RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 024297
(269 letters)
>gnl|CDD|215501 PLN02928, PLN02928, oxidoreductase family protein.
Length = 347
Score = 400 bits (1029), Expect = e-141
Identities = 156/240 (65%), Positives = 192/240 (80%), Gaps = 5/240 (2%)
Query: 1 MEGMARSSDKNITRVLFCGPHFPASHNYTKEYLQNYPSIQVDVVPISDVPDVIANYHLCV 60
++ SD TRVLFCGP FPAS++YT+EYLQ YP IQVD V DVPDVIANY +CV
Sbjct: 7 IDKRVHHSDMRPTRVLFCGPEFPASYSYTREYLQKYPFIQVDAVAREDVPDVIANYDICV 66
Query: 61 VKTMRLDSNCISRANQMKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAASCAELT 120
K MRLD++ I+RA+QMKLIMQFGVGLEGVD++AAT+ GIKVARIP + TGNAASCAE+
Sbjct: 67 PKMMRLDADIIARASQMKLIMQFGVGLEGVDVDAATKHGIKVARIPSEGTGNAASCAEMA 126
Query: 121 IYLMLGLLRKQNEMRMAIEQKKLGVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVKII 180
IYLMLGLLRKQNEM+++++ ++LG P G+TL GKTVFILG+G IG+ELAKRLRPFGVK++
Sbjct: 127 IYLMLGLLRKQNEMQISLKARRLGEPIGDTLFGKTVFILGYGAIGIELAKRLRPFGVKLL 186
Query: 181 ATKRSWASHSQVSCQSSALAVKNGIIDDLVDEKGCHEDIFEFASKADVVVCCLSLNKQTV 240
AT+RSW S + + NG +DDLVDEKG HEDI+EFA +AD+VV C +L K+T
Sbjct: 187 ATRRSWTSEPEDGLL-----IPNGDVDDLVDEKGGHEDIYEFAGEADIVVLCCTLTKETA 241
>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 = 202 bits (515), Expect = 8e-64
Identities = 79/234 (33%), Positives = 116/234 (49%), Gaps = 25/234 (10%)
Query: 14 RVLFCGPHFPASHNYTKEYLQNYPSIQVDVVPISDVP-DVIANYHLCVVKTMR-LDSNCI 71
+VLF GP FP + + L P ++V D ++A+ + V + +D+ +
Sbjct: 1 KVLFLGPEFPDAEELLRALLPPAPGVEVVTAAELDEEAALLADADVLVPGMRKVIDAELL 60
Query: 72 SRANQMKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLMLGLLRKQ 131
+ A +++LI Q GVGL+GVD+ AAT GI VA IPG GNA S AE + LML LLR+
Sbjct: 61 AAAPRLRLIQQPGVGLDGVDLEAATARGIPVANIPG---GNAESVAEHAVMLMLALLRRL 117
Query: 132 NEMRMAIEQKKLGVPTGE---TLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWAS 188
E + + G P G L GKTV I+G GNIG +A+RLR FGV++I R
Sbjct: 118 PEADRELRAGRWGRPEGRPSRELSGKTVGIVGLGNIGRAVARRLRGFGVEVIYYDRFRDP 177
Query: 189 HSQVSCQSSALAVKNGIIDDLVDEKGCHEDIFEFASKADVVVCCLSLNKQTVKL 242
+ D + ++ E +++DVV + L +T L
Sbjct: 178 -----------------EAEEKDLGVRYVELDELLAESDVVSLHVPLTPETRHL 214
>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 = 112 bits (282), Expect = 2e-29
Identities = 56/179 (31%), Positives = 87/179 (48%), Gaps = 26/179 (14%)
Query: 71 ISRANQMKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLMLGLLRK 130
+++A ++K I G G++ +D++AA + GI V +PG NA + AE + L+L LLR+
Sbjct: 58 LAKAPKLKFIQVAGAGVDNIDLDAAKKRGITVTNVPG---ANAEAVAEHALGLLLALLRR 114
Query: 131 ----QNEMRMAIEQKKLGVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSW 186
+R G P G L GKTV I+G G IG +AKRL+ FG+K++ R+
Sbjct: 115 LPRADAAVRRGWGWLWAGFP-GYELEGKTVGIVGLGRIGQRVAKRLQAFGMKVLYYDRT- 172
Query: 187 ASHSQVSCQSSALAVKNGIIDDLVDEKGCHEDIFEFASKADVVVCCLSLNKQTVKLCSS 245
K +DL + E +++DVVV L L +T L +
Sbjct: 173 --------------RKPEPEEDLGFR---VVSLDELLAQSDVVVLHLPLTPETRHLINE 214
>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 = 111 bits (279), Expect = 6e-29
Identities = 52/170 (30%), Positives = 84/170 (49%), Gaps = 23/170 (13%)
Query: 71 ISRANQMKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLMLGLLRK 130
++ A ++K+I ++GVG + +D+ AA + GI V PG N+ S AELTI LML L R+
Sbjct: 63 LAAAPRLKVISRYGVGYDNIDLEAAKKRGIVVTNTPG---ANSNSVAELTIGLMLALARQ 119
Query: 131 QNEMRMAIEQKKLGVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHS 190
+ + P G L GKT+ I+G G IG +A+RL FG+K++A
Sbjct: 120 IPQADREVRAGGWDRPVGTELYGKTLGIIGLGRIGKAVARRLSGFGMKVLAYDPYP---- 175
Query: 191 QVSCQSSALAVKNGI-IDDLVDEKGCHEDIFEFASKADVVVCCLSLNKQT 239
A ++G+ L E++ + ++D + L L +T
Sbjct: 176 -----DEEFAKEHGVEFVSL-------EELLK---ESDFISLHLPLTPET 210
>gnl|CDD|223189 COG0111, SerA, Phosphoglycerate dehydrogenase and related
dehydrogenases [Amino acid transport and metabolism].
Length = 324
Score = 108 bits (271), Expect = 1e-27
Identities = 57/210 (27%), Positives = 93/210 (44%), Gaps = 30/210 (14%)
Query: 39 IQVDVVPISDVPDVIANYHLCVVKTMRLDSNCISRANQMKLIMQFGVGLEGVDINAATRC 98
+ ++ + +A+ +V + ++ A +K I + G G++ +D+ AAT+
Sbjct: 29 PDGPDLDEEELLEALADADALIVSVTPVTEEVLAAAPNLKAIGRAGAGVDNIDLEAATKR 88
Query: 99 GIKVARIPGDVTGNAASCAELTIYLMLGLLRK----QNEMRMAIEQKKLGVPTGETLLGK 154
GI V PG GNA S AEL + L+L L R+ R +K G L GK
Sbjct: 89 GILVVNAPG---GNAISVAELVLALLLALARRIPDADASQRRGEWDRKAF--RGTELAGK 143
Query: 155 TVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEKG 214
TV I+G G IG +AKRL+ FG+K+I + +S + G
Sbjct: 144 TVGIIGLGRIGRAVAKRLKAFGMKVIG----YDPYS---------------PRERAGVDG 184
Query: 215 CH--EDIFEFASKADVVVCCLSLNKQTVKL 242
+ + E ++AD++ L L +T L
Sbjct: 185 VVGVDSLDELLAEADILTLHLPLTPETRGL 214
>gnl|CDD|223980 COG1052, LdhA, Lactate dehydrogenase and related dehydrogenases
[Energy production and conversion / Coenzyme metabolism
/ General function prediction only].
Length = 324
Score = 105 bits (264), Expect = 1e-26
Identities = 49/208 (23%), Positives = 92/208 (44%), Gaps = 28/208 (13%)
Query: 39 IQVDVVPISDVPDVIANYH-LCVVKTMRLDSNCISRANQMKLIMQFGVGLEGVDINAATR 97
+ D+ P +++ + + + + R+D+ + + +KLI G + VD+ AA
Sbjct: 28 YEDDLTPDTELAERLKDADAVITFVNDRIDAEVLEKLPGLKLIATRSAGYDNVDLEAAKE 87
Query: 98 CGIKVARIPGDVTGNAASCAELTIYLMLGLLRK--QNEMRMA----IEQKKLGVPTGETL 151
GI V +PG T + AE + L+L L R+ + + R+ G L
Sbjct: 88 RGITVTNVPGYST---EAVAEHAVALILALARRIHEGDRRVREGNWSLSGGPDPLLGFDL 144
Query: 152 LGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVD 211
GKT+ I+G G IG +A+RL+ FG+K++ RS N + +
Sbjct: 145 RGKTLGIIGLGRIGQAVARRLKGFGMKVLYYDRS----------------PNPEAEKELG 188
Query: 212 EKGCHEDIFEFASKADVVVCCLSLNKQT 239
+ + D+ E +++D++ L +T
Sbjct: 189 AR--YVDLDELLAESDIISLHCPLTPET 214
>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 = 102 bits (257), Expect = 1e-25
Identities = 55/216 (25%), Positives = 94/216 (43%), Gaps = 41/216 (18%)
Query: 36 YPSIQVDVVPISD--VPDVIANYHLCVVKTMRLDSNCISRANQMKLIMQFGVGLEGVDIN 93
+ +V + D + + + + V + + ++ ++KLI G++ + +
Sbjct: 19 LEGLYAEVPELPDEAAEEALEDADVLVGGRLTKEEA-LAALKRLKLIQVPSAGVDHLPL- 76
Query: 94 AATRCGIKVARIPGDVT-----GNAASCAELTIYLMLGLLRK----QNEMRMAI-EQKKL 143
R+P V GN+ + AE + L+L L ++ N++R I +
Sbjct: 77 ---------ERLPEGVVVANNHGNSPAVAEHALALILALAKRIVEYDNDLRRGIWHGRAG 127
Query: 144 GVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKN 203
P + L GKTV ILG+G+IG E+A+ L+ FG+++I RS
Sbjct: 128 EEPESKELRGKTVGILGYGHIGREIARLLKAFGMRVIGVSRS------------------ 169
Query: 204 GIIDDLVDEKGCHEDIFEFASKADVVVCCLSLNKQT 239
D+ D G D+ E +ADVVV L L KQT
Sbjct: 170 PKEDEGADFVGTLSDLDEALEQADVVVVALPLTKQT 205
>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 = 100 bits (251), Expect = 6e-25
Identities = 69/240 (28%), Positives = 106/240 (44%), Gaps = 42/240 (17%)
Query: 14 RVLFCGPHFPASHNYTKEYLQNYPSIQVDVVPISD---VPDVIANYHLCVVKTM-RLDSN 69
+VL P E L+ I+VDV P + +IA+ +V++ ++ +
Sbjct: 1 KVLVTDPIDEEGL----ELLREA-GIEVDVAPGLSEEELLAIIADADALIVRSATKVTAE 55
Query: 70 CISRANQMKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLMLGLLR 129
I A ++K+I + GVG++ +D+ AAT GI V PG N S AE TI LML L R
Sbjct: 56 VIEAAPRLKVIGRAGVGVDNIDVEAATARGILVVNAPG---ANTISVAEHTIALMLALAR 112
Query: 130 KQNEMRMAI-----EQKKLGVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKR 184
+ ++ ++KK G L GKT+ I+G G IG E+A+R R FG+K++A
Sbjct: 113 NIPQADASLRAGKWDRKKF---MGVELRGKTLGIVGLGRIGREVARRARAFGMKVLAYDP 169
Query: 185 SWASHSQVSCQSSALAVKNGIIDDLVDEKGCHE--DIFEFASKADVVVCCLSLNKQTVKL 242
I G E + E ++AD + L +T L
Sbjct: 170 --------------------YISAERAAAGGVELVSLDELLAEADFISLHTPLTPETRGL 209
>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 = 95.3 bits (238), Expect = 4e-23
Identities = 56/161 (34%), Positives = 85/161 (52%), Gaps = 16/161 (9%)
Query: 31 EYLQNYPSIQVDVVPISD---VPDVIANYHLCVVKT-MRLDSNCISRANQMKLIMQFGVG 86
E L+ +VD P+ + + I +Y + +V++ ++ I A +K+I + GVG
Sbjct: 15 EKLEE-AGFEVDYEPLIAKEELLEKIKDYDVLIVRSRTKVTKEVIDAAKNLKIIARAGVG 73
Query: 87 LEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLMLGLLRK----QNEMRMAI-EQK 141
L+ +D+ A + GIKV PG ++ S AEL I LML L R EM++ +K
Sbjct: 74 LDNIDVEYAKKKGIKVINTPG---ASSNSVAELVIGLMLSLARFIHRANREMKLGKWNKK 130
Query: 142 KLGVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVKIIAT 182
K G L GKT+ I+GFG IG E+AK R G+ +IA
Sbjct: 131 KY---KGIELRGKTLGIIGFGRIGREVAKIARALGMNVIAY 168
>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 = 95.2 bits (238), Expect = 5e-23
Identities = 51/191 (26%), Positives = 83/191 (43%), Gaps = 26/191 (13%)
Query: 58 LCVVKTMRLDSNCISRANQMKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAASCA 117
L T ++D+ + A +K+I + VG + +D++AA GI V P +T + A
Sbjct: 47 LLCTLTDKIDAELLDAAPPLKVIANYSVGYDHIDVDAAKARGIPVTNTPDVLT---DATA 103
Query: 118 ELTIYLMLGLLRKQNEM-RMAIEQKKLGV-PT---GETLLGKTVFILGFGNIGVELAKRL 172
+L L+L R+ E R + G PT G L GKT+ I+G G IG +A+R
Sbjct: 104 DLAFALLLAAARRVVEGDRFVRAGEWKGWSPTLLLGTDLHGKTLGIVGMGRIGQAVARRA 163
Query: 173 RPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEKGCHEDIFEFASKADVVVCC 232
+ FG+KI+ R S+ L + + + E +++D V
Sbjct: 164 KGFGMKILYHNR-----SRKPEAEEELGAR-------------YVSLDELLAESDFVSLH 205
Query: 233 LSLNKQTVKLC 243
L +T L
Sbjct: 206 CPLTPETRHLI 216
>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 = 93.9 bits (234), Expect = 2e-22
Identities = 50/174 (28%), Positives = 82/174 (47%), Gaps = 17/174 (9%)
Query: 15 VLFCGPHFPASHNYTKEYLQNYPSIQV-DVVPISDVPDVIANYH-LCVVKTMRLDSNCIS 72
VL P E L+ ++V D + ++ + + L V T + + +
Sbjct: 1 VLITDP----LRPEELELLKEGGEVEVHDELLTEELLEAAKDADALIVRSTTPVTAEVLE 56
Query: 73 RANQMKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLMLGLLRKQN 132
A +K+I + GVG++ +D++AAT GI V +PG + S AELT+ L+L L R+
Sbjct: 57 AAPGLKVIARRGVGVDNIDLDAATERGILVTNVPG---YSTESVAELTVGLILALARRIP 113
Query: 133 EMRMAIEQKKLGV-----PTGETLLGKTVFILGFGNIGVELAKRLRPFGVKIIA 181
E A + G P G L GKT+ ++G G IG A + G+ ++A
Sbjct: 114 E---ADASVRAGDWKKGGPIGLELYGKTLGVIGGGGIGGIGAAIAKALGMGVVA 164
>gnl|CDD|237436 PRK13581, PRK13581, D-3-phosphoglycerate dehydrogenase;
Provisional.
