RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1119
(1392 letters)
>gnl|CDD|214840 smart00829, PKS_ER, Enoylreductase. Enoylreductase in Polyketide
synthases.
Length = 287
Score = 366 bits (943), Expect = e-117
Identities = 127/300 (42%), Positives = 178/300 (59%), Gaps = 23/300 (7%)
Query: 462 QIYYSSINFRDIMLTTAKLAPEVIESRRLYQHCVIGFEYSGRLR---------DSGKRVM 512
++ + +NFRD+++ E V+G E +G + G RVM
Sbjct: 2 EVRAAGLNFRDVLIALGLYPGEA----------VLGGECAGVVTRVGPGVTGLAVGDRVM 51
Query: 513 GLTSGRSLANCCETDVEMAWEIPDQWTLEDAATVPCVYATAVYAMFICGQMQKGESILIH 572
GL G + A TD + IPD W+ E+AATVP V+ TA YA+ +++ GES+LIH
Sbjct: 52 GLAPG-AFATRVVTDARLVVPIPDGWSFEEAATVPVVFLTAYYALVDLARLRPGESVLIH 110
Query: 573 AGSGGVGQAAINLARYMDAEIFTTVGTPEKREFIRKTFPFIKEENIGNSRDTSFEQLVMK 632
A +GGVGQAAI LAR++ AE+F T G+PEKR+F+R I +++I +SRD SF +++
Sbjct: 111 AAAGGVGQAAIQLARHLGAEVFATAGSPEKRDFLR--ALGIPDDHIFSSRDLSFADEILR 168
Query: 633 RTKGRGVDLVLNSLAEEKLQASVRCLAQGGRFLEIGKFDLANNNMLGMEVFMRETSFHGV 692
T GRGVD+VLNSL+ E L AS+RCLA GGRF+EIGK D+ +N+ L M F S+H V
Sbjct: 169 ATGGRGVDVVLNSLSGEFLDASLRCLAPGGRFVEIGKRDIRDNSQLAMAPFRPNVSYHAV 228
Query: 693 MLDNFFFAEQEWKMSLQKALQKAIDAGAVQPLVRTIFPEDKVEEAFRYMAAGKHIGKVII 752
LD + L + + G ++PL T+FP E+AFRYM GKHIGKV++
Sbjct: 229 DLD-ALEEGPDRIRELLAEVLELFAEGVLRPLPVTVFPISDAEDAFRYMQQGKHIGKVVL 287
>gnl|CDD|176179 cd05195, enoyl_red, enoyl reductase of polyketide synthase.
Putative enoyl reductase of polyketide synthase.
Polyketide synthases produce polyketides in step by step
mechanism that is similar to fatty acid synthesis. Enoyl
reductase reduces a double to single bond. Erythromycin
is one example of a polyketide generated by 3 complex
enzymes (megasynthases). 2-enoyl thioester reductase
(ETR) catalyzes the NADPH-dependent dependent conversion
of trans-2-enoyl acyl carrier protein/coenzyme A
(ACP/CoA) to acyl-(ACP/CoA) in fatty acid synthesis.
2-enoyl thioester reductase activity has been linked in
Candida tropicalis as essential in maintaining
mitiochondrial respiratory function. This ETR family is
a part of the medium chain dehydrogenase/reductase
family, but lack the zinc coordination sites
characteristic of the alcohol dehydrogenases in this
family. NAD(P)(H)-dependent oxidoreductases are the
major enzymes in the interconversion of alcohols and
aldehydes or ketones. Alcohol dehydrogenase in the liver
converts ethanol and NAD+ to acetaldehyde and NADH,
while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which has a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. The N-terminal catalytic domain has a
distant homology to GroES. These proteins typically
form dimers (typically higher plants, mammals) or
tetramers (yeast, bacteria), and have 2 tightly bound
zinc atoms per subunit, a catalytic zinc at the active
site, and a structural zinc in a lobe of the catalytic
domain. NAD(H) binding occurs in the cleft between the
catalytic and coenzyme-binding domains, at the active
site, and coenzyme binding induces a conformational
closing of this cleft. Coenzyme binding typically
precedes and contributes to substrate binding.
Length = 293
Score = 339 bits (872), Expect = e-107
Identities = 126/303 (41%), Positives = 179/303 (59%), Gaps = 27/303 (8%)
Query: 462 QIYYSSINFRDIMLTTAKLAPEVIESRRLYQHCVIGFEYSGRLRD---------SGKRVM 512
++ + +NFRD++ V +G E SG + G RVM
Sbjct: 6 EVKAAGLNFRDVL---------VALGLLPGDETPLGLECSGIVTRVGSGVTGLKVGDRVM 56
Query: 513 GLTSGRSLANCCETDVEMAWEIPDQWTLEDAATVPCVYATAVYAMFICGQMQKGESILIH 572
GL G + A D + +IPD + E+AAT+P Y TA YA+ ++QKGES+LIH
Sbjct: 57 GLAPG-AFATHVRVDARLVVKIPDSLSFEEAATLPVAYLTAYYALVDLARLQKGESVLIH 115
Query: 573 AGSGGVGQAAINLARYMDAEIFTTVGTPEKREFIRKTFPFIKEENIGNSRDTSFEQLVMK 632
A +GGVGQAAI LA+++ AE+F TVG+ EKREF+R+ ++I +SRD SF +++
Sbjct: 116 AAAGGVGQAAIQLAQHLGAEVFATVGSEEKREFLRELGGP--VDHIFSSRDLSFADGILR 173
Query: 633 RTKGRGVDLVLNSLAEEKLQASVRCLAQGGRFLEIGKFDLANNNMLGMEVFMRETSFHGV 692
T GRGVD+VLNSL+ E L+AS RCLA GRF+EIGK D+ +N+ LGM F+R SF V
Sbjct: 174 ATGGRGVDVVLNSLSGELLRASWRCLAPFGRFVEIGKRDILSNSKLGMRPFLRNVSFSSV 233
Query: 693 MLDNFFFAEQEWKMSLQKALQKAID---AGAVQPLVRTIFPEDKVEEAFRYMAAGKHIGK 749
LD E L++ L++ ++ AG ++PL T+ P +AFR M +GKHIGK
Sbjct: 234 DLDQLARERPEL---LRELLREVLELLEAGVLKPLPPTVVPSASEIDAFRLMQSGKHIGK 290
Query: 750 VII 752
V++
Sbjct: 291 VVL 293
>gnl|CDD|187657 cd08954, KR_1_FAS_SDR_x, beta-ketoacyl reductase (KR) domain of fatty
acid synthase (FAS), subgroup 1, complex (x) SDRs.
NADP-dependent KR domain of the multidomain type I FAS, a
complex SDR family. This subfamily also includes proteins
identified as polyketide synthase (PKS), a protein with
related modular protein architecture and similar
function. It includes the KR domains of mammalian and
chicken FAS, and Dictyostelium discoideum putative
polyketide synthases (PKSs). These KR domains contain two
subdomains, each of which is related to SDR Rossmann fold
domains. However, while the C-terminal subdomain has an
active site similar to the other SDRs and a NADP-binding
capability, the N-terminal SDR-like subdomain is
truncated and lacks these functions, serving a supportive
structural role. In some instances, such as porcine FAS,
an enoyl reductase (a Rossman fold NAD-binding domain of
the medium-chain dehydrogenase/reductase, MDR family)
module is inserted between the sub-domains. Fatty acid
synthesis occurs via the stepwise elongation of a chain
(which is attached to acyl carrier protein, ACP) with
2-carbon units. Eukaryotic systems consists of large,
multifunctional synthases (type I) while bacterial, type
II systems, use single function proteins. Fungal fatty
acid synthesis uses a dodecamer of 6 alpha and 6 beta
subunits. In mammalian type FAS cycles, ketoacyl
synthase forms acetoacetyl-ACP which is reduced by the
NADP-dependent beta-ketoacyl reductase (KR), forming
beta-hydroxyacyl-ACP, which is in turn dehydrated by
dehydratase to a beta-enoyl intermediate, which is
reduced by NADP-dependent beta-enoyl reductase (ER); this
KR and ER are members of the SDR family. This KR
subfamily has an active site tetrad with a similar 3D
orientation compared to archetypical SDRs, but the active
site Lys and Asn residue positions are swapped. The
characteristic NADP-binding is typical of the multidomain
complex SDRs, with a GGXGXXG NADP 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 prostaglandin dehydrogenase
(PGDH) numbering). In addition to the Tyr and Lys, there
is often an upstream Ser (Ser-138, PGDH numbering) and/or
an Asn (Asn-107, 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 KRs 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 = 452
Score = 263 bits (673), Expect = 3e-77
Identities = 92/245 (37%), Positives = 138/245 (56%), Gaps = 11/245 (4%)
Query: 774 PRYYADSNKSYIICGGLGGFGLELADWLVLRGARK-LVLTSRSGVKNGYQALRIKIWKSY 832
Y + KSY+I GG GG GLE+ WLV RGA + +++ SRSG+K L I+ WKS
Sbjct: 211 TNYPINLGKSYLITGGSGGLGLEILKWLVKRGAVENIIILSRSGMKWE-LELLIREWKSQ 269
Query: 833 D---VQVLISTDDITTEAGVVNLLTEANKLGPVDGIFNLAVVLKDALFENQTPEDFNASL 889
+ V + D+++ +NL+ A K+GP+ GIF+LA VL D + E T F +
Sbjct: 270 NIKFHFVSVDVSDVSSLEKAINLILNAPKIGPIGGIFHLAFVLIDKVLEIDTESLFISVN 329
Query: 890 GPKANATKYFDKYSRTMCPTLGQFVVFSSVSCGRGNAGQTNYGMANSIMERICEARRAEG 949
K S C L FV+FSSVS RG+AGQ NY ANS+++ + R++ G
Sbjct: 330 KAKVMGAINLHNQSIKRCWKLDYFVLFSSVSSIRGSAGQCNYVCANSVLDSLSRYRKSIG 389
Query: 950 LPGLAVEWGAVGEVGLVADMAEDNLEVVIG--GTLQQRISNCLECLNEFL--IQSEPIVA 1005
LP +A+ WGA+G+VG V+ ++++ ++G G L Q I++CL L+ FL +++
Sbjct: 390 LPSIAINWGAIGDVGFVSRN--ESVDTLLGGQGLLPQSINSCLGTLDLFLQNPSPNLVLS 447
Query: 1006 SMVVA 1010
S A
Sbjct: 448 SFNFA 452
Score = 58.6 bits (142), Expect = 1e-08
Identities = 28/117 (23%), Positives = 53/117 (45%), Gaps = 6/117 (5%)
Query: 300 KSPVKISPLVIKVSGVDFHWIPILQKALAAEETSTKQKIILLSQLEPLSGIIGFFNCIRK 359
+ V F ++ IL+ LA T++ + ++L + SG+IG R+
Sbjct: 92 IQSPTDKSEFLPVEEQTFEYVEILKSLLA---TASCKPVLLTADGCESSGVIGAVRYFRE 148
Query: 360 ETGGERTRCFEILDKNA--PPFNPEDPFYKVQVEKDLAV-NILRNGQWGTYRHSILQ 413
E + RC + + N+ P Y +V+K+ + N+ ++G WG +RH +L
Sbjct: 149 EPQLKLIRCLFVSNLNSQKEPIIRNGKVYYERVKKNSNIKNVYKSGSWGDFRHLLLD 205
>gnl|CDD|214833 smart00822, PKS_KR, This enzymatic domain is part of bacterial
polyketide synthases. It catalyses the first step in
the reductive modification of the beta-carbonyl centres
in the growing polyketide chain. It uses NADPH to reduce
the keto group to a hydroxy group.
Length = 180
Score = 196 bits (502), Expect = 1e-57
Identities = 68/182 (37%), Positives = 96/182 (52%), Gaps = 3/182 (1%)
Query: 782 KSYIICGGLGGFGLELADWLVLRGARKLVLTSRSGVKNGYQALRIKIWKSYDVQVLISTD 841
+Y+I GGLGG G LA WL RGAR+LVL SRSG A + ++ +V +
Sbjct: 1 GTYLITGGLGGLGRALARWLAERGARRLVLLSRSGPDAPGAAALLAELEAAGARVTVVAC 60
Query: 842 DITTEAGVVNLLTEA-NKLGPVDGIFNLAVVLKDALFENQTPEDFNASLGPKANATKYFD 900
D+ + +L GP+ G+ + A VL D + + TPE F A L PKA
Sbjct: 61 DVADRDALAAVLAAIPAVEGPLTGVIHAAGVLDDGVLASLTPERFAAVLAPKAAGAWNLH 120
Query: 901 KYSRTMCPTLGQFVVFSSVSCGRGNAGQTNYGMANSIMERICEARRAEGLPGLAVEWGAV 960
+ + L FV+FSS++ G+ GQ NY AN+ ++ + E RRA GLP L++ WGA
Sbjct: 121 ELTA--DLPLDFFVLFSSIAGVLGSPGQANYAAANAFLDALAEYRRARGLPALSIAWGAW 178
Query: 961 GE 962
E
Sbjct: 179 AE 180
>gnl|CDD|187582 cd05274, KR_FAS_SDR_x, ketoreductase (KR) and fatty acid synthase
(FAS), complex (x) SDRs. Ketoreductase, a module of the
multidomain polyketide synthase (PKS), has 2 subdomains,
each corresponding to a SDR family monomer. The
C-terminal subdomain catalyzes the NADPH-dependent
reduction of the beta-carbonyl of a polyketide to a
hydroxyl group, a step in the biosynthesis of
polyketides, such as erythromycin. The N-terminal
subdomain, an interdomain linker, is a truncated Rossmann
fold which acts to stabilizes the catalytic subdomain.
Unlike typical SDRs, the isolated domain does not
oligomerize but is composed of 2 subdomains, each
resembling an SDR monomer. The active site resembles that
of typical SDRs, except that the usual positions of the
catalytic Asn and Tyr are swapped, so that the canonical
YXXXK motif changes to YXXXN. Modular PKSs are
multifunctional structures in which the makeup
recapitulates that found in (and may have evolved from)
FAS. In some instances, such as porcine FAS, an enoyl
reductase (ER) module is inserted between the
sub-domains. Fatty acid synthesis occurs via the stepwise
elongation of a chain (which is attached to acyl carrier
protein, ACP) with 2-carbon units. Eukaryotic systems
consist of large, multifunctional synthases (type I)
while bacterial, type II systems, use single function
proteins. Fungal fatty acid synthase uses a dodecamer of
6 alpha and 6 beta subunits. In mammalian type FAS
cycles, ketoacyl synthase forms acetoacetyl-ACP which is
reduced by the NADP-dependent beta-KR, forming
beta-hydroxyacyl-ACP, which is in turn dehydrated by
dehydratase to a beta-enoyl intermediate, which is
reduced by NADP-dependent beta-ER. Polyketide synthesis
also proceeds via the addition of 2-carbon units as in
fatty acid synthesis. The complex SDR NADP-binding motif,
GGXGXXG, is often present, but is not strictly conserved
in each instance of the module. 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 prostaglandin
dehydrogenase (PGDH) numbering). In addition to the Tyr
and Lys, there is often an upstream Ser (Ser-138, PGDH
numbering) and/or an Asn (Asn-107, 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 KRs 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 = 375
Score = 190 bits (485), Expect = 5e-53
Identities = 80/238 (33%), Positives = 111/238 (46%), Gaps = 18/238 (7%)
Query: 778 ADSNKSYIICGGLGGFGLELADWLVLRGARKLVLTSRSGVKNGYQALRIKIWKSYDVQVL 837
+ +Y+I GGLGG GL +A WL RGAR LVL SR G A R + ++ +V
Sbjct: 147 GGLDGTYLITGGLGGLGLLVARWLAARGARHLVLLSRRGPAPRAAA-RAALLRAGGARVS 205
Query: 838 ISTDDITTEAGVVNLLTEANKLGPVDGIFNLAVVLKDALFENQTPEDFNASLGPKANATK 897
+ D+T A + LL E GP+ G+ + A VL+DAL TP F A L K
Sbjct: 206 VVRCDVTDPAALAALLAELAAGGPLAGVIHAAGVLRDALLAELTPAAFAAVLAAKVAGA- 264
Query: 898 YFDKYSRTMCPTLGQ-----FVVFSSVSCGRGNAGQTNYGMANSIMERICEARRAEGLPG 952
+ FV+FSSV+ G AGQ Y AN+ ++ + RR GLP
Sbjct: 265 ------LNLHELTPDLPLDFFVLFSSVAALLGGAGQAAYAAANAFLDALAAQRRRRGLPA 318
Query: 953 LAVEWGAVGEVGLVADMAEDNLEVVIGGTLQQRISNCLECLNEFLI---QSEPIVASM 1007
+V+WGA G+ A A + G + LE L E L+ + +VAS+
Sbjct: 319 TSVQWGAWAGGGMAAAAALRAR-LARSGLGPLAPAEALEAL-EALLASDAPQAVVASV 374
>gnl|CDD|176180 cd05276, p53_inducible_oxidoreductase, PIG3 p53-inducible quinone
oxidoreductase. PIG3 p53-inducible quinone
oxidoreductase, a medium chain dehydrogenase/reductase
family member, acts in the apoptotic pathway. PIG3
reduces ortho-quinones, but its apoptotic activity has
been attributed to oxidative stress generation, since
overexpression of PIG3 accumulates reactive oxygen
species. PIG3 resembles the MDR family member quinone
reductases, which catalyze the reduction of quinone to
hydroxyquinone. NAD(P)(H)-dependent oxidoreductases are
the major enzymes in the interconversion of alcohols and
aldehydes or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which has a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES.
These proteins typically form dimers (typically higher
plants, mammals) or tetramers (yeast, bacteria), and
have 2 tightly bound zinc atoms per subunit, a catalytic
zinc at the active site, and a structural zinc in a lobe
of the catalytic domain. NAD(H) binding occurs in the
cleft between the catalytic and coenzyme-binding domains
at the active site, and coenzyme binding induces a
conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
In human ADH catalysis, the zinc ion helps coordinate
the alcohol, followed by deprotonation of a histidine,
the ribose of NAD, a serine, then the alcohol, which
allows the transfer of a hydride to NAD+, creating NADH
and a zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 323
Score = 179 bits (457), Expect = 7e-50
Identities = 77/259 (29%), Positives = 125/259 (48%), Gaps = 31/259 (11%)
Query: 508 GKRVMGLTSGRSLANCCETDVEMAWEIPDQWTLEDAATVPCVYATAVYAMFICGQMQKGE 567
G RV L +G A +P+ +L +AA +P V+ TA +F G ++ GE
Sbjct: 82 GDRVCALLAGGGYAEYVVVPAGQLLPVPEGLSLVEAAALPEVFFTAWQNLFQLGGLKAGE 141
Query: 568 SILIHAGSGGVGQAAINLARYMDAEIFTTVGTPEKREFIRK---TFPFIKEENIGNSRDT 624
++LIH G+ GVG AAI LA+ + A + T G+ EK E R N R
Sbjct: 142 TVLIHGGASGVGTAAIQLAKALGARVIATAGSEEKLEACRALGADVAI-------NYRTE 194
Query: 625 SFEQLVMKRTKGRGVDLVLNSLAEEKLQASVRCLAQGGRFLEIG-------KFDLANNNM 677
F + V + T GRGVD++L+ + + L ++R LA GR + IG + DLA
Sbjct: 195 DFAEEVKEATGGRGVDVILDMVGGDYLARNLRALAPDGRLVLIGLLGGAKAELDLA---- 250
Query: 678 LGMEVFMRETSFHGVMLDNFFFAEQEWKMSLQKALQK----AIDAGAVQPLVRTIFPEDK 733
+ + + G L + E K +L A ++ +G ++P++ +FP ++
Sbjct: 251 ---PLLRKRLTLTGSTLRS---RSLEEKAALAAAFREHVWPLFASGRIRPVIDKVFPLEE 304
Query: 734 VEEAFRYMAAGKHIGKVII 752
EA R M + +HIGK+++
Sbjct: 305 AAEAHRRMESNEHIGKIVL 323
>gnl|CDD|219957 pfam08659, KR, KR domain. This enzymatic domain is part of
bacterial polyketide synthases and catalyzes the first
step in the reductive modification of the beta-carbonyl
centres in the growing polyketide chain. It uses NADPH
to reduce the keto group to a hydroxy group.
