RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 017490
(370 letters)
>gnl|CDD|215501 PLN02928, PLN02928, oxidoreductase family protein.
Length = 347
Score = 612 bits (1579), Expect = 0.0
Identities = 242/348 (69%), Positives = 287/348 (82%), Gaps = 5/348 (1%)
Query: 23 SKMEGMARSSDKNITRVLFCGPHFPASHNYTKEYLQNYPSIQVDVVPISDVPDVIANYHL 82
K++ SD TRVLFCGP FPAS++YT+EYLQ YP IQVD V DVPDVIANY +
Sbjct: 5 VKIDKRVHHSDMRPTRVLFCGPEFPASYSYTREYLQKYPFIQVDAVAREDVPDVIANYDI 64
Query: 83 CVVKTMRLDSNCISRANQMKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAASCAE 142
CV K MRLD++ I+RA+QMKLIMQFGVGLEGVD++AAT+ GIKVARIP + TGNAASCAE
Sbjct: 65 CVPKMMRLDADIIARASQMKLIMQFGVGLEGVDVDAATKHGIKVARIPSEGTGNAASCAE 124
Query: 143 LTIYLMLGLLRKQNEMRMAIEQKKLGVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVK 202
+ IYLMLGLLRKQNEM+++++ ++LG P G+TL GKTVFILG+G IG+ELAKRLRPFGVK
Sbjct: 125 MAIYLMLGLLRKQNEMQISLKARRLGEPIGDTLFGKTVFILGYGAIGIELAKRLRPFGVK 184
Query: 203 IIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEKGCHEDIFEFASKADVVVCCLSLNKQ 262
++AT+RSW S + + NG +DDLVDEKG HEDI+EFA +AD+VV C +L K+
Sbjct: 185 LLATRRSWTSEPEDGLL-----IPNGDVDDLVDEKGGHEDIYEFAGEADIVVLCCTLTKE 239
Query: 263 TAGIVNKSFLSSMKKGSLLVNIARGGLLDYEAIAHYLECGHLGGLGIDVAWTEPFDPNDP 322
TAGIVN FLSSMKKG+LLVNIARGGLLDY+A+ LE GHLGGL IDVAW+EPFDP+DP
Sbjct: 240 TAGIVNDEFLSSMKKGALLVNIARGGLLDYDAVLAALESGHLGGLAIDVAWSEPFDPDDP 299
Query: 323 ILKFKNVLITPHVGGVTEHSYRSMAKVVGDVALQLHAGTPLTGLEFVN 370
ILK NV+ITPHV GVTE+SYRSM K+VGD ALQLHAG PLTG+EFVN
Sbjct: 300 ILKHPNVIITPHVAGVTEYSYRSMGKIVGDAALQLHAGRPLTGIEFVN 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 = 333 bits (856), Expect = e-114
Identities = 123/331 (37%), Positives = 181/331 (54%), Gaps = 25/331 (7%)
Query: 38 RVLFCGPHFPASHNYTKEYLQNYPSIQVDVVPISDVP-DVIANYHLCVVKTMR-LDSNCI 95
+VLF GP FP + + L P ++V D ++A+ + V + +D+ +
Sbjct: 1 KVLFLGPEFPDAEELLRALLPPAPGVEVVTAAELDEEAALLADADVLVPGMRKVIDAELL 60
Query: 96 SRANQMKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLMLGLLRKQ 155
+ A +++LI Q GVGL+GVD+ AAT GI VA IPG GNA S AE + LML LLR+
Sbjct: 61 AAAPRLRLIQQPGVGLDGVDLEAATARGIPVANIPG---GNAESVAEHAVMLMLALLRRL 117
Query: 156 NEMRMAIEQKKLGVPTGE---TLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWAS 212
E + + G P G L GKTV I+G GNIG +A+RLR FGV++I R
Sbjct: 118 PEADRELRAGRWGRPEGRPSRELSGKTVGIVGLGNIGRAVARRLRGFGVEVIYYDRFRDP 177
Query: 213 HSQVSCQSSALAVKNGIIDDLVDEKGCHEDIFEFASKADVVVCCLSLNKQTAGIVNKSFL 272
+ D + ++ E +++DVV + L +T ++ L
Sbjct: 178 -----------------EAEEKDLGVRYVELDELLAESDVVSLHVPLTPETRHLIGAEEL 220
Query: 273 SSMKKGSLLVNIARGGLLDYEAIAHYLECGHLGGLGIDVAWTEPFDPNDPILKFKNVLIT 332
++MK G++L+N ARGGL+D EA+ L GHL G G+DV W EP P+DP+L+ NV++T
Sbjct: 221 AAMKPGAILINTARGGLVDEEALLAALRSGHLAGAGLDVFWQEPLPPDDPLLRLDNVILT 280
Query: 333 PHVGGVTEHSYRSMAKVVGDVALQLHAGTPL 363
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 = 203 bits (518), Expect = 6e-63
Identities = 89/260 (34%), Positives = 140/260 (53%), Gaps = 26/260 (10%)
Query: 95 ISRANQMKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLMLGLLRK 154
+++A ++K I G G++ +D++AA + GI V +PG NA + AE + L+L LLR+
Sbjct: 58 LAKAPKLKFIQVAGAGVDNIDLDAAKKRGITVTNVPG---ANAEAVAEHALGLLLALLRR 114
Query: 155 ----QNEMRMAIEQKKLGVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSW 210
+R G P G L GKTV I+G G IG +AKRL+ FG+K++ R+
Sbjct: 115 LPRADAAVRRGWGWLWAGFP-GYELEGKTVGIVGLGRIGQRVAKRLQAFGMKVLYYDRT- 172
Query: 211 ASHSQVSCQSSALAVKNGIIDDLVDEKGCHEDIFEFASKADVVVCCLSLNKQTAGIVNKS 270
K +DL + E +++DVVV L L +T ++N+
Sbjct: 173 --------------RKPEPEEDLGFR---VVSLDELLAQSDVVVLHLPLTPETRHLINEE 215
Query: 271 FLSSMKKGSLLVNIARGGLLDYEAIAHYLECGHLGGLGIDVAWTEPFDPNDPILKFKNVL 330
L+ MK G++LVN ARGGL+D +A+ L+ G + G +DV EP + P+L+ NV+
Sbjct: 216 ELALMKPGAVLVNTARGGLVDEDALLRALKSGKIAGAALDVFEPEPLPADHPLLELPNVI 275
Query: 331 ITPHVGGVTEHSYRSMAKVV 350
+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 = 203 bits (519), Expect = 7e-63
Identities = 87/294 (29%), Positives = 144/294 (48%), Gaps = 30/294 (10%)
Query: 63 IQVDVVPISDVPDVIANYHLCVVKTMRLDSNCISRANQMKLIMQFGVGLEGVDINAATRC 122
+ ++ + +A+ +V + ++ A +K I + G G++ +D+ AAT+
Sbjct: 29 PDGPDLDEEELLEALADADALIVSVTPVTEEVLAAAPNLKAIGRAGAGVDNIDLEAATKR 88
Query: 123 GIKVARIPGDVTGNAASCAELTIYLMLGLLRK----QNEMRMAIEQKKLGVPTGETLLGK 178
GI V PG GNA S AEL + L+L L R+ R +K G L GK
Sbjct: 89 GILVVNAPG---GNAISVAELVLALLLALARRIPDADASQRRGEWDRKAF--RGTELAGK 143
Query: 179 TVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEKG 238
TV I+G G IG +AKRL+ FG+K+I + G
Sbjct: 144 TVGIIGLGRIGRAVAKRLKAFGMKVIGYDPY-------------------SPRERAGVDG 184
Query: 239 CH--EDIFEFASKADVVVCCLSLNKQTAGIVNKSFLSSMKKGSLLVNIARGGLLDYEAIA 296
+ + E ++AD++ L L +T G++N L+ MK G++L+N ARGG++D +A+
Sbjct: 185 VVGVDSLDELLAEADILTLHLPLTPETRGLINAEELAKMKPGAILINAARGGVVDEDALL 244
Query: 297 HYLECGHLGGLGIDVAWTEPFDPNDPILKFKNVLITPHVGGVTEHSYRSMAKVV 350
L+ G + G +DV EP + P+ NV++TPH+GG T+ + +A++V
Sbjct: 245 AALDSGKIAGAALDVFEEEPLPADSPLWDLPNVILTPHIGGSTDEAQERVAEIV 298
>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 = 197 bits (504), Expect = 7e-61
Identities = 84/254 (33%), Positives = 136/254 (53%), Gaps = 23/254 (9%)
Query: 95 ISRANQMKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLMLGLLRK 154
++ A ++K+I ++GVG + +D+ AA + GI V PG N+ S AELTI LML L R+
Sbjct: 63 LAAAPRLKVISRYGVGYDNIDLEAAKKRGIVVTNTPG---ANSNSVAELTIGLMLALARQ 119
Query: 155 QNEMRMAIEQKKLGVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHS 214
+ + P G L GKT+ I+G G IG +A+RL FG+K++A
Sbjct: 120 IPQADREVRAGGWDRPVGTELYGKTLGIIGLGRIGKAVARRLSGFGMKVLAYDPYP---- 175
Query: 215 QVSCQSSALAVKNGI-IDDLVDEKGCHEDIFEFASKADVVVCCLSLNKQTAGIVNKSFLS 273
A ++G+ L E++ + ++D + L L +T ++N + L+
Sbjct: 176 -----DEEFAKEHGVEFVSL-------EELLK---ESDFISLHLPLTPETRHLINAAELA 220
Query: 274 SMKKGSLLVNIARGGLLDYEAIAHYLECGHLGGLGIDVAWTEPFDPNDPILKFKNVLITP 333
MK G++L+N ARGGL+D EA+ L+ G + G +DV EP + P+L+ NV++TP
Sbjct: 221 LMKPGAILINTARGGLVDEEALYEALKSGRIAGAALDVFEEEPPPADSPLLELPNVILTP 280
Query: 334 HVGGVTEHSYRSMA 347
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 = 190 bits (486), Expect = 4e-58
Identities = 105/333 (31%), Positives = 162/333 (48%), Gaps = 45/333 (13%)
Query: 38 RVLFCGPHFPASHNYTKEYLQNYPSIQVDVVPISD---VPDVIANYHLCVVKTM-RLDSN 93
+VL P E L+ I+VDV P + +IA+ +V++ ++ +
Sbjct: 1 KVLVTDPIDEEGL----ELLREA-GIEVDVAPGLSEEELLAIIADADALIVRSATKVTAE 55
Query: 94 CISRANQMKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLMLGLLR 153
I A ++K+I + GVG++ +D+ AAT GI V PG N S AE TI LML L R
Sbjct: 56 VIEAAPRLKVIGRAGVGVDNIDVEAATARGILVVNAPG---ANTISVAEHTIALMLALAR 112
Query: 154 KQNEMRMAI-----EQKKLGVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKR 208
+ ++ ++KK G L GKT+ I+G G IG E+A+R R FG+K++A
Sbjct: 113 NIPQADASLRAGKWDRKKF---MGVELRGKTLGIVGLGRIGREVARRARAFGMKVLAYDP 169
Query: 209 SWASHSQVSCQSSALAVKNGIIDDLVDEKGCHE--DIFEFASKADVVVCCLSLNKQTAGI 266
I G E + E ++AD + L +T G+
Sbjct: 170 --------------------YISAERAAAGGVELVSLDELLAEADFISLHTPLTPETRGL 209
Query: 267 VNKSFLSSMKKGSLLVNIARGGLLDYEAIAHYLECGHLGGLGIDVAWTEPFDPNDPILKF 326
+N L+ MK G++L+N ARGG++D A+A L+ G + G +DV EP + P+L
Sbjct: 210 INAEELAKMKPGAILINTARGGIVDEAALADALKSGKIAGAALDVFEQEPPPADSPLLGL 269
Query: 327 KNVLITPHVGGVTEHSYRSMAKVVGDVALQLHA 359
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 = 190 bits (484), Expect = 1e-57
Identities = 84/298 (28%), Positives = 149/298 (50%), Gaps = 31/298 (10%)
Query: 63 IQVDVVPISDVPDVIANYH-LCVVKTMRLDSNCISRANQMKLIMQFGVGLEGVDINAATR 121
+ D+ P +++ + + + + R+D+ + + +KLI G + VD+ AA
Sbjct: 28 YEDDLTPDTELAERLKDADAVITFVNDRIDAEVLEKLPGLKLIATRSAGYDNVDLEAAKE 87
Query: 122 CGIKVARIPGDVTGNAASCAELTIYLMLGLLRK--QNEMRMA----IEQKKLGVPTGETL 175
GI V +PG T + AE + L+L L R+ + + R+ G L
Sbjct: 88 RGITVTNVPGYST---EAVAEHAVALILALARRIHEGDRRVREGNWSLSGGPDPLLGFDL 144
Query: 176 LGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVD 235
GKT+ I+G G IG +A+RL+ FG+K++ RS N + +
Sbjct: 145 RGKTLGIIGLGRIGQAVARRLKGFGMKVLYYDRS----------------PNPEAEKELG 188
Query: 236 EKGCHEDIFEFASKADVVVCCLSLNKQTAGIVNKSFLSSMKKGSLLVNIARGGLLDYEAI 295
+ + D+ E +++D++ L +T ++N L+ MK G++LVN ARGGL+D +A+
Sbjct: 189 AR--YVDLDELLAESDIISLHCPLTPETRHLINAEELAKMKPGAILVNTARGGLVDEQAL 246
Query: 296 AHYLECGHLGGLGIDVAWTEPFDPNDPILK---FKNVLITPHVGGVTEHSYRSMAKVV 350
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 = 178 bits (454), Expect = 2e-53
Identities = 88/325 (27%), Positives = 148/325 (45%), Gaps = 47/325 (14%)
Query: 60 YPSIQVDVVPISD--VPDVIANYHLCVVKTMRLDSNCISRANQMKLIMQFGVGLEGVDIN 117
+ +V + D + + + + V + + ++ ++KLI G++ + +
Sbjct: 19 LEGLYAEVPELPDEAAEEALEDADVLVGGRLTKEEA-LAALKRLKLIQVPSAGVDHLPL- 76
Query: 118 AATRCGIKVARIPGDVT-----GNAASCAELTIYLMLGLLRK----QNEMRMAI-EQKKL 167
R+P V GN+ + AE + L+L L ++ N++R I +
Sbjct: 77 ---------ERLPEGVVVANNHGNSPAVAEHALALILALAKRIVEYDNDLRRGIWHGRAG 127
Query: 168 GVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKN 227
P + L GKTV ILG+G+IG E+A+ L+ FG+++I RS
Sbjct: 128 EEPESKELRGKTVGILGYGHIGREIARLLKAFGMRVIGVSRS------------------ 169
Query: 228 GIIDDLVDEKGCHEDIFEFASKADVVVCCLSLNKQTAGIVNKSFLSSMKKGSLLVNIARG 287
D+ D G D+ E +ADVVV L L KQT G++ + L++MK G++LVN+ RG
Sbjct: 170 PKEDEGADFVGTLSDLDEALEQADVVVVALPLTKQTRGLIGAAELAAMKPGAILVNVGRG 229
Query: 288 GLLDYEAIAHYLECGHLGGLGIDVAWTEP------FDPNDPILKFKNVLITPHVGGVTEH 341
++D EA+ L+ + G IDV W P P + NV+++PH G TE
Sbjct: 230 PVVDEEALYEALKERPIAGAAIDVWWRYPSRGDPVAPSRYPFHELPNVIMSPHNAGWTEE 289
Query: 342 SYRSMAKVVGDVALQLHAGTPLTGL 366
++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 = 177 bits (451), Expect = 6e-53
Identities = 87/290 (30%), Positives = 133/290 (45%), Gaps = 37/290 (12%)
Query: 75 DVIANYHLCVVKTMRLDSNCISRANQMKLIMQFGV---GLEGVDINAATRCGIKVARIPG 131
+ + + + + + I A ++KLI GV G E VD+ AAT GI V PG