Length = 526
Score = 92.8 bits (232), Expect = 2e-21
Identities = 62/164 (37%), Positives = 90/164 (54%), Gaps = 23/164 (14%)
Query: 31 EYLQNYPSIQVDVVPISDVP---DVIANYHLCVVKTM-RLDSNCISRANQMKLIMQFGVG 86
E L++ P ++VDV D ++I +Y +V++ ++ + + A +K+I + GVG
Sbjct: 15 EILKDAPGVEVDVKTGLDKEELLEIIGDYDALIVRSATKVTAEVLEAAKNLKVIGRAGVG 74
Query: 87 LEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLMLGLLR---------KQNEMRMA 137
++ VD+ AATR GI V P TGN S AE TI LML L R K +
Sbjct: 75 VDNVDVPAATRRGIIVVNAP---TGNTISAAEHTIALMLALARNIPQAHASLKAGKW--- 128
Query: 138 IEQKKLGVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVKIIA 181
E+KK G L GKT+ I+G G IG E+AKR + FG+K+IA
Sbjct: 129 -ERKKF---MGVELYGKTLGIIGLGRIGSEVAKRAKAFGMKVIA 168
>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 = 90.8 bits (226), Expect = 2e-21
Identities = 51/187 (27%), Positives = 76/187 (40%), Gaps = 25/187 (13%)
Query: 58 LCVVKTMRLDSNCISRANQMKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAASCA 117
L + +D I A +K+I +G G + +D++ A GI V P T A
Sbjct: 47 LITPLSTPVDKEIIDAAKNLKIIANYGAGFDNIDVDYAKEKGIPVTNTPAVST---EPTA 103
Query: 118 ELTIYLMLGLLRKQNEM-RMAIEQKKLGVP----TGETLLGKTVFILGFGNIGVELAKRL 172
ELT L+L L R+ E R+ LG G L GKT+ I+G G IG +A+R
Sbjct: 104 ELTFGLILALARRIAEGDRLMRRGGFLGWAPLFFLGHELAGKTLGIIGMGRIGQAVARRA 163
Query: 173 RPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEKGCHEDIFEFASKADVVVCC 232
+ FG+KI+ R H L +D+L+ ++D V
Sbjct: 164 KAFGMKILYYNR----HRLSEETEKELGATYVDLDELL-------------KESDFVSLH 206
Query: 233 LSLNKQT 239
+T
Sbjct: 207 APYTPET 213
>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 = 90.1 bits (224), Expect = 2e-20
Identities = 52/181 (28%), Positives = 89/181 (49%), Gaps = 28/181 (15%)
Query: 14 RVLFCGPHFPASHNYTKEYLQNYPSIQVDVVP-------ISDVPDVIANYHLCVVKTM-R 65
+VL P + L++ ++VDV + +PD Y +V++ +
Sbjct: 1 KVLIADP----ISPDGIDILED-VGVEVDVQTGLSREELLEIIPD----YDALIVRSATK 51
Query: 66 LDSNCISRANQMKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLML 125
+ I+ A ++K+I + GVG++ +DI AAT GI V P TGN S AE + ++L
Sbjct: 52 VTEEVIAAAPKLKVIGRAGVGVDNIDIEAATARGILVVNAP---TGNTISAAEHALAMLL 108
Query: 126 GLLRKQNEMRMAI-----EQKKLGVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVKII 180
R + ++ ++K G L GKT+ ++G G IG +AKR + FG+K++
Sbjct: 109 AAARNIPQADASLKEGEWDRKAF---MGTELYGKTLGVIGLGRIGSIVAKRAKAFGMKVL 165
Query: 181 A 181
A
Sbjct: 166 A 166
>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 = 87.5 bits (218), Expect = 3e-20
Identities = 48/183 (26%), Positives = 79/183 (43%), Gaps = 29/183 (15%)
Query: 64 MRLDSNCISRANQMKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYL 123
L + I+ ++LI FGVG +G+D++AA GI+V PG A+L + L
Sbjct: 52 TGLSAALIAALPALELIASFGVGYDGIDLDAARARGIRVTNTPGV---LTDDVADLAVGL 108
Query: 124 MLGLLRK--QNEMRMAIEQK--KLGVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVKI 179
+L +LR+ + R + K P + GK V I+G G IG +A+RL FG++I
Sbjct: 109 LLAVLRRIPAAD-RFVRAGRWPKGAFPLTRKVSGKRVGIVGLGRIGRAIARRLEAFGMEI 167
Query: 180 IATKRSWASHSQVSCQSSALAVKNGIIDDLVDEKGCHEDIFEFASKADVVVCCLSLNKQT 239
++ V + + + E A+++DV+V T
Sbjct: 168 -----AYHGRRPK---------------PDVPYR-YYASLLELAAESDVLVVACPGGPAT 206
Query: 240 VKL 242
L
Sbjct: 207 RHL 209
>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 = 86.4 bits (215), Expect = 9e-20
Identities = 47/140 (33%), Positives = 67/140 (47%), Gaps = 15/140 (10%)
Query: 51 DVIANYHLCVVKTMRLDSNCISRANQMKLIMQFGV---GLEGVDINAATRCGIKVARIPG 107
+ + + + + + I A ++KLI GV G E VD+ AAT GI V PG
Sbjct: 42 EALKDADILITHFAPVTKKVIEAAPKLKLI---GVCRGGPENVDVEAATERGIPVLNTPG 98
Query: 108 DVTGNAASCAELTIYLMLGLLRK----QNEMRMAIEQKKL--GVPTGETLLGKTVFILGF 161
NA + AE T+ LML R ++ +K G L GKTV I+GF
Sbjct: 99 R---NAEAVAEFTVGLMLAETRNIARAHAALKDGEWRKDYYNYDGYGPELRGKTVGIVGF 155
Query: 162 GNIGVELAKRLRPFGVKIIA 181
G IG +AKRL+ FG +++
Sbjct: 156 GAIGRRVAKRLKAFGAEVLV 175
>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 = 86.4 bits (215), Expect = 9e-20
Identities = 45/224 (20%), Positives = 85/224 (37%), Gaps = 25/224 (11%)
Query: 21 HFPASHNYTKEYLQNYPSIQVDVVPISDVPDVIANYHLCVVKTMRLDSNCISRANQMKLI 80
P + + P ++ VV ++ + +A+ V+ + A +++ I
Sbjct: 6 LSPLDDEHLERLRAAAPGAELRVVTAEELTEELADAD--VLLGNPPLPELLPAAPRLRWI 63
Query: 81 MQFGVGLEGVDINAATRCGIKVARIPGDVTG-NAASCAELTIYLMLGLLRKQNEMRMAIE 139
G++ + + + G AE + ML RK
Sbjct: 64 QSTSAGVDALLFPELLERDVVLTN----ARGIFGPPIAEYVLGYMLAFARKLPRYARNQA 119
Query: 140 QKK-LGVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSA 198
+++ L GKTV I+G G+IG E+A+R + FG+++I +RS V
Sbjct: 120 ERRWQRRGPVRELAGKTVLIVGLGDIGREIARRAKAFGMRVIGVRRSGRPAPPV------ 173
Query: 199 LAVKNGIIDDLVDEKGCHEDIFEFASKADVVVCCLSLNKQTVKL 242
+D++ +++ E +AD VV L L +T L
Sbjct: 174 -------VDEVYTP----DELDELLPEADYVVNALPLTPETRGL 206
>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 = 85.7 bits (213), Expect = 2e-19
Identities = 46/169 (27%), Positives = 72/169 (42%), Gaps = 30/169 (17%)
Query: 78 KLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLMLGLLRKQNEMRMA 137
K+I G G + +D++A T+ GI+V+ PG V + A+ ++L+LG LR + +
Sbjct: 78 KIIAHAGAGYDQIDVDALTKRGIQVSNTPGAVD---EATADTALFLILGALRNFSRAERS 134
Query: 138 IEQKKLGVPTGETLL-------GKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHS 190
+ G G L GKT+ ILG G IG +A++ FG+KII RS
Sbjct: 135 A---RAGKWRGFLDLTLAHDPRGKTLGILGLGGIGKAIARKAAAFGMKIIYHNRSRL--- 188
Query: 191 QVSCQSSALAVKNGIIDDLVDEKGCHEDIFEFASKADVVVCCLSLNKQT 239
L + + E +++DVV L T
Sbjct: 189 -----PEELEKALATY---------YVSLDELLAQSDVVSLNCPLTAAT 223
>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 = 84.7 bits (210), Expect = 5e-19
Identities = 43/109 (39%), Positives = 64/109 (58%), Gaps = 6/109 (5%)
Query: 78 KLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLMLGLLRKQNEMRMA 137
KLI + G+G + VD+ AAT G+ V R+PG V + AE + L+L +LRK N+ A
Sbjct: 71 KLIARHGIGYDNVDLKAATEHGVIVTRVPGAV--ERDAVAEHAVALILTVLRKINQASEA 128
Query: 138 IEQKKLGVPT---GETLLGKTVFILGFGNIGVELAKRLRP-FGVKIIAT 182
+++ K G L GKTV I+G+GNIG +A+ L+ F K++A
Sbjct: 129 VKEGKWTERANFVGHELSGKTVGIIGYGNIGSRVAEILKEGFNAKVLAY 177
>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 = 81.6 bits (202), Expect = 5e-18
Identities = 50/154 (32%), Positives = 77/154 (50%), Gaps = 19/154 (12%)
Query: 39 IQVDVVPIS---DVPDVIANYHLCVVKT-MRLDSNCISRANQMKLIMQFGVGLEGVDINA 94
+VD P ++ +I Y ++++ +D I +A +K I + G GLE +D+
Sbjct: 21 FEVDYDPTISREEILAIIPQYDGLIIRSRFPIDKEFIEKATNLKFIARAGAGLENIDLEY 80
Query: 95 ATRCGIKVARIPGDVTGNAASCAELTIYLMLGLLRKQN----EMRMAI---EQKKLGVPT 147
A GI++ P GN + E + ++L L K N E+R I E +
Sbjct: 81 AKEKGIELFNAP---EGNRDAVGEHALGMLLALFNKLNRADQEVRNGIWDREGNR----- 132
Query: 148 GETLLGKTVFILGFGNIGVELAKRLRPFGVKIIA 181
G L+GKTV I+G+GN+G AKRL FG K+IA
Sbjct: 133 GVELMGKTVGIIGYGNMGKAFAKRLSGFGCKVIA 166
>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 = 80.4 bits (199), Expect = 1e-17
Identities = 52/186 (27%), Positives = 80/186 (43%), Gaps = 24/186 (12%)
Query: 58 LCVVKTMRLDSNCISRANQMKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAASCA 117
L R+D++ + ++K+I G + D+ A T GI V +P +T A
Sbjct: 48 LMAFMPDRIDADFLDACPRLKIIACALKGYDNFDVEACTARGIWVTIVPDLLT---EPTA 104
Query: 118 ELTIYLMLGLLRKQNEMRMAIEQKKLG--VPT--GETLLGKTVFILGFGNIGVELAKRLR 173
ELTI L++GL R + K G P G L GKTV ILG G +G +A+RL
Sbjct: 105 ELTIGLLIGLGRHILAGDRFVRSGKFGGWRPKFYGTGLDGKTVGILGMGALGRAIARRLS 164
Query: 174 PFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEKGCHEDIFEFASKADVVVCCL 233
FG ++ + H + AL ++ +D+L+ +D +V L
Sbjct: 165 GFGATLLY----YDPHPLDQAEEQALNLRRVELDELL-------------ESSDFLVLAL 207
Query: 234 SLNKQT 239
L T
Sbjct: 208 PLTPDT 213
>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 = 76.4 bits (189), Expect = 5e-17
Identities = 33/122 (27%), Positives = 50/122 (40%), Gaps = 23/122 (18%)
Query: 121 IYLMLGLLRKQNEMRMAIEQKKL--GVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVK 178
+ L+L L R+ E + + G L GKTV I+G G IG +A+RL+ FG+K
Sbjct: 1 LALLLALARRIPEADRQVRAGRWRPDALLGRELSGKTVGIIGLGRIGRAVARRLKAFGMK 60
Query: 179 IIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEKGCH-EDIFEFASKADVVVCCLSLNK 237
+IA R + G + E +++DVV L L
Sbjct: 61 VIAYDRY--------------------PKAEAEALGARYVSLDELLAESDVVSLHLPLTP 100
Query: 238 QT 239
+T
Sbjct: 101 ET 102
>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 = 77.6 bits (192), Expect = 1e-16
Identities = 47/199 (23%), Positives = 83/199 (41%), Gaps = 38/199 (19%)
Query: 51 DVIANYHLCVVKTMRLDSNCISRANQMKLIMQFGVGLEGVDINAATRCGIKVARIPG--- 107
D + + + + I ++K+I+++GVG++ VD+ AAT GI V +P
Sbjct: 46 DALLVQYA------PVTAEVIEALPRLKVIVRYGVGVDNVDVAAATERGIPVCNVPDYCT 99
Query: 108 -DVTGNAASCAELTIYLMLGLLRKQNEMRMAIEQKKLGVPTGETLL---GKTVFILGFGN 163
+V A+ + L+L L RK + A+ G + G T+ ++GFG
Sbjct: 100 EEV-------ADHALALILALARKLPFLDRAVRAGGWDWTVGGPIRRLRGLTLGLVGFGR 152
Query: 164 IGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEKGCHEDIFEFA 223
IG +AKR + FG ++IA V +G+ +++
Sbjct: 153 IGRAVAKRAKAFGFRVIAYDPY---------------VPDGVAALGGVRVVSLDELLA-- 195
Query: 224 SKADVVVCCLSLNKQTVKL 242
++DVV L +T L
Sbjct: 196 -RSDVVSLHCPLTPETRHL 213
>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 = 75.7 bits (187), Expect = 6e-16
Identities = 50/191 (26%), Positives = 85/191 (44%), Gaps = 35/191 (18%)
Query: 74 ANQMKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLMLGLLRK--- 130
A +K I + G G+ +D++AA++ GI V PG NA + AEL I +ML L R
Sbjct: 48 APSLKAIARAGAGVNNIDVDAASKRGIVVFNTPG---ANANAVAELVIAMMLALSRNIIQ 104
Query: 131 ---------QNEMRMAIEQKKLGVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVKIIA 181
+++ +E+ K E L GKT+ ++G GNIG +A G+K+I
Sbjct: 105 AIKWVTNGDGDDISKGVEKGKKQFVGTE-LRGKTLGVIGLGNIGRLVANAALALGMKVIG 163
Query: 182 TKRSWASHSQVSCQSSALAVKNGII--DDLVDEKGCHEDIFEFASKADVVVCCLSLNKQT 239
+S + +A + + L E++ + AD + + L +T
Sbjct: 164 YDPY------LSVE-AAWKLSVEVQRVTSL-------EELL---ATADYITLHVPLTDET 206
Query: 240 VKLCSSSLSSK 250
L ++ L +K
Sbjct: 207 RGLINAELLAK 217
>gnl|CDD|183914 PRK13243, PRK13243, glyoxylate reductase; Reviewed.
