RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6348
(333 letters)
>gnl|CDD|237436 PRK13581, PRK13581, D-3-phosphoglycerate dehydrogenase;
Provisional.
Length = 526
Score = 454 bits (1172), Expect = e-159
Identities = 165/307 (53%), Positives = 217/307 (70%), Gaps = 8/307 (2%)
Query: 2 YDGLVVRSDTKVTAEVLQ-ASNLQVVGRAGTGVDNIDLTAATRKGVLVLNAPGGNFISAC 60
YD L+VRS TKVTAEVL+ A NL+V+GRAG GVDN+D+ AATR+G++V+NAP GN ISA
Sbjct: 43 YDALIVRSATKVTAEVLEAAKNLKVIGRAGVGVDNVDVPAATRRGIIVVNAPTGNTISAA 102
Query: 61 ELTCSLISALSRNVPQGCQSLKEGKWDRKLYTGTELYGKTLAVLGLGRIGREVALRMQAF 120
E T +L+ AL+RN+PQ SLK GKW+RK + G ELYGKTL ++GLGRIG EVA R +AF
Sbjct: 103 EHTIALMLALARNIPQAHASLKAGKWERKKFMGVELYGKTLGIIGLGRIGSEVAKRAKAF 162
Query: 121 GMKVIGFDPMVSVEDAAKLNIASLGLEDIWPLADYITVHTPLIPQTKNLINAEVLKKCKK 180
GMKVI +DP +S E AA+L + + L+++ AD+IT+HTPL P+T+ LI AE L K K
Sbjct: 163 GMKVIAYDPYISPERAAQLGVELVSLDELLARADFITLHTPLTPETRGLIGAEELAKMKP 222
Query: 181 GVRVVNVARGGIVDENALLDSLKCGHCGGAALDVFCEEPPKSEQTFELIKHPKVIVTPHL 240
GVR++N ARGGI+DE AL ++LK G GAALDVF +EPP L + P V+VTPHL
Sbjct: 223 GVRIINCARGGIIDEAALAEALKSGKVAGAALDVFEKEPPTDS---PLFELPNVVVTPHL 279
Query: 241 GASTKEAQIRVAVEIAEQFIALANTNPQYTSIQGVLNAPALAASRNPENTSWISLARSLG 300
GAST EAQ VA+++AEQ I P + +N P++ A + ++ LA LG
Sbjct: 280 GASTAEAQENVAIQVAEQVIDALRGGP----VPNAVNLPSITAEEAEKLKPYLDLAEKLG 335
Query: 301 KISSQLL 307
+++QL
Sbjct: 336 SLAAQLA 342
>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 = 418 bits (1078), Expect = e-148
Identities = 152/262 (58%), Positives = 196/262 (74%), Gaps = 3/262 (1%)
Query: 2 YDGLVVRSDTKVTAEVLQAS-NLQVVGRAGTGVDNIDLTAATRKGVLVLNAPGGNFISAC 60
D L+VRS TKVTAEV++A+ L+V+GRAG GVDNID+ AAT +G+LV+NAPG N IS
Sbjct: 41 ADALIVRSATKVTAEVIEAAPRLKVIGRAGVGVDNIDVEAATARGILVVNAPGANTISVA 100
Query: 61 ELTCSLISALSRNVPQGCQSLKEGKWDRKLYTGTELYGKTLAVLGLGRIGREVALRMQAF 120
E T +L+ AL+RN+PQ SL+ GKWDRK + G EL GKTL ++GLGRIGREVA R +AF
Sbjct: 101 EHTIALMLALARNIPQADASLRAGKWDRKKFMGVELRGKTLGIVGLGRIGREVARRARAF 160
Query: 121 GMKVIGFDPMVSVEDAAKLNIASLGLEDIWPLADYITVHTPLIPQTKNLINAEVLKKCKK 180
GMKV+ +DP +S E AA + + L+++ AD+I++HTPL P+T+ LINAE L K K
Sbjct: 161 GMKVLAYDPYISAERAAAGGVELVSLDELLAEADFISLHTPLTPETRGLINAEELAKMKP 220
Query: 181 GVRVVNVARGGIVDENALLDSLKCGHCGGAALDVFCEEPPKSEQTFELIKHPKVIVTPHL 240
G ++N ARGGIVDE AL D+LK G GAALDVF +EPP ++ L+ P VI+TPHL
Sbjct: 221 GAILINTARGGIVDEAALADALKSGKIAGAALDVFEQEPPPAD--SPLLGLPNVILTPHL 278
Query: 241 GASTKEAQIRVAVEIAEQFIAL 262
GAST+EAQ RVAV+ AEQ +A+
Sbjct: 279 GASTEEAQERVAVDAAEQVLAV 300
>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 = 379 bits (975), Expect = e-129
Identities = 162/309 (52%), Positives = 209/309 (67%), Gaps = 9/309 (2%)
Query: 1 KYDGLVVRSDTKVTAEVLQ-ASNLQVVGRAGTGVDNIDLTAATRKGVLVLNAPGGNFISA 59
YD L+VRS TKVT EV+ A L+V+GRAG GVDNID+ AAT +G+LV+NAP GN ISA
Sbjct: 40 DYDALIVRSATKVTEEVIAAAPKLKVIGRAGVGVDNIDIEAATARGILVVNAPTGNTISA 99
Query: 60 CELTCSLISALSRNVPQGCQSLKEGKWDRKLYTGTELYGKTLAVLGLGRIGREVALRMQA 119
E +++ A +RN+PQ SLKEG+WDRK + GTELYGKTL V+GLGRIG VA R +A
Sbjct: 100 AEHALAMLLAAARNIPQADASLKEGEWDRKAFMGTELYGKTLGVIGLGRIGSIVAKRAKA 159
Query: 120 FGMKVIGFDPMVSVEDAAKLNIASLG-LEDIWPLADYITVHTPLIPQTKNLINAEVLKKC 178
FGMKV+ +DP +S E A +L + + L+++ AD+ITVHTPL P+T+ LI AE L K
Sbjct: 160 FGMKVLAYDPYISPERAEQLGVELVDDLDELLARADFITVHTPLTPETRGLIGAEELAKM 219
Query: 179 KKGVRVVNVARGGIVDENALLDSLKCGHCGGAALDVFCEEPPKSEQTFELIKHPKVIVTP 238
KKGV +VN ARGGI+DE AL ++L+ GH AALDVF +EPP L VI TP
Sbjct: 220 KKGVIIVNCARGGIIDEAALYEALEEGHVRAAALDVFEKEPPTDNP---LFDLDNVIATP 276
Query: 239 HLGASTKEAQIRVAVEIAEQFIALANTNPQYTSIQGVLNAPALAASRNPENTSWISLARS 298
HLGAST+EAQ VA ++AEQ + P + +NAP + A + ++ LA
Sbjct: 277 HLGASTREAQENVATQVAEQVLDALKGLP----VPNAVNAPGIDADVMEKLKPYLDLAEK 332
Query: 299 LGKISSQLL 307
LGK++ QLL
Sbjct: 333 LGKLAGQLL 341
>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 = 324 bits (832), Expect = e-111
Identities = 123/262 (46%), Positives = 178/262 (67%), Gaps = 4/262 (1%)
Query: 2 YDGLVVRSDTKVTAEVLQAS-NLQVVGRAGTGVDNIDLTAATRKGVLVLNAPGGNFISAC 60
YD L+VRS TKVT EV+ A+ NL+++ RAG G+DNID+ A +KG+ V+N PG + S
Sbjct: 42 YDVLIVRSRTKVTKEVIDAAKNLKIIARAGVGLDNIDVEYAKKKGIKVINTPGASSNSVA 101
Query: 61 ELTCSLISALSRNVPQGCQSLKEGKWDRKLYTGTELYGKTLAVLGLGRIGREVALRMQAF 120
EL L+ +L+R + + + +K GKW++K Y G EL GKTL ++G GRIGREVA +A
Sbjct: 102 ELVIGLMLSLARFIHRANREMKLGKWNKKKYKGIELRGKTLGIIGFGRIGREVAKIARAL 161
Query: 121 GMKVIGFDPMVSVEDAAKLNIASLGLEDIWPLADYITVHTPLIPQTKNLINAEVLKKCKK 180
GM VI +DP E A +L + ++ LE++ +D+I++H PL P+TK++IN + L+ K
Sbjct: 162 GMNVIAYDPYPKDEQAVELGVKTVSLEELLKNSDFISLHVPLTPETKHMINKKELELMKD 221
Query: 181 GVRVVNVARGGIVDENALLDSLKCGHCGGAALDVFCEEPPKSEQTFELIKHPKVIVTPHL 240
G ++N +RGG++DE ALL++LK G GAALDVF EPP +L++ P V +TPH+
Sbjct: 222 GAIIINTSRGGVIDEEALLEALKSGKLAGAALDVFENEPPPGS---KLLELPNVSLTPHI 278
Query: 241 GASTKEAQIRVAVEIAEQFIAL 262
GASTKEAQ R+ E+A + I
Sbjct: 279 GASTKEAQERIGEELANKIIEF 300
>gnl|CDD|223189 COG0111, SerA, Phosphoglycerate dehydrogenase and related
dehydrogenases [Amino acid transport and metabolism].
Length = 324
Score = 313 bits (803), Expect = e-106
Identities = 145/289 (50%), Positives = 186/289 (64%), Gaps = 11/289 (3%)
Query: 1 KYDGLVVRSDTKVTAEVLQ-ASNLQVVGRAGTGVDNIDLTAATRKGVLVLNAPGGNFISA 59
D L+V S T VT EVL A NL+ +GRAG GVDNIDL AAT++G+LV+NAPGGN IS
Sbjct: 45 DADALIV-SVTPVTEEVLAAAPNLKAIGRAGAGVDNIDLEAATKRGILVVNAPGGNAISV 103
Query: 60 CELTCSLISALSRNVPQGCQSLKEGKWDRKLYTGTELYGKTLAVLGLGRIGREVALRMQA 119
EL +L+ AL+R +P S + G+WDRK + GTEL GKT+ ++GLGRIGR VA R++A
Sbjct: 104 AELVLALLLALARRIPDADASQRRGEWDRKAFRGTELAGKTVGIIGLGRIGRAVAKRLKA 163
Query: 120 FGMKVIGFDPMVSVEDAAKLNIASL-GLEDIWPLADYITVHTPLIPQTKNLINAEVLKKC 178
FGMKVIG+DP E A + + L+++ AD +T+H PL P+T+ LINAE L K
Sbjct: 164 FGMKVIGYDPYSPRERAGVDGVVGVDSLDELLAEADILTLHLPLTPETRGLINAEELAKM 223
Query: 179 KKGVRVVNVARGGIVDENALLDSLKCGHCGGAALDVFCEEPPKSEQTFELIKHPKVIVTP 238
K G ++N ARGG+VDE+ALL +L G GAALDVF EEP ++ L P VI+TP
Sbjct: 224 KPGAILINAARGGVVDEDALLAALDSGKIAGAALDVFEEEPLPADS--PLWDLPNVILTP 281
Query: 239 HLGASTKEAQIRVAVEIAEQFIALANTNPQYTSIQGVLNAPALAASRNP 287
H+G ST EAQ RVA +AE + P V NAP + R
Sbjct: 282 HIGGSTDEAQERVAEIVAENIVRYLAGGPV------VNNAPEVDLERGY 324
>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 = 300 bits (771), Expect = e-101
Identities = 123/256 (48%), Positives = 170/256 (66%), Gaps = 6/256 (2%)
Query: 3 DGLVVRSDTKVTAEVL-QASNLQVVGRAGTGVDNIDLTAATRKGVLVLNAPGGNFISACE 61
DG++ D +T EVL A L+V+ R G G DNIDL AA ++G++V N PG N S E
Sbjct: 49 DGVIAGLD-PITEEVLAAAPRLKVISRYGVGYDNIDLEAAKKRGIVVTNTPGANSNSVAE 107
Query: 62 LTCSLISALSRNVPQGCQSLKEGKWDRKLYTGTELYGKTLAVLGLGRIGREVALRMQAFG 121
LT L+ AL+R +PQ + ++ G WDR GTELYGKTL ++GLGRIG+ VA R+ FG
Sbjct: 108 LTIGLMLALARQIPQADREVRAGGWDR--PVGTELYGKTLGIIGLGRIGKAVARRLSGFG 165
Query: 122 MKVIGFDPMVSVEDAAKLNIASLGLEDIWPLADYITVHTPLIPQTKNLINAEVLKKCKKG 181
MKV+ +DP E A + + + LE++ +D+I++H PL P+T++LINA L K G
Sbjct: 166 MKVLAYDPYPDEEFAKEHGVEFVSLEELLKESDFISLHLPLTPETRHLINAAELALMKPG 225
Query: 182 VRVVNVARGGIVDENALLDSLKCGHCGGAALDVFCEEPPKSEQTFELIKHPKVIVTPHLG 241
++N ARGG+VDE AL ++LK G GAALDVF EEPP ++ L++ P VI+TPH+G
Sbjct: 226 AILINTARGGLVDEEALYEALKSGRIAGAALDVFEEEPPPADS--PLLELPNVILTPHIG 283
Query: 242 ASTKEAQIRVAVEIAE 257
ASTKEA +R+ A+
Sbjct: 284 ASTKEAVLRMGTMAAQ 299
>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 = 287 bits (738), Expect = 1e-96
Identities = 112/263 (42%), Positives = 157/263 (59%), Gaps = 4/263 (1%)
Query: 2 YDGLVVRSDTKVTAEVLQAS-NLQVVGRAGTGVDNIDLTAATRKGVLVLNAPGGNFISAC 60
D L+V S T VTAEVL + L+ + AG GVDNIDL AA ++G+ V N PG N +
Sbjct: 42 ADALIVSSTTPVTAEVLAKAPKLKFIQVAGAGVDNIDLDAAKKRGITVTNVPGANAEAVA 101
Query: 61 ELTCSLISALSRNVPQGCQSLKEGKWDRKL-YTGTELYGKTLAVLGLGRIGREVALRMQA 119
E L+ AL R +P+ +++ G + G EL GKT+ ++GLGRIG+ VA R+QA
Sbjct: 102 EHALGLLLALLRRLPRADAAVRRGWGWLWAGFPGYELEGKTVGIVGLGRIGQRVAKRLQA 161
Query: 120 FGMKVIGFDPMVSVEDAAKLNIASLGLEDIWPLADYITVHTPLIPQTKNLINAEVLKKCK 179
FGMKV+ +D E L + L+++ +D + +H PL P+T++LIN E L K
Sbjct: 162 FGMKVLYYDRTRKPEPEEDLGFRVVSLDELLAQSDVVVLHLPLTPETRHLINEEELALMK 221
Query: 180 KGVRVVNVARGGIVDENALLDSLKCGHCGGAALDVFCEEPPKSEQTFELIKHPKVIVTPH 239
G +VN ARGG+VDE+ALL +LK G GAALDVF EP ++ L++ P VI+TPH
Sbjct: 222 PGAVLVNTARGGLVDEDALLRALKSGKIAGAALDVFEPEPLPADHP--LLELPNVILTPH 279
Query: 240 LGASTKEAQIRVAVEIAEQFIAL 262
+ T+EA+ R+A E
Sbjct: 280 IAGYTEEARERMAEIAVENLERF 302
>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 = 277 bits (712), Expect = 1e-92
Identities = 122/272 (44%), Positives = 160/272 (58%), Gaps = 22/272 (8%)
Query: 2 YDGLVVRSDTKVTAEVLQASNLQVVGRAGTGVDNIDLTAATRKGVLVLNAPGGNFISACE 61
D L+VRSD K+ A +L+ + RAG GV+NID+ AA+++G++V N PG N + E
Sbjct: 32 PDALIVRSD-KLHDMDF-APSLKAIARAGAGVNNIDVDAASKRGIVVFNTPGANANAVAE 89
Query: 62 LTCSLISALSRNVPQGCQ---------SLKEGKWDRKLYTGTELYGKTLAVLGLGRIGRE 112
L +++ ALSRN+ Q + K + +K + GTEL GKTL V+GLG IGR
Sbjct: 90 LVIAMMLALSRNIIQAIKWVTNGDGDDISKGVEKGKKQFVGTELRGKTLGVIGLGNIGRL 149
Query: 113 VALRMQAFGMKVIGFDPMVSVEDAAKLN---IASLGLEDIWPLADYITVHTPLIPQTKNL 169
VA A GMKVIG+DP +SVE A KL+ LE++ ADYIT+H PL +T+ L
Sbjct: 150 VANAALALGMKVIGYDPYLSVEAAWKLSVEVQRVTSLEELLATADYITLHVPLTDETRGL 209
Query: 170 INAEVLKKCKKGVRVVNVARGGIVDENALLDSLKCGHCGGAALDVFCEEPPKSEQTFELI 229
INAE+L K K G ++N ARG IVDE ALL++L G GG D EP
Sbjct: 210 INAELLAKMKPGAILLNFARGEIVDEEALLEALDEGKLGGYVTDF--PEPALLG------ 261
Query: 230 KHPKVIVTPHLGASTKEAQIRVAVEIAEQFIA 261
P VI TPHLGAST+EA+ AV A Q +
Sbjct: 262 HLPNVIATPHLGASTEEAEENCAVMAARQIMD 293
>gnl|CDD|223980 COG1052, LdhA, Lactate dehydrogenase and related dehydrogenases
[Energy production and conversion / Coenzyme metabolism
/ General function prediction only].
Length = 324
Score = 260 bits (666), Expect = 2e-85
Identities = 103/278 (37%), Positives = 159/278 (57%), Gaps = 6/278 (2%)
Query: 2 YDGLVVRSDTKVTAEVL-QASNLQVVGRAGTGVDNIDLTAATRKGVLVLNAPGGNFISAC 60
D ++ + ++ AEVL + L+++ G DN+DL AA +G+ V N PG + +
Sbjct: 45 ADAVITFVNDRIDAEVLEKLPGLKLIATRSAGYDNVDLEAAKERGITVTNVPGYSTEAVA 104
Query: 61 ELTCSLISALSRNVPQGCQSLKEGKWDRKLY----TGTELYGKTLAVLGLGRIGREVALR 116
E +LI AL+R + +G + ++EG W G +L GKTL ++GLGRIG+ VA R
Sbjct: 105 EHAVALILALARRIHEGDRRVREGNWSLSGGPDPLLGFDLRGKTLGIIGLGRIGQAVARR 164
Query: 117 MQAFGMKVIGFDPMVSVEDAAKLNIASLGLEDIWPLADYITVHTPLIPQTKNLINAEVLK 176
++ FGMKV+ +D + E +L + L+++ +D I++H PL P+T++LINAE L
Sbjct: 165 LKGFGMKVLYYDRSPNPEAEKELGARYVDLDELLAESDIISLHCPLTPETRHLINAEELA 224
Query: 177 KCKKGVRVVNVARGGIVDENALLDSLKCGHCGGAALDVFCEEPPKSEQTF-ELIKHPKVI 235
K K G +VN ARGG+VDE AL+D+LK G GA LDVF EP + L P V+
Sbjct: 225 KMKPGAILVNTARGGLVDEQALIDALKSGKIAGAGLDVFENEPALFDHPLLRLDNFPNVV 284
Query: 236 VTPHLGASTKEAQIRVAVEIAEQFIALANTNPQYTSIQ 273
+TPH+ ++T+EA+ +A E A + +
Sbjct: 285 LTPHIASATEEARKAMAELALENLEAFFDGGVPPNEVN 322
>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 = 251 bits (642), Expect = 5e-82
Identities = 107/271 (39%), Positives = 146/271 (53%), Gaps = 8/271 (2%)
Query: 2 YDGLVVRSDTKVTAEVLQ-ASNLQVVGRAGTGVDNIDLTAATRKGVLVLNAPGGNFISAC 60
D L+VRS T VTAEVL+ A L+V+ R G GVDNIDL AAT +G+LV N PG + S
Sbjct: 39 ADALIVRSTTPVTAEVLEAAPGLKVIARRGVGVDNIDLDAATERGILVTNVPGYSTESVA 98
Query: 61 ELTCSLISALSRNVPQGCQSLKEGKWDRKLYTGTELYGKTLAVLGLGRIGREVALRMQAF 120
ELT LI AL+R +P+ S++ G W + G ELYGKTL V+G G IG A +A
Sbjct: 99 ELTVGLILALARRIPEADASVRAGDWKKGGPIGLELYGKTLGVIGGGGIGGIGAAIAKAL 158
Query: 121 GMKVIGFDPMVSVEDAAKLNIASLGLEDIWPLA----DYITVHTPLIPQTKNLINAEVLK 176
GM V+ +DP + E A + + L L+ + D I + P +T ++I E
Sbjct: 159 GMGVVAYDPYPNPERAEEGGVEVLLLDLLLLDLKESDDLINLAPPTTMKTGHIIINEARG 218
Query: 177 KCKKGVRVVNVARGGIVDENALLDSLKCGHCGGAALDVFCEEPPKSEQTFELIKHPKVIV 236
K V + N GG+++E AL L+ G A V E PP + L+ P VI+
Sbjct: 219 MLKDAVAINNARGGGVIEEAALDALLEEGIAAAALDVVEEEPPPVNS---PLLDLPNVIL 275
Query: 237 TPHLGASTKEAQIRVAVEIAEQFIALANTNP 267
TPH+ +T+EAQ +A E AE +A
Sbjct: 276 TPHIAGATEEAQENMAEEAAENLLAFLKGGT 306
>gnl|CDD|240624 cd05299, CtBP_dh, C-terminal binding protein (CtBP),
D-isomer-specific 2-hydroxyacid dehydrogenases related
repressor. The transcriptional corepressor CtBP is a
dehydrogenase with sequence and structural similarity to
the d2-hydroxyacid dehydrogenase family. CtBP was
initially identified as a protein that bound the PXDLS
sequence at the adenovirus E1A C terminus, causing the
loss of CR-1-mediated transactivation. CtBP binds NAD(H)
within a deep cleft, undergoes a conformational change
upon NAD binding, and has NAD-dependent dehydrogenase
activity.
