RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy755
(183 letters)
>gnl|CDD|224995 COG2084, MmsB, 3-hydroxyisobutyrate dehydrogenase and related
beta-hydroxyacid dehydrogenases [Lipid metabolism].
Length = 286
Score = 212 bits (542), Expect = 1e-69
Identities = 87/184 (47%), Positives = 116/184 (63%), Gaps = 1/184 (0%)
Query: 1 MGSHMARNLLKNGHDVIVYDKNTDAS-QTLAKEGANMALSLSTLASGAEFIISMLPASQD 59
MGS MA NLLK GH+V VY++ + + + LA GA +A S + A+ A+ +I+MLP
Sbjct: 11 MGSPMAANLLKAGHEVTVYNRTPEKAAELLAAAGATVAASPAEAAAEADVVITMLPDDAA 70
Query: 60 VLDAYDGSDGILKHAKPGVIVIDSSTVDPQVPQTLSNLAREKQITFLDAPVSGGTKAAQE 119
V G +G+L+ KPG IVID ST+ P+ + L+ K + FLDAPVSGG A
Sbjct: 71 VRAVLFGENGLLEGLKPGAIVIDMSTISPETARELAAALAAKGLEFLDAPVSGGVPGAAA 130
Query: 120 ATLTFMVGGDKSSLEKAKPILKCMGRNIVHCGDSGNGQVAKLCNNMLLGVTMMGVAEAMN 179
TLT MVGGD + E+AKP+L+ MG+NIVH G G GQ AKL NN+LL + +AEA+
Sbjct: 131 GTLTIMVGGDAEAFERAKPVLEAMGKNIVHVGPVGAGQAAKLANNILLAGNIAALAEALA 190
Query: 180 LGVK 183
L K
Sbjct: 191 LAEK 194
>gnl|CDD|130753 TIGR01692, HIBADH, 3-hydroxyisobutyrate dehydrogenase.
3-hydroxyisobutyrate dehydrogenase is an enzyme that
catalyzes the NAD+-dependent oxidation of
3-hydroxyisobutyrate to methylmalonate semialdehyde of
the valine catabolism pathway. In Pseudomonas
aeruginosa, 3-hydroxyisobutyrate dehydrogenase (mmsB) is
co-induced with methylmalonate-semialdehyde
dehydrogenase (mmsA) when grown on medium containing
valine as the sole carbon source. The positive
transcriptional regulator of this operon (mmsR) is
located upstream of these genes and has been identified
as a member of the XylS/AraC family of transcriptional
regulators. 3-hydroxyisobutyrate dehydrogenase shares
high sequence homology to the characterized
3-hydroxyisobutyrate dehydrogenase from rat liver with
conservation of proposed NAD+ binding residues at the
N-terminus (G-8,10,13,24 and D-31). This enzyme belongs
to the 3-hydroxyacid dehydrogenase family, sharing a
common evolutionary origin and enzymatic mechanism with
6-phosphogluconate. HIBADH exhibits sequence similarity
to the NAD binding domain of 6-phosphogluconate
dehydrogenase above trusted (pfam03446) [Energy
metabolism, Amino acids and amines].
Length = 288
Score = 212 bits (542), Expect = 1e-69
Identities = 95/183 (51%), Positives = 116/183 (63%)
Query: 1 MGSHMARNLLKNGHDVIVYDKNTDASQTLAKEGANMALSLSTLASGAEFIISMLPASQDV 60
MG MA NLLK GH V V+D DA + GA A S + A GA+ +I+MLPA Q V
Sbjct: 7 MGGPMAANLLKAGHPVRVFDLFPDAVEEAVAAGAQAAASPAEAAEGADRVITMLPAGQHV 66
Query: 61 LDAYDGSDGILKHAKPGVIVIDSSTVDPQVPQTLSNLAREKQITFLDAPVSGGTKAAQEA 120
+ Y G +GIL G ++ID ST+DP + L+ LA F+DAPVSGG A+
Sbjct: 67 ISVYSGDEGILPKVAKGSLLIDCSTIDPDSARKLAELAAAHGAVFMDAPVSGGVGGARAG 126
Query: 121 TLTFMVGGDKSSLEKAKPILKCMGRNIVHCGDSGNGQVAKLCNNMLLGVTMMGVAEAMNL 180
TLTFMVGG A+P+L MGRNIVHCGD G GQ AK+CNNMLLG++M+G AEAM L
Sbjct: 127 TLTFMVGGVAEEFAAAEPVLGPMGRNIVHCGDHGAGQAAKICNNMLLGISMIGTAEAMAL 186
Query: 181 GVK 183
G K
Sbjct: 187 GEK 189
>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 = 184 bits (469), Expect = 4e-60
Identities = 67/150 (44%), Positives = 90/150 (60%)
Query: 1 MGSHMARNLLKNGHDVIVYDKNTDASQTLAKEGANMALSLSTLASGAEFIISMLPASQDV 60
MGS MA NLLK G+ V VY++ + + L EGA A S + + A+ +I+M+PA V
Sbjct: 11 MGSPMALNLLKAGYTVTVYNRTPEKVEELVAEGAVGAASPAEFVASADVVITMVPAGAAV 70
Query: 61 LDAYDGSDGILKHAKPGVIVIDSSTVDPQVPQTLSNLAREKQITFLDAPVSGGTKAAQEA 120
G DG+L KPG I+ID ST DP + + EK I FLDAPVSGG + A+
Sbjct: 71 DAVILGEDGLLPGLKPGDIIIDGSTSDPDDTRRRAKELAEKGIHFLDAPVSGGEEGAEAG 130
Query: 121 TLTFMVGGDKSSLEKAKPILKCMGRNIVHC 150
TL+ MVGGD+ + E+ KPIL+ MG + H
Sbjct: 131 TLSIMVGGDEEAFERVKPILEAMGACVTHY 160
>gnl|CDD|183197 PRK11559, garR, tartronate semialdehyde reductase; Provisional.
Length = 296
Score = 168 bits (427), Expect = 4e-52
Identities = 72/183 (39%), Positives = 111/183 (60%)
Query: 1 MGSHMARNLLKNGHDVIVYDKNTDASQTLAKEGANMALSLSTLASGAEFIISMLPASQDV 60
MG M++NLLK G+ ++VYD+N +A + GA A + +A + II+MLP S V
Sbjct: 13 MGKPMSKNLLKAGYSLVVYDRNPEAVAEVIAAGAETASTAKAVAEQCDVIITMLPNSPHV 72
Query: 61 LDAYDGSDGILKHAKPGVIVIDSSTVDPQVPQTLSNLAREKQITFLDAPVSGGTKAAQEA 120
+ G +GI++ AKPG +VID S++ P + ++ + K I LDAPVSGG A +
Sbjct: 73 KEVALGENGIIEGAKPGTVVIDMSSIAPLASREIAAALKAKGIEMLDAPVSGGEPKAIDG 132
Query: 121 TLTFMVGGDKSSLEKAKPILKCMGRNIVHCGDSGNGQVAKLCNNMLLGVTMMGVAEAMNL 180
TL+ MVGGDK+ +K ++K M ++VH GD G G V KL N +++ + + ++EA+ L
Sbjct: 133 TLSVMVGGDKAIFDKYYDLMKAMAGSVVHTGDIGAGNVTKLANQVIVALNIAAMSEALVL 192
Query: 181 GVK 183
K
Sbjct: 193 ATK 195
>gnl|CDD|130569 TIGR01505, tartro_sem_red, 2-hydroxy-3-oxopropionate reductase.
This model represents 2-hydroxy-3-oxopropionate
reductase (EC 1.1.1.60), also called tartronate
semialdehyde reductase. It follows glyoxylate
carboligase and precedes glycerate kinase in D-glycerate
pathway of glyoxylate degradation. The eventual product,
3-phosphoglycerate, is an intermediate of glycolysis and
is readily metabolized. Tartronic semialdehyde, the
substrate of this enzyme, may also come from other
pathways, such as D-glucarate catabolism.
Length = 291
Score = 149 bits (378), Expect = 7e-45
Identities = 65/183 (35%), Positives = 106/183 (57%)
Query: 1 MGSHMARNLLKNGHDVIVYDKNTDASQTLAKEGANMALSLSTLASGAEFIISMLPASQDV 60
MGS M+ NL K G+ + V + + L GA A + + A+ I +M+P S V
Sbjct: 10 MGSPMSINLAKAGYQLHVTTIGPEVADELLAAGAVTAETARQVTEQADVIFTMVPDSPQV 69
Query: 61 LDAYDGSDGILKHAKPGVIVIDSSTVDPQVPQTLSNLAREKQITFLDAPVSGGTKAAQEA 120
+ G +GI++ AKPG ++D S++ P + + +EK I +LDAPVSGG A E
Sbjct: 70 EEVAFGENGIIEGAKPGKTLVDMSSISPIESKRFAKAVKEKGIDYLDAPVSGGEIGAIEG 129
Query: 121 TLTFMVGGDKSSLEKAKPILKCMGRNIVHCGDSGNGQVAKLCNNMLLGVTMMGVAEAMNL 180
TL+ MVGGD++ ++ KP+ + +G+NIV G +G+GQ K+ N +++ + + V+EA+
Sbjct: 130 TLSIMVGGDQAVFDRVKPLFEALGKNIVLVGGNGDGQTCKVANQIIVALNIEAVSEALVF 189
Query: 181 GVK 183
K
Sbjct: 190 ASK 192
>gnl|CDD|185358 PRK15461, PRK15461, NADH-dependent gamma-hydroxybutyrate
dehydrogenase; Provisional.
Length = 296
Score = 125 bits (315), Expect = 1e-35
Identities = 62/166 (37%), Positives = 85/166 (51%)
Query: 1 MGSHMARNLLKNGHDVIVYDKNTDASQTLAKEGANMALSLSTLASGAEFIISMLPASQDV 60
MGS MA NLLK GH + V+D N A L +GA A S + A+GAEF+I+MLP V
Sbjct: 12 MGSPMASNLLKQGHQLQVFDVNPQAVDALVDKGATPAASPAQAAAGAEFVITMLPNGDLV 71
Query: 61 LDAYDGSDGILKHAKPGVIVIDSSTVDPQVPQTLSNLAREKQITFLDAPVSGGTKAAQEA 120
G +G+ + +VID ST+ P L + K + +D PV + A
Sbjct: 72 RSVLFGENGVCEGLSRDALVIDMSTIHPLQTDKLIADMQAKGFSMMDVPVGRTSDNAITG 131
Query: 121 TLTFMVGGDKSSLEKAKPILKCMGRNIVHCGDSGNGQVAKLCNNML 166
TL + GG +E+A PIL MG +++ G G G KL NN +
Sbjct: 132 TLLLLAGGTAEQVERATPILMAMGNELINAGGPGMGIRVKLINNYM 177
>gnl|CDD|236582 PRK09599, PRK09599, 6-phosphogluconate dehydrogenase-like protein;
Reviewed.
Length = 301
Score = 101 bits (254), Expect = 3e-26
Identities = 60/177 (33%), Positives = 87/177 (49%), Gaps = 23/177 (12%)
Query: 1 MGSHMARNLLKNGHDVIVYDKNTDASQTLAKEGANMALSLSTLAS--GAEFII-SMLPAS 57
MG +MAR LL+ GH+V+ YD+N +A + LA+EGA A SL L + A ++ M+PA
Sbjct: 11 MGGNMARRLLRGGHEVVGYDRNPEAVEALAEEGATGADSLEELVAKLPAPRVVWLMVPAG 70
Query: 58 Q---DVLDAYDGSDGILKHAKPGVIVID---SSTVDPQVPQTLSNLAREKQITFLDAPVS 111
+ +D + PG IVID S D + L EK I F+D S
Sbjct: 71 EITDATIDE------LAPLLSPGDIVIDGGNSYYKDDIR---RAELLAEKGIHFVDVGTS 121
Query: 112 GGTKAAQEATLTFMVGGDKSSLEKAKPILKCM----GRNIVHCGDSGNGQVAKLCNN 164
GG + M+GGDK ++E+ +PI K + +H G G G K+ +N
Sbjct: 122 GGVWGLERG-YCLMIGGDKEAVERLEPIFKALAPRAEDGYLHAGPVGAGHFVKMVHN 177
>gnl|CDD|185019 PRK15059, PRK15059, tartronate semialdehyde reductase; Provisional.