Length = 333
Score = 75.6 bits (186), Expect = 7e-16
Identities = 47/151 (31%), Positives = 76/151 (50%), Gaps = 15/151 (9%)
Query: 44 VPISDVPDVIANYHLCVVKTMRLDSNCISRANQMKLIMQFGVGLEGVDINAATRCGIKVA 103
V + V DV A L + + R+D A +++++ + VG + +D+ ATR GI V
Sbjct: 38 VLLEKVRDVDA---LVTMLSERIDCEVFEAAPRLRIVANYAVGYDNIDVEEATRRGIYVT 94
Query: 104 RIPGDVTGNAASCAELTIYLMLGLLRKQNEMRMAI---EQKKLGVP------TGETLLGK 154
PG +T A A+ L+L R+ E + E K+ GV G + GK
Sbjct: 95 NTPGVLT-EAT--ADFAWALLLATARRLVEADHFVRSGEWKRRGVAWHPLMFLGYDVYGK 151
Query: 155 TVFILGFGNIGVELAKRLRPFGVKIIATKRS 185
T+ I+GFG IG +A+R + FG++I+ R+
Sbjct: 152 TIGIIGFGRIGQAVARRAKGFGMRILYYSRT 182
>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 = 75.2 bits (186), Expect = 8e-16
Identities = 42/138 (30%), Positives = 64/138 (46%), Gaps = 20/138 (14%)
Query: 60 VVKTMR----LDSNCISRANQMKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAAS 115
+ MR + + R +KL++ G+ +D+ AA GI V G T +
Sbjct: 49 AIVLMRERTPFPAALLERLPNLKLLVTTGMRNASIDLAAAKERGIVVCGTGGGPT----A 104
Query: 116 CAELTIYLMLGLLRK----QNEMRMAIEQKKLGVPTGETLLGKTVFILGFGNIGVELAKR 171
AELT L+L L R +R Q LG L GKT+ I+G G IG +A+
Sbjct: 105 TAELTWALILALARNLPEEDAALRAGGWQTTLGT----GLAGKTLGIVGLGRIGARVARI 160
Query: 172 LRPFGVKIIATKRSWASH 189
+ FG+++IA W+S+
Sbjct: 161 GQAFGMRVIA----WSSN 174
>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 = 74.7 bits (184), Expect = 2e-15
Identities = 59/195 (30%), Positives = 86/195 (44%), Gaps = 45/195 (23%)
Query: 71 ISRANQMKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTG-NAASCAELTIYLMLGLLR 129
I++A +KL + G+G + VD+ AA GI VA +VTG N S AE + ++L L+R
Sbjct: 79 IAKAKNLKLALTAGIGSDHVDLQAANDRGITVA----EVTGSNVVSVAEHVVMMILILVR 134
Query: 130 K-QNEMRMAIEQKKLGVPTGE-----------TLLGKTVFILGFGNIGVELAKRLRPFGV 177
AIE G L GKTV +G G IG+ + +RL+PF V
Sbjct: 135 NYVPGHEQAIE--------GGWNVADVVKRAYDLEGKTVGTVGAGRIGLRVLRRLKPFDV 186
Query: 178 KIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEKGC--HEDIFEFASKADVVVCCLSL 235
++ R H +++ E G H D+ + SK DVV L
Sbjct: 187 HLLYYDR----HRLP--------------EEVEKELGLTRHADLEDMVSKCDVVTINCPL 228
Query: 236 NKQTVKLCSSSLSSK 250
+ +T L + L SK
Sbjct: 229 HPETEGLFNKELLSK 243
>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 = 72.7 bits (179), Expect = 7e-15
Identities = 46/179 (25%), Positives = 78/179 (43%), Gaps = 16/179 (8%)
Query: 13 TRVLFCGPHFPASHNYTKEYLQNYPSIQVDVVPISDVPDVIANYHL-------CVVKTMR 65
+VL + KE L+ VDV ++ + + L T +
Sbjct: 1 MKVLIYD-YRDDELEIEKEILKAGG---VDVEIVTYLLNDDETAELAKGADAILTAFTDK 56
Query: 66 LDSNCISRANQMKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLML 125
+D+ + +A +K I G + +D++ A GI V +P + AE TI L+L
Sbjct: 57 IDAELLDKAPGLKFISLRATGYDNIDLDYAKELGIGVTNVPEYSPN---AVAEHTIALIL 113
Query: 126 GLLRKQ--NEMRMAIEQKKLGVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVKIIAT 182
LLR + + R + + G L +TV ++G G IG +A+R + FG+K+IA
Sbjct: 114 ALLRNRKYIDERDKNQDLQDAGVIGRELEDQTVGVVGTGKIGRAVAQRAKGFGMKVIAY 172
>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 = 69.6 bits (171), Expect = 1e-13
Identities = 56/198 (28%), Positives = 84/198 (42%), Gaps = 43/198 (21%)
Query: 52 VIANYHLCVVKTMRLDSNCISRANQMKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTG 111
+IAN M L I +K+I G++ VD+ A GI V+
Sbjct: 53 MIAN--------MPLPGEVIEACKNLKMISVAFTGVDHVDLEACKERGITVS-------- 96
Query: 112 NAA-----SCAELTIYLMLGLLRK--QNEMRMAIEQKKLGVPTGETLLGKTVFILGFGNI 164
NAA + AELTI L + LLR + + K G+ G L GKTV I+G G I
Sbjct: 97 NAAGYSTEAVAELTIGLAIDLLRNIVPCDAAVRAGGTKAGL-IGRELAGKTVGIVGTGAI 155
Query: 165 GVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEKGCHEDIFEFAS 224
G+ +A+ + FG K++A RS K ++ + + E +
Sbjct: 156 GLRVARLFKAFGCKVLAYSRS---------------EKEEAKALGIE----YVSLDELLA 196
Query: 225 KADVVVCCLSLNKQTVKL 242
++D+V L LN +T L
Sbjct: 197 ESDIVSLHLPLNDETKGL 214
>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 = 69.2 bits (170), Expect = 1e-13
Identities = 37/128 (28%), Positives = 47/128 (36%), Gaps = 19/128 (14%)
Query: 113 AASCAELTIYLMLGLLRKQNEMRMAIE-QKKLGVPTGETLLGKTVFILGFGNIGVELAKR 171
A + AE + L+L LR+ A L G TV I+G G IG L
Sbjct: 84 AETVAEHALALLLAGLRQLPARARATTWDPAEEDDLVTLLRGSTVAIVGAGGIGRALIPL 143
Query: 172 LRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEKGCHEDIFEFASKADVVVC 231
L PFG K+IA RS G + DE + + E AD VV
Sbjct: 144 LAPFGAKVIAVNRS------------------GRPVEGADETVPADRLDEVWPDADHVVL 185
Query: 232 CLSLNKQT 239
L +T
Sbjct: 186 AAPLTPET 193
>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 = 64.4 bits (158), Expect = 4e-12
Identities = 41/130 (31%), Positives = 62/130 (47%), Gaps = 13/130 (10%)
Query: 65 RLDSNCISRANQMKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLM 124
LD+ +++ +KLI G VD+ AA GI V +PG T S A+ T L+
Sbjct: 54 VLDAEVLAQLPNLKLIGVLATGYNNVDLAAAKERGITVTNVPGYST---DSVAQHTFALL 110
Query: 125 LGLLRKQNEMRMAIEQKK---------LGVPTGETLLGKTVFILGFGNIGVELAKRLRPF 175
L L R ++ + P E L GKT+ I+G+GNIG +A+ R F
Sbjct: 111 LALARLVAYHNDVVKAGEWQKSPDFCFWDYPIIE-LAGKTLGIIGYGNIGQAVARIARAF 169
Query: 176 GVKIIATKRS 185
G+K++ +R
Sbjct: 170 GMKVLFAERK 179
>gnl|CDD|181041 PRK07574, PRK07574, formate dehydrogenase; Provisional.
Length = 385
Score = 64.7 bits (158), Expect = 6e-12
Identities = 44/122 (36%), Positives = 65/122 (53%), Gaps = 15/122 (12%)
Query: 71 ISRANQMKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTG-NAASCAELTIYLMLGLLR 129
I++A +KL + G+G + VD+ AA+ GI VA +VTG N+ S AE + ++L L+R
Sbjct: 109 IAKAPNLKLAITAGIGSDHVDLQAASEHGITVA----EVTGSNSISVAEHVVMMILALVR 164
Query: 130 KQNEMRMAIEQKKLG-------VPTGETLLGKTVFILGFGNIGVELAKRLRPFGVKIIAT 182
+ Q G V L G TV I+G G IG+ + +RL+PF VK+ T
Sbjct: 165 NYEP---SHRQAVEGGWNIADCVSRSYDLEGMTVGIVGAGRIGLAVLRRLKPFDVKLHYT 221
Query: 183 KR 184
R
Sbjct: 222 DR 223
>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 = 63.4 bits (155), Expect = 1e-11
Identities = 40/151 (26%), Positives = 60/151 (39%), Gaps = 35/151 (23%)
Query: 102 VARIPGDVT-GNA-----ASCAELTIYLMLGLLRKQNEMRMAIEQKKLGVPTGETLLGKT 155
+ +P VT NA AS AEL + L+L LR A + + +L +
Sbjct: 75 LPLLPEGVTLCNARGVHDASTAELAVALILASLRGLPRFVRAQARGRWEPRRTPSLADRR 134
Query: 156 VFILGFGNIGVELAKRLRPFGVKIIATKRS----WASHSQVSCQSSALAVKNGIIDDLVD 211
V I+G+G+IG + +RL PF V++ R+ H ID+L
Sbjct: 135 VLIVGYGSIGRAIERRLAPFEVRVTRVARTARPGEQVHG---------------IDELP- 178
Query: 212 EKGCHEDIFEFASKADVVVCCLSLNKQTVKL 242
+ADVVV + L +T L
Sbjct: 179 ---------ALLPEADVVVLIVPLTDETRGL 200
>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 = 62.6 bits (153), Expect = 2e-11
Identities = 42/153 (27%), Positives = 66/153 (43%), Gaps = 25/153 (16%)
Query: 94 AATRCGIKVARIPGDVTGNAASCAELTIYLMLGLLRKQNEMRMAIEQ-KKLGVPT---GE 149
A GI V D NA AE T+ +L LR+ A + G PT G
Sbjct: 90 AVWERGILVTS-AADA--NAEPVAEFTLAAILLALRRIPRFAAAYRAGRDWGWPTRRGGR 146
Query: 150 TLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDL 209
L G+TV I+GFG IG + + LRPFG++++ + ++ +AL V
Sbjct: 147 GLYGRTVGIVGFGRIGRAVVELLRPFGLRVLVYDP-YLPAAEA----AALGV-------- 193
Query: 210 VDEKGCHEDIFEFASKADVVVCCLSLNKQTVKL 242
E +++ +++DVV L +T +
Sbjct: 194 --ELVSLDELL---ARSDVVSLHAPLTPETRGM 221
>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 = 62.3 bits (152), Expect = 3e-11
Identities = 42/129 (32%), Positives = 62/129 (48%), Gaps = 11/129 (8%)
Query: 58 LCVVKTMRLDSNCISRANQMKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAASCA 117
+ V RLD+ + + ++KLI G + +D+ A GI V +P G A + A
Sbjct: 45 ISVFVYSRLDAEVLEKLPRLKLIATRSTGFDHIDLEACRERGIAVCNVPD--YGEA-TVA 101
Query: 118 ELTIYLMLGLLRKQNEM-----RMAIEQKKLGVPTGETLLGKTVFILGFGNIGVELAKRL 172
E L+L L RK E R Q L G L GKT+ ++G G IG +A+
Sbjct: 102 EHAFALLLALSRKLREAIERTRRGDFSQAGL---RGFELAGKTLGVVGTGRIGRRVARIA 158
Query: 173 RPFGVKIIA 181
R FG+K++A
Sbjct: 159 RGFGMKVLA 167
>gnl|CDD|178684 PLN03139, PLN03139, formate dehydrogenase; Provisional.
Length = 386
Score = 60.6 bits (147), Expect = 1e-10
Identities = 51/184 (27%), Positives = 75/184 (40%), Gaps = 45/184 (24%)
Query: 71 ISRANQMKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTG-NAASCAELTIYLMLGLLR 129
I +A ++L++ G+G + +D+ AA G+ VA +VTG N S AE + +L LLR
Sbjct: 116 IKKAKNLELLLTAGIGSDHIDLPAAAAAGLTVA----EVTGSNVVSVAEDELMRILILLR 171
Query: 130 K-QNEMRMAIEQKKLGVPTGE-----------TLLGKTVFILGFGNIGVELAKRLRPFGV 177
+ GE L GKTV +G G IG L +RL+PF
Sbjct: 172 NFLPGYHQVVS--------GEWNVAGIAYRAYDLEGKTVGTVGAGRIGRLLLQRLKPFNC 223
Query: 178 KIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEKGC--HEDIFEFASKADVVVCCLSL 235
++ R + +L E G ED+ K DVVV L
Sbjct: 224 NLLYHDR------------------LKMDPELEKETGAKFEEDLDAMLPKCDVVVINTPL 265
Query: 236 NKQT 239
++T
Sbjct: 266 TEKT 269
>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 = 59.1 bits (144), Expect = 3e-10
Identities = 37/99 (37%), Positives = 53/99 (53%), Gaps = 6/99 (6%)
Query: 85 VGLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLMLGLLRKQNEM--RMAIEQKK 142
+G + +D++AA GIKV +VT + S A+ T+ LML LRK ++ R +
Sbjct: 77 IGYDHIDLDAAKELGIKV----SNVTYSPNSVADYTVMLMLMALRKYKQIMKRAEVNDYS 132
Query: 143 LGVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVKIIA 181
LG G L TV ++G G IG + K L FG KI+A
Sbjct: 133 LGGLQGRELRNLTVGVIGTGRIGQAVIKNLSGFGCKILA 171
>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 = 58.7 bits (143), Expect = 5e-10
Identities = 42/175 (24%), Positives = 79/175 (45%), Gaps = 32/175 (18%)
Query: 71 ISRANQMKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLMLGLLRK 130
+++ +K I + G++ + + + GI + G ++ AE + +L + +
Sbjct: 55 LAKMKNLKWIQLYSAGVDYLPLEYIKKKGILLTNNSG---IHSIPIAEWIVGYILEIYKG 111
Query: 131 QNEMRMAIEQKK----LGVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSW 186
++ A + +K + L GKT+ LG G+IG E+AKRL+ FG+K+I S
Sbjct: 112 ---LKKAYKNQKEKKWKMDSSLLELYGKTILFLGTGSIGQEIAKRLKAFGMKVIGVNTS- 167
Query: 187 ASHSQVSCQSSALAVKNGIIDDLVDEKGCH--EDIFEFASKADVVVCCLSLNKQT 239
V+ D+ C+ E++ E +AD+VV L L ++T
Sbjct: 168 -GR----------DVEY------FDK--CYPLEELDEVLKEADIVVNVLPLTEET 203
>gnl|CDD|180588 PRK06487, PRK06487, glycerate dehydrogenase; Provisional.
