLILPRSADYS 307
A+ + L + LD E +M+ + +M N +++P A S
Sbjct: 281 ALVEHLKANPMFRVGLDVFEDEPYMKPGLADMKNAVVVPHIASAS 325
>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 = 71.2 bits (175), Expect = 2e-13
Identities = 52/230 (22%), Positives = 89/230 (38%), Gaps = 30/230 (13%)
Query: 95 VDSALAADLGLRLIHVDTSRAEEIADTVMALLLGL---LRRTHLLARHALSASGWLGSVQ 151
+D A + G+ L + + + + + +LL L L R R+ + W
Sbjct: 76 IDLEYAKEKGIELFNAPEGNRDAVGEHALGMLLALFNKLNRADQEVRNGI----WDREGN 131
Query: 152 PLCRGMRRCRGLVLGIVGRSASARALATRSLSFKMSVLYFDVPEGKGKVTFPSAARRMDT 211
RG+ G +GI+G +A A R F V+ +D + F A +
Sbjct: 132 ---RGVE-LMGKTVGIIGYGNMGKAFAKRLSGFGCKVIAYDKYK-----NFGDAYAEQVS 182
Query: 212 LNDLLAASDVISLHCAVTDETIQIINAECLQHIKPGAFLVNT--GSSQLLDDCAVKQLLI 269
L L +D++SLH +T ET ++N E + K + +NT G + D + + L
Sbjct: 183 LETLFKEADILSLHIPLTPETRGMVNKEFISSFKKPFYFINTARGKVVVTKD--LVKALK 240
Query: 270 DGTLAGCALD-------GAEGPQWMEAWVREM---PNVLILPRSADYSEE 309
G + G LD E + P V++ P A ++ E
Sbjct: 241 SGKILGACLDVLEYEKASFESIFNQPEAFEYLIKSPKVILTPHIAGWTFE 290
>gnl|CDD|237436 PRK13581, PRK13581, D-3-phosphoglycerate dehydrogenase;
Provisional.
Length = 526
Score = 70.1 bits (173), Expect = 1e-12
Identities = 42/127 (33%), Positives = 68/127 (53%), Gaps = 18/127 (14%)
Query: 161 RGLVLGIVG--RSASARALATRSLSFKMSVLYFD--VPEGKGKVTFPSAARRMD----TL 212
G LGI+G R S +A R+ +F M V+ +D + + A ++ +L
Sbjct: 139 YGKTLGIIGLGRIGSE--VAKRAKAFGMKVIAYDPYISPER--------AAQLGVELVSL 188
Query: 213 NDLLAASDVISLHCAVTDETIQIINAECLQHIKPGAFLVNTGSSQLLDDCAVKQLLIDGT 272
++LLA +D I+LH +T ET +I AE L +KPG ++N ++D+ A+ + L G
Sbjct: 189 DELLARADFITLHTPLTPETRGLIGAEELAKMKPGVRIINCARGGIIDEAALAEALKSGK 248
Query: 273 LAGCALD 279
+AG ALD
Sbjct: 249 VAGAALD 255
>gnl|CDD|181041 PRK07574, PRK07574, formate dehydrogenase; Provisional.
Length = 385
Score = 69.3 bits (170), Expect = 2e-12
Identities = 55/212 (25%), Positives = 97/212 (45%), Gaps = 5/212 (2%)
Query: 69 AYLPRAAQRRLRPYQLILCLGSSDRTVDSALAADLGLRLIHVDTSRAEEIADTVMALLLG 128
AYL + +L + G VD A++ G+ + V S + +A+ V+ ++L
Sbjct: 102 AYLTAERIAKAPNLKLAITAGIGSDHVDLQAASEHGITVAEVTGSNSISVAEHVVMMILA 161
Query: 129 LLRRTHLLARHALSASG-WLGSVQPLCRGMRRCRGLVLGIVGRSASARALATRSLSFKMS 187
L+R + H + G W ++ G+ +GIVG A+ R F +
Sbjct: 162 LVR--NYEPSHRQAVEGGW--NIADCVSRSYDLEGMTVGIVGAGRIGLAVLRRLKPFDVK 217
Query: 188 VLYFDVPEGKGKVTFPSAARRMDTLNDLLAASDVISLHCAVTDETIQIINAECLQHIKPG 247
+ Y D +V + + L++ DV+++HC + ET + +A+ L +K G
Sbjct: 218 LHYTDRHRLPEEVEQELGLTYHVSFDSLVSVCDVVTIHCPLHPETEHLFDADVLSRMKRG 277
Query: 248 AFLVNTGSSQLLDDCAVKQLLIDGTLAGCALD 279
++LVNT +++D AV + L G LAG A D
Sbjct: 278 SYLVNTARGKIVDRDAVVRALESGHLAGYAGD 309
>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 = 67.7 bits (166), Expect = 3e-12
Identities = 63/241 (26%), Positives = 99/241 (41%), Gaps = 35/241 (14%)
Query: 93 RTV-----DSALAADLGLRLIHVDTSRAEEIADTVMALLLGLLRRTHLLARHALSASGWL 147
RTV D A +LG ++ V + IA+ L + L R T A + +
Sbjct: 75 RTVGFNHIDLEAAKELGFKMARVPSYSPNAIAELAFTLAMTLSRHTAYTASRT-ANKNFK 133
Query: 148 GSVQPLCRGMRRCRGLVLGIVGRSASARALATRSLSFKMSVLYFDVPEGKGK---VTFPS 204
+ +R ++G GR A + L K V+ +D+ VTF S
Sbjct: 134 VDPFMFSKEIRNSTVGIIGT-GRIGLTAAKLFKGLGAK--VIGYDIYPSDAAKDVVTFVS 190
Query: 205 AARRMDTLNDLLAASDVISLHCA-VTDETIQIINAECLQHIKPGAFLVNTGSSQLLDDCA 263
L++LL SD+ISLH + + ++IN E + +K GA L+NT +L D+ A
Sbjct: 191 -------LDELLKKSDIISLHVPYIKGKNDKLINKEFISKMKDGAILINTARGELQDEEA 243
Query: 264 VKQLLIDGTLAGCALD--------------GAEGP-QWMEAWVREMPNVLILPRSADYSE 308
+ + L G LAG D G + +E + P VL+ P Y++
Sbjct: 244 ILEALESGKLAGFGTDVLNNEKEIFFKDFDGDKIEDPVVEKLLDLYPRVLLTPHIGSYTD 303
Query: 309 E 309
E
Sbjct: 304 E 304
>gnl|CDD|181414 PRK08410, PRK08410, 2-hydroxyacid dehydrogenase; Provisional.