Sbjct: 42 EALKDADILITHFAPVTKKVIEAAPKLKLI---GVCRGGPENVDVEAATERGIPVLNTPG 98
Query: 132 DVTGNAASCAELTIYLMLGLLRK----QNEMRMAIEQKKL--GVPTGETLLGKTVFILGF 185
NA + AE T+ LML R ++ +K G L GKTV I+GF
Sbjct: 99 R---NAEAVAEFTVGLMLAETRNIARAHAALKDGEWRKDYYNYDGYGPELRGKTVGIVGF 155
Query: 186 GNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEKGCHEDIFE 245
G IG +AKRL+ FG +++ + I+ +K E++ +
Sbjct: 156 GAIGRRVAKRLKAFGAEVLVYD-PYVDPE--------------KIEADGVKKVSLEELLK 200
Query: 246 FASKADVVVCCLSLNKQTAGIVNKSFLSSMKKGSLLVNIARGGLLDYEAIAHYLECGHLG 305
++DVV L +T G++ + MK + +N AR GL+D +A+ LE G +G
Sbjct: 201 ---RSDVVSLHARLTPETRGMIGAEEFALMKPTAYFINTARAGLVDEDALIEALEEGKIG 257
Query: 306 GLGIDVAWTEPFDPNDPILKFKNVLITPHVGG----VTEHSYRSMAKVVG 351
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 (432), Expect = 9e-52
Identities = 62/195 (31%), Positives = 97/195 (49%), Gaps = 23/195 (11%)
Query: 145 IYLMLGLLRKQNEMRMAIEQKKL--GVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVK 202
+ L+L L R+ E + + G L GKTV I+G G IG +A+RL+ FG+K
Sbjct: 1 LALLLALARRIPEADRQVRAGRWRPDALLGRELSGKTVGIIGLGRIGRAVARRLKAFGMK 60
Query: 203 IIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEKGCH-EDIFEFASKADVVVCCLSLNK 261
+IA R + G + E +++DVV L L
Sbjct: 61 VIAYDRY--------------------PKAEAEALGARYVSLDELLAESDVVSLHLPLTP 100
Query: 262 QTAGIVNKSFLSSMKKGSLLVNIARGGLLDYEAIAHYLECGHLGGLGIDVAWTEPFDPND 321
+T ++N L+ MK G++L+N ARGGL+D +A+ L+ G + G +DV EP P+
Sbjct: 101 ETRHLINAERLALMKPGAILINTARGGLVDEDALIAALKSGRIAGAALDVFEPEPLPPDH 160
Query: 322 PILKFKNVLITPHVG 336
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 (441), Expect = 2e-51
Identities = 90/269 (33%), Positives = 138/269 (51%), Gaps = 24/269 (8%)
Query: 102 KLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLMLGLLRKQNEMRMA 161
KLI + G+G + VD+ AAT G+ V R+PG V + AE + L+L +LRK N+ A
Sbjct: 71 KLIARHGIGYDNVDLKAATEHGVIVTRVPGAV--ERDAVAEHAVALILTVLRKINQASEA 128
Query: 162 IEQKKLGVPT---GETLLGKTVFILGFGNIGVELAKRLRP-FGVKIIATKRSWASHSQVS 217
+++ K G L GKTV I+G+GNIG +A+ L+ F K++A +
Sbjct: 129 VKEGKWTERANFVGHELSGKTVGIIGYGNIGSRVAEILKEGFNAKVLAYDPYVSE----- 183
Query: 218 CQSSALAVKNGIIDDLVDEKGCHEDIFEFASKADVVVCCLSLNKQTAGIVNKSFLSSMKK 277
+ K L E++ ++D++ L ++T ++N+ S MKK
Sbjct: 184 ---EVIKKKGAKPVSL-------EELLA---ESDIISLHAPLTEETYHMINEKAFSKMKK 230
Query: 278 GSLLVNIARGGLLDYEAIAHYLECGHLGGLGIDVAWTEPFDPNDPILKFKNVLITPHVGG 337
G +LVN ARG L+D EA+ L+ G + G G+DV EP + P+L ++NV+ITPH+G
Sbjct: 231 GVILVNTARGELIDEEALIEALKSGKIAGAGLDVLEEEPIKADHPLLHYENVVITPHIGA 290
Query: 338 VTEHSYRSMAKVVGDVALQLHAGTPLTGL 366
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 = 171 bits (435), Expect = 2e-50
Identities = 80/274 (29%), Positives = 134/274 (48%), Gaps = 26/274 (9%)
Query: 82 LCVVKTMRLDSNCISRANQMKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAASCA 141
L T ++D+ + A +K+I + VG + +D++AA GI V P +T + A
Sbjct: 47 LLCTLTDKIDAELLDAAPPLKVIANYSVGYDHIDVDAAKARGIPVTNTPDVLT---DATA 103
Query: 142 ELTIYLMLGLLRKQNEM-RMAIEQKKLGV-PT---GETLLGKTVFILGFGNIGVELAKRL 196
+L L+L R+ E R + G PT G L GKT+ I+G G IG +A+R
Sbjct: 104 DLAFALLLAAARRVVEGDRFVRAGEWKGWSPTLLLGTDLHGKTLGIVGMGRIGQAVARRA 163
Query: 197 RPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEKGCHEDIFEFASKADVVVCC 256
+ FG+KI+ RS + L + + + E +++D V
Sbjct: 164 KGFGMKILYHNRS-----RKPEAEEELGAR-------------YVSLDELLAESDFVSLH 205
Query: 257 LSLNKQTAGIVNKSFLSSMKKGSLLVNIARGGLLDYEAIAHYLECGHLGGLGIDVAWTEP 316
L +T ++N L+ MK ++L+N ARGG++D +A+ L+ G + G G+DV EP
Sbjct: 206 CPLTPETRHLINAERLALMKPTAILINTARGGVVDEDALVEALKSGKIAGAGLDVFEPEP 265
Query: 317 FDPNDPILKFKNVLITPHVGGVTEHSYRSMAKVV 350
+ 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 (433), Expect = 3e-50
Identities = 75/324 (23%), Positives = 139/324 (42%), Gaps = 25/324 (7%)
Query: 45 HFPASHNYTKEYLQNYPSIQVDVVPISDVPDVIANYHLCVVKTMRLDSNCISRANQMKLI 104
P + + P ++ VV ++ + +A+ V+ + A +++ I
Sbjct: 6 LSPLDDEHLERLRAAAPGAELRVVTAEELTEELADAD--VLLGNPPLPELLPAAPRLRWI 63
Query: 105 MQFGVGLEGVDINAATRCGIKVARIPGDVTG-NAASCAELTIYLMLGLLRKQNEMRMAIE 163
G++ + + + G AE + ML RK
Sbjct: 64 QSTSAGVDALLFPELLERDVVLTN----ARGIFGPPIAEYVLGYMLAFARKLPRYARNQA 119
Query: 164 QKK-LGVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSA 222
+++ L GKTV I+G G+IG E+A+R + FG+++I +RS V
Sbjct: 120 ERRWQRRGPVRELAGKTVLIVGLGDIGREIARRAKAFGMRVIGVRRSGRPAPPV------ 173
Query: 223 LAVKNGIIDDLVDEKGCHEDIFEFASKADVVVCCLSLNKQTAGIVNKSFLSSMKKGSLLV 282
+D++ +++ E +AD VV L L +T G+ N ++MK G++L+
Sbjct: 174 -------VDEVYTP----DELDELLPEADYVVNALPLTPETRGLFNAERFAAMKPGAVLI 222
Query: 283 NIARGGLLDYEAIAHYLECGHLGGLGIDVAWTEPFDPNDPILKFKNVLITPHVGGVTEHS 342
N+ RG ++D +A+ LE G + G +DV EP + P+ NV+ITPH+ G +
Sbjct: 223 NVGRGSVVDEDALIEALESGRIAGAALDVFEEEPLPADSPLWDLPNVIITPHISGDSPSY 282
Query: 343 YRSMAKVVGDVALQLHAGTPLTGL 366
+ ++ + + 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 = 168 bits (429), Expect = 1e-49
Identities = 77/279 (27%), Positives = 129/279 (46%), Gaps = 38/279 (13%)
Query: 75 DVIANYHLCVVKTMRLDSNCISRANQMKLIMQFGVGLEGVDINAATRCGIKVARIPG--- 131
D + + + + I ++K+I+++GVG++ VD+ AAT GI V +P
Sbjct: 46 DALLVQYA------PVTAEVIEALPRLKVIVRYGVGVDNVDVAAATERGIPVCNVPDYCT 99
Query: 132 -DVTGNAASCAELTIYLMLGLLRKQNEMRMAIEQKKLGVPTGETLL---GKTVFILGFGN 187
+V A+ + L+L L RK + A+ G + G T+ ++GFG
Sbjct: 100 EEV-------ADHALALILALARKLPFLDRAVRAGGWDWTVGGPIRRLRGLTLGLVGFGR 152
Query: 188 IGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEKGCHEDIFEFA 247
IG +AKR + FG ++IA V +G+ +++
Sbjct: 153 IGRAVAKRAKAFGFRVIAYDPY---------------VPDGVAALGGVRVVSLDELLA-- 195
Query: 248 SKADVVVCCLSLNKQTAGIVNKSFLSSMKKGSLLVNIARGGLLDYEAIAHYLECGHLGGL 307
++DVV L +T +++ L+ MK G+ LVN ARGGL+D A+A L+ G + G
Sbjct: 196 -RSDVVSLHCPLTPETRHLIDAEALALMKPGAFLVNTARGGLVDEAALARALKSGRIAGA 254
Query: 308 GIDVAWTEPFDPNDPILKFKNVLITPHVGGVTEHSYRSM 346
+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 (424), Expect = 4e-49
Identities = 94/307 (30%), Positives = 152/307 (49%), Gaps = 35/307 (11%)
Query: 55 EYLQNYPSIQVDVVPISD---VPDVIANYHLCVVKT-MRLDSNCISRANQMKLIMQFGVG 110
E L+ +VD P+ + + I +Y + +V++ ++ I A +K+I + GVG
Sbjct: 15 EKLEE-AGFEVDYEPLIAKEELLEKIKDYDVLIVRSRTKVTKEVIDAAKNLKIIARAGVG 73
Query: 111 LEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLMLGLLRK----QNEMRMAI-EQK 165
L+ +D+ A + GIKV PG ++ S AEL I LML L R EM++ +K
Sbjct: 74 LDNIDVEYAKKKGIKVINTPG---ASSNSVAELVIGLMLSLARFIHRANREMKLGKWNKK 130
Query: 166 KLGVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAV 225
K G L GKT+ I+GFG IG E+AK R G+ +IA AV
Sbjct: 131 KY---KGIELRGKTLGIIGFGRIGREVAKIARALGMNVIAYDPY---------PKDEQAV 178
Query: 226 KNGIIDDLVDEKGCHEDIFEFASKADVVVCCLSLNKQTAGIVNKSFLSSMKKGSLLVNIA 285
+ G+ K + E +D + + L +T ++NK L MK G++++N +
Sbjct: 179 ELGV-------KTV--SLEELLKNSDFISLHVPLTPETKHMINKKELELMKDGAIIINTS 229
Query: 286 RGGLLDYEAIAHYLECGHLGGLGIDVAWTEPFDPNDPILKFKNVLITPHVGGVTEHSYRS 345
RGG++D EA+ L+ G L G +DV EP P +L+ NV +TPH+G T+ +
Sbjct: 230 RGGVIDEEALLEALKSGKLAGAALDVFENEP-PPGSKLLELPNVSLTPHIGASTKEAQER 288
Query: 346 MAKVVGD 352
+ + + +
Sbjct: 289 IGEELAN 295
>gnl|CDD|233358 TIGR01327, PGDH, D-3-phosphoglycerate dehydrogenase. This model
represents a long form of D-3-phosphoglycerate
dehydrogenase, the serA gene of one pathway of serine
biosynthesis. Shorter forms, scoring between trusted and
noise cutoff, include SerA from E. coli [Amino acid
biosynthesis, Serine family].
Length = 525
Score = 164 bits (417), Expect = 4e-46
Identities = 99/341 (29%), Positives = 163/341 (47%), Gaps = 46/341 (13%)
Query: 38 RVLFCGPHFPASHNYTKEYLQNYPSIQVDVVP-------ISDVPDVIANYHLCVVKTM-R 89
+VL P + L++ ++VDV + +PD Y +V++ +
Sbjct: 1 KVLIADP----ISPDGIDILED-VGVEVDVQTGLSREELLEIIPD----YDALIVRSATK 51
Query: 90 LDSNCISRANQMKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLML 149
+ I+ A ++K+I + GVG++ +DI AAT GI V P TGN S AE + ++L
Sbjct: 52 VTEEVIAAAPKLKVIGRAGVGVDNIDIEAATARGILVVNAP---TGNTISAAEHALAMLL 108
Query: 150 GLLRKQNEMRMAI-----EQKKLGVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVKII 204
R + ++ ++K G L GKT+ ++G G IG +AKR + FG+K++
Sbjct: 109 AAARNIPQADASLKEGEWDRKAF---MGTELYGKTLGVIGLGRIGSIVAKRAKAFGMKVL 165
Query: 205 ATKRSWASHSQVSCQSSALAVKNGIIDDLVDEKGCHEDIFEFASKADVVVCCLSLNKQTA 264
A S A + G+ LVD D+ E ++AD + L +T
Sbjct: 166 AYD---------PYISPERAEQLGVE--LVD------DLDELLARADFITVHTPLTPETR 208
Query: 265 GIVNKSFLSSMKKGSLLVNIARGGLLDYEAIAHYLECGHLGGLGIDVAWTEPFDPNDPIL 324
G++ L+ MKKG ++VN ARGG++D A+ LE GH+ +DV EP ++P+
Sbjct: 209 GLIGAEELAKMKKGVIIVNCARGGIIDEAALYEALEEGHVRAAALDVFEKEP-PTDNPLF 267
Query: 325 KFKNVLITPHVGGVTEHSYRSMAKVVGDVALQLHAGTPLTG 365
NV+ TPH+G T + ++A V + L G P+
Sbjct: 268 DLDNVIATPHLGASTREAQENVATQVAEQVLDALKGLPVPN 308
>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 (405), Expect = 5e-46
Identities = 76/252 (30%), Positives = 118/252 (46%), Gaps = 31/252 (12%)
Query: 102 KLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLMLGLLRKQNEMRMA 161
K+I G G + +D++A T+ GI+V+ PG V + A+ ++L+LG LR + +
Sbjct: 78 KIIAHAGAGYDQIDVDALTKRGIQVSNTPGAVD---EATADTALFLILGALRNFSRAERS 134
Query: 162 IEQKKLGVPTGETLL-------GKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHS 214
+ G G L GKT+ ILG G IG +A++ FG+KII RS
Sbjct: 135 A---RAGKWRGFLDLTLAHDPRGKTLGILGLGGIGKAIARKAAAFGMKIIYHNRSRLP-- 189
Query: 215 QVSCQSSALAVKNGIIDDLVDEKGCHEDIFEFASKADVVVCCLSLNKQTAGIVNKSFLSS 274
L + + E +++DVV L T ++NK +
Sbjct: 190 ------EELEKALATY---------YVSLDELLAQSDVVSLNCPLTAATRHLINKKEFAK 234
Query: 275 MKKGSLLVNIARGGLLDYEAIAHYLECGHLGGLGIDVAWTEPFDPNDPILKFKNVLITPH 334
MK G ++VN ARG ++D +A+ LE G + G+DV EP N +LK NV + PH
Sbjct: 235 MKDGVIIVNTARGAVIDEDALVDALESGKVASAGLDVFENEPE-VNPGLLKMPNVTLLPH 293
Query: 335 VGGVTEHSYRSM 346
+G +T + M
Sbjct: 294 MGTLTVETQEKM 305
>gnl|CDD|237436 PRK13581, PRK13581, D-3-phosphoglycerate dehydrogenase;
Provisional.
