RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 019092
(346 letters)
>gnl|CDD|215501 PLN02928, PLN02928, oxidoreductase family protein.
Length = 347
Score = 608 bits (1571), Expect = 0.0
Identities = 241/346 (69%), Positives = 286/346 (82%), Gaps = 5/346 (1%)
Query: 1 MEGMARSSDKNITRVLFCGPHFPASHNYTKEYLQNYPSIQVDVVPISDVPDVIANYHLCV 60
++ SD TRVLFCGP FPAS++YT+EYLQ YP IQVD V DVPDVIANY +CV
Sbjct: 7 IDKRVHHSDMRPTRVLFCGPEFPASYSYTREYLQKYPFIQVDAVAREDVPDVIANYDICV 66
Query: 61 VKTMRLDSNCISRANQMKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAASCAELT 120
K MRLD++ I+RA+QMKLIMQFGVGLEGVD++AAT+ GIKVARIP + TGNAASCAE+
Sbjct: 67 PKMMRLDADIIARASQMKLIMQFGVGLEGVDVDAATKHGIKVARIPSEGTGNAASCAEMA 126
Query: 121 IYLMLGLLRKQNEMRMAIEQKKLGVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVKII 180
IYLMLGLLRKQNEM+++++ ++LG P G+TL GKTVFILG+G IG+ELAKRLRPFGVK++
Sbjct: 127 IYLMLGLLRKQNEMQISLKARRLGEPIGDTLFGKTVFILGYGAIGIELAKRLRPFGVKLL 186
Query: 181 ATKRSWASHSQVSCQSSALAVKNGIIDDLVDEKGCHEDIFEFASKADVVVCCLSLNKQTA 240
AT+RSW S + + NG +DDLVDEKG HEDI+EFA +AD+VV C +L K+TA
Sbjct: 187 ATRRSWTSEPEDGLL-----IPNGDVDDLVDEKGGHEDIYEFAGEADIVVLCCTLTKETA 241
Query: 241 GIVNKSFLSSMKKGSLLVNIARGGLLDYEAIAHYLECGHLGGLGIDVAWTEPFDPNDPIL 300
GIVN FLSSMKKG+LLVNIARGGLLDY+A+ LE GHLGGL IDVAW+EPFDP+DPIL
Sbjct: 242 GIVNDEFLSSMKKGALLVNIARGGLLDYDAVLAALESGHLGGLAIDVAWSEPFDPDDPIL 301
Query: 301 KFKNVLITPHVGGVTEHSYRSMAKVVGDVALQLHAGTPLTGLEFVN 346
K NV+ITPHV GVTE+SYRSM K+VGD ALQLHAG PLTG+EFVN
Sbjct: 302 KHPNVIITPHVAGVTEYSYRSMGKIVGDAALQLHAGRPLTGIEFVN 347
>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 = 330 bits (849), Expect = e-113
Identities = 123/331 (37%), Positives = 181/331 (54%), Gaps = 25/331 (7%)
Query: 14 RVLFCGPHFPASHNYTKEYLQNYPSIQVDVVPISDVP-DVIANYHLCVVKTMR-LDSNCI 71
+VLF GP FP + + L P ++V D ++A+ + V + +D+ +
Sbjct: 1 KVLFLGPEFPDAEELLRALLPPAPGVEVVTAAELDEEAALLADADVLVPGMRKVIDAELL 60
Query: 72 SRANQMKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLMLGLLRKQ 131
+ A +++LI Q GVGL+GVD+ AAT GI VA IPG GNA S AE + LML LLR+
Sbjct: 61 AAAPRLRLIQQPGVGLDGVDLEAATARGIPVANIPG---GNAESVAEHAVMLMLALLRRL 117
Query: 132 NEMRMAIEQKKLGVPTGE---TLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWAS 188
E + + G P G L GKTV I+G GNIG +A+RLR FGV++I R
Sbjct: 118 PEADRELRAGRWGRPEGRPSRELSGKTVGIVGLGNIGRAVARRLRGFGVEVIYYDRFRDP 177
Query: 189 HSQVSCQSSALAVKNGIIDDLVDEKGCHEDIFEFASKADVVVCCLSLNKQTAGIVNKSFL 248
+ D + ++ E +++DVV + L +T ++ L
Sbjct: 178 -----------------EAEEKDLGVRYVELDELLAESDVVSLHVPLTPETRHLIGAEEL 220
Query: 249 SSMKKGSLLVNIARGGLLDYEAIAHYLECGHLGGLGIDVAWTEPFDPNDPILKFKNVLIT 308
++MK G++L+N ARGGL+D EA+ L GHL G G+DV W EP P+DP+L+ NV++T
Sbjct: 221 AAMKPGAILINTARGGLVDEEALLAALRSGHLAGAGLDVFWQEPLPPDDPLLRLDNVILT 280
Query: 309 PHVGGVTEHSYRSMAKVVGDVALQLHAGTPL 339
PH+ GVT+ SY+ MA +V + +L G P
Sbjct: 281 PHIAGVTDESYQRMAAIVAENIARLLRGEPP 311
>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 = 201 bits (514), Expect = 1e-62
Identities = 89/260 (34%), Positives = 140/260 (53%), Gaps = 26/260 (10%)
Query: 71 ISRANQMKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLMLGLLRK 130
+++A ++K I G G++ +D++AA + GI V +PG NA + AE + L+L LLR+
Sbjct: 58 LAKAPKLKFIQVAGAGVDNIDLDAAKKRGITVTNVPG---ANAEAVAEHALGLLLALLRR 114
Query: 131 ----QNEMRMAIEQKKLGVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSW 186
+R G P G L GKTV I+G G IG +AKRL+ FG+K++ R+
Sbjct: 115 LPRADAAVRRGWGWLWAGFP-GYELEGKTVGIVGLGRIGQRVAKRLQAFGMKVLYYDRT- 172
Query: 187 ASHSQVSCQSSALAVKNGIIDDLVDEKGCHEDIFEFASKADVVVCCLSLNKQTAGIVNKS 246
K +DL + E +++DVVV L L +T ++N+
Sbjct: 173 --------------RKPEPEEDLGFR---VVSLDELLAQSDVVVLHLPLTPETRHLINEE 215
Query: 247 FLSSMKKGSLLVNIARGGLLDYEAIAHYLECGHLGGLGIDVAWTEPFDPNDPILKFKNVL 306
L+ MK G++LVN ARGGL+D +A+ L+ G + G +DV EP + P+L+ NV+
Sbjct: 216 ELALMKPGAVLVNTARGGLVDEDALLRALKSGKIAGAALDVFEPEPLPADHPLLELPNVI 275
Query: 307 ITPHVGGVTEHSYRSMAKVV 326
+TPH+ G TE + MA++
Sbjct: 276 LTPHIAGYTEEARERMAEIA 295
>gnl|CDD|223189 COG0111, SerA, Phosphoglycerate dehydrogenase and related
dehydrogenases [Amino acid transport and metabolism].
Length = 324
Score = 202 bits (515), Expect = 1e-62
Identities = 90/311 (28%), Positives = 151/311 (48%), Gaps = 30/311 (9%)
Query: 39 IQVDVVPISDVPDVIANYHLCVVKTMRLDSNCISRANQMKLIMQFGVGLEGVDINAATRC 98
+ ++ + +A+ +V + ++ A +K I + G G++ +D+ AAT+
Sbjct: 29 PDGPDLDEEELLEALADADALIVSVTPVTEEVLAAAPNLKAIGRAGAGVDNIDLEAATKR 88
Query: 99 GIKVARIPGDVTGNAASCAELTIYLMLGLLRK----QNEMRMAIEQKKLGVPTGETLLGK 154
GI V PG GNA S AEL + L+L L R+ R +K G L GK
Sbjct: 89 GILVVNAPG---GNAISVAELVLALLLALARRIPDADASQRRGEWDRKAF--RGTELAGK 143
Query: 155 TVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEKG 214
TV I+G G IG +AKRL+ FG+K+I + G
Sbjct: 144 TVGIIGLGRIGRAVAKRLKAFGMKVIGYDPY-------------------SPRERAGVDG 184
Query: 215 CH--EDIFEFASKADVVVCCLSLNKQTAGIVNKSFLSSMKKGSLLVNIARGGLLDYEAIA 272
+ + E ++AD++ L L +T G++N L+ MK G++L+N ARGG++D +A+
Sbjct: 185 VVGVDSLDELLAEADILTLHLPLTPETRGLINAEELAKMKPGAILINAARGGVVDEDALL 244
Query: 273 HYLECGHLGGLGIDVAWTEPFDPNDPILKFKNVLITPHVGGVTEHSYRSMAKVVGDVALQ 332
L+ G + G +DV EP + P+ NV++TPH+GG T+ + +A++V + ++
Sbjct: 245 AALDSGKIAGAALDVFEEEPLPADSPLWDLPNVILTPHIGGSTDEAQERVAEIVAENIVR 304
Query: 333 LHAGTPLTGLE 343
AG P+
Sbjct: 305 YLAGGPVVNNA 315
>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 = 196 bits (501), Expect = 1e-60
Identities = 84/254 (33%), Positives = 136/254 (53%), Gaps = 23/254 (9%)
Query: 71 ISRANQMKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLMLGLLRK 130
++ A ++K+I ++GVG + +D+ AA + GI V PG N+ S AELTI LML L R+
Sbjct: 63 LAAAPRLKVISRYGVGYDNIDLEAAKKRGIVVTNTPG---ANSNSVAELTIGLMLALARQ 119
Query: 131 QNEMRMAIEQKKLGVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHS 190
+ + P G L GKT+ I+G G IG +A+RL FG+K++A
Sbjct: 120 IPQADREVRAGGWDRPVGTELYGKTLGIIGLGRIGKAVARRLSGFGMKVLAYDPYP---- 175
Query: 191 QVSCQSSALAVKNGI-IDDLVDEKGCHEDIFEFASKADVVVCCLSLNKQTAGIVNKSFLS 249
A ++G+ L E++ + ++D + L L +T ++N + L+
Sbjct: 176 -----DEEFAKEHGVEFVSL-------EELLK---ESDFISLHLPLTPETRHLINAAELA 220
Query: 250 SMKKGSLLVNIARGGLLDYEAIAHYLECGHLGGLGIDVAWTEPFDPNDPILKFKNVLITP 309
MK G++L+N ARGGL+D EA+ L+ G + G +DV EP + P+L+ NV++TP
Sbjct: 221 LMKPGAILINTARGGLVDEEALYEALKSGRIAGAALDVFEEEPPPADSPLLELPNVILTP 280
Query: 310 HVGGVTEHSYRSMA 323
H+G T+ + M
Sbjct: 281 HIGASTKEAVLRMG 294
>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 = 188 bits (481), Expect = 9e-58
Identities = 105/333 (31%), Positives = 162/333 (48%), Gaps = 45/333 (13%)
Query: 14 RVLFCGPHFPASHNYTKEYLQNYPSIQVDVVPISD---VPDVIANYHLCVVKTM-RLDSN 69
+VL P E L+ I+VDV P + +IA+ +V++ ++ +
Sbjct: 1 KVLVTDPIDEEGL----ELLREA-GIEVDVAPGLSEEELLAIIADADALIVRSATKVTAE 55
Query: 70 CISRANQMKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLMLGLLR 129
I A ++K+I + GVG++ +D+ AAT GI V PG N S AE TI LML L R
Sbjct: 56 VIEAAPRLKVIGRAGVGVDNIDVEAATARGILVVNAPG---ANTISVAEHTIALMLALAR 112
Query: 130 KQNEMRMAI-----EQKKLGVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKR 184
+ ++ ++KK G L GKT+ I+G G IG E+A+R R FG+K++A
Sbjct: 113 NIPQADASLRAGKWDRKKF---MGVELRGKTLGIVGLGRIGREVARRARAFGMKVLAYDP 169
Query: 185 SWASHSQVSCQSSALAVKNGIIDDLVDEKGCHE--DIFEFASKADVVVCCLSLNKQTAGI 242
I G E + E ++AD + L +T G+
Sbjct: 170 --------------------YISAERAAAGGVELVSLDELLAEADFISLHTPLTPETRGL 209
Query: 243 VNKSFLSSMKKGSLLVNIARGGLLDYEAIAHYLECGHLGGLGIDVAWTEPFDPNDPILKF 302
+N L+ MK G++L+N ARGG++D A+A L+ G + G +DV EP + P+L
Sbjct: 210 INAEELAKMKPGAILINTARGGIVDEAALADALKSGKIAGAALDVFEQEPPPADSPLLGL 269
Query: 303 KNVLITPHVGGVTEHSYRSMAKVVGDVALQLHA 335
NV++TPH+G TE + +A D A Q+ A
Sbjct: 270 PNVILTPHLGASTEEAQERVAV---DAAEQVLA 299
>gnl|CDD|223980 COG1052, LdhA, Lactate dehydrogenase and related dehydrogenases
[Energy production and conversion / Coenzyme metabolism
/ General function prediction only].
Length = 324
Score = 188 bits (481), Expect = 2e-57
Identities = 84/298 (28%), Positives = 149/298 (50%), Gaps = 31/298 (10%)
Query: 39 IQVDVVPISDVPDVIANYH-LCVVKTMRLDSNCISRANQMKLIMQFGVGLEGVDINAATR 97
+ D+ P +++ + + + + R+D+ + + +KLI G + VD+ AA
Sbjct: 28 YEDDLTPDTELAERLKDADAVITFVNDRIDAEVLEKLPGLKLIATRSAGYDNVDLEAAKE 87
Query: 98 CGIKVARIPGDVTGNAASCAELTIYLMLGLLRK--QNEMRMA----IEQKKLGVPTGETL 151
GI V +PG T + AE + L+L L R+ + + R+ G L
Sbjct: 88 RGITVTNVPGYST---EAVAEHAVALILALARRIHEGDRRVREGNWSLSGGPDPLLGFDL 144
Query: 152 LGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVD 211
GKT+ I+G G IG +A+RL+ FG+K++ RS N + +
Sbjct: 145 RGKTLGIIGLGRIGQAVARRLKGFGMKVLYYDRS----------------PNPEAEKELG 188
Query: 212 EKGCHEDIFEFASKADVVVCCLSLNKQTAGIVNKSFLSSMKKGSLLVNIARGGLLDYEAI 271
+ + D+ E +++D++ L +T ++N L+ MK G++LVN ARGGL+D +A+
Sbjct: 189 AR--YVDLDELLAESDIISLHCPLTPETRHLINAEELAKMKPGAILVNTARGGLVDEQAL 246
Query: 272 AHYLECGHLGGLGIDVAWTEPFDPNDPILK---FKNVLITPHVGGVTEHSYRSMAKVV 326
L+ G + G G+DV EP + P+L+ F NV++TPH+ TE + ++MA++
Sbjct: 247 IDALKSGKIAGAGLDVFENEPALFDHPLLRLDNFPNVVLTPHIASATEEARKAMAELA 304
>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 = 177 bits (452), Expect = 2e-53
Identities = 88/325 (27%), Positives = 148/325 (45%), Gaps = 47/325 (14%)
Query: 36 YPSIQVDVVPISD--VPDVIANYHLCVVKTMRLDSNCISRANQMKLIMQFGVGLEGVDIN 93
+ +V + D + + + + V + + ++ ++KLI G++ + +
Sbjct: 19 LEGLYAEVPELPDEAAEEALEDADVLVGGRLTKEEA-LAALKRLKLIQVPSAGVDHLPL- 76
Query: 94 AATRCGIKVARIPGDVT-----GNAASCAELTIYLMLGLLRK----QNEMRMAI-EQKKL 143
R+P V GN+ + AE + L+L L ++ N++R I +
Sbjct: 77 ---------ERLPEGVVVANNHGNSPAVAEHALALILALAKRIVEYDNDLRRGIWHGRAG 127
Query: 144 GVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKN 203
P + L GKTV ILG+G+IG E+A+ L+ FG+++I RS
Sbjct: 128 EEPESKELRGKTVGILGYGHIGREIARLLKAFGMRVIGVSRS------------------ 169
Query: 204 GIIDDLVDEKGCHEDIFEFASKADVVVCCLSLNKQTAGIVNKSFLSSMKKGSLLVNIARG 263
D+ D G D+ E +ADVVV L L KQT G++ + L++MK G++LVN+ RG
Sbjct: 170 PKEDEGADFVGTLSDLDEALEQADVVVVALPLTKQTRGLIGAAELAAMKPGAILVNVGRG 229
Query: 264 GLLDYEAIAHYLECGHLGGLGIDVAWTEP------FDPNDPILKFKNVLITPHVGGVTEH 317
++D EA+ L+ + G IDV W P P + NV+++PH G TE
Sbjct: 230 PVVDEEALYEALKERPIAGAAIDVWWRYPSRGDPVAPSRYPFHELPNVIMSPHNAGWTEE 289
Query: 318 SYRSMAKVVGDVALQLHAGTPLTGL 342
++R + + G PL L
Sbjct: 290 TFRRRIDEAAENIRRYLRGEPLLNL 314
>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 = 176 bits (448), Expect = 7e-53
Identities = 87/290 (30%), Positives = 133/290 (45%), Gaps = 37/290 (12%)
Query: 51 DVIANYHLCVVKTMRLDSNCISRANQMKLIMQFGV---GLEGVDINAATRCGIKVARIPG 107
+ + + + + + I A ++KLI GV G E VD+ AAT GI V PG
Sbjct: 42 EALKDADILITHFAPVTKKVIEAAPKLKLI---GVCRGGPENVDVEAATERGIPVLNTPG 98
Query: 108 DVTGNAASCAELTIYLMLGLLRKQNEMRMAIEQKK------LGVPTGETLLGKTVFILGF 161
NA + AE T+ LML R A++ + G L GKTV I+GF
Sbjct: 99 R---NAEAVAEFTVGLMLAETRNIARAHAALKDGEWRKDYYNYDGYGPELRGKTVGIVGF 155
Query: 162 GNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEKGCHEDIFE 221
G IG +AKRL+ FG +++ + I+ +K E++ +
Sbjct: 156 GAIGRRVAKRLKAFGAEVLVYD-PYVDPE--------------KIEADGVKKVSLEELLK 200
Query: 222 FASKADVVVCCLSLNKQTAGIVNKSFLSSMKKGSLLVNIARGGLLDYEAIAHYLECGHLG 281
++DVV L +T G++ + MK + +N AR GL+D +A+ LE G +G
Sbjct: 201 ---RSDVVSLHARLTPETRGMIGAEEFALMKPTAYFINTARAGLVDEDALIEALEEGKIG 257
Query: 282 GLGIDVAWTEPFDPNDPILKFKNVLITPHVGG----VTEHSYRSMAKVVG 327
G +DV EP + P+LK NV +TPH+ G V E S +A+ +
Sbjct: 258 GAALDVFPEEPLPADHPLLKLDNVTLTPHIAGATRDVAERSPEIIAEELK 307
>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 = 169 bits (430), Expect = 8e-52
Identities = 62/195 (31%), Positives = 97/195 (49%), Gaps = 23/195 (11%)
Query: 121 IYLMLGLLRKQNEMRMAIEQKKL--GVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVK 178
+ L+L L R+ E + + G L GKTV I+G G IG +A+RL+ FG+K
Sbjct: 1 LALLLALARRIPEADRQVRAGRWRPDALLGRELSGKTVGIIGLGRIGRAVARRLKAFGMK 60
Query: 179 IIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEKGCH-EDIFEFASKADVVVCCLSLNK 237
+IA R + G + E +++DVV L L
Sbjct: 61 VIAYDRY--------------------PKAEAEALGARYVSLDELLAESDVVSLHLPLTP 100
Query: 238 QTAGIVNKSFLSSMKKGSLLVNIARGGLLDYEAIAHYLECGHLGGLGIDVAWTEPFDPND 297
+T ++N L+ MK G++L+N ARGGL+D +A+ L+ G + G +DV EP P+
Sbjct: 101 ETRHLINAERLALMKPGAILINTARGGLVDEDALIAALKSGRIAGAALDVFEPEPLPPDH 160
Query: 298 PILKFKNVLITPHVG 312
P+L+ NV++TPH+
Sbjct: 161 PLLELPNVILTPHIA 175
>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 = 173 bits (440), Expect = 2e-51
Identities = 90/269 (33%), Positives = 138/269 (51%), Gaps = 24/269 (8%)
Query: 78 KLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLMLGLLRKQNEMRMA 137
KLI + G+G + VD+ AAT G+ V R+PG V + AE + L+L +LRK N+ A
Sbjct: 71 KLIARHGIGYDNVDLKAATEHGVIVTRVPGAV--ERDAVAEHAVALILTVLRKINQASEA 128
Query: 138 IEQKKLGVPT---GETLLGKTVFILGFGNIGVELAKRLRP-FGVKIIATKRSWASHSQVS 193
+++ K G L GKTV I+G+GNIG +A+ L+ F K++A +
Sbjct: 129 VKEGKWTERANFVGHELSGKTVGIIGYGNIGSRVAEILKEGFNAKVLAYDPYVSE----- 183
Query: 194 CQSSALAVKNGIIDDLVDEKGCHEDIFEFASKADVVVCCLSLNKQTAGIVNKSFLSSMKK 253
+ K L E++ ++D++ L ++T ++N+ S MKK
Sbjct: 184 ---EVIKKKGAKPVSL-------EELLA---ESDIISLHAPLTEETYHMINEKAFSKMKK 230
Query: 254 GSLLVNIARGGLLDYEAIAHYLECGHLGGLGIDVAWTEPFDPNDPILKFKNVLITPHVGG 313
G +LVN ARG L+D EA+ L+ G + G G+DV EP + P+L ++NV+ITPH+G
Sbjct: 231 GVILVNTARGELIDEEALIEALKSGKIAGAGLDVLEEEPIKADHPLLHYENVVITPHIGA 290
Query: 314 VTEHSYRSMAKVVGDVALQLHAGTPLTGL 342
T S M + V D AG G+
Sbjct: 291 YTYESLYGMGEKVVDDIEDFLAGKEPKGI 319
>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 = 169 bits (432), Expect = 2e-50
Identities = 80/274 (29%), Positives = 134/274 (48%), Gaps = 26/274 (9%)
Query: 58 LCVVKTMRLDSNCISRANQMKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAASCA 117
L T ++D+ + A +K+I + VG + +D++AA GI V P +T + A
Sbjct: 47 LLCTLTDKIDAELLDAAPPLKVIANYSVGYDHIDVDAAKARGIPVTNTPDVLT---DATA 103
Query: 118 ELTIYLMLGLLRKQNEM-RMAIEQKKLGV-PT---GETLLGKTVFILGFGNIGVELAKRL 172
+L L+L R+ E R + G PT G L GKT+ I+G G IG +A+R
Sbjct: 104 DLAFALLLAAARRVVEGDRFVRAGEWKGWSPTLLLGTDLHGKTLGIVGMGRIGQAVARRA 163
Query: 173 RPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEKGCHEDIFEFASKADVVVCC 232
+ FG+KI+ RS + L + + + E +++D V
Sbjct: 164 KGFGMKILYHNRS-----RKPEAEEELGAR-------------YVSLDELLAESDFVSLH 205
Query: 233 LSLNKQTAGIVNKSFLSSMKKGSLLVNIARGGLLDYEAIAHYLECGHLGGLGIDVAWTEP 292
L +T ++N L+ MK ++L+N ARGG++D +A+ L+ G + G G+DV EP
Sbjct: 206 CPLTPETRHLINAERLALMKPTAILINTARGGVVDEDALVEALKSGKIAGAGLDVFEPEP 265
Query: 293 FDPNDPILKFKNVLITPHVGGVTEHSYRSMAKVV 326
+ P+L NV++ PH+G T + +MA++
Sbjct: 266 LPADHPLLTLPNVVLLPHIGSATVETRTAMAELA 299
>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 = 170 bits (432), Expect = 2e-50
Identities = 75/324 (23%), Positives = 139/324 (42%), Gaps = 25/324 (7%)
Query: 21 HFPASHNYTKEYLQNYPSIQVDVVPISDVPDVIANYHLCVVKTMRLDSNCISRANQMKLI 80
P + + P ++ VV ++ + +A+ V+ + A +++ I
Sbjct: 6 LSPLDDEHLERLRAAAPGAELRVVTAEELTEELADAD--VLLGNPPLPELLPAAPRLRWI 63
Query: 81 MQFGVGLEGVDINAATRCGIKVARIPGDVTG-NAASCAELTIYLMLGLLRKQNEMRMAIE 139
G++ + + + G AE + ML RK
Sbjct: 64 QSTSAGVDALLFPELLERDVVLTN----ARGIFGPPIAEYVLGYMLAFARKLPRYARNQA 119
Query: 140 QKK-LGVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSA 198
+++ L GKTV I+G G+IG E+A+R + FG+++I +RS V
Sbjct: 120 ERRWQRRGPVRELAGKTVLIVGLGDIGREIARRAKAFGMRVIGVRRSGRPAPPV------ 173
Query: 199 LAVKNGIIDDLVDEKGCHEDIFEFASKADVVVCCLSLNKQTAGIVNKSFLSSMKKGSLLV 258
+D++ +++ E +AD VV L L +T G+ N ++MK G++L+
Sbjct: 174 -------VDEVYTP----DELDELLPEADYVVNALPLTPETRGLFNAERFAAMKPGAVLI 222
Query: 259 NIARGGLLDYEAIAHYLECGHLGGLGIDVAWTEPFDPNDPILKFKNVLITPHVGGVTEHS 318
N+ RG ++D +A+ LE G + G +DV EP + P+ NV+ITPH+ G +
Sbjct: 223 NVGRGSVVDEDALIEALESGRIAGAALDVFEEEPLPADSPLWDLPNVIITPHISGDSPSY 282
Query: 319 YRSMAKVVGDVALQLHAGTPLTGL 342
+ ++ + + AG PL +
Sbjct: 283 PERVVEIFLENLRRYLAGEPLLNV 306
>gnl|CDD|240624 cd05299, CtBP_dh, C-terminal binding protein (CtBP),
D-isomer-specific 2-hydroxyacid dehydrogenases related
repressor. The transcriptional corepressor CtBP is a
dehydrogenase with sequence and structural similarity to
the d2-hydroxyacid dehydrogenase family. CtBP was
initially identified as a protein that bound the PXDLS
sequence at the adenovirus E1A C terminus, causing the
loss of CR-1-mediated transactivation. CtBP binds NAD(H)
within a deep cleft, undergoes a conformational change
upon NAD binding, and has NAD-dependent dehydrogenase
activity.