Length = 312
Score = 245 bits (628), Expect = 8e-80
Identities = 107/265 (40%), Positives = 154/265 (58%), Gaps = 19/265 (7%)
Query: 3 DGLVVRSDTKVTAEVLQA-SNLQVVGRAGTGVDNIDLTAATRKGVLVLNAPGGNFISAC- 60
D L+V+ VTAEV++A L+V+ R G GVDN+D+ AAT +G+ V N P C
Sbjct: 46 DALLVQY-APVTAEVIEALPRLKVIVRYGVGVDNVDVAAATERGIPVCNVPD-----YCT 99
Query: 61 ----ELTCSLISALSRNVPQGCQSLKEGKWDRKLYTGT-ELYGKTLAVLGLGRIGREVAL 115
+ +LI AL+R +P ++++ G WD + L G TL ++G GRIGR VA
Sbjct: 100 EEVADHALALILALARKLPFLDRAVRAGGWDWTVGGPIRRLRGLTLGLVGFGRIGRAVAK 159
Query: 116 RMQAFGMKVIGFDPMVSVEDAAKLNIASLGLEDIWPLADYITVHTPLIPQTKNLINAEVL 175
R +AFG +VI +DP V AA + + L+++ +D +++H PL P+T++LI+AE L
Sbjct: 160 RAKAFGFRVIAYDPYVPDGVAALGGVRVVSLDELLARSDVVSLHCPLTPETRHLIDAEAL 219
Query: 176 KKCKKGVRVVNVARGGIVDENALLDSLKCGHCGGAALDVFCEEPPKSEQTFELIKHPKVI 235
K G +VN ARGG+VDE AL +LK G GAALDV EEPP ++ L+ P VI
Sbjct: 220 ALMKPGAFLVNTARGGLVDEAALARALKSGRIAGAALDVLEEEPPPADS--PLLSAPNVI 277
Query: 236 VTPHLG----ASTKEAQIRVAVEIA 256
+TPH S E + + A E+
Sbjct: 278 LTPHAAWYSEESLAELRRKAAEEVV 302
>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 = 243 bits (622), Expect = 6e-79
Identities = 103/259 (39%), Positives = 151/259 (58%), Gaps = 5/259 (1%)
Query: 2 YDGLVVRSDTKVTAEVLQ-ASNLQVVGRAGTGVDNIDLTAATRKGVLVLNAPGGNFISAC 60
D LV + AE+L A L+++ + G G+D +DL AAT +G+ V N PGGN S
Sbjct: 44 ADVLVPGMRKVIDAELLAAAPRLRLIQQPGVGLDGVDLEAATARGIPVANIPGGNAESVA 103
Query: 61 ELTCSLISALSRNVPQGCQSLKEGKWDRKLY-TGTELYGKTLAVLGLGRIGREVALRMQA 119
E L+ AL R +P+ + L+ G+W R EL GKT+ ++GLG IGR VA R++
Sbjct: 104 EHAVMLMLALLRRLPEADRELRAGRWGRPEGRPSRELSGKTVGIVGLGNIGRAVARRLRG 163
Query: 120 FGMKVIGFDPMVSVEDAAKLNIASL-GLEDIWPLADYITVHTPLIPQTKNLINAEVLKKC 178
FG++VI +D E K L+++ +D +++H PL P+T++LI AE L
Sbjct: 164 FGVEVIYYDRFRDPEAEEKDLGVRYVELDELLAESDVVSLHVPLTPETRHLIGAEELAAM 223
Query: 179 KKGVRVVNVARGGIVDENALLDSLKCGHCGGAALDVFCEEPPKSEQTFELIKHPKVIVTP 238
K G ++N ARGG+VDE ALL +L+ GH GA LDVF +EP + L++ VI+TP
Sbjct: 224 KPGAILINTARGGLVDEEALLAALRSGHLAGAGLDVFWQEPLPPDD--PLLRLDNVILTP 281
Query: 239 HLGASTKEAQIRVAVEIAE 257
H+ T E+ R+A +AE
Sbjct: 282 HIAGVTDESYQRMAAIVAE 300
>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 = 241 bits (618), Expect = 2e-78
Identities = 98/266 (36%), Positives = 153/266 (57%), Gaps = 8/266 (3%)
Query: 2 YDGLVVRSDTKVTAEVL-QASNLQVVGRAGTGVDNIDLTAATRKGVLVLNAPGGNFISAC 60
D L+ VT +V+ A L+++G G +N+D+ AAT +G+ VLN PG N +
Sbjct: 47 ADILITHFAP-VTKKVIEAAPKLKLIGVCRGGPENVDVEAATERGIPVLNTPGRNAEAVA 105
Query: 61 ELTCSLISALSRNVPQGCQSLKEGKWDRKLY----TGTELYGKTLAVLGLGRIGREVALR 116
E T L+ A +RN+ + +LK+G+W + Y G EL GKT+ ++G G IGR VA R
Sbjct: 106 EFTVGLMLAETRNIARAHAALKDGEWRKDYYNYDGYGPELRGKTVGIVGFGAIGRRVAKR 165
Query: 117 MQAFGMKVIGFDPMVSVEDAAKLNIASLGLEDIWPLADYITVHTPLIPQTKNLINAEVLK 176
++AFG +V+ +DP V E + + LE++ +D +++H L P+T+ +I AE
Sbjct: 166 LKAFGAEVLVYDPYVDPEKIEADGVKKVSLEELLKRSDVVSLHARLTPETRGMIGAEEFA 225
Query: 177 KCKKGVRVVNVARGGIVDENALLDSLKCGHCGGAALDVFCEEPPKSEQTFELIKHPKVIV 236
K +N AR G+VDE+AL+++L+ G GGAALDVF EEP ++ L+K V +
Sbjct: 226 LMKPTAYFINTARAGLVDEDALIEALEEGKIGGAALDVFPEEPLPADH--PLLKLDNVTL 283
Query: 237 TPHLGASTKEAQIRVAVEIAEQFIAL 262
TPH+ +T++ R IAE+
Sbjct: 284 TPHIAGATRDVAERSPEIIAEELKRY 309
>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 = 228 bits (585), Expect = 2e-75
Identities = 77/177 (43%), Positives = 115/177 (64%), Gaps = 3/177 (1%)
Query: 65 SLISALSRNVPQGCQSLKEGKWDRKLYTGTELYGKTLAVLGLGRIGREVALRMQAFGMKV 124
+L+ AL+R +P+ + ++ G+W G EL GKT+ ++GLGRIGR VA R++AFGMKV
Sbjct: 2 ALLLALARRIPEADRQVRAGRWRPDALLGRELSGKTVGIIGLGRIGRAVARRLKAFGMKV 61
Query: 125 IGFDPMVSVEDAAKLNIASLGLEDIWPLADYITVHTPLIPQTKNLINAEVLKKCKKGVRV 184
I +D +A L + L+++ +D +++H PL P+T++LINAE L K G +
Sbjct: 62 IAYDRYPK-AEAEALGARYVSLDELLAESDVVSLHLPLTPETRHLINAERLALMKPGAIL 120
Query: 185 VNVARGGIVDENALLDSLKCGHCGGAALDVFCEEPPKSEQTFELIKHPKVIVTPHLG 241
+N ARGG+VDE+AL+ +LK G GAALDVF EP + L++ P VI+TPH+
Sbjct: 121 INTARGGLVDEDALIAALKSGRIAGAALDVFEPEPLPPDH--PLLELPNVILTPHIA 175
>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 = 227 bits (582), Expect = 7e-73
Identities = 95/256 (37%), Positives = 152/256 (59%), Gaps = 8/256 (3%)
Query: 2 YDGLVVRSDTKVTAEVL-QASNLQVVGRAGTGVDNIDLTAATRKGVLVLNAPGGNFISAC 60
DGL+ K+ AE+L A L+V+ G D+ID+ AA +G+ V N P +
Sbjct: 44 ADGLLCTLTDKIDAELLDAAPPLKVIANYSVGYDHIDVDAAKARGIPVTNTPDVLTDATA 103
Query: 61 ELTCSLISALSRNVPQGCQSLKEGKWDR---KLYTGTELYGKTLAVLGLGRIGREVALRM 117
+L +L+ A +R V +G + ++ G+W L GT+L+GKTL ++G+GRIG+ VA R
Sbjct: 104 DLAFALLLAAARRVVEGDRFVRAGEWKGWSPTLLLGTDLHGKTLGIVGMGRIGQAVARRA 163
Query: 118 QAFGMKVIGFDPMVSVEDAAKLNIASLGLEDIWPLADYITVHTPLIPQTKNLINAEVLKK 177
+ FGMK++ + E +L + L+++ +D++++H PL P+T++LINAE L
Sbjct: 164 KGFGMKILYHNRSRKPEAEEELGARYVSLDELLAESDFVSLHCPLTPETRHLINAERLAL 223
Query: 178 CKKGVRVVNVARGGIVDENALLDSLKCGHCGGAALDVFCEEP-PKSEQTFELIKHPKVIV 236
K ++N ARGG+VDE+AL+++LK G GA LDVF EP P L+ P V++
Sbjct: 224 MKPTAILINTARGGVVDEDALVEALKSGKIAGAGLDVFEPEPLPADH---PLLTLPNVVL 280
Query: 237 TPHLGASTKEAQIRVA 252
PH+G++T E + +A
Sbjct: 281 LPHIGSATVETRTAMA 296
>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 = 217 bits (555), Expect = 8e-69
Identities = 105/269 (39%), Positives = 157/269 (58%), Gaps = 8/269 (2%)
Query: 1 KYDGLVVRSDTKVTAEVLQAS-NLQVVGRAGTGVDNIDLTAATRKGVLVLNAPGGNFISA 59
YD L+ T V E++ A+ NL+++ G G DNID+ A KG+ V N P +
Sbjct: 43 DYDALITPLSTPVDKEIIDAAKNLKIIANYGAGFDNIDVDYAKEKGIPVTNTPAVSTEPT 102
Query: 60 CELTCSLISALSRNVPQGCQSLKEGK---WDRKLYTGTELYGKTLAVLGLGRIGREVALR 116
ELT LI AL+R + +G + ++ G W + G EL GKTL ++G+GRIG+ VA R
Sbjct: 103 AELTFGLILALARRIAEGDRLMRRGGFLGWAPLFFLGHELAGKTLGIIGMGRIGQAVARR 162
Query: 117 MQAFGMKVIGFDPM-VSVEDAAKLNIASLGLEDIWPLADYITVHTPLIPQTKNLINAEVL 175
+AFGMK++ ++ +S E +L + L+++ +D++++H P P+T +LI+A
Sbjct: 163 AKAFGMKILYYNRHRLSEETEKELGATYVDLDELLKESDFVSLHAPYTPETHHLIDAAAF 222
Query: 176 KKCKKGVRVVNVARGGIVDENALLDSLKCGHCGGAALDVFCEEPPKSEQTFELIKHPKVI 235
K K ++N ARG +VDE AL+D+LK G GAALDVF EP S EL K VI
Sbjct: 223 KLMKPTAYLINAARGPLVDEKALVDALKTGEIAGAALDVFEFEPEVSP---ELKKLDNVI 279
Query: 236 VTPHLGASTKEAQIRVAVEIAEQFIALAN 264
+TPH+G +T EA+ +A E A+ I+
Sbjct: 280 LTPHIGNATVEARDAMAKEAADNIISFLE 308
>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 = 211 bits (541), Expect = 8e-67
Identities = 102/263 (38%), Positives = 151/263 (57%), Gaps = 12/263 (4%)
Query: 5 LVVRSDTKVTAEVLQA-SNLQVVGRAGTGVDNIDLTAATRKGVLVLNAPGGNFISACELT 63
+++R T A +L+ NL+++ G +IDL AA +G++V GG + ELT
Sbjct: 51 VLMRERTPFPAALLERLPNLKLLVTTGMRNASIDLAAAKERGIVVCGTGGGP-TATAELT 109
Query: 64 CSLISALSRNVPQGCQSLKEGKWDRKLYTGTELYGKTLAVLGLGRIGREVALRMQAFGMK 123
+LI AL+RN+P+ +L+ G W L GT L GKTL ++GLGRIG VA QAFGM+
Sbjct: 110 WALILALARNLPEEDAALRAGGWQTTL--GTGLAGKTLGIVGLGRIGARVARIGQAFGMR 167
Query: 124 VIGFDPMVSVEDAAKLNI-ASLGLEDIWPLADYITVHTPLIPQTKNLINAEVLKKCKKGV 182
VI + ++ E AA + A++ E+++ +D +++H L +T+ L+ AE L K
Sbjct: 168 VIAWSSNLTAERAAAAGVEAAVSKEELFATSDVVSLHLVLSDRTRGLVGAEDLALMKPTA 227
Query: 183 RVVNVARGGIVDENALLDSLKCGHCGGAALDVFCEEP-PKSEQTFELIKHPKVIVTPHLG 241
+VN +RG +VDE ALL +L+ G GAALDVF EP P L P V++TPH+G
Sbjct: 228 LLVNTSRGPLVDEGALLAALRAGRIAGAALDVFDVEPLPADH---PLRGLPNVLLTPHIG 284
Query: 242 ASTKEA---QIRVAVEIAEQFIA 261
T+EA AVE ++A
Sbjct: 285 YVTEEAYEGFYGQAVENIAAWLA 307
>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 = 210 bits (538), Expect = 2e-66
Identities = 105/265 (39%), Positives = 158/265 (59%), Gaps = 21/265 (7%)
Query: 7 VRSDTKVTAEVLQAS-NLQVVGRAGTGVDNIDLTAATRKGVLVLNAPGGNFISACELTCS 65
+RS T++T EVL+A+ L +G G + +DL AA ++G+ V NAP N S EL
Sbjct: 48 IRSKTQLTEEVLEAAPKLLAIGCFCIGTNQVDLDAAAKRGIPVFNAPFSNTRSVAELVIG 107
Query: 66 LISALSRNVPQGCQSLKEGKWDRKLYTGT-ELYGKTLAVLGLGRIGREVALRMQAFGMKV 124
I L+R +P + G W+ K TG+ E+ GKTL ++G G IG ++++ +A GM+V
Sbjct: 108 EIIMLARRLPDRNAAAHRGIWN-KSATGSHEVRGKTLGIIGYGHIGSQLSVLAEALGMRV 166
Query: 125 IGFDPMVSVEDAAKLNIASLG-------LEDIWPLADYITVHTPLIPQTKNLINAEVLKK 177
I +D A KL LG LE++ AD++T+H P P TKN+I AE + +
Sbjct: 167 IFYDI------AEKL---PLGNARQVSSLEELLAEADFVTLHVPATPSTKNMIGAEEIAQ 217
Query: 178 CKKGVRVVNVARGGIVDENALLDSLKCGHCGGAALDVFCEEPPKSEQTF--ELIKHPKVI 235
KKG ++N +RG +VD +AL ++L+ GH GAA+DVF EEP + + F L P VI
Sbjct: 218 MKKGAILINASRGTVVDIDALAEALRSGHLAGAAVDVFPEEPASNGEPFSSPLQGLPNVI 277
Query: 236 VTPHLGASTKEAQIRVAVEIAEQFI 260
+TPH+G ST+EAQ + +E+A + +
Sbjct: 278 LTPHIGGSTEEAQENIGLEVAGKLV 302
>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 = 208 bits (531), Expect = 2e-65
Identities = 102/259 (39%), Positives = 155/259 (59%), Gaps = 15/259 (5%)
Query: 6 VVRSDTKVTAEVL-QASNLQVVGRAGTGVDNIDLTAATRKGVLVLNAPGGNFISACELTC 64
V+ + + AEVL Q NL+++G TG +N+DL AA +G+ V N PG + S + T
Sbjct: 48 VITNKVVLDAEVLAQLPNLKLIGVLATGYNNVDLAAAKERGITVTNVPGYSTDSVAQHTF 107
Query: 65 SLISALSRNVPQGCQSLKEGKWDRK------LYTGTELYGKTLAVLGLGRIGREVALRMQ 118
+L+ AL+R V +K G+W + Y EL GKTL ++G G IG+ VA +
Sbjct: 108 ALLLALARLVAYHNDVVKAGEWQKSPDFCFWDYPIIELAGKTLGIIGYGNIGQAVARIAR 167
Query: 119 AFGMKVIGFDPMVSVEDAAKLNIASLGLEDIWPLADYITVHTPLIPQTKNLINAEVLKKC 178
AFGMKV+ + + A L + L+++ +D I++H PL P+T+NLINAE L K
Sbjct: 168 AFGMKVLFAER----KGAPPLREGYVSLDELLAQSDVISLHCPLTPETRNLINAEELAKM 223
Query: 179 KKGVRVVNVARGGIVDENALLDSLKCGHCGGAALDVFCEEPPKSEQTFELIK-HPKVIVT 237
K G ++N ARGG+VDE AL D+L G GA LDV +EPP+++ L+K P +I+T
Sbjct: 224 KPGAILINTARGGLVDEQALADALNSGKIAGAGLDVLSQEPPRADN--PLLKAAPNLIIT 281
Query: 238 PHLGASTKEAQIRVAVEIA 256
PH+ +++EA+ R+ ++I
Sbjct: 282 PHIAWASREARQRL-MDIL 299
>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 = 204 bits (520), Expect = 1e-63
Identities = 97/248 (39%), Positives = 145/248 (58%), Gaps = 8/248 (3%)
Query: 20 ASNLQVVGRAGTGVDNIDLTAATRKGVLVLNAPG-GNFISACELTCSLISALSRNVPQGC 78
L+++ R G G DN+DL AAT GV+V PG + E +LI + R + Q
Sbjct: 67 NDGLKLIARHGIGYDNVDLKAATEHGVIVTRVPGAVERDAVAEHAVALILTVLRKINQAS 126
Query: 79 QSLKEGKW-DRKLYTGTELYGKTLAVLGLGRIGREVA-LRMQAFGMKVIGFDPMVSVEDA 136
+++KEGKW +R + G EL GKT+ ++G G IG VA + + F KV+ +DP VS E
Sbjct: 127 EAVKEGKWTERANFVGHELSGKTVGIIGYGNIGSRVAEILKEGFNAKVLAYDPYVSEEVI 186
Query: 137 AKLNIASLGLEDIWPLADYITVHTPLIPQTKNLINAEVLKKCKKGVRVVNVARGGIVDEN 196
K + LE++ +D I++H PL +T ++IN + K KKGV +VN ARG ++DE
Sbjct: 187 KKKGAKPVSLEELLAESDIISLHAPLTEETYHMINEKAFSKMKKGVILVNTARGELIDEE 246
Query: 197 ALLDSLKCGHCGGAALDVFCEEPPKSEQTFELIKHPKVIVTPHLGASTKEAQIRV---AV 253
AL+++LK G GA LDV EEP K++ L+ + V++TPH+GA T E+ + V
Sbjct: 247 ALIEALKSGKIAGAGLDVLEEEPIKADHP--LLHYENVVITPHIGAYTYESLYGMGEKVV 304
Query: 254 EIAEQFIA 261
+ E F+A
Sbjct: 305 DDIEDFLA 312
>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 = 204 bits (520), Expect = 2e-63
Identities = 97/273 (35%), Positives = 143/273 (52%), Gaps = 22/273 (8%)
Query: 11 TKVTAEVL-QASNLQVVGRAGTGVDNIDLTAATRKGVLVLNAPGGNFISACELTCSLISA 69
+++ AEVL + L+++ TG D+IDL A +G+ V N P + E +L+ A
Sbjct: 51 SRLDAEVLEKLPRLKLIATRSTGFDHIDLEACRERGIAVCNVPDYGEATVAEHAFALLLA 110
Query: 70 LSRNVPQGCQSLKEGKWDRKLYTGTELYGKTLAVLGLGRIGREVALRMQAFGMKVIGFDP 129
LSR + + + + G + + G EL GKTL V+G GRIGR VA + FGMKV+ +D
Sbjct: 111 LSRKLREAIERTRRGDFSQAGLRGFELAGKTLGVVGTGRIGRRVARIARGFGMKVLAYDV 170
Query: 130 MVSVEDAAKLNIASLGLEDIWPLADYITVHTPLIPQTKNLINAEVLKKCKKGVRVVNVAR 189
+ E A +L + LE++ +D I++H P PQT +LIN E K G ++N AR
Sbjct: 171 VPDEELAERLGFRYVSLEELLQESDIISLHVPYTPQTHHLINRENFALMKPGAVLINTAR 230
Query: 190 GGIVDENALLDSLKCGHCGGAALDVFCEEPPKSEQ------------------TFELIKH 231
G +VD AL+ +LK G GA LDV +E E+ L++
Sbjct: 231 GAVVDTEALVRALKEGKLAGAGLDVLEQEEVLREEAELFREDVSPEDLKKLLADHALLRK 290
Query: 232 PKVIVTPHLGASTKEAQIRV---AVEIAEQFIA 261
P VI+TPH+ +TKEA R+ VE + F A
Sbjct: 291 PNVIITPHVAYNTKEALERILDTTVENIKAFAA 323
>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 = 203 bits (518), Expect = 2e-63
Identities = 98/270 (36%), Positives = 150/270 (55%), Gaps = 11/270 (4%)
Query: 1 KYDGLVVRSDTKVTAEVLQ-ASNLQVVGRAGTGVDNIDLTAATRKGVLVLNAPGGNFISA 59