Length = 292
Score = 100 bits (251), Expect = 4e-26
Identities = 58/183 (31%), Positives = 97/183 (53%), Gaps = 1/183 (0%)
Query: 1 MGSHMARNLLKNGHDVIVYDKNTDASQTLAKEGANMALSLSTLASGAEFIISMLPASQDV 60
MG+ MA NL + GH + V A + L GA + + ++ I M+P + V
Sbjct: 11 MGTPMAINLARAGHQLHVTTIGPVADELL-SLGAVSVETARQVTEASDIIFIMVPDTPQV 69
Query: 61 LDAYDGSDGILKHAKPGVIVIDSSTVDPQVPQTLSNLAREKQITFLDAPVSGGTKAAQEA 120
+ G +G K + G ++D S++ P + + E +LDAPVSGG A+E
Sbjct: 70 EEVLFGENGCTKASLKGKTIVDMSSISPIETKRFARQVNELGGDYLDAPVSGGEIGAREG 129
Query: 121 TLTFMVGGDKSSLEKAKPILKCMGRNIVHCGDSGNGQVAKLCNNMLLGVTMMGVAEAMNL 180
TL+ MVGGD++ E+ KP+ + +G+NI G +G+GQ K+ N +++ + + V+EA+
Sbjct: 130 TLSIMVGGDEAVFERVKPLFELLGKNITLVGGNGDGQTCKVANQIIVALNIEAVSEALLF 189
Query: 181 GVK 183
K
Sbjct: 190 ASK 192
>gnl|CDD|223954 COG1023, Gnd, Predicted 6-phosphogluconate dehydrogenase
[Carbohydrate transport and metabolism].
Length = 300
Score = 95.9 bits (239), Expect = 3e-24
Identities = 64/186 (34%), Positives = 91/186 (48%), Gaps = 10/186 (5%)
Query: 1 MGSHMARNLLKNGHDVIVYDKNTDASQTLAKEGANMALSLSTLAS--GAEFII-SMLPAS 57
MG+++ R LL GHDV+ YD N A + L EGA A SL L + A I+ M+PA
Sbjct: 11 MGANLVRRLLDGGHDVVGYDVNQTAVEELKDEGATGAASLDELVAKLSAPRIVWLMVPAG 70
Query: 58 QDVLDAYDGSDGILKHAKPGVIVIDSSTVDPQVPQTLSNLAREKQITFLDAPVSGGTKAA 117
D +L G IVID + + + L EK I FLD SGG A
Sbjct: 71 DITDAVIDDLAPLL---SAGDIVIDGGNSNYKDSLRRAKLLAEKGIHFLDVGTSGGVWGA 127
Query: 118 QEATLTFMVGGDKSSLEKAKPILK--CMGRN-IVHCGDSGNGQVAKLCNNMLLGVTMMGV 174
+ M+GGD+ ++E+ +PI K G + ++CG SG+G K+ +N + M +
Sbjct: 128 ERG-YCLMIGGDEEAVERLEPIFKALAPGEDGYLYCGPSGSGHFVKMVHNGIEYGMMQAI 186
Query: 175 AEAMNL 180
AE L
Sbjct: 187 AEGFEL 192
>gnl|CDD|215463 PLN02858, PLN02858, fructose-bisphosphate aldolase.
Length = 1378
Score = 90.3 bits (224), Expect = 2e-21
Identities = 58/186 (31%), Positives = 81/186 (43%), Gaps = 3/186 (1%)
Query: 1 MGSHMARNLLKNGHDVIVYDKNTDASQTLAKEGANMALSLSTLASGAEFIISMLPASQDV 60
MG MA +LLK+ V YD G S + +A + ++ M+
Sbjct: 335 MGFGMASHLLKSNFSVCGYDVYKPTLVRFENAGGLAGNSPAEVAKDVDVLVIMVANEVQA 394
Query: 61 LDAYDGSDGILKHAKPGVIVIDSSTVDPQ-VPQTLSNLARE-KQITFLDAPVSGGTKAAQ 118
+ G G + G ++ SSTV P V Q L E + I +DAPVSGG K A
Sbjct: 395 ENVLFGDLGAVSALPAGASIVLSSTVSPGFVIQLERRLENEGRDIKLVDAPVSGGVKRAA 454
Query: 119 EATLTFMVGGDKSSLEKAKPILKCMGRNI-VHCGDSGNGQVAKLCNNMLLGVTMMGVAEA 177
TLT M G +L+ A +L + + V G G G K+ N +L GV + AEA
Sbjct: 455 MGTLTIMASGTDEALKSAGSVLSALSEKLYVIKGGCGAGSGVKMVNQLLAGVHIASAAEA 514
Query: 178 MNLGVK 183
M G +
Sbjct: 515 MAFGAR 520
Score = 80.3 bits (198), Expect = 7e-18
Identities = 51/186 (27%), Positives = 88/186 (47%), Gaps = 3/186 (1%)
Query: 1 MGSHMARNLLKNGHDVIVYDKNTDASQTLAKEGANMALSLSTLASGAEFIISMLPASQDV 60
+ +A +LL++G V ++ +T + + G + S + A A ++ +L V
Sbjct: 15 LSFELASSLLRSGFKVQAFEISTPLMEKFCELGGHRCDSPAEAAKDAAALVVVLSHPDQV 74
Query: 61 LDAYDGSDGILKHAKPGVIVIDSSTVDPQVPQTLSN-LAREKQITFL-DAPVSGGTKAAQ 118
D + G +G K + G +++ ST+ P Q L L K+ FL DA VS G
Sbjct: 75 DDVFFGDEGAAKGLQKGAVILIRSTILPLQLQKLEKKLTERKEQIFLVDAYVSKGMSDLL 134
Query: 119 EATLTFMVGGDKSSLEKAKPILKCMGRNI-VHCGDSGNGQVAKLCNNMLLGVTMMGVAEA 177
L + G ++ +A+P L M + + G+ G G K+ N +L G+ ++ AEA
Sbjct: 135 NGKLMIIASGRSDAITRAQPFLSAMCQKLYTFEGEIGAGSKVKMVNELLEGIHLVASAEA 194
Query: 178 MNLGVK 183
M LGV+
Sbjct: 195 MALGVR 200
>gnl|CDD|233163 TIGR00872, gnd_rel, 6-phosphogluconate dehydrogenase
(decarboxylating). This family resembles a larger
family (gnd) of bacterial and eukaryotic
6-phosphogluconate dehydrogenases but differs from it by
a deep split in a UPGMA similarity clustering tree and
the lack of a central region of about 140 residues.
Among complete genomes, it is found is found in Bacillus
subtilis and Mycobacterium tuberculosis, both of which
also contain gnd, and in Aquifex aeolicus. The protein
from Methylobacillus flagellatus KT has been
characterized as a decarboxylating 6-phosphogluconate
dehydrogenase as part of an unusual formaldehyde
oxidation cycle. In some sequenced organisms members of
this family are the sole 6-phosphogluconate
dehydrogenase present and are probably active in the
pentose phosphate cycle [Energy metabolism, Pentose
phosphate pathway].
Length = 298
Score = 85.3 bits (211), Expect = 3e-20
Identities = 51/190 (26%), Positives = 82/190 (43%), Gaps = 19/190 (10%)
Query: 1 MGSHMARNLLKNGHDVIVYDKNTDASQTLAKEGANMALSL---STLASGAEFIISMLPAS 57
MG+++ R L K GHD + YD + DA + + ++ +L S S + M+P
Sbjct: 11 MGANIVRRLAKRGHDCVGYDHDQDAVKAMKEDRTTGVANLRELSQRLSAPRVVWVMVPHG 70
Query: 58 QDVLDAYDGSDGILKHAKP----GVIVIDSSTVDPQVPQTLSNLAREKQITFLDAPVSGG 113
D +L+ P G IVID + L +EK I LD SGG
Sbjct: 71 --------IVDAVLEELAPTLEKGDIVIDGGNSYYKDSLRRYKLLKEKGIHLLDCGTSGG 122
Query: 114 TKAAQEATLTFMVGGDKSSLEKAKPILKCMG---RNIVHCGDSGNGQVAKLCNNMLLGVT 170
E FM+GGD + +A+P+ + + ++CG G+G K+ +N +
Sbjct: 123 VWGR-ERGYCFMIGGDGEAFARAEPLFADVAPEEQGYLYCGPCGSGHFVKMVHNGIEYGM 181
Query: 171 MMGVAEAMNL 180
M +AE +
Sbjct: 182 MAAIAEGFEI 191
>gnl|CDD|237116 PRK12490, PRK12490, 6-phosphogluconate dehydrogenase-like protein;
Reviewed.
Length = 299
Score = 84.4 bits (209), Expect = 6e-20
Identities = 54/186 (29%), Positives = 80/186 (43%), Gaps = 10/186 (5%)
Query: 1 MGSHMARNLLKNGHDVIVYDKNTDASQTLAKEGANMALSLSTLAS---GAEFIISMLPAS 57
MG +MA L ++GH+V+ YD N +A K G SL L S I M+PA
Sbjct: 11 MGGNMAERLREDGHEVVGYDVNQEAVDVAGKLGITARHSLEELVSKLEAPRTIWVMVPAG 70
Query: 58 QDVLDAYDGSDGILKHAKPGVIVIDSSTVDPQVPQTLSNLAREKQITFLDAPVSGGTKAA 117
+ +L PG IV+D + + E+ I ++D SGG
Sbjct: 71 EVTESVIKDLYPLL---SPGDIVVDGGNSRYKDDLRRAEELAERGIHYVDCGTSGGVWGL 127
Query: 118 QEATLTFMVGGDKSSLEKAKPILKCM---GRNIVHCGDSGNGQVAKLCNNMLLGVTMMGV 174
+ MVGGDK ++ +P+ K + G VH G G+G K+ +N + M
Sbjct: 128 RNG-YCLMVGGDKEIYDRLEPVFKALAPEGPGYVHAGPVGSGHFLKMVHNGIEYGMMQAY 186
Query: 175 AEAMNL 180
AE + L
Sbjct: 187 AEGLEL 192
>gnl|CDD|223439 COG0362, Gnd, 6-phosphogluconate dehydrogenase [Carbohydrate
transport and metabolism].
Length = 473
Score = 49.9 bits (120), Expect = 1e-07
Identities = 46/151 (30%), Positives = 70/151 (46%), Gaps = 18/151 (11%)
Query: 1 MGSHMARNLLKNGHDVIVYDKNTDASQTLAKEGANM-----ALSLSTLASGAE---FIIS 52
MGS++A N+ +G+ V VY++ T+ + E A A S+ + E I+
Sbjct: 14 MGSNLALNIADHGYTVAVYNRTTEKTDEFLAERAKGKNIVPAYSIEEFVASLEKPRKILL 73
Query: 53 MLPASQDVLDAYDGSDGILKHAKPGVIVID---SSTVDPQVPQTLSNLAREKQITFLDAP 109
M+ A V DA + +L + G I+ID S D + L+ EK I F+
Sbjct: 74 MVKAGTPV-DAV--IEQLLPLLEKGDIIIDGGNSHYKDTI--RRNKELS-EKGILFVGMG 127
Query: 110 VSGGTKAAQEATLTFMVGGDKSSLEKAKPIL 140
VSGG + A+ + M GG K + E PIL
Sbjct: 128 VSGGEEGARHGP-SIMPGGQKEAYELVAPIL 157
>gnl|CDD|129951 TIGR00873, gnd, 6-phosphogluconate dehydrogenase (decarboxylating).
This model does not specify whether the cofactor is
NADP only (EC 1.1.1.44), NAD only, or both. The model
does not assign an EC number for that reason [Energy
metabolism, Pentose phosphate pathway].
Length = 467
Score = 45.4 bits (108), Expect = 4e-06
Identities = 38/149 (25%), Positives = 62/149 (41%), Gaps = 14/149 (9%)
Query: 1 MGSHMARNLLKNGHDVIVYDKNTDASQTLAKEGANMALSLSTLASGAEF---------II 51
MGS++A N+ +G V VY++ + + E A + S EF I+
Sbjct: 10 MGSNLALNMADHGFTVSVYNRTPEKTDEFLAEHAK-GKKIVGAYSIEEFVQSLERPRKIM 68
Query: 52 SMLPASQDVLDAYDGSDGILKHAKPGVIVIDSSTVDPQVPQTLSNLAREKQITFLDAPVS 111
M+ A V DA + +L + G I+ID + + K I F+ + VS
Sbjct: 69 LMVKAGAPV-DAV--INQLLPLLEKGDIIIDGGNSHYPDTERRYKELKAKGILFVGSGVS 125
Query: 112 GGTKAAQEATLTFMVGGDKSSLEKAKPIL 140
GG + A++ + M GG + PI
Sbjct: 126 GGEEGARKGP-SIMPGGSAEAWPLVAPIF 153
>gnl|CDD|240287 PTZ00142, PTZ00142, 6-phosphogluconate dehydrogenase; Provisional.