Length = 317
Score = 57.8 bits (140), Expect = 9e-10
Identities = 41/144 (28%), Positives = 66/144 (45%), Gaps = 20/144 (13%)
Query: 46 ISDVPDVIANYHLCVVKTMRLDSNCISRANQMKLIMQFGVGLEGVDINAATRCGIKVARI 105
+ I+N K LD+ ++ A Q+KLI+ G VD+ AA GI V
Sbjct: 43 LRGAQVAISN------KVA-LDAAALAAAPQLKLILVAATGTNNVDLAAARERGITVCNC 95
Query: 106 PGDVTGNAASCAELTIYLMLGLLRKQNEMRMAIEQKK---------LGVPTGETLLGKTV 156
G T S A+ T+ L+L L + + + A+ + L P E L GKT+
Sbjct: 96 QGYGT---PSVAQHTLALLLALATRLPDYQQAVAAGRWQQSSQFCLLDFPIVE-LEGKTL 151
Query: 157 FILGFGNIGVELAKRLRPFGVKII 180
+LG G +G +A+ FG++++
Sbjct: 152 GLLGHGELGGAVARLAEAFGMRVL 175
>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 = 57.1 bits (139), Expect = 2e-09
Identities = 42/129 (32%), Positives = 62/129 (48%), Gaps = 23/129 (17%)
Query: 65 RLDSNCISR--ANQMKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAAS---CAEL 119
LD+ + + +KLI G VD+ AA GI V R+P A S AE
Sbjct: 55 DLDAPVLEKLAELGVKLIALRCAGFNNVDLKAAKELGITVVRVP------AYSPYAVAEH 108
Query: 120 TIYLMLGLLRK----QNEMRM---AIEQKKLGVPTGETLLGKTVFILGFGNIGVELAKRL 172
+ L+L L RK N +R +++ G+ G L GKTV ++G G IG A+ L
Sbjct: 109 AVALLLALNRKIHRAYNRVREGNFSLD----GL-LGFDLHGKTVGVIGTGKIGQAFARIL 163
Query: 173 RPFGVKIIA 181
+ FG +++A
Sbjct: 164 KGFGCRVLA 172
>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 = 54.1 bits (131), Expect = 2e-08
Identities = 40/174 (22%), Positives = 69/174 (39%), Gaps = 29/174 (16%)
Query: 74 ANQMKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLMLGLLRKQNE 133
+K I G++ +D++ A G+K+ +P + + AE + L LLR E
Sbjct: 66 EYGIKQIALRSAGVDMIDLDLAKENGLKITNVP---AYSPRAIAEFAVTQALNLLRNTPE 122
Query: 134 MRMAIEQKKLGVPTGETLLGK-----TVFILGFGNIGVELAKRLRPFGVKIIATKRSWAS 188
+ + + G L+G+ TV I+G G IG AK + FG K+IA
Sbjct: 123 IDRRVAKGDFRWAPG--LIGREIRDLTVGIIGTGRIGSAAAKIFKGFGAKVIAYDP---- 176
Query: 189 HSQVSCQSSALAVKNGIIDDLVDEKGCHEDIFEFASKADVVVCCLSLNKQTVKL 242
N ++ + ED+ +AD++ + L K+ L
Sbjct: 177 ------------YPNPELEKFLLYYDSLEDLL---KQADIISLHVPLTKENHHL 215
>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 = 52.2 bits (126), Expect = 6e-08
Identities = 46/178 (25%), Positives = 81/178 (45%), Gaps = 26/178 (14%)
Query: 15 VLFCGPHFPASHNYTKEYLQNYPSIQVDVVPIS----DVPDVIANYHLCVV--KTMRLDS 68
+L H P++ + I+V+ + + ++ + + + HL + KT +L
Sbjct: 4 LLLENIH-PSADELFRAG-----GIEVERLKGALDEDELIEALKDVHLLGIRSKT-QLTE 56
Query: 69 NCISRANQMKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLMLGLL 128
+ A ++ I F +G VD++AA + GI V P N S AEL I ++ L
Sbjct: 57 EVLEAAPKLLAIGCFCIGTNQVDLDAAAKRGIPVFNAP---FSNTRSVAELVIGEIIMLA 113
Query: 129 R----KQNEMRMAIEQKKLGVPTG--ETLLGKTVFILGFGNIGVELAKRLRPFGVKII 180
R + I K TG E + GKT+ I+G+G+IG +L+ G+++I
Sbjct: 114 RRLPDRNAAAHRGIWNK---SATGSHE-VRGKTLGIIGYGHIGSQLSVLAEALGMRVI 167
>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 = 51.1 bits (122), Expect = 1e-07
Identities = 29/120 (24%), Positives = 53/120 (44%), Gaps = 14/120 (11%)
Query: 78 KLIMQFGVGLEGVDIN-AATRCGIKVARIPGDVTG----NAASCAELTIYLMLGLLRKQN 132
+L+ + +G + D+ A R G+ + G N+ EL++ + L Q
Sbjct: 89 RLLFTYTIGADHRDLTEALARAGLTAIAVEGVELPLLTSNSIGAGELSVQFIARFLEVQQ 148
Query: 133 EMRMAIEQKKLGVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQV 192
R+ G P + GKTV ++G G +G E A+ LR G +++ T + + Q+
Sbjct: 149 PGRLG------GAPD---VAGKTVVVVGAGVVGKEAAQMLRGLGAQVLITDINVEALEQL 199
>gnl|CDD|235800 PRK06436, PRK06436, glycerate dehydrogenase; Provisional.
Length = 303
Score = 48.0 bits (114), Expect = 2e-06
Identities = 41/154 (26%), Positives = 64/154 (41%), Gaps = 27/154 (17%)
Query: 100 IKVARIPGDVT--GNAA----SCAELTIYLMLGLLRKQNEMRMAIEQKKLGVPTGETLLG 153
I V+ IP +V NA S AE L+L + E ++ + L
Sbjct: 63 IDVSGIPENVVLCSNAGAYSISVAEHAFALLLAWAKNICENNYNMKNGNFKQSPTKLLYN 122
Query: 154 KTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEK 213
K++ ILG+G IG +A + FG+ I A RS+ V +G I + E
Sbjct: 123 KSLGILGYGGIGRRVALLAKAFGMNIYAYTRSY--------------VNDG-ISSIYMEP 167
Query: 214 GCHEDIFEFASKADVVVCCLSLNKQTVKLCSSSL 247
DI + K+D V+ L L +T + +S +
Sbjct: 168 E---DIMK---KSDFVLISLPLTDETRGMINSKM 195
>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 = 47.7 bits (114), Expect = 3e-06
Identities = 37/136 (27%), Positives = 57/136 (41%), Gaps = 18/136 (13%)
Query: 57 HLCVVKTMRLDSNCISRANQMKLIMQFG--------VGLEGVDINAATRCGIKVARIPGD 108
H V+ + NC + +++ ++G VG +D+ AA G K+AR+P
Sbjct: 45 HDAVI----VRGNCFADKENLEIYKEYGIKYVFTRTVGFNHIDLEAAKELGFKMARVPS- 99
Query: 109 VTGNAASCAELTIYLMLGLLRKQNEMRMAIEQKKLGVPT---GETLLGKTVFILGFGNIG 165
+ NA AEL L + L R K V + + TV I+G G IG
Sbjct: 100 YSPNAI--AELAFTLAMTLSRHTAYTASRTANKNFKVDPFMFSKEIRNSTVGIIGTGRIG 157
Query: 166 VELAKRLRPFGVKIIA 181
+ AK + G K+I
Sbjct: 158 LTAAKLFKGLGAKVIG 173
>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 = 46.2 bits (110), Expect = 7e-06
Identities = 23/78 (29%), Positives = 41/78 (52%), Gaps = 9/78 (11%)
Query: 112 NAASCAELTIYLMLGLLRKQNEMRMAI----EQKKLGVPTGETLLGKTVFILGFGNIGVE 167
A + AE + +L ++ E+ + ++ LG +L G T+ I+GFG IG
Sbjct: 95 AAEAIAEFVLAAILAAAKRLPEIWVKGAEQWRREPLG-----SLAGSTLGIVGFGAIGQA 149
Query: 168 LAKRLRPFGVKIIATKRS 185
LA+R G++++A +RS
Sbjct: 150 LARRALALGMRVLALRRS 167
>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 = 46.0 bits (110), Expect = 8e-06
Identities = 33/95 (34%), Positives = 46/95 (48%), Gaps = 19/95 (20%)
Query: 86 GLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLMLGLLRKQNEMRMAIEQKKLGV 145
G + +D + GI A PG NA S AE Y++ LL +A Q
Sbjct: 67 GTDHIDTDYLKERGIGFANAPG---CNANSVAE---YVLSALLV------LAQRQ----- 109
Query: 146 PTGETLLGKTVFILGFGNIGVELAKRLRPFGVKII 180
G +L GKTV I+G GN+G LA+RL G+ ++
Sbjct: 110 --GFSLKGKTVGIVGVGNVGSRLARRLEALGMNVL 142
>gnl|CDD|177941 PLN02306, PLN02306, hydroxypyruvate reductase.
Length = 386
Score = 45.6 bits (108), Expect = 1e-05
Identities = 33/95 (34%), Positives = 44/95 (46%), Gaps = 12/95 (12%)
Query: 83 FGVGLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLMLGLLRKQNE----MRMAI 138
VG VD+ AA + GI V PG +T + AEL L L R+ E MR +
Sbjct: 93 MAVGYNNVDVEAANKYGIAVGNTPGVLT---ETTAELAASLSLAAARRIVEADEFMRAGL 149
Query: 139 EQKKLGVPT---GETLLGKTVFILGFGNIGVELAK 170
+ L P G L G+TV ++G G IG A+
Sbjct: 150 YEGWL--PHLFVGNLLKGQTVGVIGAGRIGSAYAR 182
>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 = 44.1 bits (105), Expect = 2e-05
Identities = 21/73 (28%), Positives = 31/73 (42%), Gaps = 11/73 (15%)
Query: 148 GETLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGI-I 206
G L G V I GFGN+G A+ L G K++A VS + +G+ +
Sbjct: 26 GIGLAGARVAIQGFGNVGSHAARFLHEAGAKVVA----------VSDSDGTIYNPDGLDV 75
Query: 207 DDLVDEKGCHEDI 219
L+ K H +
Sbjct: 76 PALLAYKKEHGSV 88
>gnl|CDD|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 = 43.5 bits (103), Expect = 5e-05
Identities = 31/80 (38%), Positives = 41/80 (51%), Gaps = 11/80 (13%)
Query: 117 AELTIYLMLGLLRKQNEMRMAIEQKK----LG-----VPTGE--TLLGKTVFILGFGNIG 165
AE T+ L+L +R+ +EMR A + + LG P G TLLG V I GFG+IG
Sbjct: 96 AEHTLALILAAVRRLDEMREAQREHRWAGELGGLQPLRPAGRLTTLLGARVLIWGFGSIG 155
Query: 166 VELAKRLRPFGVKIIATKRS 185
LA L G ++ RS
Sbjct: 156 QRLAPLLTALGARVTGVARS 175
>gnl|CDD|181414 PRK08410, PRK08410, 2-hydroxyacid dehydrogenase; Provisional.
Length = 311
Score = 43.0 bits (102), Expect = 7e-05
Identities = 37/124 (29%), Positives = 57/124 (45%), Gaps = 13/124 (10%)
Query: 66 LDSNCISRANQMKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLML 125
+D +S+ +KLI G VDI A + GI V + G T S A+ T ++L
Sbjct: 53 IDKEVLSQLPNLKLICITATGTNNVDIEYAKKKGIAVKNVAGYST---ESVAQHTFAMLL 109
Query: 126 GLLRKQNEMRMAIEQKK---------LGVPTGETLLGKTVFILGFGNIGVELAKRLRPFG 176
LL + N ++ + + P GE + GK I+G G IG +AK + FG
Sbjct: 110 SLLGRINYYDRYVKSGEYSESPIFTHISRPLGE-IKGKKWGIIGLGTIGKRVAKIAQAFG 168
Query: 177 VKII 180
K++
Sbjct: 169 AKVV 172
>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 = 41.3 bits (98), Expect = 2e-04
Identities = 37/168 (22%), Positives = 60/168 (35%), Gaps = 33/168 (19%)
Query: 78 KLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLMLGLLRKQNEMRMA 137
K I G G++ + + + + R+ G A AE Y++ +LR +M
Sbjct: 60 KAIFSLGAGVDHLLADPDLP-DVPIVRLVDP--GLAQGMAE---YVLAAVLRLHRDMDRY 113
Query: 138 IEQ------KKLGVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQ 191
Q K L V +LG G +G +A+RL G + RS
Sbjct: 114 AAQQRRGVWKPLPQRPAAER---RVGVLGLGELGAAVARRLAALGFPVSGWSRSPKDIEG 170
Query: 192 VSCQSSALAVKNGIIDDLVDEKGCHEDIFEFASKADVVVCCLSLNKQT 239
V+C + L F ++ D++VC L L +T
Sbjct: 171 VTCFHGE--------EGLDA----------FLAQTDILVCLLPLTPET 200
>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 = 41.1 bits (97), Expect = 3e-04
Identities = 35/159 (22%), Positives = 63/159 (39%), Gaps = 27/159 (16%)
Query: 117 AELTI--YLML--GLLRKQNEMRMAIEQKKLGVPTGETLLGKTVFILGFGNIGVELAKRL 172
AE I +L+L L+ + ++ + E +GK V ILG+G+IG + A+
Sbjct: 93 AEWVIGTWLVLSHHFLQYIELQKEQTWGRRQEAYSVEDSVGKRVGILGYGSIGRQTARLA 152
Query: 173 RPFGVKIIATKRSWASHSQVSCQSSALAVKNGII-------DDLVDEKGCH----EDIFE 221
+ G+++ A RS + + +S +G I D + + E
Sbjct: 153 QALGMEVYAYTRS----PRPTPES---RKDDGYIVPGTGDPDGSIPSAWFSGTDKASLHE 205
Query: 222 F-ASKADVVVCCLSLNKQTVKLCSSS----LSSKSMFFA 255
F D++V L L T L + L+ + F +
Sbjct: 206 FLRQDLDLLVVSLPLTPATKHLLGAEEFEILAKRKTFVS 244
>gnl|CDD|181499 PRK08605, PRK08605, D-lactate dehydrogenase; Validated.