Length = 181
Score = 173 bits (441), Expect = 2e-49
Identities = 70/182 (38%), Positives = 99/182 (54%), Gaps = 3/182 (1%)
Query: 783 SYIICGGLGGFGLELADWLVLRGARKLVLTSRSGVKNGYQALRIKIWKSYDVQVLISTDD 842
+Y++ GGLGG GLELA WL RGAR LVL SRSG + + ++ +V + D
Sbjct: 2 TYLVTGGLGGLGLELARWLAERGARHLVLLSRSGAPDPEAEALLAELEARGAEVTVVACD 61
Query: 843 ITTEAGVVNLLTEANK-LGPVDGIFNLAVVLKDALFENQTPEDFNASLGPKANATKYFDK 901
++ V LL E P+ G+ + A VL+DAL N T EDF L PK +
Sbjct: 62 VSDRDAVRALLAEIRADGPPLRGVIHAAGVLRDALLANMTAEDFARVLAPKVTGAWNLHE 121
Query: 902 YSRTMCPTLGQFVVFSSVSCGRGNAGQTNYGMANSIMERICEARRAEGLPGLAVEWGAVG 961
+R P L FV+FSS++ G+ GQ NY AN+ ++ + RRA+GLP ++ WG
Sbjct: 122 ATR-DRP-LDFFVLFSSIAGVLGSPGQANYAAANAFLDALAHYRRAQGLPATSINWGPWA 179
Query: 962 EV 963
+V
Sbjct: 180 DV 181
>gnl|CDD|215720 pfam00106, adh_short, short chain dehydrogenase. This family
contains a wide variety of dehydrogenases.
Length = 167
Score = 171 bits (436), Expect = 4e-49
Identities = 66/170 (38%), Positives = 89/170 (52%), Gaps = 4/170 (2%)
Query: 782 KSYIICGGLGGFGLELADWLVLRGARKLVLTSRSGVKNGYQALRIKIWKSYDVQVLISTD 841
+ +I GG GG GL LA WL GAR LVL SR G G L + ++ +V ++
Sbjct: 1 GTVLITGGTGGLGLALARWLAAEGARHLVLVSRRGPAPGAAEL-VAELEALGAEVTVAAC 59
Query: 842 DITTEAGVVNLLTEANK-LGPVDGIFNLAVVLKDALFENQTPEDFNASLGPKANATKYFD 900
D+ + LL LGP+DG+ + A VL D E TPE F L PK
Sbjct: 60 DVADRDALAALLAALPAALGPLDGVVHNAGVLDDGPLEELTPERFERVLAPKVTGAWNLH 119
Query: 901 KYSRTMCPTLGQFVVFSSVSCGRGNAGQTNYGMANSIMERICEARRAEGL 950
+ +R + LG FV+FSSV+ G+ GQ NY AN+ ++ + E RRAEGL
Sbjct: 120 ELTRDL--DLGAFVLFSSVAGVLGSPGQANYAAANAALDALAEHRRAEGL 167
>gnl|CDD|176203 cd08241, QOR1, Quinone oxidoreductase (QOR). QOR catalyzes the
conversion of a quinone + NAD(P)H to a hydroquinone +
NAD(P)+. Quinones are cyclic diones derived from
aromatic compounds. Membrane bound QOR acts in the
respiratory chains of bacteria and mitochondria, while
soluble QOR acts to protect from toxic quinones (e.g.
DT-diaphorase) or as a soluble eye-lens protein in some
vertebrates (e.g. zeta-crystalin). QOR reduces quinones
through a semi-quinone intermediate via a
NAD(P)H-dependent single electron transfer. QOR is a
member of the medium chain dehydrogenase/reductase
family, but lacks the zinc-binding sites of the
prototypical alcohol dehydrogenases of this group.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which has a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES. These
proteins typically form dimers (typically higher plants,
mammals) or tetramers (yeast, bacteria), and have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site, and a structural zinc in a lobe of
the catalytic domain. NAD(H)-binding occurs in the
cleft between the catalytic and coenzyme-binding domains
at the active site, and coenzyme binding induces a
conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
In human ADH catalysis, the zinc ion helps coordinate
the alcohol, followed by deprotonation of a histidine,
the ribose of NAD, a serine, then the alcohol, which
allows the transfer of a hydride to NAD+, creating NADH
and a zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 323
Score = 169 bits (431), Expect = 2e-46
Identities = 85/318 (26%), Positives = 138/318 (43%), Gaps = 53/318 (16%)
Query: 462 QIYYSSINFRDIMLTTAKLAPEVIESRRLYQHC-----VIGFEYSGRLRDSGK------- 509
++ + +NF D+++ K YQ V G E +G + G+
Sbjct: 33 RVEAAGVNFPDLLMIQGK-----------YQVKPPLPFVPGSEVAGVVEAVGEGVTGFKV 81
Query: 510 --RVMGLTSGRSLANCCETDVEMAWEIPDQWTLEDAATVPCVYATAVYAMFICGQMQKGE 567
RV+ LT A + +PD + E+AA +P Y TA +A+ ++Q GE
Sbjct: 82 GDRVVALTGQGGFAEEVVVPAAAVFPLPDGLSFEEAAALPVTYGTAYHALVRRARLQPGE 141
Query: 568 SILIHAGSGGVGQAAINLARYMDAEIFTTVGTPEKREFIRKTFPFIKEENIG-----NSR 622
++L+ +GGVG AA+ LA+ + A + + EK R +G + R
Sbjct: 142 TVLVLGAAGGVGLAAVQLAKALGARVIAAASSEEKLALARA---------LGADHVIDYR 192
Query: 623 DTSFEQLVMKRTKGRGVDLVLNSLAEEKLQASVRCLAQGGRFLEIG-------KFDLANN 675
D + V T GRGVD+V + + + +AS+R LA GGR L IG +
Sbjct: 193 DPDLRERVKALTGGRGVDVVYDPVGGDVFEASLRSLAWGGRLLVIGFASGEIPQIPA--- 249
Query: 676 NMLGMEVFMRETSFHGVMLDNFFFAEQEWKMSLQKALQKAIDAGAVQPLVRTIFPEDKVE 735
N+L ++ S GV + E E + L + G ++P V +FP ++
Sbjct: 250 NLL----LLKNISVVGVYWGAYARREPELLRANLAELFDLLAEGKIRPHVSAVFPLEQAA 305
Query: 736 EAFRYMAAGKHIGKVIIK 753
EA R +A K GKV++
Sbjct: 306 EALRALADRKATGKVVLT 323
>gnl|CDD|176213 cd08251, polyketide_synthase, polyketide synthase. Polyketide
synthases produce polyketides in step by step mechanism
that is similar to fatty acid synthesis. Enoyl reductase
reduces a double to single bond. Erythromycin is one
example of a polyketide generated by 3 complex enzymes
(megasynthases). 2-enoyl thioester reductase (ETR)
catalyzes the NADPH-dependent dependent conversion of
trans-2-enoyl acyl carrier protein/coenzyme A (ACP/CoA)
to acyl-(ACP/CoA) in fatty acid synthesis. 2-enoyl
thioester reductase activity has been linked in Candida
tropicalis as essential in maintaining mitiochondrial
respiratory function. This ETR family is a part of the
medium chain dehydrogenase/reductase family, but lack
the zinc coordination sites characteristic of the
alcohol dehydrogenases in this family.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which have a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. The N-terminal catalytic domain has a
distant homology to GroES. These proteins typically form
dimers (typically higher plants, mammals) or tetramers
(yeast, bacteria), and have 2 tightly bound zinc atoms
per subunit, a catalytic zinc at the active site, and a
structural zinc in a lobe of the catalytic domain.
NAD(H)-binding occurs in the cleft between the catalytic
and coenzyme-binding domains at the active site, and
coenzyme binding induces a conformational closing of
this cleft. Coenzyme binding typically precedes and
contributes to substrate binding.
Length = 303
Score = 167 bits (424), Expect = 9e-46
Identities = 87/270 (32%), Positives = 137/270 (50%), Gaps = 22/270 (8%)
Query: 497 GFEYSGRLRDSGKRVMGLTSG--------------RSLANCCETDVEMAWEIPDQWTLED 542
GFE SG +R G V L G +L E V P + E+
Sbjct: 42 GFEASGVVRAVGPHVTRLAVGDEVIAGTGESMGGHATLVTVPEDQVVRK---PASLSFEE 98
Query: 543 AATVPCVYATAVYAMFICGQMQKGESILIHAGSGGVGQAAINLARYMDAEIFTTVGTPEK 602
A +P V+ T + A F + KGE ILI +GG G A+ LAR AEI+ T + +K
Sbjct: 99 ACALPVVFLTVIDA-FARAGLAKGEHILIQTATGGTGLMAVQLARLKGAEIYATASSDDK 157
Query: 603 REFIRKTFPFIKEENIGNSRDTSFEQLVMKRTKGRGVDLVLNSLAEEKLQASVRCLAQGG 662
E++++ + ++ N + FE+ +M+ T GRGVD+V+N+L+ E +Q + CLA GG
Sbjct: 158 LEYLKQ----LGVPHVINYVEEDFEEEIMRLTGGRGVDVVINTLSGEAIQKGLNCLAPGG 213
Query: 663 RFLEIGKFDLANNNMLGMEVFMRETSFHGVMLDNFFFAEQEWKMSLQKALQKAIDAGAVQ 722
R++EI L + + + V SFH V L + E+ Q + ++ G ++
Sbjct: 214 RYVEIAMTALKSAPSVDLSVLSNNQSFHSVDLRKLLLLDPEFIADYQAEMVSLVEEGELR 273
Query: 723 PLVRTIFPEDKVEEAFRYMAAGKHIGKVII 752
P V IFP D + EA+RY++ ++IGKV++
Sbjct: 274 PTVSRIFPFDDIGEAYRYLSDRENIGKVVV 303
>gnl|CDD|187658 cd08955, KR_2_FAS_SDR_x, beta-ketoacyl reductase (KR) domain of
fatty acid synthase (FAS), subgroup 2, complex (x).
Ketoreductase, a module of the multidomain polyketide
synthase, has 2 subdomains, each corresponding to a
short-chain dehydrogenases/reductase (SDR) family
monomer. The C-terminal subdomain catalyzes the
NADPH-dependent reduction of the beta-carbonyl of a
polyketide to a hydroxyl group, a step in the
biosynthesis of polyketides, such as erythromycin. The
N-terminal subdomain, an interdomain linker, is a
truncated Rossmann fold which acts to stabilizes the
catalytic subdomain. Unlike typical SDRs, the isolated
domain does not oligomerizes but is composed of 2
subdomains, each resembling an SDR monomer. In some
instances, as in porcine FAS, an enoyl reductase (a
Rossman fold NAD binding domain of the MDR family)
module is inserted between the sub-domains. The active
site resembles that of typical SDRs, except that the
usual positions of the catalytic asparagine and tyrosine
are swapped, so that the canonical YXXXK motif changes
to YXXXN. Modular polyketide synthases are
multifunctional structures in which the makeup
recapitulates that found in (and may have evolved from)
fatty acid synthase. In some instances, such as
porcine FAS , an enoyl reductase module is inserted
between the sub-domains. Fatty acid synthesis occurs via
the stepwise elongation of a chain (which is attached to
acyl carrier protein, ACP) with 2-carbon units.
Eukaryotic systems consists of large, multifunctional
synthases (type I) while bacterial, type II systems, use
single function proteins. Fungal fatty acid synthesis
uses dodecamer of 6 alpha and 6 beta subunits. In
mammalian type FAS cycles, ketoacyl synthase forms
acetoacetyl-ACP which is reduced by the NADP-dependent
beta-ketoacyl reductase (KR), forming
beta-hydroxyacyl-ACP, which is in turn dehydrated by
dehydratase to a beta-enoyl intermediate, which is
reduced by NADP-dependent beta-enoyl reductase (ER).
Polyketide syntheses also proceeds via the addition of
2-carbon units as in fatty acid synthesis. The complex
SDR NADP binding motif, GGXGXXG, is often present, but
is not strictly conserved in each instance of the
module. This subfamily includes the KR domain of the
Lyngbya majuscule Jam J, -K, and #L which are encoded
on the jam gene cluster and are involved in the
synthesis of the Jamaicamides (neurotoxins); Lyngbya
majuscule Jam P belongs to a different KR_FAS_SDR_x
subfamily. 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
prostaglandin dehydrogenase (PGDH) numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser (Ser-138, PGDH numbering) and/or an Asn (Asn-107,
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 KRs 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 = 376
Score = 152 bits (387), Expect = 5e-40
Identities = 69/195 (35%), Positives = 101/195 (51%), Gaps = 4/195 (2%)
Query: 780 SNKSYIICGGLGGFGLELADWLVLRGARKLVLTSRSGVKNGYQALRIKIWKSYDVQVLIS 839
+ +Y+I GGLGG GL +A+WLV RGAR LVLT R + I + +V++
Sbjct: 148 PDATYLITGGLGGLGLLVAEWLVERGARHLVLTGRRAPSAAARQ-AIAALEEAGAEVVVL 206
Query: 840 TDDITTEAGVVNLLTEANK-LGPVDGIFNLAVVLKDALFENQTPEDFNASLGPKANATKY 898
D++ + L + L P+ G+ + A VL D + NQ E F L PK
Sbjct: 207 AADVSDRDALAAALAQIRASLPPLRGVIHAAGVLDDGVLANQDWERFRKVLAPKVQGAWN 266
Query: 899 FDKYSRTMCPTLGQFVVFSSVSCGRGNAGQTNYGMANSIMERICEARRAEGLPGLAVEWG 958
+ ++ P L FV+FSSV+ G+ GQ NY AN+ ++ + RRA GLP L++ WG
Sbjct: 267 LHQLTQD-LP-LDFFVLFSSVASLLGSPGQANYAAANAFLDALAHYRRARGLPALSINWG 324
Query: 959 AVGEVGLVADMAEDN 973
EVG+ A +A
Sbjct: 325 PWAEVGMAASLARQA 339
>gnl|CDD|223677 COG0604, Qor, NADPH:quinone reductase and related Zn-dependent
oxidoreductases [Energy production and conversion /
General function prediction only].
Length = 326
Score = 150 bits (382), Expect = 6e-40
Identities = 72/307 (23%), Positives = 129/307 (42%), Gaps = 33/307 (10%)
Query: 465 YSSINFRDIMLTTAKLAPEVIESRRLYQHCVIGFEYSGRLRDS---------GKRVMGLT 515
+ +N D+++ P + G E +G + G RV L
Sbjct: 36 AAGVNPIDVLVRQGLAPPVRPLPF------IPGSEAAGVVVAVGSGVTGFKVGDRVAALG 89
Query: 516 SGR---SLANCCETDVEMAWEIPDQWTLEDAATVPCVYATAVYAMFICGQMQKGESILIH 572
A + +PD + E+AA +P TA A+F ++ GE++L+H
Sbjct: 90 GVGRDGGYAEYVVVPADWLVPLPDGLSFEEAAALPLAGLTAWLALFDRAGLKPGETVLVH 149
Query: 573 AGSGGVGQAAINLARYMDAEIFTTVGTPEKREFIRKTFPFIKEENIGNSRDTSFEQLVMK 632
+GGVG AAI LA+ + A + V + EK E +++ + N R+ F + V +
Sbjct: 150 GAAGGVGSAAIQLAKALGATVVAVVSSSEKLELLKELGADH----VINYREEDFVEQVRE 205
Query: 633 RTKGRGVDLVLNSLAEEKLQASVRCLAQGGRFLEIG----KFDLANNNMLGMEVFMRETS 688
T G+GVD+VL+++ + AS+ LA GGR + IG + N + + +
Sbjct: 206 LTGGKGVDVVLDTVGGDTFAASLAALAPGGRLVSIGALSGGPPVPLNLLPLLGKRLTLRG 265
Query: 689 FHGVMLDNFFFAEQEWKMSLQKALQKAIDAGAVQPLVRTIFP-EDKVEEAFRYMAAGKHI 747
D AE L + +G ++P++ ++P + A + +
Sbjct: 266 VTLGSRDPEALAEAL------AELFDLLASGKLKPVIDRVYPLAEAPAAAAHLLLERRTT 319
Query: 748 GKVIIKI 754
GKV++K+
Sbjct: 320 GKVVLKV 326
>gnl|CDD|176227 cd08266, Zn_ADH_like1, Alcohol dehydrogenases of the MDR family.
This group contains proteins related to the
zinc-dependent alcohol dehydrogenases. However, while
the group has structural zinc site characteristic of
these enzymes, it lacks the consensus site for a
catalytic zinc. NAD(P)(H)-dependent oxidoreductases are
the major enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which has a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES. These
proteins typically form dimers (typically higher plants,
mammals) or tetramers (yeast, bacteria), and have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site, and a structural zinc in a lobe of
the catalytic domain. NAD(H)-binding occurs in the cleft
between the catalytic and coenzyme-binding domains at
the active site, and coenzyme binding induces a
conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
In human ADH catalysis, the zinc ion helps coordinate
the alcohol, followed by deprotonation of a histidine,
the ribose of NAD, a serine, then the alcohol, which
allows the transfer of a hydride to NAD+, creating NADH
and a zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 342
Score = 150 bits (381), Expect = 1e-39
Identities = 63/233 (27%), Positives = 112/233 (48%), Gaps = 37/233 (15%)
Query: 534 IPDQWTLEDAATVPCVYATAVYAMFICGQMQKGESILIHAGSGGVGQAAINLARYMDAEI 593
IPD + E+AA P + TA + + +++ GE++L+H GVG AAI +A+ A +
Sbjct: 135 IPDNLSFEEAAAAPLTFLTAWHMLVTRARLRPGETVLVHGAGSGVGSAAIQIAKLFGATV 194
Query: 594 FTTVGTPEKREFIRKTFPFIKEENIG-----NSRDTSFEQLVMKRTKGRGVDLVLNSLAE 648
T G+ +K E + + +G + R F + V + T RGVD+V+ +
Sbjct: 195 IATAGSEDKLE---------RAKELGADYVIDYRKEDFVREVRELTGKRGVDVVVEHVGA 245
Query: 649 EKLQASVRCLAQGGRFLEIG-------KFDLANNNMLGMEVFMRETSFHGVMLDNFFFAE 701
+ S++ LA+GGR + G DL VF R+ S G + AE
Sbjct: 246 ATWEKSLKSLARGGRLVTCGATTGYEAPIDL-------RHVFWRQLSILGSTMGT--KAE 296
Query: 702 QEWKMSLQKALQKAIDAGAVQPLVRTIFPEDKVEEAFRYMAAGKHIGKVIIKI 754
L +AL+ + G ++P++ ++FP ++ EA R + + + GK+++
Sbjct: 297 ------LDEALRL-VFRGKLKPVIDSVFPLEEAAEAHRRLESREQFGKIVLTP 342
>gnl|CDD|234027 TIGR02824, quinone_pig3, putative NAD(P)H quinone oxidoreductase,
PIG3 family. Members of this family are putative
quinone oxidoreductases that belong to the broader
superfamily (modeled by Pfam pfam00107) of
zinc-dependent alcohol (of medium chain length)
dehydrogenases and quinone oxiooreductases. The
alignment shows no motif of conserved Cys residues as
are found in zinc-binding members of the superfamily,
and members are likely to be quinone oxidoreductases
instead. A member of this family in Homo sapiens, PIG3,
is induced by p53 but is otherwise uncharacterized
[Unknown function, Enzymes of unknown specificity].