Length = 311
Score = 65.8 bits (161), Expect = 1e-11
Identities = 52/201 (25%), Positives = 90/201 (44%), Gaps = 15/201 (7%)
Query: 84 LILCLGSSDRTVDSALAADLGLRLIHVDTSRAEEIADTVMALLLGLLRRTHLLARHALSA 143
LI + VD A G+ + +V E +A A+LL LL R + R+ S
Sbjct: 66 LICITATGTNNVDIEYAKKKGIAVKNVAGYSTESVAQHTFAMLLSLLGRINYYDRYVKSG 125
Query: 144 SGWLGSVQP----LCRGMRRCRGLVLGIVGRSASARALATRSLSFKMSVLYFDVPEGKGK 199
+ S P + R + +G GI+G + +A + +F V+Y+ GK K
Sbjct: 126 E-Y--SESPIFTHISRPLGEIKGKKWGIIGLGTIGKRVAKIAQAFGAKVVYYS-TSGKNK 181
Query: 200 -VTFPSAARRMDTLNDLLAASDVISLHCAVTDETIQIINAECLQHIKPGAFLVNTGSSQL 258
+ +L +LL SD+IS+H + ++T +I + L+ +K GA L+N G +
Sbjct: 182 NEEYERV-----SLEELLKTSDIISIHAPLNEKTKNLIAYKELKLLKDGAILINVGRGGI 236
Query: 259 LDDCAVKQLLIDGTLAGCALD 279
+++ + + L D LD
Sbjct: 237 VNEKDLAKAL-DEKDIYAGLD 256
>gnl|CDD|215501 PLN02928, PLN02928, oxidoreductase family protein.
Length = 347
Score = 63.9 bits (156), Expect = 6e-11
Identities = 37/102 (36%), Positives = 51/102 (50%), Gaps = 9/102 (8%)
Query: 212 LNDLLAASDVISLHCAVTDETIQIINAECLQHIKPGAFLVNTGSSQLLDDCAVKQLLIDG 271
+ + +D++ L C +T ET I+N E L +K GA LVN LLD AV L G
Sbjct: 220 IYEFAGEADIVVLCCTLTKETAGIVNDEFLSSMKKGALLVNIARGGLLDYDAVLAALESG 279
Query: 272 TLAGCALDGAEGPQWMEAW-----VREMPNVLILPRSADYSE 308
L G A+D A W E + + + PNV+I P A +E
Sbjct: 280 HLGGLAIDVA----WSEPFDPDDPILKHPNVIITPHVAGVTE 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 = 61.8 bits (151), Expect = 3e-10
Identities = 40/125 (32%), Positives = 61/125 (48%), Gaps = 13/125 (10%)
Query: 161 RGLVLGIVGRSASARALATRSLSFKMSVLYFDVP--EGKGKVTFPSAARRMDTLNDLLAA 218
+G +GIVG LA R + M+VL D P E +G F S L +LLA
Sbjct: 114 KGKTVGIVGVGNVGSRLARRLEALGMNVLLCDPPRAEAEGDPGFVS-------LEELLAE 166
Query: 219 SDVISLHCAVTDE----TIQIINAECLQHIKPGAFLVNTGSSQLLDDCAVKQLLIDGTLA 274
+D+I+LH +T + T +++ + L +KPG L+N ++D+ A+ LL G
Sbjct: 167 ADIITLHVPLTRDGEHPTYHLLDEDFLAALKPGQILINASRGAVIDNQALLALLQRGKDL 226
Query: 275 GCALD 279
LD
Sbjct: 227 RVVLD 231
>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 = 59.7 bits (145), Expect = 1e-09
Identities = 56/200 (28%), Positives = 86/200 (43%), Gaps = 24/200 (12%)
Query: 118 IADTVMALLLGLLRRTHLLARHALSASGW---LGSVQPL--CRGMRRCRGLVLGIVGRSA 172
+A+ +AL+L +RR + R A W LG +QPL + G + I G +
Sbjct: 95 VAEHTLALILAAVRRLDEM-REAQREHRWAGELGGLQPLRPAGRLTTLLGARVLIWGFGS 153
Query: 173 SARALATRSLSFKMSVLYFDVPEGKG-KVTFPSAARRMDTLNDLLAASDVISLHCAVTDE 231
+ LA + V V G + FP A D L +LL +DV+ + T
Sbjct: 154 IGQRLAPLLTALGARVT--GVARSAGERAGFPVVAE--DELPELLPETDVLVMILPATPS 209
Query: 232 TIQIINAECLQHIKPGAFLVNTGSSQLLDDCAVKQLLIDGTLAGCALD-------GAEGP 284
T ++AE L + A++VN G +D+ A+ L G L G ALD A P
Sbjct: 210 TAHALDAEVLAALPKHAWVVNVGRGATVDEDALVAALESGRLGGAALDVTATEPLPASSP 269
Query: 285 QWMEAWVREMPNVLILPRSA 304
W + PN+++ P +A
Sbjct: 270 LW------DAPNLILTPHAA 283
>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 = 59.4 bits (145), Expect = 1e-09
Identities = 79/287 (27%), Positives = 108/287 (37%), Gaps = 62/287 (21%)
Query: 38 LAGVALVEHVPLGRLADGKIEAAAAVLLHSLAYLPRAAQRRLRPYQLILCLGSSDRTVDS 97
L + +V AD ++ A P RL + I LG+ VD
Sbjct: 23 LPDIEVVVWPDPADPAD--VDYALV------WKPPPGLLARLPNLKAIFSLGAG---VD- 70
Query: 98 ALAADLGL------RLIHVDTSRAEEIADTVMALLLGLLRRTHLLARHALSASGWLGSVQ 151
L AD L RL VD A+ +A+ V+A +L L R A W
Sbjct: 71 HLLADPDLPDVPIVRL--VDPGLAQGMAEYVLAAVLRLHRDMDRYAAQQRRGV-W--KPL 125
Query: 152 PLCRGMRRCRGLV-LGIVGRSASARALATRSLSFKMSVLYFDV------P-EGKGKVTFP 203
P R G++ LG +G A AR LA L F V P + +G F
Sbjct: 126 PQRPAAERRVGVLGLGELGA-AVARRLAA---------LGFPVSGWSRSPKDIEGVTCFH 175
Query: 204 SAARRMDTLNDLLAASDVISLHCAV--TDETIQIINAECLQHIKPGAFLVNTGSSQLLDD 261
+ L+ LA +D+ L C + T ET I+NAE L + GA L+N G L +
Sbjct: 176 GE----EGLDAFLAQTDI--LVCLLPLTPETRGILNAELLARLPRGAALINVGRGPHLVE 229
Query: 262 CAVKQLLIDGTLAGCALD-------GAEGPQWMEAWVREMPNVLILP 301
+ L G L+G LD A+ P W P V + P
Sbjct: 230 ADLLAALDSGHLSGAVLDVFEQEPLPADHPLW------RHPRVTVTP 270
>gnl|CDD|178684 PLN03139, PLN03139, formate dehydrogenase; Provisional.