Length = 332
Score = 40.5 bits (95), Expect = 5e-04
Identities = 27/124 (21%), Positives = 57/124 (45%), Gaps = 13/124 (10%)
Query: 66 LDSNCISRANQM--KLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYL 123
L N++ K I Q G + D+ AT+ + ++ +P + + S AE T+
Sbjct: 57 LSEAIYKLLNELGIKQIAQRSAGFDTYDLELATKYNLIISNVP---SYSPESIAEFTVTQ 113
Query: 124 MLGLLRKQNEMRMAIEQKKLGVPTGETLLGK-----TVFILGFGNIGVELAKRL-RPFGV 177
+ L+R N+++ + ++ +L + V ++G G IG+ +AK + +G
Sbjct: 114 AINLVRHFNQIQTKV--REHDFRWEPPILSRSIKDLKVAVIGTGRIGLAVAKIFAKGYGS 171
Query: 178 KIIA 181
++A
Sbjct: 172 DVVA 175
>gnl|CDD|237820 PRK14806, PRK14806, bifunctional cyclohexadienyl dehydrogenase/
3-phosphoshikimate 1-carboxyvinyltransferase;
Provisional.
Length = 735
Score = 40.7 bits (96), Expect = 5e-04
Identities = 27/77 (35%), Positives = 37/77 (48%), Gaps = 16/77 (20%)
Query: 156 VFILGFGNIGVELAKRLRPFGV--KIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEK 213
V ++G G IG AK LR G+ +++A R +S LAV G+ID
Sbjct: 6 VVVIGLGLIGGSFAKALRERGLAREVVAVDRR--------AKSLELAVSLGVIDR----- 52
Query: 214 GCHEDIFEFASKADVVV 230
ED+ E S ADV+V
Sbjct: 53 -GEEDLAEAVSGADVIV 68
>gnl|CDD|223411 COG0334, GdhA, Glutamate dehydrogenase/leucine dehydrogenase [Amino
acid transport and metabolism].
Length = 411
Score = 40.7 bits (96), Expect = 5e-04
Identities = 21/77 (27%), Positives = 38/77 (49%), Gaps = 11/77 (14%)
Query: 148 GETLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGI-I 206
G+ L G V + GFGN+G A++L G K++A VS + ++G+ +
Sbjct: 202 GDDLEGARVAVQGFGNVGQYAAEKLHELGAKVVA----------VSDSKGGIYDEDGLDV 251
Query: 207 DDLVDEKGCHEDIFEFA 223
+ L++ K + E+A
Sbjct: 252 EALLELKERRGSVAEYA 268
>gnl|CDD|235890 PRK06932, PRK06932, glycerate dehydrogenase; Provisional.
Length = 314
Score = 39.0 bits (91), Expect = 0.001
Identities = 40/180 (22%), Positives = 72/180 (40%), Gaps = 27/180 (15%)
Query: 20 PHFPASHNYTKEYLQNYPSIQVDVVPISDVPDVIANYHLCVVKTMRLDSNCISRANQMKL 79
P FP H + EY ++ +D+ VI + K + +++ ++KL
Sbjct: 21 PSFP--HEWI-EYDHTSAEQTIERAKDADI--VITS------KVL-FTRETLAQLPKLKL 68
Query: 80 IMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLMLGL-------LRKQN 132
I G VD+ AA GI V + G + + E + ++ L R Q
Sbjct: 69 IAITATGTNNVDLVAAKELGIAVKNVTGYSS---TTVPEHVLGMIFALKHSLMGWYRDQL 125
Query: 133 EMRMAIEQKKLGV---PTGETLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASH 189
R A K+ P + + G T+ + G G +G E+ + + G+K++ + AS
Sbjct: 126 SDRWA-TCKQFCYFDYPITD-VRGSTLGVFGKGCLGTEVGRLAQALGMKVLYAEHKGASV 183
>gnl|CDD|215789 pfam00208, ELFV_dehydrog, Glutamate/Leucine/Phenylalanine/Valine
dehydrogenase.
Length = 237
Score = 37.5 bits (88), Expect = 0.003
Identities = 29/74 (39%), Positives = 42/74 (56%), Gaps = 14/74 (18%)
Query: 141 KKLGVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALA 200
KKLG G++L GKTV + GFGN+G A++L G K++A VS S +
Sbjct: 23 KKLG---GDSLEGKTVAVQGFGNVGSYAAEKLLELGAKVVA----------VSDSSGYIY 69
Query: 201 VKNGI-IDDLVDEK 213
NGI I++L++ K
Sbjct: 70 DPNGIDIEELLELK 83
>gnl|CDD|181371 PRK08306, PRK08306, dipicolinate synthase subunit A; Reviewed.
Length = 296
Score = 36.7 bits (86), Expect = 0.007
Identities = 17/44 (38%), Positives = 23/44 (52%), Gaps = 6/44 (13%)
Query: 136 MAIEQKKLGVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVKI 179
MAIE T T+ G V +LGFG G+ LA+ L+ G +
Sbjct: 141 MAIEH------TPITIHGSNVLVLGFGRTGMTLARTLKALGANV 178
Score = 31.0 bits (71), Expect = 0.58
Identities = 13/66 (19%), Positives = 25/66 (37%), Gaps = 2/66 (3%)
Query: 44 VPISDVPDVIANYHLCV--VKTMRLDSNCISRANQMKLIMQFGVGLEGVDINAATRCGIK 101
+S++ + + + + + L +S+ LI+ G D A + GIK
Sbjct: 199 FHLSELAEEVGKIDIIFNTIPALVLTKEVLSKMPPEALIIDLASKPGGTDFEYAEKRGIK 258
Query: 102 VARIPG 107
PG
Sbjct: 259 ALLAPG 264
>gnl|CDD|183550 PRK12480, PRK12480, D-lactate dehydrogenase; Provisional.
Length = 330
Score = 36.0 bits (83), Expect = 0.016
Identities = 28/108 (25%), Positives = 47/108 (43%), Gaps = 6/108 (5%)
Query: 77 MKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLMLGLLRK--QNEM 134
+K I Q G + D++ A + I ++ +P + + + AE ++ + L L+R+ E
Sbjct: 70 IKQIAQRTAGFDMYDLDLAKKHNIVISNVP---SYSPETIAEYSVSIALQLVRRFPDIER 126
Query: 135 RMAIEQKKLGVPTGET-LLGKTVFILGFGNIGVELAKRLRPFGVKIIA 181
R+ + TV I+G G IG AK FG I A
Sbjct: 127 RVQAHDFTWQAEIMSKPVKNMTVAIIGTGRIGAATAKIYAGFGATITA 174
>gnl|CDD|237220 PRK12828, PRK12828, short chain dehydrogenase; Provisional.
Length = 239
Score = 35.5 bits (82), Expect = 0.017
Identities = 27/84 (32%), Positives = 36/84 (42%), Gaps = 5/84 (5%)
Query: 151 LLGKTVFILG-FGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDL 209
L GK V I G FG +G A L G ++ R A SQ A A++ G I DL
Sbjct: 5 LQGKVVAITGGFGGLGRATAAWLAARGARVALIGRGAAPLSQTLPGVPADALRIGGI-DL 63
Query: 210 VDEKGCHEDIFEFAS---KADVVV 230
VD + + E + D +V
Sbjct: 64 VDPQAARRAVDEVNRQFGRLDALV 87
>gnl|CDD|215144 PLN02256, PLN02256, arogenate dehydrogenase.
Length = 304
Score = 35.4 bits (82), Expect = 0.023
Identities = 25/86 (29%), Positives = 35/86 (40%), Gaps = 26/86 (30%)
Query: 155 TVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGI-----IDDL 209
+ I+GFGN G LAK G ++AT RS S +A + G+ DD
Sbjct: 38 KIGIVGFGNFGQFLAKTFVKQGHTVLATSRS---------DYSDIAAELGVSFFRDPDDF 88
Query: 210 VDEKGCHEDIFEFASKADVVVCCLSL 235
+E DVV+ C S+
Sbjct: 89 CEE------------HPDVVLLCTSI 102
>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 = 34.6 bits (80), Expect = 0.030
Identities = 18/78 (23%), Positives = 27/78 (34%), Gaps = 13/78 (16%)
Query: 156 VFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEKGC 215
V ILG G +G LA++L G ++ T RS + + DL
Sbjct: 1 VLILGCGYLGQRLARQLLAQGWQVTGTTRSPEKLAADRPAGVT-----PLAADLTQ---- 51
Query: 216 HEDIFEFASKADVVVCCL 233
+ D +V L
Sbjct: 52 ----PGLLADVDHLVISL 65
>gnl|CDD|178095 PLN02477, PLN02477, glutamate dehydrogenase.
Length = 410
Score = 35.1 bits (81), Expect = 0.033
Identities = 19/58 (32%), Positives = 31/58 (53%), Gaps = 10/58 (17%)
Query: 148 GETLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGI 205
G+++ G+T I GFGN+G A+ + G KI+A VS + A+ +NG+
Sbjct: 201 GKSIAGQTFVIQGFGNVGSWAAQLIHEKGGKIVA----------VSDITGAVKNENGL 248
>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 = 33.7 bits (77), Expect = 0.067
Identities = 16/34 (47%), Positives = 23/34 (67%)
Query: 148 GETLLGKTVFILGFGNIGVELAKRLRPFGVKIIA 181
G++L G TV + G GN+G LAK+L G K++A
Sbjct: 18 GDSLEGLTVAVQGLGNVGWGLAKKLAEEGGKVLA 51
>gnl|CDD|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 = 33.9 bits (78), Expect = 0.074
Identities = 23/87 (26%), Positives = 40/87 (45%), Gaps = 14/87 (16%)
Query: 149 ETLLGKTVFILGFGNIGVELAKRLRPFGV-KIIATKRSWASHSQVSCQSSALAVKNGIID 207
+L GK ++G G +G +AK L GV KI+ R++ ++ + AVK
Sbjct: 176 GSLKGKKALLIGAGEMGELVAKHLLRKGVGKILIANRTYERAEDLAKELGGEAVK----- 230
Query: 208 DLVDEKGCHEDIFEFASKADVVVCCLS 234
ED+ E+ ++AD+V+
Sbjct: 231 --------FEDLEEYLAEADIVISSTG 249
>gnl|CDD|184511 PRK14106, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
synthetase; Provisional.
Length = 450
Score = 33.8 bits (78), Expect = 0.082
Identities = 15/32 (46%), Positives = 20/32 (62%)
Query: 151 LLGKTVFILGFGNIGVELAKRLRPFGVKIIAT 182
L GK V ++G G G+ LAK L+ G K+I T
Sbjct: 3 LKGKKVLVVGAGVSGLALAKFLKKLGAKVILT 34
>gnl|CDD|131900 TIGR02853, spore_dpaA, dipicolinic acid synthetase, A subunit.
This predicted Rossman fold-containing protein is the A
subunit of dipicolinic acid synthetase as found in most,
though not all, endospore-forming low-GC Gram-positive
bacteria; it is absent in Clostridium. The B subunit is
represented by TIGR02852. This protein is also known as
SpoVFA [Cellular processes, Sporulation and
germination].
Length = 287
Score = 33.5 bits (77), Expect = 0.089
Identities = 17/50 (34%), Positives = 24/50 (48%), Gaps = 6/50 (12%)
Query: 136 MAIEQKKLGVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRS 185
MAIE T T+ G V +LGFG G+ +A+ G ++ RS
Sbjct: 140 MAIEH------TDFTIHGSNVMVLGFGRTGMTIARTFSALGARVFVGARS 183
Score = 28.1 bits (63), Expect = 4.9
Identities = 13/66 (19%), Positives = 30/66 (45%), Gaps = 2/66 (3%)
Query: 44 VPISDVPDVIANYHLCV--VKTMRLDSNCISRANQMKLIMQFGVGLEGVDINAATRCGIK 101
P++ + + +A + + + + L ++ +S+ + +I+ G D A + GIK
Sbjct: 198 FPLNKLEEKVAEIDIVINTIPALVLTADVLSKLPKHAVIIDLASKPGGTDFEYAKKRGIK 257
Query: 102 VARIPG 107
PG
Sbjct: 258 ALLAPG 263
>gnl|CDD|236985 PRK11790, PRK11790, D-3-phosphoglycerate dehydrogenase;
Provisional.
Length = 409
Score = 33.2 bits (77), Expect = 0.13
Identities = 31/95 (32%), Positives = 43/95 (45%), Gaps = 19/95 (20%)
Query: 83 FGVGLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLMLGLLRKQNEMRMAIEQKK 142
F +G VD++AA + GI V P N S AEL I ++ LLR I +K
Sbjct: 82 FCIGTNQVDLDAAAKRGIPVFNAP---FSNTRSVAELVIGEIILLLRG-------IPEKN 131
Query: 143 LGVPTGETL---------LGKTVFILGFGNIGVEL 168
G GKT+ I+G+G+IG +L
Sbjct: 132 AKAHRGGWNKSAAGSFEVRGKTLGIVGYGHIGTQL 166
>gnl|CDD|235824 PRK06545, PRK06545, prephenate dehydrogenase; Validated.
Length = 359
Score = 33.0 bits (76), Expect = 0.13
Identities = 22/77 (28%), Positives = 35/77 (45%), Gaps = 12/77 (15%)
Query: 154 KTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEK 213
+TV I+G G IG LA ++ G + S A A+ G+ID+L
Sbjct: 1 RTVLIVGLGLIGGSLALAIKAAGPDVFIIGYD------PSAAQLARALGFGVIDELA--- 51
Query: 214 GCHEDIFEFASKADVVV 230
D+ A++AD++V
Sbjct: 52 ---ADLQRAAAEADLIV 65
>gnl|CDD|185335 PRK15438, PRK15438, erythronate-4-phosphate dehydrogenase PdxB;
Provisional.
Length = 378
Score = 32.6 bits (74), Expect = 0.20
Identities = 14/33 (42%), Positives = 20/33 (60%)
Query: 148 GETLLGKTVFILGFGNIGVELAKRLRPFGVKII 180
G +L +TV I+G GN+G L RL G+K +
Sbjct: 111 GFSLHDRTVGIVGVGNVGRRLQARLEALGIKTL 143
>gnl|CDD|240258 PTZ00075, PTZ00075, Adenosylhomocysteinase; Provisional.
Length = 476
Score = 32.7 bits (75), Expect = 0.20
Identities = 13/30 (43%), Positives = 21/30 (70%)
Query: 153 GKTVFILGFGNIGVELAKRLRPFGVKIIAT 182
GKTV + G+G++G A+ LR FG +++ T
Sbjct: 254 GKTVVVCGYGDVGKGCAQALRGFGARVVVT 283
>gnl|CDD|198065 smart00997, AdoHcyase_NAD, S-adenosyl-L-homocysteine hydrolase, NAD
binding domain.