Length = 325
Score = 148 bits (377), Expect = 3e-39
Identities = 74/285 (25%), Positives = 130/285 (45%), Gaps = 44/285 (15%)
Query: 495 VIGFEYSGRLRD---------SGKRVMGLTSGRSLANCCETDVEMAWEIPDQWTLEDAAT 545
++G E +G + G RV L +G A +P+ +L +AA
Sbjct: 60 ILGLEVAGEVVAVGEGVSRWKVGDRVCALVAGGGYAEYVAVPAGQVLPVPEGLSLVEAAA 119
Query: 546 VPCVYATAVYAMFICGQMQKGESILIHAGSGGVGQAAINLARYMDAEIFTTVGTPEKREF 605
+P + T +F G ++ GE++LIH G+ G+G AI LA+ A +FTT G+ EK
Sbjct: 120 LPETFFTVWSNLFQRGGLKAGETVLIHGGASGIGTTAIQLAKAFGARVFTTAGSDEKCAA 179
Query: 606 IRKTFPFIKEENIG-----NSRDTSFEQLVMKRTKGRGVDLVLNSLAEEKLQASVRCLAQ 660
+G N R+ F ++V T G+GVD++L+ + L +++ LA
Sbjct: 180 CEA---------LGADIAINYREEDFVEVVKAETGGKGVDVILDIVGGSYLNRNIKALAL 230
Query: 661 GGRFLEIG-------KFDLANNNMLGMEVFMRETSFHGVMLDNFFFAEQEWKMSLQKALQ 713
GR ++IG + DL + + + G L AE K ++ L+
Sbjct: 231 DGRIVQIGFQGGRKAELDLG-------PLLAKRLTITGSTLRARPVAE---KAAIAAELR 280
Query: 714 KA----IDAGAVQPLVRTIFPEDKVEEAFRYMAAGKHIGKVIIKI 754
+ + +G V+P++ +FP + +A M +G HIGK+++ +
Sbjct: 281 EHVWPLLASGRVRPVIDKVFPLEDAAQAHALMESGDHIGKIVLTV 325
>gnl|CDD|176236 cd08275, MDR3, Medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family.
This group is a member of the medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, but lacks the zinc-binding
sites of the zinc-dependent alcohol dehydrogenases. The
medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P)-binding Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 337
Score = 136 bits (346), Expect = 5e-35
Identities = 88/321 (27%), Positives = 141/321 (43%), Gaps = 55/321 (17%)
Query: 467 SINFRDIMLTTAKLAPEVIESRR-LYQ-----HCVIGFEYSGRLRDSGK---------RV 511
+NF D+M +R+ LY V GFE +G + G+ RV
Sbjct: 37 GLNFADLM------------ARQGLYDSAPKPPFVPGFECAGTVEAVGEGVKDFKVGDRV 84
Query: 512 MGLTSGRSLANCCETDVEMAWEIPDQWTLEDAATVPCVYATAVYAMFICGQMQKGESILI 571
MGLT A + + +PD + E+AA P Y TA YA+F G ++ G+S+L+
Sbjct: 85 MGLTRFGGYAEVVNVPADQVFPLPDGMSFEEAAAFPVNYLTAYYALFELGNLRPGQSVLV 144
Query: 572 HAGSGGVGQAAINLARYMDAEIFTTVGT--PEKREFIRKTFPFIKEENIGNSRDTSFEQL 629
H+ +GGVG AA L + T VGT K E +KE + + D +
Sbjct: 145 HSAAGGVGLAAGQLCK--TVPNVTVVGTASASKHE-------ALKENGVTHVIDYRTQDY 195
Query: 630 V--MKRTKGRGVDLVLNSLAEEKLQASVRCLAQGGRFLEIGKFDLANNNMLGM----EVF 683
V +K+ GVD+VL++L E + S L GR + G +L + +
Sbjct: 196 VEEVKKISPEGVDIVLDALGGEDTRKSYDLLKPMGRLVVYGAANLVTGEKRSWFKLAKKW 255
Query: 684 MRETSFHGVML--DN---------FFFAEQEWKMSLQKALQKAIDAGAVQPLVRTIFPED 732
+ L +N + F E+E + L K + G ++P + ++FP +
Sbjct: 256 WNRPKVDPMKLISENKSVLGFNLGWLFEERELLTEVMDKLLKLYEEGKIKPKIDSVFPFE 315
Query: 733 KVEEAFRYMAAGKHIGKVIIK 753
+V EA R + + K+IGKV++
Sbjct: 316 EVGEAMRRLQSRKNIGKVVLT 336
>gnl|CDD|176233 cd08272, MDR6, Medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family.
This group is a member of the medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, but lacks the zinc-binding
sites of the zinc-dependent alcohol dehydrogenases. The
medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P)-binding Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 326
Score = 127 bits (321), Expect = 9e-32
Identities = 60/233 (25%), Positives = 103/233 (44%), Gaps = 33/233 (14%)
Query: 535 PDQWTLEDAATVPCVYATAVYAMFICGQMQKGESILIHAGSGGVGQAAINLARYMDAEIF 594
P ++ +AA +P V TA + +Q G+++LIH G+GGVG A+ LA+ A ++
Sbjct: 114 PANLSMREAAALPLVGITAWEGLVDRAAVQAGQTVLIHGGAGGVGHVAVQLAKAAGARVY 173
Query: 595 TTVGTPEKREFIRKTFPFIKEENIG----NSRDTSFEQLVMKRTKGRGVDLVLNSLAEEK 650
T + EK F R +G + + V + T GRG D+V +++ E
Sbjct: 174 ATASS-EKAAFARS---------LGADPIIYYRETVVEYVAEHTGGRGFDVVFDTVGGET 223
Query: 651 LQASVRCLAQGGRF---LEIGKFDLANNNMLGMEVFMRETSFHGV-----MLDNFFFAEQ 702
L AS +A GR L DLA + R ++ GV +L A
Sbjct: 224 LDASFEAVALYGRVVSILGGATHDLA-------PLSFRNATYSGVFTLLPLLTGEGRAHH 276
Query: 703 EWKMSLQKALQKAIDAGAVQPLV-RTIFPEDKVEEAFRYMAAGKHIGKVIIKI 754
+ + + ++ G ++PL+ FP ++ A + +G GK++I +
Sbjct: 277 GEIL---REAARLVERGQLRPLLDPRTFPLEEAAAAHARLESGSARGKIVIDV 326
>gnl|CDD|176178 cd05188, MDR, Medium chain reductase/dehydrogenase
(MDR)/zinc-dependent alcohol dehydrogenase-like family.
The medium chain reductase/dehydrogenases
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH) , quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. ADH-like proteins
typically form dimers (typically higher plants, mammals)
or tetramers (yeast, bacteria), and generally have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site and a structural zinc in a lobe of
the catalytic domain. The active site zinc is
coordinated by a histidine, two cysteines, and a water
molecule. The second zinc seems to play a structural
role, affects subunit interactions, and is typically
coordinated by 4 cysteines. Other MDR members have only
a catalytic zinc, and some contain no coordinated zinc.
Length = 271
Score = 121 bits (305), Expect = 3e-30
Identities = 54/265 (20%), Positives = 101/265 (38%), Gaps = 51/265 (19%)
Query: 465 YSSINFRDIMLTTAKLAPEVIESRRLYQHCVIGFEYSGRLRDS---------GKRVMGLT 515
+ + D+ + P ++G E +G + + G RV+ L
Sbjct: 8 AAGLCGTDLHIRRGGYPP------PPKLPLILGHEGAGVVVEVGPGVTGVKVGDRVVVLP 61
Query: 516 --SGRSLANCCET---------------------DVEMAWEIPDQWTLEDAATVPCVYAT 552
+ C E + +PD +LE+AA +P AT
Sbjct: 62 NLGCGTCELCRELCPGGGILGEGLDGGFAEYVVVPADNLVPLPDGLSLEEAALLPEPLAT 121
Query: 553 AVYAMFICGQMQKGESILIHAGSGGVGQAAINLARYMDAEIFTTVGTPEKREFIRK---T 609
A +A+ G ++ G+++L+ G+GGVG A LA+ A + T + EK E ++
Sbjct: 122 AYHALRRAGVLKPGDTVLVL-GAGGVGLLAAQLAKAAGARVIVTDRSDEKLELAKELGAD 180
Query: 610 FPFIKEENIGNSRDTSFEQLVMKRTKGRGVDLVLNSL-AEEKLQASVRCLAQGGRFLEIG 668
+ ++ E+ + T G G D+V++++ E L ++R L GGR + +G
Sbjct: 181 HVI-------DYKEEDLEEELR-LTGGGGADVVIDAVGGPETLAQALRLLRPGGRIVVVG 232
Query: 669 KFDLANNNMLGMEVFMRETSFHGVM 693
+ +E + G
Sbjct: 233 GTSGGPPLDDLRRLLFKELTIIGST 257
>gnl|CDD|176215 cd08253, zeta_crystallin, Zeta-crystallin with NADP-dependent
quinone reductase activity (QOR). Zeta-crystallin is a
eye lens protein with NADP-dependent quinone reductase
activity (QOR). It has been cited as a structural
component in mammalian eyes, but also has homology to
quinone reductases in unrelated species. QOR catalyzes
the conversion of a quinone and NAD(P)H to a
hydroquinone and NAD(P+. Quinones are cyclic diones
derived from aromatic compounds. Membrane bound QOR acts
in the respiratory chains of bacteria and mitochondria,
while soluble QOR acts to protect from toxic quinones
(e.g. DT-diaphorase) or as a soluble eye-lens protein in
some vertebrates (e.g. zeta-crystalin). QOR reduces
quinones through a semi-quinone intermediate via a
NAD(P)H-dependent single electron transfer. QOR is a
member of the medium chain dehydrogenase/reductase
family, but lacks the zinc-binding sites of the
prototypical alcohol dehydrogenases of this group.
Alcohol dehydrogenase in the liver converts ethanol and
NAD+ to acetaldehyde and NADH, while in yeast and some
other microorganisms ADH catalyzes the conversion
acetaldehyde to ethanol in alcoholic fermentation. ADH
is a member of the medium chain alcohol dehydrogenase
family (MDR), which has a NAD(P)(H)-binding domain in a
Rossmann fold of a beta-alpha form. The NAD(H)-binding
region is comprised of 2 structurally similar halves,
each of which contacts a mononucleotide. The N-terminal
catalytic domain has a distant homology to GroES. These
proteins typically form dimers (typically higher plants,
mammals) or tetramers (yeast, bacteria), and have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site, and a structural zinc in a lobe of
the catalytic domain. NAD(H)-binding occurs in the
cleft between the catalytic and coenzyme-binding domains
at the active site, and coenzyme binding induces a
conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
In human ADH catalysis, the zinc ion helps coordinate
the alcohol, followed by deprotonation of a histidine,
the ribose of NAD, a serine, then the alcohol, which
allows the transfer of a hydride to NAD+, creating NADH
and a zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 325
Score = 121 bits (307), Expect = 5e-30
Identities = 62/230 (26%), Positives = 110/230 (47%), Gaps = 16/230 (6%)
Query: 529 EMAWEIPDQWTLEDAATVPCVYATAVYAMFICGQMQKGESILIHAGSGGVGQAAINLARY 588
+ +PD + E A + TA A+F + GE++L+H GSG VG AA+ LAR+
Sbjct: 108 DQLVPLPDGVSFEQGAALGIPALTAYRALFHRAGAKAGETVLVHGGSGAVGHAAVQLARW 167
Query: 589 MDAEIFTTVGTPEKREFIRKTFPFIKEENIGNSRDTSFEQLVMKRTKGRGVDLVLNSLAE 648
A + T + E E +R+ + + N R ++ T G+GVD+++ LA
Sbjct: 168 AGARVIATASSAEGAELVRQ----AGADAVFNYRAEDLADRILAATAGQGVDVIIEVLAN 223
Query: 649 EKLQASVRCLAQGGRFLEIGKFDLANNNMLG-MEVF---MRETSFHGVMLDNFFFAEQEW 704
L + LA GGR + G + + G + + +E S GV+L + A E
Sbjct: 224 VNLAKDLDVLAPGGRIVVYG-----SGGLRGTIPINPLMAKEASIRGVLL---YTATPEE 275
Query: 705 KMSLQKALQKAIDAGAVQPLVRTIFPEDKVEEAFRYMAAGKHIGKVIIKI 754
+ + +A+ + GA++P++ +P ++ A + +G IGKV++
Sbjct: 276 RAAAAEAIAAGLADGALRPVIAREYPLEEAAAAHEAVESGGAIGKVVLDP 325
>gnl|CDD|187656 cd08953, KR_2_SDR_x, ketoreductase (KR), subgroup 2, complex (x)
SDRs. Ketoreductase, a module of the multidomain
polyketide synthase (PKS), has 2 subdomains, each
corresponding to a SDR family monomer. The C-terminal
subdomain catalyzes the NADPH-dependent reduction of the
beta-carbonyl of a polyketide to a hydroxyl group, a
step in the biosynthesis of polyketides, such as
erythromycin. The N-terminal subdomain, an interdomain
linker, is a truncated Rossmann fold which acts to
stabilizes the catalytic subdomain. Unlike typical SDRs,
the isolated domain does not oligomerize but is composed
of 2 subdomains, each resembling an SDR monomer. The
active site resembles that of typical SDRs, except that
the usual positions of the catalytic Asn and Tyr are
swapped, so that the canonical YXXXK motif changes to
YXXXN. Modular PKSs are multifunctional structures in
which the makeup recapitulates that found in (and may
have evolved from) FAS. Polyketide synthesis also
proceeds via the addition of 2-carbon units as in fatty
acid synthesis. The complex SDR NADP-binding motif,
GGXGXXG, is often present, but is not strictly conserved
in each instance of the module. This subfamily includes
both KR domains of the Bacillus subtilis Pks J,-L, and
PksM, and all three KR domains of PksN, components of
the megacomplex bacillaene synthase, which synthesizes
the antibiotic bacillaene. 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 prostaglandin dehydrogenase
(PGDH) numbering). In addition to the Tyr and Lys, there
is often an upstream Ser (Ser-138, PGDH numbering)
and/or an Asn (Asn-107, 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 KRs 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 = 436
Score = 123 bits (311), Expect = 1e-29
Identities = 66/190 (34%), Positives = 96/190 (50%), Gaps = 7/190 (3%)
Query: 784 YIICGGLGGFGLELADWLVLRGARKLVLTSRSGV--KNGYQALRIKIWKSYDVQVLISTD 841
Y++ GG GG G LA L R +LVL RS + + ++A + ++ +VL +
Sbjct: 208 YLVTGGAGGIGRALARALARRYGARLVLLGRSPLPPEEEWKAQTLAALEALGARVLYISA 267
Query: 842 DITTEAGVVNLLTEA-NKLGPVDGIFNLAVVLKDALFENQTPEDFNASLGPKANATKYFD 900
D+T A V LL + + G +DG+ + A VL+DAL +T EDF A L PK +
Sbjct: 268 DVTDAAAVRRLLEKVRERYGAIDGVIHAAGVLRDALLAQKTAEDFEAVLAPKVDGLLNLA 327
Query: 901 KYSRTMCPTLGQFVVFSSVSCGRGNAGQTNYGMANSIMERICEARRAEGLPG--LAVEWG 958
+ L FV+FSSVS G AGQ +Y AN+ ++ R G G L++ W
Sbjct: 328 QALADE--PLDFFVLFSSVSAFFGGAGQADYAAANAFLDAFAAYLRQRGPQGRVLSINWP 385
Query: 959 AVGEVGLVAD 968
A E G+ AD
Sbjct: 386 AWREGGMAAD 395
>gnl|CDD|176237 cd08276, MDR7, Medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family.
This group is a member of the medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, but lacks the zinc-binding
sites of the zinc-dependent alcohol dehydrogenases. The
medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P)-binding Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 336
Score = 119 bits (300), Expect = 5e-29
Identities = 65/230 (28%), Positives = 116/230 (50%), Gaps = 31/230 (13%)
Query: 534 IPDQWTLEDAATVPCVYATAVYAMFICGQMQKGESILIHAGSGGVGQAAINLARYMDAEI 593
PD + E+AAT+PC TA A+F G ++ G+++L+ G+GGV A+ A+ A +
Sbjct: 129 APDHLSFEEAATLPCAGLTAWNALFGLGPLKPGDTVLVQ-GTGGVSLFALQFAKAAGARV 187
Query: 594 FTTVGTPEKREFIRKTFPFIKEENIG-----NSRDTS-FEQLVMKRTKGRGVDLVLNSLA 647
T + EK E + +G N R T + + V+K T GRGVD V+
Sbjct: 188 IATSSSDEKLERAKA---------LGADHVINYRTTPDWGEEVLKLTGGRGVDHVVEVGG 238
Query: 648 EEKLQASVRCLAQGGRFLEIG---KFDLANNNMLGMEVFMRETSFHGVMLDNFFFAEQEW 704
L S++ +A GG IG F+ + + + + G+ + +
Sbjct: 239 PGTLAQSIKAVAPGGVISLIGFLSGFEAPVLLLP---LLTKGATLRGIAVGS-------- 287
Query: 705 KMSLQKALQKAIDAGAVQPLVRTIFPEDKVEEAFRYMAAGKHIGKVIIKI 754
+ +A+ +AI+A ++P++ +FP ++ +EA+RY+ +G H GKV+I++
Sbjct: 288 -RAQFEAMNRAIEAHRIRPVIDRVFPFEEAKEAYRYLESGSHFGKVVIRV 336
>gnl|CDD|176229 cd08268, MDR2, Medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family.
This group is a member of the medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, but lacks the zinc-binding
sites of the zinc-dependent alcohol dehydrogenases. The
medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P)-binding Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 328
Score = 115 bits (290), Expect = 1e-27
Identities = 61/227 (26%), Positives = 101/227 (44%), Gaps = 19/227 (8%)
Query: 535 PDQWTLEDAATVPCVYATAVYAMFICGQMQKGESILIHAGSGGVGQAAINLARYMDAEIF 594
PD + +AA + Y TA A+ ++ G+S+LI A S VG AAI +A A +
Sbjct: 114 PDGLSFVEAAALWMQYLTAYGALVELAGLRPGDSVLITAASSSVGLAAIQIANAAGATVI 173
Query: 595 TTVGTPEKREFIR----KTFPFIKEENIGNSRDTSFEQLVMKRTKGRGVDLVLNSLAEEK 650
T T EKR+ + EE++ V++ T G+GVD+V + + +
Sbjct: 174 ATTRTSEKRDALLALGAAHVIVTDEEDLVAE--------VLRITGGKGVDVVFDPVGGPQ 225
Query: 651 LQASVRCLAQGGRFLEIGKFDLANNNMLGMEVFMRETSFHGVMLDNFFFAEQEWKMSLQK 710
LA GG + G + +F G LD + ++
Sbjct: 226 FAKLADALAPGGTLVVYGALSGEPTPFPLKAALKKSLTFRGYSLDEITLDPEA----RRR 281
Query: 711 ALQKAIDA---GAVQPLVRTIFPEDKVEEAFRYMAAGKHIGKVIIKI 754
A+ +D GA++P+V +FP D + EA RY+ +G+ IGK+++
Sbjct: 282 AIAFILDGLASGALKPVVDRVFPFDDIVEAHRYLESGQQIGKIVVTP 328
>gnl|CDD|173547 PTZ00354, PTZ00354, alcohol dehydrogenase; Provisional.
Length = 334
Score = 113 bits (284), Expect = 6e-27
Identities = 79/289 (27%), Positives = 128/289 (44%), Gaps = 38/289 (13%)
Query: 495 VIGFEYSGRLRDS---------GKRVMGLTSGRSLANCCETDVEMAWEIPDQWTLEDAAT 545
++G E +G + D G RVM L G A IP +T E+AA
Sbjct: 61 ILGLEVAGYVEDVGSDVKRFKEGDRVMALLPGGGYAEYAVAHKGHVMHIPQGYTFEEAAA 120
Query: 546 VPCVYATAVYAMFICGQMQKGESILIHAGSGGVGQAAINLARYMDAEIFTTVGTPEKREF 605
+P + TA + G ++KG+S+LIHAG+ GVG AA LA A T + EK +F
Sbjct: 121 IPEAFLTAWQLLKKHGDVKKGQSVLIHAGASGVGTAAAQLAEKYGAATIITTSSEEKVDF 180
Query: 606 IRKTFPFIKEENIGNSRD-TSFEQLVMKRTKGRGVDLVLNSLAEEKLQASVRCLAQGGRF 664
+K + + D F V K T +GV+LVL+ + L + LA G++
Sbjct: 181 CKK----LAAIILIRYPDEEGFAPKVKKLTGEKGVNLVLDCVGGSYLSETAEVLAVDGKW 236
Query: 665 LEIG--------KFDLANNNMLGMEVFMRETSFHGVMLDNFFFAEQEWKMSLQKALQKAI 716
+ G KF+L + + S L + E+K L + ++ +
Sbjct: 237 IVYGFMGGAKVEKFNLL-------PLLRKRASIIFSTLRS---RSDEYKADLVASFEREV 286
Query: 717 ----DAGAVQPLVRTIFPEDKVEEAFRYMAAGKHIGKVIIKIRDEEPTK 761
+ G ++P+V +P ++V EA ++ K+IGKV++ + EP
Sbjct: 287 LPYMEEGEIKPIVDRTYPLEEVAEAHTFLEQNKNIGKVVLTV--NEPLS 333
>gnl|CDD|176191 cd05289, MDR_like_2, alcohol dehydrogenase and quinone
reductase-like medium chain degydrogenases/reductases.