Length = 526
Score = 161 bits (411), Expect = 5e-45
Identities = 99/305 (32%), Positives = 154/305 (50%), Gaps = 54/305 (17%)
Query: 55 EYLQNYPSIQVDVVPISDVP---DVIANYHLCVVKTM-RLDSNCISRANQMKLIMQFGVG 110
E L++ P ++VDV D ++I +Y +V++ ++ + + A +K+I + GVG
Sbjct: 15 EILKDAPGVEVDVKTGLDKEELLEIIGDYDALIVRSATKVTAEVLEAAKNLKVIGRAGVG 74
Query: 111 LEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLMLGLLR---------KQNEMRMA 161
++ VD+ AATR GI V P TGN S AE TI LML L R K +
Sbjct: 75 VDNVDVPAATRRGIIVVNAP---TGNTISAAEHTIALMLALARNIPQAHASLKAGKW--- 128
Query: 162 IEQKKLGVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVKIIA------TKRSWASHSQ 215
E+KK G L GKT+ I+G G IG E+AKR + FG+K+IA +R
Sbjct: 129 -ERKKF---MGVELYGKTLGIIGLGRIGSEVAKRAKAFGMKVIAYDPYISPER------- 177
Query: 216 VSCQSSALAVKNGIIDDLVDEKGCHEDIFEFASKADVVVCCLSLNKQTAGIVNKSFLSSM 275
A + G+ +LV +++ +AD + L +T G++ L+ M
Sbjct: 178 --------AAQLGV--ELVS----LDELLA---RADFITLHTPLTPETRGLIGAEELAKM 220
Query: 276 KKGSLLVNIARGGLLDYEAIAHYLECGHLGGLGIDVAWTEPFDPNDPILKFKNVLITPHV 335
K G ++N ARGG++D A+A L+ G + G +DV EP + P+ + NV++TPH+
Sbjct: 221 KPGVRIINCARGGIIDEAALAEALKSGKVAGAALDVFEKEP-PTDSPLFELPNVVVTPHL 279
Query: 336 GGVTE 340
G T
Sbjct: 280 GASTA 284
>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 = 156 bits (396), Expect = 8e-45
Identities = 81/284 (28%), Positives = 127/284 (44%), Gaps = 26/284 (9%)
Query: 82 LCVVKTMRLDSNCISRANQMKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAASCA 141
L + +D I A +K+I +G G + +D++ A GI V P T A
Sbjct: 47 LITPLSTPVDKEIIDAAKNLKIIANYGAGFDNIDVDYAKEKGIPVTNTPAVST---EPTA 103
Query: 142 ELTIYLMLGLLRKQNEM-RMAIEQKKLGVP----TGETLLGKTVFILGFGNIGVELAKRL 196
ELT L+L L R+ E R+ LG G L GKT+ I+G G IG +A+R
Sbjct: 104 ELTFGLILALARRIAEGDRLMRRGGFLGWAPLFFLGHELAGKTLGIIGMGRIGQAVARRA 163
Query: 197 RPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEKGCHEDIFEFASKADVVVCC 256
+ FG+KI+ R H L +D+L+ ++D V
Sbjct: 164 KAFGMKILYYNR----HRLSEETEKELGATYVDLDELL-------------KESDFVSLH 206
Query: 257 LSLNKQTAGIVNKSFLSSMKKGSLLVNIARGGLLDYEAIAHYLECGHLGGLGIDVAWTEP 316
+T +++ + MK + L+N ARG L+D +A+ L+ G + G +DV EP
Sbjct: 207 APYTPETHHLIDAAAFKLMKPTAYLINAARGPLVDEKALVDALKTGEIAGAALDVFEFEP 266
Query: 317 FDPNDPILKFKNVLITPHVGGVTEHSYRSMAKVVGDVALQLHAG 360
+ + + K NV++TPH+G T + +MAK D + G
Sbjct: 267 -EVSPELKKLDNVILTPHIGNATVEARDAMAKEAADNIISFLEG 309
>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 = 153 bits (389), Expect = 6e-44
Identities = 89/280 (31%), Positives = 138/280 (49%), Gaps = 34/280 (12%)
Query: 84 VVKTMR----LDSNCISRANQMKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAAS 139
+ MR + + R +KL++ G+ +D+ AA GI V G T +
Sbjct: 49 AIVLMRERTPFPAALLERLPNLKLLVTTGMRNASIDLAAAKERGIVVCGTGGGPT----A 104
Query: 140 CAELTIYLMLGLLRK----QNEMRMAIEQKKLGVPTGETLLGKTVFILGFGNIGVELAKR 195
AELT L+L L R +R Q LG L GKT+ I+G G IG +A+
Sbjct: 105 TAELTWALILALARNLPEEDAALRAGGWQTTLGT----GLAGKTLGIVGLGRIGARVARI 160
Query: 196 LRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEKGCHEDIFEFASKADVVVC 255
+ FG+++IA W+S+ ++ + +A A G+ + K E++F +DVV
Sbjct: 161 GQAFGMRVIA----WSSN--LTAERAAAA---GV--EAAVSK---EELFA---TSDVVSL 203
Query: 256 CLSLNKQTAGIVNKSFLSSMKKGSLLVNIARGGLLDYEAIAHYLECGHLGGLGIDVAWTE 315
L L+ +T G+V L+ MK +LLVN +RG L+D A+ L G + G +DV E
Sbjct: 204 HLVLSDRTRGLVGAEDLALMKPTALLVNTSRGPLVDEGALLAALRAGRIAGAALDVFDVE 263
Query: 316 PFDPNDPILKFKNVLITPHVGGVTEHSYRSM-AKVVGDVA 354
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 = 150 bits (381), Expect = 9e-43
Identities = 77/267 (28%), Positives = 126/267 (47%), Gaps = 30/267 (11%)
Query: 88 MRLDSNCISRANQMKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYL 147
L + I+ ++LI FGVG +G+D++AA GI+V PG A+L + L
Sbjct: 52 TGLSAALIAALPALELIASFGVGYDGIDLDAARARGIRVTNTPGV---LTDDVADLAVGL 108
Query: 148 MLGLLRK--QNEMRMAIEQK--KLGVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVKI 203
+L +LR+ + R + K P + GK V I+G G IG +A+RL FG++I
Sbjct: 109 LLAVLRRIPAAD-RFVRAGRWPKGAFPLTRKVSGKRVGIVGLGRIGRAIARRLEAFGMEI 167
Query: 204 IATKRSWASHSQVSCQSSALAVKNGIIDDLVDEKGCHEDIFEFASKADVVVCCLSLNKQT 263
++ V + + + E A+++DV+V T
Sbjct: 168 -----AYHGRRPK---------------PDVPYR-YYASLLELAAESDVLVVACPGGPAT 206
Query: 264 AGIVNKSFLSSMKKGSLLVNIARGGLLDYEAIAHYLECGHLGGLGIDVAWTEPFDPNDPI 323
+VN L ++ +LVN+ARG ++D A+ L+ G + G G+DV EP P +
Sbjct: 207 RHLVNAEVLEALGPDGVLVNVARGSVVDEAALIAALQEGRIAGAGLDVFENEPNVP-AAL 265
Query: 324 LKFKNVLITPHVGGVTEHSYRSMAKVV 350
L NV++TPH+ T + R+M +V
Sbjct: 266 LDLDNVVLTPHIASATVETRRAMGDLV 292
>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 = 147 bits (372), Expect = 2e-41
Identities = 79/333 (23%), Positives = 133/333 (39%), Gaps = 40/333 (12%)
Query: 50 HNYTKEYLQNYPSIQV-DVVPISDVPDVIANYH-LCVVKTMRLDSNCISRANQMKLIMQF 107
E L+ ++V D + ++ + + L V T + + + A +K+I +
Sbjct: 8 RPEELELLKEGGEVEVHDELLTEELLEAAKDADALIVRSTTPVTAEVLEAAPGLKVIARR 67
Query: 108 GVGLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLMLGLLRKQNEMRMAIEQKKL 167
GVG++ +D++AAT GI V +PG + S AELT+ L+L L R+ E A +
Sbjct: 68 GVGVDNIDLDAATERGILVTNVPG---YSTESVAELTVGLILALARRIPE---ADASVRA 121
Query: 168 GV-----PTGETLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSA 222
G P G L GKT+ ++G G IG A + G+ ++
Sbjct: 122 GDWKKGGPIGLELYGKTLGVIGGGGIGGIGAAIAKALGMGVV------------------ 163
Query: 223 LAVKNGIIDDLVDEKGCHEDIFEFASKA-----DVVVCCLSLNKQTAGIVNKSFLSSMKK 277
A + +E G + + D++ +T I+ +K
Sbjct: 164 -AYDPYPNPERAEEGGVEVLLLDLLLLDLKESDDLINLAPPTTMKTGHIIINEARGMLKD 222
Query: 278 GSLLVNIARGGLLDYEAIAHYLECGHLGGLGIDVAWTEPFDPNDPILKFKNVLITPHVGG 337
+ N GG+++ A+ LE G V P N P+L NV++TPH+ G
Sbjct: 223 AVAINNARGGGVIEEAALDALLEEGIAAAALDVVEEEPP-PVNSPLLDLPNVILTPHIAG 281
Query: 338 VTEHSYRSMAKVVGDVALQLHAGTPLTGLEFVN 370
TE + +MA+ + L G VN
Sbjct: 282 ATEEAQENMAEEAAENLLAFLKGGTPPNA--VN 312
>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 (371), Expect = 3e-41
Identities = 77/257 (29%), Positives = 124/257 (48%), Gaps = 36/257 (14%)
Query: 89 RLDSNCISRANQMKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLM 148
LD+ +++ +KLI G VD+ AA GI V +PG T S A+ T L+
Sbjct: 54 VLDAEVLAQLPNLKLIGVLATGYNNVDLAAAKERGITVTNVPGYST---DSVAQHTFALL 110
Query: 149 LGLLRKQNEMRMAIEQKK---------LGVPTGETLLGKTVFILGFGNIGVELAKRLRPF 199
L L R ++ + P E L GKT+ I+G+GNIG +A+ R F
Sbjct: 111 LALARLVAYHNDVVKAGEWQKSPDFCFWDYPIIE-LAGKTLGIIGYGNIGQAVARIARAF 169
Query: 200 GVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEKGCHEDIFEFASKADVVVCCLSL 259
G+K++ +R + + V +++ ++DV+ L
Sbjct: 170 GMKVLFAERK---------------GAPPLREGYVS----LDELLA---QSDVISLHCPL 207
Query: 260 NKQTAGIVNKSFLSSMKKGSLLVNIARGGLLDYEAIAHYLECGHLGGLGIDVAWTEPFDP 319
+T ++N L+ MK G++L+N ARGGL+D +A+A L G + G G+DV EP
Sbjct: 208 TPETRNLINAEELAKMKPGAILINTARGGLVDEQALADALNSGKIAGAGLDVLSQEPPRA 267
Query: 320 NDPILKF-KNVLITPHV 335
++P+LK N++ITPH+
Sbjct: 268 DNPLLKAAPNLIITPHI 284
>gnl|CDD|183914 PRK13243, PRK13243, glyoxylate reductase; Reviewed.
Length = 333
Score = 143 bits (363), Expect = 7e-40
Identities = 86/292 (29%), Positives = 146/292 (50%), Gaps = 34/292 (11%)
Query: 68 VPISDVPDVIANYHLCVVKTMRLDSNCISRANQMKLIMQFGVGLEGVDINAATRCGIKVA 127
V + V DV A L + + R+D A +++++ + VG + +D+ ATR GI V
Sbjct: 38 VLLEKVRDVDA---LVTMLSERIDCEVFEAAPRLRIVANYAVGYDNIDVEEATRRGIYVT 94
Query: 128 RIPGDVTGNAASCAELTIYLMLGLLRKQNEMRMAI---EQKKLGVP------TGETLLGK 178
PG +T A A+ L+L R+ E + E K+ GV G + GK
Sbjct: 95 NTPGVLT-EAT--ADFAWALLLATARRLVEADHFVRSGEWKRRGVAWHPLMFLGYDVYGK 151
Query: 179 TVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEKG 238
T+ I+GFG IG +A+R + FG++I+ R+ ++ L + +++L+ E
Sbjct: 152 TIGIIGFGRIGQAVARRAKGFGMRILYYSRTRKPEAE-----KELGAEYRPLEELLRE-- 204
Query: 239 CHEDIFEFASKADVVVCCLSLNKQTAGIVNKSFLSSMKKGSLLVNIARGGLLDYEAIAHY 298
+D V + L K+T ++N+ L MK ++LVN ARG ++D +A+
Sbjct: 205 -----------SDFVSLHVPLTKETYHMINEERLKLMKPTAILVNTARGKVVDTKALVKA 253
Query: 299 LECGHLGGLGIDVAWTEPFDPNDPILKFKNVLITPHVGGVTEHSYRSMAKVV 350
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 = 142 bits (360), Expect = 2e-39
Identities = 95/295 (32%), Positives = 140/295 (47%), Gaps = 44/295 (14%)
Query: 76 VIANYHLCVVKTMRLDSNCISRANQMKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTG 135
+IAN M L I +K+I G++ VD+ A GI V+
Sbjct: 53 MIAN--------MPLPGEVIEACKNLKMISVAFTGVDHVDLEACKERGITVS-------- 96
Query: 136 NAA-----SCAELTIYLMLGLLRK--QNEMRMAIEQKKLGVPTGETLLGKTVFILGFGNI 188
NAA + AELTI L + LLR + + K G+ G L GKTV I+G G I
Sbjct: 97 NAAGYSTEAVAELTIGLAIDLLRNIVPCDAAVRAGGTKAGL-IGRELAGKTVGIVGTGAI 155
Query: 189 GVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEKGCHEDIFEFAS 248
G+ +A+ + FG K++A RS K ++ + + E +
Sbjct: 156 GLRVARLFKAFGCKVLAYSRS---------------EKEEAKALGIE----YVSLDELLA 196
Query: 249 KADVVVCCLSLNKQTAGIVNKSFLSSMKKGSLLVNIARGGLLDYEAIAHYLECGHLGGLG 308
++D+V L LN +T G++ K L+ MK+ ++L+N ARG ++D EA+A L G + G G
Sbjct: 197 ESDIVSLHLPLNDETKGLIGKEKLALMKESAILINTARGPVVDNEALADALNEGKIAGAG 256
Query: 309 IDVAWTEPFDPND-PILKFKNVLITPHVGGVTEHSYRSMAKVVGDVALQLHAGTP 362
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 = 139 bits (353), Expect = 1e-38
Identities = 93/314 (29%), Positives = 145/314 (46%), Gaps = 57/314 (18%)
Query: 63 IQVDVVPIS---DVPDVIANYHLCVVKT-MRLDSNCISRANQMKLIMQFGVGLEGVDINA 118
+VD P ++ +I Y ++++ +D I +A +K I + G GLE +D+
Sbjct: 21 FEVDYDPTISREEILAIIPQYDGLIIRSRFPIDKEFIEKATNLKFIARAGAGLENIDLEY 80
Query: 119 ATRCGIKVARIPGDVTGNAASCAELTIYLMLGLLRKQN----EMRMAI---EQKKLGVPT 171
A GI++ P GN + E + ++L L K N E+R I E +
Sbjct: 81 AKEKGIELFNAP---EGNRDAVGEHALGMLLALFNKLNRADQEVRNGIWDREGNR----- 132
Query: 172 GETLLGKTVFILGFGNIGVELAKRLRPFGVKIIA----TKRSWASHSQVSCQSSALAVKN 227
G L+GKTV I+G+GN+G AKRL FG K+IA A QVS
Sbjct: 133 GVELMGKTVGIIGYGNMGKAFAKRLSGFGCKVIAYDKYKNFGDAYAEQVSL--------- 183
Query: 228 GIIDDLVDEKGCHEDIFEFASKADVVVCCLSLNKQTAGIVNKSFLSSMKKGSLLVNIARG 287
E +F+ +AD++ + L +T G+VNK F+SS KK +N ARG
Sbjct: 184 -------------ETLFK---EADILSLHIPLTPETRGMVNKEFISSFKKPFYFINTARG 227
Query: 288 GLLDYEAIAHYLECGHLGGLGIDVAWTEPF----DPNDP-----ILKFKNVLITPHVGGV 338
++ + + L+ G + G +DV E N P ++K V++TPH+ G
Sbjct: 228 KVVVTKDLVKALKSGKILGACLDVLEYEKASFESIFNQPEAFEYLIKSPKVILTPHIAGW 287
Query: 339 TEHSYRSMAKVVGD 352
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 = 139 bits (352), Expect = 2e-38
Identities = 81/268 (30%), Positives = 120/268 (44%), Gaps = 32/268 (11%)
Query: 82 LCVVKTMRLDSNCISRANQMKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAASCA 141
L R+D++ + ++K+I G + D+ A T GI V +P +T A
Sbjct: 48 LMAFMPDRIDADFLDACPRLKIIACALKGYDNFDVEACTARGIWVTIVPDLLT---EPTA 104
Query: 142 ELTIYLMLGLLRKQNEMRMAIEQKKLG--VPT--GETLLGKTVFILGFGNIGVELAKRLR 197
ELTI L++GL R + K G P G L GKTV ILG G +G +A+RL
Sbjct: 105 ELTIGLLIGLGRHILAGDRFVRSGKFGGWRPKFYGTGLDGKTVGILGMGALGRAIARRLS 164
Query: 198 PFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEKGCHEDIFEFASKADVVVCCL 257
FG ++ + H + AL ++ +D+L+ +D +V L
Sbjct: 165 GFGATLLY----YDPHPLDQAEEQALNLRRVELDELL-------------ESSDFLVLAL 207
Query: 258 SLNKQTAGIVNKSFLSSMKKGSLLVNIARGGLLDYEAIAHYLECGHLGGLGIDVAWTE-- 315
L T ++N L+ MK G+LLVN RG ++D A+A L+ GHLGG DV E
Sbjct: 208 PLTPDTLHLINAEALAKMKPGALLVNPCRGSVVDEAAVAEALKSGHLGGYAADVFEMEDW 267
Query: 316 -----PFDPNDPILKFK-NVLITPHVGG 337
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 = 138 bits (351), Expect = 2e-38
Identities = 73/231 (31%), Positives = 100/231 (43%), Gaps = 19/231 (8%)
Query: 137 AASCAELTIYLMLGLLRKQNEMRMAIE-QKKLGVPTGETLLGKTVFILGFGNIGVELAKR 195
A + AE + L+L LR+ A L G TV I+G G IG L
Sbjct: 84 AETVAEHALALLLAGLRQLPARARATTWDPAEEDDLVTLLRGSTVAIVGAGGIGRALIPL 143
Query: 196 LRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEKGCHEDIFEFASKADVVVC 255
L PFG K+IA RS G + DE + + E AD VV
Sbjct: 144 LAPFGAKVIAVNRS------------------GRPVEGADETVPADRLDEVWPDADHVVL 185
Query: 256 CLSLNKQTAGIVNKSFLSSMKKGSLLVNIARGGLLDYEAIAHYLECGHLGGLGIDVAWTE 315
L +T +V+ + L++MK + LVN+ARG L+D +A+ L G + G +DV E
Sbjct: 186 AAPLTPETRHLVDAAALAAMKPHAWLVNVARGPLVDTDALVDALRSGEIAGAALDVTDPE 245
Query: 316 PFDPNDPILKFKNVLITPHVGGVTEHSYRSMAKVVGDVALQLHAGTPLTGL 366
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 (348), Expect = 2e-37
Identities = 88/253 (34%), Positives = 127/253 (50%), Gaps = 31/253 (12%)
Query: 95 ISRANQMKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTG-NAASCAELTIYLMLGLLR 153
I++A +KL + G+G + VD+ AA GI VA +VTG N S AE + ++L L+R
Sbjct: 79 IAKAKNLKLALTAGIGSDHVDLQAANDRGITVA----EVTGSNVVSVAEHVVMMILILVR 134
Query: 154 K-QNEMRMAIEQK----KLGVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKR 208
AIE + + L GKTV +G G IG+ + +RL+PF V ++ R
Sbjct: 135 NYVPGHEQAIEGGWNVADVVKRAYD-LEGKTVGTVGAGRIGLRVLRRLKPFDVHLLYYDR 193
Query: 209 SWASHSQVSCQSSALAVKNGIIDDLVDEKGC--HEDIFEFASKADVVVCCLSLNKQTAGI 266
+ + +++ E G H D+ + SK DVV L+ +T G+
Sbjct: 194 ------------------HRLPEEVEKELGLTRHADLEDMVSKCDVVTINCPLHPETEGL 235
Query: 267 VNKSFLSSMKKGSLLVNIARGGLLDYEAIAHYLECGHLGGLGIDVAWTEPFDPNDPILKF 326
NK LS MKKG+ LVN ARG + D EA+A LE GHL G DV + +P + P
Sbjct: 236 FNKELLSKMKKGAYLVNTARGKICDREAVAEALESGHLAGYAGDVWFPQPAPKDHPWRTM 295