+YDGL++RS + E ++ A+NL+ + RAG G++NIDL A KG+ + NAP GN +
Sbjct: 40 QYDGLIIRSRFPIDKEFIEKATNLKFIARAGAGLENIDLEYAKEKGIELFNAPEGNRDAV 99
Query: 60 CELTCSLISALSRNVPQGCQSLKEGKWDRKLYTGTELYGKTLAVLGLGRIGREVALRMQA 119
E ++ AL + + Q ++ G WDR+ G EL GKT+ ++G G +G+ A R+
Sbjct: 100 GEHALGMLLALFNKLNRADQEVRNGIWDREGNRGVELMGKTVGIIGYGNMGKAFAKRLSG 159
Query: 120 FGMKVIGFDPMVSVEDAAKLNIASLGLEDIWPLADYITVHTPLIPQTKNLINAEVLKKCK 179
FG KVI +D + DA + LE ++ AD +++H PL P+T+ ++N E + K
Sbjct: 160 FGCKVIAYDKYKNFGDA---YAEQVSLETLFKEADILSLHIPLTPETRGMVNKEFISSFK 216
Query: 180 KGVRVVNVARGGIVDENALLDSLKCGHCGGAALDVFCEEPPKSEQTF-------ELIKHP 232
K +N ARG +V L+ +LK G GA LDV E E F LIK P
Sbjct: 217 KPFYFINTARGKVVVTKDLVKALKSGKILGACLDVLEYEKASFESIFNQPEAFEYLIKSP 276
Query: 233 KVIVTPHLGASTKEAQIRVAVEIAEQFIAL 262
KVI+TPH+ T E+ ++A + ++ AL
Sbjct: 277 KVILTPHIAGWTFESYEKIAEVLVDKIKAL 306
>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 = 195 bits (498), Expect = 2e-60
Identities = 93/270 (34%), Positives = 147/270 (54%), Gaps = 12/270 (4%)
Query: 3 DGLVVRSDTKVTAEVLQAS-NLQVVGRAGTGVDNIDLTAATRKGVLVLNAPGGNFISACE 61
DGL+ ++ A+ L A L+++ A G DN D+ A T +G+ V P E
Sbjct: 46 DGLMAFMPDRIDADFLDACPRLKIIACALKGYDNFDVEACTARGIWVTIVPDLLTEPTAE 105
Query: 62 LTCSLISALSRNVPQGCQSLKEGK---WDRKLYTGTELYGKTLAVLGLGRIGREVALRMQ 118
LT L+ L R++ G + ++ GK W K Y GT L GKT+ +LG+G +GR +A R+
Sbjct: 106 LTIGLLIGLGRHILAGDRFVRSGKFGGWRPKFY-GTGLDGKTVGILGMGALGRAIARRLS 164
Query: 119 AFGMKVIGFDPM-VSVEDAAKLNIASLGLEDIWPLADYITVHTPLIPQTKNLINAEVLKK 177
FG ++ +DP + + LN+ + L+++ +D++ + PL P T +LINAE L K
Sbjct: 165 GFGATLLYYDPHPLDQAEEQALNLRRVELDELLESSDFLVLALPLTPDTLHLINAEALAK 224
Query: 178 CKKGVRVVNVARGGIVDENALLDSLKCGHCGGAALDVFCEEP------PKSEQTFELIKH 231
K G +VN RG +VDE A+ ++LK GH GG A DVF E P+S L +H
Sbjct: 225 MKPGALLVNPCRGSVVDEAAVAEALKSGHLGGYAADVFEMEDWARPDRPRSIPQELLDQH 284
Query: 232 PKVIVTPHLGASTKEAQIRVAVEIAEQFIA 261
+ + TPH+G++ E ++ + +E A +
Sbjct: 285 DRTVFTPHIGSAVDEVRLEIELEAALNILQ 314
>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 = 194 bits (496), Expect = 5e-60
Identities = 88/260 (33%), Positives = 135/260 (51%), Gaps = 21/260 (8%)
Query: 14 TAEVLQA--SNLQVVGRAGTGVDNIDLTAATRKGVLVLNAPGGNFISAC-----ELTCSL 66
E++ +L+++ AG G D ID+ A T++G+ V N PG A + L
Sbjct: 66 DEELISPLPPSLKIIAHAGAGYDQIDVDALTKRGIQVSNTPG-----AVDEATADTALFL 120
Query: 67 ISALSRNVPQGCQSLKEGKW-DRKLYTGTE-LYGKTLAVLGLGRIGREVALRMQAFGMKV 124
I RN + +S + GKW T GKTL +LGLG IG+ +A + AFGMK+
Sbjct: 121 ILGALRNFSRAERSARAGKWRGFLDLTLAHDPRGKTLGILGLGGIGKAIARKAAAFGMKI 180
Query: 125 IGFDPM-VSVEDAAKLNIASLGLEDIWPLADYITVHTPLIPQTKNLINAEVLKKCKKGVR 183
I + + E L + L+++ +D ++++ PL T++LIN + K K GV
Sbjct: 181 IYHNRSRLPEELEKALATYYVSLDELLAQSDVVSLNCPLTAATRHLINKKEFAKMKDGVI 240
Query: 184 VVNVARGGIVDENALLDSLKCGHCGGAALDVFCEEPPKSEQTFELIKHPKVIVTPHLGAS 243
+VN ARG ++DE+AL+D+L+ G A LDVF EP + L+K P V + PH+G
Sbjct: 241 IVNTARGAVIDEDALVDALESGKVASAGLDVFENEPEVNP---GLLKMPNVTLLPHMGTL 297
Query: 244 TKEAQI---RVAVEIAEQFI 260
T E Q + +E E F+
Sbjct: 298 TVETQEKMEELVLENIEAFL 317
>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 = 194 bits (495), Expect = 7e-60
Identities = 91/255 (35%), Positives = 138/255 (54%), Gaps = 4/255 (1%)
Query: 15 AEVLQA-SNLQVVGRAGTGVDNIDLTAATRKGVLVLNAPGGNFISACELTCSLISALSRN 73
EV++A NL+++ A TGVD++DL A +G+ V NA G + + ELT L L RN
Sbjct: 61 GEVIEACKNLKMISVAFTGVDHVDLEACKERGITVSNAAGYSTEAVAELTIGLAIDLLRN 120
Query: 74 VPQGCQSLKEGKWDRKLYTGTELYGKTLAVLGLGRIGREVALRMQAFGMKVIGFDPMVSV 133
+ +++ G + G EL GKT+ ++G G IG VA +AFG KV+ +
Sbjct: 121 IVPCDAAVRAGG-TKAGLIGRELAGKTVGIVGTGAIGLRVARLFKAFGCKVLAYSRSEK- 178
Query: 134 EDAAKLNIASLGLEDIWPLADYITVHTPLIPQTKNLINAEVLKKCKKGVRVVNVARGGIV 193
E+A L I + L+++ +D +++H PL +TK LI E L K+ ++N ARG +V
Sbjct: 179 EEAKALGIEYVSLDELLAESDIVSLHLPLNDETKGLIGKEKLALMKESAILINTARGPVV 238
Query: 194 DENALLDSLKCGHCGGAALDVFCEEPPKSEQTFELIKHPKVIVTPHLGASTKEAQIRVAV 253
D AL D+L G GA +DVF EPP + L+ P I+TPH+ +T+EA + A
Sbjct: 239 DNEALADALNEGKIAGAGIDVFDMEPPLPAD-YPLLHAPNTILTPHVAFATEEAMEKRAE 297
Query: 254 EIAEQFIALANTNPQ 268
+ + A PQ
Sbjct: 298 IVFDNIEAWLAGKPQ 312
>gnl|CDD|236985 PRK11790, PRK11790, D-3-phosphoglycerate dehydrogenase;
Provisional.
Length = 409
Score = 196 bits (501), Expect = 1e-59
Identities = 102/265 (38%), Positives = 151/265 (56%), Gaps = 21/265 (7%)
Query: 7 VRSDTKVTAEVLQASN-LQVVGRAGTGVDNIDLTAATRKGVLVLNAPGGNFISACELTCS 65
+RS T++T EVL A+ L +G G + +DL AA ++G+ V NAP N S EL
Sbjct: 59 IRSRTQLTEEVLAAAEKLVAIGCFCIGTNQVDLDAAAKRGIPVFNAPFSNTRSVAELVIG 118
Query: 66 LISALSRNVPQGCQSLKEGKWDRKLYTGT-ELYGKTLAVLGLGRIGREVALRMQAFGMKV 124
I L R +P+ G W+ K G+ E+ GKTL ++G G IG ++++ ++ GM+V
Sbjct: 119 EIILLLRGIPEKNAKAHRGGWN-KSAAGSFEVRGKTLGIVGYGHIGTQLSVLAESLGMRV 177
Query: 125 IGFDPMVSVEDAAKLNIASLG-------LEDIWPLADYITVHTPLIPQTKNLINAEVLKK 177
+D +ED KL LG LE++ +D +++H P P TKN+I AE L
Sbjct: 178 YFYD----IED--KL---PLGNARQVGSLEELLAQSDVVSLHVPETPSTKNMIGAEELAL 228
Query: 178 CKKGVRVVNVARGGIVDENALLDSLKCGHCGGAALDVFCEEPPKSEQTFE--LIKHPKVI 235
K G ++N +RG +VD +AL D+LK GH GAA+DVF EP + FE L VI
Sbjct: 229 MKPGAILINASRGTVVDIDALADALKSGHLAGAAIDVFPVEPKSNGDPFESPLRGLDNVI 288
Query: 236 VTPHLGASTKEAQIRVAVEIAEQFI 260
+TPH+G ST+EAQ + +E+A + +
Sbjct: 289 LTPHIGGSTQEAQENIGLEVAGKLV 313
>gnl|CDD|183914 PRK13243, PRK13243, glyoxylate reductase; Reviewed.
Length = 333
Score = 192 bits (489), Expect = 6e-59
Identities = 94/270 (34%), Positives = 148/270 (54%), Gaps = 11/270 (4%)
Query: 3 DGLVVRSDTKVTAEVL-QASNLQVVGRAGTGVDNIDLTAATRKGVLVLNAPGGNFISACE 61
D LV ++ EV A L++V G DNID+ ATR+G+ V N PG + +
Sbjct: 47 DALVTMLSERIDCEVFEAAPRLRIVANYAVGYDNIDVEEATRRGIYVTNTPGVLTEATAD 106
Query: 62 LTCSLISALSRNVPQGCQSLKEGKWDR-------KLYTGTELYGKTLAVLGLGRIGREVA 114
+L+ A +R + + ++ G+W R ++ G ++YGKT+ ++G GRIG+ VA
Sbjct: 107 FAWALLLATARRLVEADHFVRSGEWKRRGVAWHPLMFLGYDVYGKTIGIIGFGRIGQAVA 166
Query: 115 LRMQAFGMKVIGFDPMVSVEDAAKLNIASLGLEDIWPLADYITVHTPLIPQTKNLINAEV 174
R + FGM+++ + E +L LE++ +D++++H PL +T ++IN E
Sbjct: 167 RRAKGFGMRILYYSRTRKPEAEKELGAEYRPLEELLRESDFVSLHVPLTKETYHMINEER 226
Query: 175 LKKCKKGVRVVNVARGGIVDENALLDSLKCGHCGGAALDVFCEEPPKSEQTFELIKHPKV 234
LK K +VN ARG +VD AL+ +LK G GA LDVF EEP +E EL V
Sbjct: 227 LKLMKPTAILVNTARGKVVDTKALVKALKEGWIAGAGLDVFEEEPYYNE---ELFSLKNV 283
Query: 235 IVTPHLGASTKEAQIRVAVEIAEQFIALAN 264
++ PH+G++T EA+ +A +AE IA
Sbjct: 284 VLAPHIGSATFEAREGMAELVAENLIAFKR 313
>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 = 189 bits (481), Expect = 9e-58
Identities = 94/259 (36%), Positives = 137/259 (52%), Gaps = 17/259 (6%)
Query: 3 DGLVVRSDTKVTAEVLQ-ASNLQVVGRAGTGVDNIDLTAATRKGVLVLNAPGGNFISACE 61
D ++ K+ AE+L A L+ + TG DNIDL A G+ V N P + + E
Sbjct: 47 DAILTAFTDKIDAELLDKAPGLKFISLRATGYDNIDLDYAKELGIGVTNVPEYSPNAVAE 106
Query: 62 LTCSLISALSRNVPQGCQSLKEGKWDRKLYT--GTELYGKTLAVLGLGRIGREVALRMQA 119
T +LI AL RN + ++ D + G EL +T+ V+G G+IGR VA R +
Sbjct: 107 HTIALILALLRN--RKYIDERDKNQDLQDAGVIGRELEDQTVGVVGTGKIGRAVAQRAKG 164
Query: 120 FGMKVIGFDPMVSVEDAAKLNIASLGLEDIWPLADYITVHTPLIPQTKNLINAEVLKKCK 179
FGMKVI +DP + E K + + LE+++ +D I++H PL P+ ++IN E K K
Sbjct: 165 FGMKVIAYDPFRNPELEDKG-VKYVSLEELFKNSDIISLHVPLTPENHHMINEEAFKLMK 223
Query: 180 KGVRVVNVARGGIVDENALLDSLKCGHCGGAALDVFCEEPP-----KSEQTF------EL 228
KGV ++N ARG +VD AL+++L G GA LDV +E P + F L
Sbjct: 224 KGVIIINTARGSLVDTEALIEALDSGKIFGAGLDVLEDETPDLLKDLEGEIFKDALNALL 283
Query: 229 IKHPKVIVTPHLGASTKEA 247
+ P VI+TPH T +A
Sbjct: 284 GRRPNVIITPHTAFYTDDA 302
>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 = 182 bits (465), Expect = 3e-55
Identities = 93/271 (34%), Positives = 134/271 (49%), Gaps = 19/271 (7%)
Query: 2 YDGLVVRSDTKVTAEVLQ---ASNLQVVGRAGTGVDNIDLTAATRKGVLVLNAPGGNFIS 58
YDG+VV+ EV + ++ + GVD IDL A G+ + N P + +
Sbjct: 45 YDGVVVQQTLPYDEEVYEKLAEYGIKQIALRSAGVDMIDLDLAKENGLKITNVPAYSPRA 104
Query: 59 ACELTCSLISALSRNVPQGCQSLKEG--KWDRKLYTGTELYGKTLAVLGLGRIGREVALR 116
E + L RN P+ + + +G +W L G E+ T+ ++G GRIG A
Sbjct: 105 IAEFAVTQALNLLRNTPEIDRRVAKGDFRWAPGL-IGREIRDLTVGIIGTGRIGSAAAKI 163
Query: 117 MQAFGMKVIGFDPMVSVEDAAKLNIASLGLEDIWPLADYITVHTPLIPQTKNLINAEVLK 176
+ FG KVI +DP + K + LED+ AD I++H PL + +LINAE
Sbjct: 164 FKGFGAKVIAYDP-YPNPELEKFLLYYDSLEDLLKQADIISLHVPLTKENHHLINAEAFA 222
Query: 177 KCKKGVRVVNVARGGIVDENALLDSLKCGHCGGAALDVF-CEEP--PK--SEQTF----- 226
K K G +VN ARGG+VD AL+D+L G GAALD + E K S +
Sbjct: 223 KMKDGAILVNAARGGLVDTKALIDALDSGKIAGAALDTYENETGYFNKDWSGKEIEDEVL 282
Query: 227 -ELIKHPKVIVTPHLGASTKEAQIRVAVEIA 256
ELI P V++TPH+ T A ++ VEI+
Sbjct: 283 KELIAMPNVLITPHIAFYTDTA-VKNMVEIS 312
>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 = 176 bits (448), Expect = 4e-53
Identities = 90/252 (35%), Positives = 137/252 (54%), Gaps = 20/252 (7%)
Query: 4 GLVVRSDTKVTAEVLQA-SNLQVVGRAGTGVDNIDLTAATRKGVLVLNAPGGNFISACEL 62
+V +T ++A ++ A L+++ G G D IDL AA +G+ V N PG +L
Sbjct: 45 AVVTNGETGLSAALIAALPALELIASFGVGYDGIDLDAARARGIRVTNTPGVLTDDVADL 104
Query: 63 TCSLISALSRNVPQGCQSLKEGKWDRKLYT-GTELYGKTLAVLGLGRIGREVALRMQAFG 121
L+ A+ R +P + ++ G+W + + ++ GK + ++GLGRIGR +A R++AFG
Sbjct: 105 AVGLLLAVLRRIPAADRFVRAGRWPKGAFPLTRKVSGKRVGIVGLGRIGRAIARRLEAFG 164
Query: 122 MKVIGFDPMVSVEDAAKLNIASLGLEDIWPLA---DYITVHTPLIPQTKNLINAEVLKKC 178
M++ D ASL LE LA D + V P P T++L+NAEVL+
Sbjct: 165 MEIAYHGR-RPKPDVPYRYYASL-LE----LAAESDVLVVACPGGPATRHLVNAEVLEAL 218
Query: 179 -KKGVRVVNVARGGIVDENALLDSLKCGHCGGAALDVFCEEP--PKSEQTFELIKHPKVI 235
GV +VNVARG +VDE AL+ +L+ G GA LDVF EP P L+ V+
Sbjct: 219 GPDGV-LVNVARGSVVDEAALIAALQEGRIAGAGLDVFENEPNVPA-----ALLDLDNVV 272
Query: 236 VTPHLGASTKEA 247
+TPH+ ++T E
Sbjct: 273 LTPHIASATVET 284
>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 = 175 bits (447), Expect = 9e-53
Identities = 88/261 (33%), Positives = 133/261 (50%), Gaps = 35/261 (13%)
Query: 15 AEVL-QASNLQVVGRAGTGVDNIDLTAATRKGVLVLNAPG--GNFISACELTCSLISALS 71
E+L A L+ + GVD + + V++ NA G G I+ E + A +
Sbjct: 51 PELLPAAPRLRWIQSTSAGVDALLFPELLERDVVLTNARGIFGPPIA--EYVLGYMLAFA 108
Query: 72 RNVPQGCQSLKEGKWDRKLYTGTELYGKTLAVLGLGRIGREVALRMQAFGMKVIG----- 126
R +P+ ++ E +W R+ EL GKT+ ++GLG IGRE+A R +AFGM+VIG
Sbjct: 109 RKLPRYARNQAERRWQRRGPV-RELAGKTVLIVGLGDIGREIARRAKAFGMRVIGVRRSG 167
Query: 127 ------FDPMVSVEDAAKLNIASLGLEDIWPLADYITVHTPLIPQTKNLINAEVLKKCKK 180
D + + ++ L+++ P ADY+ PL P+T+ L NAE K
Sbjct: 168 RPAPPVVDEVYTPDE----------LDELLPEADYVVNALPLTPETRGLFNAERFAAMKP 217
Query: 181 GVRVVNVARGGIVDENALLDSLKCGHCGGAALDVFCEEP-PKSEQTFELIKHPKVIVTPH 239
G ++NV RG +VDE+AL+++L+ G GAALDVF EEP P L P VI+TPH
Sbjct: 218 GAVLINVGRGSVVDEDALIEALESGRIAGAALDVFEEEPLPADS---PLWDLPNVIITPH 274
Query: 240 LGASTKEAQIRVAVEIAEQFI 260
+ + + E F+
Sbjct: 275 ISGDSP----SYPERVVEIFL 291
>gnl|CDD|240642 cd12165, 2-Hacid_dh_6, Putative D-isomer specific 2-hydroxyacid
dehydrogenases. 2-Hydroxyacid dehydrogenases catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 314
Score = 172 bits (437), Expect = 2e-51
Identities = 87/255 (34%), Positives = 125/255 (49%), Gaps = 13/255 (5%)
Query: 22 NLQVVGRAGTGVDNIDLTAATRKGVLVLNAPGGNFISACELTCSLISALSRNVPQGCQSL 81
L+++ GVD++ L +GV+V N G N + E +LI AL++ + + L
Sbjct: 60 RLKLIQVPSAGVDHLPL-ERLPEGVVVANNHG-NSPAVAEHALALILALAKRIVEYDNDL 117
Query: 82 KEGKWDRKLYTGT---ELYGKTLAVLGLGRIGREVALRMQAFGMKVIGFD--PMVSVEDA 136
+ G W + EL GKT+ +LG G IGRE+A ++AFGM+VIG P E A
Sbjct: 118 RRGIWHGRAGEEPESKELRGKTVGILGYGHIGREIARLLKAFGMRVIGVSRSP-KEDEGA 176
Query: 137 AKLNIASLGLEDIWPLADYITVHTPLIPQTKNLINAEVLKKCKKGVRVVNVARGGIVDEN 196
+ S L++ AD + V PL QT+ LI A L K G +VNV RG +VDE
Sbjct: 177 DFVGTLS-DLDEALEQADVVVVALPLTKQTRGLIGAAELAAMKPGAILVNVGRGPVVDEE 235
Query: 197 ALLDSLKCGHCGGAALDVFCEEPPKSEQTFE----LIKHPKVIVTPHLGASTKEAQIRVA 252
AL ++LK GAA+DV+ P + + + P VI++PH T+E R
Sbjct: 236 ALYEALKERPIAGAAIDVWWRYPSRGDPVAPSRYPFHELPNVIMSPHNAGWTEETFRRRI 295
Query: 253 VEIAEQFIALANTNP 267
E AE P
Sbjct: 296 DEAAENIRRYLRGEP 310
>gnl|CDD|180588 PRK06487, PRK06487, glycerate dehydrogenase; Provisional.