Length = 312
Score = 167 bits (425), Expect = 2e-49
Identities = 77/279 (27%), Positives = 129/279 (46%), Gaps = 38/279 (13%)
Query: 51 DVIANYHLCVVKTMRLDSNCISRANQMKLIMQFGVGLEGVDINAATRCGIKVARIPG--- 107
D + + + + I ++K+I+++GVG++ VD+ AAT GI V +P
Sbjct: 46 DALLVQYA------PVTAEVIEALPRLKVIVRYGVGVDNVDVAAATERGIPVCNVPDYCT 99
Query: 108 -DVTGNAASCAELTIYLMLGLLRKQNEMRMAIEQKKLGVPTGETLL---GKTVFILGFGN 163
+V A+ + L+L L RK + A+ G + G T+ ++GFG
Sbjct: 100 EEV-------ADHALALILALARKLPFLDRAVRAGGWDWTVGGPIRRLRGLTLGLVGFGR 152
Query: 164 IGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEKGCHEDIFEFA 223
IG +AKR + FG ++IA V +G+ +++
Sbjct: 153 IGRAVAKRAKAFGFRVIAYDPY---------------VPDGVAALGGVRVVSLDELLA-- 195
Query: 224 SKADVVVCCLSLNKQTAGIVNKSFLSSMKKGSLLVNIARGGLLDYEAIAHYLECGHLGGL 283
++DVV L +T +++ L+ MK G+ LVN ARGGL+D A+A L+ G + G
Sbjct: 196 -RSDVVSLHCPLTPETRHLIDAEALALMKPGAFLVNTARGGLVDEAALARALKSGRIAGA 254
Query: 284 GIDVAWTEPFDPNDPILKFKNVLITPHVGGVTEHSYRSM 322
+DV EP + P+L NV++TPH +E S +
Sbjct: 255 ALDVLEEEPPPADSPLLSAPNVILTPHAAWYSEESLAEL 293
>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 = 166 bits (422), Expect = 4e-49
Identities = 94/307 (30%), Positives = 152/307 (49%), Gaps = 35/307 (11%)
Query: 31 EYLQNYPSIQVDVVPISD---VPDVIANYHLCVVKT-MRLDSNCISRANQMKLIMQFGVG 86
E L+ +VD P+ + + I +Y + +V++ ++ I A +K+I + GVG
Sbjct: 15 EKLEE-AGFEVDYEPLIAKEELLEKIKDYDVLIVRSRTKVTKEVIDAAKNLKIIARAGVG 73
Query: 87 LEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLMLGLLRK----QNEMRMAI-EQK 141
L+ +D+ A + GIKV PG ++ S AEL I LML L R EM++ +K
Sbjct: 74 LDNIDVEYAKKKGIKVINTPG---ASSNSVAELVIGLMLSLARFIHRANREMKLGKWNKK 130
Query: 142 KLGVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAV 201
K G L GKT+ I+GFG IG E+AK R G+ +IA AV
Sbjct: 131 KY---KGIELRGKTLGIIGFGRIGREVAKIARALGMNVIAYDPY---------PKDEQAV 178
Query: 202 KNGIIDDLVDEKGCHEDIFEFASKADVVVCCLSLNKQTAGIVNKSFLSSMKKGSLLVNIA 261
+ G+ K + E +D + + L +T ++NK L MK G++++N +
Sbjct: 179 ELGV-------KTV--SLEELLKNSDFISLHVPLTPETKHMINKKELELMKDGAIIINTS 229
Query: 262 RGGLLDYEAIAHYLECGHLGGLGIDVAWTEPFDPNDPILKFKNVLITPHVGGVTEHSYRS 321
RGG++D EA+ L+ G L G +DV EP P +L+ NV +TPH+G T+ +
Sbjct: 230 RGGVIDEEALLEALKSGKLAGAALDVFENEP-PPGSKLLELPNVSLTPHIGASTKEAQER 288
Query: 322 MAKVVGD 328
+ + + +
Sbjct: 289 IGEELAN 295
>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 = 159 bits (404), Expect = 4e-46
Identities = 76/252 (30%), Positives = 118/252 (46%), Gaps = 31/252 (12%)
Query: 78 KLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLMLGLLRKQNEMRMA 137
K+I G G + +D++A T+ GI+V+ PG V + A+ ++L+LG LR + +
Sbjct: 78 KIIAHAGAGYDQIDVDALTKRGIQVSNTPGAVD---EATADTALFLILGALRNFSRAERS 134
Query: 138 IEQKKLGVPTGETLL-------GKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHS 190
+ G G L GKT+ ILG G IG +A++ FG+KII RS
Sbjct: 135 A---RAGKWRGFLDLTLAHDPRGKTLGILGLGGIGKAIARKAAAFGMKIIYHNRSRLP-- 189
Query: 191 QVSCQSSALAVKNGIIDDLVDEKGCHEDIFEFASKADVVVCCLSLNKQTAGIVNKSFLSS 250
L + + E +++DVV L T ++NK +
Sbjct: 190 ------EELEKALATY---------YVSLDELLAQSDVVSLNCPLTAATRHLINKKEFAK 234
Query: 251 MKKGSLLVNIARGGLLDYEAIAHYLECGHLGGLGIDVAWTEPFDPNDPILKFKNVLITPH 310
MK G ++VN ARG ++D +A+ LE G + G+DV EP N +LK NV + PH
Sbjct: 235 MKDGVIIVNTARGAVIDEDALVDALESGKVASAGLDVFENEPE-VNPGLLKMPNVTLLPH 293
Query: 311 VGGVTEHSYRSM 322
+G +T + M
Sbjct: 294 MGTLTVETQEKM 305
>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 = 162 bits (413), Expect = 8e-46
Identities = 99/341 (29%), Positives = 163/341 (47%), Gaps = 46/341 (13%)
Query: 14 RVLFCGPHFPASHNYTKEYLQNYPSIQVDVVP-------ISDVPDVIANYHLCVVKTM-R 65
+VL P + L++ ++VDV + +PD Y +V++ +
Sbjct: 1 KVLIADP----ISPDGIDILED-VGVEVDVQTGLSREELLEIIPD----YDALIVRSATK 51
Query: 66 LDSNCISRANQMKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLML 125
+ I+ A ++K+I + GVG++ +DI AAT GI V P TGN S AE + ++L
Sbjct: 52 VTEEVIAAAPKLKVIGRAGVGVDNIDIEAATARGILVVNAP---TGNTISAAEHALAMLL 108
Query: 126 GLLRKQNEMRMAI-----EQKKLGVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVKII 180
R + ++ ++K G L GKT+ ++G G IG +AKR + FG+K++
Sbjct: 109 AAARNIPQADASLKEGEWDRKAF---MGTELYGKTLGVIGLGRIGSIVAKRAKAFGMKVL 165
Query: 181 ATKRSWASHSQVSCQSSALAVKNGIIDDLVDEKGCHEDIFEFASKADVVVCCLSLNKQTA 240
A S A + G+ LVD D+ E ++AD + L +T
Sbjct: 166 AYD---------PYISPERAEQLGVE--LVD------DLDELLARADFITVHTPLTPETR 208
Query: 241 GIVNKSFLSSMKKGSLLVNIARGGLLDYEAIAHYLECGHLGGLGIDVAWTEPFDPNDPIL 300
G++ L+ MKKG ++VN ARGG++D A+ LE GH+ +DV EP ++P+
Sbjct: 209 GLIGAEELAKMKKGVIIVNCARGGIIDEAALYEALEEGHVRAAALDVFEKEP-PTDNPLF 267
Query: 301 KFKNVLITPHVGGVTEHSYRSMAKVVGDVALQLHAGTPLTG 341
NV+ TPH+G T + ++A V + L G P+
Sbjct: 268 DLDNVIATPHLGASTREAQENVATQVAEQVLDALKGLPVPN 308
>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 = 155 bits (394), Expect = 8e-45
Identities = 81/284 (28%), Positives = 127/284 (44%), Gaps = 26/284 (9%)
Query: 58 LCVVKTMRLDSNCISRANQMKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAASCA 117
L + +D I A +K+I +G G + +D++ A GI V P T A
Sbjct: 47 LITPLSTPVDKEIIDAAKNLKIIANYGAGFDNIDVDYAKEKGIPVTNTPAVST---EPTA 103
Query: 118 ELTIYLMLGLLRKQNEM-RMAIEQKKLGVP----TGETLLGKTVFILGFGNIGVELAKRL 172
ELT L+L L R+ E R+ LG G L GKT+ I+G G IG +A+R
Sbjct: 104 ELTFGLILALARRIAEGDRLMRRGGFLGWAPLFFLGHELAGKTLGIIGMGRIGQAVARRA 163
Query: 173 RPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEKGCHEDIFEFASKADVVVCC 232
+ FG+KI+ R H L +D+L+ ++D V
Sbjct: 164 KAFGMKILYYNR----HRLSEETEKELGATYVDLDELL-------------KESDFVSLH 206
Query: 233 LSLNKQTAGIVNKSFLSSMKKGSLLVNIARGGLLDYEAIAHYLECGHLGGLGIDVAWTEP 292
+T +++ + MK + L+N ARG L+D +A+ L+ G + G +DV EP
Sbjct: 207 APYTPETHHLIDAAAFKLMKPTAYLINAARGPLVDEKALVDALKTGEIAGAALDVFEFEP 266
Query: 293 FDPNDPILKFKNVLITPHVGGVTEHSYRSMAKVVGDVALQLHAG 336
+ + + K NV++TPH+G T + +MAK D + G
Sbjct: 267 -EVSPELKKLDNVILTPHIGNATVEARDAMAKEAADNIISFLEG 309
>gnl|CDD|237436 PRK13581, PRK13581, D-3-phosphoglycerate dehydrogenase;
Provisional.
Length = 526
Score = 160 bits (407), Expect = 9e-45
Identities = 99/305 (32%), Positives = 154/305 (50%), Gaps = 54/305 (17%)
Query: 31 EYLQNYPSIQVDVVPISDVP---DVIANYHLCVVKTM-RLDSNCISRANQMKLIMQFGVG 86
E L++ P ++VDV D ++I +Y +V++ ++ + + A +K+I + GVG
Sbjct: 15 EILKDAPGVEVDVKTGLDKEELLEIIGDYDALIVRSATKVTAEVLEAAKNLKVIGRAGVG 74
Query: 87 LEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLMLGLLR---------KQNEMRMA 137
++ VD+ AATR GI V P TGN S AE TI LML L R K +
Sbjct: 75 VDNVDVPAATRRGIIVVNAP---TGNTISAAEHTIALMLALARNIPQAHASLKAGKW--- 128
Query: 138 IEQKKLGVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVKIIA------TKRSWASHSQ 191
E+KK G L GKT+ I+G G IG E+AKR + FG+K+IA +R
Sbjct: 129 -ERKKF---MGVELYGKTLGIIGLGRIGSEVAKRAKAFGMKVIAYDPYISPER------- 177
Query: 192 VSCQSSALAVKNGIIDDLVDEKGCHEDIFEFASKADVVVCCLSLNKQTAGIVNKSFLSSM 251
A + G+ +LV +++ +AD + L +T G++ L+ M
Sbjct: 178 --------AAQLGV--ELVS----LDELLA---RADFITLHTPLTPETRGLIGAEELAKM 220
Query: 252 KKGSLLVNIARGGLLDYEAIAHYLECGHLGGLGIDVAWTEPFDPNDPILKFKNVLITPHV 311
K G ++N ARGG++D A+A L+ G + G +DV EP + P+ + NV++TPH+
Sbjct: 221 KPGVRIINCARGGIIDEAALAEALKSGKVAGAALDVFEKEP-PTDSPLFELPNVVVTPHL 279
Query: 312 GGVTE 316
G T
Sbjct: 280 GASTA 284
>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 = 152 bits (387), Expect = 8e-44
Identities = 89/280 (31%), Positives = 138/280 (49%), Gaps = 34/280 (12%)
Query: 60 VVKTMR----LDSNCISRANQMKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAAS 115
+ MR + + R +KL++ G+ +D+ AA GI V G T +
Sbjct: 49 AIVLMRERTPFPAALLERLPNLKLLVTTGMRNASIDLAAAKERGIVVCGTGGGPT----A 104
Query: 116 CAELTIYLMLGLLRK----QNEMRMAIEQKKLGVPTGETLLGKTVFILGFGNIGVELAKR 171
AELT L+L L R +R Q LG L GKT+ I+G G IG +A+
Sbjct: 105 TAELTWALILALARNLPEEDAALRAGGWQTTLGT----GLAGKTLGIVGLGRIGARVARI 160
Query: 172 LRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEKGCHEDIFEFASKADVVVC 231
+ FG+++IA W+S+ ++ + +A A G+ + K E++F +DVV
Sbjct: 161 GQAFGMRVIA----WSSN--LTAERAAAA---GV--EAAVSK---EELFA---TSDVVSL 203
Query: 232 CLSLNKQTAGIVNKSFLSSMKKGSLLVNIARGGLLDYEAIAHYLECGHLGGLGIDVAWTE 291
L L+ +T G+V L+ MK +LLVN +RG L+D A+ L G + G +DV E
Sbjct: 204 HLVLSDRTRGLVGAEDLALMKPTALLVNTSRGPLVDEGALLAALRAGRIAGAALDVFDVE 263
Query: 292 PFDPNDPILKFKNVLITPHVGGVTEHSYRSM-AKVVGDVA 330
P + P+ NVL+TPH+G VTE +Y + V ++A
Sbjct: 264 PLPADHPLRGLPNVLLTPHIGYVTEEAYEGFYGQAVENIA 303
>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 = 148 bits (377), Expect = 2e-42
Identities = 77/267 (28%), Positives = 126/267 (47%), Gaps = 30/267 (11%)
Query: 64 MRLDSNCISRANQMKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYL 123
L + I+ ++LI FGVG +G+D++AA GI+V PG A+L + L
Sbjct: 52 TGLSAALIAALPALELIASFGVGYDGIDLDAARARGIRVTNTPGV---LTDDVADLAVGL 108
Query: 124 MLGLLRK--QNEMRMAIEQK--KLGVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVKI 179
+L +LR+ + R + K P + GK V I+G G IG +A+RL FG++I
Sbjct: 109 LLAVLRRIPAAD-RFVRAGRWPKGAFPLTRKVSGKRVGIVGLGRIGRAIARRLEAFGMEI 167
Query: 180 IATKRSWASHSQVSCQSSALAVKNGIIDDLVDEKGCHEDIFEFASKADVVVCCLSLNKQT 239
++ V + + + E A+++DV+V T
Sbjct: 168 -----AYHGRRPK---------------PDVPYR-YYASLLELAAESDVLVVACPGGPAT 206
Query: 240 AGIVNKSFLSSMKKGSLLVNIARGGLLDYEAIAHYLECGHLGGLGIDVAWTEPFDPNDPI 299
+VN L ++ +LVN+ARG ++D A+ L+ G + G G+DV EP P +
Sbjct: 207 RHLVNAEVLEALGPDGVLVNVARGSVVDEAALIAALQEGRIAGAGLDVFENEPNVP-AAL 265
Query: 300 LKFKNVLITPHVGGVTEHSYRSMAKVV 326
L NV++TPH+ T + R+M +V
Sbjct: 266 LDLDNVVLTPHIASATVETRRAMGDLV 292
>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 = 146 bits (370), Expect = 3e-41
Identities = 77/257 (29%), Positives = 124/257 (48%), Gaps = 36/257 (14%)
Query: 65 RLDSNCISRANQMKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLM 124
LD+ +++ +KLI G VD+ AA GI V +PG T S A+ T L+
Sbjct: 54 VLDAEVLAQLPNLKLIGVLATGYNNVDLAAAKERGITVTNVPGYST---DSVAQHTFALL 110
Query: 125 LGLLRKQNEMRMAIEQKK---------LGVPTGETLLGKTVFILGFGNIGVELAKRLRPF 175
L L R ++ + P E L GKT+ I+G+GNIG +A+ R F
Sbjct: 111 LALARLVAYHNDVVKAGEWQKSPDFCFWDYPIIE-LAGKTLGIIGYGNIGQAVARIARAF 169
Query: 176 GVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEKGCHEDIFEFASKADVVVCCLSL 235
G+K++ +R + + V +++ ++DV+ L
Sbjct: 170 GMKVLFAERK---------------GAPPLREGYVS----LDELLA---QSDVISLHCPL 207
Query: 236 NKQTAGIVNKSFLSSMKKGSLLVNIARGGLLDYEAIAHYLECGHLGGLGIDVAWTEPFDP 295
+T ++N L+ MK G++L+N ARGGL+D +A+A L G + G G+DV EP
Sbjct: 208 TPETRNLINAEELAKMKPGAILINTARGGLVDEQALADALNSGKIAGAGLDVLSQEPPRA 267
Query: 296 NDPILKF-KNVLITPHV 311
++P+LK N++ITPH+
Sbjct: 268 DNPLLKAAPNLIITPHI 284
>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 = 145 bits (369), Expect = 4e-41
Identities = 79/333 (23%), Positives = 133/333 (39%), Gaps = 40/333 (12%)
Query: 26 HNYTKEYLQNYPSIQV-DVVPISDVPDVIANYH-LCVVKTMRLDSNCISRANQMKLIMQF 83
E L+ ++V D + ++ + + L V T + + + A +K+I +
Sbjct: 8 RPEELELLKEGGEVEVHDELLTEELLEAAKDADALIVRSTTPVTAEVLEAAPGLKVIARR 67
Query: 84 GVGLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLMLGLLRKQNEMRMAIEQKKL 143
GVG++ +D++AAT GI V +PG + S AELT+ L+L L R+ E A +
Sbjct: 68 GVGVDNIDLDAATERGILVTNVPG---YSTESVAELTVGLILALARRIPE---ADASVRA 121
Query: 144 GV-----PTGETLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSA 198
G P G L GKT+ ++G G IG A + G+ ++
Sbjct: 122 GDWKKGGPIGLELYGKTLGVIGGGGIGGIGAAIAKALGMGVV------------------ 163
Query: 199 LAVKNGIIDDLVDEKGCHEDIFEFASKA-----DVVVCCLSLNKQTAGIVNKSFLSSMKK 253
A + +E G + + D++ +T I+ +K
Sbjct: 164 -AYDPYPNPERAEEGGVEVLLLDLLLLDLKESDDLINLAPPTTMKTGHIIINEARGMLKD 222
Query: 254 GSLLVNIARGGLLDYEAIAHYLECGHLGGLGIDVAWTEPFDPNDPILKFKNVLITPHVGG 313
+ N GG+++ A+ LE G V P N P+L NV++TPH+ G
Sbjct: 223 AVAINNARGGGVIEEAALDALLEEGIAAAALDVVEEEPP-PVNSPLLDLPNVILTPHIAG 281
Query: 314 VTEHSYRSMAKVVGDVALQLHAGTPLTGLEFVN 346
TE + +MA+ + L G VN
Sbjct: 282 ATEEAQENMAEEAAENLLAFLKGGTPPNA--VN 312
>gnl|CDD|183914 PRK13243, PRK13243, glyoxylate reductase; Reviewed.