Query: 327 KNVLITPHVGGVT 339
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 = 133 bits (338), Expect = 2e-36
Identities = 76/269 (28%), Positives = 125/269 (46%), Gaps = 41/269 (15%)
Query: 98 ANQMKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLMLGLLRK--- 154
A +K I + G G+ +D++AA++ GI V PG NA + AEL I +ML L R
Sbjct: 48 APSLKAIARAGAGVNNIDVDAASKRGIVVFNTPG---ANANAVAELVIAMMLALSRNIIQ 104
Query: 155 ---------QNEMRMAIEQKKLGVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVKIIA 205
+++ +E+ K E L GKT+ ++G GNIG +A G+K+I
Sbjct: 105 AIKWVTNGDGDDISKGVEKGKKQFVGTE-LRGKTLGVIGLGNIGRLVANAALALGMKVIG 163
Query: 206 TKRSWASHSQVSCQSSALAVKNGII--DDLVDEKGCHEDIFEFASKADVVVCCLSLNKQT 263
+S ++ A + + L E++ + AD + + L +T
Sbjct: 164 YDPY------LSVEA-AWKLSVEVQRVTSL-------EELL---ATADYITLHVPLTDET 206
Query: 264 AGIVNKSFLSSMKKGSLLVNIARGGLLDYEAIAHYLECGHLGGLGIDVAWTEPFDPNDPI 323
G++N L+ MK G++L+N ARG ++D EA+ L+ G LGG + F +
Sbjct: 207 RGLINAELLAKMKPGAILLNFARGEIVDEEALLEALDEGKLGG-YVTD-----FPEPALL 260
Query: 324 LKFKNVLITPHVGGVTEHSYRSMAKVVGD 352
NV+ TPH+G TE + + A +
Sbjct: 261 GHLPNVIATPHLGASTEEAEENCAVMAAR 289
>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 = 134 bits (339), Expect = 2e-36
Identities = 76/252 (30%), Positives = 115/252 (45%), Gaps = 26/252 (10%)
Query: 118 AATRCGIKVARIPGDVTGNAASCAELTIYLMLGLLRKQNEMRMAIEQ-KKLGVPT---GE 173
A GI V D NA AE T+ +L LR+ A + G PT G
Sbjct: 90 AVWERGILVTS-AADA--NAEPVAEFTLAAILLALRRIPRFAAAYRAGRDWGWPTRRGGR 146
Query: 174 TLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDL 233
L G+TV I+GFG IG + + LRPFG++++ + ++ + AL V
Sbjct: 147 GLYGRTVGIVGFGRIGRAVVELLRPFGLRVLVYDP-YLPAAEAA----ALGV-------- 193
Query: 234 VDEKGCHEDIFEFASKADVVVCCLSLNKQTAGIVNKSFLSSMKKGSLLVNIARGGLLDYE 293
E +++ +++DVV L +T G+++ L+ M+ G+ +N ARG L+D
Sbjct: 194 --ELVSLDELL---ARSDVVSLHAPLTPETRGMIDARLLALMRDGATFINTARGALVDEA 248
Query: 294 AIAHYLECGHLGGLGIDVAWTEPFDPNDPILKFKNVLITPHVGGVTEHSYRSMAKVVGDV 353
A+ L G L +DV EP P+ P+ NVL+TPH+ G T R + D
Sbjct: 249 ALLAELRSGRLRAA-LDVTDPEPLPPDSPLRTLPNVLLTPHIAGSTGDERRRLGDYALDE 307
Query: 354 ALQLHAGTPLTG 365
+ 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 = 133 bits (336), Expect = 3e-36
Identities = 78/248 (31%), Positives = 111/248 (44%), Gaps = 36/248 (14%)
Query: 126 VARIPGDVT-GNA-----ASCAELTIYLMLGLLRKQNEMRMAIEQKKLGVPTGETLLGKT 179
+ +P VT NA AS AEL + L+L LR A + + +L +
Sbjct: 75 LPLLPEGVTLCNARGVHDASTAELAVALILASLRGLPRFVRAQARGRWEPRRTPSLADRR 134
Query: 180 VFILGFGNIGVELAKRLRPFGVKIIATKRS----WASHSQVSCQSSALAVKNGIIDDLVD 235
V I+G+G+IG + +RL PF V++ R+ H ID+L
Sbjct: 135 VLIVGYGSIGRAIERRLAPFEVRVTRVARTARPGEQVHG---------------IDELP- 178
Query: 236 EKGCHEDIFEFASKADVVVCCLSLNKQTAGIVNKSFLSSMKKGSLLVNIARGGLLDYEAI 295
+ADVVV + L +T G+V+ FL+ M G+LLVN+ARG ++D +A+
Sbjct: 179 ---------ALLPEADVVVLIVPLTDETRGLVDAEFLARMPDGALLVNVARGPVVDTDAL 229
Query: 296 AHYLECGHLGGLGIDVAWTEPFDPNDPILKFKNVLITPHVGGVTEHSYRSMAKVVGDVAL 355
L G L +DV EP P P+ VLITPHVGG T +V
Sbjct: 230 VAELASGRL-RAALDVTDPEPLPPGHPLWSAPGVLITPHVGGATPAFLPRAYALVRRQLR 288
Query: 356 QLHAGTPL 363
+ AG PL
Sbjct: 289 RYAAGEPL 296
>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 (335), Expect = 6e-36
Identities = 79/339 (23%), Positives = 137/339 (40%), Gaps = 60/339 (17%)
Query: 37 TRVLFCGPHFPASHNYTKEYLQNYPSIQVDVVPISDVPDVIANYHL-------CVVKTMR 89
+VL + KE L+ VDV ++ + + L T +
Sbjct: 1 MKVLIYD-YRDDELEIEKEILKAGG---VDVEIVTYLLNDDETAELAKGADAILTAFTDK 56
Query: 90 LDSNCISRANQMKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLML 149
+D+ + +A +K I G + +D++ A GI V +P + AE TI L+L
Sbjct: 57 IDAELLDKAPGLKFISLRATGYDNIDLDYAKELGIGVTNVPEYSPN---AVAEHTIALIL 113
Query: 150 GLLRKQ--NEMRMAIEQKKLGVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVKIIATK 207
LLR + + R + + G L +TV ++G G IG +A+R + FG+K+IA
Sbjct: 114 ALLRNRKYIDERDKNQDLQDAGVIGRELEDQTVGVVGTGKIGRAVAQRAKGFGMKVIAY- 172
Query: 208 RSWASHSQVSCQSSALAVKNGIIDDLVDEKGCHEDIFEFASK------ADVVVCCLSLNK 261
D + ++ S +D++ + L
Sbjct: 173 ------------------------DPFRNPELEDKGVKYVSLEELFKNSDIISLHVPLTP 208
Query: 262 QTAGIVNKSFLSSMKKGSLLVNIARGGLLDYEAIAHYLECGHLGGLGIDVAWTE------ 315
+ ++N+ MKKG +++N ARG L+D EA+ L+ G + G G+DV E
Sbjct: 209 ENHHMINEEAFKLMKKGVIIINTARGSLVDTEALIEALDSGKIFGAGLDVLEDETPDLLK 268
Query: 316 -------PFDPNDPILKFKNVLITPHVGGVTEHSYRSMA 347
N + + NV+ITPH T+ + ++M
Sbjct: 269 DLEGEIFKDALNALLGRRPNVIITPHTAFYTDDALKNMV 307
>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 = 129 bits (327), Expect = 9e-35
Identities = 71/253 (28%), Positives = 125/253 (49%), Gaps = 32/253 (12%)
Query: 95 ISRANQMKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLMLGLLRK 154
+++ +K I + G++ + + + GI + G ++ AE + +L + +
Sbjct: 55 LAKMKNLKWIQLYSAGVDYLPLEYIKKKGILLTNNSG---IHSIPIAEWIVGYILEIYKG 111
Query: 155 QNEMRMAIEQKK----LGVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSW 210
++ A + +K + L GKT+ LG G+IG E+AKRL+ FG+K+I S
Sbjct: 112 ---LKKAYKNQKEKKWKMDSSLLELYGKTILFLGTGSIGQEIAKRLKAFGMKVIGVNTS- 167
Query: 211 ASHSQVSCQSSALAVKNGIIDDLVDEKGCH--EDIFEFASKADVVVCCLSLNKQTAGIVN 268
G + D+ C+ E++ E +AD+VV L L ++T + +
Sbjct: 168 -----------------GRDVEYFDK--CYPLEELDEVLKEADIVVNVLPLTEETHHLFD 208
Query: 269 KSFLSSMKKGSLLVNIARGGLLDYEAIAHYLECGHLGGLGIDVAWTEPFDPNDPILKFKN 328
++F MKKG+L +N+ RG +D +A+ L+ + G +DV EP + P+ N
Sbjct: 209 EAFFEQMKKGALFINVGRGPSVDEDALIEALKNKQIRGAALDVFEEEPLPKDSPLWDLDN 268
Query: 329 VLITPHVGGVTEH 341
VLITPH+ GV+EH
Sbjct: 269 VLITPHISGVSEH 281
>gnl|CDD|178684 PLN03139, PLN03139, formate dehydrogenase; Provisional.
Length = 386
Score = 121 bits (306), Expect = 2e-31
Identities = 82/252 (32%), Positives = 121/252 (48%), Gaps = 29/252 (11%)
Query: 95 ISRANQMKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTG-NAASCAELTIYLMLGLLR 153
I +A ++L++ G+G + +D+ AA G+ VA +VTG N S AE + +L LLR
Sbjct: 116 IKKAKNLELLLTAGIGSDHIDLPAAAAAGLTVA----EVTGSNVVSVAEDELMRILILLR 171
Query: 154 K-QNEMRMAI--EQKKLGVPT-GETLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRS 209
+ E G+ L GKTV +G G IG L +RL+PF ++ R
Sbjct: 172 NFLPGYHQVVSGEWNVAGIAYRAYDLEGKTVGTVGAGRIGRLLLQRLKPFNCNLLYHDR- 230
Query: 210 WASHSQVSCQSSALAVKNGIIDDLVDEKGC--HEDIFEFASKADVVVCCLSLNKQTAGIV 267
+ +L E G ED+ K DVVV L ++T G+
Sbjct: 231 -----------------LKMDPELEKETGAKFEEDLDAMLPKCDVVVINTPLTEKTRGMF 273
Query: 268 NKSFLSSMKKGSLLVNIARGGLLDYEAIAHYLECGHLGGLGIDVAWTEPFDPNDPILKFK 327
NK ++ MKKG L+VN ARG ++D +A+A GH+GG G DV + +P + P
Sbjct: 274 NKERIAKMKKGVLIVNNARGAIMDTQAVADACSSGHIGGYGGDVWYPQPAPKDHPWRYMP 333
Query: 328 NVLITPHVGGVT 339
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 = 1e-30
Identities = 78/281 (27%), Positives = 126/281 (44%), Gaps = 51/281 (18%)
Query: 82 LCVVKTMRLDSNCISRANQMKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAASCA 141
+ V RLD+ + + ++KLI G + +D+ A GI V +P G A + A
Sbjct: 45 ISVFVYSRLDAEVLEKLPRLKLIATRSTGFDHIDLEACRERGIAVCNVPD--YGEA-TVA 101
Query: 142 ELTIYLMLGLLRKQNEM-----RMAIEQKKLGVPTGETLLGKTVFILGFGNIGVELAKRL 196
E L+L L RK E R Q L G L GKT+ ++G G IG +A+
Sbjct: 102 EHAFALLLALSRKLREAIERTRRGDFSQAGL---RGFELAGKTLGVVGTGRIGRRVARIA 158
Query: 197 RPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEKGC-HEDIFEFASKADVVVC 255
R FG+K++A V + ++L + G + + E ++D++
Sbjct: 159 RGFGMKVLAYDV----------------VPD---EELAERLGFRYVSLEELLQESDIISL 199
Query: 256 CLSLNKQTAGIVNKSFLSSMKKGSLLVNIARGGLLDYEAIAHYLECGHLGGLGIDV---- 311
+ QT ++N+ + MK G++L+N ARG ++D EA+ L+ G L G G+DV
Sbjct: 200 HVPYTPQTHHLINRENFALMKPGAVLINTARGAVVDTEALVRALKEGKLAGAGLDVLEQE 259
Query: 312 --------AWTEPFDP--------NDPILKFKNVLITPHVG 336
+ E P + +L+ NV+ITPHV
Sbjct: 260 EVLREEAELFREDVSPEDLKKLLADHALLRKPNVIITPHVA 300
>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 = 116 bits (292), Expect = 8e-30
Identities = 84/298 (28%), Positives = 136/298 (45%), Gaps = 52/298 (17%)
Query: 63 IQVDVVPIS----DVPDVIANYHLCVV--KTMRLDSNCISRANQMKLIMQFGVGLEGVDI 116
I+V+ + + ++ + + + HL + KT +L + A ++ I F +G VD+
Sbjct: 22 IEVERLKGALDEDELIEALKDVHLLGIRSKT-QLTEEVLEAAPKLLAIGCFCIGTNQVDL 80
Query: 117 NAATRCGIKVARIPGDVTGNAASCAELTIYLMLGLLR----KQNEMRMAIEQKKLGVPTG 172
+AA + GI V P N S AEL I ++ L R + I K TG
Sbjct: 81 DAAAKRGIPVFNAP---FSNTRSVAELVIGEIIMLARRLPDRNAAAHRGIWNK---SATG 134
Query: 173 --ETLLGKTVFILGFGNIGVELAKRLRPFGVKI----IATKRSWASHSQVSCQSSALAVK 226
E + GKT+ I+G+G+IG +L+ G+++ IA K + QVS LA
Sbjct: 135 SHE-VRGKTLGIIGYGHIGSQLSVLAEALGMRVIFYDIAEKLPLGNARQVSSLEELLA-- 191
Query: 227 NGIIDDLVDEKGCHEDIFEFASKADVVVCCLSLNKQTAGIVNKSFLSSMKKGSLLVNIAR 286
+AD V + T ++ ++ MKKG++L+N +R
Sbjct: 192 ----------------------EADFVTLHVPATPSTKNMIGAEEIAQMKKGAILINASR 229
Query: 287 GGLLDYEAIAHYLECGHLGGLGIDVAWTEPFDPND----PILKFKNVLITPHVGGVTE 340
G ++D +A+A L GHL G +DV EP + P+ NV++TPH+GG TE
Sbjct: 230 GTVVDIDALAEALRSGHLAGAAVDVFPEEPASNGEPFSSPLQGLPNVILTPHIGGSTE 287
>gnl|CDD|181041 PRK07574, PRK07574, formate dehydrogenase; Provisional.
Length = 385
Score = 117 bits (295), Expect = 1e-29
Identities = 82/253 (32%), Positives = 118/253 (46%), Gaps = 31/253 (12%)
Query: 95 ISRANQMKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTG-NAASCAELTIYLMLGLLR 153
I++A +KL + G+G + VD+ AA+ GI VA +VTG N+ S AE + ++L L+R
Sbjct: 109 IAKAPNLKLAITAGIGSDHVDLQAASEHGITVA----EVTGSNSISVAEHVVMMILALVR 164
Query: 154 KQNEMRMAIEQKKLG-------VPTGETLLGKTVFILGFGNIGVELAKRLRPFGVKIIAT 206
+ Q G V L G TV I+G G IG+ + +RL+PF VK+ T
Sbjct: 165 NYEP---SHRQAVEGGWNIADCVSRSYDLEGMTVGIVGAGRIGLAVLRRLKPFDVKLHYT 221
Query: 207 KRSWASHSQVSCQSSALAVKNGIIDDLVDEKGCHEDIFEFASKADVVVCCLSLNKQTAGI 266
R H L + H S DVV L+ +T +
Sbjct: 222 DR----HRLPEEVEQELGLTY------------HVSFDSLVSVCDVVTIHCPLHPETEHL 265
Query: 267 VNKSFLSSMKKGSLLVNIARGGLLDYEAIAHYLECGHLGGLGIDVAWTEPFDPNDPILKF 326
+ LS MK+GS LVN ARG ++D +A+ LE GHL G DV + +P + P
Sbjct: 266 FDADVLSRMKRGSYLVNTARGKIVDRDAVVRALESGHLAGYAGDVWFPQPAPADHPWRTM 325
Query: 327 KNVLITPHVGGVT 339
+TPH+ G T
Sbjct: 326 PRNGMTPHISGTT 338
>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 (289), Expect = 2e-29
Identities = 71/271 (26%), Positives = 112/271 (41%), Gaps = 35/271 (12%)
Query: 102 KLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLMLGLLRKQNEMRMA 161
K I G G++ + + + + R+ G A AE Y++ +LR +M
Sbjct: 60 KAIFSLGAGVDHLLADPDLP-DVPIVRLVDP--GLAQGMAE---YVLAAVLRLHRDMDRY 113
Query: 162 IEQ------KKLGVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQ 215
Q K L V +LG G +G +A+RL G + RS
Sbjct: 114 AAQQRRGVWKPLPQRPAAER---RVGVLGLGELGAAVARRLAALGFPVSGWSRSPKDIEG 170
Query: 216 VSCQSSALAVKNGIIDDLVDEKGCHEDIFEFASKADVVVCCLSLNKQTAGIVNKSFLSSM 275
V+C + L F ++ D++VC L L +T GI+N L+ +
Sbjct: 171 VTCFHGE--------EGLDA----------FLAQTDILVCLLPLTPETRGILNAELLARL 212
Query: 276 KKGSLLVNIARGGLLDYEAIAHYLECGHLGGLGIDVAWTEPFDPNDPILKFKNVLITPHV 335
+G+ L+N+ RG L + L+ GHL G +DV EP + P+ + V +TPH+
Sbjct: 213 PRGAALINVGRGPHLVEADLLAALDSGHLSGAVLDVFEQEPLPADHPLWRHPRVTVTPHI 272
Query: 336 GGVTEHSYRSMAKVVGDVALQLHAGTPLTGL 366
+T S A V + +L AG PL L
Sbjct: 273 AAIT--DPDSAAAQVAENIRRLEAGEPLPNL 301
>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: 109 VGLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLMLGLLRKQNEM--RMAIEQKK 166
+G + +D++AA GIKV +VT + S A+ T+ LML LRK ++ R +
Sbjct: 77 IGYDHIDLDAAKELGIKV----SNVTYSPNSVADYTVMLMLMALRKYKQIMKRAEVNDYS 132
Query: 167 LGVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVK 226
LG G L TV ++G G IG + K L FG KI+A
Sbjct: 133 LGGLQGRELRNLTVGVIGTGRIGQAVIKNLSGFGCKILAYDPY----------------P 176
Query: 227 NGIIDDLVDEKGCHEDIFEFASKADVVVCCLSLNKQTAGIVNKSFLSSMKKGSLLVNIAR 286
N + + + D+ ++D++ L ++T ++NK ++ MK G +++N AR
Sbjct: 177 NEEVKKYAE----YVDLDTLYKESDIITLHTPLTEETYHLINKESIAKMKDGVIIINTAR 232
Query: 287 GGLLDYEAIAHYLECGHLGGLGIDVAWTE--------PFD--PNDPI---LKFKNVLITP 333
G L+D EA+ LE G +GG +DV E D N + F NV++TP
Sbjct: 233 GELIDTEALIEGLESGKIGGAALDVIEGEDGIYYNDRKGDILSNRELAILRSFPNVILTP 292
Query: 334 HVGGVTEHSYRSM 346
H+ T+ + M
Sbjct: 293 HMAFYTDQAVSDM 305
>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 = 3e-28
Identities = 70/269 (26%), Positives = 118/269 (43%), Gaps = 42/269 (15%)
Query: 98 ANQMKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLMLGLLRKQNE 157
+K I G++ +D++ A G+K+ +P + + AE + L LLR E
Sbjct: 66 EYGIKQIALRSAGVDMIDLDLAKENGLKITNVP---AYSPRAIAEFAVTQALNLLRNTPE 122
Query: 158 MRMAIEQKKLGVPTGETLLGK-----TVFILGFGNIGVELAKRLRPFGVKIIATKRSWAS 212
+ + + G L+G+ TV I+G G IG AK + FG K+IA
Sbjct: 123 IDRRVAKGDFRWAPG--LIGREIRDLTVGIIGTGRIGSAAAKIFKGFGAKVIAYDP---- 176
Query: 213 HSQVSCQSSALAVKNGIIDDLVDEKGCHEDIFEFASKADVVVCCLSLNKQTAGIVNKSFL 272
N ++ + ED+ +AD++ + L K+ ++N
Sbjct: 177 ------------YPNPELEKFLLYYDSLEDLL---KQADIISLHVPLTKENHHLINAEAF 221
Query: 273 SSMKKGSLLVNIARGGLLDYEAIAHYLECGHLGGLGIDVAWTE-PFDPN--------DPI 323
+ MK G++LVN ARGGL+D +A+ L+ G + G +D E + D +
Sbjct: 222 AKMKDGAILVNAARGGLVDTKALIDALDSGKIAGAALDTYENETGYFNKDWSGKEIEDEV 281
Query: 324 LK----FKNVLITPHVGGVTEHSYRSMAK 348
LK NVLITPH+ T+ + ++M +
Sbjct: 282 LKELIAMPNVLITPHIAFYTDTAVKNMVE 310
>gnl|CDD|180588 PRK06487, PRK06487, glycerate dehydrogenase; Provisional.