Length = 470
Score = 44.4 bits (105), Expect = 1e-05
Identities = 40/178 (22%), Positives = 74/178 (41%), Gaps = 17/178 (9%)
Query: 1 MGSHMARNLLKNGHDVIVYDKNTDASQTLAKEGANMALSLSTLASGAEFIIS-------- 52
MG ++A N+ G + VY++ + ++ K+ + + E + S
Sbjct: 12 MGQNLALNIASRGFKISVYNRTYEKTEEFVKKAKEGNTRVKGYHTLEELVNSLKKPRKVI 71
Query: 53 MLPASQDVLDAYDGSDGILKHAKPGVIVIDSSTVDPQVPQTLSNLAREKQITFLDAPVSG 112
+L + + +D D +L + G I+ID + EK I +L VSG
Sbjct: 72 LLIKAGEAVDET--IDNLLPLLEKGDIIIDGGNEWYLNTERRIKRCEEKGILYLGMGVSG 129
Query: 113 GTKAAQEATLTFMVGGDKSSLEKAKPIL-KCMGRN-----IVHCGDSGNGQVAKLCNN 164
G + A+ + M GG+K + + K IL KC + + + G +G K+ +N
Sbjct: 130 GEEGARYGP-SLMPGGNKEAYDHVKDILEKCSAKVGDSPCVTYVGPGSSGHYVKMVHN 186
>gnl|CDD|236453 PRK09287, PRK09287, 6-phosphogluconate dehydrogenase; Validated.
Length = 459
Score = 43.2 bits (103), Expect = 3e-05
Identities = 42/166 (25%), Positives = 67/166 (40%), Gaps = 46/166 (27%)
Query: 1 MGSHMARNLLKNGHDVIVYDKNTDASQTLAKE---GANM--ALSLSTLASGAE---FIIS 52
MG ++A N+ +G+ V VY++ + + E G + A +L + E I+
Sbjct: 1 MGKNLALNIASHGYTVAVYNRTPEKTDEFLAEEGKGKKIVPAYTLEEFVASLEKPRKILL 60
Query: 53 MLPASQ---DVLDAYDGSDGILKHAKPGVIVIDS------STVDPQVPQTLSNLAREKQ- 102
M+ A V++ +L + G I+ID T+ REK+
Sbjct: 61 MVKAGAPVDAVIEQ------LLPLLEKGDIIIDGGNSNYKDTI-----------RREKEL 103
Query: 103 ----ITFLDAPVSGGTKAAQEATLT---FMVGGDKSSLEKAKPILK 141
I F+ VSGG + A L M GG K + E PIL+
Sbjct: 104 AEKGIHFIGMGVSGGEEGA----LHGPSIMPGGQKEAYELVAPILE 145
>gnl|CDD|223364 COG0287, TyrA, Prephenate dehydrogenase [Amino acid transport and
metabolism].
Length = 279
Score = 37.7 bits (88), Expect = 0.002
Identities = 23/93 (24%), Positives = 37/93 (39%), Gaps = 13/93 (13%)
Query: 1 MGSHMARNLLKNGHDVIVYDKNTDASQTLAKEGANMALSLST-----LASGAEFIISMLP 55
MG +AR L + G V + ++ A+ A + L+ A+ A+ +I +P
Sbjct: 14 MGGSLARALKEAGLVVRIIGRDRSAATLKAALELGVIDELTVAGLAEAAAEADLVIVAVP 73
Query: 56 ASQ--DVLDAYDGSDGILKHAKPGVIVIDSSTV 86
+VL H K G IV D +V
Sbjct: 74 IEATEEVLKELA------PHLKKGAIVTDVGSV 100
>gnl|CDD|224012 COG1087, GalE, UDP-glucose 4-epimerase [Cell envelope biogenesis,
outer membrane].
Length = 329
Score = 36.8 bits (86), Expect = 0.003
Identities = 12/19 (63%), Positives = 14/19 (73%)
Query: 2 GSHMARNLLKNGHDVIVYD 20
GSH R LLK GH+V+V D
Sbjct: 13 GSHTVRQLLKTGHEVVVLD 31
>gnl|CDD|215200 PLN02350, PLN02350, phosphogluconate dehydrogenase
(decarboxylating).
Length = 493
Score = 35.8 bits (83), Expect = 0.009
Identities = 42/190 (22%), Positives = 81/190 (42%), Gaps = 14/190 (7%)
Query: 1 MGSHMARNLLKNGHDVIVYDKNTD-ASQTLAKEGANMALSLSTLASGAEFIISMLPASQD 59
MG ++A N+ + G + VY++ T +T+ + L L +F++S+
Sbjct: 17 MGQNLALNIAEKGFPISVYNRTTSKVDETVERAKKEGNLPLYGFKDPEDFVLSIQKPRSV 76
Query: 60 VLDAYDGS------DGILKHAKPGVIVIDSSTVDPQVPQTLSNLAREKQITFLDAPVSGG 113
++ G+ + ++ +PG +ID + + A EK + +L VSGG
Sbjct: 77 IILVKAGAPVDQTIKALSEYMEPGDCIIDGGNEWYENTERRIKEAAEKGLLYLGMGVSGG 136
Query: 114 TKAAQEATLTFMVGGDKSSLEKAKPIL-KCM-----GRNIVHCGDSGNGQVAKLCNNMLL 167
+ A+ + M GG + + + IL K G + + G G G K+ +N +
Sbjct: 137 EEGARNGP-SLMPGGSFEAYKNIEDILEKVAAQVDDGPCVTYIGPGGAGNFVKMVHNGIE 195
Query: 168 GVTMMGVAEA 177
M ++EA
Sbjct: 196 YGDMQLISEA 205
>gnl|CDD|187566 cd05256, UDP_AE_SDR_e, UDP-N-acetylglucosamine 4-epimerase,
extended (e) SDRs. This subgroup contains
UDP-N-acetylglucosamine 4-epimerase of Pseudomonas
aeruginosa, WbpP, an extended SDR, that catalyzes the
NAD+ dependent conversion of UDP-GlcNAc and UDPGalNA to
UDP-Glc and UDP-Gal. This subgroup has the
characteristic active site tetrad and NAD-binding motif
of the extended SDRs. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids. Extended SDRs are a diverse collection
of proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and
their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 304
Score = 35.3 bits (82), Expect = 0.010
Identities = 11/19 (57%), Positives = 14/19 (73%)
Query: 2 GSHMARNLLKNGHDVIVYD 20
GSH+ LL+ GH+VIV D
Sbjct: 12 GSHLVERLLERGHEVIVLD 30
>gnl|CDD|223643 COG0569, TrkA, K+ transport systems, NAD-binding component
[Inorganic ion transport and metabolism].
Length = 225
Score = 34.5 bits (80), Expect = 0.015
Identities = 8/32 (25%), Positives = 19/32 (59%)
Query: 1 MGSHMARNLLKNGHDVIVYDKNTDASQTLAKE 32
+G +AR L + GH+V++ D++ + + +
Sbjct: 11 VGRSVARELSEEGHNVVLIDRDEERVEEFLAD 42
>gnl|CDD|223528 COG0451, WcaG, Nucleoside-diphosphate-sugar epimerases [Cell
envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 314
Score = 34.9 bits (80), Expect = 0.016
Identities = 15/49 (30%), Positives = 19/49 (38%)
Query: 2 GSHMARNLLKNGHDVIVYDKNTDASQTLAKEGANMALSLSTLASGAEFI 50
GSH+ LL GHDV D+ D L + L L+ E
Sbjct: 13 GSHLVERLLAAGHDVRGLDRLRDGLDPLLSGVEFVVLDLTDRDLVDELA 61
>gnl|CDD|213592 TIGR01179, galE, UDP-glucose-4-epimerase GalE. Alternate name:
UDPgalactose 4-epimerase This enzyme interconverts
UDP-glucose and UDP-galactose. A set of related
proteins, some of which are tentatively identified as
UDP-glucose-4-epimerase in Thermotoga maritima,
Bacillus halodurans, and several archaea, but deeply
branched from this set and lacking experimental
evidence, are excluded from This model and described by
a separate model [Energy metabolism, Sugars].
Length = 328
Score = 34.6 bits (80), Expect = 0.018
Identities = 10/19 (52%), Positives = 15/19 (78%)
Query: 2 GSHMARNLLKNGHDVIVYD 20
GSH R LL++GH+V++ D
Sbjct: 12 GSHTVRQLLESGHEVVILD 30
>gnl|CDD|187558 cd05247, UDP_G4E_1_SDR_e, UDP-glucose 4 epimerase, subgroup 1,
extended (e) SDRs. UDP-glucose 4 epimerase (aka
UDP-galactose-4-epimerase), is a homodimeric extended
SDR. It catalyzes the NAD-dependent conversion of
UDP-galactose to UDP-glucose, the final step in Leloir
galactose synthesis. This subgroup has the
characteristic active site tetrad and NAD-binding motif
of the extended SDRs. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids. Extended SDRs are a diverse collection
of proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and
their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 323
Score = 34.4 bits (80), Expect = 0.020
Identities = 10/39 (25%), Positives = 18/39 (46%)
Query: 2 GSHMARNLLKNGHDVIVYDKNTDASQTLAKEGANMALSL 40
GSH LL+ G+DV+V D ++ + + +
Sbjct: 12 GSHTVVELLEAGYDVVVLDNLSNGHREALPRIEKIRIEF 50
>gnl|CDD|202773 pfam03807, F420_oxidored, NADP oxidoreductase coenzyme
F420-dependent.
Length = 93
Score = 33.0 bits (76), Expect = 0.020
Identities = 20/85 (23%), Positives = 34/85 (40%), Gaps = 8/85 (9%)
Query: 1 MGSHMARNLLKNGHDVIV-YDKNTDASQTLAKE-GAN-MALSLSTLASGAEFIISMLPAS 57
MG +AR L GH+V++ +N + + LA+E G A+S A+ + +
Sbjct: 10 MGEALARGLAAAGHEVVIANSRNPEKAAALAEELGVKATAVSNEEAVEEADVVFLAVK-- 67
Query: 58 QDVLDAYDGSDGILKHAKPGVIVID 82
+ L G +VI
Sbjct: 68 ---PEDAPEVLAELADLLKGKLVIS 89
>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 = 32.9 bits (76), Expect = 0.023
Identities = 12/35 (34%), Positives = 20/35 (57%)
Query: 1 MGSHMARNLLKNGHDVIVYDKNTDASQTLAKEGAN 35
+G +A L + G DV+V DK+ + + L +EG
Sbjct: 9 VGRSLAEELREGGPDVVVIDKDPERVEELREEGVP 43
>gnl|CDD|212494 cd08946, SDR_e, extended (e) SDRs. Extended SDRs are distinct
from classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids. Extended SDRs are a diverse collection
of proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and
their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 200
Score = 33.8 bits (78), Expect = 0.026
Identities = 11/19 (57%), Positives = 15/19 (78%)
Query: 2 GSHMARNLLKNGHDVIVYD 20
GSH+ R LL+ GH+V+V D
Sbjct: 11 GSHLVRRLLERGHEVVVID 29
>gnl|CDD|191263 pfam05368, NmrA, NmrA-like family. NmrA is a negative
transcriptional regulator involved in the
post-translational modification of the transcription
factor AreA. NmrA is part of a system controlling
nitrogen metabolite repression in fungi. This family
only contains a few sequences as iteration results in
significant matches to other Rossmann fold families.
Length = 232
Score = 33.4 bits (77), Expect = 0.045
Identities = 15/68 (22%), Positives = 26/68 (38%), Gaps = 9/68 (13%)
Query: 2 GSHMARNLLKNGHDV--IVYDKNTDASQTLAKEGANMAL-------SLSTLASGAEFIIS 52
G + R LK GH V +V D ++ +++L G + SL G + + S
Sbjct: 11 GGSVVRASLKAGHPVRALVRDPKSELAKSLKAAGVELVEGDLDDHESLVEALKGVDVVFS 70
Query: 53 MLPASQDV 60
+
Sbjct: 71 VTGFWLSK 78
>gnl|CDD|183489 PRK12384, PRK12384, sorbitol-6-phosphate dehydrogenase;
Provisional.
Length = 259
Score = 31.9 bits (73), Expect = 0.14
Identities = 18/83 (21%), Positives = 37/83 (44%), Gaps = 8/83 (9%)
Query: 1 MGSHMARNLLKNGHDVIVYDKNTDASQTLAKE-----GANMALSLSTLASGAEFIISMLP 55
+G+ + L + G+ V V D N++ + +A+E G MA A+ + ++++
Sbjct: 14 LGAFLCHGLAEEGYRVAVADINSEKAANVAQEINAEYGEGMAYGFGADATSEQSVLALSR 73
Query: 56 ASQDVLDAYD---GSDGILKHAK 75
++ D + GI K A
Sbjct: 74 GVDEIFGRVDLLVYNAGIAKAAF 96
>gnl|CDD|181517 PRK08642, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 253
Score = 32.0 bits (73), Expect = 0.14
Identities = 16/60 (26%), Positives = 33/60 (55%), Gaps = 1/60 (1%)
Query: 1 MGSHMARNLLKNGHDVIV-YDKNTDASQTLAKEGANMALSLSTLASGAEFIISMLPASQD 59
+G+ +AR + G V+V Y ++ DA++ LA E + A++L + E + +M + +
Sbjct: 17 LGAAIARAFAREGARVVVNYHQSEDAAEALADELGDRAIALQADVTDREQVQAMFATATE 76
>gnl|CDD|236541 PRK09496, trkA, potassium transporter peripheral membrane
component; Reviewed.