Length = 162
Score = 31.7 bits (73), Expect = 0.21
Identities = 15/36 (41%), Positives = 22/36 (61%)
Query: 147 TGETLLGKTVFILGFGNIGVELAKRLRPFGVKIIAT 182
T L GK V + G+G++G +A RLR G ++I T
Sbjct: 17 TNVLLAGKNVVVAGYGDVGKGVAARLRGLGARVIVT 52
>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 = 31.4 bits (72), Expect = 0.28
Identities = 24/79 (30%), Positives = 32/79 (40%), Gaps = 16/79 (20%)
Query: 151 LLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLV 210
L GK + ++G+G+ G A LR GV +I R + S A K+G V
Sbjct: 2 LKGKKIAVIGYGSQGHAHALNLRDSGVNVIVGLRPGSK-------SWEKAKKDGFEVYTV 54
Query: 211 DEKGCHEDIFEFASKADVV 229
E KADVV
Sbjct: 55 AEA---------VKKADVV 64
>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 = 31.9 bits (73), Expect = 0.32
Identities = 28/97 (28%), Positives = 35/97 (36%), Gaps = 25/97 (25%)
Query: 90 VDINAATRCGIKVARIP--GDVTGNAASCAELTIYLMLGLL----RKQ-NEMRMAIEQKK 142
VDI AA GI V I GD E I ++ LL KQ E + K
Sbjct: 86 VDIAAARENGITVTGIRDYGD-----EGVVEYVISELIRLLHGFGGKQWKEEPRELTGLK 140
Query: 143 LGVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVKI 179
+G I+G G G +A L FG +
Sbjct: 141 VG-------------IIGLGTTGQMIADALSFFGADV 164
>gnl|CDD|236541 PRK09496, trkA, potassium transporter peripheral membrane
component; Reviewed.
Length = 453
Score = 32.0 bits (74), Expect = 0.33
Identities = 15/29 (51%), Positives = 18/29 (62%), Gaps = 2/29 (6%)
Query: 154 KTVFILGFGNIGVELAKRL--RPFGVKII 180
K V I+G GNIG LAK L + VK+I
Sbjct: 232 KRVMIVGGGNIGYYLAKLLEKEGYSVKLI 260
>gnl|CDD|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 = 30.6 bits (70), Expect = 0.36
Identities = 20/85 (23%), Positives = 31/85 (36%), Gaps = 15/85 (17%)
Query: 155 TVFILG-FGNIGVELAKRLR---PFG-VKIIATKRSWASHSQVSCQSSALAVKNGIIDDL 209
V I+G G +G EL + L P V ++A+ RS +A I++
Sbjct: 1 KVAIVGATGYVGQELLRLLAEHPPLELVALVASSRS---------AGKKVAFAYPILEGG 51
Query: 210 VDEKGCHEDIFEFASKADVVVCCLS 234
D D + D+V L
Sbjct: 52 KDLLLEDVDPEDL-KDVDIVFLALP 75
>gnl|CDD|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 = 0.40
Identities = 19/82 (23%), Positives = 35/82 (42%), Gaps = 4/82 (4%)
Query: 154 KTVFILGFGN-IGVELAKRLRPFGVKIIATKRSWAS--HSQVSCQSSALAVKNGIIDDLV 210
K V I G + IG+ LA L G ++IAT R+ + ++ + D+
Sbjct: 1 KVVLITGCSSGIGLALALALAAQGYRVIATARNPDKLESLGELLNDNLEVLELDVTDEES 60
Query: 211 DEKGCHEDIFEFASKADVVVCC 232
+ +++ E + DV+V
Sbjct: 61 IKAA-VKEVIERFGRIDVLVNN 81
>gnl|CDD|166874 PRK00257, PRK00257, erythronate-4-phosphate dehydrogenase;
Validated.
Length = 381
Score = 31.5 bits (72), Expect = 0.40
Identities = 23/95 (24%), Positives = 41/95 (43%), Gaps = 19/95 (20%)
Query: 85 VGLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLMLGLLRKQNEMRMAIEQKKLG 144
+G + +D++ GI + PG NA + Y++ LL +A +
Sbjct: 67 IGTDHLDLDYFAEAGITWSSAPG---CNARGVVD---YVLGSLLT------LAERE---- 110
Query: 145 VPTGETLLGKTVFILGFGNIGVELAKRLRPFGVKI 179
G L +T ++G G++G L + LR G K+
Sbjct: 111 ---GVDLAERTYGVVGAGHVGGRLVRVLRGLGWKV 142
>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 = 31.1 bits (71), Expect = 0.42
Identities = 26/89 (29%), Positives = 36/89 (40%), Gaps = 9/89 (10%)
Query: 153 GKTVFILGFGN-IGVELAKRLRPFGVKIIATKRSWA--SHSQVSCQSSALAVKN---GII 206
GK V I G + IG LAK L G +I RS + + ++ A A I
Sbjct: 1 GKHVLITGGSSGIGKALAKELVKEGANVIIVARSESKLEEAVEEIEAEANASGQKVSYIS 60
Query: 207 DDLVDEKGCHEDIFEFASKA---DVVVCC 232
DL D + + + K D+VV C
Sbjct: 61 ADLSDYEEVEQAFAQAVEKGGPPDLVVNC 89
>gnl|CDD|106361 PRK13403, PRK13403, ketol-acid reductoisomerase; Provisional.
Length = 335
Score = 31.3 bits (70), Expect = 0.44
Identities = 16/41 (39%), Positives = 24/41 (58%)
Query: 149 ETLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASH 189
E L GKTV ++G+G+ G A+ LR GV+++ R S
Sbjct: 12 ELLQGKTVAVIGYGSQGHAQAQNLRDSGVEVVVGVRPGKSF 52
>gnl|CDD|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 = 31.0 bits (71), Expect = 0.46
Identities = 28/111 (25%), Positives = 45/111 (40%), Gaps = 22/111 (19%)
Query: 134 MRMAIEQKKLGVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVS 193
M+ A E LG ++L GKTV + G G +G +LA+ L G K+I + + ++ +
Sbjct: 13 MKAAAEHL-LG---TDSLEGKTVAVQGLGKVGYKLAEHLLEEGAKLIVADINEEAVARAA 68
Query: 194 CQSSALAVKNGIIDDLVDEKGCHEDIFEFASKADVVVCC---LSLNKQTVK 241
A V I ++ ADV C +N T+
Sbjct: 69 ELFGATVVAPEEI---------------YSVDADVFAPCALGGVINDDTIP 104
>gnl|CDD|185307 PRK15409, PRK15409, bifunctional glyoxylate/hydroxypyruvate
reductase B; Provisional.
Length = 323
Score = 31.3 bits (71), Expect = 0.49
Identities = 32/129 (24%), Positives = 59/129 (45%), Gaps = 15/129 (11%)
Query: 65 RLDSNCISRANQMKLIMQFGVGLEGVDINAATRCGIKVARIPGDVTGNAASCAELTIYLM 124
++D+ + + +++ VG + D++A T I + P +T + A+ + L+
Sbjct: 55 KVDAALLEKMPKLRAASTISVGYDNFDVDALTARKILLMHTPTVLT---ETVADTLMALV 111
Query: 125 LGLLRKQNEMRMAIEQKKLGVPT--------GETLLGKTVFILGFGNIGVELAKRLR-PF 175
L R+ E+ E+ K G T G + KT+ I+G G IG+ LA+R F
Sbjct: 112 LSTARRVVEV---AERVKAGEWTASIGPDWFGTDVHHKTLGIVGMGRIGMALAQRAHFGF 168
Query: 176 GVKIIATKR 184
+ I+ R
Sbjct: 169 NMPILYNAR 177
>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 = 31.3 bits (72), Expect = 0.58
Identities = 12/30 (40%), Positives = 17/30 (56%)
Query: 153 GKTVFILGFGNIGVELAKRLRPFGVKIIAT 182
GK V + G+G +G A R R G ++I T
Sbjct: 195 GKVVVVAGYGWVGKGCAMRARGLGARVIVT 224
>gnl|CDD|223137 COG0059, IlvC, Ketol-acid reductoisomerase [Amino acid transport
and metabolism / Coenzyme metabolism].
Length = 338
Score = 31.0 bits (71), Expect = 0.60
Identities = 25/80 (31%), Positives = 36/80 (45%), Gaps = 16/80 (20%)
Query: 151 LLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLV 210
L GK V I+G+G+ G A LR G+ +I R +S S A ++G V
Sbjct: 16 LKGKKVAIIGYGSQGHAQALNLRDSGLNVIIGLRKGSS-------SWKKAKEDGFKVYTV 68
Query: 211 DEKGCHEDIFEFASKADVVV 230
+E A +ADVV+
Sbjct: 69 EEA---------AKRADVVM 79
>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 = 30.8 bits (70), Expect = 0.72
Identities = 13/32 (40%), Positives = 19/32 (59%)
Query: 151 LLGKTVFILGFGNIGVELAKRLRPFGVKIIAT 182
+ GKTV + G+G G +A R R G ++I T
Sbjct: 194 IAGKTVVVAGYGWCGKGIAMRARGMGARVIVT 225
>gnl|CDD|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 = 30.6 bits (70), Expect = 0.78
Identities = 27/107 (25%), Positives = 41/107 (38%), Gaps = 27/107 (25%)
Query: 140 QKKLGVPTGETLLGKTVFILGFGNIG---VELAKRLRPFGVKIIATKRSWASHSQVSCQS 196
Q+K G+ G+T V ++G G IG LAK G + + S ++
Sbjct: 158 QRKAGIKPGDT-----VLVIGAGPIGLLHAMLAKA---SGARKVIV-------SDLNEFR 202
Query: 197 SALAVKNGIIDDLVDEKGCHEDIFEFASK------ADVVVCCLSLNK 237
A K G D +D ED+ E + ADVV+ +
Sbjct: 203 LEFAKKLG-ADYTIDAA--EEDLVEKVRELTDGRGADVVIVATGSPE 246
>gnl|CDD|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 = 0.89
Identities = 24/85 (28%), Positives = 32/85 (37%), Gaps = 5/85 (5%)
Query: 160 GFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEKGCHEDI 219
G G+ G LA RL G KII R + +A + D K D
Sbjct: 8 GTGDQGKGLALRLAKAGNKIIIGSRDLEKAEE-----AAAKALEELGHGGSDIKVTGADN 62
Query: 220 FEFASKADVVVCCLSLNKQTVKLCS 244
E A +ADVV+ + + L S
Sbjct: 63 AEAAKRADVVILAVPWDHVLKTLES 87
>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 = 28.6 bits (65), Expect = 0.92
Identities = 9/18 (50%), Positives = 12/18 (66%)
Query: 166 VELAKRLRPFGVKIIATK 183
VE AKRL G +++AT
Sbjct: 3 VEFAKRLAELGFELLATG 20
>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 = 1.00
Identities = 14/34 (41%), Positives = 19/34 (55%)
Query: 148 GETLLGKTVFILGFGNIGVELAKRLRPFGVKIIA 181
ETL GK V I G GN+ A++L G K++
Sbjct: 33 NETLKGKRVAISGSGNVAQYAAEKLLELGAKVVT 66
>gnl|CDD|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 = 30.0 bits (68), Expect = 1.1
Identities = 14/36 (38%), Positives = 18/36 (50%), Gaps = 1/36 (2%)
Query: 151 LLGKTVFILG-FGNIGVELAKRLRPFGVKIIATKRS 185
L G TV I G IG+ LA++ G +I T R
Sbjct: 3 LTGNTVLITGGTSGIGLALARKFLEAGNTVIITGRR 38
>gnl|CDD|184463 PRK14030, PRK14030, glutamate dehydrogenase; Provisional.
Length = 445
Score = 30.2 bits (68), Expect = 1.1
Identities = 13/34 (38%), Positives = 18/34 (52%)
Query: 147 TGETLLGKTVFILGFGNIGVELAKRLRPFGVKII 180
G + GKTV I GFGN+ A + G K++
Sbjct: 222 KGIDIKGKTVAISGFGNVAWGAATKATELGAKVV 255
>gnl|CDD|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 = 28.5 bits (64), Expect = 1.1
Identities = 15/32 (46%), Positives = 20/32 (62%)
Query: 141 KKLGVPTGETLLGKTVFILGFGNIGVELAKRL 172
K G T ++L GKTV +LG G +G +AK L
Sbjct: 11 KAAGKVTNKSLKGKTVVVLGAGEVGKGIAKLL 42
>gnl|CDD|223364 COG0287, TyrA, Prephenate dehydrogenase [Amino acid transport and
metabolism].
Length = 279
Score = 30.0 bits (68), Expect = 1.2
Identities = 23/79 (29%), Positives = 38/79 (48%), Gaps = 15/79 (18%)
Query: 154 KTVFILGFGNIGVELAK--RLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVD 211
V I+G G +G LA+ + V+II RS A + A++ G+ID+L
Sbjct: 4 MKVGIVGLGLMGGSLARALKEAGLVVRIIGRDRSAA--------TLKAALELGVIDELTV 55
Query: 212 EKGCHEDIFEFASKADVVV 230
+ E A++AD+V+
Sbjct: 56 -----AGLAEAAAEADLVI 69
>gnl|CDD|235554 PRK05673, dnaE, DNA polymerase III subunit alpha; Validated.
Length = 1135
Score = 30.5 bits (70), Expect = 1.2
Identities = 12/47 (25%), Positives = 25/47 (53%), Gaps = 10/47 (21%)
Query: 200 AVKN---GIIDDLVD---EKGCHEDIFEFASKADVVVCCLSLNKQTV 240
A+K G ++ +V+ E G +D+F+F ++ D+ NK+ +
Sbjct: 824 AIKGVGEGAVEAIVEAREEGGPFKDLFDFCARVDLKKV----NKRVL 866
>gnl|CDD|224996 COG2085, COG2085, Predicted dinucleotide-binding enzymes [General
function prediction only].
Length = 211
Score = 29.6 bits (67), Expect = 1.2
Identities = 14/33 (42%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 154 KTVFILGFGNIGVELAKRLRPFGVK-IIATKRS 185
+ I+G GNIG LA RL G + II + R
Sbjct: 2 MIIAIIGTGNIGSALALRLAKAGHEVIIGSSRG 34
>gnl|CDD|223573 COG0499, SAM1, S-adenosylhomocysteine hydrolase [Coenzyme
metabolism].