Members identified as zinc-dependent alcohol
dehydrogenases and quinone oxidoreductase. QOR catalyzes
the conversion of a quinone + NAD(P)H to a hydroquinone
+ NAD(P)+. Quinones are cyclic diones derived from
aromatic compounds. Membrane bound QOR actin the
respiratory chains of bacteria and mitochondria, while
soluble QOR acts to protect from toxic quinones (e.g.
DT-diaphorase) or as a soluble eye-lens protein in some
vertebrates (e.g. zeta-crystalin). QOR reduces quinones
through a semi-quinone intermediate via a
NAD(P)H-dependent single electron transfer. QOR is a
member of the medium chain dehydrogenase/reductase
family, but lacks the zinc-binding sites of the
prototypical alcohol dehydrogenases of this group.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which has a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES. These
proteins typically form dimers (typically higher plants,
mammals) or tetramers (yeast, bacteria), and have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site and a structural zinc in a lobe of
the catalytic domain. NAD(H) binding occurs in the
cleft between the catalytic and coenzyme-binding domains
at the active site, and coenzyme binding induces a
conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
In human ADH catalysis, the zinc ion helps coordinate
the alcohol, followed by deprotonation of a histidine,
the ribose of NAD, a serine, then the alcohol, which
allows the transfer of a hydride to NAD+, creating NADH
and a zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 309
Score = 112 bits (283), Expect = 6e-27
Identities = 60/222 (27%), Positives = 98/222 (44%), Gaps = 28/222 (12%)
Query: 534 IPDQWTLEDAATVPCVYATAVYAMFICGQMQKGESILIHAGSGGVGQAAINLARYMDAEI 593
P + E+AA +P TA A+F G ++ G+++LIH +GGVG A+ LA+ A +
Sbjct: 113 KPANLSFEEAAALPLAGLTAWQALFELGGLKAGQTVLIHGAAGGVGSFAVQLAKARGARV 172
Query: 594 FTTVGTPEKREFIRKTFPFIKEENIGNSRDTSFEQLVMKRTKGRGVDLVLNSLAEEKLQA 653
T +F+R +E I + FE + GVD VL+++ E L
Sbjct: 173 IATAS-AANADFLRS---LGADEVI-DYTKGDFE----RAAAPGGVDAVLDTVGGETLAR 223
Query: 654 SVRCLAQGGRFLEIGKFDLANNNMLGMEVFMRETSFHGVMLDNFFFAEQEWKMSLQKALQ 713
S+ + GGR + I G + GV F F E + L
Sbjct: 224 SLALVKPGGRLVSI----------AGPPPAEQAAKRRGV-RAGFVFVE-----PDGEQLA 267
Query: 714 ---KAIDAGAVQPLVRTIFPEDKVEEAFRYMAAGKHIGKVII 752
+ ++AG ++P+V +FP + EA + +G GKV++
Sbjct: 268 ELAELVEAGKLRPVVDRVFPLEDAAEAHERLESGHARGKVVL 309
>gnl|CDD|176228 cd08267, MDR1, Medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family.
This group is a member of the medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, but lacks the zinc-binding
sites of the zinc-dependent alcohol dehydrogenases. The
medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P)-binding Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 319
Score = 112 bits (282), Expect = 9e-27
Identities = 63/314 (20%), Positives = 130/314 (41%), Gaps = 49/314 (15%)
Query: 462 QIYYSSINFRDIMLTTAKLAPEVIESRRLYQHCVIGFEYSGRLRDSGK---------RVM 512
+++ +S+N D L + + G +++G + G V
Sbjct: 32 KVHAASVNPVDWKLRRGPPKLLLGRPF----PPIPGMDFAGEVVAVGSGVTRFKVGDEVF 87
Query: 513 GLTSGR---SLANCCETDVEMAWEIPDQWTLEDAATVPCVYATAVYAMFICGQMQKGESI 569
G + +LA + P+ + E+AA +P TA+ A+ G+++ G+ +
Sbjct: 88 GRLPPKGGGALAEYVVAPESGLAKKPEGVSFEEAAALPVAGLTALQALRDAGKVKPGQRV 147
Query: 570 LIHAGSGGVGQAAINLARYMDAEIFTTVGTPEKREFIRKTFPFIKEENIGNSR--DTSFE 627
LI+ SGGVG A+ +A+ + A + T V + E +R ++G D + E
Sbjct: 148 LINGASGGVGTFAVQIAKALGAHV-TGVCSTRNAELVR---------SLGADEVIDYTTE 197
Query: 628 QLVMKRTKGRGVDLVLNSLAEEK--LQASVRCLAQGGRFLEIGKFDLANNNMLGMEVFMR 685
V G D++ +++ L + L GGR++ +G + L + + +
Sbjct: 198 DFVALTAGGEKYDVIFDAVGNSPFSLYRASLALKPGGRYVSVG----GGPSGLLLVLLLL 253
Query: 686 ETSFHGVMLDNFFFAEQEWKMSLQKA-------LQKAIDAGAVQPLVRTIFPEDKVEEAF 738
+ + K L K L + ++ G ++P++ +++P + EA+
Sbjct: 254 PLT--------LGGGGRRLKFFLAKPNAEDLEQLAELVEEGKLKPVIDSVYPLEDAPEAY 305
Query: 739 RYMAAGKHIGKVII 752
R + +G+ GKV+I
Sbjct: 306 RRLKSGRARGKVVI 319
>gnl|CDD|176232 cd08271, MDR5, Medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family.
This group is a member of the medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, but lacks the zinc-binding
sites of the zinc-dependent alcohol dehydrogenases. The
medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P)-binding Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 325
Score = 108 bits (273), Expect = 2e-25
Identities = 68/257 (26%), Positives = 107/257 (41%), Gaps = 22/257 (8%)
Query: 508 GKRVM---GLTSGRSLANCCETDVEMAWEIPDQWTLEDAATVPCVYATAVYAMFICGQMQ 564
G RV L G S A D +PD + E+AA +PC TA A+F +++
Sbjct: 81 GDRVAYHASLARGGSFAEYTVVDARAVLPLPDSLSFEEAAALPCAGLTAYQALFKKLRIE 140
Query: 565 KGESILIHAGSGGVGQAAINLARYMDAEIFTTVGTPEKREFIRK---TFPFIKEENIGNS 621
G +ILI G+GGVG A+ LA+ + TT + E+++ +
Sbjct: 141 AGRTILITGGAGGVGSFAVQLAKRAGLRVITTC-SKRNFEYVKSLGADHVI-------DY 192
Query: 622 RDTSFEQLVMKRTKGRGVDLVLNSLAEEKLQASVRCLAQGGRFLEIGKFDLANNNMLGME 681
D + + + T GRGVD VL+++ E A LA G + I +
Sbjct: 193 NDEDVCERIKEITGGRGVDAVLDTVGGETAAALAPTLAFNGHLVCI----QGRPDASPDP 248
Query: 682 VFMRETSFHGVMLDNFFFAEQEWKMSLQK----ALQKAIDAGAVQPLVRTIFPEDKVEEA 737
F R S H V L + L + + AG ++PLV + P +++ EA
Sbjct: 249 PFTRALSVHEVALGAAHDHGDPAAWQDLRYAGEELLELLAAGKLEPLVIEVLPFEQLPEA 308
Query: 738 FRYMAAGKHIGKVIIKI 754
R + GK+++ I
Sbjct: 309 LRALKDRHTRGKIVVTI 325
>gnl|CDD|187655 cd08952, KR_1_SDR_x, ketoreductase (KR), subgroup 1, complex (x)
SDRs. Ketoreductase, a module of the multidomain
polyketide synthase (PKS), has 2 subdomains, each
corresponding to a SDR family monomer. The C-terminal
subdomain catalyzes the NADPH-dependent reduction of the
beta-carbonyl of a polyketide to a hydroxyl group, a
step in the biosynthesis of polyketides, such as
erythromycin. The N-terminal subdomain, an interdomain
linker, is a truncated Rossmann fold which acts to
stabilizes the catalytic subdomain. Unlike typical SDRs,
the isolated domain does not oligomerize but is composed
of 2 subdomains, each resembling an SDR monomer. The
active site resembles that of typical SDRs, except that
the usual positions of the catalytic Asn and Tyr are
swapped, so that the canonical YXXXK motif changes to
YXXXN. Modular PKSs are multifunctional structures in
which the makeup recapitulates that found in (and may
have evolved from) FAS. Polyketide synthesis also
proceeds via the addition of 2-carbon units as in fatty
acid synthesis. The complex SDR NADP-binding motif,
GGXGXXG, is often present, but is not strictly conserved
in each instance of the module. This subfamily includes
KR domains found in many multidomain PKSs, including six
of seven Sorangium cellulosum PKSs (encoded by
spiDEFGHIJ) which participate in the synthesis of the
polyketide scaffold of the cytotoxic spiroketal
polyketide spirangien. These seven PKSs have either a
single PKS module (SpiF), two PKR modules
(SpiD,-E,-I,-J), or three PKS modules (SpiG,-H). This
subfamily includes the single KR domain of SpiF, the
first KR domains of SpiE,-G,H,-I,and #J, the third KR
domain of SpiG, and the second KR domain of SpiH. The
second KR domains of SpiE,-G, I, and #J, and the KR
domains of SpiD, belong to a different KR_FAS_SDR
subfamily. 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
prostaglandin dehydrogenase (PGDH) numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser (Ser-138, PGDH numbering) and/or an Asn (Asn-107,
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 KRs 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 = 480
Score = 104 bits (263), Expect = 2e-23
Identities = 61/190 (32%), Positives = 89/190 (46%), Gaps = 4/190 (2%)
Query: 786 ICGGLGGFGLELADWLVLRGARKLVLTSRSGVKN-GYQALRIKIWKSYDVQVLISTDDIT 844
+ GG G G +A WL RGA LVLTSR G G L + +V ++ D+
Sbjct: 235 VTGGTGALGAHVARWLARRGAEHLVLTSRRGPDAPGAAELV-AELTALGARVTVAACDVA 293
Query: 845 TEAGVVNLLTEANKLGPVDGIFNLAVVLKDALFENQTPEDFNASLGPKANATKYFDKYSR 904
+ LL P+ + + A VL D ++ TPE L K ++ D+ +R
Sbjct: 294 DRDALAALLAALPAGHPLTAVVHAAGVLDDGPLDDLTPERLAEVLRAKVAGARHLDELTR 353
Query: 905 TMCPTLGQFVVFSSVSCGRGNAGQTNYGMANSIMERICEARRAEGLPGLAVEWGAVGEVG 964
L FV+FSS++ G+ GQ Y AN+ ++ + E RRA GLP +V WG G
Sbjct: 354 D--RDLDAFVLFSSIAGVWGSGGQGAYAAANAYLDALAERRRARGLPATSVAWGPWAGGG 411
Query: 965 LVADMAEDNL 974
+ A A + L
Sbjct: 412 MAAGAAAERL 421
>gnl|CDD|176220 cd08259, Zn_ADH5, Alcohol dehydrogenases of the MDR family.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. This group contains proteins that
share the characteristic catalytic and structural
zinc-binding sites of the zinc-dependent alcohol
dehydrogenase family. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which have a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES. These
proteins typically form dimers (typically higher plants,
mammals) or tetramers (yeast, bacteria), and have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site and a structural zinc in a lobe of
the catalytic domain. NAD(H)-binding occurs in the cleft
between the catalytic and coenzyme-binding domains at
the active site, and coenzyme binding induces a
conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
In human ADH catalysis, the zinc ion helps coordinate
the alcohol, followed by deprotonation of a histidine
(His-51), the ribose of NAD, a serine (Ser-48), then the
alcohol, which allows the transfer of a hydride to NAD+,
creating NADH and a zinc-bound aldehyde or ketone. In
yeast and some bacteria, the active site zinc binds an
aldehyde, polarizing it, and leading to the reverse
reaction.
Length = 332
Score = 97.4 bits (243), Expect = 1e-21
Identities = 58/222 (26%), Positives = 111/222 (50%), Gaps = 21/222 (9%)
Query: 533 EIPDQWTLEDAATVPCVYATAVYAMFICGQMQKGESILIHAGSGGVGQAAINLARYMDAE 592
++PD + E AA CV TAV+A+ G ++KG+++L+ GGVG AI LA+ + A
Sbjct: 131 KLPDNVSDESAALAACVVGTAVHALKRAG-VKKGDTVLVTGAGGGVGIHAIQLAKALGAR 189
Query: 593 IFTTVGTPEKREFIRKTFPFIKEENIGNSRDTSFEQLVMKRTKGRGVDLVLNSLAEEKLQ 652
+ +PEK + +++ + I S F + V K G D+V+ + ++
Sbjct: 190 VIAVTRSPEKLKILKELG---ADYVIDGS---KFSEDVKKLG---GADVVIELVGSPTIE 240
Query: 653 ASVRCLAQGGRFLEIGKFDLANNNM-LGMEVFMRETSFHGVMLDNFFFAEQEWKMSLQKA 711
S+R L +GGR + IG + G+ + ++E G + K +++A
Sbjct: 241 ESLRSLNKGGRLVLIGNVTPDPAPLRPGL-LILKEIRIIGSISAT--------KADVEEA 291
Query: 712 LQKAIDAGAVQPLVRTIFPEDKVEEAFRYMAAGKHIGKVIIK 753
L K + G ++P++ + + + EA + +GK +G++++K
Sbjct: 292 L-KLVKEGKIKPVIDRVVSLEDINEALEDLKSGKVVGRIVLK 332
>gnl|CDD|187659 cd08956, KR_3_FAS_SDR_x, beta-ketoacyl reductase (KR) domain of
fatty acid synthase (FAS), subgroup 3, complex (x).
Ketoreductase, a module of the multidomain polyketide
synthase (PKS), has 2 subdomains, each corresponding to
a SDR family monomer. The C-terminal subdomain catalyzes
the NADPH-dependent reduction of the beta-carbonyl of a
polyketide to a hydroxyl group, a step in the
biosynthesis of polyketides, such as erythromycin. The
N-terminal subdomain, an interdomain linker, is a
truncated Rossmann fold which acts to stabilizes the
catalytic subdomain. Unlike typical SDRs, the isolated
domain does not oligomerize but is composed of 2
subdomains, each resembling an SDR monomer. The active
site resembles that of typical SDRs, except that the
usual positions of the catalytic Asn and Tyr are
swapped, so that the canonical YXXXK motif changes to
YXXXN. Modular PKSs are multifunctional structures in
which the makeup recapitulates that found in (and may
have evolved from) FAS. In some instances, such as
porcine FAS, an enoyl reductase (ER) module is inserted
between the sub-domains. Fatty acid synthesis occurs via
the stepwise elongation of a chain (which is attached to
acyl carrier protein, ACP) with 2-carbon units.
Eukaryotic systems consists of large, multifunctional
synthases (type I) while bacterial, type II systems, use
single function proteins. Fungal fatty acid synthesis
uses a dodecamer of 6 alpha and 6 beta subunits. In
mammalian type FAS cycles, ketoacyl synthase forms
acetoacetyl-ACP which is reduced by the NADP-dependent
beta-KR, forming beta-hydroxyacyl-ACP, which is in turn
dehydrated by dehydratase to a beta-enoyl intermediate,
which is reduced by NADP-dependent beta- ER. Polyketide
synthesis also proceeds via the addition of 2-carbon
units as in fatty acid synthesis. The complex SDR
NADP-binding motif, GGXGXXG, is often present, but is
not strictly conserved in each instance of the module.
This subfamily includes KR domains found in many
multidomain PKSs, including six of seven Sorangium
cellulosum PKSs (encoded by spiDEFGHIJ) which
participate in the synthesis of the polyketide scaffold
of the cytotoxic spiroketal polyketide spirangien. These
seven PKSs have either a single PKS module (SpiF), two
PKR modules (SpiD,-E,-I,-J), or three PKS modules
(SpiG,-H). This subfamily includes the second KR domains
of SpiE,-G, I, and -J, both KR domains of SpiD, and the
third KR domain of SpiH. The single KR domain of SpiF,
the first and second KR domains of SpiH, the first KR
domains of SpiE,-G,- I, and -J, and the third KR domain
of SpiG, belong to a different KR_FAS_SDR subfamily.
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
prostaglandin dehydrogenase (PGDH) numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser (Ser-138, PGDH numbering) and/or an Asn (Asn-107,
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 KRs 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 = 448
Score = 98.5 bits (246), Expect = 2e-21
Identities = 58/175 (33%), Positives = 88/175 (50%), Gaps = 5/175 (2%)
Query: 786 ICGGLGGFGLELADWLVLR-GARKLVLTSRSGV-KNGYQALRIKIWKSYDVQVLISTDDI 843
I GG G G LA LV G R L+L SR G G L ++ + +V ++ D+
Sbjct: 198 ITGGTGTLGALLARHLVTEHGVRHLLLVSRRGPDAPGAAELVAEL-AALGAEVTVAACDV 256
Query: 844 TTEAGVVNLLTEANKLGPVDGIFNLAVVLKDALFENQTPEDFNASLGPKANATKYFDKYS 903
A + LL P+ + + A VL D + + TPE +A L PK +A + + +
Sbjct: 257 ADRAALAALLAAVPADHPLTAVVHAAGVLDDGVLTSLTPERLDAVLRPKVDAAWHLHELT 316
Query: 904 RTMCPTLGQFVVFSSVSCGRGNAGQTNYGMANSIMERICEARRAEGLPGLAVEWG 958
R + L FV+FSS + G+ GQ NY AN+ ++ + + RRA GLP ++ WG
Sbjct: 317 RDL--DLAAFVLFSSAAGVLGSPGQANYAAANAFLDALAQHRRARGLPATSLAWG 369
>gnl|CDD|176189 cd05286, QOR2, Quinone oxidoreductase (QOR). Quinone
oxidoreductase (QOR) and 2-haloacrylate reductase. QOR
catalyzes the conversion of a quinone + NAD(P)H to a
hydroquinone + NAD(P)+. Quinones are cyclic diones
derived from aromatic compounds. Membrane bound QOR
actin the respiratory chains of bacteria and
mitochondria, while soluble QOR acts to protect from
toxic quinones (e.g. DT-diaphorase) or as a soluble
eye-lens protein in some vertebrates (e.g.
zeta-crystalin). QOR reduces quinones through a
semi-quinone intermediate via a NAD(P)H-dependent single
electron transfer. QOR is a member of the medium chain
dehydrogenase/reductase family, but lacks the
zinc-binding sites of the prototypical alcohol
dehydrogenases of this group. 2-haloacrylate reductase,
a member of this subgroup, catalyzes the NADPH-dependent
reduction of a carbon-carbon double bond in
organohalogen compounds. Although similar to QOR,
Burkholderia 2-haloacrylate reductase does not act on
the quinones 1,4-benzoquinone and 1,4-naphthoquinone.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which have a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES.
These proteins typically form dimers (typically higher
plants, mammals) or tetramers (yeast, bacteria), and
have 2 tightly bound zinc atoms per subunit, a catalytic
zinc at the active site and a structural zinc in a lobe
of the catalytic domain. NAD(H) binding occurs in the
cleft between the catalytic and coenzyme-binding domains
at the active site, and coenzyme binding induces a
conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
In human ADH catalysis, the zinc ion helps coordinate
the alcohol, followed by deprotonation of a histidine,
the ribose of NAD, a serine, then the alcohol, which
allows the transfer of a hydride to NAD+, creating NADH
and a zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 320
Score = 94.8 bits (237), Expect = 8e-21
Identities = 59/235 (25%), Positives = 101/235 (42%), Gaps = 33/235 (14%)
Query: 534 IPDQWTLEDAATVPCVYATAVYAMFICGQMQKGESILIHAGSGGVGQAAINLARYMDAEI 593
+PD + E AA + TA Y + ++ G+++L+HA +GGVG A+ + A +
Sbjct: 105 LPDGISDETAAALLLQGLTAHYLLRETYPVKPGDTVLVHAAAGGVGLLLTQWAKALGATV 164
Query: 594 FTTVGTPEKREFIRKTFPFIKEENIG-----NSRDTSFEQLVMKRTKGRGVDLVLNSLAE 648
TV + EK E R G N RD F + V + T GRGVD+V + + +
Sbjct: 165 IGTVSSEEKAELARA---------AGADHVINYRDEDFVERVREITGGRGVDVVYDGVGK 215
Query: 649 EKLQASVRCLAQGGRFLEIGK-------FDLANNNMLGME--VFMRETSFHGVMLDNFFF 699
+ + S+ L G + G FDL L R + FH +
Sbjct: 216 DTFEGSLDSLRPRGTLVSFGNASGPVPPFDL---LRLSKGSLFLTRPSLFH-------YI 265
Query: 700 AEQEWKMSLQKALQKAIDAGAVQPLVRTIFPEDKVEEAFRYMAAGKHIGKVIIKI 754
A +E ++ L A+ +G ++ + +P +A R + + K GK+++
Sbjct: 266 ATREELLARAAELFDAVASGKLKVEIGKRYPLADAAQAHRDLESRKTTGKLLLIP 320
>gnl|CDD|176234 cd08273, MDR8, Medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family.