Length = 317
Score = 171 bits (436), Expect = 3e-51
Identities = 94/260 (36%), Positives = 140/260 (53%), Gaps = 14/260 (5%)
Query: 6 VVRSDTKVTAEVLQASN-LQVVGRAGTGVDNIDLTAATRKGVLVLNAPGGNFISACELTC 64
+ + + A L A+ L+++ A TG +N+DL AA +G+ V N G S + T
Sbjct: 49 AISNKVALDAAALAAAPQLKLILVAATGTNNVDLAAARERGITVCNCQGYGTPSVAQHTL 108
Query: 65 SLISALSRNVPQGCQSLKEGKWDRKL------YTGTELYGKTLAVLGLGRIGREVALRMQ 118
+L+ AL+ +P Q++ G+W + + EL GKTL +LG G +G VA +
Sbjct: 109 ALLLALATRLPDYQQAVAAGRWQQSSQFCLLDFPIVELEGKTLGLLGHGELGGAVARLAE 168
Query: 119 AFGMKV-IGFDPMVSVEDAAKLNIASLGLEDIWPLADYITVHTPLIPQTKNLINAEVLKK 177
AFGM+V IG P L L+++ P D +T+H PL T++LI A L
Sbjct: 169 AFGMRVLIGQLPGRPARPD------RLPLDELLPQVDALTLHCPLTEHTRHLIGARELAL 222
Query: 178 CKKGVRVVNVARGGIVDENALLDSLKCGHCGGAALDVFCEEPPKSEQTFELIKHPKVIVT 237
K G ++N ARGG+VDE AL D+L+ GH GGAA DV EPP + P++IVT
Sbjct: 223 MKPGALLINTARGGLVDEQALADALRSGHLGGAATDVLSVEPPVNGNPLLAPDIPRLIVT 282
Query: 238 PHLGASTKEAQIRVAVEIAE 257
PH ++EA+ R+ ++AE
Sbjct: 283 PHSAWGSREARQRIVGQLAE 302
>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 = 171 bits (435), Expect = 8e-51
Identities = 79/228 (34%), Positives = 131/228 (57%), Gaps = 12/228 (5%)
Query: 31 TGVDNIDLTAATRKGVLVLNAPGGNFISACELTCSLISALSRNVPQGCQSLKEGKWDRKL 90
G +N+DL AA G+ V+ P + + E +L+ AL+R + + ++EG +
Sbjct: 77 AGFNNVDLKAAKELGITVVRVPAYSPYAVAEHAVALLLALNRKIHRAYNRVREGNFSLDG 136
Query: 91 YTGTELYGKTLAVLGLGRIGREVALRMQAFGMKVIGFDPMVSVEDAAKLNIASLGLEDIW 150
G +L+GKT+ V+G G+IG+ A ++ FG +V+ +DP + + AKL + + L+++
Sbjct: 137 LLGFDLHGKTVGVIGTGKIGQAFARILKGFGCRVLAYDPYPN-PELAKLGVEYVDLDELL 195
Query: 151 PLADYITVHTPLIPQTKNLINAEVLKKCKKGVRVVNVARGGIVDENALLDSLKCGHCGGA 210
+D I++H PL P+T +LINAE + K K GV ++N +RGG++D AL+++LK G GG
Sbjct: 196 AESDIISLHCPLTPETHHLINAETIAKMKDGVMLINTSRGGLIDTKALIEALKSGKIGGL 255
Query: 211 ALDVFCEEPP-----KSEQ-----TFE-LIKHPKVIVTPHLGASTKEA 247
LDV+ EE S++ L+ P V++T H TKEA
Sbjct: 256 GLDVYEEEAGLFFEDHSDEIIQDDVLARLLSFPNVLITGHQAFFTKEA 303
>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 = 170 bits (432), Expect = 2e-50
Identities = 82/256 (32%), Positives = 136/256 (53%), Gaps = 11/256 (4%)
Query: 13 VTAEVL-QASNLQVVGR-AGTGVDNIDLTAATRKGVLVLNAPGGNFISACELTCSLISAL 70
+ AE+L +A L+ V AG+ + A +G+LV +A N E T + I
Sbjct: 62 LDAELLARAPRLRAVVHAAGSVRGLVTD-AVWERGILVTSAADANAEPVAEFTLAAILLA 120
Query: 71 SRNVPQGCQSLKEGKWD--RKLYTGTELYGKTLAVLGLGRIGREVALRMQAFGMKVIGFD 128
R +P+ + + G+ G LYG+T+ ++G GRIGR V ++ FG++V+ +D
Sbjct: 121 LRRIPRFAAAYRAGRDWGWPTRRGGRGLYGRTVGIVGFGRIGRAVVELLRPFGLRVLVYD 180
Query: 129 PMVSVEDAAKLNIASLGLEDIWPLADYITVHTPLIPQTKNLINAEVLKKCKKGVRVVNVA 188
P + +AA L + + L+++ +D +++H PL P+T+ +I+A +L + G +N A
Sbjct: 181 PYLPAAEAAALGVELVSLDELLARSDVVSLHAPLTPETRGMIDARLLALMRDGATFINTA 240
Query: 189 RGGIVDENALLDSLKCGHCGGAALDVFCEEPPKSEQTFELIKHPKVIVTPHLGAST---K 245
RG +VDE ALL L+ G AALDV EP + L P V++TPH+ ST +
Sbjct: 241 RGALVDEAALLAELRSGR-LRAALDVTDPEPLPPDS--PLRTLPNVLLTPHIAGSTGDER 297
Query: 246 EAQIRVAVEIAEQFIA 261
A++ E+F+A
Sbjct: 298 RRLGDYALDELERFLA 313
>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 = 168 bits (428), Expect = 1e-49
Identities = 94/273 (34%), Positives = 143/273 (52%), Gaps = 16/273 (5%)
Query: 13 VTAEVLQ-ASNLQVVGRAGTGVDNIDLTAATRKGVLVLNAPGGNFISACELTCSLISALS 71
+TAE + A NL++ AG G D++DL AA +G+ V G N +S E +I L
Sbjct: 74 MTAERIAKAKNLKLALTAGIGSDHVDLQAANDRGITVAEVTGSNVVSVAEHVVMMILILV 133
Query: 72 RNVPQGCQSLKEGKWD-----RKLYTGTELYGKTLAVLGLGRIGREVALRMQAFGMKVIG 126
RN G + EG W+ ++ Y +L GKT+ +G GRIG V R++ F + ++
Sbjct: 134 RNYVPGHEQAIEGGWNVADVVKRAY---DLEGKTVGTVGAGRIGLRVLRRLKPFDVHLLY 190
Query: 127 FDPMVSVEDAAKLNIASL--GLEDIWPLADYITVHTPLIPQTKNLINAEVLKKCKKGVRV 184
+D E+ K + LED+ D +T++ PL P+T+ L N E+L K KKG +
Sbjct: 191 YDRHRLPEEVEKELGLTRHADLEDMVSKCDVVTINCPLHPETEGLFNKELLSKMKKGAYL 250
Query: 185 VNVARGGIVDENALLDSLKCGHCGGAALDVFCEEPPKSEQTFELIKHPKVIVTPHLGAST 244
VN ARG I D A+ ++L+ GH G A DV+ +P + + + P +TPH+ +T
Sbjct: 251 VNTARGKICDREAVAEALESGHLAGYAGDVWFPQPAPKDHPWRTM--PNNAMTPHISGTT 308
Query: 245 KEAQIRVAV---EIAEQFIALANTNPQYTSIQG 274
+AQ R A EI E+F P+Y +QG
Sbjct: 309 LDAQARYAAGTKEILERFFEGEPFRPEYLIVQG 341
>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 = 160 bits (407), Expect = 2e-46
Identities = 83/261 (31%), Positives = 124/261 (47%), Gaps = 29/261 (11%)
Query: 3 DGLVVRSDTKVTAEVLQASNLQVVGRAGTGVDNIDLTAATRKGVLVLNAPGGNFISACEL 62
D L+VRS TKV +L+ S ++ VG A G D+ID +G+ NAPG N S E
Sbjct: 38 DVLLVRSVTKVNEALLEGSKVKFVGTATIGTDHIDTDYLKERGIGFANAPGCNANSVAEY 97
Query: 63 TCSLISALSRNVPQGCQSLKEGKWDRKLYTGTELYGKTLAVLGLGRIGREVALRMQAFGM 122
++SAL + SLK GKT+ ++G+G +G +A R++A GM
Sbjct: 98 ---VLSALLVLAQRQGFSLK---------------GKTVGIVGVGNVGSRLARRLEALGM 139
Query: 123 KVIGFDPMVSVEDAAKLNIASLGLEDIWPLADYITVHTPLIPQ----TKNLINAEVLKKC 178
V+ DP + E SL E++ AD IT+H PL T +L++ + L
Sbjct: 140 NVLLCDPPRA-EAEGDPGFVSL--EELLAEADIITLHVPLTRDGEHPTYHLLDEDFLAAL 196
Query: 179 KKGVRVVNVARGGIVDENALLDSLKCGHCGGAALDVFCEEPPKSEQTFELIKHPKVIVTP 238
K G ++N +RG ++D ALL L+ G LDV+ EP + + + I TP
Sbjct: 197 KPGQILINASRGAVIDNQALLALLQRGKDLRVVLDVWENEPEIDLELLDKVD----IATP 252
Query: 239 HLGASTKEAQIRVAVEIAEQF 259
H+ + E + R I E
Sbjct: 253 HIAGYSLEGKARGTEMIYEAL 273
>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 = 157 bits (399), Expect = 1e-45
Identities = 82/244 (33%), Positives = 124/244 (50%), Gaps = 25/244 (10%)
Query: 19 QASNLQVVGRAGTGVDNIDLTAATRKGVLVLNAPGGNFISACELTCSLISALSRNVPQGC 78
+ NL+ + GVD + L +KG+L+ N G + I E I + + + +
Sbjct: 57 KMKNLKWIQLYSAGVDYLPLEYIKKKGILLTNNSGIHSIPIAEWIVGYILEIYKGLKKAY 116
Query: 79 QSLKEGKWDRKLYTGTELYGKTLAVLGLGRIGREVALRMQAFGMKVIG----------FD 128
++ KE KW + ELYGKT+ LG G IG+E+A R++AFGMKVIG FD
Sbjct: 117 KNQKEKKWKMDS-SLLELYGKTILFLGTGSIGQEIAKRLKAFGMKVIGVNTSGRDVEYFD 175
Query: 129 PMVSVEDAAKLNIASLGLEDIWPLADYITVHTPLIPQTKNLINAEVLKKCKKGVRVVNVA 188
+E+ L+++ AD + PL +T +L + ++ KKG +NV
Sbjct: 176 KCYPLEE----------LDEVLKEADIVVNVLPLTEETHHLFDEAFFEQMKKGALFINVG 225
Query: 189 RGGIVDENALLDSLKCGHCGGAALDVFCEEP-PKSEQTFELIKHPKVIVTPHLGASTKEA 247
RG VDE+AL+++LK GAALDVF EEP PK L V++TPH+ ++
Sbjct: 226 RGPSVDEDALIEALKNKQIRGAALDVFEEEPLPKDS---PLWDLDNVLITPHISGVSEHF 282
Query: 248 QIRV 251
R+
Sbjct: 283 NERL 286
>gnl|CDD|235890 PRK06932, PRK06932, glycerate dehydrogenase; Provisional.
Length = 314
Score = 153 bits (387), Expect = 5e-44
Identities = 84/247 (34%), Positives = 123/247 (49%), Gaps = 17/247 (6%)
Query: 5 LVVRSDTKVTAEVLQA-SNLQVVGRAGTGVDNIDLTAATRKGVLVLNAPGGNFISACELT 63
+V+ S T E L L+++ TG +N+DL AA G+ V N G + + E
Sbjct: 47 IVITSKVLFTRETLAQLPKLKLIAITATGTNNVDLVAAKELGIAVKNVTGYSSTTVPEHV 106
Query: 64 CSLISALSRNVPQGCQSLKEGKW-DRKL-----YTGTELYGKTLAVLGLGRIGREVALRM 117
+I AL ++ + +W K Y T++ G TL V G G +G EV
Sbjct: 107 LGMIFALKHSLMGWYRDQLSDRWATCKQFCYFDYPITDVRGSTLGVFGKGCLGTEVGRLA 166
Query: 118 QAFGMKVIGFDPMVSVEDAAKLNIASLGLEDIWPLADYITVHTPLIPQTKNLINAEVLKK 177
QA GMKV+ + A+ E++ AD +T+H PL T+NLINAE L
Sbjct: 167 QALGMKVL----YAEHKGASVCREGYTPFEEVLKQADIVTLHCPLTETTQNLINAETLAL 222
Query: 178 CKKGVRVVNVARGGIVDENALLDSLKCGHCGGAALDVFCEEPPKSEQTFELI----KHPK 233
K ++N RG +VDE ALLD+L+ G GAALDV +EPP+ + LI + P
Sbjct: 223 MKPTAFLINTGRGPLVDEQALLDALENGKIAGAALDVLVKEPPEKDNP--LIQAAKRLPN 280
Query: 234 VIVTPHL 240
+++TPH+
Sbjct: 281 LLITPHI 287
>gnl|CDD|181414 PRK08410, PRK08410, 2-hydroxyacid dehydrogenase; Provisional.
Length = 311
Score = 147 bits (373), Expect = 6e-42
Identities = 80/254 (31%), Positives = 134/254 (52%), Gaps = 12/254 (4%)
Query: 12 KVTAEVL-QASNLQVVGRAGTGVDNIDLTAATRKGVLVLNAPGGNFISACELTCSLISAL 70
+ EVL Q NL+++ TG +N+D+ A +KG+ V N G + S + T +++ +L
Sbjct: 52 VIDKEVLSQLPNLKLICITATGTNNVDIEYAKKKGIAVKNVAGYSTESVAQHTFAMLLSL 111
Query: 71 SRNVPQGCQSLKEGKWDR-KLYTGT-----ELYGKTLAVLGLGRIGREVALRMQAFGMKV 124
+ + +K G++ ++T E+ GK ++GLG IG+ VA QAFG KV
Sbjct: 112 LGRINYYDRYVKSGEYSESPIFTHISRPLGEIKGKKWGIIGLGTIGKRVAKIAQAFGAKV 171
Query: 125 IGFDPMVSVEDAAKLNIASLGLEDIWPLADYITVHTPLIPQTKNLINAEVLKKCKKGVRV 184
+ + ++ + LE++ +D I++H PL +TKNLI + LK K G +
Sbjct: 172 VYYSTSGKNKNE---EYERVSLEELLKTSDIISIHAPLNEKTKNLIAYKELKLLKDGAIL 228
Query: 185 VNVARGGIVDENALLDSLKCGHCGGAALDVFCEEPPKSEQTFELIK-HPKVIVTPHLGAS 243
+NV RGGIV+E L +L A LDV +EP + IK K+++TPH+ +
Sbjct: 229 INVGRGGIVNEKDLAKALDEKDI-YAGLDVLEKEPMEKNHPLLSIKNKEKLLITPHIAWA 287
Query: 244 TKEAQIRVAVEIAE 257
+KEA+ + ++ E
Sbjct: 288 SKEARKTLIEKVKE 301
>gnl|CDD|181041 PRK07574, PRK07574, formate dehydrogenase; Provisional.
Length = 385
Score = 147 bits (374), Expect = 2e-41
Identities = 91/276 (32%), Positives = 142/276 (51%), Gaps = 24/276 (8%)
Query: 14 TAE-VLQASNLQVVGRAGTGVDNIDLTAATRKGVLVLNAPGGNFISACELTCSLISALSR 72
TAE + +A NL++ AG G D++DL AA+ G+ V G N IS E +I AL R
Sbjct: 105 TAERIAKAPNLKLAITAGIGSDHVDLQAASEHGITVAEVTGSNSISVAEHVVMMILALVR 164
Query: 73 NVPQGCQSLKEGKWD-----RKLYTGTELYGKTLAVLGLGRIGREVALRMQAFGMKVIGF 127
N + EG W+ + Y +L G T+ ++G GRIG V R++ F +K+
Sbjct: 165 NYEPSHRQAVEGGWNIADCVSRSY---DLEGMTVGIVGAGRIGLAVLRRLKPFDVKLHYT 221
Query: 128 DPMVSVEDAAKLNIASLGL------EDIWPLADYITVHTPLIPQTKNLINAEVLKKCKKG 181
D E+ + LGL + + + D +T+H PL P+T++L +A+VL + K+G
Sbjct: 222 DRHRLPEEVEQ----ELGLTYHVSFDSLVSVCDVVTIHCPLHPETEHLFDADVLSRMKRG 277
Query: 182 VRVVNVARGGIVDENALLDSLKCGHCGGAALDVFCEEPPKSEQTFELIKHPKVIVTPHLG 241
+VN ARG IVD +A++ +L+ GH G A DV+ +P ++ + + +TPH+
Sbjct: 278 SYLVNTARGKIVDRDAVVRALESGHLAGYAGDVWFPQPAPADHPWRTMPRNG--MTPHIS 335
Query: 242 ASTKEAQIRVAV---EIAEQFIALANTNPQYTSIQG 274
+T AQ R A EI E F +Y + G
Sbjct: 336 GTTLSAQARYAAGTREILECFFEGRPIRDEYLIVDG 371
>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 = 143 bits (364), Expect = 2e-40
Identities = 79/263 (30%), Positives = 126/263 (47%), Gaps = 21/263 (7%)
Query: 3 DGLVVRSDTKVTAEVLQ---ASNLQVVGRAGTGVDNIDLTAATRKGVLVLNAPGGNFISA 59
D ++VR + E L+ ++ V G ++IDL AA G + P + +
Sbjct: 46 DAVIVRGNCFADKENLEIYKEYGIKYVFTRTVGFNHIDLEAAKELGFKMARVPSYSPNAI 105
Query: 60 CELTCSLISALSRNVPQGCQSLKEG--KWDRKLYTGTELYGKTLAVLGLGRIGREVALRM 117
EL +L LSR+ K D ++ E+ T+ ++G GRIG A
Sbjct: 106 AELAFTLAMTLSRHTAYTASRTANKNFKVDPFMF-SKEIRNSTVGIIGTGRIGLTAAKLF 164
Query: 118 QAFGMKVIGFDPMVSVEDAAKLNIASLGLEDIWPLADYITVHTPLIP-QTKNLINAEVLK 176
+ G KVIG+D S DAAK + + L+++ +D I++H P I + LIN E +
Sbjct: 165 KGLGAKVIGYDIYPS--DAAKDVVTFVSLDELLKKSDIISLHVPYIKGKNDKLINKEFIS 222
Query: 177 KCKKGVRVVNVARGGIVDENALLDSLKCGHCGGAALDVFCEEPPKSEQTF---------- 226
K K G ++N ARG + DE A+L++L+ G G DV E + F
Sbjct: 223 KMKDGAILINTARGELQDEEAILEALESGKLAGFGTDVLNNEKEIFFKDFDGDKIEDPVV 282
Query: 227 -ELIK-HPKVIVTPHLGASTKEA 247
+L+ +P+V++TPH+G+ T EA
Sbjct: 283 EKLLDLYPRVLLTPHIGSYTDEA 305
>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 = 143 bits (363), Expect = 2e-40
Identities = 87/270 (32%), Positives = 133/270 (49%), Gaps = 20/270 (7%)
Query: 2 YDGLVVRSDTKVTAEVLQASNLQVVGRAGT---GVDNIDLTAATRKGVLVLNAP-GGNFI 57
YDG+ + +K++AE+L+ V T G D+IDL AA G+ V N N
Sbjct: 45 YDGISILGKSKISAELLEKLKEAGVKYISTRSIGYDHIDLDAAKELGIKVSNVTYSPN-- 102
Query: 58 SACELTCSLISALSRNVPQGCQSLKEGKWDRKLYTGTELYGKTLAVLGLGRIGREVALRM 117
S + T L+ R Q + + + G EL T+ V+G GRIG+ V +
Sbjct: 103 SVADYTVMLMLMALRKYKQIMKRAEVNDYSLGGLQGRELRNLTVGVIGTGRIGQAVIKNL 162
Query: 118 QAFGMKVIGFDPMVSVEDAAKLNIASLGLEDIWPLADYITVHTPLIPQTKNLINAEVLKK 177
FG K++ +DP + + K + L+ ++ +D IT+HTPL +T +LIN E + K
Sbjct: 163 SGFGCKILAYDPYPN--EEVKKYAEYVDLDTLYKESDIITLHTPLTEETYHLINKESIAK 220
Query: 178 CKKGVRVVNVARGGIVDENALLDSLKCGHCGGAALDVFCEE-----------PPKSEQTF 226
K GV ++N ARG ++D AL++ L+ G GGAALDV E + +
Sbjct: 221 MKDGVIIINTARGELIDTEALIEGLESGKIGGAALDVIEGEDGIYYNDRKGDILSNRELA 280
Query: 227 ELIKHPKVIVTPHLGASTKEAQIRVAVEIA 256
L P VI+TPH+ T +A + VE +
Sbjct: 281 ILRSFPNVILTPHMAFYTDQA-VSDMVENS 309
>gnl|CDD|215501 PLN02928, PLN02928, oxidoreductase family protein.
Length = 347
Score = 143 bits (362), Expect = 6e-40
Identities = 88/262 (33%), Positives = 141/262 (53%), Gaps = 26/262 (9%)
Query: 2 YDGLVVRSDTKVTAEVL-QASNLQVVGRAGTGVDNIDLTAATRKGVLVLNAPG---GNFI 57
YD V + ++ A+++ +AS ++++ + G G++ +D+ AAT+ G+ V P GN
Sbjct: 62 YDICVPKM-MRLDADIIARASQMKLIMQFGVGLEGVDVDAATKHGIKVARIPSEGTGNAA 120
Query: 58 SACELTCSLISALSRNVPQGCQSLKEGKWDRKL--YTGTELYGKTLAVLGLGRIGREVAL 115
S E+ L+ L R + SLK R+L G L+GKT+ +LG G IG E+A
Sbjct: 121 SCAEMAIYLMLGLLRKQNEMQISLK----ARRLGEPIGDTLFGKTVFILGYGAIGIELAK 176
Query: 116 RMQAFGMKVIGFDPMVSVEDAAKLNIASL----------GLEDIWPL---ADYITVHTPL 162
R++ FG+K++ + E L I + G EDI+ AD + + L
Sbjct: 177 RLRPFGVKLLATRRSWTSEPEDGLLIPNGDVDDLVDEKGGHEDIYEFAGEADIVVLCCTL 236
Query: 163 IPQTKNLINAEVLKKCKKGVRVVNVARGGIVDENALLDSLKCGHCGGAALDVFCEEPPKS 222
+T ++N E L KKG +VN+ARGG++D +A+L +L+ GH GG A+DV EP
Sbjct: 237 TKETAGIVNDEFLSSMKKGALLVNIARGGLLDYDAVLAALESGHLGGLAIDVAWSEPFDP 296
Query: 223 EQTFELIKHPKVIVTPHLGAST 244
+ ++KHP VI+TPH+ T
Sbjct: 297 DD--PILKHPNVIITPHVAGVT 316
>gnl|CDD|178684 PLN03139, PLN03139, formate dehydrogenase; Provisional.