Length = 453
Score = 32.0 bits (74), Expect = 0.16
Identities = 8/24 (33%), Positives = 12/24 (50%)
Query: 2 GSHMARNLLKNGHDVIVYDKNTDA 25
G +A NL +DV V D + +
Sbjct: 12 GYTLAENLSGENNDVTVIDTDEER 35
>gnl|CDD|237008 PRK11880, PRK11880, pyrroline-5-carboxylate reductase; Reviewed.
Length = 267
Score = 31.7 bits (73), Expect = 0.17
Identities = 16/55 (29%), Positives = 25/55 (45%), Gaps = 4/55 (7%)
Query: 1 MGSHMARNLLKNG---HDVIVYDKNTDASQTLAKE-GANMALSLSTLASGAEFII 51
M S + LL +G D+IV D + + LA+E G A A A+ ++
Sbjct: 13 MASAIIGGLLASGVPAKDIIVSDPSPEKRAALAEEYGVRAATDNQEAAQEADVVV 67
>gnl|CDD|236326 PRK08655, PRK08655, prephenate dehydrogenase; Provisional.
Length = 437
Score = 31.1 bits (71), Expect = 0.33
Identities = 24/89 (26%), Positives = 43/89 (48%), Gaps = 9/89 (10%)
Query: 1 MGSHMARNLLKNGHDVIVYDKNTDASQTLAKE-GANMALSLSTLASGAEFIISMLP--AS 57
+G AR L + G +VIV ++ + +AKE G A A A+ +I +P +
Sbjct: 12 LGKWFARFLKEKGFEVIVTGRDPKKGKEVAKELGVEYANDNIDAAKDADIVIISVPINVT 71
Query: 58 QDVLDAYDGSDGILKHAKPGVIVIDSSTV 86
+DV+ + H K G +++D ++V
Sbjct: 72 EDVIKE------VAPHVKEGSLLMDVTSV 94
>gnl|CDD|187537 cd05226, SDR_e_a, Extended (e) and atypical (a) SDRs. Extended or
atypical short-chain dehydrogenases/reductases (SDRs,
aka tyrosine-dependent oxidoreductases) are distinct
from classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately 100
amino acids. Extended SDRs are a diverse collection of
proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. Atypical SDRs generally
lack the catalytic residues characteristic of the SDRs,
and their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Atypical SDRs include biliverdin IX beta
reductase (BVR-B,aka flavin reductase), NMRa (a negative
transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Complex
(multidomain) SDRs such as ketoreductase domains of
fatty acid synthase have a GGXGXXG NAD(P)-binding motif
and an altered active site motif (YXXXN). Fungal type
ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding
motif.
Length = 176
Score = 30.4 bits (69), Expect = 0.33
Identities = 24/110 (21%), Positives = 40/110 (36%), Gaps = 16/110 (14%)
Query: 2 GSHMARNLLKNGHDVIVYDKNTDASQTLAKEGANMALSLSTLASGAEFIISMLPASQDVL 61
G +AR LL+ GH+V + +NT +E + L +
Sbjct: 11 GRALARELLEQGHEVTLLVRNTKRLSKEDQEPVA-------------VVEGDLRDLDSLS 57
Query: 62 DAYDGSDGILKHAKPGVIVIDSSTVDPQVPQTLSNLARE---KQITFLDA 108
DA G D ++ A D VD + + + A+E K F+ +
Sbjct: 58 DAVQGVDVVIHLAGAPRDTRDFCEVDVEGTRNVLEAAKEAGVKHFIFISS 107
>gnl|CDD|216906 pfam02153, PDH, Prephenate dehydrogenase. Members of this family
are prephenate dehydrogenases EC:1.3.1.12 involved in
tyrosine biosynthesis.
Length = 258
Score = 30.4 bits (69), Expect = 0.41
Identities = 27/140 (19%), Positives = 53/140 (37%), Gaps = 18/140 (12%)
Query: 6 ARNLLKNGHDVIV--YDKNTDASQTLAKEGA-NMALSLSTLASGAEFIISMLPASQ--DV 60
A L + G V + YD + +A+ + G + A + A+ ++ +P +V
Sbjct: 2 ALALRRKGFKVTIIGYDIDPEAAVAAVELGLIDEATDSISAVQEADIVVLAVPIEVTLEV 61
Query: 61 LDAYDGSDGILKHAKPGVIVIDSSTVDPQVPQTLSNLAREKQITFLDAPVSGGTKAAQEA 120
L + H K G ++ D +V ++ + L + P++G K+ +A
Sbjct: 62 LKE------LAPHLKEGALITDVGSVKVKIVEDAEQLLCDGVGFIGGHPMAGTEKSGPDA 115
Query: 121 TLTFMVGGDKSSLEKAKPIL 140
+ E A IL
Sbjct: 116 -------ARANLFEGAPVIL 128
>gnl|CDD|223842 COG0771, MurD, UDP-N-acetylmuramoylalanine-D-glutamate ligase
[Cell envelope biogenesis, outer membrane].
Length = 448
Score = 30.7 bits (70), Expect = 0.44
Identities = 10/30 (33%), Positives = 12/30 (40%)
Query: 5 MARNLLKNGHDVIVYDKNTDASQTLAKEGA 34
AR LLK G +V V D A+
Sbjct: 22 AARFLLKLGAEVTVSDDRPAPEGLAAQPLL 51
>gnl|CDD|133444 cd01075, NAD_bind_Leu_Phe_Val_DH, NAD(P) binding domain of
leucine dehydrogenase, phenylalanine dehydrogenase, and
valine dehydrogenase. Amino acid dehydrogenase (DH) is
a widely distributed family of enzymes that catalyzes
the oxidative deamination of an amino acid to its keto
acid and ammonia with concomitant reduction of NADP+.
For example, leucine DH catalyzes the reversible
oxidative deamination of L-leucine and several other
straight or branched chain amino acids to the
corresponding 2-oxoacid derivative. Amino acid DH -like
NAD(P)-binding domains are members of the Rossmann fold
superfamily and include glutamate, leucine, and
phenylalanine DHs, methylene tetrahydrofolate DH,
methylene-tetrahydromethanopterin DH,
methylene-tetrahydropholate DH/cyclohydrolase,
Shikimate DH-like proteins, malate oxidoreductases, and
glutamyl tRNA reductase. Amino acid DHs catalyze the
deamination of amino acids to keto acids with NAD(P)+
as a cofactor. The NAD(P)-binding Rossmann fold
superfamily includes a wide variety of protein families
including NAD(P)- binding domains of alcohol DHs,
tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate DH, lactate/malate DHs,
formate/glycerate DHs, siroheme synthases,
6-phosphogluconate DH, amino acid DHs, repressor rex,
NAD-binding potassium channel domain, CoA-binding, and
ornithine cyclodeaminase-like domains. These domains
have an alpha-beta-alpha configuration. NAD binding
involves numerous hydrogen and van der Waals contacts.
Length = 200
Score = 30.3 bits (69), Expect = 0.46
Identities = 11/31 (35%), Positives = 17/31 (54%)
Query: 2 GSHMARNLLKNGHDVIVYDKNTDASQTLAKE 32
G +A +LL+ G +IV D N +A A+
Sbjct: 40 GYKLAEHLLEEGAKLIVADINEEAVARAAEL 70
>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 = 30.3 bits (69), Expect = 0.51
Identities = 21/89 (23%), Positives = 36/89 (40%), Gaps = 6/89 (6%)
Query: 2 GSHMARNLLKNGHDVIVYDKNTDASQTLAKEGANMALSLSTLASGAEFIISMLPASQDVL 61
G +AR L G ++ YD + + L L ++F++ LP + D L
Sbjct: 156 GRAIARRLSGFGATLLYYDPHPLDQAEEQALNLRR-VELDELLESSDFLVLALPLTPDTL 214
Query: 62 DAYDGSDGILKHAKPGVIVIDS---STVD 87
+ L KPG ++++ S VD
Sbjct: 215 HLIN--AEALAKMKPGALLVNPCRGSVVD 241
>gnl|CDD|219954 pfam08654, DASH_Dad2, DASH complex subunit Dad2. The DASH
complex is a ~10 subunit microtubule-binding complex
that is transferred to the kinetochore prior to
mitosis. In Saccharomyces cerevisiae DASH forms both
rings and spiral structures on microtubules in vitro.
Length = 97
Score = 28.9 bits (65), Expect = 0.54
Identities = 22/73 (30%), Positives = 37/73 (50%), Gaps = 2/73 (2%)
Query: 23 TDASQTLAKEGANMALSLSTLASGAEFIISMLPASQDVLDAYD-GSDGILKHAKPGVIVI 81
+ S LA + + LST+A G E + S+L +VL + S G+LK+++ V
Sbjct: 20 RELSDDLAAQLEELEEKLSTMADGTEAVASVLANWDNVLRSISLASLGLLKYSEDDYEVG 79
Query: 82 DSSTVDPQVPQTL 94
+P +P+TL
Sbjct: 80 AWDEEEP-LPETL 91
>gnl|CDD|187545 cd05234, UDP_G4E_2_SDR_e, UDP-glucose 4 epimerase, subgroup 2,
extended (e) SDRs. UDP-glucose 4 epimerase (aka
UDP-galactose-4-epimerase), is a homodimeric extended
SDR. It catalyzes the NAD-dependent conversion of
UDP-galactose to UDP-glucose, the final step in Leloir
galactose synthesis. This subgroup is comprised of
archaeal and bacterial proteins, and has the
characteristic active site tetrad and NAD-binding motif
of the extended SDRs. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids. Extended SDRs are a diverse collection
of proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and
their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 305
Score = 30.0 bits (68), Expect = 0.67
Identities = 9/19 (47%), Positives = 14/19 (73%)
Query: 2 GSHMARNLLKNGHDVIVYD 20
GSH+ LL+ G++V+V D
Sbjct: 12 GSHLVDRLLEEGNEVVVVD 30
>gnl|CDD|224996 COG2085, COG2085, Predicted dinucleotide-binding enzymes [General
function prediction only].
Length = 211
Score = 29.6 bits (67), Expect = 0.73
Identities = 26/89 (29%), Positives = 39/89 (43%), Gaps = 12/89 (13%)
Query: 1 MGSHMARNLLKNGHDVIVYDKN---TDASQTLAKEGANMALSLSTLASGAEFIISMLP-- 55
+GS +A L K GH+VI+ A+ A S A+ A+ ++ +P
Sbjct: 12 IGSALALRLAKAGHEVIIGSSRGPKALAAAAAALGPLITGGSNEDAAALADVVVLAVPFE 71
Query: 56 ASQDVLDAYDGSDGILKHAKPGVIVIDSS 84
A DVL L+ A G IVID++
Sbjct: 72 AIPDVLAE-------LRDALGGKIVIDAT 93
>gnl|CDD|187607 cd05349, BKR_2_SDR_c, putative beta-ketoacyl acyl carrier protein
[ACP]reductase (BKR), subgroup 2, classical (c) SDR.
This subgroup includes Rhizobium sp. NGR234 FabG1. The
Escherichai coli K12 BKR, FabG, belongs to a different
subgroup. BKR catalyzes the NADPH-dependent reduction
of ACP in the first reductive step of de novo fatty
acid synthesis (FAS). FAS consists of four elongation
steps, which are repeated to extend the fatty acid
chain through the addition of two-carbo units from
malonyl acyl-carrier protein (ACP): condensation,
reduction, dehydration, and a final reduction. Type II
FAS, typical of plants and many bacteria, maintains
these activities on discrete polypeptides, while type I
FAS utilizes one or two multifunctional polypeptides.
BKR resembles enoyl reductase, which catalyzes the
second reduction step in FAS. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold
(alpha/beta folding pattern with a central beta-sheet),
an NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRS are
approximately 350 residues. Sequence identity between
different SDR enzymes are typically in the 15-30%
range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes have a
3-glycine N-terminal NAD(P)(H)-binding pattern
(typically, TGxxxGxG in classical SDRs and TGxxGxxG in
extended SDRs), while substrate binding is in the
C-terminal region. A critical catalytic Tyr residue
(Tyr-151, human 15-hydroxyprostaglandin dehydrogenase
(15-PGDH) numbering), is often found in a conserved
YXXXK pattern. In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) or
additional Ser, contributing to the active site.
Substrates for these enzymes include sugars, steroids,
alcohols, and aromatic compounds. The standard reaction
mechanism is a proton relay involving the conserved Tyr
and Lys, as well as Asn (or Ser). Some SDR family
members, including 17 beta-hydroxysteroid dehydrogenase
contain an additional helix-turn-helix motif that is
not generally found among SDRs.