This group is a member of the medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, but lacks the zinc-binding
sites of the zinc-dependent alcohol dehydrogenases. The
medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P)-binding Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 331
Score = 88.1 bits (219), Expect = 1e-18
Identities = 70/324 (21%), Positives = 121/324 (37%), Gaps = 57/324 (17%)
Query: 462 QIYYSSINFRDIMLTT-----AKLAPEVIESRRLYQHCVIGFEYSGRLR---------DS 507
++ S ++F D+ + P G++ GR+ +
Sbjct: 33 KVEASGVSFADVQMRRGLYPDQPPLPFTP-----------GYDLVGRVDALGSGVTGFEV 81
Query: 508 GKRVMGLTSGRSLANCCETDVEMAWEIPDQWTLEDAATVPCVYATAVYAMFICGQMQKGE 567
G RV LT A D + +P+ +A + Y TA + ++ G+
Sbjct: 82 GDRVAALTRVGGNAEYINLDAKYLVPVPEGVDAAEAVCLVLNYVTAYQMLHRAAKVLTGQ 141
Query: 568 SILIHAGSGGVGQAAINLARYMDAEIFTTVGTPEKREFIRKTFPFIKEENIGNS---RDT 624
+LIH SGGVGQA + LA AE++ T E+ ++E +G + T
Sbjct: 142 RVLIHGASGGVGQALLELALLAGAEVYGT--ASERN------HAALRE--LGATPIDYRT 191
Query: 625 SFEQLVMKRTKGRGVDLVLNSLAEEKLQASVRCLAQGGRFLEIGK--------------- 669
M GVD+V + + E + S LA GG + G
Sbjct: 192 KDWLPAMLT--PGGVDVVFDGVGGESYEESYAALAPGGTLVCYGGNSSLLQGRRSLAALG 249
Query: 670 FDLANNNMLGMEVFMRETSFHGVMLDNFFFAEQEWKMSLQKALQKAIDAGAVQPLVRTIF 729
LA L + R +F+ V + + ++ L L + G ++P +
Sbjct: 250 SLLARLAKLKLLPTGRRATFYYVW-RDRAEDPKLFRQDL-TELLDLLAKGKIRPKIAKRL 307
Query: 730 PEDKVEEAFRYMAAGKHIGKVIIK 753
P +V EA R + +GK +GK+++
Sbjct: 308 PLSEVAEAHRLLESGKVVGKIVLL 331
>gnl|CDD|176211 cd08249, enoyl_reductase_like, enoyl_reductase_like. Member
identified as possible enoyl reductase of the MDR
family. 2-enoyl thioester reductase (ETR) catalyzes the
NADPH-dependent dependent conversion of trans-2-enoyl
acyl carrier protein/coenzyme A (ACP/CoA) to
acyl-(ACP/CoA) in fatty acid synthesis. 2-enoyl
thioester reductase activity has been linked in Candida
tropicalis as essential in maintaining mitiochondrial
respiratory function. This ETR family is a part of the
medium chain dehydrogenase/reductase family, but lack
the zinc coordination sites characteristic of the
alcohol dehydrogenases in this family.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which has a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. The N-terminal catalytic domain has a
distant homology to GroES. These proteins typically
form dimers (typically higher plants, mammals) or
tetramers (yeast, bacteria), and have 2 tightly bound
zinc atoms per subunit, a catalytic zinc at the active
site, and a structural zinc in a lobe of the catalytic
domain. NAD(H)-binding occurs in the cleft between the
catalytic and coenzyme-binding domains at the active
site, and coenzyme binding induces a conformational
closing of this cleft. Coenzyme binding typically
precedes and contributes to substrate binding. Candida
tropicalis enoyl thioester reductase (Etr1p) catalyzes
the NADPH-dependent reduction of trans-2-enoyl
thioesters in mitochondrial fatty acid synthesis. Etr1p
forms homodimers with each subunit containing a
nucleotide-binding Rossmann fold domain and a catalytic
domain.
Length = 339
Score = 86.1 bits (214), Expect = 8e-18
Identities = 61/278 (21%), Positives = 109/278 (39%), Gaps = 48/278 (17%)
Query: 508 GKRVMGLTSGRSLANCCE--------TDVEMAWEIPDQWTLEDAATVPCVYATAVYAMFI 559
G RV G G + + D ++ +IPD + E+AAT+P TA A+F
Sbjct: 79 GDRVAGFVHGGNPNDPRNGAFQEYVVADADLTAKIPDNISFEEAATLPVGLVTAALALFQ 138
Query: 560 CGQM----------QKGESILIHAGSGGVGQAAINLARYMDAEIFTTVGTPEKREFIRKT 609
+ KG+ +LI GS VG AI LA+ ++ TT K
Sbjct: 139 KLGLPLPPPKPSPASKGKPVLIWGGSSSVGTLAIQLAKLAGYKVITTASP--------KN 190
Query: 610 FPFIKEENIG-----NSRDTSFEQLVMKRTKGRGVDLVLNSLAE-EKLQASVRCLAQGGR 663
F +K +G + D + + T G+ + L+ ++ E Q L + G
Sbjct: 191 FDLVKS--LGADAVFDYHDPDVVEDIRAATGGK-LRYALDCISTPESAQLCAEALGRSGG 247
Query: 664 FLEIGKFDLANNNMLGMEVFMRET-SFHGVM---LDNFFFAEQEWKMSLQKALQKAIDAG 719
GK L + + E R+ V+ + ++E+ K L + ++ G
Sbjct: 248 ----GK--LVSLLPVPEETEPRKGVKVKFVLGYTVFGEIPEDREFGEVFWKYLPELLEEG 301
Query: 720 AVQPLVRTIFPE--DKVEEAFRYMAAGKHIG-KVIIKI 754
++P + + V+E + GK G K+++++
Sbjct: 302 KLKPHPVRVVEGGLEGVQEGLDLLRKGKVSGEKLVVRL 339
>gnl|CDD|215721 pfam00107, ADH_zinc_N, Zinc-binding dehydrogenase.
Length = 131
Score = 75.8 bits (187), Expect = 5e-16
Identities = 33/120 (27%), Positives = 61/120 (50%), Gaps = 6/120 (5%)
Query: 577 GVGQAAINLARYM-DAEIFTTVGTPEKREFIRKTFPFIKEENIGNSRDTSFEQLVMKRTK 635
GVG AA+ LA+ + A + + EK E ++ + +++ N RD F + V + T
Sbjct: 1 GVGLAAVQLAKALGAARVIAVDRSEEKLELAKE----LGADHVINYRDEDFVERVRELTG 56
Query: 636 GRGVDLVLNSL-AEEKLQASVRCLAQGGRFLEIGKFDLANNNMLGMEVFMRETSFHGVML 694
GRGVD+V++ + A L+ ++ L GGR + +G A ++ ++E + G +
Sbjct: 57 GRGVDVVIDCVGAPATLEQALELLRPGGRVVVVGLPGGAPVPFPLRDLLLKELTILGSLG 116
>gnl|CDD|176212 cd08250, Mgc45594_like, Mgc45594 gene product and other MDR family
members. Includes Human Mgc45594 gene product of
undetermined function. The medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, which contains the
zinc-dependent alcohol dehydrogenase (ADH-Zn) and
related proteins, is a diverse group of proteins related
to the first identified member, class I mammalian ADH.
MDRs display a broad range of activities and are
distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES.
Length = 329
Score = 78.8 bits (195), Expect = 2e-15
Identities = 56/212 (26%), Positives = 93/212 (43%), Gaps = 36/212 (16%)
Query: 561 GQMQKGESILIHAGSGGVGQAAINLARYMDAEIFTTVGTPEKREFIRKTFPFI------- 613
G+M+ GE++L+ A +GG GQ A+ LA+ + T + EK EF++ +
Sbjct: 135 GEMKSGETVLVTAAAGGTGQFAVQLAKLAGCHVIGTCSSDEKAEFLKS----LGCDRPIN 190
Query: 614 -KEENIGNSRDTSFEQLVMKRTKGRGVDLVLNSLAEEKLQASVRCLAQGGRFLEIG---- 668
K E++G V+K+ +GVD+V S+ E V LA GR + IG
Sbjct: 191 YKTEDLGE---------VLKKEYPKGVDVVYESVGGEMFDTCVDNLALKGRLIVIGFISG 241
Query: 669 -----KFDLANNNMLGMEVFMRETSFHGVMLDNFFFAEQEWKMSLQKALQKAIDAGAVQP 723
L ++ + S G L ++ + L + LQ G +
Sbjct: 242 YQSGTGPSPVKGATLPPKLLAKSASVRGFFLPHYA---KLIPQHLDRLLQ-LYQRGKLVC 297
Query: 724 LV-RTIFPE-DKVEEAFRYMAAGKHIGKVIIK 753
V T F + V +A Y+ +GK+IGKV+++
Sbjct: 298 EVDPTRFRGLESVADAVDYLYSGKNIGKVVVE 329
>gnl|CDD|222256 pfam13602, ADH_zinc_N_2, Zinc-binding dehydrogenase.
Length = 129
Score = 72.8 bits (179), Expect = 4e-15
Identities = 37/133 (27%), Positives = 66/133 (49%), Gaps = 11/133 (8%)
Query: 620 NSRDTSFEQLVMKRTKGRGVDLVLNSLAEEKLQASVRCLAQGGRFLEIGKFDLANNNMLG 679
+ FE+ T G GVD+VL+++ E L ++ L GGR + IG + +L
Sbjct: 8 DYTTEDFEEA----TAGEGVDVVLDTVGGETLLRALLALKPGGRLVSIG----GPDLLLS 59
Query: 680 MEVFMRETSFHGVMLDNFFFAEQEWKMSLQKALQKAIDAGAVQPLVRTIFPEDKVEEAFR 739
+ GV L F + E L + + ++AG ++P++ +FP ++ EA R
Sbjct: 60 VAAKAGGRGVRGVFL--FPVSPGEAGADLAELAE-LVEAGKLRPVIDRVFPLEEAAEAHR 116
Query: 740 YMAAGKHIGKVII 752
Y+ +G+ GKV++
Sbjct: 117 YLESGRARGKVVL 129
>gnl|CDD|223992 COG1064, AdhP, Zn-dependent alcohol dehydrogenases [General
function prediction only].
Length = 339
Score = 78.0 bits (193), Expect = 4e-15
Identities = 51/229 (22%), Positives = 105/229 (45%), Gaps = 27/229 (11%)
Query: 531 AWEIPDQWTLEDAATVPCVYATAVYAMFICGQMQKGESILIHAGSGGVGQAAINLARYMD 590
+IP+ L +AA + C T A+ ++ G+ + + G+GG+G A+ A+ M
Sbjct: 133 VVKIPEGLDLAEAAPLLCAGITTYRALKKAN-VKPGKWVAVV-GAGGLGHMAVQYAKAMG 190
Query: 591 AEIFTTVGTPEKREFIRKTFPFIKEENIGNSRDTSFEQLVMKRTKGRGVDLVLNSLAEEK 650
AE+ + EK E +K + +++ NS D+ + V + D +++++
Sbjct: 191 AEVIAITRSEEKLELAKK----LGADHVINSSDSDALEAVKEI-----ADAIIDTVGPAT 241
Query: 651 LQASVRCLAQGGRFLEIGKFDLANNNMLGM-EVFMRETSFHGVMLDNFFFAEQEWKMSLQ 709
L+ S++ L +GG + +G +L + ++E S G ++ +
Sbjct: 242 LEPSLKALRRGGTLVLVGLPGGGPIPLLPAFLLILKEISIVGSLVGT------------R 289
Query: 710 KALQKAID---AGAVQPLVRTIFPEDKVEEAFRYMAAGKHIGKVIIKIR 755
L++A+D G ++P + P D++ EA+ M GK G+ +I +
Sbjct: 290 ADLEEALDFAAEGKIKPEILETIPLDEINEAYERMEKGKVRGRAVIDMS 338
>gnl|CDD|176206 cd08244, MDR_enoyl_red, Possible enoyl reductase. Member
identified as possible enoyl reductase of the MDR
family. 2-enoyl thioester reductase (ETR) catalyzes the
NADPH-dependent dependent conversion of trans-2-enoyl
acyl carrier protein/coenzyme A (ACP/CoA) to
acyl-(ACP/CoA) in fatty acid synthesis. 2-enoyl
thioester reductase activity has been linked in Candida
tropicalis as essential in maintaining mitiochondrial
respiratory function. This ETR family is a part of the
medium chain dehydrogenase/reductase family, but lack
the zinc coordination sites characteristic of the
alcohol dehydrogenases in this family.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which has a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. The N-terminal catalytic domain has a
distant homology to GroES. These proteins typically
form dimers (typically higher plants, mammals) or
tetramers (yeast, bacteria), and have 2 tightly bound
zinc atoms per subunit, a catalytic zinc at the active
site, and a structural zinc in a lobe of the catalytic
domain. NAD(H) binding occurs in the cleft between the
catalytic and coenzyme-binding domains at the active
site, and coenzyme binding induces a conformational
closing of this cleft. Coenzyme binding typically
precedes and contributes to substrate binding. Candida
tropicalis enoyl thioester reductase (Etr1p) catalyzes
the NADPH-dependent reduction of trans-2-enoyl
thioesters in mitochondrial fatty acid synthesis. Etr1p
forms homodimers, with each subunit containing a
nucleotide-binding Rossmann fold domain and a catalytic
domain.
Length = 324
Score = 77.8 bits (192), Expect = 4e-15
Identities = 59/247 (23%), Positives = 102/247 (41%), Gaps = 10/247 (4%)
Query: 508 GKRVMGLTSGRS--LANCCETDVEMAWEIPDQWTLEDAATVPCVYATAVYAMFICGQMQK 565
G+RV+ T A DV+ +PD LE A V TA+ + +
Sbjct: 84 GRRVVAHTGRAGGGYAELAVADVDSLHPVPDGLDLEAAVAVVHDGRTAL-GLLDLATLTP 142
Query: 566 GESILIHAGSGGVGQAAINLARYMDAEIFTTVGTPEKREFIRKTFPFIKEENIGNSRDTS 625
G+ +L+ A +GG+G + LA+ A + G P K +R + + +
Sbjct: 143 GDVVLVTAAAGGLGSLLVQLAKAAGATVVGAAGGPAKTALVRA----LGADVAVDYTRPD 198
Query: 626 FEQLVMKRTKGRGVDLVLNSLAEEKLQASVRCLAQGGRFLEIGKFDLANNNMLGMEVFMR 685
+ V + G GV +VL+ + +A++ LA GGRFL G + + R
Sbjct: 199 WPDQVREALGGGGVTVVLDGVGGAIGRAALALLAPGGRFLTYGWASGEWTALDEDDARRR 258
Query: 686 ETSFHGVMLDNFFFAEQEWKMSLQKALQKAIDAGAVQPLVRTIFPEDKVEEAFRYMAAGK 745
+ G++ + +AL +A G + P+V FP ++ EA + A
Sbjct: 259 GVTVVGLLGVQAE--RGGLRALEARALAEAAA-GRLVPVVGQTFPLERAAEAHAALEARS 315
Query: 746 HIGKVII 752
+GKV++
Sbjct: 316 TVGKVLL 322
>gnl|CDD|176181 cd05278, FDH_like, Formaldehyde dehydrogenases. Formaldehyde
dehydrogenase (FDH) is a member of the
zinc-dependent/medium chain alcohol dehydrogenase
family. Formaldehyde dehydrogenase (aka ADH3) may be
the ancestral form of alcohol dehydrogenase, which
evolved to detoxify formaldehyde. This CD contains
glutathione dependant FDH, glutathione independent FDH,
and related alcohol dehydrogenases. FDH converts
formaldehyde and NAD(P) to formate and NAD(P)H. The
initial step in this process the spontaneous formation
of a S-(hydroxymethyl)glutathione adduct from
formaldehyde and glutathione, followed by FDH-mediated
oxidation (and detoxification) of the adduct to
S-formylglutathione. Unlike typical FDH, Pseudomonas
putida aldehyde-dismutating FDH (PFDH) is
glutathione-independent. The medium chain alcohol
dehydrogenase family (MDR) have a NAD(P)(H)-binding
domain in a Rossmann fold of a beta-alpha form. The
N-terminal region typically has an all-beta catalytic
domain. These proteins typically form dimers (typically
higher plants, mammals) or tetramers (yeast, bacteria),
and have 2 tightly bound zinc atoms per subunit.
Length = 347
Score = 75.4 bits (186), Expect = 4e-14
Identities = 50/224 (22%), Positives = 92/224 (41%), Gaps = 20/224 (8%)
Query: 534 IPDQWTLEDAATVPCVYATAVYAMFICGQMQKGESILIHAGSGGVGQAAINLARYMDAEI 593
IPD EDA + + T + ++ G ++ + G+G VG A+ AR + A
Sbjct: 137 IPDGLPDEDALMLSDILPTGFHGA-ELAGIKPGSTVAV-IGAGPVGLCAVAGARLLGAAR 194
Query: 594 FTTVG-TPEKREFIRKTFPFIKEENIGNSRDTSFEQLVMKRTKGRGVDLVLNSLA-EEKL 651
V PE+ + ++ I N ++ + +++ T GRGVD V+ ++ EE
Sbjct: 195 IIAVDSNPERLDLAKEAGATD----IINPKNGDIVEQILELTGGRGVDCVIEAVGFEETF 250
Query: 652 QASVRCLAQGGRFLEIGKFDLANNNMLGMEVFMRETSFHGVMLDNFFFAEQEWKMSLQKA 711
+ +V+ + GG +G + + L E F + +F ++
Sbjct: 251 EQAVKVVRPGGTIANVGVYGKPDPLPLLGEWFGKNLTFKTGLVPVRARMP---------E 301
Query: 712 LQKAIDAGAV--QPLVRTIFPEDKVEEAFRYMAAGK-HIGKVII 752
L I+ G + L+ FP D + +A+R KV+I
Sbjct: 302 LLDLIEEGKIDPSKLITHRFPLDDILKAYRLFDNKPDGCIKVVI 345
>gnl|CDD|216224 pfam00975, Thioesterase, Thioesterase domain. Peptide synthetases
are involved in the non-ribosomal synthesis of peptide
antibiotics. Next to the operons encoding these enzymes,
in almost all cases, are genes that encode proteins that
have similarity to the type II fatty acid thioesterases
of vertebrates. There are also modules within the peptide
synthetases that also share this similarity. With respect
to antibiotic production, thioesterases are required for
the addition of the last amino acid to the peptide
antibiotic, thereby forming a cyclic antibiotic.
Thioesterases (non-integrated) have molecular masses of
25-29 kDa.