Length = 386
Score = 142 bits (360), Expect = 2e-39
Identities = 86/248 (34%), Positives = 129/248 (52%), Gaps = 13/248 (5%)
Query: 13 VTAEVLQ-ASNLQVVGRAGTGVDNIDLTAATRKGVLVLNAPGGNFISACELTCSLISALS 71
VTAE ++ A NL+++ AG G D+IDL AA G+ V G N +S E I L
Sbjct: 111 VTAERIKKAKNLELLLTAGIGSDHIDLPAAAAAGLTVAEVTGSNVVSVAEDELMRILILL 170
Query: 72 RNVPQGCQSLKEGKWDRK--LYTGTELYGKTLAVLGLGRIGREVALRMQAFGMKV----- 124
RN G + G+W+ Y +L GKT+ +G GRIGR + R++ F +
Sbjct: 171 RNFLPGYHQVVSGEWNVAGIAYRAYDLEGKTVGTVGAGRIGRLLLQRLKPFNCNLLYHDR 230
Query: 125 IGFDPMVSVEDAAKLNIASLGLEDIWPLADYITVHTPLIPQTKNLINAEVLKKCKKGVRV 184
+ DP + E AK L+ + P D + ++TPL +T+ + N E + K KKGV +
Sbjct: 231 LKMDPELEKETGAKF---EEDLDAMLPKCDVVVINTPLTEKTRGMFNKERIAKMKKGVLI 287
Query: 185 VNVARGGIVDENALLDSLKCGHCGGAALDVFCEEPPKSEQTFELIKHPKVIVTPHLGAST 244
VN ARG I+D A+ D+ GH GG DV+ +P + + + P +TPH+ +T
Sbjct: 288 VNNARGAIMDTQAVADACSSGHIGGYGGDVWYPQPAPKDHPWRYM--PNHAMTPHISGTT 345
Query: 245 KEAQIRVA 252
+AQ+R A
Sbjct: 346 IDAQLRYA 353
>gnl|CDD|185307 PRK15409, PRK15409, bifunctional glyoxylate/hydroxypyruvate
reductase B; Provisional.
Length = 323
Score = 127 bits (320), Expect = 3e-34
Identities = 77/273 (28%), Positives = 130/273 (47%), Gaps = 16/273 (5%)
Query: 9 SDTKVTAEVLQ-ASNLQVVGRAGTGVDNIDLTAATRKGVLVLNAPGGNFISACELTCSLI 67
S KV A +L+ L+ G DN D+ A T + +L+++ P + + +L+
Sbjct: 52 SGEKVDAALLEKMPKLRAASTISVGYDNFDVDALTARKILLMHTPTVLTETVADTLMALV 111
Query: 68 SALSRNVPQGCQSLKEGKWDRKL---YTGTELYGKTLAVLGLGRIGREVALRMQ-AFGMK 123
+ +R V + + +K G+W + + GT+++ KTL ++G+GRIG +A R F M
Sbjct: 112 LSTARRVVEVAERVKAGEWTASIGPDWFGTDVHHKTLGIVGMGRIGMALAQRAHFGFNMP 171
Query: 124 VIGFDPMVSVEDAAKLNIASLGLEDIWPLADYITVHTPLIPQTKNLINAEVLKKCKKGVR 183
++ E + N L+ + +D++ + PL +T +L AE K K
Sbjct: 172 ILYNARRHHKEAEERFNARYCDLDTLLQESDFVCIILPLTDETHHLFGAEQFAKMKSSAI 231
Query: 184 VVNVARGGIVDENALLDSLKCGHCGGAALDVFCEEP-PKSEQTFELIKHPKVIVTPHLGA 242
+N RG +VDENAL+ +L+ G A LDVF +EP L+ P V+ PH+G+
Sbjct: 232 FINAGRGPVVDENALIAALQKGEIHAAGLDVFEQEPLSVDS---PLLSLPNVVAVPHIGS 288
Query: 243 STKEAQIRVAVEIAEQFIALAN-------TNPQ 268
+T E + +A + I NPQ
Sbjct: 289 ATHETRYNMAACAVDNLIDALQGKVEKNCVNPQ 321
>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 = 125 bits (317), Expect = 1e-33
Identities = 75/262 (28%), Positives = 111/262 (42%), Gaps = 38/262 (14%)
Query: 22 NLQVVGRAGTGVDNIDLTAATRKGVLV--LNAPG-----GNFISACELTCSLISALSRNV 74
NL+ + G GVD++ L V + L PG ++ A L L R++
Sbjct: 58 NLKAIFSLGAGVDHL-LADPDLPDVPIVRLVDPGLAQGMAEYVLAAVL------RLHRDM 110
Query: 75 PQGCQSLKEGKWDRKLY-TGTELYGKTLAVLGLGRIGREVALRMQAFGMKVIG------- 126
+ + G W E + VLGLG +G VA R+ A G V G
Sbjct: 111 DRYAAQQRRGVWKPLPQRPAAER---RVGVLGLGELGAAVARRLAALGFPVSGWSRSPKD 167
Query: 127 FDPMVSVEDAAKLNIASLGLEDIWPLADYITVHTPLIPQTKNLINAEVLKKCKKGVRVVN 186
+ + GL+ D + PL P+T+ ++NAE+L + +G ++N
Sbjct: 168 IEGVTCFHGEE-------GLDAFLAQTDILVCLLPLTPETRGILNAELLARLPRGAALIN 220
Query: 187 VARGGIVDENALLDSLKCGHCGGAALDVFCEEPPKSEQTFELIKHPKVIVTPHLGASTKE 246
V RG + E LL +L GH GA LDVF +EP ++ +HP+V VTPH+ A T
Sbjct: 221 VGRGPHLVEADLLAALDSGHLSGAVLDVFEQEPLPADHPL--WRHPRVTVTPHIAAIT-- 276
Query: 247 AQIRVAVE-IAEQFIALANTNP 267
A +AE L P
Sbjct: 277 -DPDSAAAQVAENIRRLEAGEP 297
>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 = 123 bits (310), Expect = 8e-33
Identities = 69/222 (31%), Positives = 113/222 (50%), Gaps = 20/222 (9%)
Query: 45 GVLVLNAPGGNFISACELTCSLISALSRNVPQGCQSLKE-GKWDRKLYTGTELYGKTLAV 103
G +V A G + E + I A ++ +P+ +K +W R+ L G TL +
Sbjct: 85 GPVVTCARGVAAEAIAEFVLAAILAAAKRLPE--IWVKGAEQWRRE--PLGSLAGSTLGI 140
Query: 104 LGLGRIGREVALRMQAFGMKVI------GFDPMVSVEDAAKLNIASLGLEDIWPLADYIT 157
+G G IG+ +A R A GM+V+ + VE AA L +++ +D++
Sbjct: 141 VGFGAIGQALARRALALGMRVLALRRSGRPSDVPGVEAAADL-------AELFARSDHLV 193
Query: 158 VHTPLIPQTKNLINAEVLKKCKKGVRVVNVARGGIVDENALLDSLKCGHCGGAALDVFCE 217
+ PL P+T++LINA+VL + K G+ ++N+ARGG+VD+ ALL++L G A+LDV
Sbjct: 194 LAAPLTPETRHLINADVLAQAKPGLHLINIARGGLVDQEALLEALDSGRISLASLDVTDP 253
Query: 218 EPPKSEQTFELIKHPKVIVTPHLGASTKEAQIRVAVEIAEQF 259
EP HP+V ++PH A + + +A E
Sbjct: 254 EPLPEGHPL--YTHPRVRLSPHTSAIAPDGRRNLADRFLENL 293
>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 = 121 bits (305), Expect = 4e-32
Identities = 73/264 (27%), Positives = 118/264 (44%), Gaps = 26/264 (9%)
Query: 9 SDTKVTAEVLQASNLQVVGRAGTGVDNIDLTAATRKGVLVLNAPGGNFISACELTCSLIS 68
+ V + L+VV G D + +GV + NA G + S EL +LI
Sbjct: 47 AAPPVLEALRALPRLRVVQTLSAGYDGV--LPLLPEGVTLCNARGVHDASTAELAVALIL 104
Query: 69 ALSRNVPQGCQSLKEGKWDRKLYTGTELYGKTLAVLGLGRIGREVALRMQAFGMKVIGF- 127
A R +P+ ++ G+W+ + L + + ++G G IGR + R+ F ++V
Sbjct: 105 ASLRGLPRFVRAQARGRWEPR--RTPSLADRRVLIVGYGSIGRAIERRLAPFEVRVTRVA 162
Query: 128 ------DPMVSVEDAAKLNIASLGLEDIWPLADYITVHTPLIPQTKNLINAEVLKKCKKG 181
+ + +++ L + P AD + + PL +T+ L++AE L + G
Sbjct: 163 RTARPGEQVHGIDE----------LPALLPEADVVVLIVPLTDETRGLVDAEFLARMPDG 212
Query: 182 VRVVNVARGGIVDENALLDSLKCGHCGGAALDVFCEEP-PKSEQTFELIKHPKVIVTPHL 240
+VNVARG +VD +AL+ L G AALDV EP P L P V++TPH+
Sbjct: 213 ALLVNVARGPVVDTDALVAELASGRL-RAALDVTDPEPLPPGH---PLWSAPGVLITPHV 268
Query: 241 GASTKEAQIRVAVEIAEQFIALAN 264
G +T R + Q A
Sbjct: 269 GGATPAFLPRAYALVRRQLRRYAA 292
>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 = 120 bits (303), Expect = 2e-31
Identities = 80/271 (29%), Positives = 112/271 (41%), Gaps = 49/271 (18%)
Query: 19 QASNLQVVGRAGTGVDN-IDLTAATRKGVLVLNAPGGNFISACELTCSLISALSRNVPQG 77
NL++V G D+ + V + A G + E LS + Q
Sbjct: 51 DVPNLRLVQLFSAGADHWLGHPLYKDPEVPLCTASGIHGPQIAEWVIGTWLVLSHHFLQY 110
Query: 78 CQSLKEGKWDRKL--YTGTELYGKTLAVLGLGRIGREVALRMQAFGMKVIGF-------- 127
+ KE W R+ Y+ + GK + +LG G IGR+ A QA GM+V +
Sbjct: 111 IELQKEQTWGRRQEAYSVEDSVGKRVGILGYGSIGRQTARLAQALGMEVYAYTRSPRPTP 170
Query: 128 --------------DPMVSV-------EDAAKLN-IASLGLEDIWPLADYITVHTPLIPQ 165
DP S+ D A L+ L D + V PL P
Sbjct: 171 ESRKDDGYIVPGTGDPDGSIPSAWFSGTDKASLHEFLRQDL-------DLLVVSLPLTPA 223
Query: 166 TKNLINAE---VLKKCKKGVRVVNVARGGIVDENALLDSLKCGHCGGAALDVFCEEP-PK 221
TK+L+ AE +L K + V N+ARG +VD +AL+ +L+ G GAALDV EP P
Sbjct: 224 TKHLLGAEEFEILAK--RKTFVSNIARGSLVDTDALVAALESGQIRGAALDVTDPEPLPA 281
Query: 222 SEQTFELIKHPKVIVTPHLGASTKEAQIRVA 252
L P VI+TPH+ T+E R
Sbjct: 282 DH---PLWSAPNVIITPHVSWQTQEYFDRAL 309
>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 = 119 bits (301), Expect = 2e-31
Identities = 61/168 (36%), Positives = 92/168 (54%), Gaps = 7/168 (4%)
Query: 86 WDRKLYT--GTELYGKTLAVLGLGRIGREVALRMQAFGMKVIGFDPMVSVEDAAKLNIAS 143
WD T L G T+A++G G IGR + + FG KVI + + A + +
Sbjct: 111 WDPAEEDDLVTLLRGSTVAIVGAGGIGRALIPLLAPFGAKVIAVNRSGRPVEGADETVPA 170
Query: 144 LGLEDIWPLADYITVHTPLIPQTKNLINAEVLKKCKKGVRVVNVARGGIVDENALLDSLK 203
L+++WP AD++ + PL P+T++L++A L K +VNVARG +VD +AL+D+L+
Sbjct: 171 DRLDEVWPDADHVVLAAPLTPETRHLVDAAALAAMKPHAWLVNVARGPLVDTDALVDALR 230
Query: 204 CGHCGGAALDVFCEEP-PKSEQTFELIKHPKVIVTPHLGASTKEAQIR 250
G GAALDV EP P + L P ++TPH+ A+T E
Sbjct: 231 SGEIAGAALDVTDPEPLPDGHPLWSL---PNALITPHV-ANTPEVIRP 274
>gnl|CDD|181499 PRK08605, PRK08605, D-lactate dehydrogenase; Validated.
Length = 332
Score = 120 bits (302), Expect = 2e-31
Identities = 74/230 (32%), Positives = 110/230 (47%), Gaps = 16/230 (6%)
Query: 32 GVDNIDLTAATRKGVLVLNAPGGNFISACELTCSLISALSRNVPQGCQSLKEG--KWDRK 89
G D DL AT+ +++ N P + S E T + L R+ Q ++E +W+
Sbjct: 79 GFDTYDLELATKYNLIISNVPSYSPESIAEFTVTQAINLVRHFNQIQTKVREHDFRWEPP 138
Query: 90 LYTGTELYGKTLAVLGLGRIGREVA-LRMQAFGMKVIGFDPMVSVEDAAKLNIASLGLED 148
+ + +AV+G GRIG VA + + +G V+ +DP + + A ++ +E+
Sbjct: 139 I-LSRSIKDLKVAVIGTGRIGLAVAKIFAKGYGSDVVAYDPFPNAKAATYVDYKD-TIEE 196
Query: 149 IWPLADYITVHTPLIPQTKNLINAEVLKKCKKGVRVVNVARGGIVDENALLDSLKCGHCG 208
AD +T+H P L NA++ K KKG VN ARG +VD ALLD+L G
Sbjct: 197 AVEGADIVTLHMPATKYNHYLFNADLFKHFKKGAVFVNCARGSLVDTKALLDALDNGLIK 256
Query: 209 GAALDVFCEEPP-----KSEQTF------ELIKHPKVIVTPHLGASTKEA 247
GAALD + E P + QT LI VI+TPH+ T A
Sbjct: 257 GAALDTYEFERPLFPSDQRGQTINDPLLESLINREDVILTPHIAFYTDAA 306
>gnl|CDD|235800 PRK06436, PRK06436, glycerate dehydrogenase; Provisional.
Length = 303
Score = 110 bits (276), Expect = 5e-28
Identities = 74/251 (29%), Positives = 126/251 (50%), Gaps = 22/251 (8%)
Query: 15 AEVLQASNLQVVGRA-------GTGVDNIDLTAATRKGVLVLNAPGGNFISACELTCSLI 67
AE + V G+ GVD+ID++ VL NA G IS E +L+
Sbjct: 35 AEAILIKGRYVPGKKTKMIQSLSAGVDHIDVSGIPENVVLCSNA-GAYSISVAEHAFALL 93
Query: 68 SALSRNVPQGCQSLKEGKWDRKLYTGTELYGKTLAVLGLGRIGREVALRMQAFGMKVIGF 127
A ++N+ + ++K G + + LY K+L +LG G IGR VAL +AFGM + +
Sbjct: 94 LAWAKNICENNYNMKNGNFKQSPTK--LLYNKSLGILGYGGIGRRVALLAKAFGMNIYAY 151
Query: 128 DPMVSVEDAAKLNIASLGLE--DIWPLADYITVHTPLIPQTKNLINAEVLKKCKKGVRVV 185
I+S+ +E DI +D++ + PL +T+ +IN+++L +KG+ ++
Sbjct: 152 -----TRSYVNDGISSIYMEPEDIMKKSDFVLISLPLTDETRGMINSKMLSLFRKGLAII 206
Query: 186 NVARGGIVDENALLDSLKCGHCGGAALDVFCEEPPKSEQTFELIKHPKVIVTPHLGASTK 245
NVAR +VD+N +L+ L+ + DV+ EP +E + VI++PH+
Sbjct: 207 NVARADVVDKNDMLNFLRNHNDKYYLSDVWWNEPIITETNPD-----NVILSPHVAGGMS 261
Query: 246 EAQIRVAVEIA 256
++ AV +A
Sbjct: 262 GEIMQPAVALA 272
>gnl|CDD|166874 PRK00257, PRK00257, erythronate-4-phosphate dehydrogenase;
Validated.
Length = 381
Score = 108 bits (273), Expect = 5e-27
Identities = 77/288 (26%), Positives = 126/288 (43%), Gaps = 38/288 (13%)
Query: 3 DGLVVRSDTKVTAEVLQASNLQVVGRAGTGVDNIDLTAATRKGVLVLNAPGGNFISACEL 62
D L+VRS T+V +L+ S ++ VG G D++DL G+ +APG N
Sbjct: 39 DVLLVRSVTRVDRALLEGSRVRFVGTCTIGTDHLDLDYFAEAGITWSSAPGCN------- 91
Query: 63 TCSLISALSRNVPQGCQS----LKEGKWDRKLYTGTELYGKTLAVLGLGRIGREVALRMQ 118
+R V L E + G +L +T V+G G +G + ++
Sbjct: 92 --------ARGVVDYVLGSLLTLAERE-------GVDLAERTYGVVGAGHVGGRLVRVLR 136
Query: 119 AFGMKVIGFDPMVSVEDAAKLNIASLGLEDIWPLADYITVHTPLIPQ----TKNLINAEV 174
G KV+ DP A+ + + LE I D I++HTPL + T++L++
Sbjct: 137 GLGWKVLVCDP---PRQEAEGDGDFVSLERILEECDVISLHTPLTKEGEHPTRHLLDEAF 193
Query: 175 LKKCKKGVRVVNVARGGIVDENALLDSLKCGHCGGAALDVFCEEPPKSEQTFELIKHPKV 234
L + G ++N +RG +VD AL ++L G A LDV+ EP + +L
Sbjct: 194 LASLRPGAWLINASRGAVVDNQALREALLSGEDLDAVLDVWEGEPQIDLELADLC----T 249
Query: 235 IVTPHLGASTKEAQIRVAVEIAEQFIALANTNPQYTSIQGVLNAPALA 282
I TPH+ + + + R +I + + S+ +L P LA
Sbjct: 250 IATPHIAGYSLDGKARGTAQIYQALCRFFGIPARV-SLTDLLPPPWLA 296
>gnl|CDD|177941 PLN02306, PLN02306, hydroxypyruvate reductase.
Length = 386
Score = 104 bits (260), Expect = 3e-25
Identities = 96/332 (28%), Positives = 149/332 (44%), Gaps = 33/332 (9%)
Query: 1 KYDGLVVRSDTKVTAEVLQASNLQVVGRA----GTGVDNIDLTAATRKGVLVLNAPGGNF 56
K DG V+ T+ E L ++ + G+A G +N+D+ AA + G+ V N PG
Sbjct: 62 KCDG-VIGQLTEDWGETLFSALSKAGGKAFSNMAVGYNNVDVEAANKYGIAVGNTPGVLT 120
Query: 57 ISACELTCSLISALSRNVPQGCQSLKEGK---WDRKLYTGTELYGKTLAVLGLGRIGREV 113
+ EL SL A +R + + + ++ G W L+ G L G+T+ V+G GRIG
Sbjct: 121 ETTAELAASLSLAAARRIVEADEFMRAGLYEGWLPHLFVGNLLKGQTVGVIGAGRIGSAY 180
Query: 114 ALRM-QAFGMKVIGFDPMVSV-----------------EDAAKLNIASLGLEDIWPLADY 155
A M + F M +I +D S E AS +E++ AD
Sbjct: 181 ARMMVEGFKMNLIYYDLYQSTRLEKFVTAYGQFLKANGEQPVTWKRAS-SMEEVLREADV 239
Query: 156 ITVHTPLIPQTKNLINAEVLKKCKKGVRVVNVARGGIVDENALLDSLKCGHCGGAALDVF 215
I++H L T +LIN E L KK +VN +RG ++DE AL++ LK LDVF
Sbjct: 240 ISLHPVLDKTTYHLINKERLALMKKEAVLVNASRGPVIDEVALVEHLKANPMFRVGLDVF 299
Query: 216 CEEPPKSEQTFELIKHPKVIVTPHLGASTKEAQIRVAVEIAEQFIALANTNPQYTSIQGV 275
+EP ++ +V PH+ +++K + +A A + P + V
Sbjct: 300 EDEPYMKPGLADM---KNAVVVPHIASASKWTREGMATLAALNVLGKLKGYPVWGDPNRV 356
Query: 276 LNAPALAASRNPENTS-WISLARSLGKISSQL 306
P L + P S I A++LG S+L
Sbjct: 357 --EPFLNENAPPPAASPSIVNAKALGLPVSKL 386
>gnl|CDD|183550 PRK12480, PRK12480, D-lactate dehydrogenase; Provisional.