Length = 317
Score = 109 bits (274), Expect = 3e-27
Identities = 81/305 (26%), Positives = 130/305 (42%), Gaps = 45/305 (14%)
Query: 70 ISDVPDVIANYHLCVVKTMRLDSNCISRANQMKLIMQFGVGLEGVDINAATRCGIKVARI 129
+ I+N K LD+ ++ A Q+KLI+ G VD+ AA GI V
Sbjct: 43 LRGAQVAISN------KVA-LDAAALAAAPQLKLILVAATGTNNVDLAAARERGITVCNC 95
Query: 130 PGDVTGNAASCAELTIYLMLGLLRKQNEMRMAIEQKK---------LGVPTGETLLGKTV 180
G T S A+ T+ L+L L + + + A+ + L P E L GKT+
Sbjct: 96 QGYGT---PSVAQHTLALLLALATRLPDYQQAVAAGRWQQSSQFCLLDFPIVE-LEGKTL 151
Query: 181 FILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEKGCH 240
+LG G +G +A+ FG++++ + L +
Sbjct: 152 GLLGHGELGGAVARLAEAFGMRVLI-----GQLPGRPARPDRLPLD-------------- 192
Query: 241 EDIFEFASKADVVVCCLSLNKQTAGIVNKSFLSSMKKGSLLVNIARGGLLDYEAIAHYLE 300
E + D + L + T ++ L+ MK G+LL+N ARGGL+D +A+A L
Sbjct: 193 ----ELLPQVDALTLHCPLTEHTRHLIGARELALMKPGALLINTARGGLVDEQALADALR 248
Query: 301 CGHLGGLGIDVAWTEPFDPNDPIL--KFKNVLITPHVGGVTEHSYRSMAKVVGDVALQLH 358
GHLGG DV EP +P+L +++TPH + + + + + + A
Sbjct: 249 SGHLGGAATDVLSVEPPVNGNPLLAPDIPRLIVTPHSAWGSREARQRIVGQLAENARAFF 308
Query: 359 AGTPL 363
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 = 106 bits (266), Expect = 3e-26
Identities = 63/233 (27%), Positives = 104/233 (44%), Gaps = 24/233 (10%)
Query: 136 NAASCAELTIYLMLGLLRKQNEMRMAIEQKKLGVPTGETLLGKTVFILGFGNIGVELAKR 195
A + AE + +L ++ E+ + ++ P G +L G T+ I+GFG IG LA+R
Sbjct: 95 AAEAIAEFVLAAILAAAKRLPEIWVKGAEQWRREPLG-SLAGSTLGIVGFGAIGQALARR 153
Query: 196 LRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEKGCH--EDIFEFASKADVV 253
G++++A +RS D G D+ E +++D +
Sbjct: 154 ALALGMRVLALRRS---------------------GRPSDVPGVEAAADLAELFARSDHL 192
Query: 254 VCCLSLNKQTAGIVNKSFLSSMKKGSLLVNIARGGLLDYEAIAHYLECGHLGGLGIDVAW 313
V L +T ++N L+ K G L+NIARGGL+D EA+ L+ G + +DV
Sbjct: 193 VLAAPLTPETRHLINADVLAQAKPGLHLINIARGGLVDQEALLEALDSGRISLASLDVTD 252
Query: 314 TEPFDPNDPILKFKNVLITPHVGGVTEHSYRSMAKVVGDVALQLHAGTPLTGL 366
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: 89 RLDSNCISR--ANQMKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAAS---CAEL 143
LD+ + + +KLI G VD+ AA GI V R+P A S AE
Sbjct: 55 DLDAPVLEKLAELGVKLIALRCAGFNNVDLKAAKELGITVVRVP------AYSPYAVAEH 108
Query: 144 TIYLMLGLLRK----QNEMRM---AIEQKKLGVPTGETLLGKTVFILGFGNIGVELAKRL 196
+ L+L L RK N +R +++ G+ G L GKTV ++G G IG A+ L
Sbjct: 109 AVALLLALNRKIHRAYNRVREGNFSLD----GL-LGFDLHGKTVGVIGTGKIGQAFARIL 163
Query: 197 RPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEKGCHEDIFEFAS------KA 250
+ FG +++A D + E+ ++
Sbjct: 164 KGFGCRVLAY-------------------------DPYPNPELAKLGVEYVDLDELLAES 198
Query: 251 DVVVCCLSLNKQTAGIVNKSFLSSMKKGSLLVNIARGGLLDYEAIAHYLECGHLGGLGID 310
D++ L +T ++N ++ MK G +L+N +RGGL+D +A+ L+ G +GGLG+D
Sbjct: 199 DIISLHCPLTPETHHLINAETIAKMKDGVMLINTSRGGLIDTKALIEALKSGKIGGLGLD 258
Query: 311 VAWTEPF----DPNDPI---------LKFKNVLITPHVGGVTEHSYRSMAKVVGDVALQL 357
V E D +D I L F NVLIT H T+ + ++A+ +
Sbjct: 259 VYEEEAGLFFEDHSDEIIQDDVLARLLSFPNVLITGHQAFFTKEALTNIAETTLENLDDF 318
Query: 358 HAGTPLT 364
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 (257), Expect = 8e-25
Identities = 78/298 (26%), Positives = 121/298 (40%), Gaps = 65/298 (21%)
Query: 81 HLCVVKTMRLDSNCISRANQMKLIMQFG--------VGLEGVDINAATRCGIKVARIPGD 132
H V+ + NC + +++ ++G VG +D+ AA G K+AR+P
Sbjct: 45 HDAVI----VRGNCFADKENLEIYKEYGIKYVFTRTVGFNHIDLEAAKELGFKMARVPS- 99
Query: 133 VTGNAASCAELTIYLMLGLLRKQNEMRMAIEQKKLGVPT---GETLLGKTVFILGFGNIG 189
+ NA AEL L + L R K V + + TV I+G G IG
Sbjct: 100 YSPNAI--AELAFTLAMTLSRHTAYTASRTANKNFKVDPFMFSKEIRNSTVGIIGTGRIG 157
Query: 190 VELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEKGCHEDIFEFAS- 248
+ AK + G K+I D+ +D+ F S
Sbjct: 158 LTAAKLFKGLGAKVIGY-------------------------DIYPSDAA-KDVVTFVSL 191
Query: 249 -----KADVV-VCCLSLNKQTAGIVNKSFLSSMKKGSLLVNIARGGLLDYEAIAHYLECG 302
K+D++ + + + ++NK F+S MK G++L+N ARG L D EAI LE G
Sbjct: 192 DELLKKSDIISLHVPYIKGKNDKLINKEFISKMKDGAILINTARGELQDEEAILEALESG 251
Query: 303 HLGGLGIDV------------AWTEPFDP--NDPILKFKNVLITPHVGGVTEHSYRSM 346
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 = 6e-24
Identities = 59/220 (26%), Positives = 98/220 (44%), Gaps = 28/220 (12%)
Query: 141 AELTI--YLML--GLLRKQNEMRMAIEQKKLGVPTGETLLGKTVFILGFGNIGVELAKRL 196
AE I +L+L L+ + ++ + E +GK V ILG+G+IG + A+
Sbjct: 93 AEWVIGTWLVLSHHFLQYIELQKEQTWGRRQEAYSVEDSVGKRVGILGYGSIGRQTARLA 152
Query: 197 RPFGVKIIATKRSWASHSQVSCQSSALAVKNGII-------DDLVDEKGCH----EDIFE 245
+ G+++ A RS + + +S +G I D + + E
Sbjct: 153 QALGMEVYAYTRS----PRPTPES---RKDDGYIVPGTGDPDGSIPSAWFSGTDKASLHE 205
Query: 246 F-ASKADVVVCCLSLNKQTAGIVNK---SFLSSMKKGSLLVNIARGGLLDYEAIAHYLEC 301
F D++V L L T ++ L+ K+ + + NIARG L+D +A+ LE
Sbjct: 206 FLRQDLDLLVVSLPLTPATKHLLGAEEFEILA--KRKTFVSNIARGSLVDTDALVAALES 263
Query: 302 GHLGGLGIDVAWTEPFDPNDPILKFKNVLITPHVGGVTEH 341
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 = 98.2 bits (245), Expect = 2e-23
Identities = 66/208 (31%), Positives = 100/208 (48%), Gaps = 30/208 (14%)
Query: 141 AELTIYLMLGLLRKQNEMRMAIEQKK----LG-----VPTGE--TLLGKTVFILGFGNIG 189
AE T+ L+L +R+ +EMR A + + LG P G TLLG V I GFG+IG
Sbjct: 96 AEHTLALILAAVRRLDEMREAQREHRWAGELGGLQPLRPAGRLTTLLGARVLIWGFGSIG 155
Query: 190 VELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEKGCHEDIFEFASK 249
LA L G ++ RS + G +V E +++ E +
Sbjct: 156 QRLAPLLTALGARVTGVARS-------------AGERAGF--PVVAE----DELPELLPE 196
Query: 250 ADVVVCCLSLNKQTAGIVNKSFLSSMKKGSLLVNIARGGLLDYEAIAHYLECGHLGGLGI 309
DV+V L TA ++ L+++ K + +VN+ RG +D +A+ LE G LGG +
Sbjct: 197 TDVLVMILPATPSTAHALDAEVLAALPKHAWVVNVGRGATVDEDALVAALESGRLGGAAL 256
Query: 310 DVAWTEPFDPNDPILKFKNVLITPHVGG 337
DV TEP + P+ N+++TPH G
Sbjct: 257 DVTATEPLPASSPLWDAPNLILTPHAAG 284
>gnl|CDD|236985 PRK11790, PRK11790, D-3-phosphoglycerate dehydrogenase;
Provisional.
Length = 409
Score = 97.2 bits (243), Expect = 2e-22
Identities = 75/255 (29%), Positives = 116/255 (45%), Gaps = 59/255 (23%)
Query: 107 FGVGLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLMLGLLRKQNEMRMAIEQKK 166
F +G VD++AA + GI V P N S AEL I ++ LLR I +K
Sbjct: 82 FCIGTNQVDLDAAAKRGIPVFNAP---FSNTRSVAELVIGEIILLLRG-------IPEKN 131
Query: 167 LGVPTGETL---------LGKTVFILGFGNIGVELAKRLRPFGVKI----IATKRSWASH 213
G GKT+ I+G+G+IG +L+ G+++ I K +
Sbjct: 132 AKAHRGGWNKSAAGSFEVRGKTLGIVGYGHIGTQLSVLAESLGMRVYFYDIEDKLPLGNA 191
Query: 214 SQVSCQSSALAVKNGIIDDLVDEKGCHEDIFEFASKADVVVCCLSL----NKQTAGIVNK 269
QV G +++L+ +++DVV SL T ++
Sbjct: 192 RQV-----------GSLEELL-------------AQSDVV----SLHVPETPSTKNMIGA 223
Query: 270 SFLSSMKKGSLLVNIARGGLLDYEAIAHYLECGHLGGLGIDVAWTEPFDPND----PILK 325
L+ MK G++L+N +RG ++D +A+A L+ GHL G IDV EP D P+
Sbjct: 224 EELALMKPGAILINASRGTVVDIDALADALKSGHLAGAAIDVFPVEPKSNGDPFESPLRG 283
Query: 326 FKNVLITPHVGGVTE 340
NV++TPH+GG T+
Sbjct: 284 LDNVILTPHIGGSTQ 298
>gnl|CDD|235890 PRK06932, PRK06932, glycerate dehydrogenase; Provisional.
Length = 314
Score = 94.9 bits (236), Expect = 4e-22
Identities = 73/306 (23%), Positives = 127/306 (41%), Gaps = 53/306 (17%)
Query: 44 PHFPASHNYTKEYLQNYPSIQVDVVPISDVPDVIANYHLCVVKTMRLDSNCISRANQMKL 103
P FP H + EY ++ +D+ VI + K + +++ ++KL
Sbjct: 21 PSFP--HEWI-EYDHTSAEQTIERAKDADI--VITS------KVL-FTRETLAQLPKLKL 68
Query: 104 IMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLMLGL-------LRKQN 156
I G VD+ AA GI V + G + + E + ++ L R Q
Sbjct: 69 IAITATGTNNVDLVAAKELGIAVKNVTGYSS---TTVPEHVLGMIFALKHSLMGWYRDQL 125
Query: 157 EMRMAIEQKKLGV---PTGETLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASH 213
R A K+ P + + G T+ + G G +G E+ + + G+K++ + AS
Sbjct: 126 SDRWA-TCKQFCYFDYPITD-VRGSTLGVFGKGCLGTEVGRLAQALGMKVLYAEHKGASV 183
Query: 214 SQVSCQSSALAVKNGIIDDLVDEKGCHEDIFEFASKADVVVCCLSLNKQTAGIVNKSFLS 273
C+ E +AD+V L + T ++N L+
Sbjct: 184 ----CREGYT------------------PFEEVLKQADIVTLHCPLTETTQNLINAETLA 221
Query: 274 SMKKGSLLVNIARGGLLDYEAIAHYLECGHLGGLGIDVAWTEPFDPNDPIL----KFKNV 329
MK + L+N RG L+D +A+ LE G + G +DV EP + ++P++ + N+
Sbjct: 222 LMKPTAFLINTGRGPLVDEQALLDALENGKIAGAALDVLVKEPPEKDNPLIQAAKRLPNL 281
Query: 330 LITPHV 335
LITPH+
Sbjct: 282 LITPHI 287
>gnl|CDD|181414 PRK08410, PRK08410, 2-hydroxyacid dehydrogenase; Provisional.
Length = 311
Score = 93.1 bits (232), Expect = 2e-21
Identities = 70/262 (26%), Positives = 121/262 (46%), Gaps = 46/262 (17%)
Query: 90 LDSNCISRANQMKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLML 149
+D +S+ +KLI G VDI A + GI V + G T S A+ T ++L
Sbjct: 53 IDKEVLSQLPNLKLICITATGTNNVDIEYAKKKGIAVKNVAGYST---ESVAQHTFAMLL 109
Query: 150 GLLRKQNEMRMAIEQKK---------LGVPTGETLLGKTVFILGFGNIGVELAKRLRPFG 200
LL + N ++ + + P GE + GK I+G G IG +AK + FG
Sbjct: 110 SLLGRINYYDRYVKSGEYSESPIFTHISRPLGE-IKGKKWGIIGLGTIGKRVAKIAQAFG 168
Query: 201 VKII----ATKRSWASHSQVSCQSSALAVKNGIIDDLVDEKGCHEDIFEFASKADVVVCC 256
K++ + K + +VS +++L+ +D++
Sbjct: 169 AKVVYYSTSGKNKNEEYERVS------------LEELL-------------KTSDIISIH 203
Query: 257 LSLNKQTAGIVNKSFLSSMKKGSLLVNIARGGLLDYEAIAHYLECGHLGGLGIDVAWTEP 316
LN++T ++ L +K G++L+N+ RGG+++ + +A L+ + G+DV EP
Sbjct: 204 APLNEKTKNLIAYKELKLLKDGAILINVGRGGIVNEKDLAKALDEKDI-YAGLDVLEKEP 262
Query: 317 FDPNDPILKFKN---VLITPHV 335
+ 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: 124 IKVARIPGDVT--GNAA----SCAELTIYLMLGLLRKQNEMRMAIEQKKLGVPTGETLLG 177
I V+ IP +V NA S AE L+L + E ++ + L
Sbjct: 63 IDVSGIPENVVLCSNAGAYSISVAEHAFALLLAWAKNICENNYNMKNGNFKQSPTKLLYN 122
Query: 178 KTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEK 237
K++ ILG+G IG +A + FG+ I A RS+ + S
Sbjct: 123 KSLGILGYGGIGRRVALLAKAFGMNIYAYTRSYVNDGISSIYMEP--------------- 167
Query: 238 GCHEDIFEFASKADVVVCCLSLNKQTAGIVNKSFLSSMKKGSLLVNIARGGLLDYEAIAH 297
EDI + K+D V+ L L +T G++N LS +KG ++N+AR ++D + +
Sbjct: 168 ---EDIMK---KSDFVLISLPLTDETRGMINSKMLSLFRKGLAIINVARADVVDKNDMLN 221
Query: 298 YLECGHLGGLGIDVAWTEPFDPNDPILKFKNVLITPHVGG 337
+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 = 84.5 bits (210), Expect = 2e-18
Identities = 71/262 (27%), Positives = 114/262 (43%), Gaps = 70/262 (26%)
Query: 110 GLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLMLGLLRKQNEMRMAIEQKKLGV 169
G + +D + GI A PG NA S AE Y++ LL +A Q
Sbjct: 67 GTDHIDTDYLKERGIGFANAPG---CNANSVAE---YVLSALLV------LAQRQ----- 109
Query: 170 PTGETLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGI 229
G +L GKTV I+G GN+G LA+RL G+ ++ C
Sbjct: 110 --GFSLKGKTVGIVGVGNVGSRLARRLEALGMNVLL------------C----------- 144
Query: 230 IDDLVDEKGCHEDIFEFAS------KADVVVCCLSLNKQ----TAGIVNKSFLSSMKKGS 279
D E E F S +AD++ + L + T ++++ FL+++K G
Sbjct: 145 -DPPRAEA---EGDPGFVSLEELLAEADIITLHVPLTRDGEHPTYHLLDEDFLAALKPGQ 200
Query: 280 LLVNIARGGLLDYEAIAHYLECGHLGGLGIDVAW-TEPFDPNDPILKFKNVLI-TPHVGG 337
+L+N +RG ++D +A+ L+ G + +DV W EP + + +L V I TPH+ G
Sbjct: 201 ILINASRGAVIDNQALLALLQRGKDLRVVLDV-WENEP-EIDLELLDK--VDIATPHIAG 256
Query: 338 V--------TEHSYRSMAKVVG 351
TE Y ++ + +G
Sbjct: 257 YSLEGKARGTEMIYEALCQFLG 278
>gnl|CDD|185307 PRK15409, PRK15409, bifunctional glyoxylate/hydroxypyruvate
reductase B; Provisional.