Length = 224
Score = 72.8 bits (179), Expect = 4e-14
Identities = 39/226 (17%), Positives = 69/226 (30%), Gaps = 33/226 (14%)
Query: 1159 TIFMVPGIEGIATVLEPLAKNINAQVLV-------FQFDHTNPPDTIPEMADSLLPHFKK 1211
+F P G A+ LA+ + + P +I E+A+ ++
Sbjct: 2 RLFCFPPAGGSASYFRNLARRLPGTAEFNAVQLPGRERGE-PPLTSIEELAEEYAEALRR 60
Query: 1212 RLVHGTDEIKLVGFSFGGMVALELAIKLEQLG-TKCHLYLVDSAPDYVLTSLRKLPDWNA 1270
G L G S GG++A E+A +LE+ G L L D+ + R+
Sbjct: 61 IQPEG--PYALFGHSMGGLLAFEVARRLERRGEEPAGLILSDAYAPH---FGRREASHLL 115
Query: 1271 KLNYFLDLMPEDATHSRTYQRNLAH-----------AAYKRITSILKYTDPKHKAFGGNI 1319
+ L + T + L A R + Y A +
Sbjct: 116 GDDELLAELRRIG---GTPEALLEDEELLSLLLPALRADYRA--LENYPIHP-IAAPSDA 169
Query: 1320 TLL--RPTEQALPTAEDYGLSKVCKKPVKVHFVDGNHFTVLDNIKS 1363
TL + H + G+HF + ++ +
Sbjct: 170 TLFYGADDPLNTLDWLAAWWREYTPGEFDTHVLPGDHFYLNEHAEE 215
>gnl|CDD|176645 cd05282, ETR_like, 2-enoyl thioester reductase-like. 2-enoyl
thioester reductase (ETR) catalyzes the NADPH-dependent
conversion of trans-2-enoyl acyl carrier
protein/coenzyme A (ACP/CoA) to acyl-(ACP/CoA) in fatty
acid synthesis. 2-enoyl thioester reductase activity has
been linked in Candida tropicalis as essential in
maintaining mitiochondrial respiratory function. This
ETR family is a part of the medium chain
dehydrogenase/reductase family, but lack the zinc
coordination sites characteristic of the alcohol
dehydrogenases in this family. NAD(P)(H)-dependent
oxidoreductases are the major enzymes in the
interconversion of alcohols and aldehydes, or ketones.
Alcohol dehydrogenase in the liver converts ethanol and
NAD+ to acetaldehyde and NADH, while in yeast and some
other microorganisms ADH catalyzes the conversion
acetaldehyde to ethanol in alcoholic fermentation. ADH
is a member of the medium chain alcohol dehydrogenase
family (MDR), which has a NAD(P)(H)-binding domain in a
Rossmann fold of a beta-alpha form. The NAD(H)-binding
region is comprised of 2 structurally similar halves,
each of which contacts a mononucleotide. The N-terminal
catalytic domain has a distant homology to GroES.
These proteins typically form dimers (typically higher
plants, mammals) or tetramers (yeast, bacteria), and
have 2 tightly bound zinc atoms per subunit, a catalytic
zinc at the active site and a structural zinc in a lobe
of the catalytic domain. NAD(H) binding occurs in the
cleft between the catalytic and coenzyme-binding domains
at the active site, and coenzyme binding induces a
conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
Candida tropicalis enoyl thioester reductase (Etr1p)
catalyzes the NADPH-dependent reduction of trans-2-enoyl
thioesters in mitochondrial fatty acid synthesis. Etr1p
forms homodimers with each subunit containing a
nucleotide-binding Rossmann fold domain and a catalytic
domain.
Length = 323
Score = 73.9 bits (182), Expect = 8e-14
Identities = 59/285 (20%), Positives = 104/285 (36%), Gaps = 48/285 (16%)
Query: 495 VIGFEYSGRLRDSGKRVMGLTSG------------RSLANCCETDVEMAWEIPDQWTLED 542
V G E G + + G V GL G + D+ +PD + E
Sbjct: 59 VPGNEGVGVVVEVGSGVSGLLVGQRVLPLGGEGTWQEYVVAPADDL---IPVPDSISDEQ 115
Query: 543 AATVPCVYATAVYAMFICGQ---MQKGESILIHAGSGGVGQAAINLARYMDAEIFTTVGT 599
AA + Y + A + + + G+ ++ +A + VG+ I LA+ + F T+
Sbjct: 116 AAML---YINPLTAWLMLTEYLKLPPGDWVIQNAANSAVGRMLIQLAKLLG---FKTINV 169
Query: 600 PEKREFIRKTFPFIKE----ENIGNSRDTSFEQLVMKRTKGRGVDLVLNSLAEEKLQASV 655
+ E + + +K E I +S Q V + T G G L L+++ E
Sbjct: 170 VRRDEQVEE----LKALGADEVI-DSSPEDLAQRVKEATGGAGARLALDAVGGESATRLA 224
Query: 656 RCLAQGGRFLEIGKFDLANNNMLG--MEVFMRETSFHGVMLDNFFFAEQEWKMSLQK--- 710
R L GG + G + G + F + + F+ + + +
Sbjct: 225 RSLRPGGTLVNYG-------LLSGEPVPFPRSVFIFKDITVRGFWLRQWLHSATKEAKQE 277
Query: 711 ---ALQKAIDAGAVQPLVRTIFPEDKVEEAFRYMAAGKHIGKVII 752
+ K ++AG + V FP + EEA GKV++
Sbjct: 278 TFAEVIKLVEAGVLTTPVGAKFPLEDFEEAVAAAEQPGRGGKVLL 322
>gnl|CDD|176210 cd08248, RTN4I1, Human Reticulon 4 Interacting Protein 1. Human
Reticulon 4 Interacting Protein 1 is a member of the
medium chain dehydrogenase/ reductase (MDR) family.
Riticulons are endoplasmic reticulum associated proteins
involved in membrane trafficking and neuroendocrine
secretion. The MDR/zinc-dependent alcohol
dehydrogenase-like family, which contains the
zinc-dependent alcohol dehydrogenase (ADH-Zn) and
related proteins, is a diverse group of proteins related
to the first identified member, class I mammalian ADH.
MDRs display a broad range of activities and are
distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES.
Length = 350
Score = 74.2 bits (183), Expect = 9e-14
Identities = 59/238 (24%), Positives = 112/238 (47%), Gaps = 34/238 (14%)
Query: 535 PDQWTLEDAATVPCVYATAVYAMFICGQMQ----KGESILIHAGSGGVGQAAINLARYMD 590
P + E+AA++P TA A+ G + G+ +LI GSGGVG AI L +
Sbjct: 128 PKNLSHEEAASLPYAGLTAWSALVNVGGLNPKNAAGKRVLILGGSGGVGTFAIQLLKAWG 187
Query: 591 AEIFTTVGTPEKREFIRKTFPFIKE---ENIGNSRDTSFEQLVMKRTKGRGVDLVLNSLA 647
A + TT T P +K +++ + + FE+ + +R K D++L+++
Sbjct: 188 AHVTTTCST--------DAIPLVKSLGADDVIDYNNEDFEEELTERGK---FDVILDTVG 236
Query: 648 EEKLQASVRCLAQGGRFLEIGKFDLANNNMLGMEVF------------MRETSFHGVMLD 695
+ + +++ L +GG ++ + L N + LG+ V ++ G
Sbjct: 237 GDTEKWALKLLKKGGTYVTLVSPLLKNTDKLGL-VGGMLKSAVDLLKKNVKSLLKGSHYR 295
Query: 696 NFFFAEQEWKMSLQKALQKAIDAGAVQPLVRTIFPEDKVEEAFRYMAAGKHIGKVIIK 753
FF+ +L + L K ++ G ++P++ +FP ++V EA+ + +G GK +IK
Sbjct: 296 WGFFSPSG--SALDE-LAKLVEDGKIKPVIDKVFPFEEVPEAYEKVESGHARGKTVIK 350
>gnl|CDD|184316 PRK13771, PRK13771, putative alcohol dehydrogenase; Provisional.
Length = 334
Score = 73.1 bits (180), Expect = 2e-13
Identities = 51/223 (22%), Positives = 102/223 (45%), Gaps = 23/223 (10%)
Query: 534 IPDQWTLEDAATVPCVYATAVYAMFICGQMQKGESILIHAGSGGVGQAAINLARYMDAEI 593
+P + E A VPCV + G ++KGE++L+ GGVG AI +A+ + A++
Sbjct: 132 VPPNVSDEGAVIVPCVTGMVYRGLRRAG-VKKGETVLVTGAGGGVGIHAIQVAKALGAKV 190
Query: 594 FTTVGTPEKREFIRKTFPFIKEENIGNSRDTSFEQLVMKRTKGRGVDLVLNSLAEEKLQA 653
+ K + + K ++ + F + V K G D+V+ ++ L+
Sbjct: 191 IAVTSSESKAKIVSKYADYVIVGS-------KFSEEVKKIG---GADIVIETVGTPTLEE 240
Query: 654 SVRCLAQGGRFLEIGKFD--LANNNMLGMEVFMRETSFHGVMLDNFFFAEQEWKMSLQKA 711
S+R L GG+ ++IG D + LG + +++ G + K +++A
Sbjct: 241 SLRSLNMGGKIIQIGNVDPSPTYSLRLGY-IILKDIEIIGHI--------SATKRDVEEA 291
Query: 712 LQKAIDAGAVQPLVRTIFPEDKVEEAFRYMAAGKHIGKVIIKI 754
L K + G ++P++ ++++A + IGK+++K
Sbjct: 292 L-KLVAEGKIKPVIGAEVSLSEIDKALEELKDKSRIGKILVKP 333
>gnl|CDD|225041 COG2130, COG2130, Putative NADP-dependent oxidoreductases [General
function prediction only].
Length = 340
Score = 71.2 bits (175), Expect = 8e-13
Identities = 46/214 (21%), Positives = 88/214 (41%), Gaps = 19/214 (8%)
Query: 552 TAVYAMFICGQMQKGESILIHAGSGGVGQAAINLARYMDAEIFTTVGTPEKREFIRKTFP 611
TA + + GQ + GE++++ A +G VG +A+ + G EK +F+ +
Sbjct: 137 TAYFGLLDIGQPKAGETVVVSAAAGAVGSVVGQIAKLKGCRVVGIAGGAEKCDFLTEELG 196
Query: 612 FIKEENIGNSRDTSFEQLVMKRTKGRGVDLVLNSLAEEKLQASVRCLAQGGRFLEIGKFD 671
F + + + F Q +K +G+D+ ++ E L A + L R G
Sbjct: 197 F---DAGIDYKAEDFAQ-ALKEACPKGIDVYFENVGGEVLDAVLPLLNLFARIPVCGAIS 252
Query: 672 LANNNMLGM------EVFMRETSFHGVMLDNFFFAEQEWKMSLQKALQKAIDAGAVQPLV 725
N L + + G ++ + + + + L + G +Q
Sbjct: 253 QYNAPELPPGPRRLPLLMAKRLRVQGFIVASDY---DQRFPEALRELGGWVKEGKIQYRE 309
Query: 726 RTIFPEDKVE---EAFRYMAAGKHIGKVIIKIRD 756
TI D +E EAF + +GK+ GK+++K+ D
Sbjct: 310 -TI--VDGLENAPEAFIGLLSGKNFGKLVVKVAD 340
>gnl|CDD|176205 cd08243, quinone_oxidoreductase_like_1, Quinone oxidoreductase
(QOR). NAD(P)(H)-dependent oxidoreductases are the
major enzymes in the interconversion of alcohols and
aldehydes, or ketones. The medium chain alcohol
dehydrogenase family (MDR) have a NAD(P)(H)-binding
domain in a Rossmann fold of a beta-alpha form. The
N-terminal region typically has an all-beta catalytic
domain. These proteins typically form dimers (typically
higher plants, mammals) or tetramers (yeast, bacteria),
and have 2 tightly bound zinc atoms per subunit.
Length = 320
Score = 70.3 bits (173), Expect = 1e-12
Identities = 57/218 (26%), Positives = 93/218 (42%), Gaps = 28/218 (12%)
Query: 544 ATVPCVYATAVYAMFICGQMQKGESILIHAGSGGVGQAAINLARYMDAEIFTTVGTPEKR 603
A +P Y TA ++F +Q G+++LI G+ VG AA+ LA+ + A + T +PE+
Sbjct: 121 AALPETYYTAWGSLFRSLGLQPGDTLLIRGGTSSVGLAALKLAKALGATVTATTRSPERA 180
Query: 604 EFIRKT---FPFIKEENIGNSRDTSFEQLVMKRTKGRGVDLVLNSLAEEKLQASVRCLAQ 660
+++ I + I EQL R G D VL + L+ S+R L
Sbjct: 181 ALLKELGADEVVIDDGAIA-------EQL---RAAPGGFDKVLELVGTATLKDSLRHLRP 230
Query: 661 GGRFLEIGKFDLANNNMLGMEVFMR-----ETSFHGVMLDNF-FFAEQEWKMSLQKALQK 714
GG G +LG + + + GV L + + LQ L
Sbjct: 231 GGIVCMTG--------LLGGQWTLEDFNPMDDIPSGVNLTLTGSSSGDVPQTPLQ-ELFD 281
Query: 715 AIDAGAVQPLVRTIFPEDKVEEAFRYMAAGKHIGKVII 752
+ AG + +F D++ EA YM + + GKV++
Sbjct: 282 FVAAGHLDIPPSKVFTFDEIVEAHAYMESNRAFGKVVV 319
>gnl|CDD|223991 COG1063, Tdh, Threonine dehydrogenase and related Zn-dependent
dehydrogenases [Amino acid transport and metabolism /
General function prediction only].
Length = 350
Score = 69.3 bits (170), Expect = 3e-12
Identities = 49/227 (21%), Positives = 93/227 (40%), Gaps = 20/227 (8%)
Query: 534 IPDQWTLEDAATVPCVYATAVYA-MFICGQMQKGESILIHAGSGGVGQAAINLARYMDAE 592
+PD E AA ATA + + G ++++ G+G +G AI LA+ + A
Sbjct: 138 LPDGIDEEAAALTEP-LATAYHGHAERAAV-RPGGTVVV-VGAGPIGLLAIALAKLLGAS 194
Query: 593 IFTTVGT-PEKREFIRKTFPFIKEENIGNSRDTSFEQLVMKRTKGRGVDLVLNSL-AEEK 650
+ V PE+ E ++ + + N + +++ T GRG D+V+ ++ +
Sbjct: 195 VVIVVDRSPERLELAKEAGGA---DVVVNPSEDDAGAEILELTGGRGADVVIEAVGSPPA 251
Query: 651 LQASVRCLAQGGRFLEIG--KFDLANNNMLGMEVFMRETSFHGVMLDNFFFAEQEWKMSL 708
L ++ L GG + +G + V +E + G + ++++ +L
Sbjct: 252 LDQALEALRPGGTVVVVGVYGGEDIPLPA--GLVVSKELTLRGSL---RPSGREDFERAL 306
Query: 709 QKALQKAIDAGAVQPLVRTIFPEDKVEEAFRYMAAGK-HIGKVIIKI 754
ID + L+ P D EA+ A K KV++K
Sbjct: 307 DLLASGKID---PEKLITHRLPLDDAAEAYELFADRKEEAIKVVLKP 350
>gnl|CDD|176190 cd05288, PGDH, Prostaglandin dehydrogenases. Prostaglandins and
related eicosanoids are metabolized by the oxidation of
the 15(S)-hydroxyl group of the NAD+-dependent (type I
15-PGDH) 15-prostaglandin dehydrogenase (15-PGDH)
followed by reduction by NADPH/NADH-dependent (type II
15-PGDH) delta-13 15-prostaglandin reductase (13-PGR) to
15-keto-13,14,-dihydroprostaglandins. 13-PGR is a
bifunctional enzyme, since it also has leukotriene B(4)
12-hydroxydehydrogenase activity. These 15-PGDH and
related enzymes are members of the medium chain
dehydrogenase/reductase family. The medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, which contains the
zinc-dependent alcohol dehydrogenase (ADH-Zn) and
related proteins, is a diverse group of proteins related
to the first identified member, class I mammalian ADH.
MDRs display a broad range of activities and are
distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES.
Length = 329
Score = 69.0 bits (170), Expect = 3e-12
Identities = 43/210 (20%), Positives = 88/210 (41%), Gaps = 21/210 (10%)
Query: 552 TAVYAMFICGQMQKGESILIHAGSGGVGQAAINLARYMDAEIFTTVGTPEKREFIRKTFP 611
TA + + G+ + GE++++ A +G VG +A+ + A + G+ EK ++ +
Sbjct: 132 TAYFGLTEIGKPKPGETVVVSAAAGAVGSVVGQIAKLLGARVVGIAGSDEKCRWLVEELG 191
Query: 612 F---IKEENIGNSRDTSFEQLVMKRTKGRGVDLVLNSLAEEKLQASVRCLAQGGRFLEIG 668
F I N + + + + G+D+ +++ E L A++ L +GGR G
Sbjct: 192 FDAAI------NYKTPDLAEALKEAAPD-GIDVYFDNVGGEILDAALTLLNKGGRIALCG 244
Query: 669 ------KFDLANNNMLGMEVFMRETSFHGVMLDNFFFAEQEWKMSLQKALQKAIDAGAVQ 722
+ LG + R T G ++ ++ E L K + G ++
Sbjct: 245 AISQYNATEPPGPKNLGNIITKRLT-MQGFIVSDYADRFPEA----LAELAKWLAEGKLK 299
Query: 723 PLVRTIFPEDKVEEAFRYMAAGKHIGKVII 752
+ + EAF + GK+ GK+++
Sbjct: 300 YREDVVEGLENAPEAFLGLFTGKNTGKLVV 329
>gnl|CDD|176235 cd08274, MDR9, Medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family.
This group is a member of the medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, but lacks the zinc-binding
sites of the zinc-dependent alcohol dehydrogenases. The
medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P)-binding Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 350
Score = 68.5 bits (168), Expect = 5e-12
Identities = 54/236 (22%), Positives = 95/236 (40%), Gaps = 37/236 (15%)
Query: 529 EMAWEIPDQWTLEDAATVPCVYATAVYAMFICGQMQKGESILIHAGSGGVGQAAINLARY 588
E A+ + + + AT PC Y+TA M + GE++L+ SGGVG A + LA+
Sbjct: 142 ENAYPVNSPLSDVELATFPCSYSTA-ENMLERAGVGAGETVLVTGASGGVGSALVQLAKR 200
Query: 589 MDAEIFTTVGTPEKREFIRK--TFPFIKEENIGNSRDTSFEQLVMKRTKGRGVDLVLNSL 646
A + G K E +R I + + K G VD+V + +
Sbjct: 201 RGAIVIAVAG-AAKEEAVRALGADTVILRDAPLLADA--------KALGGEPVDVVADVV 251
Query: 647 AEEKLQASVRCLAQGGRFLEIG-------KFDLANNNMLGMEVFMRETSFHG-VMLDNFF 698
+R L GGR++ G + DL +++++ + G +
Sbjct: 252 GGPLFPDLLRLLRPGGRYVTAGAIAGPVVELDLR-------TLYLKDLTLFGSTLGTREV 304
Query: 699 FAEQEWKMSLQKALQKAIDAGAVQPLVRTIFPEDKVEEAFRYMAAGKHIGKVIIKI 754
F L + I+ G ++P+V FP ++ EA +H+GK+++
Sbjct: 305 FRR----------LVRYIEEGEIRPVVAKTFPLSEIREAQAEFLEKRHVGKLVLVP 350
>gnl|CDD|176221 cd08260, Zn_ADH6, Alcohol dehydrogenases of the MDR family.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. This group has the characteristic
catalytic and structural zinc sites of the
zinc-dependent alcohol dehydrogenases. Alcohol
dehydrogenase in the liver converts ethanol and NAD+ to
acetaldehyde and NADH, while in yeast and some other
microorganisms ADH catalyzes the conversion acetaldehyde
to ethanol in alcoholic fermentation. ADH is a member of
the medium chain alcohol dehydrogenase family (MDR),
which has a NAD(P)(H)-binding domain in a Rossmann fold
of a beta-alpha form. The NAD(H)-binding region is
comprised of 2 structurally similar halves, each of
which contacts a mononucleotide. A GxGxxG motif after
the first mononucleotide contact half allows the close
contact of the coenzyme with the ADH backbone. The
N-terminal catalytic domain has a distant homology to
GroES. These proteins typically form dimers (typically
higher plants, mammals) or tetramers (yeast, bacteria),
and have 2 tightly bound zinc atoms per subunit, a
catalytic zinc at the active site and a structural zinc
in a lobe of the catalytic domain. NAD(H)-binding occurs
in the cleft between the catalytic and coenzyme-binding
domains at the active site, and coenzyme binding induces
a conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
In human ADH catalysis, the zinc ion helps coordinate
the alcohol, followed by deprotonation of a histidine,
the ribose of NAD, a serine, then the alcohol, which
allows the transfer of a hydride to NAD+, creating NADH
and a zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 345
Score = 68.0 bits (167), Expect = 9e-12
Identities = 57/232 (24%), Positives = 90/232 (38%), Gaps = 35/232 (15%)
Query: 534 IPDQWTLEDAATVPCVYATAVYAMFICGQMQKGESILIHAGSGGVGQAAINLARYMDAEI 593
+PD AA + C +ATA A+ +++ GE + +H G GGVG +A+ +A + A +
Sbjct: 134 LPDDVDFVTAAGLGCRFATAFRALVHQARVKPGEWVAVH-GCGGVGLSAVMIASALGARV 192
Query: 594 FTTVGTPEKREFIRKTFPFIKEENIGNSRDTSFEQLVMKRTKGRGVDLVLNSL-AEEKLQ 652
+K E R+ + S V T G G + +++L E +
Sbjct: 193 IAVDIDDDKLELARE---LGAVATVNASEVEDVAAAVRDLTGG-GAHVSVDALGIPETCR 248
Query: 653 ASVRCLAQGGRFLEIGKFDLANNNMLGME---------VFMRETSFHGVMLDNFFFAEQE 703
SV L + GR +++G LG E V RE G
Sbjct: 249 NSVASLRKRGRHVQVGL-------TLGEEAGVALPMDRVVARELEIVGS------HGMPA 295
Query: 704 WKMSLQKALQKAIDAGAVQP--LV-RTIFPEDKVEEAFRYMAAGKHIGKVII 752
+ A+ I +G + P LV RTI D+ +A M G +I
Sbjct: 296 HRYD---AMLALIASGKLDPEPLVGRTI-SLDEAPDALAAMDDYATAGITVI 343
>gnl|CDD|176197 cd08235, iditol_2_DH_like, L-iditol 2-dehydrogenase. Putative
L-iditol 2-dehydrogenase based on annotation of some
members in this subgroup. L-iditol 2-dehydrogenase
catalyzes the NAD+-dependent conversion of L-iditol to
L-sorbose in fructose and mannose metabolism. This
enzyme is related to sorbitol dehydrogenase, alcohol
dehydrogenase, and other medium chain
dehydrogenase/reductases. The zinc-dependent alcohol
dehydrogenase (ADH-Zn)-like family of proteins is a
diverse group of proteins related to the first
identified member, class I mammalian ADH. This group is
also called the medium chain dehydrogenases/reductase
family (MDR) to highlight its broad range of activities
and to distinguish from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal GroES-like catalytic
domain. The MDR group contains a host of activities,
including the founding alcohol dehydrogenase (ADH),
quinone reductase, sorbitol dehydrogenase, formaldehyde
dehydrogenase, butanediol DH, ketose reductase, cinnamyl
reductase, and numerous others. The zinc-dependent
alcohol dehydrogenases (ADHs) catalyze the
NAD(P)(H)-dependent interconversion of alcohols to
aldehydes or ketones. Active site zinc has a catalytic
role, while structural zinc aids in stability. ADH-like
proteins typically form dimers (typically higher
plants, mammals) or tetramers (yeast, bacteria), and
generally have 2 tightly bound zinc atoms per subunit.