Length = 386
Score = 58.7 bits (142), Expect = 4e-09
Identities = 58/236 (24%), Positives = 100/236 (42%), Gaps = 8/236 (3%)
Query: 69 AYLPRAAQRRLRPYQLILCLGSSDRTVDSALAADLGLRLIHVDTSRAEEIA-DTVMALLL 127
AY+ ++ + +L+L G +D AA GL + V S +A D +M +L+
Sbjct: 109 AYVTAERIKKAKNLELLLTAGIGSDHIDLPAAAAAGLTVAEVTGSNVVSVAEDELMRILI 168
Query: 128 GLLRRTHLLARHALSASGWLGSVQPLCRGMRRCRGLVLGIVGRSASARALATRSLSFKMS 187
L R L H + + W +V + G +G VG R L R F +
Sbjct: 169 --LLRNFLPGYHQVVSGEW--NVAGIAYRAYDLEGKTVGTVGAGRIGRLLLQRLKPFNCN 224
Query: 188 VLYFDVPEGKGKVTFPSAARRMDTLNDLLAASDVISLHCAVTDETIQIINAECLQHIKPG 247
+LY D + ++ + A+ + L+ +L DV+ ++ +T++T + N E + +K G
Sbjct: 225 LLYHDRLKMDPELEKETGAKFEEDLDAMLPKCDVVVINTPLTEKTRGMFNKERIAKMKKG 284
Query: 248 AFLVNTGSSQLLDDCAVKQLLIDGTLAGCALD--GAEGPQWMEAWVREMPNVLILP 301
+VN ++D AV G + G D + W R MPN + P
Sbjct: 285 VLIVNNARGAIMDTQAVADACSSGHIGGYGGDVWYPQPAPKDHPW-RYMPNHAMTP 339
>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 = 56.8 bits (138), Expect = 1e-08
Identities = 51/244 (20%), Positives = 97/244 (39%), Gaps = 41/244 (16%)
Query: 115 AEEIADTVMALLLGLLRRTHLLARHALSASGWLGSVQPLCRGMRRCRGLVLGIVGRSASA 174
+ IA+ ++ +L + + + W + G + +G +
Sbjct: 94 SIPIAEWIVGYILEIYKGLKKAYK-NQKEKKWKMD-----SSLLELYGKTILFLGTGSIG 147
Query: 175 RALATRSLSFKMSVL----------YFDVPEGKGKVTFPSAARRMDTLNDLLAASDVISL 224
+ +A R +F M V+ YFD +P + L+++L +D++
Sbjct: 148 QEIAKRLKAFGMKVIGVNTSGRDVEYFDK-------CYPL-----EELDEVLKEADIVVN 195
Query: 225 HCAVTDETIQIINAECLQHIKPGAFLVNTGSSQLLDDCAVKQLLIDGTLAGCALDGAE-- 282
+T+ET + + + +K GA +N G +D+ A+ + L + + G ALD E
Sbjct: 196 VLPLTEETHHLFDEAFFEQMKKGALFINVGRGPSVDEDALIEALKNKQIRGAALDVFEEE 255
Query: 283 -----GPQWMEAWVREMPNVLILPRSADYSEEVWMEIRDKAISVLQTFFFDGVIPKNAIS 337
P W ++ NVLI P + SE + D L++F DG + KN +
Sbjct: 256 PLPKDSPLW------DLDNVLITPHISGVSEHFNERLFDIFYENLKSFLEDGELLKNVVD 309
Query: 338 DTEG 341
+G
Sbjct: 310 LNKG 313
>gnl|CDD|183550 PRK12480, PRK12480, D-lactate dehydrogenase; Provisional.
Length = 330
Score = 54.9 bits (132), Expect = 5e-08
Identities = 53/252 (21%), Positives = 100/252 (39%), Gaps = 36/252 (14%)
Query: 96 DSALAADLGLRLIHVDTSRAEEIADTVMALLLGLLRRTHLLARHALSAS-GWLGSVQPLC 154
D LA + + +V + E IA+ +++ L L+RR + R + W +
Sbjct: 84 DLDLAKKHNIVISNVPSYSPETIAEYSVSIALQLVRRFPDIERRVQAHDFTWQAEIMS-- 141
Query: 155 RGMRRCRGLVLGIVGRSASARALATRSLSFKMSVLYFDVPEGKGKVTFPSAA----RRMD 210
+ + + + I+G A A F ++ +D +P+ D
Sbjct: 142 ---KPVKNMTVAIIGTGRIGAATAKIYAGFGATITAYDA--------YPNKDLDFLTYKD 190
Query: 211 TLNDLLAASDVISLHCAVTDETIQIINAECLQHIKPGAFLVNTGSSQLLDDCAVKQLLID 270
++ + + +D+ISLH E+ + + H+K GA LVN +++ + + D
Sbjct: 191 SVKEAIKDADIISLHVPANKESYHLFDKAMFDHVKKGAILVNAARGAVINTPDLIAAVND 250
Query: 271 GTLAGCALDG--AEGPQWMEAWVR------------EMPNVLILPRSADYSEEVWMEI-- 314
GTL G A+D E + W E +L+ P A +S+E +
Sbjct: 251 GTLLGAAIDTYENEAAYFTNDWTNKDIDDKTLLELIEHERILVTPHIAFFSDEAVQNLVE 310
Query: 315 --RDKAISVLQT 324
+ A+SV+ T
Sbjct: 311 GGLNAALSVINT 322
>gnl|CDD|181499 PRK08605, PRK08605, D-lactate dehydrogenase; Validated.
Length = 332
Score = 46.7 bits (111), Expect = 2e-05
Identities = 24/74 (32%), Positives = 38/74 (51%)
Query: 210 DTLNDLLAASDVISLHCAVTDETIQIINAECLQHIKPGAFLVNTGSSQLLDDCAVKQLLI 269
DT+ + + +D+++LH T + NA+ +H K GA VN L+D A+ L
Sbjct: 192 DTIEEAVEGADIVTLHMPATKYNHYLFNADLFKHFKKGAVFVNCARGSLVDTKALLDALD 251
Query: 270 DGTLAGCALDGAEG 283
+G + G ALD E
Sbjct: 252 NGLIKGAALDTYEF 265
>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 = 46.1 bits (110), Expect = 3e-05
Identities = 40/172 (23%), Positives = 71/172 (41%), Gaps = 24/172 (13%)
Query: 162 GLVLGIVGRSASARALATRSLSFKMSVLYF------DVPEGKGKVTFPSAARRMDTLNDL 215
GL +GI+G + + +A F V Y+ D E KG P LN+L
Sbjct: 138 GLKVGIIGLGTTGQMIADALSFFGADVYYYSRTRKPDA-EAKGIRYLP--------LNEL 188
Query: 216 LAASDVISLHCAVTDETIQIINAECLQHIKPGAFLVNTGSSQLLDDCAVKQLL--IDGTL 273
L DVI + + ++ E + + G L NT + A+K+ L +
Sbjct: 189 LKTVDVICTC---LPKNVILLGEEEFELLGDGKILFNTSLGPSFEVEALKKWLKASGYNI 245
Query: 274 AGCALDGAEGPQWMEAWVREMPNVLILPRSADYSEEVWMEIRDKAISVLQTF 325
C GA G + + + PNV+ +SA ++ + + + K ++ L+ +
Sbjct: 246 FDCDTAGALGDEELLRY----PNVICTNKSAGWTRQAFERLSQKVLANLEEY 293
>gnl|CDD|166874 PRK00257, PRK00257, erythronate-4-phosphate dehydrogenase;
Validated.