Length = 323
Score = 77.9 bits (192), Expect = 5e-16
Identities = 66/269 (24%), Positives = 118/269 (43%), Gaps = 33/269 (12%)
Query: 89 RLDSNCISRANQMKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLM 148
++D+ + + +++ VG + D++A T I + P +T + A+ + L+
Sbjct: 55 KVDAALLEKMPKLRAASTISVGYDNFDVDALTARKILLMHTPTVLT---ETVADTLMALV 111
Query: 149 LGLLRKQNEMRMAIEQKKLGVPT--------GETLLGKTVFILGFGNIGVELAKRLR-PF 199
L R+ E+ E+ K G T G + KT+ I+G G IG+ LA+R F
Sbjct: 112 LSTARRVVEV---AERVKAGEWTASIGPDWFGTDVHHKTLGIVGMGRIGMALAQRAHFGF 168
Query: 200 GVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEKGCHEDIFEFASKADVVVCCLSL 259
+ I+ R H + + +A + +D L+ E +D V L L
Sbjct: 169 NMPILYNARR--HHKEAEERFNA---RYCDLDTLLQE-------------SDFVCIILPL 210
Query: 260 NKQTAGIVNKSFLSSMKKGSLLVNIARGGLLDYEAIAHYLECGHLGGLGIDVAWTEPFDP 319
+T + + MK ++ +N RG ++D A+ L+ G + G+DV EP
Sbjct: 211 TDETHHLFGAEQFAKMKSSAIFINAGRGPVVDENALIAALQKGEIHAAGLDVFEQEPLSV 270
Query: 320 NDPILKFKNVLITPHVGGVTEHSYRSMAK 348
+ P+L NV+ PH+G T + +MA
Sbjct: 271 DSPLLSLPNVVAVPHIGSATHETRYNMAA 299
>gnl|CDD|177941 PLN02306, PLN02306, hydroxypyruvate reductase.
Length = 386
Score = 76.0 bits (187), Expect = 3e-15
Identities = 69/261 (26%), Positives = 120/261 (45%), Gaps = 40/261 (15%)
Query: 107 FGVGLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLMLGLLRKQNE----MRMAI 162
VG VD+ AA + GI V PG +T + AEL L L R+ E MR +
Sbjct: 93 MAVGYNNVDVEAANKYGIAVGNTPGVLT---ETTAELAASLSLAAARRIVEADEFMRAGL 149
Query: 163 EQKKLGVPT---GETLLGKTVFILGFGNIGVELAKRL-RPFGVKII------ATK----- 207
+ L P G L G+TV ++G G IG A+ + F + +I +T+
Sbjct: 150 YEGWL--PHLFVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYYDLYQSTRLEKFV 207
Query: 208 RSWASHSQVSCQSSALAVKNGIIDDLVDEKGCHEDIFEFASKADVVVCCLSLNKQTAGIV 267
++ + + + + +++++ E ADV+ L+K T ++
Sbjct: 208 TAYGQFLKANGEQPVTWKRASSMEEVLRE-------------ADVISLHPVLDKTTYHLI 254
Query: 268 NKSFLSSMKKGSLLVNIARGGLLDYEAIAHYLECGHLGGLGIDVAWTEPF-DPNDPILKF 326
NK L+ MKK ++LVN +RG ++D A+ +L+ + +G+DV EP+ P +
Sbjct: 255 NKERLALMKKEAVLVNASRGPVIDEVALVEHLKANPMFRVGLDVFEDEPYMKPG--LADM 312
Query: 327 KNVLITPHVGGVTEHSYRSMA 347
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 = 75.0 bits (184), Expect = 3e-15
Identities = 54/217 (24%), Positives = 93/217 (42%), Gaps = 32/217 (14%)
Query: 102 KLIMQFGVGLEGVDIN-AATRCGIKVARIPGDVTG----NAASCAELTIYLMLGLLRKQN 156
+L+ + +G + D+ A R G+ + G N+ EL++ + L Q
Sbjct: 89 RLLFTYTIGADHRDLTEALARAGLTAIAVEGVELPLLTSNSIGAGELSVQFIARFLEVQQ 148
Query: 157 EMRMAIEQKKLGVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQV 216
R+ G P + GKTV ++G G +G E A+ LR G +++ T + + Q+
Sbjct: 149 PGRLG------GAPD---VAGKTVVVVGAGVVGKEAAQMLRGLGAQVLITDINVEALEQL 199
Query: 217 SCQSSALAVKNGIIDDLVDEKGCHEDIFEFASKADVVVCCLSLNKQTAGIVN-KSFLSSM 275
E++ E ++ADV+V L + AGI+ + + M
Sbjct: 200 EELGGKNV----------------EELEEALAEADVIVTTTLLPGKRAGILVPEELVEQM 243
Query: 276 KKGSLLVNIARGGLLDYEAIAHY-LECGHLGGLGIDV 311
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: 90 LDSNCISRANQM--KLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYL 147
L N++ K I Q G + D+ AT+ + ++ +P + + S AE T+
Sbjct: 57 LSEAIYKLLNELGIKQIAQRSAGFDTYDLELATKYNLIISNVP---SYSPESIAEFTVTQ 113
Query: 148 MLGLLRKQNEMRMAIEQKKLGVPTGETLLGK-----TVFILGFGNIGVELAKRL-RPFGV 201
+ L+R N+++ + ++ +L + V ++G G IG+ +AK + +G
Sbjct: 114 AINLVRHFNQIQTKV--REHDFRWEPPILSRSIKDLKVAVIGTGRIGLAVAKIFAKGYGS 171
Query: 202 KIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEKGCHEDIFEFASKADVVVCCLSLNK 261
++A N VD K + I E AD+V + K
Sbjct: 172 DVVAYD----------------PFPNAKAATYVDYK---DTIEEAVEGADIVTLHMPATK 212
Query: 262 QTAGIVNKSFLSSMKKGSLLVNIARGGLLDYEAIAHYLECGHLGGLGIDVAWTE-PFDP- 319
+ N KKG++ VN ARG L+D +A+ L+ G + G +D E P P
Sbjct: 213 YNHYLFNADLFKHFKKGAVFVNCARGSLVDTKALLDALDNGLIKGAALDTYEFERPLFPS 272
Query: 320 -------NDPILK----FKNVLITPHVGGVTE 340
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: 101 MKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLMLGLLRK--QNEM 158
+K I Q G + D++ A + I ++ +P + + + AE ++ + L L+R+ E
Sbjct: 70 IKQIAQRTAGFDMYDLDLAKKHNIVISNVP---SYSPETIAEYSVSIALQLVRRFPDIER 126
Query: 159 RMAIEQKKLGVPTGET-LLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVS 217
R+ + TV I+G G IG AK FG I A ++ +
Sbjct: 127 RVQAHDFTWQAEIMSKPVKNMTVAIIGTGRIGAATAKIYAGFGATITAYD-AYPNKDL-- 183
Query: 218 CQSSALAVKNGIIDDLVDEKGCHEDIFEFASKADVVVCCLSLNKQTAGIVNKSFLSSMKK 277
L K+ + + + D AD++ + NK++ + +K+ +KK
Sbjct: 184 ---DFLTYKDSVKEAIKD--------------ADIISLHVPANKESYHLFDKAMFDHVKK 226
Query: 278 GSLLVNIARGGLLDYEAIAHYLECGHLGGLGIDV----------AWTEPFDPNDPIL--- 324
G++LVN ARG +++ + + G L G ID WT D +D L
Sbjct: 227 GAILVNAARGAVINTPDLIAAVNDGTLLGAAIDTYENEAAYFTNDWTNK-DIDDKTLLEL 285
Query: 325 -KFKNVLITPHVGGVTEHSYRSM 346
+ + +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 = 5e-14
Identities = 55/189 (29%), Positives = 85/189 (44%), Gaps = 24/189 (12%)
Query: 179 TVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEKG 238
T+ ILG G +G ++A+ L+ +G + RS S V QS A
Sbjct: 138 TIGILGAGVLGSKVAQSLQTWGFPLRCWSRSRKSWPGV--QSFAGR-------------- 181
Query: 239 CHEDIFEFASKADVVVCCLSLNKQTAGIVNKSFLSSMKKGSLLVNIARGGLLDYEAIAHY 298
E++ F S+ V++ L +T GI+N+ L + G+ L+N+ARG + + +
Sbjct: 182 --EELSAFLSQTRVLINLLPNTPETVGIINQQLLEQLPDGAYLLNLARGVHVVEDDLLAA 239
Query: 299 LECGHLGGLGIDVAWTEPFDPNDPILKFKNVLITPHVGGVTEHSYRSMAKV--VGDVALQ 356
L+ G + G +DV EP P P+ + V ITPHV VT R V + Q
Sbjct: 240 LDSGKVKGAMLDVFSREPLPPESPLWQHPRVAITPHVAAVT----RPAEAVEYISRTIAQ 295
Query: 357 LHAGTPLTG 365
L G + G
Sbjct: 296 LEKGERVCG 304
>gnl|CDD|185335 PRK15438, PRK15438, erythronate-4-phosphate dehydrogenase PdxB;
Provisional.
Length = 378
Score = 52.6 bits (126), Expect = 1e-07
Identities = 45/172 (26%), Positives = 76/172 (44%), Gaps = 27/172 (15%)
Query: 172 GETLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIID 231
G +L +TV I+G GN+G L RL G+K + A
Sbjct: 111 GFSLHDRTVGIVGVGNVGRRLQARLEALGIKTLLCDPPRADRG----------------- 153
Query: 232 DLVDEKGCHEDIFEFASKADVVVCCLSLNK----QTAGIVNKSFLSSMKKGSLLVNIARG 287
++G + E +AD++ L K +T + ++ + S+K G++L+N RG
Sbjct: 154 ----DEGDFRSLDELVQEADILTFHTPLFKDGPYKTLHLADEKLIRSLKPGAILINACRG 209
Query: 288 GLLDYEAIAHYLECGHLGGLGIDVAWTEPFDPNDPILKFKNVLITPHVGGVT 339
++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 = 55/239 (23%), Positives = 97/239 (40%), Gaps = 58/239 (24%)
Query: 109 VGLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLMLGLLRKQNEMRMAIEQKKLG 168
+G + +D++ GI + PG NA + Y++ LL +A +
Sbjct: 67 IGTDHLDLDYFAEAGITWSSAPG---CNARGVVD---YVLGSLLT------LAERE---- 110
Query: 169 VPTGETLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNG 228
G L +T ++G G++G L + LR G K++
Sbjct: 111 ---GVDLAERTYGVVGAGHVGGRLVRVLRGLGWKVL------------------------ 143
Query: 229 IIDDLVDEKGCHEDIFEFAS------KADVVVCCLSLNKQ----TAGIVNKSFLSSMKKG 278
+ D E E +F S + DV+ L K+ T +++++FL+S++ G
Sbjct: 144 VCDPPRQEA---EGDGDFVSLERILEECDVISLHTPLTKEGEHPTRHLLDEAFLASLRPG 200
Query: 279 SLLVNIARGGLLDYEAIAHYLECGHLGGLGIDVAWTEPFDPNDPILKFKNVLITPHVGG 337
+ L+N +RG ++D +A+ L G +DV EP D L + TPH+ G
Sbjct: 201 AWLINASRGAVVDNQALREALLSGEDLDAVLDVWEGEP--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 = 6e-05
Identities = 21/73 (28%), Positives = 31/73 (42%), Gaps = 11/73 (15%)
Query: 172 GETLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGI-I 230
G L G V I GFGN+G A+ L G K++A VS + +G+ +
Sbjct: 26 GIGLAGARVAIQGFGNVGSHAARFLHEAGAKVVA----------VSDSDGTIYNPDGLDV 75
Query: 231 DDLVDEKGCHEDI 243
L+ K H +
Sbjct: 76 PALLAYKKEHGSV 88
>gnl|CDD|181371 PRK08306, PRK08306, dipicolinate synthase subunit A; Reviewed.
Length = 296
Score = 43.7 bits (104), Expect = 8e-05
Identities = 38/141 (26%), Positives = 58/141 (41%), Gaps = 36/141 (25%)
Query: 160 MAIEQKKLGVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQ 219
MAIE T T+ G V +LGFG G+ LA+ L+ G + R
Sbjct: 141 MAIEH------TPITIHGSNVLVLGFGRTGMTLARTLKALGANVTVGARK---------- 184
Query: 220 SSALAVKNGIIDDLVDEKGCH----EDIFEFASKADVVVCCLSLNKQTAGIVNKSFLSSM 275
S+ LA + E G ++ E K D++ N A ++ K LS M
Sbjct: 185 SAHLAR--------ITEMGLSPFHLSELAEEVGKIDIIF-----NTIPALVLTKEVLSKM 231
Query: 276 KKGSLLVNIAR--GGLLDYEA 294
+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: 68 VPISDVPDVIANYHLCV--VKTMRLDSNCISRANQMKLIMQFGVGLEGVDINAATRCGIK 125
+S++ + + + + + L +S+ LI+ G D A + GIK
Sbjct: 199 FHLSELAEEVGKIDIIFNTIPALVLTKEVLSKMPPEALIIDLASKPGGTDFEYAEKRGIK 258
Query: 126 VARIPG 131
PG
Sbjct: 259 ALLAPG 264
>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 = 41.7 bits (99), Expect = 1e-04
Identities = 26/116 (22%), Positives = 49/116 (42%), Gaps = 18/116 (15%)
Query: 179 TVFILGFGNIG---VELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVD 235
V ++G G +G AK L G ++ A Q+ ++ L
Sbjct: 22 KVVVIGAGVVGLGAAATAKGL---GAEVTVLDVRPARLRQLE------SLLGARFTTLYS 72
Query: 236 EKGCHEDIFEFASKADVVVCCLSL-NKQTAGIVNKSFLSSMKKGSLLVNIA--RGG 288
+ E E +AD+V+ + + + +V + + SMK GS++V++A +GG
Sbjct: 73 QAELLE---EAVKEADLVIGAVLIPGAKAPKLVTREMVKSMKPGSVIVDVAADQGG 125
>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 = 43.2 bits (102), Expect = 1e-04
Identities = 20/108 (18%), Positives = 46/108 (42%), Gaps = 12/108 (11%)
Query: 179 TVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEKG 238
V I+G G +G+ AK + G ++ V G +K
Sbjct: 164 KVLIIGAGVVGLGAAKIAKKLGANVLVYDIKEEKLKGVE--------TLGGSRLRYSQK- 214
Query: 239 CHEDIFEFASKADVVVCCLSLNKQTAGIV-NKSFLSSMKKGSLLVNIA 285
E++ + + D+++ + ++ A I+ + + MK+G+++V++A
Sbjct: 215 --EELEKELKQTDILINAILVDGPRAPILIMEELVGPMKRGAVIVDLA 260
>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: 114 VDINAATRCGIKVARIP--GDVTGNAASCAELTIYLMLGLL----RKQ-NEMRMAIEQKK 166
VDI AA GI V I GD E I ++ LL KQ E + K
Sbjct: 86 VDIAAARENGITVTGIRDYGD-----EGVVEYVISELIRLLHGFGGKQWKEEPRELTGLK 140
Query: 167 LGVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVK 226
+G I+G G G +A L FG + R+ + ++ +
Sbjct: 141 VG-------------IIGLGTTGQMIADALSFFGADVYYYSRT----RKPDAEAKGIRYL 183
Query: 227 NGIIDDLVDEKGCHEDIFEFASKADVVVCCLSLNKQTAGIVNKSFLSSMKKGSLLVNIAR 286
+++L+ DV+ CL N ++ + + G +L N +
Sbjct: 184 P--LNELLKT-------------VDVICTCLPKNVI---LLGEEEFELLGDGKILFNTSL 225
Query: 287 GGLLDYEAIAHYLE--------CGHLGGLGIDVAWTEPFDPNDPILKFKNVLITPHVGGV 338
G + EA+ +L+ C G LG ++ +L++ NV+ T G
Sbjct: 226 GPSFEVEALKKWLKASGYNIFDCDTAGALG-----------DEELLRYPNVICTNKSAGW 274
Query: 339 TEHSYRSMAKVV 350
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: 180 VFILGFGNIGVELAKRLRPFGV--KIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEK 237
V ++G G IG AK LR G+ +++A R +S LAV G+ID
Sbjct: 6 VVVIGLGLIGGSFAKALRERGLAREVVAVDRR--------AKSLELAVSLGVIDR----- 52
Query: 238 GCHEDIFEFASKADVVV 254
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 = 40.3 bits (95), Expect = 0.001
Identities = 21/77 (27%), Positives = 38/77 (49%), Gaps = 11/77 (14%)
Query: 172 GETLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGI-I 230
G+ L G V + GFGN+G A++L G K++A VS + ++G+ +
Sbjct: 202 GDDLEGARVAVQGFGNVGQYAAEKLHELGAKVVA----------VSDSKGGIYDEDGLDV 251
Query: 231 DDLVDEKGCHEDIFEFA 247
+ L++ K + E+A
Sbjct: 252 EALLELKERRGSVAEYA 268
>gnl|CDD|178095 PLN02477, PLN02477, glutamate dehydrogenase.
Length = 410
Score = 38.6 bits (90), Expect = 0.004
Identities = 45/174 (25%), Positives = 71/174 (40%), Gaps = 38/174 (21%)
Query: 172 GETLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGI-I 230
G+++ G+T I GFGN+G A+ + G KI+A VS + A+ +NG+ I
Sbjct: 201 GKSIAGQTFVIQGFGNVGSWAAQLIHEKGGKIVA----------VSDITGAVKNENGLDI 250
Query: 231 DDLVDEKGCHEDIFEFASKADVVVCCLSLNKQTAGIVNKSFLSSMKKGSLLVNIARGGLL 290
L + F I L ++ +L+ A GG++
Sbjct: 251 PALRKHVAEGGGLKGFPG--------------GDPIDPDDIL--VEPCDVLIPAALGGVI 294
Query: 291 DYEAIAHYLECGHLGGLGIDVAWTEPFDPN-DPILKFKNVLITPHV----GGVT 339
+ 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 = 37.5 bits (88), Expect = 0.006
Identities = 29/74 (39%), Positives = 42/74 (56%), Gaps = 14/74 (18%)
Query: 165 KKLGVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALA 224
KKLG G++L GKTV + GFGN+G A++L G K++A VS S +
Sbjct: 23 KKLG---GDSLEGKTVAVQGFGNVGSYAAEKLLELGAKVVA----------VSDSSGYIY 69
Query: 225 VKNGI-IDDLVDEK 237
NGI I++L++ K
Sbjct: 70 DPNGIDIEELLELK 83
>gnl|CDD|215144 PLN02256, PLN02256, arogenate dehydrogenase.