Length = 333
Score = 143 bits (361), Expect = 6e-40
Identities = 85/292 (29%), Positives = 146/292 (50%), Gaps = 34/292 (11%)
Query: 44 VPISDVPDVIANYHLCVVKTMRLDSNCISRANQMKLIMQFGVGLEGVDINAATRCGIKVA 103
V + V DV A L + + R+D A +++++ + VG + +D+ ATR GI V
Sbjct: 38 VLLEKVRDVDA---LVTMLSERIDCEVFEAAPRLRIVANYAVGYDNIDVEEATRRGIYVT 94
Query: 104 RIPGDVTGNAASCAELTIYLMLGLLRKQNEMRMAI---EQKKLGVP------TGETLLGK 154
PG +T + A+ L+L R+ E + E K+ GV G + GK
Sbjct: 95 NTPGVLTE---ATADFAWALLLATARRLVEADHFVRSGEWKRRGVAWHPLMFLGYDVYGK 151
Query: 155 TVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEKG 214
T+ I+GFG IG +A+R + FG++I+ R+ ++ L + +++L+ E
Sbjct: 152 TIGIIGFGRIGQAVARRAKGFGMRILYYSRTRKPEAE-----KELGAEYRPLEELLRE-- 204
Query: 215 CHEDIFEFASKADVVVCCLSLNKQTAGIVNKSFLSSMKKGSLLVNIARGGLLDYEAIAHY 274
+D V + L K+T ++N+ L MK ++LVN ARG ++D +A+
Sbjct: 205 -----------SDFVSLHVPLTKETYHMINEERLKLMKPTAILVNTARGKVVDTKALVKA 253
Query: 275 LECGHLGGLGIDVAWTEPFDPNDPILKFKNVLITPHVGGVTEHSYRSMAKVV 326
L+ G + G G+DV EP+ N+ + KNV++ PH+G T + MA++V
Sbjct: 254 LKEGWIAGAGLDVFEEEPY-YNEELFSLKNVVLAPHIGSATFEAREGMAELV 304
>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 = 141 bits (357), Expect = 2e-39
Identities = 95/295 (32%), Positives = 140/295 (47%), Gaps = 44/295 (14%)
Query: 52 VIANYHLCVVKTMRLDSNCISRANQMKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTG 111
+IAN M L I +K+I G++ VD+ A GI V+
Sbjct: 53 MIAN--------MPLPGEVIEACKNLKMISVAFTGVDHVDLEACKERGITVS-------- 96
Query: 112 NAA-----SCAELTIYLMLGLLRK--QNEMRMAIEQKKLGVPTGETLLGKTVFILGFGNI 164
NAA + AELTI L + LLR + + K G+ G L GKTV I+G G I
Sbjct: 97 NAAGYSTEAVAELTIGLAIDLLRNIVPCDAAVRAGGTKAGL-IGRELAGKTVGIVGTGAI 155
Query: 165 GVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEKGCHEDIFEFAS 224
G+ +A+ + FG K++A RS K ++ + + E +
Sbjct: 156 GLRVARLFKAFGCKVLAYSRS---------------EKEEAKALGIE----YVSLDELLA 196
Query: 225 KADVVVCCLSLNKQTAGIVNKSFLSSMKKGSLLVNIARGGLLDYEAIAHYLECGHLGGLG 284
++D+V L LN +T G++ K L+ MK+ ++L+N ARG ++D EA+A L G + G G
Sbjct: 197 ESDIVSLHLPLNDETKGLIGKEKLALMKESAILINTARGPVVDNEALADALNEGKIAGAG 256
Query: 285 IDVAWTEPFDPND-PILKFKNVLITPHVGGVTEHSYRSMAKVVGDVALQLHAGTP 338
IDV EP P D P+L N ++TPHV TE + A++V D AG P
Sbjct: 257 IDVFDMEPPLPADYPLLHAPNTILTPHVAFATEEAMEKRAEIVFDNIEAWLAGKP 311
>gnl|CDD|240656 cd12179, 2-Hacid_dh_14, Putative D-isomer specific 2-hydroxyacid
dehydrogenases, NAD-binding and catalytic domains.
2-Hydroxyacid dehydrogenases catalyze the conversion of
a wide variety of D-2-hydroxy acids to their
corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 306
Score = 140 bits (354), Expect = 4e-39
Identities = 93/314 (29%), Positives = 145/314 (46%), Gaps = 57/314 (18%)
Query: 39 IQVDVVPIS---DVPDVIANYHLCVVKT-MRLDSNCISRANQMKLIMQFGVGLEGVDINA 94
+VD P ++ +I Y ++++ +D I +A +K I + G GLE +D+
Sbjct: 21 FEVDYDPTISREEILAIIPQYDGLIIRSRFPIDKEFIEKATNLKFIARAGAGLENIDLEY 80
Query: 95 ATRCGIKVARIPGDVTGNAASCAELTIYLMLGLLRKQN----EMRMAI---EQKKLGVPT 147
A GI++ P GN + E + ++L L K N E+R I E +
Sbjct: 81 AKEKGIELFNAP---EGNRDAVGEHALGMLLALFNKLNRADQEVRNGIWDREGNR----- 132
Query: 148 GETLLGKTVFILGFGNIGVELAKRLRPFGVKIIA----TKRSWASHSQVSCQSSALAVKN 203
G L+GKTV I+G+GN+G AKRL FG K+IA A QVS
Sbjct: 133 GVELMGKTVGIIGYGNMGKAFAKRLSGFGCKVIAYDKYKNFGDAYAEQVSL--------- 183
Query: 204 GIIDDLVDEKGCHEDIFEFASKADVVVCCLSLNKQTAGIVNKSFLSSMKKGSLLVNIARG 263
E +F+ +AD++ + L +T G+VNK F+SS KK +N ARG
Sbjct: 184 -------------ETLFK---EADILSLHIPLTPETRGMVNKEFISSFKKPFYFINTARG 227
Query: 264 GLLDYEAIAHYLECGHLGGLGIDVAWTEPF----DPNDP-----ILKFKNVLITPHVGGV 314
++ + + L+ G + G +DV E N P ++K V++TPH+ G
Sbjct: 228 KVVVTKDLVKALKSGKILGACLDVLEYEKASFESIFNQPEAFEYLIKSPKVILTPHIAGW 287
Query: 315 TEHSYRSMAKVVGD 328
T SY +A+V+ D
Sbjct: 288 TFESYEKIAEVLVD 301
>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 = 138 bits (351), Expect = 2e-38
Identities = 81/268 (30%), Positives = 120/268 (44%), Gaps = 32/268 (11%)
Query: 58 LCVVKTMRLDSNCISRANQMKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAASCA 117
L R+D++ + ++K+I G + D+ A T GI V +P +T A
Sbjct: 48 LMAFMPDRIDADFLDACPRLKIIACALKGYDNFDVEACTARGIWVTIVPDLLT---EPTA 104
Query: 118 ELTIYLMLGLLRKQNEMRMAIEQKKLG--VPT--GETLLGKTVFILGFGNIGVELAKRLR 173
ELTI L++GL R + K G P G L GKTV ILG G +G +A+RL
Sbjct: 105 ELTIGLLIGLGRHILAGDRFVRSGKFGGWRPKFYGTGLDGKTVGILGMGALGRAIARRLS 164
Query: 174 PFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEKGCHEDIFEFASKADVVVCCL 233
FG ++ + H + AL ++ +D+L+ +D +V L
Sbjct: 165 GFGATLLY----YDPHPLDQAEEQALNLRRVELDELL-------------ESSDFLVLAL 207
Query: 234 SLNKQTAGIVNKSFLSSMKKGSLLVNIARGGLLDYEAIAHYLECGHLGGLGIDVAWTE-- 291
L T ++N L+ MK G+LLVN RG ++D A+A L+ GHLGG DV E
Sbjct: 208 PLTPDTLHLINAEALAKMKPGALLVNPCRGSVVDEAAVAEALKSGHLGGYAADVFEMEDW 267
Query: 292 -----PFDPNDPILKFK-NVLITPHVGG 313
P +L + TPH+G
Sbjct: 268 ARPDRPRSIPQELLDQHDRTVFTPHIGS 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 = 137 bits (348), Expect = 4e-38
Identities = 73/231 (31%), Positives = 100/231 (43%), Gaps = 19/231 (8%)
Query: 113 AASCAELTIYLMLGLLRKQNEMRMAIE-QKKLGVPTGETLLGKTVFILGFGNIGVELAKR 171
A + AE + L+L LR+ A L G TV I+G G IG L
Sbjct: 84 AETVAEHALALLLAGLRQLPARARATTWDPAEEDDLVTLLRGSTVAIVGAGGIGRALIPL 143
Query: 172 LRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEKGCHEDIFEFASKADVVVC 231
L PFG K+IA RS G + DE + + E AD VV
Sbjct: 144 LAPFGAKVIAVNRS------------------GRPVEGADETVPADRLDEVWPDADHVVL 185
Query: 232 CLSLNKQTAGIVNKSFLSSMKKGSLLVNIARGGLLDYEAIAHYLECGHLGGLGIDVAWTE 291
L +T +V+ + L++MK + LVN+ARG L+D +A+ L G + G +DV E
Sbjct: 186 AAPLTPETRHLVDAAALAAMKPHAWLVNVARGPLVDTDALVDALRSGEIAGAALDVTDPE 245
Query: 292 PFDPNDPILKFKNVLITPHVGGVTEHSYRSMAKVVGDVALQLHAGTPLTGL 342
P P+ N LITPHV E +A+ V + AG PL G+
Sbjct: 246 PLPDGHPLWSLPNALITPHVANTPEVIRPLLAERVAENVRAFAAGEPLLGV 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 = 137 bits (347), Expect = 1e-37
Identities = 88/253 (34%), Positives = 127/253 (50%), Gaps = 31/253 (12%)
Query: 71 ISRANQMKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTG-NAASCAELTIYLMLGLLR 129
I++A +KL + G+G + VD+ AA GI VA +VTG N S AE + ++L L+R
Sbjct: 79 IAKAKNLKLALTAGIGSDHVDLQAANDRGITVA----EVTGSNVVSVAEHVVMMILILVR 134
Query: 130 K-QNEMRMAIEQK----KLGVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKR 184
AIE + + L GKTV +G G IG+ + +RL+PF V ++ R
Sbjct: 135 NYVPGHEQAIEGGWNVADVVKRAYD-LEGKTVGTVGAGRIGLRVLRRLKPFDVHLLYYDR 193
Query: 185 SWASHSQVSCQSSALAVKNGIIDDLVDEKGC--HEDIFEFASKADVVVCCLSLNKQTAGI 242
+ + +++ E G H D+ + SK DVV L+ +T G+
Sbjct: 194 ------------------HRLPEEVEKELGLTRHADLEDMVSKCDVVTINCPLHPETEGL 235
Query: 243 VNKSFLSSMKKGSLLVNIARGGLLDYEAIAHYLECGHLGGLGIDVAWTEPFDPNDPILKF 302
NK LS MKKG+ LVN ARG + D EA+A LE GHL G DV + +P + P
Sbjct: 236 FNKELLSKMKKGAYLVNTARGKICDREAVAEALESGHLAGYAGDVWFPQPAPKDHPWRTM 295
Query: 303 KNVLITPHVGGVT 315
N +TPH+ G T
Sbjct: 296 PNNAMTPHISGTT 308
>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 = 132 bits (335), Expect = 3e-36
Identities = 76/269 (28%), Positives = 125/269 (46%), Gaps = 41/269 (15%)
Query: 74 ANQMKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLMLGLLRK--- 130
A +K I + G G+ +D++AA++ GI V PG NA + AEL I +ML L R
Sbjct: 48 APSLKAIARAGAGVNNIDVDAASKRGIVVFNTPG---ANANAVAELVIAMMLALSRNIIQ 104
Query: 131 ---------QNEMRMAIEQKKLGVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVKIIA 181
+++ +E+ K E L GKT+ ++G GNIG +A G+K+I
Sbjct: 105 AIKWVTNGDGDDISKGVEKGKKQFVGTE-LRGKTLGVIGLGNIGRLVANAALALGMKVIG 163
Query: 182 TKRSWASHSQVSCQSSALAVKNGII--DDLVDEKGCHEDIFEFASKADVVVCCLSLNKQT 239
+S ++ A + + L E++ + AD + + L +T
Sbjct: 164 YDPY------LSVEA-AWKLSVEVQRVTSL-------EELL---ATADYITLHVPLTDET 206
Query: 240 AGIVNKSFLSSMKKGSLLVNIARGGLLDYEAIAHYLECGHLGGLGIDVAWTEPFDPNDPI 299
G++N L+ MK G++L+N ARG ++D EA+ L+ G LGG + F +
Sbjct: 207 RGLINAELLAKMKPGAILLNFARGEIVDEEALLEALDEGKLGG-YVTD-----FPEPALL 260
Query: 300 LKFKNVLITPHVGGVTEHSYRSMAKVVGD 328
NV+ TPH+G TE + + A +
Sbjct: 261 GHLPNVIATPHLGASTEEAEENCAVMAAR 289
>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 = 132 bits (334), Expect = 5e-36
Identities = 79/339 (23%), Positives = 137/339 (40%), Gaps = 60/339 (17%)
Query: 13 TRVLFCGPHFPASHNYTKEYLQNYPSIQVDVVPISDVPDVIANYHL-------CVVKTMR 65
+VL + KE L+ VDV ++ + + L T +
Sbjct: 1 MKVLIYD-YRDDELEIEKEILKAGG---VDVEIVTYLLNDDETAELAKGADAILTAFTDK 56
Query: 66 LDSNCISRANQMKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLML 125
+D+ + +A +K I G + +D++ A GI V +P + AE TI L+L
Sbjct: 57 IDAELLDKAPGLKFISLRATGYDNIDLDYAKELGIGVTNVPEYSPN---AVAEHTIALIL 113
Query: 126 GLLRKQ--NEMRMAIEQKKLGVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVKIIATK 183
LLR + + R + + G L +TV ++G G IG +A+R + FG+K+IA
Sbjct: 114 ALLRNRKYIDERDKNQDLQDAGVIGRELEDQTVGVVGTGKIGRAVAQRAKGFGMKVIAY- 172
Query: 184 RSWASHSQVSCQSSALAVKNGIIDDLVDEKGCHEDIFEFASK------ADVVVCCLSLNK 237
D + ++ S +D++ + L
Sbjct: 173 ------------------------DPFRNPELEDKGVKYVSLEELFKNSDIISLHVPLTP 208
Query: 238 QTAGIVNKSFLSSMKKGSLLVNIARGGLLDYEAIAHYLECGHLGGLGIDVAWTE------ 291
+ ++N+ MKKG +++N ARG L+D EA+ L+ G + G G+DV E
Sbjct: 209 ENHHMINEEAFKLMKKGVIIINTARGSLVDTEALIEALDSGKIFGAGLDVLEDETPDLLK 268
Query: 292 -------PFDPNDPILKFKNVLITPHVGGVTEHSYRSMA 323
N + + NV+ITPH T+ + ++M
Sbjct: 269 DLEGEIFKDALNALLGRRPNVIITPHTAFYTDDALKNMV 307
>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 = 132 bits (335), Expect = 6e-36
Identities = 76/252 (30%), Positives = 115/252 (45%), Gaps = 26/252 (10%)
Query: 94 AATRCGIKVARIPGDVTGNAASCAELTIYLMLGLLRKQNEMRMAIEQ-KKLGVPT---GE 149
A GI V D NA AE T+ +L LR+ A + G PT G
Sbjct: 90 AVWERGILVTS-AADA--NAEPVAEFTLAAILLALRRIPRFAAAYRAGRDWGWPTRRGGR 146
Query: 150 TLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDL 209
L G+TV I+GFG IG + + LRPFG++++ + ++ + AL V
Sbjct: 147 GLYGRTVGIVGFGRIGRAVVELLRPFGLRVLVYDP-YLPAAEAA----ALGV-------- 193
Query: 210 VDEKGCHEDIFEFASKADVVVCCLSLNKQTAGIVNKSFLSSMKKGSLLVNIARGGLLDYE 269
E +++ +++DVV L +T G+++ L+ M+ G+ +N ARG L+D
Sbjct: 194 --ELVSLDELL---ARSDVVSLHAPLTPETRGMIDARLLALMRDGATFINTARGALVDEA 248
Query: 270 AIAHYLECGHLGGLGIDVAWTEPFDPNDPILKFKNVLITPHVGGVTEHSYRSMAKVVGDV 329
A+ L G L +DV EP P+ P+ NVL+TPH+ G T R + D
Sbjct: 249 ALLAELRSGRLRAA-LDVTDPEPLPPDSPLRTLPNVLLTPHIAGSTGDERRRLGDYALDE 307
Query: 330 ALQLHAGTPLTG 341
+ AG PL
Sbjct: 308 LERFLAGEPLLH 319
>gnl|CDD|240643 cd12166, 2-Hacid_dh_7, Putative D-isomer specific 2-hydroxyacid
dehydrogenases. 2-Hydroxyacid dehydrogenases catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 300
Score = 131 bits (331), Expect = 9e-36
Identities = 78/248 (31%), Positives = 111/248 (44%), Gaps = 36/248 (14%)
Query: 102 VARIPGDVT-GNA-----ASCAELTIYLMLGLLRKQNEMRMAIEQKKLGVPTGETLLGKT 155
+ +P VT NA AS AEL + L+L LR A + + +L +
Sbjct: 75 LPLLPEGVTLCNARGVHDASTAELAVALILASLRGLPRFVRAQARGRWEPRRTPSLADRR 134
Query: 156 VFILGFGNIGVELAKRLRPFGVKIIATKRS----WASHSQVSCQSSALAVKNGIIDDLVD 211
V I+G+G+IG + +RL PF V++ R+ H ID+L
Sbjct: 135 VLIVGYGSIGRAIERRLAPFEVRVTRVARTARPGEQVHG---------------IDELP- 178
Query: 212 EKGCHEDIFEFASKADVVVCCLSLNKQTAGIVNKSFLSSMKKGSLLVNIARGGLLDYEAI 271
+ADVVV + L +T G+V+ FL+ M G+LLVN+ARG ++D +A+
Sbjct: 179 ---------ALLPEADVVVLIVPLTDETRGLVDAEFLARMPDGALLVNVARGPVVDTDAL 229
Query: 272 AHYLECGHLGGLGIDVAWTEPFDPNDPILKFKNVLITPHVGGVTEHSYRSMAKVVGDVAL 331
L G L +DV EP P P+ VLITPHVGG T +V
Sbjct: 230 VAELASGRL-RAALDVTDPEPLPPGHPLWSAPGVLITPHVGGATPAFLPRAYALVRRQLR 288
Query: 332 QLHAGTPL 339
+ AG PL
Sbjct: 289 RYAAGEPL 296
>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 = 130 bits (329), Expect = 3e-35
Identities = 71/253 (28%), Positives = 125/253 (49%), Gaps = 32/253 (12%)
Query: 71 ISRANQMKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLMLGLLRK 130
+++ +K I + G++ + + + GI + G ++ AE + +L + +
Sbjct: 55 LAKMKNLKWIQLYSAGVDYLPLEYIKKKGILLTNNSG---IHSIPIAEWIVGYILEIYKG 111
Query: 131 QNEMRMAIEQKK----LGVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSW 186
++ A + +K + L GKT+ LG G+IG E+AKRL+ FG+K+I S
Sbjct: 112 ---LKKAYKNQKEKKWKMDSSLLELYGKTILFLGTGSIGQEIAKRLKAFGMKVIGVNTS- 167
Query: 187 ASHSQVSCQSSALAVKNGIIDDLVDEKGCH--EDIFEFASKADVVVCCLSLNKQTAGIVN 244
G + D+ C+ E++ E +AD+VV L L ++T + +
Sbjct: 168 -----------------GRDVEYFDK--CYPLEELDEVLKEADIVVNVLPLTEETHHLFD 208
Query: 245 KSFLSSMKKGSLLVNIARGGLLDYEAIAHYLECGHLGGLGIDVAWTEPFDPNDPILKFKN 304
++F MKKG+L +N+ RG +D +A+ L+ + G +DV EP + P+ N
Sbjct: 209 EAFFEQMKKGALFINVGRGPSVDEDALIEALKNKQIRGAALDVFEEEPLPKDSPLWDLDN 268
Query: 305 VLITPHVGGVTEH 317
VLITPH+ GV+EH
Sbjct: 269 VLITPHISGVSEH 281
>gnl|CDD|178684 PLN03139, PLN03139, formate dehydrogenase; Provisional.
Length = 386
Score = 121 bits (305), Expect = 2e-31
Identities = 82/252 (32%), Positives = 121/252 (48%), Gaps = 29/252 (11%)
Query: 71 ISRANQMKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTG-NAASCAELTIYLMLGLLR 129
I +A ++L++ G+G + +D+ AA G+ VA +VTG N S AE + +L LLR
Sbjct: 116 IKKAKNLELLLTAGIGSDHIDLPAAAAAGLTVA----EVTGSNVVSVAEDELMRILILLR 171
Query: 130 K-QNEMRMAI--EQKKLGVPT-GETLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRS 185
+ E G+ L GKTV +G G IG L +RL+PF ++ R
Sbjct: 172 NFLPGYHQVVSGEWNVAGIAYRAYDLEGKTVGTVGAGRIGRLLLQRLKPFNCNLLYHDR- 230
Query: 186 WASHSQVSCQSSALAVKNGIIDDLVDEKGC--HEDIFEFASKADVVVCCLSLNKQTAGIV 243
+ +L E G ED+ K DVVV L ++T G+
Sbjct: 231 -----------------LKMDPELEKETGAKFEEDLDAMLPKCDVVVINTPLTEKTRGMF 273
Query: 244 NKSFLSSMKKGSLLVNIARGGLLDYEAIAHYLECGHLGGLGIDVAWTEPFDPNDPILKFK 303
NK ++ MKKG L+VN ARG ++D +A+A GH+GG G DV + +P + P
Sbjct: 274 NKERIAKMKKGVLIVNNARGAIMDTQAVADACSSGHIGGYGGDVWYPQPAPKDHPWRYMP 333
Query: 304 NVLITPHVGGVT 315
N +TPH+ G T
Sbjct: 334 NHAMTPHISGTT 345
>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 = 118 bits (299), Expect = 8e-31
Identities = 78/281 (27%), Positives = 126/281 (44%), Gaps = 51/281 (18%)
Query: 58 LCVVKTMRLDSNCISRANQMKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAASCA 117
+ V RLD+ + + ++KLI G + +D+ A GI V +P G A + A
Sbjct: 45 ISVFVYSRLDAEVLEKLPRLKLIATRSTGFDHIDLEACRERGIAVCNVPD--YGEA-TVA 101
Query: 118 ELTIYLMLGLLRKQNEM-----RMAIEQKKLGVPTGETLLGKTVFILGFGNIGVELAKRL 172
E L+L L RK E R Q L G L GKT+ ++G G IG +A+
Sbjct: 102 EHAFALLLALSRKLREAIERTRRGDFSQAGL---RGFELAGKTLGVVGTGRIGRRVARIA 158
Query: 173 RPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEKGC-HEDIFEFASKADVVVC 231
R FG+K++A V + ++L + G + + E ++D++
Sbjct: 159 RGFGMKVLAYDV----------------VPD---EELAERLGFRYVSLEELLQESDIISL 199
Query: 232 CLSLNKQTAGIVNKSFLSSMKKGSLLVNIARGGLLDYEAIAHYLECGHLGGLGIDV---- 287
+ QT ++N+ + MK G++L+N ARG ++D EA+ L+ G L G G+DV
Sbjct: 200 HVPYTPQTHHLINRENFALMKPGAVLINTARGAVVDTEALVRALKEGKLAGAGLDVLEQE 259
Query: 288 --------AWTEPFDP--------NDPILKFKNVLITPHVG 312
+ E P + +L+ NV+ITPHV
Sbjct: 260 EVLREEAELFREDVSPEDLKKLLADHALLRKPNVIITPHVA 300
>gnl|CDD|181041 PRK07574, PRK07574, formate dehydrogenase; Provisional.