Length = 246
Score = 29.7 bits (67), Expect = 0.74
Identities = 11/41 (26%), Positives = 27/41 (65%), Gaps = 1/41 (2%)
Query: 1 MGSHMARNLLKNGHDVIV-YDKNTDASQTLAKEGANMALSL 40
+G+ +AR+ + G V+V Y ++T++++ +A E A+++
Sbjct: 12 LGAAIARSFAREGARVVVNYYRSTESAEAVAAEAGERAIAI 52
>gnl|CDD|187557 cd05246, dTDP_GD_SDR_e, dTDP-D-glucose 4,6-dehydratase, extended
(e) SDRs. This subgroup contains dTDP-D-glucose
4,6-dehydratase and related proteins, members of the
extended-SDR family, with the characteristic Rossmann
fold core region, active site tetrad and NAD(P)-binding
motif. dTDP-D-glucose 4,6-dehydratase is closely
related to other sugar epimerases of the SDR family.
dTDP-D-dlucose 4,6,-dehydratase catalyzes the second of
four steps in the dTDP-L-rhamnose pathway (the
dehydration of dTDP-D-glucose to
dTDP-4-keto-6-deoxy-D-glucose) in the synthesis of
L-rhamnose, a cell wall component of some pathogenic
bacteria. In many gram negative bacteria, L-rhamnose is
an important constituent of lipopoylsaccharide
O-antigen. The larger N-terminal portion of
dTDP-D-Glucose 4,6-dehydratase forms a Rossmann fold
NAD-binding domain, while the C-terminus binds the
sugar substrate. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids. Extended SDRs are a diverse collection
of proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and
their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 315
Score = 29.8 bits (68), Expect = 0.80
Identities = 11/28 (39%), Positives = 14/28 (50%), Gaps = 2/28 (7%)
Query: 1 MGSHMARNLLKNGHD--VIVYDKNTDAS 26
+GS+ R LL D +I DK T A
Sbjct: 12 IGSNFVRYLLNKYPDYKIINLDKLTYAG 39
>gnl|CDD|187579 cd05271, NDUFA9_like_SDR_a, NADH dehydrogenase (ubiquinone) 1
alpha subcomplex, subunit 9, 39 kDa, (NDUFA9) -like,
atypical (a) SDRs. This subgroup of extended SDR-like
proteins are atypical SDRs. They have a glycine-rich
NAD(P)-binding motif similar to the typical SDRs,
GXXGXXG, and have the YXXXK active site motif (though
not the other residues of the SDR tetrad). Members
identified include NDUFA9 (mitochondrial) and putative
nucleoside-diphosphate-sugar epimerase. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif
is often different from the forms normally seen in
classical or extended SDRs. Atypical SDRs include
biliverdin IX beta reductase (BVR-B,aka flavin
reductase), NMRa (a negative transcriptional regulator
of various fungi), progesterone 5-beta-reductase like
proteins, phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane
reductase, isoflavone reductases, and others. SDRs are
a functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. In addition to the Rossmann fold
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids, and typically have a TGXXGXXG cofactor
binding motif. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 273
Score = 29.5 bits (67), Expect = 0.82
Identities = 7/18 (38%), Positives = 10/18 (55%)
Query: 1 MGSHMARNLLKNGHDVIV 18
+G ++ L K G VIV
Sbjct: 12 IGRYVVNRLAKRGSQVIV 29
>gnl|CDD|187563 cd05253, UDP_GE_SDE_e, UDP glucuronic acid epimerase, extended
(e) SDRs. This subgroup contains UDP-D-glucuronic acid
4-epimerase, an extended SDR, which catalyzes the
conversion of UDP-alpha-D-glucuronic acid to
UDP-alpha-D-galacturonic acid. This group has the SDR's
canonical catalytic tetrad and the TGxxGxxG NAD-binding
motif of the extended SDRs. Extended SDRs are distinct
from classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids. Extended SDRs are a diverse collection
of proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and
their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 332
Score = 29.6 bits (67), Expect = 0.91
Identities = 18/79 (22%), Positives = 32/79 (40%), Gaps = 10/79 (12%)
Query: 2 GSHMARNLLKNGHDVIVYDKNTDASQTLAKEGANMALSLSTLASGAEFIISMLPASQDVL 61
G H+A+ LL+ G +V+ D D KE L L + G +F+ D+
Sbjct: 13 GFHVAKRLLERGDEVVGIDNLNDYYDVRLKEA---RLELLGKSGGFKFV------KGDLE 63
Query: 62 DAYDGSDGILKHAKPGVIV 80
D + + K + ++
Sbjct: 64 D-REALRRLFKDHEFDAVI 81
>gnl|CDD|187541 cd05230, UGD_SDR_e, UDP-glucuronate decarboxylase (UGD) and
related proteins, extended (e) SDRs. UGD catalyzes the
formation of UDP-xylose from UDP-glucuronate; it is an
extended-SDR, and has the characteristic glycine-rich
NAD-binding pattern, TGXXGXXG, and active site tetrad.
Extended SDRs are distinct from classical SDRs. In
addition to the Rossmann fold (alpha/beta folding
pattern with a central beta-sheet) core region typical
of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving
as a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton
relay involving the conserved Tyr and Lys, a water
molecule stabilized by Asn, and nicotinamide. Atypical
SDRs generally lack the catalytic residues
characteristic of the SDRs, and their glycine-rich
NAD(P)-binding motif is often different from the forms
normally seen in classical or extended SDRs. Complex
(multidomain) SDRs such as ketoreductase domains of
fatty acid synthase have a GGXGXXG NAD(P)-binding motif
and an altered active site motif (YXXXN). Fungal type
ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding
motif.
Length = 305
Score = 29.5 bits (67), Expect = 0.99
Identities = 10/19 (52%), Positives = 14/19 (73%)
Query: 2 GSHMARNLLKNGHDVIVYD 20
GSH+ LL++GH+VI D
Sbjct: 13 GSHLCDRLLEDGHEVICVD 31
>gnl|CDD|236044 PRK07531, PRK07531, bifunctional 3-hydroxyacyl-CoA
dehydrogenase/thioesterase; Validated.
Length = 495
Score = 29.3 bits (66), Expect = 1.1
Identities = 27/107 (25%), Positives = 39/107 (36%), Gaps = 30/107 (28%)
Query: 2 GSHMARNLLKNGHDVIVYDKNTDASQTLAKEGANMALSLSTLASGAEFIISMLPA----- 56
G AR LL G DV V+D + +A + + + AN + + L LP
Sbjct: 17 GGWAARFLL-AGIDVAVFDPHPEAERIIGEVLANAERAYAMLTDAP------LPPEGRLT 69
Query: 57 -SQDVLDAYDGSDGI---------LKH--------AKPGVIVIDSST 85
+ +A G+D I LK A +I SST
Sbjct: 70 FCASLAEAVAGADWIQESVPERLDLKRRVLAEIDAAARPDALIGSST 116
>gnl|CDD|235506 PRK05565, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 247
Score = 29.0 bits (66), Expect = 1.1
Identities = 13/33 (39%), Positives = 20/33 (60%), Gaps = 1/33 (3%)
Query: 1 MGSHMARNLLKNGHDVIV-YDKNTDASQTLAKE 32
+G +A L K G V++ YD N +A+Q L +E
Sbjct: 17 IGRAIAELLAKEGAKVVIAYDINEEAAQELLEE 49
>gnl|CDD|187608 cd05350, SDR_c6, classical (c) SDR, subgroup 6. These proteins
are members of the classical SDR family, with a
canonical active site tetrad and a fairly well
conserved typical Gly-rich NAD-binding motif. SDRs are
a functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold (alpha/beta folding pattern with a
central beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRS are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes have a
3-glycine N-terminal NAD(P)(H)-binding pattern
(typically, TGxxxGxG in classical SDRs and TGxxGxxG in
extended SDRs), while substrate binding is in the
C-terminal region. A critical catalytic Tyr residue
(Tyr-151, human 15-hydroxyprostaglandin dehydrogenase
(15-PGDH) numbering), is often found in a conserved
YXXXK pattern. In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) or
additional Ser, contributing to the active site.
Substrates for these enzymes include sugars, steroids,
alcohols, and aromatic compounds. The standard reaction
mechanism is a proton relay involving the conserved Tyr
and Lys, as well as Asn (or Ser). Some SDR family
members, including 17 beta-hydroxysteroid dehydrogenase
contain an additional helix-turn-helix motif that is
not generally found among SDRs.
Length = 239
Score = 28.8 bits (65), Expect = 1.3
Identities = 12/39 (30%), Positives = 18/39 (46%)
Query: 1 MGSHMARNLLKNGHDVIVYDKNTDASQTLAKEGANMALS 39
+G +AR K G++V + + TD L E N S
Sbjct: 10 IGRALAREFAKAGYNVALAARRTDRLDELKAELLNPNPS 48
>gnl|CDD|129557 TIGR00465, ilvC, ketol-acid reductoisomerase. This is the second
enzyme in the parallel isoleucine-valine biosynthetic
pathway [Amino acid biosynthesis, Pyruvate family].
Length = 314
Score = 28.9 bits (65), Expect = 1.4
Identities = 16/54 (29%), Positives = 25/54 (46%)
Query: 2 GSHMARNLLKNGHDVIVYDKNTDASQTLAKEGANMALSLSTLASGAEFIISMLP 55
G A NL +G +VIV + AS A E ++ A+ I+++LP
Sbjct: 15 GHAQALNLRDSGLNVIVGLRKGGASWKKATEDGFKVGTVEEAIPQADLIMNLLP 68
>gnl|CDD|233242 TIGR01035, hemA, glutamyl-tRNA reductase. This enzyme, together
with glutamate-1-semialdehyde-2,1-aminomutase
(TIGR00713), leads to the production of
delta-amino-levulinic acid from Glu-tRNA [Biosynthesis
of cofactors, prosthetic groups, and carriers, Heme,
porphyrin, and cobalamin].
Length = 417
Score = 28.9 bits (65), Expect = 1.5
Identities = 24/99 (24%), Positives = 46/99 (46%), Gaps = 8/99 (8%)
Query: 1 MGSHMARNLL-KNGHDVIVYDKNTDASQTLAKEGANMALSLSTLASG---AEFIISMLPA 56
MG +A++LL K +++ ++ + ++ LAKE A+ L A+ +IS A
Sbjct: 191 MGELVAKHLLRKGVGKILIANRTYERAEDLAKELGGEAVKFEDLEEYLAEADIVISSTGA 250
Query: 57 SQDVLDAYDGSDGILKHAKPGVIVIDSST---VDPQVPQ 92
++ D + L+ + +ID + VDP V +
Sbjct: 251 PHPIVSKED-VERALRERTRPLFIIDIAVPRDVDPAVAR 288
>gnl|CDD|187572 cd05262, SDR_a7, atypical (a) SDRs, subgroup 7. This subgroup
contains atypical SDRs of unknown function. Members of
this subgroup have a glycine-rich NAD(P)-binding motif
consensus that matches the extended SDRs, TGXXGXXG, but
lacks the characteristic active site residues of the
SDRs. This subgroup has basic residues (HXXXR) in place
of the active site motif YXXXK, these may have a
catalytic role. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and
their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Atypical SDRs include biliverdin IX beta
reductase (BVR-B,aka flavin reductase), NMRa (a
negative transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane
reductase, isoflavone reductases, and others. SDRs are
a functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. In addition to the Rossmann fold
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids, and typically have a TGXXGXXG cofactor
binding motif. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 291
Score = 28.9 bits (65), Expect = 1.5
Identities = 13/51 (25%), Positives = 22/51 (43%), Gaps = 6/51 (11%)
Query: 2 GSHMARNLLKNGHDVIVYDKNTDASQTLAKEGA-----NMALSLSTLASGA 47
GS + R L+ GH+V+ ++ + L GA ++ L L A
Sbjct: 13 GSAVVRELVAAGHEVVGLARSDAGAAKLEAAGAQVHRGDLE-DLDILRKAA 62
>gnl|CDD|183450 PRK12335, PRK12335, tellurite resistance protein TehB; Provisional.
Length = 287
Score = 28.8 bits (65), Expect = 1.6
Identities = 18/64 (28%), Positives = 26/64 (40%), Gaps = 12/64 (18%)
Query: 1 MGSHMARNLL---KNGHDVIVYDKNTDASQTLA----KEGANMALSLSTLASGA-----E 48
+G RN L G DV D N + + L KE N+ L + S + +
Sbjct: 127 LGCGQGRNSLYLALLGFDVTAVDINQQSLENLQEIAEKENLNIRTGLYDINSASIQEEYD 186
Query: 49 FIIS 52
FI+S
Sbjct: 187 FILS 190
>gnl|CDD|168796 PRK07066, PRK07066, 3-hydroxybutyryl-CoA dehydrogenase; Validated.