Length = 381
Score = 45.8 bits (109), Expect = 4e-05
Identities = 44/148 (29%), Positives = 64/148 (43%), Gaps = 17/148 (11%)
Query: 147 LGSVQPLC--RGMRRCRGLVLGIVGRSASARALATRSLSFKMSVLYFDVP--EGKGKVTF 202
LGS+ L G+ G+VG L VL D P E +G F
Sbjct: 100 LGSLLTLAEREGVD-LAERTYGVVGAGHVGGRLVRVLRGLGWKVLVCDPPRQEAEGDGDF 158
Query: 203 PSAARRMDTLNDLLAASDVISLHCAVTDE----TIQIINAECLQHIKPGAFLVNTGSSQL 258
S L +L DVISLH +T E T +++ L ++PGA+L+N +
Sbjct: 159 VS-------LERILEECDVISLHTPLTKEGEHPTRHLLDEAFLASLRPGAWLINASRGAV 211
Query: 259 LDDCAVKQLLIDGTLAGCALDGAEG-PQ 285
+D+ A+++ L+ G LD EG PQ
Sbjct: 212 VDNQALREALLSGEDLDAVLDVWEGEPQ 239
>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 = 44.1 bits (105), Expect = 1e-04
Identities = 75/285 (26%), Positives = 103/285 (36%), Gaps = 58/285 (20%)
Query: 39 AGVALVEHVPLGRLADGKIEAAAAVLLHSLAYLPRAAQRRLRPYQLILCLGSSDRTVDSA 98
GV +V G D + V + A A R L +++ L + V
Sbjct: 18 PGVEVVVWDGEGPPPDAAADVEFVVPPYMAAPPVLEALRALPRLRVVQTLSAGYDGVLPL 77
Query: 99 LAADLGL---RLIHVDTSRAEEIADTVMALLLGLLRRTHLLARHALSASGWLGSVQPLCR 155
L + L R +H D S AE +AL+L LR R A + W P
Sbjct: 78 LPEGVTLCNARGVH-DASTAE----LAVALILASLRGLPRFVR-AQARGRWEPRRTPSLA 131
Query: 156 GMRRCRGLVLGIVGRSASARALATRSLSFKMSVLYFDVPEGKGKVTFPSAARR------- 208
R VL IVG + RA+ R F++ V AR
Sbjct: 132 DRR-----VL-IVGYGSIGRAIERRLAPFEVRVTRV--------------ARTARPGEQV 171
Query: 209 --MDTLNDLLAASDVISLHCAVTDETIQIINAECLQHIKPGAFLVNTGSSQLLDDCAVKQ 266
+D L LL +DV+ L +TDET +++AE L + GA LVN ++D A
Sbjct: 172 HGIDELPALLPEADVVVLIVPLTDETRGLVDAEFLARMPDGALLVNVARGPVVDTDA--- 228
Query: 267 LLIDGTLAG---CALD-------GAEGPQWMEAWVREMPNVLILP 301
L+ +G ALD P W P VLI P
Sbjct: 229 -LVAELASGRLRAALDVTDPEPLPPGHPLW------SAPGVLITP 266
>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 = 39.1 bits (91), Expect = 0.005
Identities = 26/124 (20%), Positives = 47/124 (37%), Gaps = 2/124 (1%)
Query: 162 GLVLGIVGRSASARALATRSLSFKMSVLYFDVPEGKGKVTFPSAARRMDTLNDLLAASDV 221
G + +VG + A VL D+ + + ++ L + LA +DV
Sbjct: 160 GKTVVVVGAGVVGKEAAQMLRGLGAQVLITDINVEALEQLEELGGKNVEELEEALAEADV 219
Query: 222 ISLHCAVTDETIQIIN-AECLQHIKPGAFLVNTGSSQLLDDCAV-KQLLIDGTLAGCALD 279
I + + I+ E ++ +KPG+ +VN + A+ QLL +G D
Sbjct: 220 IVTTTLLPGKRAGILVPEELVEQMKPGSVIVNVAVGAVGCVQALHTQLLEEGHGVVHYGD 279
Query: 280 GAEG 283
Sbjct: 280 VNMP 283
>gnl|CDD|240640 cd12163, 2-Hacid_dh_5, Putative D-isomer specific 2-hydroxyacid
dehydrogenases. 2-Hydroxyacid dehydrogenases catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 334
Score = 38.8 bits (91), Expect = 0.007
Identities = 35/117 (29%), Positives = 53/117 (45%), Gaps = 24/117 (20%)
Query: 214 DLLAASDVISLHCAVTDETIQIINAECLQHI-KPGAFLVNTGSSQLLDDCAVKQLLIDGT 272
DLL V+SL +T T ++ AE + + K F+ N L+D A+ L G
Sbjct: 212 DLL----VVSL--PLTPATKHLLGAEEFEILAKRKTFVSNIARGSLVDTDALVAALESGQ 265
Query: 273 LAGCALD-------GAEGPQWMEAWVREMPNVLILPRSADYSEEVWMEIRDKAISVL 322
+ G ALD A+ P W PNV+I P + ++E + D+A+ VL
Sbjct: 266 IRGAALDVTDPEPLPADHPLW------SAPNVIITPHVSWQTQEYF----DRALDVL 312
>gnl|CDD|235800 PRK06436, PRK06436, glycerate dehydrogenase; Provisional.
Length = 303
Score = 38.7 bits (90), Expect = 0.007
Identities = 41/182 (22%), Positives = 75/182 (41%), Gaps = 20/182 (10%)
Query: 165 LGIVGRSASARALATRSLSFKMSVLYFD---VPEGKGKVTFPSAARRMDTLNDLLAASDV 221
LGI+G R +A + +F M++ + V +G + D++ SD
Sbjct: 125 LGILGYGGIGRRVALLAKAFGMNIYAYTRSYVNDG-ISSIYMEPE-------DIMKKSDF 176
Query: 222 ISLHCAVTDETIQIINAECLQHIKPGAFLVNTGSSQLLDDCAVKQLLIDGTLAGCALDGA 281
+ + +TDET +IN++ L + G ++N + ++D + L + D
Sbjct: 177 VLISLPLTDETRGMINSKMLSLFRKGLAIINVARADVVDKNDMLNFLRNHNDKYYLSD-- 234
Query: 282 EGPQWMEAWVRE--MPNVLILPR-SADYSEEVWMEIRDKAISVLQTFFFDGVIPKNAISD 338
W E + E NV++ P + S E+ A ++ FF+G PKN +
Sbjct: 235 --VWWNEPIITETNPDNVILSPHVAGGMSGEIMQPAVALAFENIKN-FFEGK-PKNIVRK 290
Query: 339 TE 340
E
Sbjct: 291 EE 292
>gnl|CDD|185335 PRK15438, PRK15438, erythronate-4-phosphate dehydrogenase PdxB;
Provisional.