Length = 385
Score = 117 bits (294), Expect = 8e-30
Identities = 82/253 (32%), Positives = 118/253 (46%), Gaps = 31/253 (12%)
Query: 71 ISRANQMKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTG-NAASCAELTIYLMLGLLR 129
I++A +KL + G+G + VD+ AA+ GI VA +VTG N+ S AE + ++L L+R
Sbjct: 109 IAKAPNLKLAITAGIGSDHVDLQAASEHGITVA----EVTGSNSISVAEHVVMMILALVR 164
Query: 130 KQNEMRMAIEQKKLG-------VPTGETLLGKTVFILGFGNIGVELAKRLRPFGVKIIAT 182
+ Q G V L G TV I+G G IG+ + +RL+PF VK+ T
Sbjct: 165 NYEP---SHRQAVEGGWNIADCVSRSYDLEGMTVGIVGAGRIGLAVLRRLKPFDVKLHYT 221
Query: 183 KRSWASHSQVSCQSSALAVKNGIIDDLVDEKGCHEDIFEFASKADVVVCCLSLNKQTAGI 242
R H L + H S DVV L+ +T +
Sbjct: 222 DR----HRLPEEVEQELGLTY------------HVSFDSLVSVCDVVTIHCPLHPETEHL 265
Query: 243 VNKSFLSSMKKGSLLVNIARGGLLDYEAIAHYLECGHLGGLGIDVAWTEPFDPNDPILKF 302
+ LS MK+GS LVN ARG ++D +A+ LE GHL G DV + +P + P
Sbjct: 266 FDADVLSRMKRGSYLVNTARGKIVDRDAVVRALESGHLAGYAGDVWFPQPAPADHPWRTM 325
Query: 303 KNVLITPHVGGVT 315
+TPH+ G T
Sbjct: 326 PRNGMTPHISGTT 338
>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 = 115 bits (290), Expect = 9e-30
Identities = 84/298 (28%), Positives = 136/298 (45%), Gaps = 52/298 (17%)
Query: 39 IQVDVVPIS----DVPDVIANYHLCVV--KTMRLDSNCISRANQMKLIMQFGVGLEGVDI 92
I+V+ + + ++ + + + HL + KT +L + A ++ I F +G VD+
Sbjct: 22 IEVERLKGALDEDELIEALKDVHLLGIRSKT-QLTEEVLEAAPKLLAIGCFCIGTNQVDL 80
Query: 93 NAATRCGIKVARIPGDVTGNAASCAELTIYLMLGLLR----KQNEMRMAIEQKKLGVPTG 148
+AA + GI V P N S AEL I ++ L R + I K TG
Sbjct: 81 DAAAKRGIPVFNAP---FSNTRSVAELVIGEIIMLARRLPDRNAAAHRGIWNK---SATG 134
Query: 149 --ETLLGKTVFILGFGNIGVELAKRLRPFGVKI----IATKRSWASHSQVSCQSSALAVK 202
E + GKT+ I+G+G+IG +L+ G+++ IA K + QVS LA
Sbjct: 135 SHE-VRGKTLGIIGYGHIGSQLSVLAEALGMRVIFYDIAEKLPLGNARQVSSLEELLA-- 191
Query: 203 NGIIDDLVDEKGCHEDIFEFASKADVVVCCLSLNKQTAGIVNKSFLSSMKKGSLLVNIAR 262
+AD V + T ++ ++ MKKG++L+N +R
Sbjct: 192 ----------------------EADFVTLHVPATPSTKNMIGAEEIAQMKKGAILINASR 229
Query: 263 GGLLDYEAIAHYLECGHLGGLGIDVAWTEPFDPND----PILKFKNVLITPHVGGVTE 316
G ++D +A+A L GHL G +DV EP + P+ NV++TPH+GG TE
Sbjct: 230 GTVVDIDALAEALRSGHLAGAAVDVFPEEPASNGEPFSSPLQGLPNVILTPHIGGSTE 287
>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 = 114 bits (289), Expect = 2e-29
Identities = 73/253 (28%), Positives = 116/253 (45%), Gaps = 39/253 (15%)
Query: 85 VGLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLMLGLLRKQNEM--RMAIEQKK 142
+G + +D++AA GIKV +VT + S A+ T+ LML LRK ++ R +
Sbjct: 77 IGYDHIDLDAAKELGIKV----SNVTYSPNSVADYTVMLMLMALRKYKQIMKRAEVNDYS 132
Query: 143 LGVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVK 202
LG G L TV ++G G IG + K L FG KI+A
Sbjct: 133 LGGLQGRELRNLTVGVIGTGRIGQAVIKNLSGFGCKILAYDPY----------------P 176
Query: 203 NGIIDDLVDEKGCHEDIFEFASKADVVVCCLSLNKQTAGIVNKSFLSSMKKGSLLVNIAR 262
N + + + D+ ++D++ L ++T ++NK ++ MK G +++N AR
Sbjct: 177 NEEVKKYAE----YVDLDTLYKESDIITLHTPLTEETYHLINKESIAKMKDGVIIINTAR 232
Query: 263 GGLLDYEAIAHYLECGHLGGLGIDVAWTE--------PFD--PNDPI---LKFKNVLITP 309
G L+D EA+ LE G +GG +DV E D N + F NV++TP
Sbjct: 233 GELIDTEALIEGLESGKIGGAALDVIEGEDGIYYNDRKGDILSNRELAILRSFPNVILTP 292
Query: 310 HVGGVTEHSYRSM 322
H+ T+ + M
Sbjct: 293 HMAFYTDQAVSDM 305
>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 = 114 bits (288), Expect = 2e-29
Identities = 71/271 (26%), Positives = 112/271 (41%), Gaps = 35/271 (12%)
Query: 78 KLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLMLGLLRKQNEMRMA 137
K I G G++ + + + + R+ G A AE Y++ +LR +M
Sbjct: 60 KAIFSLGAGVDHLLADPDLP-DVPIVRLVDP--GLAQGMAE---YVLAAVLRLHRDMDRY 113
Query: 138 IEQ------KKLGVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQ 191
Q K L V +LG G +G +A+RL G + RS
Sbjct: 114 AAQQRRGVWKPLPQRPAAER---RVGVLGLGELGAAVARRLAALGFPVSGWSRSPKDIEG 170
Query: 192 VSCQSSALAVKNGIIDDLVDEKGCHEDIFEFASKADVVVCCLSLNKQTAGIVNKSFLSSM 251
V+C + L F ++ D++VC L L +T GI+N L+ +
Sbjct: 171 VTCFHGE--------EGLDA----------FLAQTDILVCLLPLTPETRGILNAELLARL 212
Query: 252 KKGSLLVNIARGGLLDYEAIAHYLECGHLGGLGIDVAWTEPFDPNDPILKFKNVLITPHV 311
+G+ L+N+ RG L + L+ GHL G +DV EP + P+ + V +TPH+
Sbjct: 213 PRGAALINVGRGPHLVEADLLAALDSGHLSGAVLDVFEQEPLPADHPLWRHPRVTVTPHI 272
Query: 312 GGVTEHSYRSMAKVVGDVALQLHAGTPLTGL 342
+T S A V + +L AG PL L
Sbjct: 273 AAIT--DPDSAAAQVAENIRRLEAGEPLPNL 301
>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 = 112 bits (282), Expect = 2e-28
Identities = 70/269 (26%), Positives = 118/269 (43%), Gaps = 42/269 (15%)
Query: 74 ANQMKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLMLGLLRKQNE 133
+K I G++ +D++ A G+K+ +P + + AE + L LLR E
Sbjct: 66 EYGIKQIALRSAGVDMIDLDLAKENGLKITNVP---AYSPRAIAEFAVTQALNLLRNTPE 122
Query: 134 MRMAIEQKKLGVPTGETLLGK-----TVFILGFGNIGVELAKRLRPFGVKIIATKRSWAS 188
+ + + G L+G+ TV I+G G IG AK + FG K+IA
Sbjct: 123 IDRRVAKGDFRWAPG--LIGREIRDLTVGIIGTGRIGSAAAKIFKGFGAKVIAYDP---- 176
Query: 189 HSQVSCQSSALAVKNGIIDDLVDEKGCHEDIFEFASKADVVVCCLSLNKQTAGIVNKSFL 248
N ++ + ED+ +AD++ + L K+ ++N
Sbjct: 177 ------------YPNPELEKFLLYYDSLEDLL---KQADIISLHVPLTKENHHLINAEAF 221
Query: 249 SSMKKGSLLVNIARGGLLDYEAIAHYLECGHLGGLGIDVAWTE-PFDPN--------DPI 299
+ MK G++LVN ARGGL+D +A+ L+ G + G +D E + D +
Sbjct: 222 AKMKDGAILVNAARGGLVDTKALIDALDSGKIAGAALDTYENETGYFNKDWSGKEIEDEV 281
Query: 300 LK----FKNVLITPHVGGVTEHSYRSMAK 324
LK NVLITPH+ T+ + ++M +
Sbjct: 282 LKELIAMPNVLITPHIAFYTDTAVKNMVE 310
>gnl|CDD|180588 PRK06487, PRK06487, glycerate dehydrogenase; Provisional.
Length = 317
Score = 108 bits (271), Expect = 5e-27
Identities = 81/305 (26%), Positives = 130/305 (42%), Gaps = 45/305 (14%)
Query: 46 ISDVPDVIANYHLCVVKTMRLDSNCISRANQMKLIMQFGVGLEGVDINAATRCGIKVARI 105
+ I+N K LD+ ++ A Q+KLI+ G VD+ AA GI V
Sbjct: 43 LRGAQVAISN------KVA-LDAAALAAAPQLKLILVAATGTNNVDLAAARERGITVCNC 95
Query: 106 PGDVTGNAASCAELTIYLMLGLLRKQNEMRMAIEQKK---------LGVPTGETLLGKTV 156
G T S A+ T+ L+L L + + + A+ + L P E L GKT+
Sbjct: 96 QGYGT---PSVAQHTLALLLALATRLPDYQQAVAAGRWQQSSQFCLLDFPIVE-LEGKTL 151
Query: 157 FILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEKGCH 216
+LG G +G +A+ FG++++ + L +
Sbjct: 152 GLLGHGELGGAVARLAEAFGMRVLI-----GQLPGRPARPDRLPLD-------------- 192
Query: 217 EDIFEFASKADVVVCCLSLNKQTAGIVNKSFLSSMKKGSLLVNIARGGLLDYEAIAHYLE 276
E + D + L + T ++ L+ MK G+LL+N ARGGL+D +A+A L
Sbjct: 193 ----ELLPQVDALTLHCPLTEHTRHLIGARELALMKPGALLINTARGGLVDEQALADALR 248
Query: 277 CGHLGGLGIDVAWTEPFDPNDPIL--KFKNVLITPHVGGVTEHSYRSMAKVVGDVALQLH 334
GHLGG DV EP +P+L +++TPH + + + + + + A
Sbjct: 249 SGHLGGAATDVLSVEPPVNGNPLLAPDIPRLIVTPHSAWGSREARQRIVGQLAENARAFF 308
Query: 335 AGTPL 339
AG PL
Sbjct: 309 AGKPL 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 = 105 bits (264), Expect = 5e-26
Identities = 63/233 (27%), Positives = 104/233 (44%), Gaps = 24/233 (10%)
Query: 112 NAASCAELTIYLMLGLLRKQNEMRMAIEQKKLGVPTGETLLGKTVFILGFGNIGVELAKR 171
A + AE + +L ++ E+ + ++ P G +L G T+ I+GFG IG LA+R
Sbjct: 95 AAEAIAEFVLAAILAAAKRLPEIWVKGAEQWRREPLG-SLAGSTLGIVGFGAIGQALARR 153
Query: 172 LRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEKGCH--EDIFEFASKADVV 229
G++++A +RS D G D+ E +++D +
Sbjct: 154 ALALGMRVLALRRS---------------------GRPSDVPGVEAAADLAELFARSDHL 192
Query: 230 VCCLSLNKQTAGIVNKSFLSSMKKGSLLVNIARGGLLDYEAIAHYLECGHLGGLGIDVAW 289
V L +T ++N L+ K G L+NIARGGL+D EA+ L+ G + +DV
Sbjct: 193 VLAAPLTPETRHLINADVLAQAKPGLHLINIARGGLVDQEALLEALDSGRISLASLDVTD 252
Query: 290 TEPFDPNDPILKFKNVLITPHVGGVTEHSYRSMAKVVGDVALQLHAGTPLTGL 342
EP P+ V ++PH + R++A + + AG PL L
Sbjct: 253 PEPLPEGHPLYTHPRVRLSPHTSAIAPDGRRNLADRFLENLARYRAGQPLHDL 305
>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 = 103 bits (260), Expect = 3e-25
Identities = 85/307 (27%), Positives = 132/307 (42%), Gaps = 67/307 (21%)
Query: 65 RLDSNCISR--ANQMKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAAS---CAEL 119
LD+ + + +KLI G VD+ AA GI V R+P A S AE
Sbjct: 55 DLDAPVLEKLAELGVKLIALRCAGFNNVDLKAAKELGITVVRVP------AYSPYAVAEH 108
Query: 120 TIYLMLGLLRK----QNEMRM---AIEQKKLGVPTGETLLGKTVFILGFGNIGVELAKRL 172
+ L+L L RK N +R +++ G+ G L GKTV ++G G IG A+ L
Sbjct: 109 AVALLLALNRKIHRAYNRVREGNFSLD----GL-LGFDLHGKTVGVIGTGKIGQAFARIL 163
Query: 173 RPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEKGCHEDIFEFAS------KA 226
+ FG +++A D + E+ ++
Sbjct: 164 KGFGCRVLAY-------------------------DPYPNPELAKLGVEYVDLDELLAES 198
Query: 227 DVVVCCLSLNKQTAGIVNKSFLSSMKKGSLLVNIARGGLLDYEAIAHYLECGHLGGLGID 286
D++ L +T ++N ++ MK G +L+N +RGGL+D +A+ L+ G +GGLG+D
Sbjct: 199 DIISLHCPLTPETHHLINAETIAKMKDGVMLINTSRGGLIDTKALIEALKSGKIGGLGLD 258
Query: 287 VAWTEPF----DPNDPI---------LKFKNVLITPHVGGVTEHSYRSMAKVVGDVALQL 333
V E D +D I L F NVLIT H T+ + ++A+ +
Sbjct: 259 VYEEEAGLFFEDHSDEIIQDDVLARLLSFPNVLITGHQAFFTKEALTNIAETTLENLDDF 318
Query: 334 HAGTPLT 340
AG PL
Sbjct: 319 EAGKPLK 325
>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 = 102 bits (256), Expect = 8e-25
Identities = 78/298 (26%), Positives = 121/298 (40%), Gaps = 65/298 (21%)
Query: 57 HLCVVKTMRLDSNCISRANQMKLIMQFG--------VGLEGVDINAATRCGIKVARIPGD 108
H V+ + NC + +++ ++G VG +D+ AA G K+AR+P
Sbjct: 45 HDAVI----VRGNCFADKENLEIYKEYGIKYVFTRTVGFNHIDLEAAKELGFKMARVPS- 99
Query: 109 VTGNAASCAELTIYLMLGLLRKQNEMRMAIEQKKLGVPT---GETLLGKTVFILGFGNIG 165
+ NA AEL L + L R K V + + TV I+G G IG
Sbjct: 100 YSPNAI--AELAFTLAMTLSRHTAYTASRTANKNFKVDPFMFSKEIRNSTVGIIGTGRIG 157
Query: 166 VELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEKGCHEDIFEFAS- 224
+ AK + G K+I D+ +D+ F S
Sbjct: 158 LTAAKLFKGLGAKVIGY-------------------------DIYPSDAA-KDVVTFVSL 191
Query: 225 -----KADVV-VCCLSLNKQTAGIVNKSFLSSMKKGSLLVNIARGGLLDYEAIAHYLECG 278
K+D++ + + + ++NK F+S MK G++L+N ARG L D EAI LE G
Sbjct: 192 DELLKKSDIISLHVPYIKGKNDKLINKEFISKMKDGAILINTARGELQDEEAILEALESG 251
Query: 279 HLGGLGIDV------------AWTEPFDP--NDPILKFKNVLITPHVGGVTEHSYRSM 322
L G G DV + DP + + VL+TPH+G T+ + +M
Sbjct: 252 KLAGFGTDVLNNEKEIFFKDFDGDKIEDPVVEKLLDLYPRVLLTPHIGSYTDEALSNM 309
>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 = 100 bits (251), Expect = 4e-24
Identities = 59/220 (26%), Positives = 98/220 (44%), Gaps = 28/220 (12%)
Query: 117 AELTI--YLML--GLLRKQNEMRMAIEQKKLGVPTGETLLGKTVFILGFGNIGVELAKRL 172
AE I +L+L L+ + ++ + E +GK V ILG+G+IG + A+
Sbjct: 93 AEWVIGTWLVLSHHFLQYIELQKEQTWGRRQEAYSVEDSVGKRVGILGYGSIGRQTARLA 152
Query: 173 RPFGVKIIATKRSWASHSQVSCQSSALAVKNGII-------DDLVDEKGCH----EDIFE 221
+ G+++ A RS + + +S +G I D + + E
Sbjct: 153 QALGMEVYAYTRS----PRPTPES---RKDDGYIVPGTGDPDGSIPSAWFSGTDKASLHE 205
Query: 222 F-ASKADVVVCCLSLNKQTAGIVNK---SFLSSMKKGSLLVNIARGGLLDYEAIAHYLEC 277
F D++V L L T ++ L+ K+ + + NIARG L+D +A+ LE
Sbjct: 206 FLRQDLDLLVVSLPLTPATKHLLGAEEFEILA--KRKTFVSNIARGSLVDTDALVAALES 263
Query: 278 GHLGGLGIDVAWTEPFDPNDPILKFKNVLITPHVGGVTEH 317
G + G +DV EP + P+ NV+ITPHV T+
Sbjct: 264 GQIRGAALDVTDPEPLPADHPLWSAPNVIITPHVSWQTQE 303
>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 = 96.7 bits (241), Expect = 6e-23
Identities = 66/208 (31%), Positives = 100/208 (48%), Gaps = 30/208 (14%)
Query: 117 AELTIYLMLGLLRKQNEMRMAIEQKK----LG-----VPTGE--TLLGKTVFILGFGNIG 165
AE T+ L+L +R+ +EMR A + + LG P G TLLG V I GFG+IG
Sbjct: 96 AEHTLALILAAVRRLDEMREAQREHRWAGELGGLQPLRPAGRLTTLLGARVLIWGFGSIG 155
Query: 166 VELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEKGCHEDIFEFASK 225
LA L G ++ RS + G +V E +++ E +
Sbjct: 156 QRLAPLLTALGARVTGVARS-------------AGERAGF--PVVAE----DELPELLPE 196
Query: 226 ADVVVCCLSLNKQTAGIVNKSFLSSMKKGSLLVNIARGGLLDYEAIAHYLECGHLGGLGI 285
DV+V L TA ++ L+++ K + +VN+ RG +D +A+ LE G LGG +
Sbjct: 197 TDVLVMILPATPSTAHALDAEVLAALPKHAWVVNVGRGATVDEDALVAALESGRLGGAAL 256
Query: 286 DVAWTEPFDPNDPILKFKNVLITPHVGG 313
DV TEP + P+ N+++TPH G
Sbjct: 257 DVTATEPLPASSPLWDAPNLILTPHAAG 284
>gnl|CDD|236985 PRK11790, PRK11790, D-3-phosphoglycerate dehydrogenase;
Provisional.
Length = 409
Score = 96.8 bits (242), Expect = 2e-22
Identities = 75/255 (29%), Positives = 116/255 (45%), Gaps = 59/255 (23%)
Query: 83 FGVGLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLMLGLLRKQNEMRMAIEQKK 142
F +G VD++AA + GI V P N S AEL I ++ LLR I +K
Sbjct: 82 FCIGTNQVDLDAAAKRGIPVFNAP---FSNTRSVAELVIGEIILLLRG-------IPEKN 131
Query: 143 LGVPTGETL---------LGKTVFILGFGNIGVELAKRLRPFGVKI----IATKRSWASH 189
G GKT+ I+G+G+IG +L+ G+++ I K +
Sbjct: 132 AKAHRGGWNKSAAGSFEVRGKTLGIVGYGHIGTQLSVLAESLGMRVYFYDIEDKLPLGNA 191
Query: 190 SQVSCQSSALAVKNGIIDDLVDEKGCHEDIFEFASKADVVVCCLSL----NKQTAGIVNK 245
QV G +++L+ +++DVV SL T ++
Sbjct: 192 RQV-----------GSLEELL-------------AQSDVV----SLHVPETPSTKNMIGA 223
Query: 246 SFLSSMKKGSLLVNIARGGLLDYEAIAHYLECGHLGGLGIDVAWTEPFDPND----PILK 301
L+ MK G++L+N +RG ++D +A+A L+ GHL G IDV EP D P+
Sbjct: 224 EELALMKPGAILINASRGTVVDIDALADALKSGHLAGAAIDVFPVEPKSNGDPFESPLRG 283
Query: 302 FKNVLITPHVGGVTE 316
NV++TPH+GG T+
Sbjct: 284 LDNVILTPHIGGSTQ 298
>gnl|CDD|235890 PRK06932, PRK06932, glycerate dehydrogenase; Provisional.
Length = 314
Score = 94.5 bits (235), Expect = 4e-22
Identities = 73/306 (23%), Positives = 127/306 (41%), Gaps = 53/306 (17%)
Query: 20 PHFPASHNYTKEYLQNYPSIQVDVVPISDVPDVIANYHLCVVKTMRLDSNCISRANQMKL 79
P FP H + EY ++ +D+ VI + K + +++ ++KL
Sbjct: 21 PSFP--HEWI-EYDHTSAEQTIERAKDADI--VITS------KVL-FTRETLAQLPKLKL 68
Query: 80 IMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLMLGL-------LRKQN 132
I G VD+ AA GI V + G + + E + ++ L R Q
Sbjct: 69 IAITATGTNNVDLVAAKELGIAVKNVTGYSS---TTVPEHVLGMIFALKHSLMGWYRDQL 125
Query: 133 EMRMAIEQKKLGV---PTGETLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASH 189
R A K+ P + + G T+ + G G +G E+ + + G+K++ + AS
Sbjct: 126 SDRWA-TCKQFCYFDYPITD-VRGSTLGVFGKGCLGTEVGRLAQALGMKVLYAEHKGASV 183
Query: 190 SQVSCQSSALAVKNGIIDDLVDEKGCHEDIFEFASKADVVVCCLSLNKQTAGIVNKSFLS 249
C+ E +AD+V L + T ++N L+
Sbjct: 184 ----CREGYT------------------PFEEVLKQADIVTLHCPLTETTQNLINAETLA 221
Query: 250 SMKKGSLLVNIARGGLLDYEAIAHYLECGHLGGLGIDVAWTEPFDPNDPIL----KFKNV 305
MK + L+N RG L+D +A+ LE G + G +DV EP + ++P++ + N+
Sbjct: 222 LMKPTAFLINTGRGPLVDEQALLDALENGKIAGAALDVLVKEPPEKDNPLIQAAKRLPNL 281
Query: 306 LITPHV 311
LITPH+
Sbjct: 282 LITPHI 287
>gnl|CDD|181414 PRK08410, PRK08410, 2-hydroxyacid dehydrogenase; Provisional.