Length = 321
Score = 28.6 bits (64), Expect = 1.7
Identities = 30/106 (28%), Positives = 41/106 (38%), Gaps = 25/106 (23%)
Query: 1 MGSHMARNLLKNGHDVIVYDKNTDASQTLAKEGANM--ALSLSTLASG------------ 46
+GS L +G DV+ +D A L AN AL LA G
Sbjct: 18 IGSGWVARALAHGLDVVAWDPAPGAEAALRANVANAWPALERQGLAPGASPARLRFVATI 77
Query: 47 ------AEFIISMLPASQDV-LDAYDGSDGILKHAKPGVIVIDSST 85
A+FI P + + L+ + + I + AKP I I SST
Sbjct: 78 EACVADADFIQESAPEREALKLELH---ERISRAAKPDAI-IASST 119
>gnl|CDD|187567 cd05257, Arna_like_SDR_e, Arna decarboxylase_like, extended (e)
SDRs. Decarboxylase domain of ArnA. ArnA, is an enzyme
involved in the modification of outer membrane protein
lipid A of gram-negative bacteria. It is a bifunctional
enzyme that catalyzes the NAD-dependent decarboxylation
of UDP-glucuronic acid and
N-10-formyltetrahydrofolate-dependent formylation of
UDP-4-amino-4-deoxy-l-arabinose; its NAD-dependent
decaboxylating activity is in the C-terminal 360
residues. This subgroup belongs to the extended SDR
family, however the NAD binding motif is not a perfect
match and the upstream Asn of the canonical active site
tetrad is not conserved. Extended SDRs are distinct
from classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids. Extended SDRs are a diverse collection
of proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and
their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 316
Score = 28.8 bits (65), Expect = 1.7
Identities = 9/20 (45%), Positives = 12/20 (60%)
Query: 2 GSHMARNLLKNGHDVIVYDK 21
GSH+ LL+ GH+V D
Sbjct: 12 GSHLTERLLREGHEVRALDI 31
>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 = 28.8 bits (65), Expect = 1.8
Identities = 19/86 (22%), Positives = 37/86 (43%), Gaps = 10/86 (11%)
Query: 2 GSHMARNLLKNGHDVIVYDKNTDASQTLAKEGANMALSLSTLASGAEFI---ISMLPASQ 58
G +AR G V+ YD D + LA+ +SL L ++ I + P +
Sbjct: 151 GRRVARIARGFGMKVLAYDVVPD--EELAERLGFRYVSLEELLQESDIISLHVPYTPQTH 208
Query: 59 DVLDAYDGSDGILKHAKPGVIVIDSS 84
+++ + KPG ++I+++
Sbjct: 209 HLINREN-----FALMKPGAVLINTA 229
>gnl|CDD|235788 PRK06372, PRK06372, translation initiation factor IF-2B subunit
delta; Provisional.
Length = 253
Score = 28.3 bits (63), Expect = 1.9
Identities = 13/37 (35%), Positives = 20/37 (54%), Gaps = 3/37 (8%)
Query: 2 GSHMARNLLKNGHDVIVYDKNTDASQTLAKEGANMAL 38
G MA+ L+K+G DV++ TDAS A + +
Sbjct: 123 GIDMAKLLVKSGIDVVLL---TDASMCEAVLNVDAVI 156
>gnl|CDD|216461 pfam01370, Epimerase, NAD dependent epimerase/dehydratase family.
This family of proteins utilise NAD as a cofactor. The
proteins in this family use nucleotide-sugar substrates
for a variety of chemical reactions.
Length = 233
Score = 28.4 bits (64), Expect = 2.0
Identities = 10/18 (55%), Positives = 14/18 (77%)
Query: 2 GSHMARNLLKNGHDVIVY 19
GSH+ R LL+ G++VIV
Sbjct: 11 GSHLVRRLLQEGYEVIVL 28
>gnl|CDD|179297 PRK01438, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
synthetase; Provisional.
Length = 480
Score = 28.5 bits (64), Expect = 2.1
Identities = 13/52 (25%), Positives = 21/52 (40%), Gaps = 6/52 (11%)
Query: 6 ARNLLKNGHDVIVYD-----KNTDASQTLAKEGANMALS-LSTLASGAEFII 51
A LL+ G V V D ++ + L GA + L TL + ++
Sbjct: 32 ADALLELGARVTVVDDGDDERHRALAAILEALGATVRLGPGPTLPEDTDLVV 83
>gnl|CDD|182741 PRK10799, PRK10799, metal-binding protein; Provisional.
Length = 247
Score = 28.2 bits (63), Expect = 2.2
Identities = 11/31 (35%), Positives = 16/31 (51%)
Query: 131 SSLEKAKPILKCMGRNIVHCGDSGNGQVAKL 161
LE A I +GR + CGD+G V ++
Sbjct: 138 PGLELASWIEARLGRKPLWCGDTGPEVVQRV 168
>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 = 28.0 bits (63), Expect = 2.5
Identities = 13/60 (21%), Positives = 27/60 (45%), Gaps = 12/60 (20%)
Query: 5 MARNLLKNGHDVIVYDKNTDASQTLAKEGANMALSLSTLASGAE-FIISMLPASQDVLDA 63
+A L + GH+ + YD T + L + + A+ +I+ +P +V++A
Sbjct: 18 LAAPLEEQGHEFVYYDTKTTDTAELIER-----------SKDADIVMIANMPLPGEVIEA 66
>gnl|CDD|215029 PLN00016, PLN00016, RNA-binding protein; Provisional.
Length = 378
Score = 28.1 bits (63), Expect = 2.6
Identities = 11/31 (35%), Positives = 21/31 (67%)
Query: 2 GSHMARNLLKNGHDVIVYDKNTDASQTLAKE 32
G ++A+ L+K GH+V ++ + + SQ + KE
Sbjct: 69 GFYLAKELVKAGHEVTLFTRGKEPSQKMKKE 99
>gnl|CDD|235059 PRK02705, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
synthetase; Provisional.
Length = 459
Score = 28.3 bits (64), Expect = 2.6
Identities = 12/33 (36%), Positives = 17/33 (51%), Gaps = 5/33 (15%)
Query: 6 ARNLLKNGHDVIVYDKNT-----DASQTLAKEG 33
AR L G +V+V D+N + Q L +EG
Sbjct: 16 ARLLKAQGWEVVVSDRNDSPELLERQQELEQEG 48
>gnl|CDD|233433 TIGR01482, SPP-subfamily, sucrose-phosphate phosphatase subfamily.
This model includes both the members of the SPP
equivalog model (TIGR01485), encompassing plants and
cyanobacteria, as well as those archaeal sequences which
are the closest relatives (TIGR01487). It remains to be
shown whether these archaeal sequences catalyze the same
reaction as SPP.
Length = 225
Score = 27.8 bits (62), Expect = 2.8
Identities = 19/89 (21%), Positives = 27/89 (30%), Gaps = 13/89 (14%)
Query: 70 ILKHAKPGVI--VIDSSTVDPQVPQTLSNLAREKQITFLDAPVSGGTKAAQEATLTFMVG 127
LK P V +D + + L A SG G
Sbjct: 98 RLKVQYPRRASLVKMRYGIDVDTVREIIKELGLN----LVAVDSG------FDIHILPQG 147
Query: 128 GDK-SSLEKAKPILKCMGRNIVHCGDSGN 155
+K +++K K L + CGDS N
Sbjct: 148 VNKGVAVKKLKEKLGIKPGETLVCGDSEN 176
>gnl|CDD|226495 COG4007, COG4007, Predicted dehydrogenase related to H2-forming
N5,N10-methylenetetrahydromethanopterin dehydrogenase
[General function prediction only].
Length = 340
Score = 27.9 bits (62), Expect = 2.9
Identities = 21/94 (22%), Positives = 38/94 (40%), Gaps = 8/94 (8%)
Query: 2 GSHMARNLLKNGHDVIVYDKNTDAS-----QTLAKEGANMALSLSTLASGAEFIISMLPA 56
G+ MA + GHDV++ + N D + + G + + A E + P
Sbjct: 33 GARMAIEFAEAGHDVVLAEPNRDIMDDEHWKRVEDAGVEVVSDDAEAAEHGEIHVLFTPF 92
Query: 57 SQDVLDAYDGSDGILKHAKPGVIVIDSSTVDPQV 90
+ + IL+H G ++ ++ TV P V
Sbjct: 93 GKATFGI---AREILEHVPEGAVICNTCTVSPVV 123
>gnl|CDD|216400 pfam01266, DAO, FAD dependent oxidoreductase. This family
includes various FAD dependent oxidoreductases:
Glycerol-3-phosphate dehydrogenase EC:1.1.99.5,
Sarcosine oxidase beta subunit EC:1.5.3.1, D-alanine
oxidase EC:1.4.99.1, D-aspartate oxidase EC:1.4.3.1.
Length = 234
Score = 27.7 bits (62), Expect = 3.0
Identities = 7/28 (25%), Positives = 12/28 (42%)
Query: 1 MGSHMARNLLKNGHDVIVYDKNTDASQT 28
+G A L + G V + ++ AS
Sbjct: 10 VGLSTAYELARRGLSVTLLERGDLASGA 37
>gnl|CDD|187568 cd05258, CDP_TE_SDR_e, CDP-tyvelose 2-epimerase, extended (e)
SDRs. CDP-tyvelose 2-epimerase is a tetrameric SDR
that catalyzes the conversion of CDP-D-paratose to
CDP-D-tyvelose, the last step in tyvelose biosynthesis.
This subgroup is a member of the extended SDR
subfamily, with a characteristic active site tetrad and
NAD-binding motif. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids. Extended SDRs are a diverse collection
of proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and
their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 337
Score = 28.0 bits (63), Expect = 3.0
Identities = 10/19 (52%), Positives = 14/19 (73%)
Query: 2 GSHMARNLLKNGHDVIVYD 20
GS++AR LK G +VI +D
Sbjct: 13 GSNLARFFLKQGWEVIGFD 31
>gnl|CDD|182639 PRK10675, PRK10675, UDP-galactose-4-epimerase; Provisional.
Length = 338
Score = 27.9 bits (62), Expect = 3.0
Identities = 13/28 (46%), Positives = 18/28 (64%), Gaps = 2/28 (7%)
Query: 1 MGSHMARNLLKNGHDVIVYDK--NTDAS 26
+GSH LL+NGHDV++ D N+ S
Sbjct: 12 IGSHTCVQLLQNGHDVVILDNLCNSKRS 39
>gnl|CDD|168661 PRK06753, PRK06753, hypothetical protein; Provisional.
Length = 373
Score = 27.7 bits (62), Expect = 3.5
Identities = 7/19 (36%), Positives = 12/19 (63%)
Query: 9 LLKNGHDVIVYDKNTDASQ 27
L + GH+V V++KN +
Sbjct: 19 LQEQGHEVKVFEKNESVKE 37
>gnl|CDD|187542 cd05231, NmrA_TMR_like_1_SDR_a, NmrA (a transcriptional
regulator) and triphenylmethane reductase (TMR) like
proteins, subgroup 1, atypical (a) SDRs. Atypical SDRs
related to NMRa, TMR, and HSCARG (an NADPH sensor).
This subgroup resembles the SDRs and has a partially
conserved characteristic [ST]GXXGXXG NAD-binding motif,
but lacks the conserved active site residues. NmrA is a
negative transcriptional regulator of various fungi,
involved in the post-translational modulation of the
GATA-type transcription factor AreA. NmrA lacks the
canonical GXXGXXG NAD-binding motif and has altered
residues at the catalytic triad, including a Met
instead of the critical Tyr residue. NmrA may bind
nucleotides but appears to lack any dehydrogenase
activity. HSCARG has been identified as a putative
NADP-sensing molecule, and redistributes and
restructures in response to NADPH/NADP ratios. Like
NmrA, it lacks most of the active site residues of the
SDR family, but has an NAD(P)-binding motif similar to
the extended SDR family, GXXGXXG. SDRs are a
functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Atypical
SDRs are distinct from classical SDRs. Classical SDRs
have an TGXXX[AG]XG cofactor binding motif and a YXXXK
active site motif, with the Tyr residue of the active
site motif serving as a critical catalytic residue
(Tyr-151, human 15-hydroxyprostaglandin dehydrogenase
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser and/or an Asn, contributing to
the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. In addition to the Rossmann fold core
region typical of all SDRs, extended SDRs have a less
conserved C-terminal extension of approximately 100
amino acids, and typically have a TGXXGXXG cofactor
binding motif. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 259
Score = 27.7 bits (62), Expect = 3.8
Identities = 11/37 (29%), Positives = 19/37 (51%)
Query: 2 GSHMARNLLKNGHDVIVYDKNTDASQTLAKEGANMAL 38
GS +A LL+ G V ++ + + LA GA + +
Sbjct: 11 GSKVATTLLEAGRPVRALVRSDERAAALAARGAEVVV 47
>gnl|CDD|187660 cd08957, WbmH_like_SDR_e, Bordetella bronchiseptica enzymes WbmH
and WbmG-like, extended (e) SDRs. Bordetella
bronchiseptica enzymes WbmH and WbmG, and related
proteins. This subgroup exhibits the active site tetrad
and NAD-binding motif of the extended SDR family. It
has been proposed that the active site in Bordetella
WbmG and WbmH cannot function as an epimerase, and that
it plays a role in O-antigen synthesis pathway from
UDP-2,3-diacetamido-2,3-dideoxy-l-galacturonic acid.