Length = 378
Score = 36.0 bits (83), Expect = 0.046
Identities = 32/128 (25%), Positives = 58/128 (45%), Gaps = 19/128 (14%)
Query: 165 LGIVGRSASARALATRSLSFKMSVLYFDVPEGKGKVTFPSAARRMD-----TLNDLLAAS 219
+GIVG R L R + + L D P A R D +L++L+ +
Sbjct: 119 VGIVGVGNVGRRLQARLEALGIKTLLCD----------PPRADRGDEGDFRSLDELVQEA 168
Query: 220 DVISLHCAVTDE----TIQIINAECLQHIKPGAFLVNTGSSQLLDDCAVKQLLIDGTLAG 275
D+++ H + + T+ + + + ++ +KPGA L+N ++D+ A+ L +G
Sbjct: 169 DILTFHTPLFKDGPYKTLHLADEKLIRSLKPGAILINACRGAVVDNTALLTCLNEGQKLS 228
Query: 276 CALDGAEG 283
LD EG
Sbjct: 229 VVLDVWEG 236
>gnl|CDD|185366 PRK15469, ghrA, bifunctional glyoxylate/hydroxypyruvate reductase
A; Provisional.
Length = 312
Score = 33.2 bits (76), Expect = 0.38
Identities = 24/84 (28%), Positives = 37/84 (44%), Gaps = 7/84 (8%)
Query: 229 TDETIQIINAECLQHIKPGAFLVNTGSSQLLDDCAVKQLLIDGTLAGCALD-------GA 281
T ET+ IIN + L+ + GA+L+N + + + L G + G LD
Sbjct: 201 TPETVGIINQQLLEQLPDGAYLLNLARGVHVVEDDLLAALDSGKVKGAMLDVFSREPLPP 260
Query: 282 EGPQWMEAWVREMPNVLILPRSAD 305
E P W V P+V + R A+
Sbjct: 261 ESPLWQHPRVAITPHVAAVTRPAE 284
>gnl|CDD|223166 COG0088, RplD, Ribosomal protein L4 [Translation, ribosomal
structure and biogenesis].
Length = 214
Score = 32.6 bits (75), Expect = 0.47
Identities = 22/85 (25%), Positives = 36/85 (42%), Gaps = 16/85 (18%)
Query: 358 KVSTLEGSVGGQLTDDIQVS----PEDSLKKGISWSRDSPSQLQGSGFSQNSANTKSDGR 413
KV L+G G++ +V ED + + + + + QG+ +TK+ G
Sbjct: 5 KVYDLDGEEVGEVELLPEVFGPERNEDLIHRAVLAQLAN--RRQGT------HSTKTRGE 56
Query: 414 RSRSGKKAKK----RHARQKSLQKP 434
S GKK ARQ S++ P
Sbjct: 57 VSGGGKKPWGQKGTGRARQGSIRSP 81
>gnl|CDD|151621 pfam11179, DUF2967, Protein of unknown function (DUF2967). This
family of proteins with unknown function appears to be
restricted to Drosophila.
Length = 284
Score = 32.3 bits (72), Expect = 0.74
Identities = 20/97 (20%), Positives = 36/97 (37%), Gaps = 2/97 (2%)
Query: 385 GISWSRDSPSQLQGSGFSQNSANTKSDGRRSRS--GKKAKKRHARQKSLQKPDDPSALEK 442
G+ S S + G+G A ++ + + KK AR++ + +
Sbjct: 61 GVGGGGGSGSGVGGNGVMAAGAADEAADAQEEDAIANRNKKLRARERDPMAGNANANANA 120
Query: 443 ESTSHKEDDTAMSGTDQASSRCASPEELRSRKTPIES 479
S+ + + S ASP+ + R TPI S
Sbjct: 121 NGGSNSSRNHISPSVSPSHSNRASPKREKKRTTPIAS 157
>gnl|CDD|137505 PRK09751, PRK09751, putative ATP-dependent helicase Lhr; Provisional.
Length = 1490
Score = 32.6 bits (74), Expect = 0.92
Identities = 25/77 (32%), Positives = 35/77 (45%), Gaps = 10/77 (12%)
Query: 114 RAEEIADTVMALLL--GLLRRTHLLARHALSAS---GWLGSVQPLCRGM----RRCRG-L 163
+ E + DT L L +L R +++R A+ A G S+Q LCR M R RG
Sbjct: 1281 QVEPLNDTERMLALAENMLDRYGIISRQAVIAENIPGGFPSMQTLCRSMEDSGRIMRGRF 1340
Query: 164 VLGIVGRSASARALATR 180
V G+ G + R R
Sbjct: 1341 VEGLGGAQFAERLTIDR 1357
>gnl|CDD|218752 pfam05793, TFIIF_alpha, Transcription initiation factor IIF, alpha
subunit (TFIIF-alpha). Transcription initiation factor
IIF, alpha subunit (TFIIF-alpha) or RNA polymerase
II-associating protein 74 (RAP74) is the large subunit
of transcription factor IIF (TFIIF), which is essential
for accurate initiation and stimulates elongation by RNA
polymerase II.
Length = 528
Score = 32.2 bits (73), Expect = 1.0
Identities = 39/179 (21%), Positives = 63/179 (35%), Gaps = 20/179 (11%)
Query: 337 SDTEGCENEIDDEIEQYNKLDKVSTLEGSVGGQLTDDIQV-SPEDSLKKGISWSRDSPSQ 395
D + E + DD ++ + D +S + G + SPE K I DS
Sbjct: 265 GDDDADEYDSDDGDDEGREEDYISD-SSASGNDPEEREDKLSPEIPAKPEIEQDEDSEES 323
Query: 396 LQGSGFSQNSANTKSDGRRSRSGKKAKKRHARQKSLQKPDDPSALEKESTSHKEDD---- 451
+ +G S+ GKK KK ++ L K D S + + + +D
Sbjct: 324 --------EEEKNEEEGGLSKKGKKLKKLKGKKNGLDKDDSDSGDDSDDSDIDGEDSVSL 375
Query: 452 -TAMSGTDQAS-----SRCASPEELRSRKTPIESIQESTSKKLSRSSKKLSEVSGETLK 504
TA + S +SP + ES + K + SK + V + LK
Sbjct: 376 VTAKKQKEPKKEEPVDSNPSSPGNSGPARPSPESKDKGKRKAANEVSKSPASVPAKKLK 434
>gnl|CDD|99975 cd03802, GT1_AviGT4_like, This family is most closely related to
the GT1 family of glycosyltransferases. aviGT4 in
Streptomyces viridochromogenes has been shown to be
involved in biosynthesis of oligosaccharide antibiotic
avilamycin A. Inactivation of aviGT4 resulted in a
mutant that accumulated a novel avilamycin derivative
lacking the terminal eurekanate residue.