Length = 330
Score = 101 bits (252), Expect = 2e-24
Identities = 67/280 (23%), Positives = 123/280 (43%), Gaps = 42/280 (15%)
Query: 2 YDGLVVRSDTKVTAEV---LQASNLQVVGRAGTGVDNIDLTAATRKGVLVLNAPGGNFIS 58
YDG+ K+ +V L++ ++ + + G D DL A + +++ N P + +
Sbjct: 46 YDGVTTMQFGKLENDVYPKLESYGIKQIAQRTAGFDMYDLDLAKKHNIVISNVPSYSPET 105
Query: 59 ACELTCSLISALSRNVPQGCQSLKEG--KWDRKLYTGTELYGKTLAVLGLGRIGREVALR 116
E + S+ L R P + ++ W ++ + + T+A++G GRIG A
Sbjct: 106 IAEYSVSIALQLVRRFPDIERRVQAHDFTWQAEIMS-KPVKNMTVAIIGTGRIGAATAKI 164
Query: 117 MQAFGMKVIGFDPMV-----------SVEDAAKLNIASLGLEDIWPLADYITVHTPLIPQ 165
FG + +D SV++A K AD I++H P +
Sbjct: 165 YAGFGATITAYDAYPNKDLDFLTYKDSVKEAIKD-------------ADIISLHVPANKE 211
Query: 166 TKNLINAEVLKKCKKGVRVVNVARGGIVDENALLDSLKCGHCGGAALDVFCEEPP----- 220
+ +L + + KKG +VN ARG +++ L+ ++ G GAA+D + E
Sbjct: 212 SYHLFDKAMFDHVKKGAILVNAARGAVINTPDLIAAVNDGTLLGAAIDTYENEAAYFTND 271
Query: 221 ------KSEQTFELIKHPKVIVTPHLGASTKEAQIRVAVE 254
+ ELI+H +++VTPH+ + EA ++ VE
Sbjct: 272 WTNKDIDDKTLLELIEHERILVTPHIAFFSDEA-VQNLVE 310
>gnl|CDD|185335 PRK15438, PRK15438, erythronate-4-phosphate dehydrogenase PdxB;
Provisional.
Length = 378
Score = 99.6 bits (248), Expect = 1e-23
Identities = 83/283 (29%), Positives = 132/283 (46%), Gaps = 34/283 (12%)
Query: 3 DGLVVRSDTKVTAEVLQASNLQVVGRAGTGVDNIDLTAATRKGVLVLNAPGGNFISACEL 62
D L+VRS TKV +L ++ VG A G D++D + G+ APG N I+ E
Sbjct: 39 DALMVRSVTKVNESLLAGKPIKFVGTATAGTDHVDEAWLKQAGIGFSAAPGCNAIAVVEY 98
Query: 63 TCSLISALSRNVPQGCQSLKEGKWDRKLYTGTELYGKTLAVLGLGRIGREVALRMQAFGM 122
S + L+ G L+ +T+ ++G+G +GR + R++A G+
Sbjct: 99 VFSSLLMLAER------------------DGFSLHDRTVGIVGVGNVGRRLQARLEALGI 140
Query: 123 KVIGFD-PMVSVEDAAKLNIASLGLEDIWPLADYITVHTPLIP----QTKNLINAEVLKK 177
K + D P D L+++ AD +T HTPL +T +L + ++++
Sbjct: 141 KTLLCDPPRADRGDEGDFR----SLDELVQEADILTFHTPLFKDGPYKTLHLADEKLIRS 196
Query: 178 CKKGVRVVNVARGGIVDENALLDSLKCGHCGGAALDVFCEEPPKSEQTFELIKHPKV-IV 236
K G ++N RG +VD ALL L G LDV+ EP E EL+K KV I
Sbjct: 197 LKPGAILINACRGAVVDNTALLTCLNEGQKLSVVLDVWEGEP---ELNVELLK--KVDIG 251
Query: 237 TPHLGASTKEAQIRVAVEIAEQFIALANTNPQYTSIQGVLNAP 279
TPH+ T E + R ++ E + + Q+ ++ +L AP
Sbjct: 252 TPHIAGYTLEGKARGTTQVFEAYSKFIG-HEQHVALDTLLPAP 293
>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 = 92.4 bits (230), Expect = 2e-21
Identities = 62/198 (31%), Positives = 94/198 (47%), Gaps = 32/198 (16%)
Query: 61 ELTCSLISALSRNVPQGCQSLKEGKWDRKL----------YTGTELYGKTLAVLGLGRIG 110
E T +LI A R + + ++ +E +W +L T L G + + G G IG
Sbjct: 97 EHTLALILAAVRRLDEMREAQREHRWAGELGGLQPLRPAGRLTT-LLGARVLIWGFGSIG 155
Query: 111 REVALRMQAFGMKVIGFD---------PMVSVEDAAKLNIASLGLEDIWPLADYITVHTP 161
+ +A + A G +V G P+V+ ++ L ++ P D + + P
Sbjct: 156 QRLAPLLTALGARVTGVARSAGERAGFPVVAEDE----------LPELLPETDVLVMILP 205
Query: 162 LIPQTKNLINAEVLKKCKKGVRVVNVARGGIVDENALLDSLKCGHCGGAALDVFCEEPPK 221
P T + ++AEVL K VVNV RG VDE+AL+ +L+ G GGAALDV EP
Sbjct: 206 ATPSTAHALDAEVLAALPKHAWVVNVGRGATVDEDALVAALESGRLGGAALDVTATEPLP 265
Query: 222 SEQTFELIKHPKVIVTPH 239
+ L P +I+TPH
Sbjct: 266 ASSP--LWDAPNLILTPH 281
>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 = 83.8 bits (207), Expect = 2e-18
Identities = 64/249 (25%), Positives = 101/249 (40%), Gaps = 24/249 (9%)
Query: 11 TKVTAEVLQASNLQVVGRAGTGVDNIDLT-AATRKGVLVLNAPGGNFISACELTCSLISA 69
T ++Q +++ G D+ DLT A R G+ + G LT + I A
Sbjct: 76 TNAEYALIQKLGDRLLFTYTIGADHRDLTEALARAGLTAIAVEGVELPL---LTSNSIGA 132
Query: 70 LSRNVPQGCQSLKEGKWDRKLYTGTELYGKTLAVLGLGRIGREVALRMQAFGMKVIGFDP 129
+V Q E + +L ++ GKT+ V+G G +G+E A ++ G +V+ D
Sbjct: 133 GELSV-QFIARFLEVQQPGRLGGAPDVAGKTVVVVGAGVVGKEAAQMLRGLGAQVLITDI 191
Query: 130 MVSVEDAAKLNIASLG------LEDIWPLADYITVHTPLIPQTKN-LINAEVLKKCKKGV 182
V A + LG LE+ AD I T L + L+ E++++ K G
Sbjct: 192 NV----EALEQLEELGGKNVEELEEALAEADVIVTTTLLPGKRAGILVPEELVEQMKPGS 247
Query: 183 RVVNVARGGIVDENALL-DSLKCGHCGGAALDVFCEEPPKSEQTFELIKHPKVIVTPHLG 241
+VNVA G + AL L+ GH DV P + T L
Sbjct: 248 VIVNVAVGAVGCVQALHTQLLEEGHGVVHYGDVNMPGPGCAMGV-------PWDATLRLA 300
Query: 242 ASTKEAQIR 250
A+T A ++
Sbjct: 301 ANTLPALVK 309
>gnl|CDD|185366 PRK15469, ghrA, bifunctional glyoxylate/hydroxypyruvate reductase
A; Provisional.
Length = 312
Score = 74.4 bits (183), Expect = 4e-15
Identities = 41/101 (40%), Positives = 59/101 (58%), Gaps = 5/101 (4%)
Query: 161 PLIPQTKNLINAEVLKKCKKGVRVVNVARGGIVDENALLDSLKCGHCGGAALDVFCEEPP 220
P P+T +IN ++L++ G ++N+ARG V E+ LL +L G GA LDVF EP
Sbjct: 199 PNTPETVGIINQQLLEQLPDGAYLLNLARGVHVVEDDLLAALDSGKVKGAMLDVFSREPL 258
Query: 221 KSEQTFELIKHPKVIVTPHLGASTKEAQIRVAVEIAEQFIA 261
E L +HP+V +TPH+ A T+ A+ AVE + IA
Sbjct: 259 PPESP--LWQHPRVAITPHVAAVTRPAE---AVEYISRTIA 294
>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 = 50.0 bits (120), Expect = 6e-07
Identities = 62/261 (23%), Positives = 98/261 (37%), Gaps = 40/261 (15%)
Query: 3 DGLVVRSDTKVTAEVLQA-SNLQVVGRAGTGVD----NIDLTAATRKGVLVLNA-----P 52
D ++V T++ EVL+A N++ +G + N+D+ AA G+ V
Sbjct: 48 DCVLVSYTTQIDEEVLEACPNIKYIGMCCSLYSEESANVDIAAARENGITVTGIRDYGDE 107
Query: 53 G-GNFISACELTCSLISALSRNVPQGCQSLKEGKWDRKLYTGTELYGKTLAVLGLGRIGR 111
G ++ LI L +W + EL G + ++GLG G+
Sbjct: 108 GVVEYV-----ISELIRLL--------HGFGGKQWKEE---PRELTGLKVGIIGLGTTGQ 151
Query: 112 EVALRMQAFGMKVIGFDPMVSVEDAAKLNIASLGLEDIWPLADYITVHTPLIPQTKN--L 169
+A + FG V + + AK I L L ++ D I P KN L
Sbjct: 152 MIADALSFFGADVYYYSRTRKPDAEAK-GIRYLPLNELLKTVDVICTCLP-----KNVIL 205
Query: 170 INAEVLKKCKKGVRVVNVARGGIVDENALLDSLKCGHCGGAALDVFCEEPPKSEQTFELI 229
+ E + G + N + G + AL LK G D E EL+
Sbjct: 206 LGEEEFELLGDGKILFNTSLGPSFEVEALKKWLK--ASGYNIFDCDTAGALGDE---ELL 260
Query: 230 KHPKVIVTPHLGASTKEAQIR 250
++P VI T T++A R
Sbjct: 261 RYPNVICTNKSAGWTRQAFER 281
>gnl|CDD|129544 TIGR00452, TIGR00452, tRNA (mo5U34)-methyltransferase. This model
describes a set of proteins with homology in its central
region to a large number of methyltransferases active on
a variety of substrates. The similarity includes a motif
resembling ILDVGCG[SG]G. Known examples to date are
restricted to the proteobacteria [Unknown function,
Enzymes of unknown specificity].
Length = 314
Score = 38.8 bits (90), Expect = 0.002
Identities = 28/86 (32%), Positives = 39/86 (45%), Gaps = 14/86 (16%)
Query: 85 KWDRKLYTGTELYGKTLAVLGLGRIGREVALRMQAFGMK-VIGFDPMVSV----EDAAKL 139
KWDR L + L G+T+ +G G G + RM G K ++G DP V E KL
Sbjct: 109 KWDRVLPHLSPLKGRTILDVGCGS-GYHM-WRMLGHGAKSLVGIDPTVLFLCQFEAVRKL 166
Query: 140 -------NIASLGLEDIWPLADYITV 158
+ LG+E + L + TV
Sbjct: 167 LDNDKRAILEPLGIEQLHELYAFDTV 192
>gnl|CDD|198065 smart00997, AdoHcyase_NAD, S-adenosyl-L-homocysteine hydrolase, NAD
binding domain.
Length = 162
Score = 37.0 bits (87), Expect = 0.004
Identities = 31/114 (27%), Positives = 46/114 (40%), Gaps = 39/114 (34%)
Query: 92 TGTELYGKTLAVLGLGRIGREVALRMQAFGMKVI---------------GFDPMVSVEDA 136
T L GK + V G G +G+ VA R++ G +VI GF+ M +E+A
Sbjct: 17 TNVLLAGKNVVVAGYGDVGKGVAARLRGLGARVIVTEIDPIRALEAAMDGFEVM-KMEEA 75
Query: 137 AKLNIASLGLEDIWPLAD-YITVHTPLIPQT--KNLINAEVLKKCKKGVRVVNV 187
AK AD ++T T K++I E + K G + N
Sbjct: 76 AK-------------RADIFVTA-------TGNKDVITREHFRAMKDGAILANA 109
>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 = 37.4 bits (88), Expect = 0.007
Identities = 30/106 (28%), Positives = 45/106 (42%), Gaps = 37/106 (34%)
Query: 98 GKTLAVLGLGRIGREVALRMQAFGMKVI---------------GFDPMVSVEDAAKLNIA 142
GK + V G G +G+ A+R + G +VI GF+ M +E+AAK I
Sbjct: 195 GKVVVVAGYGWVGKGCAMRARGLGARVIVTEVDPICALQAAMDGFEVM-PMEEAAK--IG 251
Query: 143 SLGLEDIWPLADYITVHTPLIPQT--KNLINAEVLKKCKKGVRVVN 186
DI ++T T K++I E +K K G + N
Sbjct: 252 -----DI-----FVTA-------TGNKDVIRGEHFEKMKDGAILCN 280
>gnl|CDD|223573 COG0499, SAM1, S-adenosylhomocysteine hydrolase [Coenzyme
metabolism].
Length = 420
Score = 37.6 bits (88), Expect = 0.007
Identities = 30/106 (28%), Positives = 46/106 (43%), Gaps = 37/106 (34%)
Query: 98 GKTLAVLGLGRIGREVALRMQAFGMKVI---------------GFDPMVSVEDAAKLNIA 142
GK + V G G +GR +A+R++ G +VI GF M ++E+AAK
Sbjct: 209 GKNVVVAGYGWVGRGIAMRLRGMGARVIVTEVDPIRALEAAMDGFRVM-TMEEAAKTG-- 265
Query: 143 SLGLEDIWPLADYITVHTPLIPQT--KNLINAEVLKKCKKGVRVVN 186
DI ++T T K++I E +K K G + N
Sbjct: 266 -----DI-----FVTA-------TGNKDVIRKEHFEKMKDGAILAN 294
>gnl|CDD|223842 COG0771, MurD, UDP-N-acetylmuramoylalanine-D-glutamate ligase [Cell
envelope biogenesis, outer membrane].
Length = 448
Score = 36.9 bits (86), Expect = 0.013
Identities = 24/98 (24%), Positives = 39/98 (39%), Gaps = 13/98 (13%)
Query: 96 LYGKTLAVLGLGRIGREVALRMQAFGMKVIGFD-----PMVSVEDAAKLNIA-SLG--LE 147
GK + VLGLG+ G A + G +V D ++ + I LG +
Sbjct: 5 FQGKKVLVLGLGKSGLAAARFLLKLGAEVTVSDDRPAPEGLAAQPLLLEGIEVELGSHDD 64
Query: 148 DIWPLADYITVHTPLIPQTKNLINAEVLKKCKKGVRVV 185
+ D + V +P IP T L+ A G+ ++
Sbjct: 65 EDLAEFDLV-VKSPGIPPTHPLVEAAK----AAGIEII 97
>gnl|CDD|236190 PRK08220, PRK08220, 2,3-dihydroxybenzoate-2,3-dehydrogenase;
Validated.
Length = 252
Score = 36.4 bits (85), Expect = 0.014
Identities = 17/32 (53%), Positives = 19/32 (59%), Gaps = 1/32 (3%)
Query: 98 GKTLAVLGLGR-IGREVALRMQAFGMKVIGFD 128
GKT+ V G + IG VAL G KVIGFD
Sbjct: 8 GKTVWVTGAAQGIGYAVALAFVEAGAKVIGFD 39
>gnl|CDD|188426 TIGR03911, pyrrolys_PylD, pyrrolysine biosynthesis protein PylD.
This protein is PylD, part of a three-gene cassette that
is sufficient to direct the biosynthesis of pyrrolysine,
the twenty-second amino acid, incorporated in some
species at a UAG canonical stop codon [Amino acid
biosynthesis, Other].
Length = 266
Score = 36.3 bits (84), Expect = 0.015
Identities = 22/84 (26%), Positives = 34/84 (40%), Gaps = 8/84 (9%)
Query: 96 LYGKTLAVLGLGRIGREVALRMQAFGMKVIGFDPMVSVEDAAKLNIASLGLEDIWPLA-- 153
L K + V+GLG +GR A + G V +D + V + ++ S+G+E A
Sbjct: 143 LKSKDVLVIGLGPVGRAAAFHLVDKGFHVYVYDKNLEVSEKLAQDLCSIGIERELDEAMH 202
Query: 154 --DYITVHTPLIPQTKNLINAEVL 175
I TP I + L
Sbjct: 203 KFSAIFEATP----EAGTIREDHL 222
>gnl|CDD|235824 PRK06545, PRK06545, prephenate dehydrogenase; Validated.
Length = 359
Score = 35.7 bits (83), Expect = 0.028
Identities = 31/109 (28%), Positives = 46/109 (42%), Gaps = 17/109 (15%)
Query: 99 KTLAVLGLGRIGREVALRMQAFGMKVIGFDPMVSVEDAAKLNIASLGLEDIWPL------ 152
+T+ ++GLG IG +AL ++A G V S A +LG I L
Sbjct: 1 RTVLIVGLGLIGGSLALAIKAAGPDVFIIGYDPSAAQLA----RALGFGVIDELAADLQR 56
Query: 153 ----ADYITVHTPLIPQTKNLINAEVLKKCKKGVRVVNVA--RGGIVDE 195
AD I + P + T L+ + K GV V +V +G I+ E
Sbjct: 57 AAAEADLIVLAVP-VDATAALLAELADLELKPGVIVTDVGSVKGAILAE 104
>gnl|CDD|236582 PRK09599, PRK09599, 6-phosphogluconate dehydrogenase-like protein;
Reviewed.
Length = 301
Score = 35.5 bits (83), Expect = 0.030
Identities = 13/38 (34%), Positives = 22/38 (57%)
Query: 101 LAVLGLGRIGREVALRMQAFGMKVIGFDPMVSVEDAAK 138
L ++GLGR+G +A R+ G +V+G+D +A
Sbjct: 3 LGMIGLGRMGGNMARRLLRGGHEVVGYDRNPEAVEALA 40
>gnl|CDD|234094 TIGR03026, NDP-sugDHase, nucleotide sugar dehydrogenase. Enzymes
in this family catalyze the NAD-dependent
alcohol-to-acid oxidation of nucleotide-linked sugars.
Examples include UDP-glucose 6-dehydrogenase (1.1.1.22)
, GDP-mannose 6-dehydrogenase (1.1.1.132) ,
UDP-N-acetylglucosamine 6-dehydrogenase (1.1.1.136),
UDP-N-acetyl-D-galactosaminuronic acid dehydrogenase and
UDP-N-acetyl-D-mannosaminuronic acid dehydrogenase.
These enzymes are most often involved in the
biosynthesis of polysaccharides and are often found in
operons devoted to that purpose. All of these enzymes
contain three Pfam domains, pfam03721, pfam00984, and
pfam03720 for the N-terminal, central, and C-terminal
regions respectively.
Length = 409
Score = 35.7 bits (83), Expect = 0.032
Identities = 33/119 (27%), Positives = 44/119 (36%), Gaps = 34/119 (28%)
Query: 99 KTLAVLGLGRIGREVALRMQAFGMKVIGFDPMVSVEDAAKLN-----IASLGL------- 146
+AV+GLG +G +A + G V G D + E KLN I GL
Sbjct: 1 MKIAVIGLGYVGLPLAALLADLGHDVTGVD--IDQEKVDKLNKGKSPIYEPGLDELLAKA 58
Query: 147 ------------EDIWPLADY--ITVHTPL----IPQTKNLINA--EVLKKCKKGVRVV 185
E+ AD I V TPL P + +A + K +KG VV
Sbjct: 59 LKAGRLRATTDYEEAIRDADVIIICVPTPLKEDGSPDLSYVESAAETIAKHLRKGATVV 117
>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 = 35.5 bits (82), Expect = 0.034
Identities = 30/104 (28%), Positives = 44/104 (42%), Gaps = 33/104 (31%)
Query: 98 GKTLAVLGLGRIGREVALRMQAFGMKVI---------------GFDPMVSVEDAAKLNIA 142
GKT+ V G G G+ +A+R + G +VI GF M ++E+AAK+
Sbjct: 196 GKTVVVAGYGWCGKGIAMRARGMGARVIVTEVDPIRALEAAMDGFRVM-TMEEAAKIG-- 252
Query: 143 SLGLEDIWPLADYITVHTPLIPQTKNLINAEVLKKCKKGVRVVN 186
DI +IT K++I E + K G V N
Sbjct: 253 -----DI-----FITA-----TGNKDVIRGEHFENMKDGAIVAN 281
>gnl|CDD|235488 PRK05476, PRK05476, S-adenosyl-L-homocysteine hydrolase;
Provisional.
Length = 425
Score = 35.1 bits (82), Expect = 0.041
Identities = 28/107 (26%), Positives = 44/107 (41%), Gaps = 39/107 (36%)
Query: 98 GKTLAVLGLGRIGREVALRMQAFGMKVI---------------GFDPMVSVEDAAKLNIA 142
GK + V G G +G+ A R++ G +VI GF M ++E+AA
Sbjct: 212 GKVVVVAGYGDVGKGCAQRLRGLGARVIVTEVDPICALQAAMDGFRVM-TMEEAA----- 265
Query: 143 SLGLEDIWPLAD-YITVHTPLIPQT--KNLINAEVLKKCKKGVRVVN 186
L D ++T T K++I AE ++ K G + N
Sbjct: 266 --------ELGDIFVTA-------TGNKDVITAEHMEAMKDGAILAN 297
>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 = 34.4 bits (80), Expect = 0.048
Identities = 14/55 (25%), Positives = 25/55 (45%), Gaps = 1/55 (1%)
Query: 91 YTGTELYGKTLAVLGLGRIGREVALRMQAFGMKVIGF-DPMVSVEDAAKLNIASL 144
G L G +A+ G G +G A + G KV+ D ++ + L++ +L
Sbjct: 24 KLGIGLAGARVAIQGFGNVGSHAARFLHEAGAKVVAVSDSDGTIYNPDGLDVPAL 78
>gnl|CDD|184511 PRK14106, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
synthetase; Provisional.
Length = 450
Score = 34.9 bits (81), Expect = 0.051
Identities = 20/55 (36%), Positives = 26/55 (47%), Gaps = 2/55 (3%)
Query: 95 ELYGKTLAVLGLGRIGREVALRMQAFGMKVIGFDPMVSVEDAAKLNIASLGLEDI 149
EL GK + V+G G G +A ++ G KVI D ED K + LG I
Sbjct: 2 ELKGKKVLVVGAGVSGLALAKFLKKLGAKVILTD--EKEEDQLKEALEELGELGI 54
>gnl|CDD|181371 PRK08306, PRK08306, dipicolinate synthase subunit A; Reviewed.