Length = 304
Score = 36.2 bits (84), Expect = 0.019
Identities = 30/111 (27%), Positives = 47/111 (42%), Gaps = 27/111 (24%)
Query: 179 TVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGI-----IDDL 233
+ I+GFGN G LAK G ++AT RS S +A + G+ DD
Sbjct: 38 KIGIVGFGNFGQFLAKTFVKQGHTVLATSRS---------DYSDIAAELGVSFFRDPDDF 88
Query: 234 VDEKGCHEDIFEFASKADVVVCCLSLNKQTAGIVNKSFLSSMKKGSLLVNI 284
+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 = 34.8 bits (80), Expect = 0.047
Identities = 27/84 (32%), Positives = 36/84 (42%), Gaps = 5/84 (5%)
Query: 175 LLGKTVFILG-FGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDL 233
L GK V I G FG +G A L G ++ R A SQ A A++ G I DL
Sbjct: 5 LQGKVVAITGGFGGLGRATAAWLAARGARVALIGRGAAPLSQTLPGVPADALRIGGI-DL 63
Query: 234 VDEKGCHEDIFEFAS---KADVVV 254
VD + + E + D +V
Sbjct: 64 VDPQAARRAVDEVNRQFGRLDALV 87
>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 = 0.087
Identities = 28/118 (23%), Positives = 51/118 (43%), Gaps = 21/118 (17%)
Query: 173 ETLLGKTVFILGFGNIGVELAKRLRPFGV-KIIATKRSWASHSQVSCQSSALAVKNGIID 231
+L GK ++G G +G +AK L GV KI+ R++ ++ + AVK
Sbjct: 176 GSLKGKKALLIGAGEMGELVAKHLLRKGVGKILIANRTYERAEDLAKELGGEAVK----- 230
Query: 232 DLVDEKGCHEDIFEFASKADVVVCCLSLNKQTAGIVNKSFLS----SMKKGSLLVNIA 285
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 = 0.087
Identities = 18/78 (23%), Positives = 27/78 (34%), Gaps = 13/78 (16%)
Query: 180 VFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEKGC 239
V ILG G +G LA++L G ++ T RS + + DL
Sbjct: 1 VLILGCGYLGQRLARQLLAQGWQVTGTTRSPEKLAADRPAGVT-----PLAADLTQ---- 51
Query: 240 HEDIFEFASKADVVVCCL 257
+ 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 = 34.3 bits (79), Expect = 0.088
Identities = 32/137 (23%), Positives = 55/137 (40%), Gaps = 28/137 (20%)
Query: 160 MAIEQKKLGVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQ 219
MAIE T T+ G V +LGFG G+ +A+ G + V +
Sbjct: 140 MAIEH------TDFTIHGSNVMVLGFGRTGMTIARTFSALG-----------ARVFVGAR 182
Query: 220 SSALAVKNGIIDDLVDEKGCHEDIFEFASKADVVVCC-LSLNKQTAGIVNKSFLSSMKKG 278
SSA + + E G F + V + +N A ++ LS + K
Sbjct: 183 SSADLAR-------ITEMGLIP--FPLNKLEEKVAEIDIVINTIPALVLTADVLSKLPKH 233
Query: 279 SLLVNIA-RGGLLDYEA 294
++++++A + G D+E
Sbjct: 234 AVIIDLASKPGGTDFEY 250
Score = 27.8 bits (62), Expect = 9.7
Identities = 13/66 (19%), Positives = 30/66 (45%), Gaps = 2/66 (3%)
Query: 68 VPISDVPDVIANYHLCV--VKTMRLDSNCISRANQMKLIMQFGVGLEGVDINAATRCGIK 125
P++ + + +A + + + + L ++ +S+ + +I+ G D A + GIK
Sbjct: 198 FPLNKLEEKVAEIDIVINTIPALVLTADVLSKLPKHAVIIDLASKPGGTDFEYAKKRGIK 257
Query: 126 VARIPG 131
PG
Sbjct: 258 ALLAPG 263
>gnl|CDD|198065 smart00997, AdoHcyase_NAD, S-adenosyl-L-homocysteine hydrolase, NAD
binding domain.
Length = 162
Score = 33.2 bits (77), Expect = 0.10
Identities = 29/119 (24%), Positives = 49/119 (41%), Gaps = 31/119 (26%)
Query: 171 TGETLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGII 230
T L GK V + G+G++G +A RLR G ++I T+ I
Sbjct: 17 TNVLLAGKNVVVAGYGDVGKGVAARLRGLGARVIVTE----------------------I 54
Query: 231 DDLVDEKGCHE-----DIFEFASKADVVVCCLSLNKQTAGIVNKSFLSSMKKGSLLVNI 284
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: 175 LLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLV 234
L GK V I+G+G+ G A LR G+ +I R +S S A ++G V
Sbjct: 16 LKGKKVAIIGYGSQGHAQALNLRDSGLNVIIGLRKGSS-------SWKKAKEDGFKVYTV 68
Query: 235 DEKGCHEDIFEFASKADVVVCCLSLNKQTAGIVNKSFLSSMKKGSLLV-----NIARGG 288
+E A +ADVV+ L ++Q + K ++K+G+ L NI G
Sbjct: 69 EEA---------AKRADVVMILLP-DEQQKEVYEKEIAPNLKEGAALGFAHGFNIHFGL 117
>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 = 33.3 bits (76), Expect = 0.13
Identities = 16/34 (47%), Positives = 23/34 (67%)
Query: 172 GETLLGKTVFILGFGNIGVELAKRLRPFGVKIIA 205
G++L G TV + G GN+G LAK+L G K++A
Sbjct: 18 GDSLEGLTVAVQGLGNVGWGLAKKLAEEGGKVLA 51
>gnl|CDD|184511 PRK14106, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
synthetase; Provisional.
Length = 450
Score = 33.8 bits (78), Expect = 0.15
Identities = 15/32 (46%), Positives = 20/32 (62%)
Query: 175 LLGKTVFILGFGNIGVELAKRLRPFGVKIIAT 206
L GK V ++G G G+ LAK L+ G K+I T
Sbjct: 3 LKGKKVLVVGAGVSGLALAKFLKKLGAKVILT 34
>gnl|CDD|224995 COG2084, MmsB, 3-hydroxyisobutyrate dehydrogenase and related
beta-hydroxyacid dehydrogenases [Lipid metabolism].
Length = 286
Score = 32.6 bits (75), Expect = 0.26
Identities = 18/110 (16%), Positives = 39/110 (35%), Gaps = 19/110 (17%)
Query: 178 KTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEK 237
+ +G G +G +A L G ++ R+ + L
Sbjct: 1 MKIAFIGLGIMGSPMAANLLKAGHEVTVYNRTPEK----------------AAELLAAAG 44
Query: 238 GC-HEDIFEFASKADVVVCCLSLNKQTAGIVNKS--FLSSMKKGSLLVNI 284
E A++ADVV+ L + ++ L +K G++++++
Sbjct: 45 ATVAASPAEAAAEADVVITMLPDDAAVRAVLFGENGLLEGLKPGAIVIDM 94
>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 = 0.28
Identities = 30/108 (27%), Positives = 46/108 (42%), Gaps = 17/108 (15%)
Query: 175 LLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLV 234
L GK + ++G+G+ G A LR GV +I R + S A K+G V
Sbjct: 2 LKGKKIAVIGYGSQGHAHALNLRDSGVNVIVGLRPGSK-------SWEKAKKDGFEVYTV 54
Query: 235 DEKGCHEDIFEFASKADVVVCCLSLNKQTAGIVNKSFLSSMKKGSLLV 282
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 = 0.39
Identities = 13/30 (43%), Positives = 21/30 (70%)
Query: 177 GKTVFILGFGNIGVELAKRLRPFGVKIIAT 206
GKTV + G+G++G A+ LR FG +++ T
Sbjct: 254 GKTVVVCGYGDVGKGCAQALRGFGARVVVT 283
>gnl|CDD|235824 PRK06545, PRK06545, prephenate dehydrogenase; Validated.
Length = 359
Score = 32.2 bits (74), Expect = 0.39
Identities = 22/77 (28%), Positives = 35/77 (45%), Gaps = 12/77 (15%)
Query: 178 KTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEK 237
+TV I+G G IG LA ++ G + S A A+ G+ID+L
Sbjct: 1 RTVLIVGLGLIGGSLALAIKAAGPDVFIIGYD------PSAAQLARALGFGVIDELA--- 51
Query: 238 GCHEDIFEFASKADVVV 254
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 = 0.48
Identities = 26/89 (29%), Positives = 36/89 (40%), Gaps = 9/89 (10%)
Query: 177 GKTVFILGFGN-IGVELAKRLRPFGVKIIATKRSWA--SHSQVSCQSSALAVKN---GII 230
GK V I G + IG LAK L G +I RS + + ++ A A I
Sbjct: 1 GKHVLITGGSSGIGKALAKELVKEGANVIIVARSESKLEEAVEEIEAEANASGQKVSYIS 60
Query: 231 DDLVDEKGCHEDIFEFASKA---DVVVCC 256
DL D + + + K D+VV C
Sbjct: 61 ADLSDYEEVEQAFAQAVEKGGPPDLVVNC 89
>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 = 29.4 bits (66), Expect = 0.56
Identities = 9/41 (21%), Positives = 17/41 (41%)
Query: 24 KMEGMARSSDKNITRVLFCGPHFPASHNYTKEYLQNYPSIQ 64
K G + + R+L C P P ++ + Q S++
Sbjct: 35 KTHGFLKGGWLTLKRILRCHPLHPGGNDPVPKKKQILESLK 75
>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 = 31.4 bits (72), Expect = 0.59
Identities = 21/92 (22%), Positives = 37/92 (40%), Gaps = 11/92 (11%)
Query: 178 KTVFILGFGN-IGVELAKRLRPFGVKIIATKRSWAS--HSQVSCQSSALAVKNGIIDDLV 234
K V I G + IG+ LA L G ++IAT R+ + ++ + D+
Sbjct: 1 KVVLITGCSSGIGLALALALAAQGYRVIATARNPDKLESLGELLNDNLEVLELDVTDEES 60
Query: 235 DEKGCHEDIFEFASKADVVVCCLSLNKQTAGI 266
+ +++ E + DV+V AG
Sbjct: 61 IKAA-VKEVIERFGRIDVLVNN-------AGY 84
>gnl|CDD|215623 PLN03190, PLN03190, aminophospholipid translocase; Provisional.
Length = 1178
Score = 31.8 bits (72), Expect = 0.66
Identities = 14/27 (51%), Positives = 17/27 (62%)
Query: 241 EDIFEFASKADVVVCCLSLNKQTAGIV 267
E +F+ ASK VV+CC Q AGIV
Sbjct: 837 EQLFQLASKCSVVLCCRVAPLQKAGIV 863
>gnl|CDD|236541 PRK09496, trkA, potassium transporter peripheral membrane
component; Reviewed.
Length = 453
Score = 31.6 bits (73), Expect = 0.68
Identities = 15/29 (51%), Positives = 18/29 (62%), Gaps = 2/29 (6%)
Query: 178 KTVFILGFGNIGVELAKRL--RPFGVKII 204
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 = 0.75
Identities = 16/41 (39%), Positives = 24/41 (58%)
Query: 173 ETLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASH 213
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 = 0.85
Identities = 28/117 (23%), Positives = 41/117 (35%), Gaps = 39/117 (33%)
Query: 177 GKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDE 236
GK V + G+G +G +A RLR G ++I T+ VD
Sbjct: 209 GKNVVVAGYGWVGRGIAMRLRGMGARVIVTE--------------------------VDP 242
Query: 237 KGCHEDIF---------EFASKADVVVCCLSLNKQTAGIVNKSFLSSMKKGSLLVNI 284
E E A D+ V + NK ++ K MK G++L N
Sbjct: 243 IRALEAAMDGFRVMTMEEAAKTGDIFVTA-TGNK---DVIRKEHFEKMKDGAILANA 295
>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 = 29.8 bits (68), Expect = 0.87
Identities = 20/85 (23%), Positives = 31/85 (36%), Gaps = 15/85 (17%)
Query: 179 TVFILG-FGNIGVELAKRLR---PFG-VKIIATKRSWASHSQVSCQSSALAVKNGIIDDL 233
V I+G G +G EL + L P V ++A+ RS +A I++
Sbjct: 1 KVAIVGATGYVGQELLRLLAEHPPLELVALVASSRS---------AGKKVAFAYPILEGG 51
Query: 234 VDEKGCHEDIFEFASKADVVVCCLS 258
D D + D+V L
Sbjct: 52 KDLLLEDVDPEDL-KDVDIVFLALP 75
>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 = 31.2 bits (72), Expect = 0.93
Identities = 13/44 (29%), Positives = 26/44 (59%), Gaps = 3/44 (6%)
Query: 248 SKADVVVCC-LSLNKQTAGIVNKSFLSSMKKGSLLVNIA--RGG 288
+AD+V+ L + +V + + +MK GS++V++A +GG
Sbjct: 230 KEADLVIGAVLIPGAKAPKLVTEEMVKTMKPGSVIVDVAIDQGG 273
>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: 177 GKTVFILGFGNIGVELAKRLRPFGVKIIAT 206
GK V + G+G +G A R R G ++I T
Sbjct: 195 GKVVVVAGYGWVGKGCAMRARGLGARVIVT 224
>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 = 30.3 bits (69), Expect = 1.1
Identities = 19/49 (38%), Positives = 27/49 (55%), Gaps = 4/49 (8%)
Query: 158 MRMAIEQKKLGVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVKIIAT 206
M+ A E LG ++L GKTV + G G +G +LA+ L G K+I
Sbjct: 13 MKAAAEHL-LG---TDSLEGKTVAVQGLGKVGYKLAEHLLEEGAKLIVA 57
>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 = 30.1 bits (68), Expect = 1.2
Identities = 30/119 (25%), Positives = 43/119 (36%), Gaps = 14/119 (11%)
Query: 184 GFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEKGCHEDI 243
G G+ G LA RL G KII R + +A + D K D
Sbjct: 8 GTGDQGKGLALRLAKAGNKIIIGSRDLEKAEE-----AAAKALEELGHGGSDIKVTGADN 62
Query: 244 FEFASKADVVVCCLSLNKQTAGIVNKSFLSSMK---KGSLLVNIARGGLLDYEAIAHYL 299
E A +ADVV+ + + L S++ G L+++ D A YL
Sbjct: 63 AEAAKRADVVILAVPWDHVL------KTLESLRDELSGKLVISPVVPLASDGGKGARYL 115
>gnl|CDD|213572 TIGR00936, ahcY, adenosylhomocysteinase. This enzyme hydrolyzes
adenosylhomocysteine as part of a cycle for the
regeneration of the methyl donor S-adenosylmethionine.
Species that lack this enzyme are likely to have
adenosylhomocysteine nucleosidase (EC 3.2.2.9), an
enzyme which also acts as 5'-methyladenosine
nucleosidase (see TIGR01704) [Energy metabolism, Amino
acids and amines].
Length = 407
Score = 30.5 bits (69), Expect = 1.4
Identities = 13/32 (40%), Positives = 19/32 (59%)
Query: 175 LLGKTVFILGFGNIGVELAKRLRPFGVKIIAT 206
+ GKTV + G+G G +A R R G ++I T
Sbjct: 194 IAGKTVVVAGYGWCGKGIAMRARGMGARVIVT 225
>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 = 1.5
Identities = 27/107 (25%), Positives = 41/107 (38%), Gaps = 27/107 (25%)
Query: 164 QKKLGVPTGETLLGKTVFILGFGNIG---VELAKRLRPFGVKIIATKRSWASHSQVSCQS 220
Q+K G+ G+T V ++G G IG LAK G + + S ++
Sbjct: 158 QRKAGIKPGDT-----VLVIGAGPIGLLHAMLAKA---SGARKVIV-------SDLNEFR 202
Query: 221 SALAVKNGIIDDLVDEKGCHEDIFEFASK------ADVVVCCLSLNK 261
A K G D +D ED+ E + ADVV+ +
Sbjct: 203 LEFAKKLG-ADYTIDAA--EEDLVEKVRELTDGRGADVVIVATGSPE 246
>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 = 30.3 bits (69), Expect = 1.5
Identities = 14/34 (41%), Positives = 19/34 (55%)
Query: 172 GETLLGKTVFILGFGNIGVELAKRLRPFGVKIIA 205
ETL GK V I G GN+ A++L G K++
Sbjct: 33 NETLKGKRVAISGSGNVAQYAAEKLLELGAKVVT 66
>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 = 1.5
Identities = 11/42 (26%), Positives = 24/42 (57%), Gaps = 1/42 (2%)
Query: 245 EFASKADVVV-CCLSLNKQTAGIVNKSFLSSMKKGSLLVNIA 285
E S+ D++V C L + I+ + L +K G+L+++++
Sbjct: 193 EELSEYDIIVNCILQDTDRPDHIIYEEDLKRLKPGALIIDVS 234
>gnl|CDD|184463 PRK14030, PRK14030, glutamate dehydrogenase; Provisional.
Length = 445
Score = 30.2 bits (68), Expect = 2.0
Identities = 13/34 (38%), Positives = 18/34 (52%)
Query: 171 TGETLLGKTVFILGFGNIGVELAKRLRPFGVKII 204
G + GKTV I GFGN+ A + G K++
Sbjct: 222 KGIDIKGKTVAISGFGNVAWGAATKATELGAKVV 255
>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 = 28.1 bits (63), Expect = 2.0
Identities = 15/32 (46%), Positives = 20/32 (62%)
Query: 165 KKLGVPTGETLLGKTVFILGFGNIGVELAKRL 196
K G T ++L GKTV +LG G +G +AK L
Sbjct: 11 KAAGKVTNKSLKGKTVVVLGAGEVGKGIAKLL 42
>gnl|CDD|178263 PLN02657, PLN02657, 3,8-divinyl protochlorophyllide a 8-vinyl
reductase.
Length = 390
Score = 30.1 bits (68), Expect = 2.0
Identities = 28/129 (21%), Positives = 46/129 (35%), Gaps = 24/129 (18%)
Query: 178 KTVFILG-FGNIGVELAKRLRPFGVKIIATKRSWA---SHSQVSCQSSALAVKNGIIDDL 233
TV ++G G IG + + L G ++A R + + L + D+
Sbjct: 61 VTVLVVGATGYIGKFVVRELVRRGYNVVAVAREKSGIRGKNGKEDTKKELPGAEVVFGDV 120
Query: 234 VDEKGCHEDIFEFASKADVVVCCLSLNKQTAGIVNKSFLSSMKKGSLLVNIARGGLLDYE 293
D + +F DVVV CL+ G V S+ +DY+
Sbjct: 121 TDADSLRKVLFSEGDPVDVVVSCLA---SRTGGVKDSW-----------------KIDYQ 160
Query: 294 AIAHYLECG 302
A + L+ G
Sbjct: 161 ATKNSLDAG 169
>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 = 2.0
Identities = 14/36 (38%), Positives = 18/36 (50%), Gaps = 1/36 (2%)
Query: 175 LLGKTVFILG-FGNIGVELAKRLRPFGVKIIATKRS 209
L G TV I G IG+ LA++ G +I T R
Sbjct: 3 LTGNTVLITGGTSGIGLALARKFLEAGNTVIITGRR 38
>gnl|CDD|129557 TIGR00465, ilvC, ketol-acid reductoisomerase. This is the second
enzyme in the parallel isoleucine-valine biosynthetic
pathway [Amino acid biosynthesis, Pyruvate family].