Length = 335
Score = 31.4 bits (72), Expect = 1.4
Identities = 22/62 (35%), Positives = 24/62 (38%), Gaps = 15/62 (24%)
Query: 17 TPLPSVVALNCIEDCVLEQDSLAGVALVEHVPLGRLADGKIEAAAAVLLHSLAYLPRAAQ 76
TP V+A V E +VE G L D E AAAV L RAA
Sbjct: 269 TP---VIAFRR--GAVPE--------VVEDGVTGFLVDSVEELAAAV--ARADRLDRAAC 313
Query: 77 RR 78
RR
Sbjct: 314 RR 315
>gnl|CDD|218715 pfam05719, GPP34, Golgi phosphoprotein 3 (GPP34). This family
consists of several eukaryotic GPP34 like proteins.
GPP34 localises to the Golgi complex and is conserved
from yeast to humans. The cytosolic-ally exposed
location of GPP34 predict a role for a novel coat
protein in Golgi trafficking.
Length = 205
Score = 30.7 bits (70), Expect = 1.8
Identities = 41/172 (23%), Positives = 56/172 (32%), Gaps = 34/172 (19%)
Query: 38 LAGVALVEHVPLGRLA--DGKIEAAAA-----VLLHSLAYLPRAAQRRLRPYQLI--LCL 88
LAG AL+E GR+ G++ A LL R A R + L
Sbjct: 27 LAGAALLELALAGRVTLDGGRVVVVDARPTGDPLLDEALAELRGASRPRSVKDWLERLSG 86
Query: 89 GSSDRTVDSALAAD----------LGL----RLIHVDTSRAEEIADTVMALLLGLLRRTH 134
V + L A LGL R VD + + + A L G
Sbjct: 87 RGLRERVAAGLVARGILRREKRRFLGLFPTTRYPLVDPAAEAALRARLRAALRGGAPPD- 145
Query: 135 LLARHA-----LSASGWLGSVQPL---CRGMRRCRGLVLGIVGRSASARALA 178
R A L A+G L ++ P G R R + I S + A+
Sbjct: 146 --PRTAALAALLHAAGLLRNLLPGDPAGLGRRAVRARLKEIAEGSWAGEAVR 195
>gnl|CDD|240192 cd05687, S1_RPS1_repeat_ec1_hs1, S1_RPS1_repeat_ec1_hs1: Ribosomal
protein S1 (RPS1) domain. RPS1 is a component of the
small ribosomal subunit thought to be involved in the
recognition and binding of mRNA's during translation
initiation. The bacterial RPS1 domain architecture
consists of 4-6 tandem S1 domains. In some bacteria, the
tandem S1 array is located C-terminal to a
4-hydroxy-3-methylbut-2-enyl diphosphate reductase
(HMBPP reductase) domain. While RPS1 is found primarily
in bacteria, proteins with tandem RPS1-like domains have
been identified in plants and humans, however these lack
the N-terminal HMBPP reductase domain. This CD includes
S1 repeat 1 of the Escherichia coli and Homo sapiens
RPS1 (ec1 and hs1, respectively). Autoantibodies to
double-stranded DNA from patients with systemic lupus
erythematosus cross-react with the human RPS1 homolog.
Length = 70
Score = 28.3 bits (64), Expect = 1.9
Identities = 16/59 (27%), Positives = 28/59 (47%), Gaps = 6/59 (10%)
Query: 312 MEIRDKAISVLQTFFFDGVIPKNAISDTEGCENE----IDDEIEQYNKLDKVSTLEGSV 366
+ + D + V + +G+IP + SD E + DE+E Y + +V EG+V
Sbjct: 9 VSVDDDEVLVDIGYKSEGIIPISEFSDDPIENGEDEVKVGDEVEVY--VLRVEDEEGNV 65
>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A
(vWA) domain [General function prediction only].
Length = 4600
Score = 31.5 bits (71), Expect = 2.0
Identities = 31/128 (24%), Positives = 51/128 (39%), Gaps = 37/128 (28%)
Query: 328 DGVIPKNAISDTEGCENEIDDEIEQYNKLDKVSTLEGSVGGQLTDDIQVSPEDSLKKGIS 387
D V+ +N SD+E ++D+E+ + L S+ +L D+ E+ L +
Sbjct: 3870 DSVVSENENSDSEEENQDLDEEVNDIPE-----DLSNSLNEKLWDE---PNEEDLLE--- 3918
Query: 388 WSRDSPSQLQGSGFSQNSANTKSDGRRSRSGKKAKKRHARQKSLQKPDDPSALEKESTSH 447
+ S Q++AN +SD + K DD ALE +
Sbjct: 3919 --TEQKSN------EQSAANNESD------------------LVSKEDDNKALEDKDRQE 3952
Query: 448 KEDDTAMS 455
KED+ MS
Sbjct: 3953 KEDEEEMS 3960
>gnl|CDD|218429 pfam05097, DUF688, Protein of unknown function (DUF688). This
family contains several uncharacterized proteins found
in Arabidopsis thaliana.
Length = 446
Score = 30.9 bits (69), Expect = 2.4
Identities = 37/189 (19%), Positives = 60/189 (31%), Gaps = 24/189 (12%)
Query: 334 NAISDTEGCENEIDDEIEQYNKLDKVST-------LEGSVGGQLTDDIQVSPEDSLKKGI 386
N I D E + DD + L K L+ S+G ++P S+K+
Sbjct: 223 NDIDDEEEEDENDDDGVVYSEYLSKKGCGLLPQLCLKNSLG-------LLNPVPSMKRQK 275
Query: 387 SWSRDSPSQLQGSGFSQNSANTKSDGRRSRSGKKAKKRHARQKSLQKPDDPSALEKEST- 445
S ++ S +Q+ + +S + S KK + S ES
Sbjct: 276 PLRTVSHRAVKSSKVAQSKLSFQSVNKHSLDIVNKKKLSGIYSRPKGSSGGSKFNSESEK 335
Query: 446 -SHKEDDTAMSGTDQ-ASSRCASP-------EELRSRKTPIESIQESTSKKLSRSSKKLS 496
+D A SG+ SP L + +E S ++S
Sbjct: 336 PESFKDSQAPSGSSPYRHGGGMSPYRNVGLSSPLHAAGFGTRVEEEKMRANRLSSISRIS 395
Query: 497 EVSGETLKD 505
+ GE L
Sbjct: 396 KRFGELLAS 404
>gnl|CDD|227925 COG5638, COG5638, Uncharacterized conserved protein [Function
unknown].