Length = 296
Score = 34.4 bits (80), Expect = 0.054
Identities = 26/98 (26%), Positives = 43/98 (43%), Gaps = 11/98 (11%)
Query: 96 LYGKTLAVLGLGRIGREVALRMQAFGMKVIGFDPMVSVEDAAKL-NIASLGLEDIWP--L 152
++G + VLG GR G +A ++A G V V +A L I +GL L
Sbjct: 150 IHGSNVLVLGFGRTGMTLARTLKALGANV-----TVGARKSAHLARITEMGLSPFHLSEL 204
Query: 153 ADYITVHTPLIPQT--KNLINAEVLKKCKKGVRVVNVA 188
A+ + +I T ++ EVL K ++++A
Sbjct: 205 AEEVG-KIDIIFNTIPALVLTKEVLSKMPPEALIIDLA 241
>gnl|CDD|178111 PLN02494, PLN02494, adenosylhomocysteinase.
Length = 477
Score = 34.8 bits (80), Expect = 0.062
Identities = 28/98 (28%), Positives = 45/98 (45%), Gaps = 7/98 (7%)
Query: 92 TGTELYGKTLAVLGLGRIGREVALRMQAFGMKVI--GFDPMVSVEDAAKLNIASLGLEDI 149
T + GK + G G +G+ A M+A G +VI DP+ +++ A L LED+
Sbjct: 248 TDVMIAGKVAVICGYGDVGKGCAAAMKAAGARVIVTEIDPICALQ-ALMEGYQVLTLEDV 306
Query: 150 WPLADYITVHTPLIPQTKNLINAEVLKKCKKGVRVVNV 187
AD T K++I + ++K K V N+
Sbjct: 307 VSEADIFVTTT----GNKDIIMVDHMRKMKNNAIVCNI 340
>gnl|CDD|168796 PRK07066, PRK07066, 3-hydroxybutyryl-CoA dehydrogenase; Validated.
Length = 321
Score = 34.4 bits (79), Expect = 0.068
Identities = 19/53 (35%), Positives = 26/53 (49%), Gaps = 5/53 (9%)
Query: 99 KTLAVLGLGRIGREVALRMQAFGMKVIGFDPMVSVEDAAKLNIASLGLEDIWP 151
KT A +G G IG R A G+ V+ +DP E A + N+A + WP
Sbjct: 8 KTFAAIGSGVIGSGWVARALAHGLDVVAWDPAPGAEAALRANVA-----NAWP 55
>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 = 0.074
Identities = 35/119 (29%), Positives = 49/119 (41%), Gaps = 18/119 (15%)
Query: 93 GTELYGKTLAVLGLGRIGREVALRMQAFGMKVI--------GFDPMVSVEDAAKLNIASL 144
G L G T+AV GLG +G +A ++ G KV+ +DP ++ E+ +A L
Sbjct: 18 GDSLEGLTVAVQGLGNVGWGLAKKLAEEGGKVLAVSDPDGYIYDPGITTEELINYAVA-L 76
Query: 145 GLEDIWPLADYITVHTPL-------IP-QTKNLINAEVLKKCKKGVRVVNVARGGIVDE 195
G + DY L P N+I+ E KK K V V A DE
Sbjct: 77 GGSARVKVQDYFPGEAILGLDVDIFAPCALGNVIDLENAKKLKAKV-VAEGANNPTTDE 134
>gnl|CDD|223364 COG0287, TyrA, Prephenate dehydrogenase [Amino acid transport and
metabolism].
Length = 279
Score = 33.5 bits (77), Expect = 0.11
Identities = 23/99 (23%), Positives = 38/99 (38%), Gaps = 13/99 (13%)
Query: 99 KTLAVLGLGRIGREVALRMQAFGMKVIGFDPMVSVEDAAKLNIASLGLEDIW-------- 150
+ ++GLG +G +A ++ G+ V A LG+ D
Sbjct: 4 MKVGIVGLGLMGGSLARALKEAGLVVRIIG--RDRSAATLKAALELGVIDELTVAGLAEA 61
Query: 151 -PLADYITVHTPLIPQTKNLINAEVLKKCKKGVRVVNVA 188
AD + V P I T+ ++ E+ KKG V +V
Sbjct: 62 AAEADLVIVAVP-IEATEEVL-KELAPHLKKGAIVTDVG 98
>gnl|CDD|223411 COG0334, GdhA, Glutamate dehydrogenase/leucine dehydrogenase [Amino
acid transport and metabolism].
Length = 411
Score = 33.4 bits (77), Expect = 0.14
Identities = 12/36 (33%), Positives = 19/36 (52%)
Query: 93 GTELYGKTLAVLGLGRIGREVALRMQAFGMKVIGFD 128
G +L G +AV G G +G+ A ++ G KV+
Sbjct: 202 GDDLEGARVAVQGFGNVGQYAAEKLHELGAKVVAVS 237
>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 = 32.5 bits (75), Expect = 0.14
Identities = 28/121 (23%), Positives = 44/121 (36%), Gaps = 40/121 (33%)
Query: 96 LYGKTLAVLGLGRIGREVALRMQAFGMKVI----------------GFDPMVSVEDAAKL 139
L GK +AV+G G G AL ++ G+ VI GF+ +V +A K
Sbjct: 2 LKGKKIAVIGYGSQGHAHALNLRDSGVNVIVGLRPGSKSWEKAKKDGFEVY-TVAEAVK- 59
Query: 140 NIASLGLEDIWPLADYITVHTPLIP--QTKNLINAEVLKKCKKGVRVV-----NVARGGI 192
AD + + L+P + E+ K+G + N+ G I
Sbjct: 60 ------------KADVVMI---LLPDEVQAEVYEKEIAPNLKEGAALAFAHGFNIHFGQI 104
Query: 193 V 193
Sbjct: 105 K 105
>gnl|CDD|238315 cd00562, NifX_NifB, This CD represents a family of iron-molybdenum
cluster-binding proteins that includes NifB, NifX, and
NifY, all of which are involved in the synthesis of an
iron-molybdenum cofactor (FeMo-co) that binds the active
site of the dinitrogenase enzyme. This domain is a
predicted small-molecule-binding domain (SMBD) with an
alpha/beta fold that is present either as a stand-alone
domain (e.g. NifX and NifY) or fused to another
conserved domain (e.g. NifB) however, its function is
still undetermined.The SCOP database suggests that this
domain is most similar to structures within the
ribonuclease H superfamily. This conserved domain is
represented in two of the three major divisions of life
(bacteria and archaea).
Length = 102
Score = 31.4 bits (72), Expect = 0.15
Identities = 20/73 (27%), Positives = 31/73 (42%), Gaps = 15/73 (20%)
Query: 71 SRNVPQGCQSLKEGKWDRKLYTGTELYGKTLAVLG-----LGRIGREVALRMQAFGMKVI 125
R P C EGK +L LA+ G +G IG A +++A G+K I
Sbjct: 37 VRENPAACGGGGEGKLAARL----------LALEGCDAVLVGGIGGPAAAKLEAAGIKPI 86
Query: 126 GFDPMVSVEDAAK 138
++E+A +
Sbjct: 87 KAAEGGTIEEALE 99
>gnl|CDD|240258 PTZ00075, PTZ00075, Adenosylhomocysteinase; Provisional.
Length = 476
Score = 33.5 bits (77), Expect = 0.17
Identities = 33/120 (27%), Positives = 59/120 (49%), Gaps = 17/120 (14%)
Query: 77 GC-QSLKEGKWDRKLYTGTE--LYGKTLAVLGLGRIGREVALRMQAFGMKVI--GFDPMV 131
GC SL +G ++ T+ + GKT+ V G G +G+ A ++ FG +V+ DP+
Sbjct: 235 GCRHSLIDG-----IFRATDVMIAGKTVVVCGYGDVGKGCAQALRGFGARVVVTEIDPIC 289
Query: 132 SVEDAAKLNIASLGLEDIWPLAD-YITVHTPLIPQTKNLINAEVLKKCKKGVRVVNVARG 190
+++ AA + LED+ AD ++T K++I E +++ K V N+
Sbjct: 290 ALQ-AAMEGYQVVTLEDVVETADIFVTA-----TGNKDIITLEHMRRMKNNAIVGNIGHF 343
>gnl|CDD|237116 PRK12490, PRK12490, 6-phosphogluconate dehydrogenase-like protein;
Reviewed.
Length = 299
Score = 33.2 bits (76), Expect = 0.17
Identities = 16/51 (31%), Positives = 28/51 (54%), Gaps = 2/51 (3%)
Query: 101 LAVLGLGRIGREVALRMQAFGMKVIGFDPMVSVEDAAKLN--IASLGLEDI 149
L ++GLG++G +A R++ G +V+G+D D A A LE++
Sbjct: 3 LGLIGLGKMGGNMAERLREDGHEVVGYDVNQEAVDVAGKLGITARHSLEEL 53
>gnl|CDD|149853 pfam08916, Phe_ZIP, Phenylalanine zipper. The phenylalanine zipper
consists of aromatic side chains from ten phenylalanine
residues that are stacked within a hydrophobic core.
This zipper mediates dimerisation of various proteins,
such as APS, SH2-B and Lnk.
Length = 59
Score = 29.7 bits (67), Expect = 0.26
Identities = 8/21 (38%), Positives = 10/21 (47%)
Query: 252 AVEIAEQFIALANTNPQYTSI 272
A + A +F NPQY S
Sbjct: 15 ARDFARKFWLFLRENPQYDSP 35
>gnl|CDD|223137 COG0059, IlvC, Ketol-acid reductoisomerase [Amino acid transport
and metabolism / Coenzyme metabolism].
Length = 338
Score = 32.6 bits (75), Expect = 0.26
Identities = 32/121 (26%), Positives = 48/121 (39%), Gaps = 40/121 (33%)
Query: 96 LYGKTLAVLGLGRIGREVALRMQAFGMKVI----------------GFDPMVSVEDAAKL 139
L GK +A++G G G AL ++ G+ VI GF +VE+AAK
Sbjct: 16 LKGKKVAIIGYGSQGHAQALNLRDSGLNVIIGLRKGSSSWKKAKEDGFKVY-TVEEAAK- 73
Query: 140 NIASLGLEDIWPLADYITVHTPLIP--QTKNLINAEVLKKCKKGVRVV-----NVARGGI 192
AD + + L+P Q K + E+ K+G + N+ G I
Sbjct: 74 ------------RADVVMI---LLPDEQQKEVYEKEIAPNLKEGAALGFAHGFNIHFGLI 118
Query: 193 V 193
V
Sbjct: 119 V 119
>gnl|CDD|176217 cd08255, 2-desacetyl-2-hydroxyethyl_bacteriochlorophyllide_like,
2-desacetyl-2-hydroxyethyl bacteriochlorophyllide and
other MDR family members. This subgroup of the medium
chain dehydrogenases/reductase (MDR)/zinc-dependent
alcohol dehydrogenase-like family has members identified
as 2-desacetyl-2-hydroxyethyl bacteriochlorophyllide A
dehydrogenase and alcohol dehydrogenases. The medium
chain dehydrogenases/reductase (MDR)/zinc-dependent
alcohol dehydrogenase-like family, which contains the
zinc-dependent alcohol dehydrogenase (ADH-Zn) and
related proteins, is a diverse group of proteins related
to the first identified member, class I mammalian ADH.
MDRs display a broad range of activities and are
distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability.
Length = 277
Score = 32.2 bits (74), Expect = 0.27
Identities = 21/53 (39%), Positives = 31/53 (58%), Gaps = 7/53 (13%)
Query: 98 GKTLAVLGLGRIGREVALRMQAFG-MKVIGFDPMVSVEDAAKLNIA-SLGLED 148
G+ +AV+GLG +G A +A G +V+G DP DAA+ +A +LG D
Sbjct: 98 GERVAVVGLGLVGLLAAQLAKAAGAREVVGVDP-----DAARRELAEALGPAD 145
>gnl|CDD|234950 PRK01390, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
synthetase; Provisional.
Length = 460
Score = 32.5 bits (75), Expect = 0.32
Identities = 20/50 (40%), Positives = 24/50 (48%), Gaps = 1/50 (2%)
Query: 94 TELYGKTLAVLGLGRIGREVALRMQAFGMKVIGFDPMV-SVEDAAKLNIA 142
T GKT+AV GLG G A + A G +VI +D S AA I
Sbjct: 5 TGFAGKTVAVFGLGGSGLATARALVAGGAEVIAWDDNPASRAKAAAAGIT 54
>gnl|CDD|215789 pfam00208, ELFV_dehydrog, Glutamate/Leucine/Phenylalanine/Valine
dehydrogenase.
Length = 237
Score = 31.7 bits (73), Expect = 0.40
Identities = 18/53 (33%), Positives = 26/53 (49%), Gaps = 1/53 (1%)
Query: 93 GTELYGKTLAVLGLGRIGREVALRMQAFGMKVIGF-DPMVSVEDAAKLNIASL 144
G L GKT+AV G G +G A ++ G KV+ D + D ++I L
Sbjct: 27 GDSLEGKTVAVQGFGNVGSYAAEKLLELGAKVVAVSDSSGYIYDPNGIDIEEL 79
>gnl|CDD|180970 PRK07417, PRK07417, arogenate dehydrogenase; Reviewed.
Length = 279
Score = 31.4 bits (72), Expect = 0.49
Identities = 22/80 (27%), Positives = 36/80 (45%), Gaps = 14/80 (17%)
Query: 103 VLGLGRIGREVALRMQAFGMKVIGFDPMVS-----VEDAAKLNIASLGLEDIWPL--ADY 155
++GLG IG + L +++ G V G VS E A + + D+ L D
Sbjct: 5 IVGLGLIGGSLGLDLRSLGHTVYG----VSRRESTCERAIERGLVDEASTDLSLLKDCDL 60
Query: 156 ITVHTP---LIPQTKNLINA 172
+ + P L+P ++ LI A
Sbjct: 61 VILALPIGLLLPPSEQLIPA 80
>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 = 0.50
Identities = 28/118 (23%), Positives = 47/118 (39%), Gaps = 30/118 (25%)
Query: 96 LYGKTLAVLGLGRIGREVALRMQAFGMKVIG--FDPMVSVEDAAKLNIASLGLEDIWPLA 153
L GKT+AV GLG++G ++A + G K+I + A + E+I+
Sbjct: 26 LEGKTVAVQGLGKVGYKLAEHLLEEGAKLIVADINEEAVARAAELFGATVVAPEEIYS-- 83
Query: 154 DYITVHTPLIPQTKNLINAEVLKKCKKGVRVVNVARGGIVDENALLDSLKCGHCGGAA 211
++A+V C A GG++++ + LK GAA
Sbjct: 84 ----------------VDADVFAPC---------ALGGVIND-DTIPQLKAKAIAGAA 115
>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 = 31.6 bits (72), Expect = 0.50
Identities = 27/88 (30%), Positives = 40/88 (45%), Gaps = 3/88 (3%)
Query: 96 LYGKTLAVLGLGRIGREVALRMQAFGMKVI-GFDP-MVSVEDAAKLNIASLGLEDIWPLA 153
L GKT+A++G G G AL ++ G+ VI G S + A + +E+ P A
Sbjct: 1 LKGKTVAIIGYGSQGHAQALNLRDSGLNVIVGLRKGGASWKKATEDGFKVGTVEEAIPQA 60
Query: 154 DYITVHTPLIPQTKNLINAEVLKKCKKG 181
D I P Q + AE+ K+G
Sbjct: 61 DLIMNLLPDEVQ-HEVYEAEIQPLLKEG 87
>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 = 30.6 bits (70), Expect = 0.58
Identities = 29/112 (25%), Positives = 45/112 (40%), Gaps = 28/112 (25%)
Query: 102 AVLGLGRIGR---EVALRMQAFGMKVIGFDPMVSVEDAAKLNIASLG------------- 145
V+G G +G A + G +V D V A + SL
Sbjct: 24 VVIGAGVVGLGAAATAKGL---GAEVTVLD----VRPARLRQLESLLGARFTTLYSQAEL 76
Query: 146 LEDIWPLADYITVHTPLIP--QTKNLINAEVLKKCKKGVRVVNVA--RGGIV 193
LE+ AD + + LIP + L+ E++K K G +V+VA +GG +
Sbjct: 77 LEEAVKEAD-LVIGAVLIPGAKAPKLVTREMVKSMKPGSVIVDVAADQGGCI 127
>gnl|CDD|223749 COG0677, WecC, UDP-N-acetyl-D-mannosaminuronate dehydrogenase [Cell
envelope biogenesis, outer membrane].
Length = 436
Score = 31.5 bits (72), Expect = 0.70
Identities = 13/29 (44%), Positives = 18/29 (62%)
Query: 100 TLAVLGLGRIGREVALRMQAFGMKVIGFD 128
T+ V+GLG +G +A + G KVIG D
Sbjct: 11 TIGVIGLGYVGLPLAAAFASAGFKVIGVD 39
>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 = 31.2 bits (71), Expect = 0.74
Identities = 27/96 (28%), Positives = 43/96 (44%), Gaps = 7/96 (7%)
Query: 96 LYGKTLAVLGLGRIGREVALRMQAFGMKVIGFDPMVSVEDAAKLNIASLGLEDI-WP-LA 153
++G + VLG GR G +A A G +V F S D A+ I +GL L
Sbjct: 149 IHGSNVMVLGFGRTGMTIARTFSALGARV--FVGARSSADLAR--ITEMGLIPFPLNKLE 204
Query: 154 DYITVHTPLIPQTKNLI-NAEVLKKCKKGVRVVNVA 188
+ + +I L+ A+VL K K ++++A
Sbjct: 205 EKVAEIDIVINTIPALVLTADVLSKLPKHAVIIDLA 240
>gnl|CDD|235774 PRK06292, PRK06292, dihydrolipoamide dehydrogenase; Validated.
Length = 460
Score = 31.3 bits (72), Expect = 0.78
Identities = 23/97 (23%), Positives = 41/97 (42%), Gaps = 20/97 (20%)
Query: 99 KTLAVLGLGRIGREVALRMQAFGMKVIGF---DPMVSVEDAAKLNIASLGLEDIWPLADY 155
K+LAV+G G IG E+ + G+KV F D ++ +ED ++ + I L+
Sbjct: 170 KSLAVIGGGVIGLELGQALSRLGVKVTVFERGDRILPLEDPE---VSKQ-AQKI--LSKE 223
Query: 156 ITVHTPLIPQTKNLINAEVLK-KCKKGVRVVNVARGG 191
+ A+V + +V + +GG
Sbjct: 224 FKIKL----------GAKVTSVEKSGDEKVEELEKGG 250
>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 = 29.5 bits (67), Expect = 0.84
Identities = 9/27 (33%), Positives = 16/27 (59%)
Query: 102 AVLGLGRIGREVALRMQAFGMKVIGFD 128
++G GR+GR +A ++ G V+ D
Sbjct: 2 IIIGYGRVGRSLAEELREGGPDVVVID 28
>gnl|CDD|223936 COG1004, Ugd, Predicted UDP-glucose 6-dehydrogenase [Cell envelope
biogenesis, outer membrane].
Length = 414
Score = 30.6 bits (70), Expect = 1.1
Identities = 19/65 (29%), Positives = 29/65 (44%), Gaps = 13/65 (20%)
Query: 96 LYGKTLAVLGLG-----------RIGREVALRMQAFGMKVIGFDPMVSVEDAAKLNIASL 144
L GKT+AVLGL ++ R+Q G +VI +DP+ +E+A +
Sbjct: 308 LKGKTIAVLGLAFKPNTDDMRESPA-LDIIKRLQEKGAEVIAYDPVA-MENAFRNFPDVE 365
Query: 145 GLEDI 149
D
Sbjct: 366 LESDA 370
>gnl|CDD|223954 COG1023, Gnd, Predicted 6-phosphogluconate dehydrogenase
[Carbohydrate transport and metabolism].
Length = 300
Score = 30.1 bits (68), Expect = 1.5
Identities = 12/41 (29%), Positives = 22/41 (53%), Gaps = 1/41 (2%)
Query: 99 KTLAVLGLGRIGREVALRMQAFGMKVIGFD-PMVSVEDAAK 138
+ ++GLGR+G + R+ G V+G+D +VE+
Sbjct: 1 MQIGMIGLGRMGANLVRRLLDGGHDVVGYDVNQTAVEELKD 41
>gnl|CDD|223643 COG0569, TrkA, K+ transport systems, NAD-binding component
[Inorganic ion transport and metabolism].
Length = 225
Score = 29.9 bits (68), Expect = 1.5
Identities = 9/27 (33%), Positives = 15/27 (55%)
Query: 99 KTLAVLGLGRIGREVALRMQAFGMKVI 125
+ ++G GR+GR VA + G V+
Sbjct: 1 MKIIIIGAGRVGRSVARELSEEGHNVV 27
>gnl|CDD|176178 cd05188, MDR, Medium chain reductase/dehydrogenase
(MDR)/zinc-dependent alcohol dehydrogenase-like family.
The medium chain reductase/dehydrogenases
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH) , quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. ADH-like proteins
typically form dimers (typically higher plants, mammals)
or tetramers (yeast, bacteria), and generally have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site and a structural zinc in a lobe of
the catalytic domain. 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. Other MDR members have only
a catalytic zinc, and some contain no coordinated zinc.
Length = 271
Score = 29.6 bits (67), Expect = 1.9
Identities = 29/107 (27%), Positives = 40/107 (37%), Gaps = 19/107 (17%)
Query: 98 GKTLAVLGLGRIGREVALRMQAFGMKVIGFDPMVSVEDAAKLNIA-SLGLEDIWPLADYI 156
G T+ VLG G +G A +A G +VI D KL +A LG + + DY
Sbjct: 135 GDTVLVLGAGGVGLLAAQLAKAAGARVIVTDR-----SDEKLELAKELGADHV---IDY- 185
Query: 157 TVHTPLIPQTKNLINAEVLKKCKKGVRVVNVARGGIVDENALLDSLK 203
+ + E+ G VV A GG L L+
Sbjct: 186 ---------KEEDLEEELRLTGGGGADVVIDAVGGPETLAQALRLLR 223
>gnl|CDD|223105 COG0026, PurK, Phosphoribosylaminoimidazole carboxylase (NCAIR
synthetase) [Nucleotide transport and metabolism].