Length = 311
Score = 93.1 bits (232), Expect = 1e-21
Identities = 70/262 (26%), Positives = 121/262 (46%), Gaps = 46/262 (17%)
Query: 66 LDSNCISRANQMKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLML 125
+D +S+ +KLI G VDI A + GI V + G T S A+ T ++L
Sbjct: 53 IDKEVLSQLPNLKLICITATGTNNVDIEYAKKKGIAVKNVAGYST---ESVAQHTFAMLL 109
Query: 126 GLLRKQNEMRMAIEQKK---------LGVPTGETLLGKTVFILGFGNIGVELAKRLRPFG 176
LL + N ++ + + P GE + GK I+G G IG +AK + FG
Sbjct: 110 SLLGRINYYDRYVKSGEYSESPIFTHISRPLGE-IKGKKWGIIGLGTIGKRVAKIAQAFG 168
Query: 177 VKII----ATKRSWASHSQVSCQSSALAVKNGIIDDLVDEKGCHEDIFEFASKADVVVCC 232
K++ + K + +VS +++L+ +D++
Sbjct: 169 AKVVYYSTSGKNKNEEYERVS------------LEELL-------------KTSDIISIH 203
Query: 233 LSLNKQTAGIVNKSFLSSMKKGSLLVNIARGGLLDYEAIAHYLECGHLGGLGIDVAWTEP 292
LN++T ++ L +K G++L+N+ RGG+++ + +A L+ + G+DV EP
Sbjct: 204 APLNEKTKNLIAYKELKLLKDGAILINVGRGGIVNEKDLAKALDEKDI-YAGLDVLEKEP 262
Query: 293 FDPNDPILKFKN---VLITPHV 311
+ N P+L KN +LITPH+
Sbjct: 263 MEKNHPLLSIKNKEKLLITPHI 284
>gnl|CDD|235800 PRK06436, PRK06436, glycerate dehydrogenase; Provisional.
Length = 303
Score = 90.7 bits (225), Expect = 1e-20
Identities = 60/220 (27%), Positives = 95/220 (43%), Gaps = 30/220 (13%)
Query: 100 IKVARIPGDVT--GNAA----SCAELTIYLMLGLLRKQNEMRMAIEQKKLGVPTGETLLG 153
I V+ IP +V NA S AE L+L + E ++ + L
Sbjct: 63 IDVSGIPENVVLCSNAGAYSISVAEHAFALLLAWAKNICENNYNMKNGNFKQSPTKLLYN 122
Query: 154 KTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEK 213
K++ ILG+G IG +A + FG+ I A RS+ + S
Sbjct: 123 KSLGILGYGGIGRRVALLAKAFGMNIYAYTRSYVNDGISSIYMEP--------------- 167
Query: 214 GCHEDIFEFASKADVVVCCLSLNKQTAGIVNKSFLSSMKKGSLLVNIARGGLLDYEAIAH 273
EDI + K+D V+ L L +T G++N LS +KG ++N+AR ++D + +
Sbjct: 168 ---EDIMK---KSDFVLISLPLTDETRGMINSKMLSLFRKGLAIINVARADVVDKNDMLN 221
Query: 274 YLECGHLGGLGIDVAWTEPFDPNDPILKFKNVLITPHVGG 313
+L + DV W EP + NV+++PHV G
Sbjct: 222 FLRNHNDKYYLSDVWWNEP-IITETNP--DNVILSPHVAG 258
>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 = 84.1 bits (209), Expect = 3e-18
Identities = 71/262 (27%), Positives = 114/262 (43%), Gaps = 70/262 (26%)
Query: 86 GLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLMLGLLRKQNEMRMAIEQKKLGV 145
G + +D + GI A PG NA S AE Y++ LL +A Q
Sbjct: 67 GTDHIDTDYLKERGIGFANAPG---CNANSVAE---YVLSALLV------LAQRQ----- 109
Query: 146 PTGETLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGI 205
G +L GKTV I+G GN+G LA+RL G+ ++ C
Sbjct: 110 --GFSLKGKTVGIVGVGNVGSRLARRLEALGMNVLL------------C----------- 144
Query: 206 IDDLVDEKGCHEDIFEFAS------KADVVVCCLSLNKQ----TAGIVNKSFLSSMKKGS 255
D E E F S +AD++ + L + T ++++ FL+++K G
Sbjct: 145 -DPPRAEA---EGDPGFVSLEELLAEADIITLHVPLTRDGEHPTYHLLDEDFLAALKPGQ 200
Query: 256 LLVNIARGGLLDYEAIAHYLECGHLGGLGIDVAW-TEPFDPNDPILKFKNVLI-TPHVGG 313
+L+N +RG ++D +A+ L+ G + +DV W EP + + +L V I TPH+ G
Sbjct: 201 ILINASRGAVIDNQALLALLQRGKDLRVVLDV-WENEP-EIDLELLDK--VDIATPHIAG 256
Query: 314 V--------TEHSYRSMAKVVG 327
TE Y ++ + +G
Sbjct: 257 YSLEGKARGTEMIYEALCQFLG 278
>gnl|CDD|185307 PRK15409, PRK15409, bifunctional glyoxylate/hydroxypyruvate
reductase B; Provisional.
Length = 323
Score = 77.5 bits (191), Expect = 5e-16
Identities = 66/269 (24%), Positives = 118/269 (43%), Gaps = 33/269 (12%)
Query: 65 RLDSNCISRANQMKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLM 124
++D+ + + +++ VG + D++A T I + P +T + A+ + L+
Sbjct: 55 KVDAALLEKMPKLRAASTISVGYDNFDVDALTARKILLMHTPTVLT---ETVADTLMALV 111
Query: 125 LGLLRKQNEMRMAIEQKKLGVPT--------GETLLGKTVFILGFGNIGVELAKRLR-PF 175
L R+ E+ E+ K G T G + KT+ I+G G IG+ LA+R F
Sbjct: 112 LSTARRVVEV---AERVKAGEWTASIGPDWFGTDVHHKTLGIVGMGRIGMALAQRAHFGF 168
Query: 176 GVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEKGCHEDIFEFASKADVVVCCLSL 235
+ I+ R H + + +A + +D L+ E +D V L L
Sbjct: 169 NMPILYNARR--HHKEAEERFNA---RYCDLDTLLQE-------------SDFVCIILPL 210
Query: 236 NKQTAGIVNKSFLSSMKKGSLLVNIARGGLLDYEAIAHYLECGHLGGLGIDVAWTEPFDP 295
+T + + MK ++ +N RG ++D A+ L+ G + G+DV EP
Sbjct: 211 TDETHHLFGAEQFAKMKSSAIFINAGRGPVVDENALIAALQKGEIHAAGLDVFEQEPLSV 270
Query: 296 NDPILKFKNVLITPHVGGVTEHSYRSMAK 324
+ P+L NV+ PH+G T + +MA
Sbjct: 271 DSPLLSLPNVVAVPHIGSATHETRYNMAA 299
>gnl|CDD|177941 PLN02306, PLN02306, hydroxypyruvate reductase.
Length = 386
Score = 75.3 bits (185), Expect = 4e-15
Identities = 69/261 (26%), Positives = 120/261 (45%), Gaps = 40/261 (15%)
Query: 83 FGVGLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLMLGLLRKQNE----MRMAI 138
VG VD+ AA + GI V PG +T + AEL L L R+ E MR +
Sbjct: 93 MAVGYNNVDVEAANKYGIAVGNTPGVLT---ETTAELAASLSLAAARRIVEADEFMRAGL 149
Query: 139 EQKKLGVPT---GETLLGKTVFILGFGNIGVELAKRL-RPFGVKII------ATK----- 183
+ L P G L G+TV ++G G IG A+ + F + +I +T+
Sbjct: 150 YEGWL--PHLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQSTRLEKFV 207
Query: 184 RSWASHSQVSCQSSALAVKNGIIDDLVDEKGCHEDIFEFASKADVVVCCLSLNKQTAGIV 243
++ + + + + +++++ E ADV+ L+K T ++
Sbjct: 208 TAYGQFLKANGEQPVTWKRASSMEEVLRE-------------ADVISLHPVLDKTTYHLI 254
Query: 244 NKSFLSSMKKGSLLVNIARGGLLDYEAIAHYLECGHLGGLGIDVAWTEPF-DPNDPILKF 302
NK L+ MKK ++LVN +RG ++D A+ +L+ + +G+DV EP+ P +
Sbjct: 255 NKERLALMKKEAVLVNASRGPVIDEVALVEHLKANPMFRVGLDVFEDEPYMKPG--LADM 312
Query: 303 KNVLITPHVGGVTEHSYRSMA 323
KN ++ PH+ ++ + MA
Sbjct: 313 KNAVVVPHIASASKWTREGMA 333
>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 = 73.8 bits (181), Expect = 7e-15
Identities = 54/217 (24%), Positives = 93/217 (42%), Gaps = 32/217 (14%)
Query: 78 KLIMQFGVGLEGVDIN-AATRCGIKVARIPGDVTG----NAASCAELTIYLMLGLLRKQN 132
+L+ + +G + D+ A R G+ + G N+ EL++ + L Q
Sbjct: 89 RLLFTYTIGADHRDLTEALARAGLTAIAVEGVELPLLTSNSIGAGELSVQFIARFLEVQQ 148
Query: 133 EMRMAIEQKKLGVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQV 192
R+ G P + GKTV ++G G +G E A+ LR G +++ T + + Q+
Sbjct: 149 PGRLG------GAPD---VAGKTVVVVGAGVVGKEAAQMLRGLGAQVLITDINVEALEQL 199
Query: 193 SCQSSALAVKNGIIDDLVDEKGCHEDIFEFASKADVVVCCLSLNKQTAGIVN-KSFLSSM 251
E++ E ++ADV+V L + AGI+ + + M
Sbjct: 200 EELGGKNV----------------EELEEALAEADVIVTTTLLPGKRAGILVPEELVEQM 243
Query: 252 KKGSLLVNIARGGLLDYEAIAHY-LECGHLGGLGIDV 287
K GS++VN+A G + +A+ LE GH DV
Sbjct: 244 KPGSVIVNVAVGAVGCVQALHTQLLEEGHGVVHYGDV 280
>gnl|CDD|181499 PRK08605, PRK08605, D-lactate dehydrogenase; Validated.
Length = 332
Score = 73.2 bits (180), Expect = 1e-14
Identities = 65/272 (23%), Positives = 115/272 (42%), Gaps = 45/272 (16%)
Query: 66 LDSNCISRANQM--KLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYL 123
L N++ K I Q G + D+ AT+ + ++ +P + + S AE T+
Sbjct: 57 LSEAIYKLLNELGIKQIAQRSAGFDTYDLELATKYNLIISNVP---SYSPESIAEFTVTQ 113
Query: 124 MLGLLRKQNEMRMAIEQKKLGVPTGETLLGK-----TVFILGFGNIGVELAKRL-RPFGV 177
+ L+R N+++ + ++ +L + V ++G G IG+ +AK + +G
Sbjct: 114 AINLVRHFNQIQTKV--REHDFRWEPPILSRSIKDLKVAVIGTGRIGLAVAKIFAKGYGS 171
Query: 178 KIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEKGCHEDIFEFASKADVVVCCLSLNK 237
++A N VD K + I E AD+V + K
Sbjct: 172 DVVAYD----------------PFPNAKAATYVDYK---DTIEEAVEGADIVTLHMPATK 212
Query: 238 QTAGIVNKSFLSSMKKGSLLVNIARGGLLDYEAIAHYLECGHLGGLGIDVAWTE-PFDP- 295
+ N KKG++ VN ARG L+D +A+ L+ G + G +D E P P
Sbjct: 213 YNHYLFNADLFKHFKKGAVFVNCARGSLVDTKALLDALDNGLIKGAALDTYEFERPLFPS 272
Query: 296 -------NDPILK----FKNVLITPHVGGVTE 316
NDP+L+ ++V++TPH+ T+
Sbjct: 273 DQRGQTINDPLLESLINREDVILTPHIAFYTD 304
>gnl|CDD|183550 PRK12480, PRK12480, D-lactate dehydrogenase; Provisional.
Length = 330
Score = 72.3 bits (177), Expect = 3e-14
Identities = 59/263 (22%), Positives = 113/263 (42%), Gaps = 41/263 (15%)
Query: 77 MKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLMLGLLRK--QNEM 134
+K I Q G + D++ A + I ++ +P + + + AE ++ + L L+R+ E
Sbjct: 70 IKQIAQRTAGFDMYDLDLAKKHNIVISNVP---SYSPETIAEYSVSIALQLVRRFPDIER 126
Query: 135 RMAIEQKKLGVPTGET-LLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVS 193
R+ + TV I+G G IG AK FG I A ++ +
Sbjct: 127 RVQAHDFTWQAEIMSKPVKNMTVAIIGTGRIGAATAKIYAGFGATITAYD-AYPNKDL-- 183
Query: 194 CQSSALAVKNGIIDDLVDEKGCHEDIFEFASKADVVVCCLSLNKQTAGIVNKSFLSSMKK 253
L K+ + + + D AD++ + NK++ + +K+ +KK
Sbjct: 184 ---DFLTYKDSVKEAIKD--------------ADIISLHVPANKESYHLFDKAMFDHVKK 226
Query: 254 GSLLVNIARGGLLDYEAIAHYLECGHLGGLGIDV----------AWTEPFDPNDPIL--- 300
G++LVN ARG +++ + + G L G ID WT D +D L
Sbjct: 227 GAILVNAARGAVINTPDLIAAVNDGTLLGAAIDTYENEAAYFTNDWTNK-DIDDKTLLEL 285
Query: 301 -KFKNVLITPHVGGVTEHSYRSM 322
+ + +L+TPH+ ++ + +++
Sbjct: 286 IEHERILVTPHIAFFSDEAVQNL 308
>gnl|CDD|185366 PRK15469, ghrA, bifunctional glyoxylate/hydroxypyruvate reductase
A; Provisional.
Length = 312
Score = 71.8 bits (176), Expect = 4e-14
Identities = 55/189 (29%), Positives = 85/189 (44%), Gaps = 24/189 (12%)
Query: 155 TVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEKG 214
T+ ILG G +G ++A+ L+ +G + RS S V QS A
Sbjct: 138 TIGILGAGVLGSKVAQSLQTWGFPLRCWSRSRKSWPGV--QSFAGR-------------- 181
Query: 215 CHEDIFEFASKADVVVCCLSLNKQTAGIVNKSFLSSMKKGSLLVNIARGGLLDYEAIAHY 274
E++ F S+ V++ L +T GI+N+ L + G+ L+N+ARG + + +
Sbjct: 182 --EELSAFLSQTRVLINLLPNTPETVGIINQQLLEQLPDGAYLLNLARGVHVVEDDLLAA 239
Query: 275 LECGHLGGLGIDVAWTEPFDPNDPILKFKNVLITPHVGGVTEHSYRSMAKV--VGDVALQ 332
L+ G + G +DV EP P P+ + V ITPHV VT R V + Q
Sbjct: 240 LDSGKVKGAMLDVFSREPLPPESPLWQHPRVAITPHVAAVT----RPAEAVEYISRTIAQ 295
Query: 333 LHAGTPLTG 341
L G + G
Sbjct: 296 LEKGERVCG 304
>gnl|CDD|185335 PRK15438, PRK15438, erythronate-4-phosphate dehydrogenase PdxB;
Provisional.
Length = 378
Score = 52.2 bits (125), Expect = 2e-07
Identities = 45/172 (26%), Positives = 76/172 (44%), Gaps = 27/172 (15%)
Query: 148 GETLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIID 207
G +L +TV I+G GN+G L RL G+K + A
Sbjct: 111 GFSLHDRTVGIVGVGNVGRRLQARLEALGIKTLLCDPPRADRG----------------- 153
Query: 208 DLVDEKGCHEDIFEFASKADVVVCCLSLNK----QTAGIVNKSFLSSMKKGSLLVNIARG 263
++G + E +AD++ L K +T + ++ + S+K G++L+N RG
Sbjct: 154 ----DEGDFRSLDELVQEADILTFHTPLFKDGPYKTLHLADEKLIRSLKPGAILINACRG 209
Query: 264 GLLDYEAIAHYLECGHLGGLGIDVAWTEPFDPNDPILKFKNVLITPHVGGVT 315
++D A+ L G + +DV EP + N +LK ++ TPH+ G T
Sbjct: 210 AVVDNTALLTCLNEGQKLSVVLDVWEGEP-ELNVELLKKVDI-GTPHIAGYT 259
>gnl|CDD|166874 PRK00257, PRK00257, erythronate-4-phosphate dehydrogenase;
Validated.
Length = 381
Score = 46.2 bits (110), Expect = 1e-05
Identities = 53/235 (22%), Positives = 95/235 (40%), Gaps = 50/235 (21%)
Query: 85 VGLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLMLGLLRKQNEMRMAIEQKKLG 144
+G + +D++ GI + PG NA + Y++ LL +A +
Sbjct: 67 IGTDHLDLDYFAEAGITWSSAPG---CNARGVVD---YVLGSLLT------LAERE---- 110
Query: 145 VPTGETLLGKTVFILGFGNIGVELAKRLRPFGVKIIATK--RSWASHSQVSCQSSALAVK 202
G L +T ++G G++G L + LR G K++ R A
Sbjct: 111 ---GVDLAERTYGVVGAGHVGGRLVRVLRGLGWKVLVCDPPRQEA--------------- 152
Query: 203 NGIIDDLVDEKGCHEDIFEFASKADVVVCCLSLNKQ----TAGIVNKSFLSSMKKGSLLV 258
+ G + + DV+ L K+ T +++++FL+S++ G+ L+
Sbjct: 153 --------EGDGDFVSLERILEECDVISLHTPLTKEGEHPTRHLLDEAFLASLRPGAWLI 204
Query: 259 NIARGGLLDYEAIAHYLECGHLGGLGIDVAWTEPFDPNDPILKFKNVLITPHVGG 313
N +RG ++D +A+ L G +DV EP D L + TPH+ G
Sbjct: 205 NASRGAVVDNQALREALLSGEDLDAVLDVWEGEP--QIDLELADLCTIATPHIAG 257
>gnl|CDD|133445 cd01076, NAD_bind_1_Glu_DH, NAD(P) binding domain of glutamate
dehydrogenase, subgroup 1. Amino acid dehydrogenase
(DH) is a widely distributed family of enzymes that
catalyzes the oxidative deamination of an amino acid to
its keto acid and ammonia with concomitant reduction of
NADP+. Glutamate DH is a multidomain enzyme that
catalyzes the reaction from glutamate to 2-oxyoglutarate
and ammonia in the presence of NAD or NADP. It is
present in all organisms. Enzymes involved in ammonia
assimilation are typically NADP+-dependent, while those
involved in glutamate catabolism are generally
NAD+-dependent. Amino acid DH-like NAD(P)-binding
domains are members of the Rossmann fold superfamily and
include glutamate, leucine, and phenylalanine DHs,
methylene tetrahydrofolate DH,
methylene-tetrahydromethanopterin DH,
methylene-tetrahydropholate DH/cyclohydrolase, Shikimate
DH-like proteins, malate oxidoreductases, and glutamyl
tRNA reductase. Amino acid DHs catalyze the deamination
of amino acids to keto acids with NAD(P)+ as a cofactor.
The NAD(P)-binding Rossmann fold superfamily includes a
wide variety of protein families including NAD(P)-
binding domains of alcohol DHs, tyrosine-dependent
oxidoreductases, glyceraldehyde-3-phosphate DH,
lactate/malate DHs, formate/glycerate DHs, siroheme
synthases, 6-phosphogluconate DH, amino acid DHs,
repressor rex, NAD-binding potassium channel domain,
CoA-binding, and ornithine cyclodeaminase-like domains.
These domains have an alpha -beta-alpha configuration.
NAD binding involves numerous hydrogen and van der Waals
contacts.
Length = 227
Score = 43.3 bits (103), Expect = 7e-05
Identities = 21/73 (28%), Positives = 31/73 (42%), Gaps = 11/73 (15%)
Query: 148 GETLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGI-I 206
G L G V I GFGN+G A+ L G K++A VS + +G+ +
Sbjct: 26 GIGLAGARVAIQGFGNVGSHAARFLHEAGAKVVA----------VSDSDGTIYNPDGLDV 75
Query: 207 DDLVDEKGCHEDI 219
L+ K H +
Sbjct: 76 PALLAYKKEHGSV 88
>gnl|CDD|181371 PRK08306, PRK08306, dipicolinate synthase subunit A; Reviewed.
Length = 296
Score = 43.3 bits (103), Expect = 8e-05
Identities = 38/141 (26%), Positives = 58/141 (41%), Gaps = 36/141 (25%)
Query: 136 MAIEQKKLGVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQ 195
MAIE T T+ G V +LGFG G+ LA+ L+ G + R
Sbjct: 141 MAIEH------TPITIHGSNVLVLGFGRTGMTLARTLKALGANVTVGARK---------- 184
Query: 196 SSALAVKNGIIDDLVDEKGCH----EDIFEFASKADVVVCCLSLNKQTAGIVNKSFLSSM 251
S+ LA + E G ++ E K D++ N A ++ K LS M
Sbjct: 185 SAHLAR--------ITEMGLSPFHLSELAEEVGKIDIIF-----NTIPALVLTKEVLSKM 231
Query: 252 KKGSLLVNIAR--GGLLDYEA 270
+L++++A GG D+E
Sbjct: 232 PPEALIIDLASKPGG-TDFEY 251
Score = 30.6 bits (70), Expect = 1.2
Identities = 13/66 (19%), Positives = 25/66 (37%), Gaps = 2/66 (3%)
Query: 44 VPISDVPDVIANYHLCV--VKTMRLDSNCISRANQMKLIMQFGVGLEGVDINAATRCGIK 101
+S++ + + + + + L +S+ LI+ G D A + GIK
Sbjct: 199 FHLSELAEEVGKIDIIFNTIPALVLTKEVLSKMPPEALIIDLASKPGGTDFEYAEKRGIK 258
Query: 102 VARIPG 107
PG
Sbjct: 259 ALLAPG 264
>gnl|CDD|240621 cd01620, Ala_dh_like, Alanine dehydrogenase and related
dehydrogenases. Alanine dehydrogenase/Transhydrogenase,
such as the hexameric L-alanine dehydrogenase of
Phormidium lapideum, contain 2 Rossmann fold-like
domains linked by an alpha helical region. Related
proteins include Saccharopine Dehydrogenase (SDH),
bifunctional lysine ketoglutarate reductase
/saccharopine dehydrogenase enzyme,
N(5)-(carboxyethyl)ornithine synthase, and Rubrum
transdehydrogenase. Alanine dehydrogenase (L-AlaDH)
catalyzes the NAD-dependent conversion of pyrucate to
L-alanine via reductive amination. Transhydrogenases
found in bacterial and inner mitochondrial membranes
link NAD(P)(H)-dependent redox reactions to proton
translocation. The energy of the proton electrochemical
gradient (delta-p), generated by the respiratory
electron transport chain, is consumed by
transhydrogenase in NAD(P)+ reduction. Transhydrogenase
is likely involved in the regulation of the citric acid
cycle. Rubrum transhydrogenase has 3 components, dI,
dII, and dIII. dII spans the membrane while dI and dIII
protrude on the cytoplasmic/matirx side. DI contains 2
domains with Rossmann folds, linked by a long alpha
helix, and contains a NAD binding site. Two dI
polypeptides (represented in this sub-family)
spontaneously form a heterotrimer with one dIII in the
absence of dII. In the heterotrimer, both dI chains may
bind NAD, but only one is well-ordered. dIII also binds
a well-ordered NADP, but in a different orientation than
classical Rossmann domains.
Length = 317
Score = 42.8 bits (101), Expect = 1e-04
Identities = 20/108 (18%), Positives = 46/108 (42%), Gaps = 12/108 (11%)
Query: 155 TVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEKG 214
V I+G G +G+ AK + G ++ V G +K
Sbjct: 164 KVLIIGAGVVGLGAAKIAKKLGANVLVYDIKEEKLKGVE--------TLGGSRLRYSQK- 214
Query: 215 CHEDIFEFASKADVVVCCLSLNKQTAGIV-NKSFLSSMKKGSLLVNIA 261
E++ + + D+++ + ++ A I+ + + MK+G+++V++A
Sbjct: 215 --EELEKELKQTDILINAILVDGPRAPILIMEELVGPMKRGAVIVDLA 260
>gnl|CDD|214966 smart01002, AlaDh_PNT_C, Alanine dehydrogenase/PNT, C-terminal
domain. Alanine dehydrogenase catalyzes the
NAD-dependent reversible reductive amination of pyruvate
into alanine.