The active site zinc is coordinated by a histidine, two
cysteines, and a water molecule. The second zinc seems
to play a structural role, affects subunit interactions,
and is typically coordinated by 4 cysteines.
Length = 343
Score = 66.5 bits (163), Expect = 2e-11
Identities = 55/227 (24%), Positives = 104/227 (45%), Gaps = 24/227 (10%)
Query: 533 EIPDQWTLEDAATV-P--CVYATAVYAMFICGQMQKGESILIHAGSGGVGQAAINLARYM 589
++PD + E+AA V P C A ++ G+++L+ G+G +G LA+
Sbjct: 135 KLPDNVSFEEAALVEPLACCINAQRKA-----GIKPGDTVLV-IGAGPIGLLHAMLAKAS 188
Query: 590 DAE-IFTTVGTPEKREFIRKTFPFIKEENIGNSRDTSFEQLVMKRTKGRGVDLVLNSLAE 648
A + + + EF +K + I ++ + + V + T GRG D+V+ +
Sbjct: 189 GARKVIVSDLNEFRLEFAKK---LGADYTI-DAAEEDLVEKVRELTDGRGADVVIVATGS 244
Query: 649 EKLQA-SVRCLAQGGRFLEIGKFDLANNNMLGME-VFMRETSFHGVMLDNFFFAEQEWKM 706
+ QA ++ + +GGR L G + + + RE + G + + +++K
Sbjct: 245 PEAQAQALELVRKGGRILFFGGLPKGSTVNIDPNLIHYREITITGS----YAASPEDYKE 300
Query: 707 SLQKALQKAIDAGAVQPLVRTIFPEDKVEEAFRYMAAGKHIGKVIIK 753
+L+ ID V+ L+ FP + +EEAF A GK + K++I
Sbjct: 301 ALELIASGKID---VKDLITHRFPLEDIEEAFELAADGKSL-KIVIT 343
>gnl|CDD|176231 cd08270, MDR4, Medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family.
This group is a member of the medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, but lacks the zinc-binding
sites of the zinc-dependent alcohol dehydrogenases. The
medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P)-binding Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 305
Score = 63.9 bits (156), Expect = 1e-10
Identities = 46/161 (28%), Positives = 72/161 (44%), Gaps = 14/161 (8%)
Query: 508 GKRVMGLTSGRSLANCCETDVEMAWEIPDQWTLEDAATVPCVYATAVYAMFICGQMQKGE 567
G RV+GL + + A +PD + AAT+P TA+ A+ G G
Sbjct: 76 GARVVGLGAMGAWAELVAVPTGWLAVLPDGVSFAQAATLPVAGVTALRALRR-GGPLLGR 134
Query: 568 SILIHAGSGGVGQAAINLARYMDAEIFTTVGTPEKREFIRKTFPFIKEENIGNSRDTSFE 627
+L+ SGGVG+ A+ LA A + VG+P + E +R E +G S +
Sbjct: 135 RVLVTGASGGVGRFAVQLAALAGAHVVAVVGSPARAEGLR--ELGAAEVVVGGSELSGAP 192
Query: 628 QLVMKRTKGRGVDLVLNSLAEEKLQASVRCLAQGGRFLEIG 668
VDLV++S+ +L ++ LA GG + +G
Sbjct: 193 -----------VDLVVDSVGGPQLARALELLAPGGTVVSVG 222
>gnl|CDD|176224 cd08263, Zn_ADH10, Alcohol dehydrogenases of the MDR family.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which have a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES. These
proteins typically form dimers (typically higher plants,
mammals) or tetramers (yeast, bacteria), and have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site and a structural zinc in a lobe of
the catalytic domain. NAD(H)-binding occurs in the
cleft between the catalytic and coenzyme-binding
domains at the active site, and coenzyme binding induces
a conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
In human ADH catalysis, the zinc ion helps coordinate
the alcohol, followed by deprotonation of a histidine,
the ribose of NAD, a serine, then the alcohol, which
allows the transfer of a hydride to NAD+, creating NADH
and a zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 367
Score = 64.7 bits (158), Expect = 1e-10
Identities = 41/168 (24%), Positives = 70/168 (41%), Gaps = 9/168 (5%)
Query: 503 RLRDSGKRVMGLTSGRSLANCCETDVEMAWEIPDQWTLEDAATVPCVYATAVYAMFICGQ 562
D G M G LA +P+ ++A + C TA A+
Sbjct: 127 FRLDGGPVYMYSMGG--LAEYAVVPATALAPLPESLDYTESAVLGCAGFTAYGALKHAAD 184
Query: 563 MQKGESILIHAGSGGVGQAAINLARYMDAEIFTTVGT-PEKREFIRKTFPFIKEENIGNS 621
++ GE++ + G GGVG +AI LA+ A V EK ++ + + N+
Sbjct: 185 VRPGETVAV-IGVGGVGSSAIQLAKAFGASPIIAVDVRDEKLAKAKE----LGATHTVNA 239
Query: 622 RDTSFEQLVMKRTKGRGVDLVLNSLA-EEKLQASVRCLAQGGRFLEIG 668
+ + T GRGVD+V+ +L E + ++ + GGR + +G
Sbjct: 240 AKEDAVAAIREITGGRGVDVVVEALGKPETFKLALDVVRDGGRAVVVG 287
>gnl|CDD|235500 PRK05557, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Validated.
Length = 248
Score = 61.0 bits (149), Expect = 6e-10
Identities = 41/161 (25%), Positives = 70/161 (43%), Gaps = 12/161 (7%)
Query: 780 SNKSYIICGGLGGFGLELADWLVLRGARKLVLTSRSGVKNGYQALRIKIWKSYDVQVLIS 839
K ++ G G G +A+ L +GA +V+ S + G +AL +I + + L
Sbjct: 4 EGKVALVTGASRGIGRAIAERLAAQGA-NVVINYASS-EAGAEALVAEI-GALGGKALAV 60
Query: 840 TDDITTEAGVVNLLTEA-NKLGPVDGIFNLAVVLKDALFENQTPEDFNASLGPKANATKY 898
D++ V + EA + G VD + N A + +D L ED++ + N T
Sbjct: 61 QGDVSDAESVERAVDEAKAEFGGVDILVNNAGITRDNLLMRMKEEDWDRVI--DTNLTGV 118
Query: 899 FDKYSRTMCPTL-----GQFVVFSSVSCGRGNAGQTNYGMA 934
F ++ + + G+ + SSV GN GQ NY +
Sbjct: 119 F-NLTKAVARPMMKQRSGRIINISSVVGLMGNPGQANYAAS 158
>gnl|CDD|188164 TIGR01751, crot-CoA-red, crotonyl-CoA reductase. The enzyme
modelled by This model is responsible for the conversion
of crotonyl-CoA reductase to butyryl-CoA. In serine
cycle methylotrophic bacteria this enzyme is involved in
the process of acetyl-CoA to glyoxylate. In other
bacteria the enzyme is used to produce butyrate for
incorporation into polyketides such as tylosin from
Streptomyces fradiae and coronatine from Pseudomonas
syringae.
Length = 398
Score = 62.5 bits (152), Expect = 7e-10
Identities = 58/277 (20%), Positives = 98/277 (35%), Gaps = 34/277 (12%)
Query: 506 DSGKRVMGL-TSGRSLANCCETDVEMAWEIPDQWTLEDAATVPCVYATAVYAMFICG--- 561
S +R+ G T+ S A P T E+AA ATA Y + G
Sbjct: 127 SSEQRIWGYETNFGSFAEFALVKDYQLMPKPKHLTWEEAACPGLTGATA-YRQ-LVGWNP 184
Query: 562 -QMQKGESILIHAGSGGVGQAAINLARYMDAEIFTTVGTPEKREFI----------RKTF 610
++ G+++LI +GG+G A LAR V +PEK E+ R F
Sbjct: 185 AAVKPGDNVLIWGAAGGLGSYATQLARAGGGNPVAVVSSPEKAEYCRSLGAEAVIDRNDF 244
Query: 611 PFIKEENIGNSRD--------TSFEQLVMKRTKGRGVDLVLNSLAEEKLQASVRCLAQGG 662
N++ F + + + T G D+V SV +GG
Sbjct: 245 GHWGRLPDHNTQAPKEWTKSFKRFGKRIRELTGGEDPDIVFEHPGRATFPTSVYVCRRGG 304
Query: 663 RFLEIGKFDLANNNMLGMEVFMRETSFHGVMLDNFFFAEQEWKMSLQKALQKAIDAGAVQ 722
+ G N++ ++MR+ G N +A + G +
Sbjct: 305 MVVICGGTTGYNHDYDNRYLWMRQKRIQGSHFANL--------REAYEANRLVAK-GRID 355
Query: 723 PLVRTIFPEDKVEEAFRYMAAGKHIGKVIIKIRDEEP 759
P + +P +++ +A + + H G V + + P
Sbjct: 356 PTLSKTYPLEEIGQAHQDVHRNHHQGNVAVLVLAPRP 392
>gnl|CDD|176208 cd08246, crotonyl_coA_red, crotonyl-CoA reductase. Crotonyl-CoA
reductase, a member of the medium chain
dehydrogenase/reductase family, catalyzes the
NADPH-dependent conversion of crotonyl-CoA to
butyryl-CoA, a step in (2S)-methylmalonyl-CoA
production for straight-chain fatty acid biosynthesis.
Like enoyl reductase, another enzyme in fatty acid
synthesis, crotonyl-CoA reductase is a member of the
zinc-dependent alcohol dehydrogenase-like medium chain
dehydrogenase/reductase family. The medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, which contains the
zinc-dependent alcohol dehydrogenase (ADH-Zn) and
related proteins, is a diverse group of proteins related
to the first identified member, class I mammalian ADH.
MDRs display a broad range of activities and are
distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES.
Length = 393
Score = 60.9 bits (148), Expect = 2e-09
Identities = 61/285 (21%), Positives = 99/285 (34%), Gaps = 62/285 (21%)
Query: 506 DSGKRVMGL-TSGRSLANCCETDVEMAWEIPDQWTLEDAATVPCVYATAVYAMFIC---G 561
D +R+ G T+ S A P + E+AA V ATA Y M
Sbjct: 131 DPSQRIWGYETNYGSFAQFALVQATQLMPKPKHLSWEEAAAYMLVGATA-YRMLFGWNPN 189
Query: 562 QMQKGESILIHAGSGGVGQAAINLARYMDAEIFTTVGTPEKREFI----------RKTFP 611
++ G+++LI SGG+G AI LAR A V + EK E+ R+ F
Sbjct: 190 TVKPGDNVLIWGASGGLGSMAIQLARAAGANPVAVVSSEEKAEYCRALGAEGVINRRDFD 249
Query: 612 --FIKEE--NIGNSRDT----SFEQLVMKRT-KGRGVDLVLNSLAEEKLQASVRCLAQGG 662
+ + + + T F + + D+V SV +GG
Sbjct: 250 HWGVLPDVNSEAYTAWTKEARRFGKAIWDILGGREDPDIVFEHPGRATFPTSVFVCDRGG 309
Query: 663 RFLEIGKFDLANNNMLGMEVFMRETSFHGVMLDNFFFAEQEWKMSLQKALQ--------- 713
M V T+ + DN + W M QK +Q
Sbjct: 310 -----------------MVVICAGTTGYNHTYDNRYL----W-MR-QKRIQGSHFANDRE 346
Query: 714 -----KAIDAGAVQPLVRTIFPEDKVEEAFRYMAAGKH-IGKVII 752
+ + G + P + +F D+ +A + M +H +G + +
Sbjct: 347 AAEANRLVMKGRIDPCLSKVFSLDETPDAHQLMHRNQHHVGNMAV 391
>gnl|CDD|223959 COG1028, FabG, Dehydrogenases with different specificities (related
to short-chain alcohol dehydrogenases) [Secondary
metabolites biosynthesis, transport, and catabolism /
General function prediction only].
Length = 251
Score = 59.4 bits (144), Expect = 2e-09
Identities = 39/158 (24%), Positives = 64/158 (40%), Gaps = 5/158 (3%)
Query: 780 SNKSYIICGGLGGFGLELADWLVLRGARKLVLTSRSGVKNGYQALRIKIWKSYDVQVLIS 839
S K ++ G G G +A L GAR +V RS + +AL I ++ +
Sbjct: 4 SGKVALVTGASSGIGRAIARALAREGARVVVAARRSE-EEAAEALAAAIKEAGGGRAAAV 62
Query: 840 TDDIT-TEAGVVNLLTEA-NKLGPVDGIFNLA-VVLKDALFENQTPEDFNASLGPKANAT 896
D++ E V L+ A + G +D + N A + DA E T ED++ +
Sbjct: 63 AADVSDDEESVEALVAAAEEEFGRIDILVNNAGIAGPDAPLEELTEEDWDRVIDVNLLGA 122
Query: 897 KYFDKYSRTMCPTLGQFVVFSSVSCGRGNAGQTNYGMA 934
+ + + + V SSV+ G GQ Y +
Sbjct: 123 FLLTRAALPLMK-KQRIVNISSVAGLGGPPGQAAYAAS 159
>gnl|CDD|176216 cd08254, hydroxyacyl_CoA_DH, 6-hydroxycyclohex-1-ene-1-carboxyl-CoA
dehydrogenase, N-benzyl-3-pyrrolidinol dehydrogenase,
and other MDR family members. This group contains
enzymes of the zinc-dependent alcohol dehydrogenase
family, including members (aka MDR) identified as
6-hydroxycyclohex-1-ene-1-carboxyl-CoA dehydrogenase and
N-benzyl-3-pyrrolidinol dehydrogenase.
6-hydroxycyclohex-1-ene-1-carboxyl-CoA dehydrogenase
catalyzes the conversion of
6-Hydroxycyclohex-1-enecarbonyl-CoA and NAD+ to
6-Ketoxycyclohex-1-ene-1-carboxyl-CoA,NADH, and H+. This
group displays the characteristic catalytic and
structural zinc sites of the zinc-dependent alcohol
dehydrogenases. NAD(P)(H)-dependent oxidoreductases are
the major enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which have a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES. These
proteins typically form dimers (typically higher plants,
mammals) or tetramers (yeast, bacteria), and have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site and a structural zinc in a lobe of
the catalytic domain. NAD(H)-binding occurs in the cleft
between the catalytic and coenzyme-binding domains at
the active site, and coenzyme binding induces a
conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
In human ADH catalysis, the zinc ion helps coordinate
the alcohol, followed by deprotonation of a histidine,
the ribose of NAD, a serine, then the alcohol, which
allows the transfer of a hydride to NAD+, creating NADH
and a zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 338
Score = 60.0 bits (146), Expect = 4e-09
Identities = 49/228 (21%), Positives = 90/228 (39%), Gaps = 32/228 (14%)
Query: 534 IPDQWTLEDAATVPCVYATAVYAMFICGQMQKGESILIHAGSGGVGQAAINLARYMDAEI 593
+PD AA T +A+ G+++ GE++L+ G GG+G A+ +A+ M A +
Sbjct: 134 VPDGVPFAQAAVATDAVLTPYHAVVRAGEVKPGETVLV-IGLGGLGLNAVQIAKAMGAAV 192
Query: 594 FTTVGTPEKREFIRKTFPFIKEENIG-----NSRDTSFEQLVMKRTKGRGVDLVLN-SLA 647
EK E ++ +G NS D S + G G D++ +
Sbjct: 193 IAVDIKEEKLELAKE---------LGADEVLNSLDDSPKDKKAA-GLGGGFDVIFDFVGT 242
Query: 648 EEKLQASVRCLAQGGRFLEIGKFDLANNNMLGMEVFM-RETSFHGVMLDNFFFAEQEW-K 705
+ + + + + GGR + +G + + + + RE G +F
Sbjct: 243 QPTFEDAQKAVKPGGRIVVVGL--GRDKLTVDLSDLIARELRIIG----SF------GGT 290
Query: 706 MSLQKALQKAIDAGAVQPLVRTIFPEDKVEEAFRYMAAGKHIGKVIIK 753
+ I G + P V T P D++ E + GK G+V++
Sbjct: 291 PEDLPEVLDLIAKGKLDPQVETR-PLDEIPEVLERLHKGKVKGRVVLV 337
>gnl|CDD|212491 cd05233, SDR_c, classical (c) SDRs. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold
(alpha/beta folding pattern with a central beta-sheet),
an NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRs are approximately
350 residues. Sequence identity between different SDR
enzymes are typically in the 15-30% range, but the
enzymes share the Rossmann fold NAD-binding motif and
characteristic NAD-binding and catalytic sequence
patterns. These enzymes catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human prostaglandin dehydrogenase
(PGDH) numbering). In addition to the Tyr and Lys, there
is often an upstream Ser (Ser-138, PGDH numbering)
and/or an Asn (Asn-107, 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 = 234
Score = 56.5 bits (137), Expect = 1e-08
Identities = 42/184 (22%), Positives = 72/184 (39%), Gaps = 24/184 (13%)
Query: 785 IICGGLGGFGLELADWLVLRGARKLVLTSRSGVKNGYQALRIKIWKSYDVQVLISTDDIT 844
++ G G G +A L GA+ +VL R+ + ++ + D++
Sbjct: 2 LVTGASSGIGRAIARRLAREGAK-VVLADRNEEA----LAELAAIEALGGNAVAVQADVS 56
Query: 845 TEAGVVNLLTEA-NKLGPVDGIFNLAVVLKDALFENQTPEDFNASL-----GPKANATKY 898
E V L+ EA + G +D + N A + + E T ED++ L G T+
Sbjct: 57 DEEDVEALVEEALEEFGRLDILVNNAGIARPGPLEELTDEDWDRVLDVNLTGV-FLLTRA 115
Query: 899 FDKYSRTMCP-TLGQFVVFSSVSCGRGNAGQTNYGMANSIMERICEARRAEGLPGLAVEW 957
+ M G+ V SSV+ R GQ Y + + +E + + LA+E
Sbjct: 116 ALPH---MKKQGGGRIVNISSVAGLRPLPGQAAYAASKAALEGLTRS--------LALEL 164
Query: 958 GAVG 961
G
Sbjct: 165 APYG 168
>gnl|CDD|176222 cd08261, Zn_ADH7, Alcohol dehydrogenases of the MDR family. This
group contains members identified as related to
zinc-dependent alcohol dehydrogenase and other members
of the MDR family. The medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, which contains the
zinc-dependent alcohol dehydrogenase (ADH-Zn) and
related proteins, is a diverse group of proteins related
to the first identified member, class I mammalian ADH.