Length = 375
Score = 29.9 bits (68), Expect = 1.9
Identities = 15/32 (46%), Positives = 21/32 (65%)
Query: 98 GKTLAVLGLGRIGREVALRMQAFGMKVIGFDP 129
KT+ +LG G++GR +AL G+KVI DP
Sbjct: 1 MKTVGILGGGQLGRMMALAAARLGIKVIVLDP 32
>gnl|CDD|109716 pfam00670, AdoHcyase_NAD, S-adenosyl-L-homocysteine hydrolase, NAD
binding domain.
Length = 162
Score = 28.8 bits (65), Expect = 2.3
Identities = 26/92 (28%), Positives = 42/92 (45%), Gaps = 7/92 (7%)
Query: 98 GKTLAVLGLGRIGREVALRMQAFGMKVI--GFDPMVSVEDAAKLNIASLGLEDIWPLADY 155
GK V G G +G+ A ++ G +VI DP+ +++ AA + LE++ AD
Sbjct: 23 GKVAVVCGYGDVGKGCAASLKGQGARVIVTEIDPICALQ-AAMEGFQVVTLEEVVKKADI 81
Query: 156 ITVHTPLIPQTKNLINAEVLKKCKKGVRVVNV 187
T K++I E + K K V N+
Sbjct: 82 FVTTT----GNKDIITGEHMAKMKNDAIVCNI 109
>gnl|CDD|235546 PRK05653, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Validated.
Length = 246
Score = 29.4 bits (67), Expect = 2.3
Identities = 21/45 (46%), Positives = 26/45 (57%), Gaps = 3/45 (6%)
Query: 96 LYGKTLAVLGLGR-IGREVALRMQAFGMKVIGFDPMVSVEDAAKL 139
L GKT V G R IGR +ALR+ A G KV+ +D + E A L
Sbjct: 3 LQGKTALVTGASRGIGRAIALRLAADGAKVVIYD--SNEEAAEAL 45
>gnl|CDD|180163 PRK05611, rpmD, 50S ribosomal protein L30; Reviewed.
Length = 59
Score = 27.0 bits (61), Expect = 2.4
Identities = 16/46 (34%), Positives = 20/46 (43%), Gaps = 15/46 (32%)
Query: 99 KTLAVLGLGRIGREV------ALRMQAFGM--KVIGFDPMVSVEDA 136
TL LGL +I V A+R GM KV +V VE+
Sbjct: 21 ATLRGLGLRKINSTVELEDTPAIR----GMINKVS---HLVKVEEV 59
>gnl|CDD|235491 PRK05479, PRK05479, ketol-acid reductoisomerase; Provisional.
Length = 330
Score = 29.3 bits (67), Expect = 2.6
Identities = 16/57 (28%), Positives = 27/57 (47%), Gaps = 17/57 (29%)
Query: 98 GKTLAVLGLGRIGREVALRMQAFGMKVI----------------GFDPMVSVEDAAK 138
GK +A++G G G AL ++ G+ V+ GF+ + +V +AAK
Sbjct: 17 GKKVAIIGYGSQGHAHALNLRDSGVDVVVGLREGSKSWKKAEADGFEVL-TVAEAAK 72
>gnl|CDD|151783 pfam11342, DUF3144, Protein of unknown function (DUF3144). This
family of proteins with unknown function appears to be
restricted to Proteobacteria.
Length = 78
Score = 27.3 bits (61), Expect = 2.7
Identities = 13/33 (39%), Positives = 17/33 (51%)
Query: 253 VEIAEQFIALANTNPQYTSIQGVLNAPALAASR 285
+ A+QFIALAN + V A AA+R
Sbjct: 3 YDRADQFIALANEQNKEIDAGKVSAALLYAAAR 35
>gnl|CDD|227264 COG4927, COG4927, Predicted choloylglycine hydrolase [General
function prediction only].
Length = 336
Score = 29.1 bits (65), Expect = 2.8
Identities = 15/68 (22%), Positives = 24/68 (35%)
Query: 211 ALDVFCEEPPKSEQTFELIKHPKVIVTPHLGASTKEAQIRVAVEIAEQFIALANTNPQYT 270
A+ C P S Q ++ T LG + R+ F A ++ Y
Sbjct: 193 AVKALCRIPVASSQNVIVLDSAGNYATLELGPGQRPIITRLRNACTNHFRAATPSSFSYA 252
Query: 271 SIQGVLNA 278
Q +L+A
Sbjct: 253 RQQFILSA 260
>gnl|CDD|235633 PRK05872, PRK05872, short chain dehydrogenase; Provisional.
Length = 296
Score = 29.2 bits (66), Expect = 3.0
Identities = 19/62 (30%), Positives = 26/62 (41%), Gaps = 8/62 (12%)
Query: 92 TGTELYGKTLAVLGLGR-IGREVALRMQAFGMKV--IGFDPMVSVEDAAKLNIASLGLED 148
T L GK + V G R IG E+A R+ A G K+ + + A LG +D
Sbjct: 3 PMTSLAGKVVVVTGAARGIGAELARRLHARGAKLALVDLEE-----AELAALAAELGGDD 57
Query: 149 IW 150
Sbjct: 58 RV 59
>gnl|CDD|237898 PRK15068, PRK15068, tRNA mo(5)U34 methyltransferase; Provisional.
Length = 322
Score = 29.1 bits (66), Expect = 3.4
Identities = 25/86 (29%), Positives = 38/86 (44%), Gaps = 14/86 (16%)
Query: 85 KWDRKLYTGTELYGKTLAVLGLGRIGREVALRMQAFGMK-VIGFDPMVS----------- 132
KWDR L + L G+T+ +G G G RM G K V+G DP
Sbjct: 110 KWDRVLPHLSPLKGRTVLDVGCGN-GYH-MWRMLGAGAKLVVGIDPSQLFLCQFEAVRKL 167
Query: 133 VEDAAKLNIASLGLEDIWPLADYITV 158
+ + + ++ LG+E + L + TV
Sbjct: 168 LGNDQRAHLLPLGIEQLPALKAFDTV 193
>gnl|CDD|236016 PRK07424, PRK07424, bifunctional sterol desaturase/short chain
dehydrogenase; Validated.
Length = 406
Score = 29.3 bits (66), Expect = 3.4
Identities = 14/42 (33%), Positives = 22/42 (52%), Gaps = 1/42 (2%)
Query: 87 DRKLYTGTELYGKTLAVLGL-GRIGREVALRMQAFGMKVIGF 127
D+ + T L GKT+AV G G +G+ + + G KV+
Sbjct: 167 DKLMGTALSLKGKTVAVTGASGTLGQALLKELHQQGAKVVAL 208
>gnl|CDD|235961 PRK07200, PRK07200, aspartate/ornithine carbamoyltransferase family
protein; Validated.
Length = 395
Score = 28.9 bits (65), Expect = 3.7
Identities = 21/54 (38%), Positives = 25/54 (46%), Gaps = 11/54 (20%)
Query: 97 YGKTLAVLGLGRIGREVALRMQAFGMKVI-----GFDPMVSVEDAAKLNIASLG 145
YGK L+V G IG M FGM V G+D M V + AK N + G
Sbjct: 200 YGKPLSV-PQGIIGL-----MTRFGMDVTLAHPEGYDLMPEVVEVAKKNAKASG 247
>gnl|CDD|235558 PRK05683, flgK, flagellar hook-associated protein FlgK; Validated.
Length = 676
Score = 29.3 bits (66), Expect = 3.7
Identities = 17/62 (27%), Positives = 32/62 (51%)
Query: 269 YTSIQGVLNAPALAASRNPENTSWISLARSLGKISSQLLQTSTFSSTAFSLVTQDITNVT 328
+T++Q P A+R T L++ +SSQL Q ++ ++ S +T + N+T
Sbjct: 113 FTALQTAAANPTDTAARQLLLTQAQGLSKRFNSLSSQLNQQNSNINSQLSAMTDQVNNLT 172
Query: 329 SS 330
+S
Sbjct: 173 TS 174
>gnl|CDD|222253 pfam13597, NRDD, Anaerobic ribonucleoside-triphosphate reductase.
Length = 542
Score = 29.1 bits (66), Expect = 3.7
Identities = 12/51 (23%), Positives = 16/51 (31%), Gaps = 12/51 (23%)
Query: 208 GGAALDVFCEEPPKSEQTFELIKH------------PKVIVTPHLGASTKE 246
GG L +F E P E +L+K P + G E
Sbjct: 449 GGTILHLFLGESPDPEALKKLVKKAAKTGLPYFTITPTFSICNDCGYIDGE 499
>gnl|CDD|235693 PRK06077, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 252
Score = 28.9 bits (65), Expect = 3.8
Identities = 13/32 (40%), Positives = 18/32 (56%), Gaps = 1/32 (3%)
Query: 95 ELYGKTLAVLGLGR-IGREVALRMQAFGMKVI 125
L K + V G GR IGR +A+R+ G V+
Sbjct: 3 SLKDKVVVVTGSGRGIGRAIAVRLAKEGSLVV 34
>gnl|CDD|234405 TIGR03936, sam_1_link_chp, radical SAM-linked protein. This model
describes an uncharacterized protein encoded adjacent
to, or as a fusion protein with, an uncharacterized
radical SAM protein.
Length = 209
Score = 28.7 bits (65), Expect = 3.9
Identities = 32/141 (22%), Positives = 47/141 (33%), Gaps = 31/141 (21%)
Query: 111 REVALRMQAF---GMKVIGFDPMVSVEDAAKLNIASLGLEDIWPLADY-ITVHTPLIPQT 166
EV R+ A G++V+ + V D A L + ADY IT+
Sbjct: 75 EEVLERLNAVLPEGIEVLE---VEEVPDKAP------SLMALIDAADYRITLPLDDEEDL 125
Query: 167 KNLINA-------EVLKKCKKGVRVVNVARGGIVD------ENALLDSLKCGHCG----G 209
+ I A V KK KKG + V++ R I LL +L G G
Sbjct: 126 QEAIEAFLAAEEIIVEKKTKKGKKKVDI-RPLIKSLEVEDNGLRLLMTLSAGSEGNLRPE 184
Query: 210 AALDVFCEEPPKSEQTFELIK 230
L+ + +
Sbjct: 185 ELLEALLALLGLELALLRIHR 205
>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 = 28.9 bits (65), Expect = 4.2
Identities = 26/130 (20%), Positives = 50/130 (38%), Gaps = 19/130 (14%)
Query: 72 RNVPQGCQSLKEGKWDRKLYTGTELYGKTLAVLGLGRIGREVALRMQAFGMKVIGFDPMV 131
V G L + R G + + ++G G +G A + G V+ +D
Sbjct: 137 AGVQLGAYELARIQGGRMGGAGG-VPPAKVLIIGAGVVGLGAAKIAKKLGANVLVYD--- 192
Query: 132 SVEDAAKLNIASLG-----------LEDIWPLADYITVHTPLIPQTKN--LINAEVLKKC 178
+++ + +LG LE D I ++ L+ + LI E++
Sbjct: 193 -IKEEKLKGVETLGGSRLRYSQKEELEKELKQTD-ILINAILVDGPRAPILIMEELVGPM 250
Query: 179 KKGVRVVNVA 188
K+G +V++A
Sbjct: 251 KRGAVIVDLA 260
>gnl|CDD|223146 COG0068, HypF, Hydrogenase maturation factor [Posttranslational
modification, protein turnover, chaperones].
Length = 750
Score = 28.9 bits (65), Expect = 4.3
Identities = 30/143 (20%), Positives = 53/143 (37%), Gaps = 20/143 (13%)
Query: 130 MVSVEDAAKLNIASL-GLEDIWPLADYITVHTPLIPQTKNLINAEVLKKCKKGVRVVNVA 188
+ E A N +L L+ I ADY +H I N + V++ + + +
Sbjct: 328 NLPGEPMAIDNEEALEKLKGI---ADYFLLHNREIV---NRCDDSVVRVVAGRIAFIRRS 381
Query: 189 RGGIVDE--NALLDSLKCGHCGGAALDVFCEEPPKSEQTFELIKHPKVIVTPHLGASTKE 246
RG + +++K GA L TF L+K K ++ H+G +
Sbjct: 382 RG-YAPKPIELPFNNVKKILALGAELKN----------TFCLLKGGKAYLSQHIGDLSNL 430
Query: 247 AQIRVAVEIAEQFIALANTNPQY 269
+ E F+ + + P Y
Sbjct: 431 ETLEFFREALRHFLKIYDFEPDY 453
>gnl|CDD|217692 pfam03721, UDPG_MGDP_dh_N, UDP-glucose/GDP-mannose dehydrogenase
family, NAD binding domain. The UDP-glucose/GDP-mannose
dehydrogenaseses are a small group of enzymes which
possesses the ability to catalyze the NAD-dependent
2-fold oxidation of an alcohol to an acid without the
release of an aldehyde intermediate.
Length = 188
Score = 28.4 bits (64), Expect = 4.4
Identities = 17/56 (30%), Positives = 28/56 (50%), Gaps = 7/56 (12%)
Query: 99 KTLAVLGLGRIGREVALRMQAFGMKVIGFDPMVSVEDAAKLNIASL-----GLEDI 149
+AV+GLG +G A+ + G V+G D ++ KLN + GLE++
Sbjct: 1 MRIAVIGLGYVGLPTAVCLAEIGHDVVGVD--INQSKIDKLNNGKIPIYEPGLEEL 54
>gnl|CDD|183772 PRK12823, benD, 1,6-dihydroxycyclohexa-2,4-diene-1-carboxylate
dehydrogenase; Provisional.
Length = 260
Score = 28.4 bits (64), Expect = 4.4
Identities = 21/58 (36%), Positives = 29/58 (50%), Gaps = 2/58 (3%)
Query: 98 GKTLAVLGLGR-IGREVALRMQAFGMKVIGFDPMVSVEDAAKLNIASLGLEDIWPLAD 154
GK + V G + IGR VALR A G +V+ D V + A + + G E + AD
Sbjct: 8 GKVVVVTGAAQGIGRGVALRAAAEGARVVLVDRSELVHEVAA-ELRAAGGEALALTAD 64
>gnl|CDD|235707 PRK06130, PRK06130, 3-hydroxybutyryl-CoA dehydrogenase; Validated.
Length = 311
Score = 28.6 bits (64), Expect = 4.8
Identities = 10/32 (31%), Positives = 18/32 (56%)
Query: 99 KTLAVLGLGRIGREVALRMQAFGMKVIGFDPM 130
+ LA++G G +G +A G++V+ D M
Sbjct: 5 QNLAIIGAGTMGSGIAALFARKGLQVVLIDVM 36
>gnl|CDD|218507 pfam05221, AdoHcyase, S-adenosyl-L-homocysteine hydrolase.
Length = 430
Score = 28.5 bits (64), Expect = 5.8
Identities = 25/104 (24%), Positives = 41/104 (39%), Gaps = 7/104 (6%)
Query: 98 GKTLAVLGLGRIGREVALRMQAFGMKVI--GFDPMVSVEDAAKLNIASLGLEDIWPLADY 155
GK V G G +G+ A ++ G +VI DP+ +++ AA + LE++ AD
Sbjct: 210 GKVAVVCGYGDVGKGCAASLRGQGARVIVTEIDPICALQ-AAMEGYQVVTLEEVVKDADI 268
Query: 156 ITVHTPLIPQTKNLINAEVLKKCKKGVRVVNVARGGIVDENALL 199
T ++I KK V N+ + L
Sbjct: 269 FVTTT----GCVDIIVGRHFMNMKKDAIVCNIGHFDCEIDVGWL 308
>gnl|CDD|149213 pfam08003, Methyltransf_9, Protein of unknown function (DUF1698).
This family contains many hypothetical proteins. It also
includes two putative methyltransferase proteins.
Length = 315
Score = 28.1 bits (63), Expect = 5.9
Identities = 27/86 (31%), Positives = 38/86 (44%), Gaps = 14/86 (16%)
Query: 85 KWDRKLYTGTELYGKTLAVLGLGRIGREVALRMQAFGMK-VIGFDPMV----SVEDAAKL 139
KWDR L + L G+T+ +G G G + RM G V+G DP E KL
Sbjct: 103 KWDRVLPHLSPLKGRTILDVGCGN-GYHM-WRMLGEGAALVVGIDPSELFLCQFEAVRKL 160
Query: 140 -------NIASLGLEDIWPLADYITV 158
++ LG+E + L + TV
Sbjct: 161 LGNDQRAHLLPLGIEQLPALEAFDTV 186
>gnl|CDD|130212 TIGR01142, purT, phosphoribosylglycinamide formyltransferase 2.
This enzyme is an alternative to PurN (TIGR00639)
[Purines, pyrimidines, nucleosides, and nucleotides,
Purine ribonucleotide biosynthesis].
Length = 380
Score = 28.2 bits (63), Expect = 6.0
Identities = 14/39 (35%), Positives = 22/39 (56%), Gaps = 3/39 (7%)
Query: 104 LGLGRIGREVALRMQAFGMKVIGFDPMVSVEDAAKLNIA 142
LG G +G+EVA+ Q G++VI D +A + +A
Sbjct: 5 LGSGELGKEVAIEAQRLGVEVIAVD---RYANAPAMQVA 40
>gnl|CDD|166227 PLN02586, PLN02586, probable cinnamyl alcohol dehydrogenase.
Length = 360
Score = 28.3 bits (63), Expect = 6.5
Identities = 17/35 (48%), Positives = 23/35 (65%), Gaps = 2/35 (5%)
Query: 91 YTGTELYGKTLAVLGLGRIGREVALRM-QAFGMKV 124
Y G GK L V GLG +G VA+++ +AFG+KV
Sbjct: 177 YYGMTEPGKHLGVAGLGGLG-HVAVKIGKAFGLKV 210
>gnl|CDD|217563 pfam03446, NAD_binding_2, NAD binding domain of 6-phosphogluconate
dehydrogenase. The NAD binding domain of
6-phosphogluconate dehydrogenase adopts a Rossmann fold.
Length = 163
Score = 27.4 bits (62), Expect = 6.7
Identities = 8/40 (20%), Positives = 16/40 (40%)
Query: 99 KTLAVLGLGRIGREVALRMQAFGMKVIGFDPMVSVEDAAK 138
+ +GLG +G +AL + G V ++ +
Sbjct: 1 AKIGFIGLGVMGSPMALNLLKAGYTVTVYNRTPEKVEELV 40
>gnl|CDD|223106 COG0027, PurT, Formate-dependent phosphoribosylglycinamide
formyltransferase (GAR transformylase) [Nucleotide
transport and metabolism].
Length = 394
Score = 28.1 bits (63), Expect = 7.3
Identities = 12/30 (40%), Positives = 19/30 (63%)
Query: 99 KTLAVLGLGRIGREVALRMQAFGMKVIGFD 128
+ +LG G +G+EVA+ Q G++VI D
Sbjct: 13 TKVMLLGSGELGKEVAIEAQRLGVEVIAVD 42
>gnl|CDD|234828 PRK00742, PRK00742, chemotaxis-specific methylesterase;
Provisional.
Length = 354
Score = 27.8 bits (63), Expect = 7.4
Identities = 16/67 (23%), Positives = 21/67 (31%), Gaps = 17/67 (25%)
Query: 98 GKTLAVL--GLGRIGREVALRMQAFGMKVIGFD---------PMVSVEDAAKLNIA--SL 144
L V+ G+GR G L M+ G I D P A + L
Sbjct: 282 RNALGVILTGMGRDGAAGLLEMKQAGATTIAQDEASCVVYGMPKA----AIEAGAVDEVL 337
Query: 145 GLEDIWP 151
L+ I
Sbjct: 338 PLDQIAE 344
>gnl|CDD|132172 TIGR03128, RuMP_HxlA, 3-hexulose-6-phosphate synthase. Members of
this protein family are 3-hexulose-6-phosphate synthase
(HPS), or the HPS domain of a fusion protein. This
enzyme is part of the ribulose monophosphate (RuMP)
pathway, which in one direction removes the toxic
metabolite formaldehyde by assimilation into
fructose-6-phosphate. In the other direction, in species
lacking a complete pentose phosphate pathway, the RuMP
pathway yields ribulose-5-phosphate, necessary for
nucleotide biosynthesis, at the cost of also yielding
formaldehyde. These latter species tend usually have a
formaldehyde-activating enzyme to attach formaldehyde to
the C1 carrier tetrahydromethanopterin. In these
species, the enzyme is viewed as a lyase rather than a
synthase and is called D-arabino 3-hexulose 6-phosphate
formaldehyde lyase. Note that there is some overlap in
specificity with the Escherichia coli enzyme
3-keto-L-gulonate 6-phosphate decarboxylase.
Length = 206
Score = 27.3 bits (61), Expect = 9.3
Identities = 20/53 (37%), Positives = 27/53 (50%)
Query: 153 ADYITVHTPLIPQTKNLINAEVLKKCKKGVRVVNVARGGIVDENALLDSLKCG 205
ADYI VHT L Q K E L+ K V+ VA G ++ + + D +K G
Sbjct: 127 ADYIGVHTGLDEQAKGQNPFEDLQTILKLVKEARVAVAGGINLDTIPDVIKLG 179
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
0.316 0.132 0.374
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: 16,270,941
Number of extensions: 1562706
Number of successful extensions: 1990
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1805
Number of HSP's successfully gapped: 165
Length of query: 333
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 236
Effective length of database: 6,635,264
Effective search space: 1565922304
Effective search space used: 1565922304
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 59 (26.3 bits)