Length = 149
Score = 41.0 bits (97), Expect = 2e-04
Identities = 26/116 (22%), Positives = 49/116 (42%), Gaps = 18/116 (15%)
Query: 155 TVFILGFGNIG---VELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVD 211
V ++G G +G AK L G ++ A Q+ ++ L
Sbjct: 22 KVVVIGAGVVGLGAAATAKGL---GAEVTVLDVRPARLRQLE------SLLGARFTTLYS 72
Query: 212 EKGCHEDIFEFASKADVVVCCLSL-NKQTAGIVNKSFLSSMKKGSLLVNIA--RGG 264
+ E E +AD+V+ + + + +V + + SMK GS++V++A +GG
Sbjct: 73 QAELLE---EAVKEADLVIGAVLIPGAKAPKLVTREMVKSMKPGSVIVDVAADQGG 125
>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 = 40.4 bits (95), Expect = 8e-04
Identities = 53/252 (21%), Positives = 91/252 (36%), Gaps = 66/252 (26%)
Query: 90 VDINAATRCGIKVARIP--GDVTGNAASCAELTIYLMLGLL----RKQ-NEMRMAIEQKK 142
VDI AA GI V I GD E I ++ LL KQ E + K
Sbjct: 86 VDIAAARENGITVTGIRDYGD-----EGVVEYVISELIRLLHGFGGKQWKEEPRELTGLK 140
Query: 143 LGVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVK 202
+G I+G G G +A L FG + R+ + ++ +
Sbjct: 141 VG-------------IIGLGTTGQMIADALSFFGADVYYYSRT----RKPDAEAKGIRYL 183
Query: 203 NGIIDDLVDEKGCHEDIFEFASKADVVVCCLSLNKQTAGIVNKSFLSSMKKGSLLVNIAR 262
+++L+ DV+ CL N ++ + + G +L N +
Sbjct: 184 P--LNELLKT-------------VDVICTCLPKNVI---LLGEEEFELLGDGKILFNTSL 225
Query: 263 GGLLDYEAIAHYLE--------CGHLGGLGIDVAWTEPFDPNDPILKFKNVLITPHVGGV 314
G + EA+ +L+ C G LG ++ +L++ NV+ T G
Sbjct: 226 GPSFEVEALKKWLKASGYNIFDCDTAGALG-----------DEELLRYPNVICTNKSAGW 274
Query: 315 TEHSYRSMAKVV 326
T ++ +++ V
Sbjct: 275 TRQAFERLSQKV 286
>gnl|CDD|237820 PRK14806, PRK14806, bifunctional cyclohexadienyl dehydrogenase/
3-phosphoshikimate 1-carboxyvinyltransferase;
Provisional.
Length = 735
Score = 40.4 bits (95), Expect = 0.001
Identities = 27/77 (35%), Positives = 37/77 (48%), Gaps = 16/77 (20%)
Query: 156 VFILGFGNIGVELAKRLRPFGV--KIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEK 213
V ++G G IG AK LR G+ +++A R +S LAV G+ID
Sbjct: 6 VVVIGLGLIGGSFAKALRERGLAREVVAVDRR--------AKSLELAVSLGVIDR----- 52
Query: 214 GCHEDIFEFASKADVVV 230
ED+ E S ADV+V
Sbjct: 53 -GEEDLAEAVSGADVIV 68
>gnl|CDD|223411 COG0334, GdhA, Glutamate dehydrogenase/leucine dehydrogenase [Amino
acid transport and metabolism].
Length = 411
Score = 39.9 bits (94), Expect = 0.001
Identities = 21/77 (27%), Positives = 38/77 (49%), Gaps = 11/77 (14%)
Query: 148 GETLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGI-I 206
G+ L G V + GFGN+G A++L G K++A VS + ++G+ +
Sbjct: 202 GDDLEGARVAVQGFGNVGQYAAEKLHELGAKVVA----------VSDSKGGIYDEDGLDV 251
Query: 207 DDLVDEKGCHEDIFEFA 223
+ L++ K + E+A
Sbjct: 252 EALLELKERRGSVAEYA 268
>gnl|CDD|178095 PLN02477, PLN02477, glutamate dehydrogenase.
Length = 410
Score = 38.2 bits (89), Expect = 0.005
Identities = 45/174 (25%), Positives = 71/174 (40%), Gaps = 38/174 (21%)
Query: 148 GETLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGI-I 206
G+++ G+T I GFGN+G A+ + G KI+A VS + A+ +NG+ I
Sbjct: 201 GKSIAGQTFVIQGFGNVGSWAAQLIHEKGGKIVA----------VSDITGAVKNENGLDI 250
Query: 207 DDLVDEKGCHEDIFEFASKADVVVCCLSLNKQTAGIVNKSFLSSMKKGSLLVNIARGGLL 266
L + F I L ++ +L+ A GG++
Sbjct: 251 PALRKHVAEGGGLKGFPG--------------GDPIDPDDIL--VEPCDVLIPAALGGVI 294
Query: 267 DYEAIAHYLECGHLGGLGIDVAWTEPFDPN-DPILKFKNVLITPHV----GGVT 315
+ E A ++ I A P DP D IL+ K V++ P + GGVT
Sbjct: 295 NKEN-AADVKAKF-----IVEAANHPTDPEADEILRKKGVVVLPDIYANSGGVT 342
>gnl|CDD|215789 pfam00208, ELFV_dehydrog, Glutamate/Leucine/Phenylalanine/Valine
dehydrogenase.
Length = 237
Score = 37.1 bits (87), Expect = 0.008
Identities = 29/74 (39%), Positives = 42/74 (56%), Gaps = 14/74 (18%)
Query: 141 KKLGVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALA 200
KKLG G++L GKTV + GFGN+G A++L G K++A VS S +
Sbjct: 23 KKLG---GDSLEGKTVAVQGFGNVGSYAAEKLLELGAKVVA----------VSDSSGYIY 69
Query: 201 VKNGI-IDDLVDEK 213
NGI I++L++ K
Sbjct: 70 DPNGIDIEELLELK 83
>gnl|CDD|215144 PLN02256, PLN02256, arogenate dehydrogenase.
Length = 304
Score = 36.6 bits (85), Expect = 0.016
Identities = 30/111 (27%), Positives = 47/111 (42%), Gaps = 27/111 (24%)
Query: 155 TVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGI-----IDDL 209
+ I+GFGN G LAK G ++AT RS S +A + G+ DD
Sbjct: 38 KIGIVGFGNFGQFLAKTFVKQGHTVLATSRS---------DYSDIAAELGVSFFRDPDDF 88
Query: 210 VDEKGCHEDIFEFASKADVVVCCLSLNKQTAGIVNKSFLSSMKKGSLLVNI 260
+E DVV+ C S+ T ++ L +K+ +L V++
Sbjct: 89 CEE------------HPDVVLLCTSI-LSTEAVLRSLPLQRLKRSTLFVDV 126
>gnl|CDD|237220 PRK12828, PRK12828, short chain dehydrogenase; Provisional.
Length = 239
Score = 34.4 bits (79), Expect = 0.061
Identities = 24/62 (38%), Positives = 29/62 (46%), Gaps = 2/62 (3%)
Query: 151 LLGKTVFILG-FGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDL 209
L GK V I G FG +G A L G ++ R A SQ A A++ G I DL
Sbjct: 5 LQGKVVAITGGFGGLGRATAAWLAARGARVALIGRGAAPLSQTLPGVPADALRIGGI-DL 63
Query: 210 VD 211
VD
Sbjct: 64 VD 65
>gnl|CDD|233242 TIGR01035, hemA, glutamyl-tRNA reductase. This enzyme, together
with glutamate-1-semialdehyde-2,1-aminomutase
(TIGR00713), leads to the production of
delta-amino-levulinic acid from Glu-tRNA [Biosynthesis
of cofactors, prosthetic groups, and carriers, Heme,
porphyrin, and cobalamin].
Length = 417
Score = 34.3 bits (79), Expect = 0.086
Identities = 28/118 (23%), Positives = 51/118 (43%), Gaps = 21/118 (17%)
Query: 149 ETLLGKTVFILGFGNIGVELAKRLRPFGV-KIIATKRSWASHSQVSCQSSALAVKNGIID 207
+L GK ++G G +G +AK L GV KI+ R++ ++ + AVK
Sbjct: 176 GSLKGKKALLIGAGEMGELVAKHLLRKGVGKILIANRTYERAEDLAKELGGEAVK----- 230
Query: 208 DLVDEKGCHEDIFEFASKADVVVCCLSLNKQTAGIVNKSFLS----SMKKGSLLVNIA 261
ED+ E+ ++AD+V+ IV+K + + +++IA
Sbjct: 231 --------FEDLEEYLAEADIVISSTG---APHPIVSKEDVERALRERTRPLFIIDIA 277
>gnl|CDD|187576 cd05266, SDR_a4, atypical (a) SDRs, subgroup 4. Atypical SDRs in
this subgroup are poorly defined, one member is
identified as a putative NAD-dependent
epimerase/dehydratase. Atypical SDRs are distinct from
classical SDRs. Members of this subgroup have a
glycine-rich NAD(P)-binding motif that is related to,
but is different from, the archetypical SDRs, GXGXXG.
This subgroup also lacks most of the characteristic
active site residues of the SDRs; however, the upstream
Ser is present at the usual place, and some potential
catalytic residues are present in place of the usual
YXXXK active site motif. Atypical SDRs generally lack
the catalytic residues characteristic of the SDRs, and
their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Atypical SDRs include biliverdin IX beta
reductase (BVR-B,aka flavin reductase), NMRa (a negative
transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. In addition to the
Rossmann fold core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 251
Score = 33.8 bits (78), Expect = 0.090
Identities = 18/78 (23%), Positives = 27/78 (34%), Gaps = 13/78 (16%)
Query: 156 VFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEKGC 215
V ILG G +G LA++L G ++ T RS + + DL
Sbjct: 1 VLILGCGYLGQRLARQLLAQGWQVTGTTRSPEKLAADRPAGVT-----PLAADLTQ---- 51
Query: 216 HEDIFEFASKADVVVCCL 233
+ D +V L
Sbjct: 52 ----PGLLADVDHLVISL 65
>gnl|CDD|131900 TIGR02853, spore_dpaA, dipicolinic acid synthetase, A subunit.
This predicted Rossman fold-containing protein is the A
subunit of dipicolinic acid synthetase as found in most,
though not all, endospore-forming low-GC Gram-positive
bacteria; it is absent in Clostridium. The B subunit is
represented by TIGR02852. This protein is also known as
SpoVFA [Cellular processes, Sporulation and
germination].
Length = 287
Score = 33.9 bits (78), Expect = 0.10
Identities = 32/137 (23%), Positives = 55/137 (40%), Gaps = 28/137 (20%)
Query: 136 MAIEQKKLGVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQ 195
MAIE T T+ G V +LGFG G+ +A+ G + V +
Sbjct: 140 MAIEH------TDFTIHGSNVMVLGFGRTGMTIARTFSALG-----------ARVFVGAR 182
Query: 196 SSALAVKNGIIDDLVDEKGCHEDIFEFASKADVVVCC-LSLNKQTAGIVNKSFLSSMKKG 254
SSA + + E G F + V + +N A ++ LS + K
Sbjct: 183 SSADLAR-------ITEMGLIP--FPLNKLEEKVAEIDIVINTIPALVLTADVLSKLPKH 233
Query: 255 SLLVNIA-RGGLLDYEA 270
++++++A + G D+E
Sbjct: 234 AVIIDLASKPGGTDFEY 250
Score = 27.8 bits (62), Expect = 10.0
Identities = 13/66 (19%), Positives = 30/66 (45%), Gaps = 2/66 (3%)
Query: 44 VPISDVPDVIANYHLCV--VKTMRLDSNCISRANQMKLIMQFGVGLEGVDINAATRCGIK 101
P++ + + +A + + + + L ++ +S+ + +I+ G D A + GIK
Sbjct: 198 FPLNKLEEKVAEIDIVINTIPALVLTADVLSKLPKHAVIIDLASKPGGTDFEYAKKRGIK 257
Query: 102 VARIPG 107
PG
Sbjct: 258 ALLAPG 263
>gnl|CDD|198065 smart00997, AdoHcyase_NAD, S-adenosyl-L-homocysteine hydrolase, NAD
binding domain.
Length = 162
Score = 32.8 bits (76), Expect = 0.12
Identities = 29/119 (24%), Positives = 49/119 (41%), Gaps = 31/119 (26%)
Query: 147 TGETLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGII 206
T L GK V + G+G++G +A RLR G ++I T+ I
Sbjct: 17 TNVLLAGKNVVVAGYGDVGKGVAARLRGLGARVIVTE----------------------I 54
Query: 207 DDLVDEKGCHE-----DIFEFASKADVVVCCLSLNKQTAGIVNKSFLSSMKKGSLLVNI 260
D + + + + E A +AD+ V NK ++ + +MK G++L N
Sbjct: 55 DPIRALEAAMDGFEVMKMEEAAKRADIFVTATG-NK---DVITREHFRAMKDGAILANA 109
>gnl|CDD|223137 COG0059, IlvC, Ketol-acid reductoisomerase [Amino acid transport
and metabolism / Coenzyme metabolism].
Length = 338
Score = 33.7 bits (78), Expect = 0.13
Identities = 34/119 (28%), Positives = 52/119 (43%), Gaps = 22/119 (18%)
Query: 151 LLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLV 210
L GK V I+G+G+ G A LR G+ +I R +S S A ++G V
Sbjct: 16 LKGKKVAIIGYGSQGHAQALNLRDSGLNVIIGLRKGSS-------SWKKAKEDGFKVYTV 68
Query: 211 DEKGCHEDIFEFASKADVVVCCLSLNKQTAGIVNKSFLSSMKKGSLLV-----NIARGG 264
+E A +ADVV+ L ++Q + K ++K+G+ L NI G
Sbjct: 69 EEA---------AKRADVVMILLP-DEQQKEVYEKEIAPNLKEGAALGFAHGFNIHFGL 117
>gnl|CDD|184511 PRK14106, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
synthetase; Provisional.
Length = 450
Score = 33.4 bits (77), Expect = 0.15
Identities = 15/32 (46%), Positives = 20/32 (62%)
Query: 151 LLGKTVFILGFGNIGVELAKRLRPFGVKIIAT 182
L GK V ++G G G+ LAK L+ G K+I T
Sbjct: 3 LKGKKVLVVGAGVSGLALAKFLKKLGAKVILT 34
>gnl|CDD|133450 cd05211, NAD_bind_Glu_Leu_Phe_Val, NAD(P) binding domain of
glutamate dehydrogenase, leucine dehydrogenase,
phenylalanine dehydrogenase, and valine dehydrogenase.
Amino acid dehydrogenase (DH) is a widely distributed
family of enzymes that catalyzes the oxidative
deamination of an amino acid to its keto acid and
ammonia with concomitant reduction of NAD(P)+. This
subfamily includes glutamate, leucine, phenylalanine,
and valine DHs. Glutamate DH is a multi-domain enzyme
that catalyzes the reaction from glutamate to
2-oxyoglutarate and ammonia in the presence of NAD or
NADP. It is present in all organisms. Enzymes involved
in ammonia assimilation are typically NADP+-dependent,
while those involved in glutamate catabolism are
generally NAD+-dependent. As in other NAD+-dependent
DHs, monomers in this family have 2 domains separated by
a deep cleft. Here the c-terminal domain contains a
modified NAD-binding Rossmann fold with 7 rather than
the usual 6 beta strands and one strand anti-parrallel
to the others. Amino acid DH-like NAD(P)-binding domains
are members of the Rossmann fold superfamily and include
glutamate, leucine, and phenylalanine DHs, methylene
tetrahydrofolate DH, methylene-tetrahydromethanopterin
DH, methylene-tetrahydropholate DH/cyclohydrolase,
Shikimate DH-like proteins, malate oxidoreductases, and
glutamyl tRNA reductase. Amino acid DHs catalyze the
deamination of amino acids to keto acids with NAD(P)+ as
a cofactor. The NAD(P)-binding Rossmann fold superfamily
includes a wide variety of protein families including
NAD(P)- binding domains of alcohol DHs,
tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate DH, lactate/malate DHs,
formate/glycerate DHs, siroheme synthases,
6-phosphogluconate DH, amino acid DHs, repressor rex,
NAD-binding potassium channel domain, CoA-binding, and
ornithine cyclodeaminase-like domains. These domains
have an alpha-beta-alpha configuration. NAD binding
involves numerous hydrogen and van der Waals contacts.
Length = 217
Score = 32.9 bits (75), Expect = 0.16
Identities = 16/34 (47%), Positives = 23/34 (67%)
Query: 148 GETLLGKTVFILGFGNIGVELAKRLRPFGVKIIA 181
G++L G TV + G GN+G LAK+L G K++A
Sbjct: 18 GDSLEGLTVAVQGLGNVGWGLAKKLAEEGGKVLA 51
>gnl|CDD|116601 pfam07991, IlvN, Acetohydroxy acid isomeroreductase, catalytic
domain. Acetohydroxy acid isomeroreductase catalyzes
the conversion of acetohydroxy acids into dihydroxy
valerates. This reaction is the second in the synthetic
pathway of the essential branched side chain amino acids
valine and isoleucine.
Length = 165
Score = 31.7 bits (73), Expect = 0.31
Identities = 30/108 (27%), Positives = 46/108 (42%), Gaps = 17/108 (15%)
Query: 151 LLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLV 210
L GK + ++G+G+ G A LR GV +I R + S A K+G V
Sbjct: 2 LKGKKIAVIGYGSQGHAHALNLRDSGVNVIVGLRPGSK-------SWEKAKKDGFEVYTV 54
Query: 211 DEKGCHEDIFEFASKADVVVCCLSLNKQTAGIVNKSFLSSMKKGSLLV 258
E KADVV+ L ++ A + K ++K+G+ L
Sbjct: 55 AEA---------VKKADVVM-ILLPDEVQAEVYEKEIAPNLKEGAALA 92
>gnl|CDD|240258 PTZ00075, PTZ00075, Adenosylhomocysteinase; Provisional.
Length = 476
Score = 32.3 bits (74), Expect = 0.35
Identities = 13/30 (43%), Positives = 21/30 (70%)
Query: 153 GKTVFILGFGNIGVELAKRLRPFGVKIIAT 182
GKTV + G+G++G A+ LR FG +++ T
Sbjct: 254 GKTVVVCGYGDVGKGCAQALRGFGARVVVT 283
>gnl|CDD|224995 COG2084, MmsB, 3-hydroxyisobutyrate dehydrogenase and related
beta-hydroxyacid dehydrogenases [Lipid metabolism].
Length = 286
Score = 32.2 bits (74), Expect = 0.36
Identities = 18/110 (16%), Positives = 39/110 (35%), Gaps = 19/110 (17%)
Query: 154 KTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEK 213
+ +G G +G +A L G ++ R+ + L
Sbjct: 1 MKIAFIGLGIMGSPMAANLLKAGHEVTVYNRTPEK----------------AAELLAAAG 44
Query: 214 GC-HEDIFEFASKADVVVCCLSLNKQTAGIVNKS--FLSSMKKGSLLVNI 260
E A++ADVV+ L + ++ L +K G++++++
Sbjct: 45 ATVAASPAEAAAEADVVITMLPDDAAVRAVLFGENGLLEGLKPGAIVIDM 94
>gnl|CDD|235824 PRK06545, PRK06545, prephenate dehydrogenase; Validated.
Length = 359
Score = 31.8 bits (73), Expect = 0.44
Identities = 22/77 (28%), Positives = 35/77 (45%), Gaps = 12/77 (15%)
Query: 154 KTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEK 213
+TV I+G G IG LA ++ G + S A A+ G+ID+L
Sbjct: 1 RTVLIVGLGLIGGSLALAIKAAGPDVFIIGYD------PSAAQLARALGFGVIDELA--- 51
Query: 214 GCHEDIFEFASKADVVV 230
D+ A++AD++V
Sbjct: 52 ---ADLQRAAAEADLIV 65
>gnl|CDD|187643 cd08939, KDSR-like_SDR_c, 3-ketodihydrosphingosine reductase (KDSR)
and related proteins, classical (c) SDR. These proteins
include members identified as KDSR, ribitol type
dehydrogenase, and others. The group shows strong
conservation of the active site tetrad and glycine rich
NAD-binding motif of the classical SDRs. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold (alpha/beta folding pattern with a central
beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRs are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes catalyze a
wide range of activities including the metabolism of
steroids, cofactors, carbohydrates, lipids, aromatic
compounds, and amino acids, and act in redox sensing.
Classical SDRs have an TGXXX[AG]XG cofactor binding
motif and a YXXXK active site motif, with the Tyr
residue of the active site motif serving as a critical
catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 239
Score = 31.5 bits (72), Expect = 0.52
Identities = 26/89 (29%), Positives = 36/89 (40%), Gaps = 9/89 (10%)
Query: 153 GKTVFILGFGN-IGVELAKRLRPFGVKIIATKRSWA--SHSQVSCQSSALAVKN---GII 206
GK V I G + IG LAK L G +I RS + + ++ A A I
Sbjct: 1 GKHVLITGGSSGIGKALAKELVKEGANVIIVARSESKLEEAVEEIEAEANASGQKVSYIS 60
Query: 207 DDLVDEKGCHEDIFEFASKA---DVVVCC 232
DL D + + + K D+VV C
Sbjct: 61 ADLSDYEEVEQAFAQAVEKGGPPDLVVNC 89
>gnl|CDD|215623 PLN03190, PLN03190, aminophospholipid translocase; Provisional.
Length = 1178
Score = 31.8 bits (72), Expect = 0.58
Identities = 14/27 (51%), Positives = 17/27 (62%)
Query: 217 EDIFEFASKADVVVCCLSLNKQTAGIV 243
E +F+ ASK VV+CC Q AGIV
Sbjct: 837 EQLFQLASKCSVVLCCRVAPLQKAGIV 863
>gnl|CDD|187632 cd05374, 17beta-HSD-like_SDR_c, 17beta hydroxysteroid
dehydrogenase-like, classical (c) SDRs.
17beta-hydroxysteroid dehydrogenases are a group of
isozymes that catalyze activation and inactivation of
estrogen and androgens. SDRs are a functionally diverse
family of oxidoreductases that have a single domain with
a structurally conserved Rossmann fold (alpha/beta
folding pattern with a central beta-sheet), an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRs are approximately
350 residues. Sequence identity between different SDR
enzymes are typically in the 15-30% range, but the
enzymes share the Rossmann fold NAD-binding motif and
characteristic NAD-binding and catalytic sequence
patterns. These enzymes catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase (15-PGDH) numbering). In addition to the
Tyr and Lys, there is often an upstream Ser (Ser-138,
15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH
numbering) contributing to the active site; while
substrate binding is in the C-terminal region, which
determines specificity. The standard reaction mechanism
is a 4-pro-S hydride transfer and proton relay involving
the conserved Tyr and Lys, a water molecule stabilized
by Asn, and nicotinamide. Extended SDRs have additional
elements in the C-terminal region, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Some atypical SDRs have lost catalytic activity and/or
have an unusual NAD(P)-binding motif and missing or
unusual active site residues. Reactions catalyzed within
the SDR family include isomerization, decarboxylation,
epimerization, C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 248
Score = 31.0 bits (71), Expect = 0.63
Identities = 21/92 (22%), Positives = 37/92 (40%), Gaps = 11/92 (11%)
Query: 154 KTVFILGFGN-IGVELAKRLRPFGVKIIATKRSWAS--HSQVSCQSSALAVKNGIIDDLV 210
K V I G + IG+ LA L G ++IAT R+ + ++ + D+
Sbjct: 1 KVVLITGCSSGIGLALALALAAQGYRVIATARNPDKLESLGELLNDNLEVLELDVTDEES 60
Query: 211 DEKGCHEDIFEFASKADVVVCCLSLNKQTAGI 242
+ +++ E + DV+V AG
Sbjct: 61 IKAA-VKEVIERFGRIDVLVNN-------AGY 84
>gnl|CDD|236541 PRK09496, trkA, potassium transporter peripheral membrane
component; Reviewed.