Length = 622
Score = 30.9 bits (69), Expect = 2.6
Identities = 35/216 (16%), Positives = 74/216 (34%), Gaps = 22/216 (10%)
Query: 343 ENEIDDEIE-QYNKLDKVSTLEGSVGGQLTDDIQVSPEDSLKKGISWSRDSPSQLQGSGF 401
+ + D +E + KL + V D + G + L S
Sbjct: 370 DEDDDSVMESKMQKL-----FSEKEIDFGLNSELVDMSDDGENGEMEDTFTSH-LPASNE 423
Query: 402 SQNSANTKSDGRRSRSGKKAKKRHARQKSLQKPDDPSALEKESTSHKEDDTAMSGTDQAS 461
S++ ++ + + ++ + +++ L+K D S ++ + + G
Sbjct: 424 SESDDKLETTIEKLDRKLRERQENRKERQLKKTKDDSDVDLKDKKESINKKNKKGKHAIE 483
Query: 462 SRCASPEELR---------------SRKTPIESIQESTSKKLSRSSKKLSEVSGETLKDG 506
AS EEL K+ +++ + ++KL + + L E KD
Sbjct: 484 RTAASKEELELIKADDEDDEQLDHFDMKSILKAEKFKKNRKLKKKASNLEEGFVFDPKDP 543
Query: 507 YVVALYARDRPALHISRQRHKGGGWILETMSNVTKR 542
VA++ A+ + K G + + M KR
Sbjct: 544 RFVAIFEDHNFAIDPTHPEFKKTGGMKKIMDEKRKR 579
>gnl|CDD|182105 PRK09840, PRK09840, catecholate siderophore receptor Fiu;
Provisional.
Length = 761
Score = 30.5 bits (69), Expect = 3.5
Identities = 17/47 (36%), Positives = 22/47 (46%), Gaps = 6/47 (12%)
Query: 335 AISDTEGCENEI----DDEIEQYNKLDKVSTLEGSVGGQLTDDIQVS 377
A+ T+ ENE+ D QY K +V E SV G +T QV
Sbjct: 588 ALFRTD-IENEVEQNDDGTYSQYGK-KRVEGYELSVAGNITPAWQVI 632
>gnl|CDD|234178 TIGR03354, VI_FHA, type VI secretion system FHA domain protein.
Members of this protein family are FHA
(forkhead-associated) domain-containing proteins that
are part of type VI secretion loci in a considerable
number of bacteria, most of which are known pathogens.
Species include Pseudomonas aeruginosa PAO1, Aeromonas
hydrophila, Yersinia pestis, Burkholderia mallei, etc
[Protein fate, Protein and peptide secretion and
trafficking, Cellular processes, Pathogenesis].
Length = 396
Score = 30.0 bits (68), Expect = 3.5
Identities = 31/136 (22%), Positives = 44/136 (32%), Gaps = 11/136 (8%)
Query: 11 PHRDNPTPLPSVVALNCIEDCVLEQDSLAGVALVEHVPLGRLADGKIEAAAAVLLHSLAY 70
P L + AL+ + D L L + A A ++
Sbjct: 130 PDPAPLAQLDPLKALDQEPLSAADLDDL-SAPLFPPLDARLPAFAAPIDAEPTMVPPFVP 188
Query: 71 LPRAAQRRLRPYQLILCLGSSDRTVDSALAADLGLRLIHVDTSRA----EEIADTVMALL 126
LP Q SSD + LGL L +D+ A EE+ + A++
Sbjct: 189 LPAPEPAPAPASQA----PSSDAVALTPFLRGLGLPLELLDSQAAEDVLEELGRLLRAMV 244
Query: 127 LGLLRRTHLLARHALS 142
GLL L AR L
Sbjct: 245 EGLL--QLLRARAELK 258
>gnl|CDD|119355 cd02876, GH18_SI-CLP, Stabilin-1 interacting chitinase-like protein
(SI-CLP) is a eukaryotic chitinase-like protein of
unknown function that interacts with the
endocytic/sorting transmembrane receptor stabilin-1 and
is secreted from the lysosome. SI-CLP has a glycosyl
hydrolase family 18 (GH18) domain but lacks a
chitin-binding domain. The catalytic amino acids of the
GH18 domain are not conserved in SI-CLP, similar to the
chitolectins YKL-39, YKL-40, and YM1/2. Human SI-CLP is
sorted to late endosomes and secretory lysosomes in
alternatively activated macrophages.
Length = 318
Score = 30.0 bits (68), Expect = 4.4
Identities = 16/59 (27%), Positives = 26/59 (44%), Gaps = 12/59 (20%)
Query: 285 QWMEAWVREMPNVLILPR------SADYSEEVWM--EIRDKAISVLQTFF----FDGVI 331
W+E + N+ ILPR S + + + R+K I +L T FDG++
Sbjct: 55 GWIEEVRKANKNIKILPRVLFEGWSYQDLQSLLNDEQEREKLIKLLVTTAKKNHFDGIV 113
>gnl|CDD|215332 PLN02616, PLN02616, tetrahydrofolate dehydrogenase/cyclohydrolase,
putative.
Length = 364
Score = 30.0 bits (67), Expect = 4.6
Identities = 25/104 (24%), Positives = 41/104 (39%), Gaps = 2/104 (1%)
Query: 463 RCASPEELRSRKTPIESIQESTSKKLSRSSKKLSEVSGETLKDGYVVALYARDRPALHIS 522
RC P +R+ + S+S + G + DG VA RD + +S
Sbjct: 35 RCVGPLRVRTTASGRGCCINSSSSPSPVINADTGSEGGAKVIDGKAVAKKIRDEITIEVS 94
Query: 523 RQRHKGGGWILETMSNVTKRDPAAQFLICKSK--DTIGLRSFTA 564
R + G + V R +A ++ K K D++G+ SF
Sbjct: 95 RMKESIGVVPGLAVILVGDRKDSATYVRNKKKACDSVGINSFEV 138
>gnl|CDD|181295 PRK08213, PRK08213, gluconate 5-dehydrogenase; Provisional.
Length = 259
Score = 29.5 bits (67), Expect = 5.3
Identities = 15/31 (48%), Positives = 18/31 (58%)
Query: 39 AGVALVEHVPLGRLADGKIEAAAAVLLHSLA 69
G L+ H PLGRL D + AA+LL S A
Sbjct: 211 LGEDLLAHTPLGRLGDDEDLKGAALLLASDA 241
>gnl|CDD|135765 PRK06113, PRK06113, 7-alpha-hydroxysteroid dehydrogenase;
Validated.
Length = 255
Score = 29.4 bits (66), Expect = 5.3
Identities = 15/57 (26%), Positives = 25/57 (43%), Gaps = 7/57 (12%)
Query: 20 PSVVALNCIEDCVLEQDSLAGV-------ALVEHVPLGRLADGKIEAAAAVLLHSLA 69
+ +N I + D+L V +++H P+ RL + A AA+ L S A
Sbjct: 179 EKNIRVNGIAPGAILTDALKSVITPEIEQKMLQHTPIRRLGQPQDIANAALFLCSPA 235
>gnl|CDD|237974 PRK15489, nfrB, bacteriophage N4 adsorption protein B; Provisional.