Extended SDRs are distinct from classical SDRs. In
addition to the Rossmann fold (alpha/beta folding
pattern with a central beta-sheet) core region typical
of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving
as a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton
relay involving the conserved Tyr and Lys, a water
molecule stabilized by Asn, and nicotinamide. Atypical
SDRs generally lack the catalytic residues
characteristic of the SDRs, and their glycine-rich
NAD(P)-binding motif is often different from the forms
normally seen in classical or extended SDRs. Complex
(multidomain) SDRs such as ketoreductase domains of
fatty acid synthase have a GGXGXXG NAD(P)-binding motif
and an altered active site motif (YXXXN). Fungal type
ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding
motif.
Length = 307
Score = 27.5 bits (61), Expect = 3.9
Identities = 10/20 (50%), Positives = 15/20 (75%)
Query: 1 MGSHMARNLLKNGHDVIVYD 20
+GSH+ +LL+ GH V+V D
Sbjct: 12 IGSHLIEHLLERGHQVVVID 31
>gnl|CDD|223774 COG0702, COG0702, Predicted nucleoside-diphosphate-sugar epimerases
[Cell envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 275
Score = 27.6 bits (61), Expect = 3.9
Identities = 29/112 (25%), Positives = 41/112 (36%), Gaps = 12/112 (10%)
Query: 2 GSHMARNLLKNGHDVIVYDKNTDASQTLAKE------GANMALSLSTLASGAE--FIISM 53
G + R LL GH+V +N +A+ LA SL A G + +IS
Sbjct: 13 GGAVVRELLARGHEVRAAVRNPEAAAALAGGVEVVLGDLRDPKSLVAGAKGVDGVLLISG 72
Query: 54 LPASQDVLDAYDGSDGI--LKHAKPGVI-VIDSSTVDPQVPQTLSNLAREKQ 102
L D A + + + A GV + S + S LAR K
Sbjct: 73 LLDGSDAFRAVQVTAVVRAAEAAGAGVKHGVSLSVLGADAASP-SALARAKA 123
>gnl|CDD|237343 PRK13304, PRK13304, L-aspartate dehydrogenase; Reviewed.
Length = 265
Score = 27.6 bits (62), Expect = 4.0
Identities = 20/85 (23%), Positives = 40/85 (47%), Gaps = 5/85 (5%)
Query: 18 VYDKNTDASQTLAKE-GANMALSLSTLASGAEFIISMLPASQDVLDAYDGSDGILKHAKP 76
YD+N + ++ LA + GA LS+ L + ++ AS + + + L++ K
Sbjct: 32 FYDRNLEKAENLASKTGAKACLSIDELVEDVDLVVEC--ASVNAV--EEVVPKSLENGKD 87
Query: 77 GVIVIDSSTVDPQVPQTLSNLAREK 101
+I+ + D ++ L LA+E
Sbjct: 88 VIIMSVGALADKELFLKLYKLAKEN 112
>gnl|CDD|187583 cd05322, SDH_SDR_c_like, Sorbitol 6-phosphate dehydrogenase
(SDH), classical (c) SDRs. Sorbitol 6-phosphate
dehydrogenase (SDH, aka glucitol 6-phosphate
dehydrogenase) catalyzes the NAD-dependent
interconversion of D-fructose 6-phosphate to D-sorbitol
6-phosphate. SDH is a member of the classical SDRs,
with the characteristic catalytic tetrad, but without a
complete match to the typical NAD-binding motif. SDRs
are a functionally diverse family of oxidoreductases
that have a single domain with a structurally conserved
Rossmann fold (alpha/beta folding pattern with a
central beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRs are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes catalyze a
wide range of activities including the metabolism of
steroids, cofactors, carbohydrates, lipids, aromatic
compounds, and amino acids, and act in redox sensing.
Classical SDRs have an TGXXX[AG]XG cofactor binding
motif and a YXXXK active site motif, with the Tyr
residue of the active site motif serving as a critical
catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 257
Score = 27.4 bits (61), Expect = 4.4
Identities = 10/32 (31%), Positives = 19/32 (59%)
Query: 1 MGSHMARNLLKNGHDVIVYDKNTDASQTLAKE 32
+G + L + G+DV V D N++ ++ +A E
Sbjct: 14 LGEFLCHGLAEAGYDVAVADINSENAEKVADE 45
>gnl|CDD|205628 pfam13450, NAD_binding_8, NAD(P)-binding Rossmann-like domain.
Length = 66
Score = 25.5 bits (57), Expect = 4.5
Identities = 9/23 (39%), Positives = 11/23 (47%)
Query: 2 GSHMARNLLKNGHDVIVYDKNTD 24
G A L K G DV+V +K
Sbjct: 8 GLVAAYLLAKRGKDVLVLEKRDR 30
>gnl|CDD|237213 PRK12810, gltD, glutamate synthase subunit beta; Reviewed.
Length = 471
Score = 27.4 bits (62), Expect = 4.5
Identities = 5/14 (35%), Positives = 9/14 (64%)
Query: 9 LLKNGHDVIVYDKN 22
L + GH V V+++
Sbjct: 162 LARAGHKVTVFERA 175
>gnl|CDD|236216 PRK08277, PRK08277, D-mannonate oxidoreductase; Provisional.
Length = 278
Score = 27.2 bits (61), Expect = 4.6
Identities = 19/74 (25%), Positives = 34/74 (45%), Gaps = 7/74 (9%)
Query: 1 MGSHMARNLLKNGHDVIVYDKNTDASQTLAKE---GANMALSLSTLASGAEFIISMLPAS 57
+G MA+ L + G V + D+N + ++ + E AL++ E S+ A
Sbjct: 22 LGGAMAKELARAGAKVAILDRNQEKAEAVVAEIKAAGGEALAVKADVLDKE---SLEQAR 78
Query: 58 QDVLDAYDGSDGIL 71
Q +L+ + D IL
Sbjct: 79 QQILEDFGPCD-IL 91
>gnl|CDD|187570 cd05260, GDP_MD_SDR_e, GDP-mannose 4,6 dehydratase, extended (e)
SDRs. GDP-mannose 4,6 dehydratase, a homodimeric SDR,
catalyzes the NADP(H)-dependent conversion of
GDP-(D)-mannose to GDP-4-keto, 6-deoxy-(D)-mannose in
the fucose biosynthesis pathway. These proteins have
the canonical active site triad and NAD-binding
pattern, however the active site Asn is often missing
and may be substituted with Asp. A Glu residue has been
identified as an important active site base. Extended
SDRs are distinct from classical SDRs. In addition to
the Rossmann fold (alpha/beta folding pattern with a
central beta-sheet) core region typical of all SDRs,
extended SDRs have a less conserved C-terminal
extension of approximately 100 amino acids. Extended
SDRs are a diverse collection of proteins, and include
isomerases, epimerases, oxidoreductases, and lyases;
they typically have a TGXXGXXG cofactor binding motif.
SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving
as a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton
relay involving the conserved Tyr and Lys, a water
molecule stabilized by Asn, and nicotinamide. Atypical
SDRs generally lack the catalytic residues
characteristic of the SDRs, and their glycine-rich
NAD(P)-binding motif is often different from the forms
normally seen in classical or extended SDRs. Complex
(multidomain) SDRs such as ketoreductase domains of
fatty acid synthase have a GGXGXXG NAD(P)-binding motif
and an altered active site motif (YXXXN). Fungal type
ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding
motif.
Length = 316
Score = 27.2 bits (61), Expect = 4.6
Identities = 7/16 (43%), Positives = 12/16 (75%)
Query: 2 GSHMARNLLKNGHDVI 17
GS++A LL+ G++V
Sbjct: 12 GSYLAEFLLEKGYEVH 27
>gnl|CDD|237136 PRK12557, PRK12557, H(2)-dependent
methylenetetrahydromethanopterin dehydrogenase-related
protein; Provisional.
Length = 342
Score = 27.4 bits (61), Expect = 4.8
Identities = 9/23 (39%), Positives = 13/23 (56%)
Query: 2 GSHMARNLLKNGHDVIVYDKNTD 24
GS MA + GHDV++ + N
Sbjct: 32 GSRMAIEFAEAGHDVVLAEPNRS 54
>gnl|CDD|133057 cd06435, CESA_NdvC_like, NdvC_like proteins in this family are
putative bacterial beta-(1,6)-glucosyltransferase.
NdvC_like proteins in this family are putative
bacterial beta-(1,6)-glucosyltransferase. Bradyrhizobium
japonicum synthesizes periplasmic cyclic
beta-(1,3),beta-(1,6)-D-glucans during growth under
hypoosmotic conditions. Two genes (ndvB, ndvC) are
involved in the beta-(1, 3), beta-(1,6)-glucan
synthesis. The ndvC mutant strain resulted in synthesis
of altered cyclic beta-glucans composed almost entirely
of beta-(1, 3)-glycosyl linkages. The periplasmic cyclic
beta-(1,3),beta-(1,6)-D-glucans function for
osmoregulation. The ndvC mutation also affects the
ability of the bacteria to establish a successful
symbiotic interaction with host plant. Thus, the
beta-glucans may function as suppressors of a host
defense response.
Length = 236
Score = 27.0 bits (60), Expect = 5.1
Identities = 11/41 (26%), Positives = 19/41 (46%), Gaps = 2/41 (4%)
Query: 78 VIVIDSSTVDPQVPQTLSNLARE--KQITFLDAPVSGGTKA 116
VIVID++T D + + + + ++ F G KA
Sbjct: 31 VIVIDNNTKDEALWKPVEAHCAQLGERFRFFHVEPLPGAKA 71
>gnl|CDD|215890 pfam00386, C1q, C1q domain. C1q is a subunit of the C1 enzyme
complex that activates the serum complement system.
Length = 125
Score = 26.5 bits (59), Expect = 5.2
Identities = 9/30 (30%), Positives = 17/30 (56%), Gaps = 1/30 (3%)
Query: 2 GSHMARNLLKNGHDVI-VYDKNTDASQTLA 30
G ++ L+KNG +V+ YD+ + S +
Sbjct: 57 GKNLKVGLMKNGQEVVSFYDQAQNGSDVAS 86
>gnl|CDD|187598 cd05339, 17beta-HSDXI-like_SDR_c, human 17-beta-hydroxysteroid
dehydrogenase XI-like, classical (c) SDRs.
17-beta-hydroxysteroid dehydrogenases (17betaHSD) are a
group of isozymes that catalyze activation and
inactivation of estrogen and androgens. 17betaHSD type
XI, a classical SDR, preferentially converts
3alpha-adiol to androsterone but not numerous other
tested steroids. This subgroup of classical SDRs also
includes members identified as retinol dehydrogenases,
which convert retinol to retinal, a property that
overlaps with 17betaHSD activity. SDRs are a
functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold (alpha/beta folding pattern with a
central beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRS are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes have a
3-glycine N-terminal NAD(P)(H)-binding pattern
(typically, TGxxxGxG in classical SDRs and TGxxGxxG in
extended SDRs), while substrate binding is in the
C-terminal region. A critical catalytic Tyr residue
(Tyr-151, human 15-hydroxyprostaglandin dehydrogenase
(15-PGDH) numbering), is often found in a conserved
YXXXK pattern. In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) or
additional Ser, contributing to the active site.
Substrates for these enzymes include sugars, steroids,
alcohols, and aromatic compounds. The standard reaction
mechanism is a proton relay involving the conserved Tyr
and Lys, as well as Asn (or Ser). Some SDR family
members, including 17 beta-hydroxysteroid dehydrogenase
contain an additional helix-turn-helix motif that is
not generally found among SDRs.
Length = 243
Score = 27.2 bits (61), Expect = 5.2
Identities = 11/36 (30%), Positives = 16/36 (44%), Gaps = 4/36 (11%)
Query: 2 GSHMARNLLKNGHDVIVYDKNTDASQTLAKEGANMA 37
G +A K G V++ D N + A+E AN
Sbjct: 12 GRLLALEFAKRGAKVVILDIN----EKGAEETANNV 43
>gnl|CDD|216593 pfam01593, Amino_oxidase, Flavin containing amine oxidoreductase.