Length = 420
Score = 29.9 bits (68), Expect = 1.4
Identities = 13/30 (43%), Positives = 19/30 (63%)
Query: 153 GKTVFILGFGNIGVELAKRLRPFGVKIIAT 182
GK V + G+G +G +A RLR G ++I T
Sbjct: 209 GKNVVVAGYGWVGRGIAMRLRGMGARVIVT 238
>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 = 27.8 bits (62), Expect = 1.6
Identities = 8/39 (20%), Positives = 16/39 (41%)
Query: 2 EGMARSSDKNITRVLFCGPHFPASHNYTKEYLQNYPSIQ 40
G + + R+L C P P ++ + Q S++
Sbjct: 37 HGFLKGGWLTLKRILRCHPLHPGGNDPVPKKKQILESLK 75
>gnl|CDD|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 = 29.1 bits (66), Expect = 1.6
Identities = 13/45 (28%), Positives = 23/45 (51%), Gaps = 1/45 (2%)
Query: 31 EYLQNYPSIQVDVVPISDVPDVIANYHLCVVKTMRL-DSNCISRA 74
EYL YP ++VD+V + D++ + L DS+ ++R
Sbjct: 22 EYLARYPDVRVDLVLSDRLVDLVEEGFDAAFRIGELADSSLVARP 66
>gnl|CDD|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 = 1.7
Identities = 13/37 (35%), Positives = 18/37 (48%), Gaps = 1/37 (2%)
Query: 150 TLLGKTVFILGFGN-IGVELAKRLRPFGVKIIATKRS 185
G T+ I G + IG+ LAKR G +I R+
Sbjct: 2 KTTGNTILITGGASGIGLALAKRFLELGNTVIICGRN 38
>gnl|CDD|235488 PRK05476, PRK05476, S-adenosyl-L-homocysteine hydrolase;
Provisional.
Length = 425
Score = 29.3 bits (67), Expect = 1.9
Identities = 18/48 (37%), Positives = 26/48 (54%), Gaps = 12/48 (25%)
Query: 147 TGETLL------------GKTVFILGFGNIGVELAKRLRPFGVKIIAT 182
TGE+LL GK V + G+G++G A+RLR G ++I T
Sbjct: 194 TGESLLDGIKRATNVLIAGKVVVVAGYGDVGKGCAQRLRGLGARVIVT 241
>gnl|CDD|218507 pfam05221, AdoHcyase, S-adenosyl-L-homocysteine hydrolase.
Length = 430
Score = 29.3 bits (66), Expect = 2.1
Identities = 11/30 (36%), Positives = 17/30 (56%)
Query: 153 GKTVFILGFGNIGVELAKRLRPFGVKIIAT 182
GK + G+G++G A LR G ++I T
Sbjct: 210 GKVAVVCGYGDVGKGCAASLRGQGARVIVT 239
>gnl|CDD|235660 PRK05976, PRK05976, dihydrolipoamide dehydrogenase; Validated.
Length = 472
Score = 29.1 bits (66), Expect = 2.3
Identities = 13/28 (46%), Positives = 19/28 (67%)
Query: 152 LGKTVFILGFGNIGVELAKRLRPFGVKI 179
L K++ I+G G IG+E A L FGV++
Sbjct: 179 LPKSLVIVGGGVIGLEWASMLADFGVEV 206
>gnl|CDD|223536 COG0460, ThrA, Homoserine dehydrogenase [Amino acid transport and
metabolism].
Length = 333
Score = 29.1 bits (66), Expect = 2.4
Identities = 17/86 (19%), Positives = 32/86 (37%), Gaps = 19/86 (22%)
Query: 156 VFILGFGNIGVELAKRL--------RPFGVKIIATK---RSWASHSQVSCQSSALAVKNG 204
V +LG G +G + + L + G++I R + + ++ + +G
Sbjct: 6 VGLLGLGTVGSGVLEILAEKQEELRKRAGIEIRVVAVADRDGSLVRDLDLLNAEVWTTDG 65
Query: 205 IIDDLVDEKGCHEDIFEFASKADVVV 230
+ + EDI DVVV
Sbjct: 66 ALSLGDEVL-LDEDI-------DVVV 83
>gnl|CDD|112609 pfam03804, DUF325, Viral domain of unknown function.
Length = 71
Score = 27.1 bits (60), Expect = 2.6
Identities = 12/34 (35%), Positives = 19/34 (55%), Gaps = 2/34 (5%)
Query: 208 DLVDEKGCHEDI--FEFASKADVVVCCLSLNKQT 239
L+D K H D+ F F + +V C+++N QT
Sbjct: 27 ALIDGKVTHADVRRFGFLDRNALVSACMAVNVQT 60
>gnl|CDD|182601 PRK10632, PRK10632, transcriptional regulator; Provisional.
Length = 309
Score = 28.6 bits (64), Expect = 3.0
Identities = 16/47 (34%), Positives = 26/47 (55%), Gaps = 1/47 (2%)
Query: 29 TKEYLQNYPSIQVDVVPISDVPDVIANYHLCVVKTMRL-DSNCISRA 74
T + L+ YP + V++V PD+IA+ V++ L DS+ SR
Sbjct: 111 TAKMLKEYPGLSVNLVTGIPAPDLIADGLDVVIRVGALQDSSLFSRR 157
>gnl|CDD|223842 COG0771, MurD, UDP-N-acetylmuramoylalanine-D-glutamate ligase [Cell
envelope biogenesis, outer membrane].
Length = 448
Score = 28.8 bits (65), Expect = 3.0
Identities = 11/33 (33%), Positives = 16/33 (48%)
Query: 149 ETLLGKTVFILGFGNIGVELAKRLRPFGVKIIA 181
E GK V +LG G G+ A+ L G ++
Sbjct: 3 EDFQGKKVLVLGLGKSGLAAARFLLKLGAEVTV 35
>gnl|CDD|224995 COG2084, MmsB, 3-hydroxyisobutyrate dehydrogenase and related
beta-hydroxyacid dehydrogenases [Lipid metabolism].
Length = 286
Score = 28.7 bits (65), Expect = 3.2
Identities = 15/82 (18%), Positives = 26/82 (31%), Gaps = 17/82 (20%)
Query: 154 KTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEK 213
+ +G G +G +A L G ++ R+ + L
Sbjct: 1 MKIAFIGLGIMGSPMAANLLKAGHEVTVYNRTPEK----------------AAELLAAAG 44
Query: 214 GC-HEDIFEFASKADVVVCCLS 234
E A++ADVV+ L
Sbjct: 45 ATVAASPAEAAAEADVVITMLP 66
>gnl|CDD|178263 PLN02657, PLN02657, 3,8-divinyl protochlorophyllide a 8-vinyl
reductase.
Length = 390
Score = 28.6 bits (64), Expect = 3.5
Identities = 20/85 (23%), Positives = 33/85 (38%), Gaps = 4/85 (4%)
Query: 154 KTVFILG-FGNIGVELAKRLRPFGVKIIATKRSWA---SHSQVSCQSSALAVKNGIIDDL 209
TV ++G G IG + + L G ++A R + + L + D+
Sbjct: 61 VTVLVVGATGYIGKFVVRELVRRGYNVVAVAREKSGIRGKNGKEDTKKELPGAEVVFGDV 120
Query: 210 VDEKGCHEDIFEFASKADVVVCCLS 234
D + +F DVVV CL+
Sbjct: 121 TDADSLRKVLFSEGDPVDVVVSCLA 145
>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 = 28.5 bits (64), Expect = 3.5
Identities = 18/54 (33%), Positives = 26/54 (48%), Gaps = 7/54 (12%)
Query: 151 LLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNG 204
L GKTV I+G+G+ G A LR G+ +I R + S A ++G
Sbjct: 1 LKGKTVAIIGYGSQGHAQALNLRDSGLNVIVGLRKGGA-------SWKKATEDG 47
>gnl|CDD|109716 pfam00670, AdoHcyase_NAD, S-adenosyl-L-homocysteine hydrolase, NAD
binding domain.
Length = 162
Score = 28.1 bits (63), Expect = 3.6
Identities = 10/30 (33%), Positives = 17/30 (56%)
Query: 153 GKTVFILGFGNIGVELAKRLRPFGVKIIAT 182
GK + G+G++G A L+ G ++I T
Sbjct: 23 GKVAVVCGYGDVGKGCAASLKGQGARVIVT 52
>gnl|CDD|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 = 27.1 bits (61), Expect = 3.8
Identities = 10/17 (58%), Positives = 11/17 (64%)
Query: 166 VELAKRLRPFGVKIIAT 182
VELAK L G K+ AT
Sbjct: 3 VELAKALVELGFKLYAT 19
>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 = 28.5 bits (64), Expect = 3.9
Identities = 12/29 (41%), Positives = 17/29 (58%)
Query: 152 LGKTVFILGFGNIGVELAKRLRPFGVKII 180
L K V ++G G IG+ELA L G ++
Sbjct: 141 LPKRVVVVGGGYIGLELAAALAKLGKEVT 169
>gnl|CDD|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 = 27.5 bits (62), Expect = 4.3
Identities = 16/81 (19%), Positives = 28/81 (34%), Gaps = 15/81 (18%)
Query: 155 TVFILGFGNIG---VELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVD 211
V ++G G +G AK L G ++ A Q+ ++ L
Sbjct: 22 KVVVIGAGVVGLGAAATAKGL---GAEVTVLDVRPARLRQLE------SLLGARFTTLYS 72
Query: 212 EKGCHEDIFEFASKADVVVCC 232
+ E E +AD+V+
Sbjct: 73 QAELLE---EAVKEADLVIGA 90
>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 = 4.3
Identities = 9/17 (52%), Positives = 12/17 (70%)
Query: 166 VELAKRLRPFGVKIIAT 182
VE AK L GV+I++T
Sbjct: 16 VEFAKALVELGVEILST 32
>gnl|CDD|223552 COG0476, ThiF, Dinucleotide-utilizing enzymes involved in
molybdopterin and thiamine biosynthesis family 2
[Coenzyme metabolism].
Length = 254
Score = 28.1 bits (63), Expect = 4.4
Identities = 22/117 (18%), Positives = 35/117 (29%), Gaps = 25/117 (21%)
Query: 151 LLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWAS-----HSQV------------- 192
L V ++G G +G AK L GV + Q
Sbjct: 28 LKDSRVLVVGAGGLGSPAAKYLALAGVGKLTIVDFDTVELSNLQRQFLFTEADVGKPKAE 87
Query: 193 SCQSSALAVKNGIIDDLVDEKGCHEDIFEFASKADVVVCCLS-------LNKQTVKL 242
+ + + E+ E+ E ++ DVV+ C +N VKL
Sbjct: 88 VAAKALRKLNPLVEVVAYLERLDEENAEELIAQFDVVLDCTDNFETRYLINDACVKL 144
>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 = 28.1 bits (63), Expect = 4.4
Identities = 13/78 (16%), Positives = 27/78 (34%), Gaps = 11/78 (14%)
Query: 155 TVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEKG 214
V I+G G +G+ AK + G ++ V G +K
Sbjct: 164 KVLIIGAGVVGLGAAKIAKKLGANVLVYDIKEEKLKGVE--------TLGGSRLRYSQK- 214
Query: 215 CHEDIFEFASKADVVVCC 232
E++ + + D+++
Sbjct: 215 --EELEKELKQTDILINA 230
>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 = 4.6
Identities = 29/120 (24%), Positives = 47/120 (39%), Gaps = 17/120 (14%)
Query: 143 LGVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVK 202
LG + + V I G G +G+E+AK L GVK + H CQ+ L+
Sbjct: 14 LGDEAMQKMAKSNVLISGMGGLGLEIAKNLVLAGVKSVTL------HDTEKCQAWDLSSN 67
Query: 203 NGIIDDLVDEKGCHEDIFEFASKADVVVCCLSLNKQTVKLCSSSLSSKSMFFATYVVFMF 262
+ +D V ++A+ VV L+ V + SSS+ F + +
Sbjct: 68 FFLSEDDVGR-----------NRAEAVVKKLAELNPYVHVSSSSVPFNEEFLDKFQCVVL 116
>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 = 28.0 bits (63), Expect = 4.7
Identities = 14/42 (33%), Positives = 23/42 (54%), Gaps = 2/42 (4%)
Query: 153 GKTVFILG-FGNIGVELAKRLRPFGVK-IIATKRSWASHSQV 192
GKT+ + G G+IG EL +++ FG K +I R ++
Sbjct: 2 GKTILVTGGAGSIGSELVRQILKFGPKKLIVFDRDENKLHEL 43
>gnl|CDD|187540 cd05229, SDR_a3, atypical (a) SDRs, subgroup 3. These atypical SDR
family members of unknown function have a glycine-rich
NAD(P)-binding motif consensus that is very similar to
the extended SDRs, GXXGXXG. Generally, this group has
poor conservation of the active site tetrad, However,
individual sequences do contain matches to the YXXXK
active site motif, and generally Tyr or Asn in place of
the upstream Ser found in most SDRs. 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 = 302
Score = 28.1 bits (63), Expect = 5.1
Identities = 18/75 (24%), Positives = 28/75 (37%), Gaps = 11/75 (14%)
Query: 158 ILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEKGCHE 217
+ G IG E+A+ LR G + RS + + + A D +D
Sbjct: 5 LGASGPIGREVARELRRRGWDVRLVSRSGSKLAWLPGVEIVAA-------DAMDAS---- 53
Query: 218 DIFEFASKADVVVCC 232
+ A ADV+ C
Sbjct: 54 SVIAAARGADVIYHC 68
>gnl|CDD|180774 PRK06953, PRK06953, short chain dehydrogenase; Provisional.
Length = 222
Score = 27.7 bits (62), Expect = 5.1
Identities = 15/36 (41%), Positives = 21/36 (58%), Gaps = 1/36 (2%)
Query: 154 KTVFILGFG-NIGVELAKRLRPFGVKIIATKRSWAS 188
KTV I+G IG E ++ R G ++IAT R A+
Sbjct: 2 KTVLIVGASRGIGREFVRQYRADGWRVIATARDAAA 37
>gnl|CDD|223450 COG0373, HemA, Glutamyl-tRNA reductase [Coenzyme metabolism].
Length = 414
Score = 28.0 bits (63), Expect = 5.2
Identities = 24/87 (27%), Positives = 39/87 (44%), Gaps = 14/87 (16%)
Query: 149 ETLLGKTVFILGFGNIGVELAKRLRPFGV-KIIATKRSWASHSQVSCQSSALAVKNGIID 207
+L K V ++G G +G +AK L GV KI R+ +++ + A AV
Sbjct: 174 GSLKDKKVLVIGAGEMGELVAKHLAEKGVKKITIANRTLERAEELAKKLGAEAVA----- 228
Query: 208 DLVDEKGCHEDIFEFASKADVVVCCLS 234
E++ E ++ADVV+ S
Sbjct: 229 --------LEELLEALAEADVVISSTS 247
>gnl|CDD|236106 PRK07818, PRK07818, dihydrolipoamide dehydrogenase; Reviewed.
Length = 466
Score = 28.1 bits (63), Expect = 5.5
Identities = 12/28 (42%), Positives = 18/28 (64%)
Query: 152 LGKTVFILGFGNIGVELAKRLRPFGVKI 179
L K++ I G G IG+E A L+ +GV +
Sbjct: 171 LPKSIVIAGAGAIGMEFAYVLKNYGVDV 198
>gnl|CDD|238709 cd01421, IMPCH, Inosine monophosphate cyclohydrolase domain. This
is the N-terminal domain in the purine biosynthesis
pathway protein ATIC (purH). The bifunctional ATIC
protein contains a C-terminal ATIC formylase domain
that formylates
5-aminoimidazole-4-carboxamide-ribonucleotide. The IMPCH
domain then converts the
formyl-5-aminoimidazole-4-carboxamide-ribonucleotide to
inosine monophosphate. This is the final step in de novo
purine production.