Length = 703
Score = 29.7 bits (67), Expect = 6.4
Identities = 24/86 (27%), Positives = 32/86 (37%), Gaps = 16/86 (18%)
Query: 35 QDSLAGVALVEH--VPLGRLADGKIEAAAAVLL--HSLAYLPRAAQRRLRPYQLILCLGS 90
D L V VP DG + A A L +L + RAA R + Q I
Sbjct: 561 ADCLPRDLCVRWRVVPFSIGEDGTLNIAVASPLPGEALQEVARAAGR--KVAQFIAR--- 615
Query: 91 SDRTVDSALAADLGLRLIHVDTSRAE 116
DS ++A LRL+ +A
Sbjct: 616 -----DSEISA--ELRLLAGPERQAT 634
>gnl|CDD|218908 pfam06136, DUF966, Domain of unknown function (DUF966). Family of
plant proteins with unknown function.
Length = 308
Score = 28.9 bits (65), Expect = 8.5
Identities = 20/139 (14%), Positives = 45/139 (32%), Gaps = 23/139 (16%)
Query: 367 GGQLTDDIQVSPEDSL--KKGISWSRDSPSQLQGSGFSQNSA------NTKSDGRRSRSG 418
G ++ D + + + D+P + + S +S+ K++ S
Sbjct: 85 GSEILDSSSSKGDPEEASSRKLQEESDTPPVNRRANQSWSSSDLAEYKVYKAEEPADAST 144
Query: 419 KKAKKRHARQKSLQKPDDPSALEKESTSHKEDDTAMSGTDQASSRCASPEELRSRKT--- 475
+ +R + E EST ++ + + + S +SPE L S
Sbjct: 145 QTDDRRSRD-----------SSEAESTELSREEISPPSSSSSPSSSSSPETLESLIKADG 193
Query: 476 -PIESIQESTSKKLSRSSK 493
S + + + +
Sbjct: 194 RLSLSFRSLEEDESAGRVR 212
>gnl|CDD|240658 cd12181, ceo_syn, N(5)-(carboxyethyl)ornithine synthase.
N(5)-(carboxyethyl)ornithine synthase (ceo_syn)
catalyzes the NADP-dependent conversion of
N5-(L-1-carboxyethyl)-L-ornithine to L-ornithine +
pyruvate. Ornithine plays a key role in the urea cycle,
which in mammals is used in arginine biosynthesis, and
is a precursor in polyamine synthesis. ceo_syn is
related to the NAD-dependent L-alanine dehydrogenases.
Like formate dehydrogenase and related enzymes, ceo_syn
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. These ceo_syn proteins have a
partially conserved NAD-binding motif and active site
residues that are characteristic of related enzymes such
as Saccharopine Dehydrogenase.
Length = 295
Score = 28.7 bits (65), Expect = 8.5
Identities = 15/47 (31%), Positives = 25/47 (53%), Gaps = 3/47 (6%)
Query: 207 RRMDTLNDLLAASDVISLHCAV--TDETIQIINAECLQHIKPGAFLV 251
R + L+ D+I ++C + TD II E L+ +KPGA ++
Sbjct: 186 RTEALFKEELSEYDII-VNCILQDTDRPDHIIYEEDLKRLKPGALII 231
>gnl|CDD|215878 pfam00362, Integrin_beta, Integrin, beta chain. Integrins have
been found in animals and their homologues have also
been found in cyanobacteria, probably due to horizontal
gene transfer. The sequences repeats have been trimmed
due to an overlap with EGF.
Length = 424
Score = 28.7 bits (65), Expect = 9.1
Identities = 11/40 (27%), Positives = 18/40 (45%)
Query: 458 DQASSRCASPEELRSRKTPIESIQESTSKKLSRSSKKLSE 497
+ S RC + E L + E I+ S+ +K LS+
Sbjct: 23 EFNSPRCDTLESLLEKGCSEEDIENPRSELEVTENKPLSD 62
>gnl|CDD|237083 PRK12374, PRK12374, putative dithiobiotin synthetase; Provisional.
Length = 231
Score = 28.6 bits (64), Expect = 9.2
Identities = 16/40 (40%), Positives = 18/40 (45%), Gaps = 1/40 (2%)
Query: 61 AAVLLHSLAYLPRAAQRRLRPYQLILCLGSSDRTVDSALA 100
A L+ L YLPRA QR L Y + L S VD
Sbjct: 193 PAPLIGELPYLPRAEQRELGQYIDLSMLRSVL-AVDRVTV 231
>gnl|CDD|236315 PRK08633, PRK08633, 2-acyl-glycerophospho-ethanolamine
acyltransferase; Validated.
Length = 1146
Score = 29.1 bits (66), Expect = 9.3
Identities = 14/45 (31%), Positives = 19/45 (42%), Gaps = 8/45 (17%)
Query: 489 SRSSKKLSEVSGETLKDGYVVALYARDRPALHISRQRH----KGG 529
S SK+ E + L DG VV ++ P I+R K G
Sbjct: 494 SGGSKESLEFIRKALDDGEVVCIF----PEGAITRNGQLNEFKRG 534
>gnl|CDD|130009 TIGR00934, 2a38euk, potassium uptake protein, Trk family. The
proteins of the Trk family are derived from
Gram-negative and Gram-positive bacteria, yeast and
wheat. The proteins of E. coli K12 TrkH and TrkG as well
as several yeast proteins have been functionally
characterized.The E. coli TrkH and TrkG proteins are
complexed to two peripheral membrane proteins, TrkA, an
NAD-binding protein, and TrkE, an ATP-binding protein.
This complex forms the potassium uptake system. This
family is specific for the eukaryotic Trk system
[Transport and binding proteins, Cations and iron
carrying compounds].
Length = 800
Score = 28.8 bits (64), Expect = 9.8
Identities = 34/167 (20%), Positives = 54/167 (32%), Gaps = 20/167 (11%)
Query: 369 QLTDDIQVSPEDSLKKGISWSR--DSPSQLQGSGFS----------QNSANTKSDGRRSR 416
L +++ PE + ++ Q FS QNS + KSD R
Sbjct: 153 LLQRELEDRPETGVAGRVTVPHGSAKRRDFQDKLFSGEFVKRDEPDQNSPDVKSDTRADE 212
Query: 417 SGKKAKKRHARQKSLQKPDDPSALEKESTSHKEDDTAMSGTDQASSRCASPEELRSRKTP 476
S + ++ + DP L + + + R S RS +
Sbjct: 213 SISDLEFEKFAKRRGSRDVDPEDLYRSIMMLQGIHERI--------REKSSANSRSDERS 264
Query: 477 IESIQESTSKKLSRSSKKLSEVSGETLKDGYVVALYARDRPALHISR 523
ESIQE ++ S S + + S D R R + I R
Sbjct: 265 SESIQEQVERRPSTSDIERNSQSLTRRYDDKSFDKAVRLRRSKTIDR 311
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.317 0.132 0.385
Gapped
Lambda K H
0.267 0.0724 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 32,233,375
Number of extensions: 3185888
Number of successful extensions: 3041
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2944
Number of HSP's successfully gapped: 114
Length of query: 632
Length of database: 10,937,602
Length adjustment: 103
Effective length of query: 529
Effective length of database: 6,369,140
Effective search space: 3369275060
Effective search space used: 3369275060
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 62 (27.7 bits)