This family consists of various amine oxidases,
including maze polyamine oxidase (PAO) and various
flavin containing monoamine oxidases (MAO). The aligned
region includes the flavin binding site of these
enzymes. The family also contains phytoene
dehydrogenases and related enzymes. In vertebrates MAO
plays an important role regulating the intracellular
levels of amines via there oxidation; these include
various neurotransmitters, neurotoxins and trace
amines. In lower eukaryotes such as aspergillus and in
bacteria the main role of amine oxidases is to provide
a source of ammonium. PAOs in plants, bacteria and
protozoa oxidase spermidine and spermine to an
aminobutyral, diaminopropane and hydrogen peroxide and
are involved in the catabolism of polyamines. Other
members of this family include tryptophan
2-monooxygenase, putrescine oxidase, corticosteroid
binding proteins and antibacterial glycoproteins.
Length = 444
Score = 27.1 bits (60), Expect = 6.7
Identities = 8/14 (57%), Positives = 9/14 (64%)
Query: 6 ARNLLKNGHDVIVY 19
AR LL+ G DV V
Sbjct: 7 ARELLRAGFDVTVL 20
>gnl|CDD|187538 cd05227, AR_SDR_e, aldehyde reductase, extended (e) SDRs. This
subgroup contains aldehyde reductase of the extended
SDR-type and related proteins. Aldehyde reductase I (aka
carbonyl reductase) is an NADP-binding SDR; it has an
NADP-binding motif consensus that is slightly different
from the canonical SDR form and lacks the Asn of the
extended SDR active site tetrad. Aldehyde reductase I
catalyzes the NADP-dependent reduction of ethyl
4-chloro-3-oxobutanoate to ethyl
(R)-4-chloro-3-hydroxybutanoate. Extended SDRs are
distinct from classical SDRs. In addition to the
Rossmann fold (alpha/beta folding pattern with a central
beta-sheet) core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids. Extended SDRs are a
diverse collection of proteins, and include isomerases,
epimerases, oxidoreductases, and lyases; they typically
have a TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 301
Score = 26.8 bits (60), Expect = 6.7
Identities = 25/101 (24%), Positives = 34/101 (33%), Gaps = 15/101 (14%)
Query: 2 GSHMARNLLKNGHDVIV----YDKNTDASQTLAKEGANMALSLSTLASGAEFIISMLPAS 57
SH+ LLK G+ V K+ L G N L I+ L A
Sbjct: 12 ASHIVEQLLKAGYKVRGTVRSLSKSAKLKALLKAAGYNDRLEF--------VIVDDLTAP 63
Query: 58 QDVLDAYDGSDGILKHAKPGVIVID---SSTVDPQVPQTLS 95
+A G D ++ A P +DP V TL+
Sbjct: 64 NAWDEALKGVDYVIHVASPFPFTGPDAEDDVIDPAVEGTLN 104
>gnl|CDD|217642 pfam03618, Kinase-PPPase, Kinase/pyrophosphorylase. This family of
regulatory proteins has ADP-dependent kinase and
inorganic phosphate-dependent pyrophosphorylase
activity.
Length = 255
Score = 26.6 bits (60), Expect = 7.4
Identities = 16/73 (21%), Positives = 31/73 (42%), Gaps = 14/73 (19%)
Query: 41 STLA--SGAEFIISMLP--ASQDVLDAYDGSDGILKHAK--PGVIVIDSSTVDPQVPQTL 94
+ L+ G EF I P +++ L+ +L+ G++ + VDP++ + L
Sbjct: 18 AALSQFPGVEFEIHRFPFIRTEEKLEE------VLEEINEEDGIVF--YTLVDPELREIL 69
Query: 95 SNLAREKQITFLD 107
A I +D
Sbjct: 70 EEFAEALGIPCVD 82
>gnl|CDD|187640 cd08935, mannonate_red_SDR_c, putative D-mannonate oxidoreductase,
classical (c) SDR. D-mannonate oxidoreductase catalyzes
the NAD-dependent interconversion of D-mannonate and
D-fructuronate. This subgroup includes Bacillus
subtitils UxuB/YjmF, a putative D-mannonate
oxidoreductase; the B. subtilis UxuB gene is part of a
putative ten-gene operon (the Yjm operon) involved in
hexuronate catabolism. Escherichia coli UxuB does not
belong to this subgroup. This subgroup has a canonical
active site tetrad and a typical Gly-rich NAD-binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold (alpha/beta folding
pattern with a central beta-sheet), an NAD(P)(H)-binding
region, and a structurally diverse C-terminal region.
Classical SDRs are typically about 250 residues long,
while extended SDRs are approximately 350 residues.
Sequence identity between different SDR enzymes are
typically in the 15-30% range, but the enzymes share the
Rossmann fold NAD-binding motif and characteristic
NAD-binding and catalytic sequence patterns. These
enzymes catalyze a wide range of activities including
the metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 271
Score = 26.7 bits (59), Expect = 7.7
Identities = 26/122 (21%), Positives = 47/122 (38%), Gaps = 4/122 (3%)
Query: 1 MGSHMARNLLKNGHDVIVYDKNTDASQTLAKEGANMALSLSTLASGAEFIISMLPASQDV 60
+G MAR L + G V +N + +AKE + LA+ S+ A +++
Sbjct: 17 LGGAMARALAQAGAKVAALGRNQEKGDKVAKEITALGGRAIALAADVLDRASLERAREEI 76
Query: 61 LDAYDGSDGILKHA---KPGVIVIDSSTVDPQVPQTLSNLAREKQITFLDAPVSGGTKAA 117
+ + D ++ A P D +P+ Q +L E D ++G +
Sbjct: 77 VAQFGTVDILINGAGGNHPDAT-TDPEHYEPETEQNFFDLDEEGWEFVFDLNLNGSFLPS 135
Query: 118 QE 119
Q
Sbjct: 136 QV 137
>gnl|CDD|202367 pfam02737, 3HCDH_N, 3-hydroxyacyl-CoA dehydrogenase, NAD binding
domain. This family also includes lambda crystallin.
Length = 180
Score = 26.3 bits (59), Expect = 8.3
Identities = 13/45 (28%), Positives = 24/45 (53%), Gaps = 3/45 (6%)
Query: 1 MGSHMARNLLKNGHDVIVYDKNTDASQTLAKEGANMALSLSTLAS 45
MG+ +A+ + G +V++ D + +A L K A + SL+ L
Sbjct: 10 MGAGIAQVFARAGLEVVLVDISEEA---LEKARARIEKSLARLVE 51
>gnl|CDD|169390 PRK08340, PRK08340, glucose-1-dehydrogenase; Provisional.
Length = 259
Score = 26.3 bits (58), Expect = 8.4
Identities = 11/32 (34%), Positives = 19/32 (59%)
Query: 1 MGSHMARNLLKNGHDVIVYDKNTDASQTLAKE 32
+G ++AR LLK G V++ +N + + KE
Sbjct: 12 IGFNVARELLKKGARVVISSRNEENLEKALKE 43
>gnl|CDD|187553 cd05242, SDR_a8, atypical (a) SDRs, subgroup 8. This subgroup
contains atypical SDRs of unknown function. Proteins in
this subgroup have a glycine-rich NAD(P)-binding motif
consensus that resembles that of the extended SDRs,
(GXXGXXG or GGXGXXG), but lacks the characteristic
active site residues of the SDRs. A Cys often replaces
the usual Lys of the YXXXK active site motif, while the
upstream Ser is generally present and Arg replaces the
usual Asn. Atypical SDRs generally lack the catalytic
residues characteristic of the SDRs, and their
glycine-rich NAD(P)-binding motif is often different
from the forms normally seen in classical or extended
SDRs. Atypical SDRs include biliverdin IX beta
reductase (BVR-B,aka flavin reductase), NMRa (a
negative transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane
reductase, isoflavone reductases, and others. SDRs are
a functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. In addition to the Rossmann fold
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids, and typically have a TGXXGXXG cofactor
binding motif. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 296
Score = 26.4 bits (59), Expect = 8.6
Identities = 7/17 (41%), Positives = 10/17 (58%)
Query: 2 GSHMARNLLKNGHDVIV 18
G + R L GH+V+V
Sbjct: 12 GRALTRRLTAAGHEVVV 28
>gnl|CDD|214954 smart00984, UDPG_MGDP_dh_C, UDP binding domain. The
UDP-glucose/GDP-mannose dehydrogenases are a small
group of enzymes which possesses the ability to
catalyse the NAD-dependent 2-fold oxidation of an
alcohol to an acid without the release of an aldehyde
intermediate.
Length = 99
Score = 25.5 bits (57), Expect = 9.2
Identities = 12/47 (25%), Positives = 21/47 (44%), Gaps = 2/47 (4%)
Query: 5 MARNLLKNGHDVIVYDKNTDASQTLAKEGANMALSLSTLASGAEFII 51
+ LL+ G +V+VYD A + + G L GA+ ++
Sbjct: 22 IIEELLEAGAEVVVYDPY--AMEEAREYGLTYVSDLEEALKGADAVV 66
>gnl|CDD|235226 PRK04148, PRK04148, hypothetical protein; Provisional.
Length = 134
Score = 25.7 bits (57), Expect = 9.3
Identities = 13/30 (43%), Positives = 17/30 (56%)
Query: 6 ARNLLKNGHDVIVYDKNTDASQTLAKEGAN 35
A+ L ++G DVIV D N A + K G N
Sbjct: 32 AKKLKESGFDVIVIDINEKAVEKAKKLGLN 61
>gnl|CDD|99993 cd03823, GT1_ExpE7_like, This family is most closely related to
the GT1 family of glycosyltransferases. ExpE7 in
Sinorhizobium meliloti has been shown to be involved in
the biosynthesis of galactoglucans (exopolysaccharide
II).
Length = 359
Score = 26.5 bits (59), Expect = 9.5
Identities = 7/16 (43%), Positives = 9/16 (56%)
Query: 4 HMARNLLKNGHDVIVY 19
+A L K GH+V V
Sbjct: 23 DLAEALAKRGHEVAVL 38
>gnl|CDD|187604 cd05346, SDR_c5, classical (c) SDR, subgroup 5. These proteins
are members of the classical SDR family, with a
canonical active site tetrad and a typical Gly-rich
NAD-binding motif. SDRs are a functionally diverse
family of oxidoreductases that have a single domain
with a structurally conserved Rossmann fold (alpha/beta
folding pattern with a central beta-sheet), an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRs are
approximately 350 residues. Sequence identity between
different SDR enzymes are typically in the 15-30%
range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes catalyze a
wide range of activities including the metabolism of
steroids, cofactors, carbohydrates, lipids, aromatic
compounds, and amino acids, and act in redox sensing.
Classical SDRs have an TGXXX[AG]XG cofactor binding
motif and a YXXXK active site motif, with the Tyr
residue of the active site motif serving as a critical
catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 249
Score = 26.1 bits (58), Expect = 9.7
Identities = 18/61 (29%), Positives = 25/61 (40%), Gaps = 12/61 (19%)
Query: 2 GSHMARNLLKNGHDVIVYDKNTDASQTLAKEGANMALSLSTLASGAEFIISMLPASQDVL 61
G AR K G +I+ + + Q LA E GA+F + +LP DV
Sbjct: 13 GEATARRFAKAGAKLILTGRRAERLQELADE------------LGAKFPVKVLPLQLDVS 60
Query: 62 D 62
D
Sbjct: 61 D 61
>gnl|CDD|221938 pfam13149, DUF3988, Protein of unknown function (DUF3988). A
family of uncharacterized proteins found by clustering
human gut metagenomic sequences.
Length = 308
Score = 26.3 bits (58), Expect = 9.7
Identities = 11/44 (25%), Positives = 17/44 (38%)
Query: 81 IDSSTVDPQVPQTLSNLAREKQITFLDAPVSGGTKAAQEATLTF 124
+S+ T K I L A + TK++ +LTF
Sbjct: 121 ASASSTGTPTFLTTQLYDAAKDIDLLVAKATNVTKSSPAVSLTF 164
>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 = 26.4 bits (59), Expect = 9.9
Identities = 24/102 (23%), Positives = 34/102 (33%), Gaps = 26/102 (25%)
Query: 13 GHDVIVYDKNTD----------------ASQTLAKEGANMALSLST----LASGAEFIIS 52
GHDV D + + + LAK L +T A+ II
Sbjct: 23 GHDVTGVDIDQEKVDKLNKGKSPIYEPGLDELLAKALKAGRLRATTDYEEAIRDADVIII 82
Query: 53 MLPASQDV-----LDA-YDGSDGILKHAKPGVIVIDSSTVDP 88
+P L ++ I KH + G V+ STV P
Sbjct: 83 CVPTPLKEDGSPDLSYVESAAETIAKHLRKGATVVLESTVPP 124
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
0.314 0.130 0.362
Gapped
Lambda K H
0.267 0.0832 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,836,854
Number of extensions: 787073
Number of successful extensions: 980
Number of sequences better than 10.0: 1
Number of HSP's gapped: 953
Number of HSP's successfully gapped: 124
Length of query: 183
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 92
Effective length of database: 6,901,388
Effective search space: 634927696
Effective search space used: 634927696
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: 42 (22.0 bits)
S2: 56 (25.2 bits)