Length = 187
Score = 27.6 bits (62), Expect = 5.6
Identities = 9/17 (52%), Positives = 12/17 (70%)
Query: 166 VELAKRLRPFGVKIIAT 182
VE AK L GV+I++T
Sbjct: 14 VEFAKELVELGVEILST 30
>gnl|CDD|222002 pfam13241, NAD_binding_7, Putative NAD(P)-binding. This domain is
found in fungi, plants, archaea and bacteria.
Length = 104
Score = 26.6 bits (60), Expect = 5.7
Identities = 19/94 (20%), Positives = 35/94 (37%), Gaps = 21/94 (22%)
Query: 153 GKTVFILGFGNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDE 212
GK V ++G G + + + L G K+ VS + G++ L+
Sbjct: 7 GKRVLVVGGGEVALRKIRALLEAGAKVTV----------VSPEILEAE---GLV-RLIQR 52
Query: 213 KGCHEDIFEFASKADVVVCCLS---LNKQTVKLC 243
+ D+ AD+V+ LN++ L
Sbjct: 53 EFEPGDL----DGADLVIAATDDPELNERIAALA 82
>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 = 28.0 bits (63), Expect = 5.8
Identities = 26/99 (26%), Positives = 43/99 (43%), Gaps = 21/99 (21%)
Query: 137 AIE--QKKLGVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVK-IIATKRSWASHSQVS 193
A+E +K G L GK V ++G G +G AK L GV I R++ +++
Sbjct: 165 AVELAEKIFG-----NLKGKKVLVIGAGEMGELAAKHLAAKGVAEITIANRTYERAEELA 219
Query: 194 CQSSALAVKNGIIDDLVDEKGCHEDIFEFASKADVVVCC 232
+ AV +D+L++ +ADVV+
Sbjct: 220 KELGGNAVP---LDELLELLN----------EADVVISA 245
>gnl|CDD|234592 PRK00045, hemA, glutamyl-tRNA reductase; Reviewed.
Length = 423
Score = 27.8 bits (63), Expect = 5.9
Identities = 24/113 (21%), Positives = 45/113 (39%), Gaps = 21/113 (18%)
Query: 149 ETLLGKTVFILGFGNIGVELAKRLRPFGVK-IIATKRSWASHSQVSCQSSALAVK-NGII 206
L GK V ++G G +G +AK L GV+ I R+ ++ LA + G
Sbjct: 178 GDLSGKKVLVIGAGEMGELVAKHLAEKGVRKITVANRT-LERAE------ELAEEFGGEA 230
Query: 207 DDLVDEKGCHEDIFEFASKADVVVCCLS-----LNKQTVKLCSSSLSSKSMFF 254
L +++ E ++AD+V+ + K V+ + + +
Sbjct: 231 IPL-------DELPEALAEADIVISSTGAPHPIIGKGMVERALKARRHRPLLL 276
>gnl|CDD|224433 COG1516, FliS, Flagellin-specific chaperone FliS [Cell motility and
secretion / Intracellular trafficking and secretion /
Posttranslational modification, protein turnover,
chaperones].
Length = 132
Score = 26.9 bits (60), Expect = 6.2
Identities = 11/31 (35%), Positives = 16/31 (51%)
Query: 112 NAASCAELTIYLMLGLLRKQNEMRMAIEQKK 142
N AS +L + L G L+ + AIEQ+
Sbjct: 16 NTASPHKLILMLYEGALKFLKRAKEAIEQED 46
>gnl|CDD|130488 TIGR01421, gluta_reduc_1, glutathione-disulfide reductase,
animal/bacterial. The tripeptide glutathione is an
important reductant, e.g., for maintaining the cellular
thiol/disulfide status and for protecting against
reactive oxygen species such as hydrogen peroxide.
Glutathione-disulfide reductase regenerates reduced
glutathione from oxidized glutathione (glutathione
disulfide) + NADPH. This model represents one of two
closely related subfamilies of glutathione-disulfide
reductase. Both are closely related to trypanothione
reductase, and separate models are built so each of the
three can describe proteins with conserved function.
This model describes glutathione-disulfide reductases of
animals, yeast, and a number of animal-resident bacteria
[Energy metabolism, Electron transport].
Length = 450
Score = 27.9 bits (62), Expect = 6.8
Identities = 13/27 (48%), Positives = 15/27 (55%)
Query: 152 LGKTVFILGFGNIGVELAKRLRPFGVK 178
L K V I+G G I VELA L G +
Sbjct: 165 LPKRVVIVGAGYIAVELAGVLHGLGSE 191
>gnl|CDD|215691 pfam00070, Pyr_redox, 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 = 82
Score = 26.0 bits (58), Expect = 7.0
Identities = 10/24 (41%), Positives = 14/24 (58%)
Query: 156 VFILGFGNIGVELAKRLRPFGVKI 179
V ++G G IG+E A L G K+
Sbjct: 2 VVVVGGGYIGLEFASALAKLGSKV 25
>gnl|CDD|178323 PLN02721, PLN02721, threonine aldolase.
Length = 353
Score = 27.7 bits (62), Expect = 7.5
Identities = 13/33 (39%), Positives = 15/33 (45%), Gaps = 8/33 (24%)
Query: 141 KKLGVPTGETLLGKTVFILGFGNIGVELAKRLR 173
K LG P G ++G FI AKRLR
Sbjct: 208 KGLGAPVGSVIVGSKSFI--------RKAKRLR 232
>gnl|CDD|216949 pfam02254, TrkA_N, TrkA-N domain. This domain is found in a wide
variety of proteins. These protein include potassium
channels, phosphoesterases, and various other
transporters. This domain binds to NAD.
Length = 116
Score = 26.4 bits (59), Expect = 7.9
Identities = 8/18 (44%), Positives = 13/18 (72%)
Query: 156 VFILGFGNIGVELAKRLR 173
+ I+G+G +G LA+ LR
Sbjct: 1 IIIIGYGRVGRSLAEELR 18
>gnl|CDD|238768 cd01491, Ube1_repeat1, Ubiquitin activating enzyme (E1), repeat 1.
E1, a highly conserved small protein present universally
in eukaryotic cells, is part of cascade to attach
ubiquitin (Ub) covalently to substrate proteins. This
cascade consists of activating (E1), conjugating (E2),
and/or ligating (E3) enzymes and then targets them for
degradation by the 26S proteasome. E1 activates
ubiquitin by C-terminal adenylation, and subsequently
forms a highly reactive thioester bond between its
catalytic cysteine and ubiquitin's C-terminus. E1 also
associates with E2 and promotes ubiquitin transfer to
the E2's catalytic cysteine. Ubiquitin-E1 is a
single-chain protein with a weakly conserved two-fold
repeat. This CD represents the first repeat of Ub-E1.
Length = 286
Score = 27.2 bits (61), Expect = 8.1
Identities = 16/36 (44%), Positives = 19/36 (52%)
Query: 143 LGVPTGETLLGKTVFILGFGNIGVELAKRLRPFGVK 178
LG + L V I G G +GVE+AK L GVK
Sbjct: 9 LGHEAMKKLQKSNVLISGLGGLGVEIAKNLILAGVK 44
>gnl|CDD|215281 PLN02507, PLN02507, glutathione reductase.
Length = 499
Score = 27.5 bits (61), Expect = 8.1
Identities = 17/49 (34%), Positives = 22/49 (44%), Gaps = 4/49 (8%)
Query: 135 RMAIEQKKLGVPTGETL----LGKTVFILGFGNIGVELAKRLRPFGVKI 179
R I K+L + + E L L K +LG G I VE A R G +
Sbjct: 181 RPNIPGKELAITSDEALSLEELPKRAVVLGGGYIAVEFASIWRGMGATV 229
>gnl|CDD|182130 PRK09880, PRK09880, L-idonate 5-dehydrogenase; Provisional.
Length = 343
Score = 27.3 bits (61), Expect = 8.1
Identities = 25/98 (25%), Positives = 40/98 (40%), Gaps = 19/98 (19%)
Query: 151 LLGKTVFILGFGNIGVELAKRLRPFGVK-IIATKRSWASHSQVSCQSSALAVK------- 202
L GK VF+ G G IG + ++ G I+ + VS +S +LA +
Sbjct: 168 LQGKRVFVSGVGPIGCLIVAAVKTLGAAEIVC--------ADVSPRSLSLAREMGADKLV 219
Query: 203 ---NGIIDDLVDEKGCHEDIFEFASKADVVVCCLSLNK 237
N +D EKG + FE + + CL + +
Sbjct: 220 NPQNDDLDHYKAEKGYFDVSFEVSGHPSSINTCLEVTR 257
>gnl|CDD|187593 cd05332, 11beta-HSD1_like_SDR_c, 11beta-hydroxysteroid
dehydrogenase type 1 (11beta-HSD1)-like, classical (c)
SDRs. Human 11beta_HSD1 catalyzes the NADP(H)-dependent
interconversion of cortisone and cortisol. This subgroup
also includes human dehydrogenase/reductase SDR family
member 7C (DHRS7C) and DHRS7B. These proteins have the
GxxxGxG nucleotide binding motif and S-Y-K catalytic
triad characteristic of the SDRs, but have an atypical
C-terminal domain that contributes to homodimerization
contacts. 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 = 257
Score = 27.2 bits (61), Expect = 8.2
Identities = 14/38 (36%), Positives = 18/38 (47%), Gaps = 1/38 (2%)
Query: 151 LLGKTVFILG-FGNIGVELAKRLRPFGVKIIATKRSWA 187
L GK V I G IG ELA L G +++ + R
Sbjct: 1 LQGKVVIITGASSGIGEELAYHLARLGARLVLSARREE 38
>gnl|CDD|178111 PLN02494, PLN02494, adenosylhomocysteinase.
Length = 477
Score = 27.5 bits (61), Expect = 8.5
Identities = 10/31 (32%), Positives = 18/31 (58%)
Query: 153 GKTVFILGFGNIGVELAKRLRPFGVKIIATK 183
GK I G+G++G A ++ G ++I T+
Sbjct: 254 GKVAVICGYGDVGKGCAAAMKAAGARVIVTE 284
>gnl|CDD|181452 PRK08507, PRK08507, prephenate dehydrogenase; Validated.
Length = 275
Score = 27.2 bits (61), Expect = 9.1
Identities = 17/77 (22%), Positives = 31/77 (40%), Gaps = 18/77 (23%)
Query: 156 VFILGFGNIGVELAKRLRP--FGVKIIATKRSWASHSQVSCQSSALAVKNGIIDDLVDEK 213
+ I+G G +G L L+ K+ + H + A++ G++D++V
Sbjct: 3 IGIIGLGLMGGSLGLALKEKGLISKVYGYDHN-ELHLK-------KALELGLVDEIVS-- 52
Query: 214 GCHEDIFEFASKADVVV 230
FE K DV+
Sbjct: 53 ------FEELKKCDVIF 63
>gnl|CDD|237079 PRK12367, PRK12367, short chain dehydrogenase; Provisional.
Length = 245
Score = 27.3 bits (61), Expect = 9.3
Identities = 15/45 (33%), Positives = 23/45 (51%), Gaps = 1/45 (2%)
Query: 153 GKTVFILGF-GNIGVELAKRLRPFGVKIIATKRSWASHSQVSCQS 196
GK + I G G +G L K R G K+I S ++S+ + +S
Sbjct: 14 GKRIGITGASGALGKALTKAFRAKGAKVIGLTHSKINNSESNDES 58
>gnl|CDD|176198 cd08236, sugar_DH, NAD(P)-dependent sugar dehydrogenases. This
group contains proteins identified as sorbitol
dehydrogenases and other sugar dehydrogenases of the
medium-chain dehydrogenase/reductase family (MDR), which
includes zinc-dependent alcohol dehydrogenase and
related proteins. Sorbitol and aldose reductase are
NAD(+) binding proteins of the polyol pathway, which
interconverts glucose and fructose. Sorbitol
dehydrogenase is tetrameric and has a single catalytic
zinc per subunit. NAD(P)(H)-dependent oxidoreductases
are the major enzymes in the interconversion of alcohols
and aldehydes, or ketones. Related proteins include
threonine dehydrogenase, formaldehyde dehydrogenase, and
butanediol dehydrogenase. The medium chain alcohol
dehydrogenase family (MDR) has a NAD(P)(H)-binding
domain in a Rossmann fold of a beta-alpha form. The
N-terminal region typically has an all-beta catalytic
domain. These proteins typically form dimers (typically
higher plants, mammals) or tetramers (yeast, bacteria),
and have 2 tightly bound zinc atoms per subunit. Horse
liver alcohol dehydrogenase is a dimeric enzyme and each
subunit has two domains. The NAD binding domain is in a
Rossmann fold and the catalytic domain contains a zinc
ion to which substrates bind. There is a cleft between
the domains that closes upon formation of the ternary
complex.
Length = 343
Score = 27.2 bits (61), Expect = 9.5
Identities = 24/83 (28%), Positives = 39/83 (46%), Gaps = 13/83 (15%)
Query: 152 LGKTVFILGFGNIGVELAKRLRPFGVK-IIATKRSWASHSQVSCQSSALAVKNGIIDDLV 210
LG TV ++G G IG+ + L+ G K +IA + + A+A + G DD +
Sbjct: 159 LGDTVVVIGAGTIGLLAIQWLKILGAKRVIAV--------DIDDEKLAVARELG-ADDTI 209
Query: 211 DEKGC-HEDIFEFAS--KADVVV 230
+ K E + E AD+V+
Sbjct: 210 NPKEEDVEKVRELTEGRGADLVI 232
>gnl|CDD|238712 cd01424, MGS_CPS_II, Methylglyoxal synthase-like domain from type
II glutamine-dependent carbamoyl phosphate synthetase
(CSP). CSP, a CarA and CarB heterodimer, catalyzes the
production of carbamoyl phosphate which is subsequently
employed in the metabolic pathways responsible for the
synthesis of pyrimidine nucleotides or arginine. The
MGS-like domain is the C-terminal domain of CarB and
appears to play a regulatory role in CPS function by
binding allosteric effector molecules, including UMP and
ornithine.
Length = 110
Score = 26.3 bits (59), Expect = 9.7
Identities = 10/18 (55%), Positives = 14/18 (77%)
Query: 166 VELAKRLRPFGVKIIATK 183
VE+AKRL G K++AT+
Sbjct: 16 VEIAKRLAELGFKLVATE 33
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
0.323 0.136 0.402
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: 13,233,038
Number of extensions: 1231936
Number of successful extensions: 1543
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1452
Number of HSP's successfully gapped: 155
Length of query: 269
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 174
Effective length of database: 6,723,972
Effective search space: 1169971128
Effective search space used: 1169971128
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 58 (25.9 bits)