Length = 453
Score = 31.6 bits (73), Expect = 0.64
Identities = 15/29 (51%), Positives = 18/29 (62%), Gaps = 2/29 (6%)
Query: 154 KTVFILGFGNIGVELAKRL--RPFGVKII 180
K V I+G GNIG LAK L + VK+I
Sbjct: 232 KRVMIVGGGNIGYYLAKLLEKEGYSVKLI 260
>gnl|CDD|106361 PRK13403, PRK13403, ketol-acid reductoisomerase; Provisional.
Length = 335
Score = 31.3 bits (70), Expect = 0.74
Identities = 16/41 (39%), Positives = 24/41 (58%)
Query: 149 ETLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASH 189
E L GKTV ++G+G+ G A+ LR GV+++ R S
Sbjct: 12 ELLQGKTVAVIGYGSQGHAQAQNLRDSGVEVVVGVRPGKSF 52
>gnl|CDD|223573 COG0499, SAM1, S-adenosylhomocysteine hydrolase [Coenzyme
metabolism].
Length = 420
Score = 31.1 bits (71), Expect = 0.88
Identities = 28/117 (23%), Positives = 41/117 (35%), Gaps = 39/117 (33%)
Query: 153 GKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDE 212
GK V + G+G +G +A RLR G ++I T+ VD
Sbjct: 209 GKNVVVAGYGWVGRGIAMRLRGMGARVIVTE--------------------------VDP 242
Query: 213 KGCHEDIF---------EFASKADVVVCCLSLNKQTAGIVNKSFLSSMKKGSLLVNI 260
E E A D+ V + NK ++ K MK G++L N
Sbjct: 243 IRALEAAMDGFRVMTMEEAAKTGDIFVTA-TGNK---DVIRKEHFEKMKDGAILANA 295
>gnl|CDD|240630 cd05305, L-AlaDH, Alanine dehydrogenase NAD-binding and catalytic
domains. Alanine dehydrogenase (L-AlaDH) catalyzes the
NAD-dependent conversion of pyruvate to L-alanine via
reductive amination. Like formate dehydrogenase and
related enzymes, L-AlaDH is comprised of 2 domains
connected by a long alpha helical stretch, each
resembling a Rossmann fold NAD-binding domain. The
NAD-binding domain is inserted within the linear
sequence of the more divergent catalytic domain. Ligand
binding and active site residues are found in the cleft
between the subdomains. L-AlaDH is typically hexameric
and is critical in carbon and nitrogen metabolism in
micro-organisms.
Length = 359
Score = 30.8 bits (71), Expect = 1.0
Identities = 13/44 (29%), Positives = 26/44 (59%), Gaps = 3/44 (6%)
Query: 224 SKADVVVCC-LSLNKQTAGIVNKSFLSSMKKGSLLVNIA--RGG 264
+AD+V+ L + +V + + +MK GS++V++A +GG
Sbjct: 230 KEADLVIGAVLIPGAKAPKLVTEEMVKTMKPGSVIVDVAIDQGG 273
>gnl|CDD|201603 pfam01118, Semialdhyde_dh, Semialdehyde dehydrogenase, NAD binding
domain. This Pfam entry contains the following members:
N-acetyl-glutamine semialdehyde dehydrogenase (AgrC)
Aspartate-semialdehyde dehydrogenase.
Length = 121
Score = 29.4 bits (67), Expect = 1.0
Identities = 20/85 (23%), Positives = 31/85 (36%), Gaps = 15/85 (17%)
Query: 155 TVFILG-FGNIGVELAKRLR---PFG-VKIIATKRSWASHSQVSCQSSALAVKNGIIDDL 209
V I+G G +G EL + L P V ++A+ RS +A I++
Sbjct: 1 KVAIVGATGYVGQELLRLLAEHPPLELVALVASSRS---------AGKKVAFAYPILEGG 51
Query: 210 VDEKGCHEDIFEFASKADVVVCCLS 234
D D + D+V L
Sbjct: 52 KDLLLEDVDPEDL-KDVDIVFLALP 75
>gnl|CDD|240619 cd00401, SAHH, S-Adenosylhomocysteine Hydrolase, NAD-binding and
catalytic domains. S-adenosyl-L-homocysteine hydrolase
(SAHH, AdoHycase) catalyzes the hydrolysis of
S-adenosyl-L-homocysteine (AdoHyc) to form adenosine
(Ado) and homocysteine (Hcy). The equilibrium lies far
on the side of AdoHyc synthesis, but in nature the
removal of Ado and Hyc is sufficiently fast, so that the
net reaction is in the direction of hydrolysis. Since
AdoHyc is a potent inhibitor of S-adenosyl-L-methionine
dependent methyltransferases, AdoHycase plays a critical
role in the modulation of the activity of various
methyltransferases. The enzyme forms homotetramers, with
each monomer binding one molecule of NAD+.
Length = 402
Score = 30.9 bits (71), Expect = 1.1
Identities = 12/30 (40%), Positives = 17/30 (56%)
Query: 153 GKTVFILGFGNIGVELAKRLRPFGVKIIAT 182
GK V + G+G +G A R R G ++I T
Sbjct: 195 GKVVVVAGYGWVGKGCAMRARGLGARVIVT 224
>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 = 30.3 bits (69), Expect = 1.3
Identities = 11/42 (26%), Positives = 24/42 (57%), Gaps = 1/42 (2%)
Query: 221 EFASKADVVV-CCLSLNKQTAGIVNKSFLSSMKKGSLLVNIA 261
E S+ D++V C L + I+ + L +K G+L+++++
Sbjct: 193 EELSEYDIIVNCILQDTDRPDHIIYEEDLKRLKPGALIIDVS 234
>gnl|CDD|133444 cd01075, NAD_bind_Leu_Phe_Val_DH, NAD(P) binding domain of leucine
dehydrogenase, phenylalanine dehydrogenase, and valine
dehydrogenase. Amino acid dehydrogenase (DH) is a
widely distributed family of enzymes that catalyzes the
oxidative deamination of an amino acid to its keto acid
and ammonia with concomitant reduction of NADP+. For
example, leucine DH catalyzes the reversible oxidative
deamination of L-leucine and several other straight or
branched chain amino acids to the corresponding
2-oxoacid derivative. Amino acid DH -like NAD(P)-binding
domains are members of the Rossmann fold superfamily and
include glutamate, leucine, and phenylalanine DHs,
methylene tetrahydrofolate DH,
methylene-tetrahydromethanopterin DH,
methylene-tetrahydropholate DH/cyclohydrolase, Shikimate
DH-like proteins, malate oxidoreductases, and glutamyl
tRNA reductase. Amino acid DHs catalyze the deamination
of amino acids to keto acids with NAD(P)+ as a cofactor.
The NAD(P)-binding Rossmann fold superfamily includes a
wide variety of protein families including NAD(P)-
binding domains of alcohol DHs, tyrosine-dependent
oxidoreductases, glyceraldehyde-3-phosphate DH,
lactate/malate DHs, formate/glycerate DHs, siroheme
synthases, 6-phosphogluconate DH, amino acid DHs,
repressor rex, NAD-binding potassium channel domain,
CoA-binding, and ornithine cyclodeaminase-like domains.
These domains have an alpha-beta-alpha configuration.
NAD binding involves numerous hydrogen and van der Waals
contacts.
Length = 200
Score = 29.9 bits (68), Expect = 1.3
Identities = 19/49 (38%), Positives = 27/49 (55%), Gaps = 4/49 (8%)
Query: 134 MRMAIEQKKLGVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVKIIAT 182
M+ A E LG ++L GKTV + G G +G +LA+ L G K+I
Sbjct: 13 MKAAAEHL-LG---TDSLEGKTVAVQGLGKVGYKLAEHLLEEGAKLIVA 57
>gnl|CDD|213572 TIGR00936, ahcY, adenosylhomocysteinase. This enzyme hydrolyzes
adenosylhomocysteine as part of a cycle for the
regeneration of the methyl donor S-adenosylmethionine.
Species that lack this enzyme are likely to have
adenosylhomocysteine nucleosidase (EC 3.2.2.9), an
enzyme which also acts as 5'-methyladenosine
nucleosidase (see TIGR01704) [Energy metabolism, Amino
acids and amines].
Length = 407
Score = 30.5 bits (69), Expect = 1.3
Identities = 13/32 (40%), Positives = 19/32 (59%)
Query: 151 LLGKTVFILGFGNIGVELAKRLRPFGVKIIAT 182
+ GKTV + G+G G +A R R G ++I T
Sbjct: 194 IAGKTVVVAGYGWCGKGIAMRARGMGARVIVT 225
>gnl|CDD|133455 cd05313, NAD_bind_2_Glu_DH, NAD(P) binding domain of glutamate
dehydrogenase, subgroup 2. Amino acid dehydrogenase
(DH) is a widely distributed family of enzymes that
catalyzes the oxidative deamination of an amino acid to
its keto acid and ammonia with concomitant reduction of
NADP+. Glutamate DH is a multidomain enzyme that
catalyzes the reaction from glutamate to 2-oxyoglutarate
and ammonia in the presence of NAD or NADP. It is
present in all organisms. Enzymes involved in ammonia
asimilation are typically NADP+-dependent, while those
involved in glutamate catabolism are generally
NAD+-dependent. Amino acid DH-like NAD(P)-binding
domains are members of the Rossmann fold superfamily and
include glutamate, leucine, and phenylalanine DHs,
methylene tetrahydrofolate DH,
methylene-tetrahydromethanopterin DH,
methylene-tetrahydropholate DH/cyclohydrolase, Shikimate
DH-like proteins, malate oxidoreductases, and glutamyl
tRNA reductase. Amino acid DHs catalyze the deamination
of amino acids to keto acids with NAD(P)+ as a cofactor.
The NAD(P)-binding Rossmann fold superfamily includes a
wide variety of protein families including NAD(P)-
binding domains of alcohol DHs, tyrosine-dependent
oxidoreductases, glyceraldehyde-3-phosphate DH,
lactate/malate DHs, formate/glycerate DHs, siroheme
synthases, 6-phosphogluconate DH, amino acid DHs,
repressor rex, NAD-binding potassium channel domain,
CoA-binding, and ornithine cyclodeaminase-like domains.
These domains have an alpha -beta-alpha configuration.
NAD binding involves numerous hydrogen and van der Waals
contacts.
Length = 254
Score = 29.9 bits (68), Expect = 1.5
Identities = 14/34 (41%), Positives = 19/34 (55%)
Query: 148 GETLLGKTVFILGFGNIGVELAKRLRPFGVKIIA 181
ETL GK V I G GN+ A++L G K++
Sbjct: 33 NETLKGKRVAISGSGNVAQYAAEKLLELGAKVVT 66
>gnl|CDD|233635 TIGR01915, npdG, NADPH-dependent F420 reductase. This model
represents a subset of a parent family described by
pfam03807. Unlike the parent family, members of this
family are found only in species with evidence of
coenzyme F420. All members of this family are believed
to act as NADPH-dependent F420 reductase [Energy
metabolism, Electron transport].
Length = 219
Score = 29.8 bits (67), Expect = 1.6
Identities = 30/119 (25%), Positives = 43/119 (36%), Gaps = 14/119 (11%)
Query: 160 GFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEKGCHEDI 219
G G+ G LA RL G KII R + +A + D K D
Sbjct: 8 GTGDQGKGLALRLAKAGNKIIIGSRDLEKAEE-----AAAKALEELGHGGSDIKVTGADN 62
Query: 220 FEFASKADVVVCCLSLNKQTAGIVNKSFLSSMK---KGSLLVNIARGGLLDYEAIAHYL 275
E A +ADVV+ + + L S++ G L+++ D A YL
Sbjct: 63 AEAAKRADVVILAVPWDHVL------KTLESLRDELSGKLVISPVVPLASDGGKGARYL 115
>gnl|CDD|232903 TIGR00278, TIGR00278, putative membrane protein insertion
efficiency factor. This model describes a family,
YidD, of small, non-essential proteins now suggested to
improve YidC-dependent inner membrane protein
insertion. A related protein is found in the
temperature phage HP1 of Haemophilus influenzae.
Annotation of some members of this family as hemolysins
appears to represent propagation from an unpublished
GenBank submission, L36462, attributed to Aeromonas
hydrophila but a close match to E. coli [Hypothetical
proteins, Conserved].
Length = 75
Score = 28.2 bits (63), Expect = 1.6
Identities = 8/39 (20%), Positives = 16/39 (41%)
Query: 2 EGMARSSDKNITRVLFCGPHFPASHNYTKEYLQNYPSIQ 40
G + + R+L C P P ++ + Q S++
Sbjct: 37 HGFLKGGWLTLKRILRCHPLHPGGNDPVPKKKQILESLK 75
>gnl|CDD|176197 cd08235, iditol_2_DH_like, L-iditol 2-dehydrogenase. Putative
L-iditol 2-dehydrogenase based on annotation of some
members in this subgroup. L-iditol 2-dehydrogenase
catalyzes the NAD+-dependent conversion of L-iditol to
L-sorbose in fructose and mannose metabolism. This
enzyme is related to sorbitol dehydrogenase, alcohol
dehydrogenase, and other medium chain
dehydrogenase/reductases. The zinc-dependent alcohol
dehydrogenase (ADH-Zn)-like family of proteins is a
diverse group of proteins related to the first
identified member, class I mammalian ADH. This group is
also called the medium chain dehydrogenases/reductase
family (MDR) to highlight its broad range of activities
and to distinguish from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal GroES-like catalytic
domain. The MDR group contains a host of activities,
including the founding alcohol dehydrogenase (ADH),
quinone reductase, sorbitol dehydrogenase, formaldehyde
dehydrogenase, butanediol DH, ketose reductase, cinnamyl
reductase, and numerous others. The zinc-dependent
alcohol dehydrogenases (ADHs) catalyze the
NAD(P)(H)-dependent interconversion of alcohols to
aldehydes or ketones. Active site zinc has a catalytic
role, while structural zinc aids in stability. ADH-like
proteins typically form dimers (typically higher
plants, mammals) or tetramers (yeast, bacteria), and
generally have 2 tightly bound zinc atoms per subunit.
The active site zinc is coordinated by a histidine, two
cysteines, and a water molecule. The second zinc seems
to play a structural role, affects subunit interactions,
and is typically coordinated by 4 cysteines.
Length = 343
Score = 30.3 bits (69), Expect = 1.6
Identities = 27/107 (25%), Positives = 41/107 (38%), Gaps = 27/107 (25%)
Query: 140 QKKLGVPTGETLLGKTVFILGFGNIG---VELAKRLRPFGVKIIATKRSWASHSQVSCQS 196
Q+K G+ G+T V ++G G IG LAK G + + S ++
Sbjct: 158 QRKAGIKPGDT-----VLVIGAGPIGLLHAMLAKA---SGARKVIV-------SDLNEFR 202
Query: 197 SALAVKNGIIDDLVDEKGCHEDIFEFASK------ADVVVCCLSLNK 237
A K G D +D ED+ E + ADVV+ +
Sbjct: 203 LEFAKKLG-ADYTIDAA--EEDLVEKVRELTDGRGADVVIVATGSPE 246
>gnl|CDD|184463 PRK14030, PRK14030, glutamate dehydrogenase; Provisional.
Length = 445
Score = 30.2 bits (68), Expect = 1.9
Identities = 13/34 (38%), Positives = 18/34 (52%)
Query: 147 TGETLLGKTVFILGFGNIGVELAKRLRPFGVKII 180
G + GKTV I GFGN+ A + G K++
Sbjct: 222 KGIDIKGKTVAISGFGNVAWGAATKATELGAKVV 255
>gnl|CDD|178263 PLN02657, PLN02657, 3,8-divinyl protochlorophyllide a 8-vinyl
reductase.
Length = 390
Score = 29.7 bits (67), Expect = 2.1
Identities = 28/129 (21%), Positives = 46/129 (35%), Gaps = 24/129 (18%)
Query: 154 KTVFILG-FGNIGVELAKRLRPFGVKIIATKRSWA---SHSQVSCQSSALAVKNGIIDDL 209
TV ++G G IG + + L G ++A R + + L + D+
Sbjct: 61 VTVLVVGATGYIGKFVVRELVRRGYNVVAVAREKSGIRGKNGKEDTKKELPGAEVVFGDV 120
Query: 210 VDEKGCHEDIFEFASKADVVVCCLSLNKQTAGIVNKSFLSSMKKGSLLVNIARGGLLDYE 269
D + +F DVVV CL+ G V S+ +DY+
Sbjct: 121 TDADSLRKVLFSEGDPVDVVVSCLA---SRTGGVKDSW-----------------KIDYQ 160
Query: 270 AIAHYLECG 278
A + L+ G
Sbjct: 161 ATKNSLDAG 169
>gnl|CDD|214855 smart00851, MGS, MGS-like domain. This domain composes the whole
protein of methylglyoxal synthetase and the domain is
also found in Carbamoyl phosphate synthetase (CPS) where
it forms a regulatory domain that binds to the
allosteric effector ornithine. This family also includes
inosicase. The known structures in this family show a
common phosphate binding site.
Length = 91
Score = 27.8 bits (63), Expect = 2.1
Identities = 9/18 (50%), Positives = 12/18 (66%)
Query: 166 VELAKRLRPFGVKIIATK 183
VE AKRL G +++AT
Sbjct: 3 VEFAKRLAELGFELLATG 20
>gnl|CDD|187628 cd05370, SDR_c2, classical (c) SDR, subgroup 2. Short-chain
dehydrogenases/reductases (SDRs, aka Tyrosine-dependent
oxidoreductases) are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold (alpha/beta folding
pattern with a central beta-sheet), an NAD(P)(H)-binding
region, and a structurally diverse C-terminal region.
Classical SDRs are typically about 250 residues long,
while extended SDRs are approximately 350 residues.
Sequence identity between different SDR enzymes are
typically in the 15-30% range, but the enzymes share the
Rossmann fold NAD-binding motif and characteristic
NAD-binding and catalytic sequence patterns. These
enzymes catalyze a wide range of activities including
the metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 228
Score = 29.6 bits (67), Expect = 2.1
Identities = 14/36 (38%), Positives = 18/36 (50%), Gaps = 1/36 (2%)
Query: 151 LLGKTVFILG-FGNIGVELAKRLRPFGVKIIATKRS 185
L G TV I G IG+ LA++ G +I T R
Sbjct: 3 LTGNTVLITGGTSGIGLALARKFLEAGNTVIITGRR 38
>gnl|CDD|223364 COG0287, TyrA, Prephenate dehydrogenase [Amino acid transport and
metabolism].
Length = 279
Score = 29.6 bits (67), Expect = 2.2
Identities = 27/110 (24%), Positives = 53/110 (48%), Gaps = 17/110 (15%)
Query: 154 KTVFILGFGNIGVELAK--RLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVD 211
V I+G G +G LA+ + V+II RS A + A++ G+ID+L
Sbjct: 4 MKVGIVGLGLMGGSLARALKEAGLVVRIIGRDRSAA--------TLKAALELGVIDELTV 55
Query: 212 EKGCHEDIFEFASKADVVVCCLSLNKQTAGIVNKSFLSSMKKGSLLVNIA 261
+ E A++AD+V+ + + T ++ + +KKG+++ ++
Sbjct: 56 -----AGLAEAAAEADLVIVAVPIE-ATEEVLKELA-PHLKKGAIVTDVG 98
>gnl|CDD|129557 TIGR00465, ilvC, ketol-acid reductoisomerase. This is the second
enzyme in the parallel isoleucine-valine biosynthetic
pathway [Amino acid biosynthesis, Pyruvate family].
Length = 314
Score = 29.7 bits (67), Expect = 2.2
Identities = 26/110 (23%), Positives = 43/110 (39%), Gaps = 21/110 (19%)
Query: 151 LLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLV 210
L GKTV I+G+G+ G A LR G+ +I R + S A ++G
Sbjct: 1 LKGKTVAIIGYGSQGHAQALNLRDSGLNVIVGLRKGGA-------SWKKATEDG------ 47
Query: 211 DEKGCHE--DIFEFASKADVVVCCLSLNKQTAGIVNKSFLSSMKKGSLLV 258
+ + E +AD+++ L Q + +K+G L
Sbjct: 48 -----FKVGTVEEAIPQADLIMNLLPDEVQHE-VYEAEIQPLLKEGKTLG 91
>gnl|CDD|133449 cd05191, NAD_bind_amino_acid_DH, NAD(P) binding domain of amino
acid dehydrogenase-like proteins. Amino acid
dehydrogenase(DH)-like NAD(P)-binding domains are
members of the Rossmann fold superfamily and are found
in glutamate, leucine, and phenylalanine DHs (DHs),
methylene tetrahydrofolate DH,
methylene-tetrahydromethanopterin DH,
methylene-tetrahydropholate DH/cyclohydrolase, Shikimate
DH-like proteins, malate oxidoreductases, and glutamyl
tRNA reductase. Amino acid DHs catalyze the deamination
of amino acids to keto acids with NAD(P)+ as a cofactor.
The NAD(P)-binding Rossmann fold superfamily includes a
wide variety of protein families including NAD(P)-
binding domains of alcohol DHs, tyrosine-dependent
oxidoreductases, glyceraldehyde-3-phosphate DH,
lactate/malate DHs, formate/glycerate DHs, siroheme
synthases, 6-phosphogluconate DH, amino acid DHs,
repressor rex, NAD-binding potassium channel domain,
CoA-binding, and ornithine cyclodeaminase-like domains.
These domains have an alpha-beta-alpha configuration.
NAD binding involves numerous hydrogen and van der Waals
contacts.
Length = 86
Score = 27.7 bits (62), Expect = 2.5
Identities = 15/32 (46%), Positives = 20/32 (62%)
Query: 141 KKLGVPTGETLLGKTVFILGFGNIGVELAKRL 172
K G T ++L GKTV +LG G +G +AK L
Sbjct: 11 KAAGKVTNKSLKGKTVVVLGAGEVGKGIAKLL 42
>gnl|CDD|224996 COG2085, COG2085, Predicted dinucleotide-binding enzymes [General
function prediction only].
Length = 211
Score = 28.8 bits (65), Expect = 3.1
Identities = 12/27 (44%), Positives = 16/27 (59%)
Query: 154 KTVFILGFGNIGVELAKRLRPFGVKII 180
+ I+G GNIG LA RL G ++I
Sbjct: 2 MIIAIIGTGNIGSALALRLAKAGHEVI 28
>gnl|CDD|226476 COG3967, DltE, Short-chain dehydrogenase involved in D-alanine
esterification of lipoteichoic acid and wall teichoic
acid (D-alanine transfer protein) [Cell envelope
biogenesis, outer membrane].