Length = 314
Score = 30.0 bits (68), Expect = 2.1
Identities = 26/110 (23%), Positives = 43/110 (39%), Gaps = 21/110 (19%)
Query: 175 LLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLV 234
L GKTV I+G+G+ G A LR G+ +I R + S A ++G
Sbjct: 1 LKGKTVAIIGYGSQGHAQALNLRDSGLNVIVGLRKGGA-------SWKKATEDG------ 47
Query: 235 DEKGCHE--DIFEFASKADVVVCCLSLNKQTAGIVNKSFLSSMKKGSLLV 282
+ + E +AD+++ L Q + +K+G L
Sbjct: 48 -----FKVGTVEEAIPQADLIMNLLPDEVQHE-VYEAEIQPLLKEGKTLG 91
>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 = 28.2 bits (64), Expect = 2.2
Identities = 9/18 (50%), Positives = 12/18 (66%)
Query: 190 VELAKRLRPFGVKIIATK 207
VE AKRL G +++AT
Sbjct: 3 VEFAKRLAELGFELLATG 20
>gnl|CDD|223364 COG0287, TyrA, Prephenate dehydrogenase [Amino acid transport and
metabolism].
Length = 279
Score = 29.6 bits (67), Expect = 2.4
Identities = 27/110 (24%), Positives = 53/110 (48%), Gaps = 17/110 (15%)
Query: 178 KTVFILGFGNIGVELAK--RLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVD 235
V I+G G +G LA+ + V+II RS A + A++ G+ID+L
Sbjct: 4 MKVGIVGLGLMGGSLARALKEAGLVVRIIGRDRSAA--------TLKAALELGVIDELTV 55
Query: 236 EKGCHEDIFEFASKADVVVCCLSLNKQTAGIVNKSFLSSMKKGSLLVNIA 285
+ E A++AD+V+ + + T ++ + +KKG+++ ++
Sbjct: 56 -----AGLAEAAAEADLVIVAVPIE-ATEEVLKELA-PHLKKGAIVTDVG 98
>gnl|CDD|224996 COG2085, COG2085, Predicted dinucleotide-binding enzymes [General
function prediction only].
Length = 211
Score = 29.2 bits (66), Expect = 2.6
Identities = 14/33 (42%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 178 KTVFILGFGNIGVELAKRLRPFGVK-IIATKRS 209
+ I+G GNIG LA RL G + II + R
Sbjct: 2 MIIAIIGTGNIGSALALRLAKAGHEVIIGSSRG 34
>gnl|CDD|223758 COG0686, Ald, Alanine dehydrogenase [Amino acid transport and
metabolism].
Length = 371
Score = 29.6 bits (67), Expect = 2.8
Identities = 30/124 (24%), Positives = 48/124 (38%), Gaps = 23/124 (18%)
Query: 168 GVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKN 227
GVP +L V +LG G +G AK G + + Q
Sbjct: 162 GVPG---VLPAKVVVLGGGVVGTNAAKIAIGLGADVTILDLNIDRLRQ------------ 206
Query: 228 GIIDDLVDEK-----GCHEDIFEFASKADVVVCC-LSLNKQTAGIVNKSFLSSMKKGSLL 281
+DDL + +I E KAD+V+ L + +V + + MK GS++
Sbjct: 207 --LDDLFGGRVHTLYSTPSNIEEAVKKADLVIGAVLIPGAKAPKLVTREMVKQMKPGSVI 264
Query: 282 VNIA 285
V++A
Sbjct: 265 VDVA 268
>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 = 29.3 bits (66), Expect = 3.2
Identities = 13/37 (35%), Positives = 18/37 (48%), Gaps = 1/37 (2%)
Query: 174 TLLGKTVFILGFGN-IGVELAKRLRPFGVKIIATKRS 209
G T+ I G + IG+ LAKR G +I R+
Sbjct: 2 KTTGNTILITGGASGIGLALAKRFLELGNTVIICGRN 38
>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 = 3.2
Identities = 13/45 (28%), Positives = 23/45 (51%), Gaps = 1/45 (2%)
Query: 55 EYLQNYPSIQVDVVPISDVPDVIANYHLCVVKTMRL-DSNCISRA 98
EYL YP ++VD+V + D++ + L DS+ ++R
Sbjct: 22 EYLARYPDVRVDLVLSDRLVDLVEEGFDAAFRIGELADSSLVARP 66
>gnl|CDD|112609 pfam03804, DUF325, Viral domain of unknown function.
Length = 71
Score = 27.1 bits (60), Expect = 3.4
Identities = 12/34 (35%), Positives = 19/34 (55%), Gaps = 2/34 (5%)
Query: 232 DLVDEKGCHEDI--FEFASKADVVVCCLSLNKQT 263
L+D K H D+ F F + +V C+++N QT
Sbjct: 27 ALIDGKVTHADVRRFGFLDRNALVSACMAVNVQT 60
>gnl|CDD|235554 PRK05673, dnaE, DNA polymerase III subunit alpha; Validated.
Length = 1135
Score = 29.3 bits (67), Expect = 3.7
Identities = 12/46 (26%), Positives = 24/46 (52%), Gaps = 10/46 (21%)
Query: 224 AVKN---GIIDDLVD---EKGCHEDIFEFASKADVVVCCLSLNKQT 263
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 = 3.8
Identities = 11/30 (36%), Positives = 17/30 (56%)
Query: 177 GKTVFILGFGNIGVELAKRLRPFGVKIIAT 206
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 = 4.0
Identities = 18/48 (37%), Positives = 26/48 (54%), Gaps = 12/48 (25%)
Query: 171 TGETLL------------GKTVFILGFGNIGVELAKRLRPFGVKIIAT 206
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 = 4.2
Identities = 16/47 (34%), Positives = 26/47 (55%), Gaps = 1/47 (2%)
Query: 53 TKEYLQNYPSIQVDVVPISDVPDVIANYHLCVVKTMRL-DSNCISRA 98
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 = 29.1 bits (66), Expect = 4.6
Identities = 13/28 (46%), Positives = 19/28 (67%)
Query: 176 LGKTVFILGFGNIGVELAKRLRPFGVKI 203
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 = 4.8
Identities = 26/104 (25%), Positives = 42/104 (40%), Gaps = 19/104 (18%)
Query: 175 LLGKTVFILGFGNIGVELAKRLRPFGVK-IIATKRSWASHSQVSCQSSALAVK------- 226
L GK VF+ G G IG + ++ G I+ + VS +S +LA +
Sbjct: 168 LQGKRVFVSGVGPIGCLIVAAVKTLGAAEIVC--------ADVSPRSLSLAREMGADKLV 219
Query: 227 ---NGIIDDLVDEKGCHEDIFEFASKADVVVCCLSLNKQTAGIV 267
N +D EKG + FE + + CL + + +V
Sbjct: 220 NPQNDDLDHYKAEKGYFDVSFEVSGHPSSINTCLEVTRAKGVMV 263
>gnl|CDD|223842 COG0771, MurD, UDP-N-acetylmuramoylalanine-D-glutamate ligase [Cell
envelope biogenesis, outer membrane].
Length = 448
Score = 28.8 bits (65), Expect = 5.7
Identities = 11/33 (33%), Positives = 16/33 (48%)
Query: 173 ETLLGKTVFILGFGNIGVELAKRLRPFGVKIIA 205
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 = 28.1 bits (63), Expect = 5.8
Identities = 10/30 (33%), Positives = 17/30 (56%)
Query: 177 GKTVFILGFGNIGVELAKRLRPFGVKIIAT 206
GK + G+G++G A L+ G ++I T
Sbjct: 23 GKVAVVCGYGDVGKGCAASLKGQGARVIVT 52
>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 = 28.5 bits (65), Expect = 5.8
Identities = 16/56 (28%), Positives = 29/56 (51%), Gaps = 17/56 (30%)
Query: 243 IFEFASKADVVVCCLSLNKQTAGI--------VNKSFLSSMKKGSLLVNIA--RGG 288
+ + ++AD+V+ TA I + K + SMK GS++V++A +GG
Sbjct: 243 LAKHIAEADIVIT-------TALIPGRKAPKLITKEMVESMKPGSVIVDLAAEQGG 291
>gnl|CDD|223536 COG0460, ThrA, Homoserine dehydrogenase [Amino acid transport and
metabolism].
Length = 333
Score = 28.3 bits (64), Expect = 5.9
Identities = 14/86 (16%), Positives = 29/86 (33%), Gaps = 19/86 (22%)
Query: 180 VFILGFGNIGVELAKRL--------RPFGVKIIATK---RSWASHSQVSCQSSALAVKNG 228
V +LG G +G + + L + G++I R + + ++ + +G
Sbjct: 6 VGLLGLGTVGSGVLEILAEKQEELRKRAGIEIRVVAVADRDGSLVRDLDLLNAEVWTTDG 65
Query: 229 IIDDLVDEKGCHEDIFEFASKADVVV 254
+ + DVVV
Sbjct: 66 ALSLGDE--------VLLDEDIDVVV 83
>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 = 6.3
Identities = 11/27 (40%), Positives = 18/27 (66%), Gaps = 3/27 (11%)
Query: 340 EHSYRSMAKVVGDVALQLH--AGTPLT 364
+YR + KV+ ++A ++H AG PLT
Sbjct: 176 PSTYRFVDKVIDEIA-RMHQEAGQPLT 201
>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 = 6.4
Identities = 14/42 (33%), Positives = 23/42 (54%), Gaps = 2/42 (4%)
Query: 177 GKTVFILG-FGNIGVELAKRLRPFGVK-IIATKRSWASHSQV 216
GKT+ + G G+IG EL +++ FG K +I R ++
Sbjct: 2 GKTILVTGGAGSIGSELVRQILKFGPKKLIVFDRDENKLHEL 43
>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 = 7.4
Identities = 9/17 (52%), Positives = 12/17 (70%)
Query: 190 VELAKRLRPFGVKIIAT 206
VE AK L GV+I++T
Sbjct: 16 VEFAKALVELGVEILST 32
>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 = 27.3 bits (61), Expect = 7.5
Identities = 27/120 (22%), Positives = 48/120 (40%), Gaps = 23/120 (19%)
Query: 172 GETLLGKTVFILGFGNIGVELAKRLRPFGVK-IIATKRSWASHSQVSCQSSALAVKNGII 230
L GK V ++G G + AK L G K I R+ ++ LA + +
Sbjct: 7 FGDLKGKKVLLIGAGEMARLAAKHLLSKGAKKITIANRT-LEKAK------ELAEEFPVG 59
Query: 231 DDLVDEKGCHEDIFEFASKADVVVCCLSLNKQTAG---IVNKSFLSSMKKGS--LLVNIA 285
+ + +++ E ++AD+V+ T+ I+ K + K L V+IA
Sbjct: 60 GEALP----LDELEELLAEADIVISA------TSAPTPIITKEMVEEALKARPLLFVDIA 109
>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 = 8.1
Identities = 16/53 (30%), Positives = 22/53 (41%), Gaps = 19/53 (35%)
Query: 302 GHLGGLGIDVAWTEPFDPNDPILKFKNVLITPHVGGVTEHSYRSMAKVVGDVA 354
GHL GL I +W E G++EH Y+ +A V G +A
Sbjct: 63 GHLVGLLIPHSWYEAL-------------------GISEHLYQLLAIVAGGIA 96
>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 = 8.3
Identities = 10/17 (58%), Positives = 11/17 (64%)
Query: 190 VELAKRLRPFGVKIIAT 206
VELAK L G K+ AT
Sbjct: 3 VELAKALVELGFKLYAT 19
>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 = 27.4 bits (62), Expect = 8.3
Identities = 12/55 (21%), Positives = 23/55 (41%), Gaps = 3/55 (5%)
Query: 231 DDLVDEKGC-HEDIFEFASKADVVVCCLSLNKQTAGIVN--KSFLSSMKKGSLLV 282
++LV E EF + ADVV+ + ++ L +K G +++
Sbjct: 37 EELVAEGAVGAASPAEFVASADVVITMVPAGAAVDAVILGEDGLLPGLKPGDIII 91
>gnl|CDD|223450 COG0373, HemA, Glutamyl-tRNA reductase [Coenzyme metabolism].
Length = 414
Score = 28.0 bits (63), Expect = 8.4
Identities = 24/87 (27%), Positives = 39/87 (44%), Gaps = 14/87 (16%)
Query: 173 ETLLGKTVFILGFGNIGVELAKRLRPFGV-KIIATKRSWASHSQVSCQSSALAVKNGIID 231
+L K V ++G G +G +AK L GV KI R+ +++ + A AV
Sbjct: 174 GSLKDKKVLVIGAGEMGELVAKHLAEKGVKKITIANRTLERAEELAKKLGAEAVA----- 228
Query: 232 DLVDEKGCHEDIFEFASKADVVVCCLS 258
E++ E ++ADVV+ S
Sbjct: 229 --------LEELLEALAEADVVISSTS 247
>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 = 8.4
Identities = 14/36 (38%), Positives = 19/36 (52%)
Query: 167 LGVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVK 202
LG + + V I G G +G+E+AK L GVK
Sbjct: 14 LGDEAMQKMAKSNVLISGMGGLGLEIAKNLVLAGVK 49
>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 = 28.1 bits (63), Expect = 8.4
Identities = 12/29 (41%), Positives = 17/29 (58%)
Query: 176 LGKTVFILGFGNIGVELAKRLRPFGVKII 204
L K V ++G G IG+ELA L G ++
Sbjct: 141 LPKRVVVVGGGYIGLELAAALAKLGKEVT 169
>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 = 27.9 bits (63), Expect = 8.5
Identities = 28/95 (29%), Positives = 43/95 (45%), Gaps = 12/95 (12%)
Query: 188 IGVELAKRLRPFGVKIIATKRSWASHSQ-VSCQSSALAVKN-GIIDDLVDEKGCH---ED 242
IG +A +L G K+I T RS ++ V + A VK G++ D+ D + E+
Sbjct: 10 IGRAIALKLAKEGAKVIITYRSSEEGAEEVVEELKAYGVKALGVVCDVSDREDVKAVVEE 69
Query: 243 IFEFASKADVVVCCLSLNKQTAGIVNKSFLSSMKK 277
I E D++V AGI + L MK+
Sbjct: 70 IEEELGPIDILVN-------NAGITRDNLLMRMKE 97
>gnl|CDD|216396 pfam01262, AlaDh_PNT_C, Alanine dehydrogenase/PNT, C-terminal
domain. This family now also contains the lysine
2-oxoglutarate reductases.
Length = 150
Score = 27.1 bits (61), Expect = 8.6
Identities = 23/112 (20%), Positives = 46/112 (41%), Gaps = 15/112 (13%)
Query: 178 KTVFILGFGNIG---VELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLV 234
V ++G G +G AK L G + Q+ ++ ++
Sbjct: 21 AKVVVIGGGVVGLGAAATAKGL---GAPVTILDVRPERLEQLD------SLFAEFVE--T 69
Query: 235 DEKGCHEDIFEFASKADVVVC-CLSLNKQTAGIVNKSFLSSMKKGSLLVNIA 285
D E + E ++AD+V+ L + +V + + +MK GS++V++A
Sbjct: 70 DIFSNCEYLAEAIAEADLVIGTVLIPGARAPKLVTREMVKTMKPGSVIVDVA 121
>gnl|CDD|236106 PRK07818, PRK07818, dihydrolipoamide dehydrogenase; Reviewed.
Length = 466
Score = 28.1 bits (63), Expect = 9.8
Identities = 12/28 (42%), Positives = 18/28 (64%)
Query: 176 LGKTVFILGFGNIGVELAKRLRPFGVKI 203
L K++ I G G IG+E A L+ +GV +
Sbjct: 171 LPKSIVIAGAGAIGMEFAYVLKNYGVDV 198
>gnl|CDD|180774 PRK06953, PRK06953, short chain dehydrogenase; Provisional.
Length = 222
Score = 27.3 bits (61), Expect = 9.8
Identities = 15/36 (41%), Positives = 21/36 (58%), Gaps = 1/36 (2%)
Query: 178 KTVFILGFG-NIGVELAKRLRPFGVKIIATKRSWAS 212
KTV I+G IG E ++ R G ++IAT R A+
Sbjct: 2 KTVLIVGASRGIGREFVRQYRADGWRVIATARDAAA 37
>gnl|CDD|133452 cd05213, NAD_bind_Glutamyl_tRNA_reduct, NADP-binding domain of
glutamyl-tRNA reductase. Glutamyl-tRNA reductase
catalyzes the conversion of glutamyl-tRNA to
glutamate-1-semialdehyde, initiating the synthesis of
tetrapyrrole. Whereas tRNAs are generally associated
with peptide bond formation in protein translation, here
the tRNA activates glutamate in the initiation of
tetrapyrrole biosynthesis in archaea, plants and many
bacteria. In the first step, activated glutamate is
reduced to glutamate-1-semi-aldehyde via the NADPH
dependent glutamyl-tRNA reductase. Glutamyl-tRNA
reductase forms a V-shaped dimer. Each monomer has 3
domains: an N-terminal catalytic domain, a classic
nucleotide binding domain, and a C-terminal dimerization
domain. Although the representative structure 1GPJ lacks
a bound NADPH, a theoretical binding pocket has been
described. (PMID 11172694). Amino acid dehydrogenase
(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 = 311
Score = 27.6 bits (62), Expect = 9.9
Identities = 26/99 (26%), Positives = 43/99 (43%), Gaps = 21/99 (21%)
Query: 161 AIE--QKKLGVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVK-IIATKRSWASHSQVS 217
A+E +K G L GK V ++G G +G AK L GV I R++ +++
Sbjct: 165 AVELAEKIFG-----NLKGKKVLVIGAGEMGELAAKHLAAKGVAEITIANRTYERAEELA 219
Query: 218 CQSSALAVKNGIIDDLVDEKGCHEDIFEFASKADVVVCC 256
+ AV +D+L++ +ADVV+
Sbjct: 220 KELGGNAVP---LDELLELLN----------EADVVISA 245
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
0.322 0.138 0.414
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: 18,782,165
Number of extensions: 1812929
Number of successful extensions: 2043
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1892
Number of HSP's successfully gapped: 178
Length of query: 370
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 272
Effective length of database: 6,590,910
Effective search space: 1792727520
Effective search space used: 1792727520
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: 60 (26.7 bits)