Length = 245
Score = 28.9 bits (65), Expect = 3.2
Identities = 13/37 (35%), Positives = 18/37 (48%), Gaps = 1/37 (2%)
Query: 150 TLLGKTVFILGFGN-IGVELAKRLRPFGVKIIATKRS 185
G T+ I G + IG+ LAKR G +I R+
Sbjct: 2 KTTGNTILITGGASGIGLALAKRFLELGNTVIICGRN 38
>gnl|CDD|112609 pfam03804, DUF325, Viral domain of unknown function.
Length = 71
Score = 27.1 bits (60), Expect = 3.2
Identities = 12/34 (35%), Positives = 19/34 (55%), Gaps = 2/34 (5%)
Query: 208 DLVDEKGCHEDI--FEFASKADVVVCCLSLNKQT 239
L+D K H D+ F F + +V C+++N QT
Sbjct: 27 ALIDGKVTHADVRRFGFLDRNALVSACMAVNVQT 60
>gnl|CDD|223758 COG0686, Ald, Alanine dehydrogenase [Amino acid transport and
metabolism].
Length = 371
Score = 29.2 bits (66), Expect = 3.3
Identities = 14/46 (30%), Positives = 25/46 (54%), Gaps = 1/46 (2%)
Query: 217 EDIFEFASKADVVVCC-LSLNKQTAGIVNKSFLSSMKKGSLLVNIA 261
+I E KAD+V+ L + +V + + MK GS++V++A
Sbjct: 223 SNIEEAVKKADLVIGAVLIPGAKAPKLVTREMVKQMKPGSVIVDVA 268
>gnl|CDD|176166 cd08477, PBP2_CrgA_like_8, The C-terminal substrate binding
domain of an uncharacterized LysR-type transcriptional
regulator CrgA-like, contains the type 2 periplasmic
binding fold. This CD represents the substrate binding
domain of an uncharacterized LysR-type transcriptional
regulator (LTTR) CrgA-like 8. The LTTRs are acting as
both auto-repressors and activators of target
promoters, controlling operons involved in a wide
variety of cellular processes such as amino acid
biosynthesis, CO2 fixation, antibiotic resistance,
degradation of aromatic compounds, nodule formation of
nitrogen-fixing bacteria, and synthesis of virulence
factors, to name a few. In contrast to the tetrameric
form of other LTTRs, CrgA from Neisseria meningitides
assembles into an octameric ring, which can bind up to
four 63-bp DNA oligonucleotides. Phylogenetic cluster
analysis showed that the CrgA-like regulators form a
subclass of the LTTRs that function as octamers. The
CrgA is an auto-repressor of its own gene and activates
the expression of the mdaB gene which coding for an
NADPH-quinone reductase and that its action is
increased by MBL (alpha-methylene-gamma-butyrolactone),
an inducer of NADPH-quinone oxidoreductase. The
structural topology of this substrate-binding domain is
most similar to that of the type 2 periplasmic binding
proteins (PBP2), which are responsible for the uptake
of a variety of substrates such as phosphate, sulfate,
polysaccharides, lysine/arginine/ornithine, and
histidine. The PBP2 bind their ligand in the cleft
between these domains in a manner resembling a Venus
flytrap. After binding their specific ligand with high
affinity, they can interact with a cognate membrane
transport complex comprised of two integral membrane
domains and two cytoplasmically located ATPase domains.
This interaction triggers the ligand translocation
across the cytoplasmic membrane energized by ATP
hydrolysis.
Length = 197
Score = 28.7 bits (65), Expect = 3.3
Identities = 13/45 (28%), Positives = 23/45 (51%), Gaps = 1/45 (2%)
Query: 31 EYLQNYPSIQVDVVPISDVPDVIANYHLCVVKTMRL-DSNCISRA 74
EYL YP ++VD+V + D++ + L DS+ ++R
Sbjct: 22 EYLARYPDVRVDLVLSDRLVDLVEEGFDAAFRIGELADSSLVARP 66
>gnl|CDD|235554 PRK05673, dnaE, DNA polymerase III subunit alpha; Validated.
Length = 1135
Score = 29.3 bits (67), Expect = 3.4
Identities = 12/46 (26%), Positives = 24/46 (52%), Gaps = 10/46 (21%)
Query: 200 AVKN---GIIDDLVD---EKGCHEDIFEFASKADVVVCCLSLNKQT 239
A+K G ++ +V+ E G +D+F+F ++ D+ NK+
Sbjct: 824 AIKGVGEGAVEAIVEAREEGGPFKDLFDFCARVDLKKV----NKRV 865
>gnl|CDD|218507 pfam05221, AdoHcyase, S-adenosyl-L-homocysteine hydrolase.
Length = 430
Score = 29.3 bits (66), Expect = 3.6
Identities = 11/30 (36%), Positives = 17/30 (56%)
Query: 153 GKTVFILGFGNIGVELAKRLRPFGVKIIAT 182
GK + G+G++G A LR G ++I T
Sbjct: 210 GKVAVVCGYGDVGKGCAASLRGQGARVIVT 239
>gnl|CDD|235488 PRK05476, PRK05476, S-adenosyl-L-homocysteine hydrolase;
Provisional.
Length = 425
Score = 28.9 bits (66), Expect = 3.9
Identities = 18/48 (37%), Positives = 26/48 (54%), Gaps = 12/48 (25%)
Query: 147 TGETLL------------GKTVFILGFGNIGVELAKRLRPFGVKIIAT 182
TGE+LL GK V + G+G++G A+RLR G ++I T
Sbjct: 194 TGESLLDGIKRATNVLIAGKVVVVAGYGDVGKGCAQRLRGLGARVIVT 241
>gnl|CDD|182601 PRK10632, PRK10632, transcriptional regulator; Provisional.
Length = 309
Score = 29.0 bits (65), Expect = 4.1
Identities = 16/47 (34%), Positives = 26/47 (55%), Gaps = 1/47 (2%)
Query: 29 TKEYLQNYPSIQVDVVPISDVPDVIANYHLCVVKTMRL-DSNCISRA 74
T + L+ YP + V++V PD+IA+ V++ L DS+ SR
Sbjct: 111 TAKMLKEYPGLSVNLVTGIPAPDLIADGLDVVIRVGALQDSSLFSRR 157
>gnl|CDD|235660 PRK05976, PRK05976, dihydrolipoamide dehydrogenase; Validated.
Length = 472
Score = 28.7 bits (65), Expect = 4.6
Identities = 13/28 (46%), Positives = 19/28 (67%)
Query: 152 LGKTVFILGFGNIGVELAKRLRPFGVKI 179
L K++ I+G G IG+E A L FGV++
Sbjct: 179 LPKSLVIVGGGVIGLEWASMLADFGVEV 206
>gnl|CDD|182130 PRK09880, PRK09880, L-idonate 5-dehydrogenase; Provisional.
Length = 343
Score = 28.9 bits (65), Expect = 4.6
Identities = 26/104 (25%), Positives = 42/104 (40%), Gaps = 19/104 (18%)
Query: 151 LLGKTVFILGFGNIGVELAKRLRPFGVK-IIATKRSWASHSQVSCQSSALAVK------- 202
L GK VF+ G G IG + ++ G I+ + VS +S +LA +
Sbjct: 168 LQGKRVFVSGVGPIGCLIVAAVKTLGAAEIVC--------ADVSPRSLSLAREMGADKLV 219
Query: 203 ---NGIIDDLVDEKGCHEDIFEFASKADVVVCCLSLNKQTAGIV 243
N +D EKG + FE + + CL + + +V
Sbjct: 220 NPQNDDLDHYKAEKGYFDVSFEVSGHPSSINTCLEVTRAKGVMV 263
>gnl|CDD|119337 cd06569, GH20_Sm-chitobiase-like, The chitobiase of Serratia
marcescens is a beta-N-1,4-acetylhexosaminidase with a
glycosyl hydrolase family 20 (GH20) domain that
hydrolyzes the beta-1,4-glycosidic linkages in oligomers
derived from chitin. Chitin is degraded by a two step
process: i) a chitinase hydrolyzes the chitin to
oligosaccharides and disaccharides such as
di-N-acetyl-D-glucosamine and chitobiose, ii) chitobiase
then further degrades these oligomers into monomers. The
GH20 hexosaminidases are thought to act via a catalytic
mechanism in which the catalytic nucleophile is not
provided by solvent or the enzyme, but by the substrate
itself.
Length = 445
Score = 28.4 bits (64), Expect = 5.4
Identities = 11/27 (40%), Positives = 18/27 (66%), Gaps = 3/27 (11%)
Query: 316 EHSYRSMAKVVGDVALQLH--AGTPLT 340
+YR + KV+ ++A ++H AG PLT
Sbjct: 176 PSTYRFVDKVIDEIA-RMHQEAGQPLT 201
>gnl|CDD|223842 COG0771, MurD, UDP-N-acetylmuramoylalanine-D-glutamate ligase [Cell
envelope biogenesis, outer membrane].
Length = 448
Score = 28.4 bits (64), Expect = 5.6
Identities = 11/33 (33%), Positives = 16/33 (48%)
Query: 149 ETLLGKTVFILGFGNIGVELAKRLRPFGVKIIA 181
E GK V +LG G G+ A+ L G ++
Sbjct: 3 EDFQGKKVLVLGLGKSGLAAARFLLKLGAEVTV 35
>gnl|CDD|109716 pfam00670, AdoHcyase_NAD, S-adenosyl-L-homocysteine hydrolase, NAD
binding domain.
Length = 162
Score = 27.7 bits (62), Expect = 5.6
Identities = 10/30 (33%), Positives = 17/30 (56%)
Query: 153 GKTVFILGFGNIGVELAKRLRPFGVKIIAT 182
GK + G+G++G A L+ G ++I T
Sbjct: 23 GKVAVVCGYGDVGKGCAASLKGQGARVIVT 52
>gnl|CDD|187548 cd05237, UDP_invert_4-6DH_SDR_e, UDP-Glcnac (UDP-linked
N-acetylglucosamine) inverting 4,6-dehydratase, extended
(e) SDRs. UDP-Glcnac inverting 4,6-dehydratase was
identified in Helicobacter pylori as the hexameric flaA1
gene product (FlaA1). FlaA1 is hexameric, possesses
UDP-GlcNAc-inverting 4,6-dehydratase activity, and
catalyzes the first step in the creation of a
pseudaminic acid derivative in protein glycosylation.
Although this subgroup has the NADP-binding motif
characteristic of extended SDRs, its members tend to
have a Met substituted for the active site Tyr found in
most SDR families. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately 100
amino acids. Extended SDRs are a diverse collection of
proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 287
Score = 28.4 bits (64), Expect = 5.8
Identities = 14/42 (33%), Positives = 23/42 (54%), Gaps = 2/42 (4%)
Query: 153 GKTVFILG-FGNIGVELAKRLRPFGVK-IIATKRSWASHSQV 192
GKT+ + G G+IG EL +++ FG K +I R ++
Sbjct: 2 GKTILVTGGAGSIGSELVRQILKFGPKKLIVFDRDENKLHEL 43
>gnl|CDD|145687 pfam02665, Nitrate_red_gam, Nitrate reductase gamma subunit. This
family is the gamma subunit of the nitrate reductase
enzyme, the gamma subunit is a b-type cytochrome that
receives electrons from the quinone pool. It then
transfers these via the iron-sulfur clusters of the beta
subunit to the molybdenum cofactor found in the alpha
subunit. The nitrate reductase enzyme, EC:1.7.99.4
catalyzes the conversion of nitrite to nitrate via the
reduction of an acceptor. The nitrate reductase enzyme
is composed of three subunits. Nitrate is the most
widely used alternative electron acceptor after oxygen.
Length = 222
Score = 27.9 bits (63), Expect = 6.9
Identities = 16/53 (30%), Positives = 22/53 (41%), Gaps = 19/53 (35%)
Query: 278 GHLGGLGIDVAWTEPFDPNDPILKFKNVLITPHVGGVTEHSYRSMAKVVGDVA 330
GHL GL I +W E G++EH Y+ +A V G +A
Sbjct: 63 GHLVGLLIPHSWYEAL-------------------GISEHLYQLLAIVAGGIA 96
>gnl|CDD|240629 cd05304, Rubrum_tdh, Rubrum transdehydrogenase NAD-binding and
catalytic domains. Transhydrogenases found in bacterial
and inner mitochondrial membranes link
NAD(P)(H)-dependent redox reactions to proton
translocation. The energy of the proton electrochemical
gradient (delta-p), generated by the respiratory
electron transport chain, is consumed by
transhydrogenase in NAD(P)+ reduction. Transhydrogenase
is likely involved in the regulation of the citric acid
cycle. Rubrum transhydrogenase has 3 components, dI,
dII, and dIII. dII spans the membrane while dI and dIII
protrude on the cytoplasmic/matrix side. DI contains 2
domains in Rossmann-like folds, linked by a long alpha
helix, and contains a NAD binding site. Two dI
polypeptides (represented in this sub-family)
spontaneously form a heterotrimer with dIII in the
absence of dII. In the heterotrimer, both dI chains may
bind NAD, but only one is well-ordered. dIII also binds
a well-ordered NADP, but in a different orientation than
a classical Rossmann domain.
Length = 363
Score = 28.1 bits (64), Expect = 6.9
Identities = 16/56 (28%), Positives = 29/56 (51%), Gaps = 17/56 (30%)
Query: 219 IFEFASKADVVVCCLSLNKQTAGI--------VNKSFLSSMKKGSLLVNIA--RGG 264
+ + ++AD+V+ TA I + K + SMK GS++V++A +GG
Sbjct: 243 LAKHIAEADIVIT-------TALIPGRKAPKLITKEMVESMKPGSVIVDLAAEQGG 291
>gnl|CDD|223216 COG0138, PurH, AICAR transformylase/IMP cyclohydrolase PurH (only
IMP cyclohydrolase domain in Aful) [Nucleotide transport
and metabolism].
Length = 515
Score = 28.4 bits (64), Expect = 7.2
Identities = 9/17 (52%), Positives = 12/17 (70%)
Query: 166 VELAKRLRPFGVKIIAT 182
VE AK L GV+I++T
Sbjct: 16 VEFAKALVELGVEILST 32
>gnl|CDD|223536 COG0460, ThrA, Homoserine dehydrogenase [Amino acid transport and
metabolism].
Length = 333
Score = 27.9 bits (63), Expect = 7.2
Identities = 14/86 (16%), Positives = 29/86 (33%), Gaps = 19/86 (22%)
Query: 156 VFILGFGNIGVELAKRL--------RPFGVKIIATK---RSWASHSQVSCQSSALAVKNG 204
V +LG G +G + + L + G++I R + + ++ + +G
Sbjct: 6 VGLLGLGTVGSGVLEILAEKQEELRKRAGIEIRVVAVADRDGSLVRDLDLLNAEVWTTDG 65
Query: 205 IIDDLVDEKGCHEDIFEFASKADVVV 230
+ + DVVV
Sbjct: 66 ALSLGDE--------VLLDEDIDVVV 83
>gnl|CDD|130475 TIGR01408, Ube1, ubiquitin-activating enzyme E1. This model
represents the full length, over a thousand amino acids,
of a multicopy family of eukaryotic proteins, many of
which are designated ubiquitin-activating enzyme E1.
Members have two copies of the ThiF family domain
(pfam00899), a repeat found in ubiquitin-activating
proteins (pfam02134), and other regions.
Length = 1008
Score = 28.3 bits (63), Expect = 7.6
Identities = 14/36 (38%), Positives = 19/36 (52%)
Query: 143 LGVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVK 178
LG + + V I G G +G+E+AK L GVK
Sbjct: 14 LGDEAMQKMAKSNVLISGMGGLGLEIAKNLVLAGVK 49
>gnl|CDD|223450 COG0373, HemA, Glutamyl-tRNA reductase [Coenzyme metabolism].
Length = 414
Score = 28.0 bits (63), Expect = 7.9
Identities = 24/87 (27%), Positives = 39/87 (44%), Gaps = 14/87 (16%)
Query: 149 ETLLGKTVFILGFGNIGVELAKRLRPFGV-KIIATKRSWASHSQVSCQSSALAVKNGIID 207
+L K V ++G G +G +AK L GV KI R+ +++ + A AV
Sbjct: 174 GSLKDKKVLVIGAGEMGELVAKHLAEKGVKKITIANRTLERAEELAKKLGAEAVA----- 228
Query: 208 DLVDEKGCHEDIFEFASKADVVVCCLS 234
E++ E ++ADVV+ S
Sbjct: 229 --------LEELLEALAEADVVISSTS 247
>gnl|CDD|216899 pfam02142, MGS, MGS-like domain. This domain composes the whole
protein of methylglyoxal synthetase and the domain is
also found in Carbamoyl phosphate synthetase (CPS) where
it forms a regulatory domain that binds to the
allosteric effector ornithine. This family also includes
inosicase. The known structures in this family show a
common phosphate binding site.
Length = 92
Score = 26.3 bits (59), Expect = 8.0
Identities = 10/17 (58%), Positives = 11/17 (64%)
Query: 166 VELAKRLRPFGVKIIAT 182
VELAK L G K+ AT
Sbjct: 3 VELAKALVELGFKLYAT 19
>gnl|CDD|216527 pfam01488, Shikimate_DH, Shikimate / quinate 5-dehydrogenase. This
family contains both shikimate and quinate
dehydrogenases. Shikimate 5-dehydrogenase catalyzes the
conversion of shikimate to 5-dehydroshikimate. This
reaction is part of the shikimate pathway which is
involved in the biosynthesis of aromatic amino acids.
Quinate 5-dehydrogenase catalyzes the conversion of
quinate to 5-dehydroquinate. This reaction is part of
the quinate pathway where quinic acid is exploited as a
source of carbon in prokaryotes and microbial
eukaryotes. Both the shikimate and quinate pathways
share two common pathway metabolites 3-dehydroquinate
and dehydroshikimate.
Length = 133
Score = 26.9 bits (60), Expect = 9.1
Identities = 27/120 (22%), Positives = 48/120 (40%), Gaps = 23/120 (19%)
Query: 148 GETLLGKTVFILGFGNIGVELAKRLRPFGVK-IIATKRSWASHSQVSCQSSALAVKNGII 206
L GK V ++G G + AK L G K I R+ ++ LA + +
Sbjct: 7 FGDLKGKKVLLIGAGEMARLAAKHLLSKGAKKITIANRT-LEKAK------ELAEEFPVG 59
Query: 207 DDLVDEKGCHEDIFEFASKADVVVCCLSLNKQTAG---IVNKSFLSSMKKGS--LLVNIA 261
+ + +++ E ++AD+V+ T+ I+ K + K L V+IA
Sbjct: 60 GEALP----LDELEELLAEADIVISA------TSAPTPIITKEMVEEALKARPLLFVDIA 109
>gnl|CDD|219686 pfam07992, Pyr_redox_2, Pyridine nucleotide-disulphide
oxidoreductase. This family includes both class I and
class II oxidoreductases and also NADH oxidases and
peroxidases. This domain is actually a small NADH
binding domain within a larger FAD binding domain.
Length = 283
Score = 27.7 bits (62), Expect = 9.1
Identities = 12/29 (41%), Positives = 17/29 (58%)
Query: 152 LGKTVFILGFGNIGVELAKRLRPFGVKII 180
L K V ++G G IG+ELA L G ++
Sbjct: 141 LPKRVVVVGGGYIGLELAAALAKLGKEVT 169
>gnl|CDD|217563 pfam03446, NAD_binding_2, NAD binding domain of 6-phosphogluconate
dehydrogenase. The NAD binding domain of
6-phosphogluconate dehydrogenase adopts a Rossmann fold.
Length = 163
Score = 27.0 bits (61), Expect = 9.4
Identities = 12/55 (21%), Positives = 23/55 (41%), Gaps = 3/55 (5%)
Query: 207 DDLVDEKGC-HEDIFEFASKADVVVCCLSLNKQTAGIVN--KSFLSSMKKGSLLV 258
++LV E EF + ADVV+ + ++ L +K G +++
Sbjct: 37 EELVAEGAVGAASPAEFVASADVVITMVPAGAAVDAVILGEDGLLPGLKPGDIII 91
>gnl|CDD|224433 COG1516, FliS, Flagellin-specific chaperone FliS [Cell motility and
secretion / Intracellular trafficking and secretion /
Posttranslational modification, protein turnover,
chaperones].
Length = 132
Score = 26.9 bits (60), Expect = 9.5
Identities = 11/31 (35%), Positives = 16/31 (51%)
Query: 112 NAASCAELTIYLMLGLLRKQNEMRMAIEQKK 142
N AS +L + L G L+ + AIEQ+
Sbjct: 16 NTASPHKLILMLYEGALKFLKRAKEAIEQED 46
>gnl|CDD|233590 TIGR01830, 3oxo_ACP_reduc, 3-oxoacyl-(acyl-carrier-protein)
reductase. This model represents 3-oxoacyl-[ACP]
reductase, also called 3-ketoacyl-acyl carrier protein
reductase, an enzyme of fatty acid biosynthesis [Fatty
acid and phospholipid metabolism, Biosynthesis].
Length = 239
Score = 27.6 bits (62), Expect = 9.7
Identities = 28/95 (29%), Positives = 43/95 (45%), Gaps = 12/95 (12%)
Query: 164 IGVELAKRLRPFGVKIIATKRSWASHSQ-VSCQSSALAVKN-GIIDDLVDEKGCH---ED 218
IG +A +L G K+I T RS ++ V + A VK G++ D+ D + E+
Sbjct: 10 IGRAIALKLAKEGAKVIITYRSSEEGAEEVVEELKAYGVKALGVVCDVSDREDVKAVVEE 69
Query: 219 IFEFASKADVVVCCLSLNKQTAGIVNKSFLSSMKK 253
I E D++V AGI + L MK+
Sbjct: 70 IEEELGPIDILVN-------NAGITRDNLLMRMKE 97
>gnl|CDD|238709 cd01421, IMPCH, Inosine monophosphate cyclohydrolase domain. This
is the N-terminal domain in the purine biosynthesis
pathway protein ATIC (purH). The bifunctional ATIC
protein contains a C-terminal ATIC formylase domain
that formylates
5-aminoimidazole-4-carboxamide-ribonucleotide. The IMPCH
domain then converts the
formyl-5-aminoimidazole-4-carboxamide-ribonucleotide to
inosine monophosphate. This is the final step in de novo
purine production.
Length = 187
Score = 27.2 bits (61), Expect = 9.8
Identities = 9/17 (52%), Positives = 12/17 (70%)
Query: 166 VELAKRLRPFGVKIIAT 182
VE AK L GV+I++T
Sbjct: 14 VEFAKELVELGVEILST 30
>gnl|CDD|236106 PRK07818, PRK07818, dihydrolipoamide dehydrogenase; Reviewed.
Length = 466
Score = 27.7 bits (62), Expect = 9.9
Identities = 12/28 (42%), Positives = 18/28 (64%)
Query: 152 LGKTVFILGFGNIGVELAKRLRPFGVKI 179
L K++ I G G IG+E A L+ +GV +
Sbjct: 171 LPKSIVIAGAGAIGMEFAYVLKNYGVDV 198
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
0.321 0.137 0.409
Gapped
Lambda K H
0.267 0.0831 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 17,574,108
Number of extensions: 1698015
Number of successful extensions: 1977
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1826
Number of HSP's successfully gapped: 183
Length of query: 346
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 248
Effective length of database: 6,590,910
Effective search space: 1634545680
Effective search space used: 1634545680
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 59 (26.3 bits)