MDRs display a broad range of activities and are
distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P)-binding Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group includes
various activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has a
catalytic role, while structural zinc aids in stability.
ADH-like proteins typically form dimers (typically
higher plants, mammals) or tetramers (yeast, bacteria),
and generally have 2 tightly bound zinc atoms per
subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 337
Score = 57.6 bits (140), Expect = 2e-08
Identities = 67/304 (22%), Positives = 117/304 (38%), Gaps = 66/304 (21%)
Query: 495 VIGFEYSGRLRDSGKRVMGLTSG------------------RSLANCCET-DV------- 528
++G E SG + + G+ V GL G + NCCE V
Sbjct: 56 ILGHELSGEVVEVGEGVAGLKVGDRVVVDPYISCGECYACRKGRPNCCENLQVLGVHRDG 115
Query: 529 ---------EMAWEIPDQWTLEDAATVPC--VYATAVYAMFICGQMQKGESILIHAGSGG 577
A +P+ +L+ AA V + A AV + G+++L+ G+G
Sbjct: 116 GFAEYIVVPADALLVPEGLSLDQAALVEPLAIGAHAVRR----AGVTAGDTVLV-VGAGP 170
Query: 578 VGQAAINLARYMDAEIFTTVGTPEKREFIRKTFPFIKEENIGNSRDTSFEQLVMKRTKGR 637
+G I +A+ A + E+ EF R+ ++ I N D + + T G
Sbjct: 171 IGLGVIQVAKARGARVIVVDIDDERLEFARE---LGADDTI-NVGDEDVAARLRELTDGE 226
Query: 638 GVDLVLNSL-AEEKLQASVRCLAQGGR--FLEIGKFDLANNNMLGMEVFMRETSFHGVML 694
G D+V+++ ++ +V +A GGR + + K + E +E + G
Sbjct: 227 GADVVIDATGNPASMEEAVELVAHGGRVVLVGLSKGPVTFP---DPEFHKKELTILGSRN 283
Query: 695 -DNFFFAEQEWKMSLQKALQKAIDAGAVQP--LVRTIFPEDKVEEAFRYMAA-GKHIGKV 750
F + + +++G V P L+ FP + V EAF A + KV
Sbjct: 284 ATREDFPD----------VIDLLESGKVDPEALITHRFPFEDVPEAFDLWEAPPGGVIKV 333
Query: 751 IIKI 754
+I+
Sbjct: 334 LIEF 337
>gnl|CDD|176198 cd08236, sugar_DH, NAD(P)-dependent sugar dehydrogenases. This
group contains proteins identified as sorbitol
dehydrogenases and other sugar dehydrogenases of the
medium-chain dehydrogenase/reductase family (MDR), which
includes zinc-dependent alcohol dehydrogenase and
related proteins. Sorbitol and aldose reductase are
NAD(+) binding proteins of the polyol pathway, which
interconverts glucose and fructose. Sorbitol
dehydrogenase is tetrameric and has a single catalytic
zinc per subunit. NAD(P)(H)-dependent oxidoreductases
are the major enzymes in the interconversion of alcohols
and aldehydes, or ketones. Related proteins include
threonine dehydrogenase, formaldehyde dehydrogenase, and
butanediol dehydrogenase. The medium chain alcohol
dehydrogenase family (MDR) has a NAD(P)(H)-binding
domain in a Rossmann fold of a beta-alpha form. The
N-terminal region typically has an all-beta catalytic
domain. These proteins typically form dimers (typically
higher plants, mammals) or tetramers (yeast, bacteria),
and have 2 tightly bound zinc atoms per subunit. Horse
liver alcohol dehydrogenase is a dimeric enzyme and each
subunit has two domains. The NAD binding domain is in a
Rossmann fold and the catalytic domain contains a zinc
ion to which substrates bind. There is a cleft between
the domains that closes upon formation of the ternary
complex.
Length = 343
Score = 57.6 bits (140), Expect = 2e-08
Identities = 52/227 (22%), Positives = 104/227 (45%), Gaps = 19/227 (8%)
Query: 533 EIPDQWTLEDAATV-PCVYATAVYAMFICGQMQKGESILIHAGSGGVGQAAINLARYMDA 591
+IPD E+AA + P A A++A+ + + G+++++ G+G +G AI + + A
Sbjct: 129 KIPDHVDYEEAAMIEPA--AVALHAVRL-AGITLGDTVVV-IGAGTIGLLAIQWLKILGA 184
Query: 592 EIFTTVG-TPEKREFIRKTFPFIKEENIGNSRDTSFEQLVMKRTKGRGVDLVLNSL-AEE 649
+ V EK R+ + ++ N ++ E+ V + T+GRG DLV+ + +
Sbjct: 185 KRVIAVDIDDEKLAVARE----LGADDTINPKEEDVEK-VRELTEGRGADLVIEAAGSPA 239
Query: 650 KLQASVRCLAQGGR--FLEIGKFDLANNNMLGMEVFMRETSFHGV-MLDNFFFAEQEWKM 706
++ ++ GG+ + I D+ + ++ +E + G + F EW+
Sbjct: 240 TIEQALALARPGGKVVLVGIPYGDVTLSEEAFEKILRKELTIQGSWNSYSAPFPGDEWRT 299
Query: 707 SLQKALQKAIDAGAVQPLVRTIFPEDKVEEAFRYMAAGK-HIGKVII 752
+L I V+PL+ P + AF +A + GKV++
Sbjct: 300 ALDLLASGKIK---VEPLITHRLPLEDGPAAFERLADREEFSGKVLL 343
>gnl|CDD|214834 smart00823, PKS_PP, Phosphopantetheine attachment site.
Phosphopantetheine (or pantetheine 4' phosphate) is the
prosthetic group of acyl carrier proteins (ACP) in some
multienzyme complexes where it serves as a 'swinging arm'
for the attachment of activated fatty acid and amino-acid
groups.
Length = 86
Score = 52.3 bits (126), Expect = 2e-08
Identities = 14/53 (26%), Positives = 26/53 (49%)
Query: 1022 IVDAVINILGLRDLKTVSLHSTLAELGMDSMMAVEIKQTLEREFEVFLTPQDI 1074
+ + V +LG + + +LG+DS+MAVE++ LE + L +
Sbjct: 17 VREQVAAVLGHAAAEAIDPDRPFRDLGLDSLMAVELRNRLEAATGLRLPATLV 69
>gnl|CDD|236372 PRK09072, PRK09072, short chain dehydrogenase; Provisional.
Length = 263
Score = 56.1 bits (136), Expect = 3e-08
Identities = 36/111 (32%), Positives = 55/111 (49%), Gaps = 5/111 (4%)
Query: 780 SNKSYIICGGLGGFGLELADWLVLRGARKLVLTSRSGVKNGYQALRIKIWKSYDVQVLIS 839
+K ++ G GG G LA+ L GAR L+L R+ K +AL ++ Y +
Sbjct: 4 KDKRVLLTGASGGIGQALAEALAAAGAR-LLLVGRNAEK--LEALAARL--PYPGRHRWV 58
Query: 840 TDDITTEAGVVNLLTEANKLGPVDGIFNLAVVLKDALFENQTPEDFNASLG 890
D+T+EAG +L A ++G ++ + N A V AL E+Q PE L
Sbjct: 59 VADLTSEAGREAVLARAREMGGINVLINNAGVNHFALLEDQDPEAIERLLA 109
>gnl|CDD|225856 COG3319, COG3319, Thioesterase domains of type I polyketide synthases
or non-ribosomal peptide synthetases [Secondary
metabolites biosynthesis, transport, and catabolism].
Length = 257
Score = 55.9 bits (135), Expect = 3e-08
Identities = 50/238 (21%), Positives = 76/238 (31%), Gaps = 42/238 (17%)
Query: 1159 TIFMVPGIEGIATVLEPLAKNINAQVLVFQFD------HTNPPDTIPEMADSLLPHFKKR 1212
+F G PLA + + V+ P ++ +MA + + R
Sbjct: 2 PLFCFHPAGGSVLAYAPLAAALGPLLPVYGLQAPGYGAGEQPFASLDDMAAAYVA--AIR 59
Query: 1213 LVHGTDEIKLVGFSFGGMVALELAIKLEQLGTKC-HLYLVDSAPDY------VLTSLRKL 1265
V L+G+S GG VA E+A +LE G + L L+D+ P + R+
Sbjct: 60 RVQPEGPYVLLGWSLGGAVAFEVAAQLEAQGEEVAFLGLLDAVPPHNGRKEETRNRWRRY 119
Query: 1266 PDWNAKLNYFLDL---------MPEDATH--SRTYQRNLAHAAYKRITSILKYTDPK--- 1311
K LD + +A +R + LA A + IL+
Sbjct: 120 ARTAEKTANGLDPEVLAEILASLGAEAAEYLARALEA-LAQAGLDKAAFILELEAALLLR 178
Query: 1312 --------HKAFGGNITLLRPTEQALPTA--EDYGLSKVCKKPVKVHFVDGNHFTVLD 1359
K G TL G S V +DG HF +L
Sbjct: 179 VRALGTALFKPSDGLPTLFAADRL-HDEGFPPLAGWSGWIADLDIVR-IDGTHFDMLK 234
>gnl|CDD|176193 cd08231, MDR_TM0436_like, Hypothetical enzyme TM0436 resembles the
zinc-dependent alcohol dehydrogenases (ADH). This group
contains the hypothetical TM0436 alcohol dehydrogenase
from Thermotoga maritima, proteins annotated as
5-exo-alcohol dehydrogenase, and other members of the
medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family.
MDR, which contains the zinc-dependent alcohol
dehydrogenase (ADH-Zn) and related proteins, is a
diverse group of proteins related to the first
identified member, class I mammalian ADH. MDRs display
a broad range of activities and are distinguished from
the smaller short chain dehydrogenases (~ 250 amino
acids vs. the ~ 350 amino acids of the MDR). The MDR
proteins have 2 domains: a C-terminal NAD(P)
binding-Rossmann fold domain of a beta-alpha form and an
N-terminal catalytic domain with distant homology to
GroES. The MDR group contains a host of activities,
including the founding alcohol dehydrogenase (ADH),
quinone reductase, sorbitol dehydrogenase, formaldehyde
dehydrogenase, butanediol DH, ketose reductase, cinnamyl
reductase, and numerous others. The zinc-dependent
alcohol dehydrogenases (ADHs) catalyze the
NAD(P)(H)-dependent interconversion of alcohols to
aldehydes or ketones. Active site zinc has a catalytic
role, while structural zinc aids in stability.
Length = 361
Score = 56.5 bits (137), Expect = 5e-08
Identities = 34/142 (23%), Positives = 62/142 (43%), Gaps = 14/142 (9%)
Query: 534 IPDQWTLEDAATVPCVYATAVYAMFICGQMQKGESILIHAGSGGVGQAAINLARYMDAEI 593
+PD E AA C AT + A+ G + G+++++ G+G +G A+ A+ A
Sbjct: 146 VPDNVPDEVAAPANCALATVLAALDRAGPVGAGDTVVVQ-GAGPLGLYAVAAAKLAGARR 204
Query: 594 FTTVGTPEKREFIRKTF---PFIKEENIGNSRDTSFEQLVMKRTKGRGVDLVL----NSL 646
+ +R + + F I +I D +V T GRG D+V+ +
Sbjct: 205 VIVIDGSPERLELAREFGADATI---DIDELPDPQRRAIVRDITGGRGADVVIEASGHPA 261
Query: 647 AEEKLQASVRCLAQGGRFLEIG 668
A + + L +GG ++ +G
Sbjct: 262 A---VPEGLELLRRGGTYVLVG 280
>gnl|CDD|176257 cd08297, CAD3, Cinnamyl alcohol dehydrogenases (CAD). These
alcohol dehydrogenases are related to the cinnamyl
alcohol dehydrogenases (CAD), members of the medium
chain dehydrogenase/reductase family.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. Cinnamyl alcohol dehydrogenases
(CAD) reduce cinnamaldehydes to cinnamyl alcohols in the
last step of monolignal metabolism in plant cells walls.
CAD binds 2 zinc ions and is NADPH- dependent. CAD
family members are also found in non-plant species, e.g.
in yeast where they have an aldehyde reductase activity.
The medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 341
Score = 55.6 bits (135), Expect = 8e-08
Identities = 52/231 (22%), Positives = 94/231 (40%), Gaps = 34/231 (14%)
Query: 534 IPDQWTLEDAATVPCVYATAVYAMFICGQMQKGESILIHAGSGGVGQAAINLARYMDAEI 593
IPD + E AA + C T VY ++ G+ ++I GG+G + A+ M +
Sbjct: 135 IPDGLSFEQAAPLLCAGVT-VYKALKKAGLKPGDWVVISGAGGGLGHLGVQYAKAMGLRV 193
Query: 594 FTTVGTPEKREFIRKTFP--FIKEENIGNSRDTSFEQLVMKRTKGRGVDLVLN-SLAEEK 650
EK E ++ F+ + + + + V + T G G V+ +++
Sbjct: 194 IAIDVGDEKLELAKELGADAFV------DFKKSDDVEAVKELTGGGGAHAVVVTAVSAAA 247
Query: 651 LQASVRCLAQGGRFLEIGKFDLANNNMLGMEVF---MRET----SFHGVMLDNFFFAEQE 703
+ ++ L GG + +G L + ++ F +R S G D
Sbjct: 248 YEQALDYLRPGGTLVCVG---LPPGGFIPLDPFDLVLRGITIVGSLVGTRQD-------- 296
Query: 704 WKMSLQKALQKAIDAGAVQPLVRTIFPEDKVEEAFRYMAAGKHIGKVIIKI 754
LQ+AL+ A G V+P ++ P + + E F M GK G+V++
Sbjct: 297 ----LQEALEFA-ARGKVKPHIQV-VPLEDLNEVFEKMEEGKIAGRVVVDF 341
>gnl|CDD|233590 TIGR01830, 3oxo_ACP_reduc, 3-oxoacyl-(acyl-carrier-protein)
reductase. This model represents 3-oxoacyl-[ACP]
reductase, also called 3-ketoacyl-acyl carrier protein
reductase, an enzyme of fatty acid biosynthesis [Fatty
acid and phospholipid metabolism, Biosynthesis].
Length = 239
Score = 54.1 bits (131), Expect = 1e-07
Identities = 47/166 (28%), Positives = 76/166 (45%), Gaps = 18/166 (10%)
Query: 785 IICGGLGGFGLELADWLVLRGARKLVLTSRSGVKNGYQALRIKIWKSYDVQVLISTDDIT 844
++ G G G +A L GA K+++T RS + + + ++ K+Y V+ L D++
Sbjct: 2 LVTGASRGIGRAIALKLAKEGA-KVIITYRSSEEGA-EEVVEEL-KAYGVKALGVVCDVS 58
Query: 845 TEAGVVNLLTEA-NKLGPVDGIFNLAVVLKDALFENQTPEDFNASLGPKANATKYFD--- 900
V ++ E +LGP+D + N A + +D L ED++A + N T F+
Sbjct: 59 DREDVKAVVEEIEEELGPIDILVNNAGITRDNLLMRMKEEDWDAVI--DTNLTGVFNLTQ 116
Query: 901 KYSRTMCPT-LGQFVVFSSVSCGRGNAGQTNY--------GMANSI 937
R M G+ + SSV GNAGQ NY G S+
Sbjct: 117 AVLRIMIKQRSGRIINISSVVGLMGNAGQANYAASKAGVIGFTKSL 162
>gnl|CDD|176201 cd08239, THR_DH_like, L-threonine dehydrogenase (TDH)-like.
MDR/AHD-like proteins, including a protein annotated as
a threonine dehydrogenase. L-threonine dehydrogenase
(TDH) catalyzes the zinc-dependent formation of
2-amino-3-ketobutyrate from L-threonine via
NAD(H)-dependent oxidation. The zinc-dependent alcohol
dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent
interconversion of alcohols to aldehydes or ketones.
Zinc-dependent ADHs are medium chain
dehydrogenase/reductase type proteins (MDRs) and have a
NAD(P)(H)-binding domain in a Rossmann fold of an
beta-alpha form. The N-terminal region typically has an
all-beta catalytic domain. In addition to alcohol
dehydrogenases, this group includes quinone reductase,
sorbitol dehydrogenase, formaldehyde dehydrogenase,
butanediol DH, ketose reductase, cinnamyl reductase, and
numerous others. These proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 339
Score = 55.0 bits (133), Expect = 1e-07
Identities = 47/226 (20%), Positives = 100/226 (44%), Gaps = 28/226 (12%)
Query: 534 IPDQWTLEDAATVPCVYATAVYAMFICGQMQKGESILIHAGSGGVGQAAINLARYMDAE- 592
+PD + D A + C TA Y + +++L+ G+G VG A+ LAR + AE
Sbjct: 133 LPDDLSFADGALLLCGIGTA-YHALRRVGVSGRDTVLV-VGAGPVGLGALMLARALGAED 190
Query: 593 IFTTVGTPEKREFIRKTFPFIKEENIGNSRDTSFEQLVMKRTKGRGVDLVLN-SLAEEKL 651
+ +PE+ E + + + + NS ++ + + T G G D+ + S
Sbjct: 191 VIGVDPSPERLELAKA----LGADFVINSGQDDVQE-IRELTSGAGADVAIECSGNTAAR 245
Query: 652 QASVRCLAQGGRFLEIGK-----FDLANNNMLGMEVFMRETSFHGVMLDNFFFAEQEWKM 706
+ ++ + GR + +G+ +++N ++ ++ + G +++F+ + +
Sbjct: 246 RLALEAVRPWGRLVLVGEGGELTIEVSN------DLIRKQRTLIG----SWYFSVPDMEE 295
Query: 707 SLQKALQKAIDAGAVQPLVRTIFPEDKVEEAFRYMAAGKHIGKVII 752
+ + ++ V LV F D+ EA+ A G+ GKV+
Sbjct: 296 CAEFLARHKLE---VDRLVTHRFGLDQAPEAYALFAQGE-SGKVVF 337
>gnl|CDD|176209 cd08247, AST1_like, AST1 is a cytoplasmic protein associated with
the periplasmic membrane in yeast. This group contains
members identified in targeting of yeast membrane
proteins ATPase. AST1 is a cytoplasmic protein
associated with the periplasmic membrane in yeast,
identified as a multicopy suppressor of pma1 mutants
which cause temperature sensitive growth arrest due to
the inability of ATPase to target to the cell surface.
This family is homologous to the medium chain family of
dehydrogenases and reductases. Medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, which contains the
zinc-dependent alcohol dehydrogenase (ADH-Zn) and
related proteins, is a diverse group of proteins related
to the first identified member, class I mammalian ADH.
MDRs display a broad range of activities and are
distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of an
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES.
Length = 352
Score = 54.2 bits (131), Expect = 2e-07
Identities = 59/246 (23%), Positives = 105/246 (42%), Gaps = 37/246 (15%)
Query: 534 IPDQWTLEDAATVPCVYATAVYAMFICGQ-MQKGESILIHAGSGGVGQAAINLARYMDAE 592
P+ +LE+AA P V TA + GQ + +L+ GS VG+ AI LA+
Sbjct: 119 KPENISLEEAAAWPLVLGTAYQILEDLGQKLGPDSKVLVLGGSTSVGRFAIQLAKNHYN- 177
Query: 593 IFTTVGTPEKREFIRKTFPFIKE---ENIGNSRDTSFEQL---VMKRTKGRG-VDLVLNS 645
I T VGT R + K+ ++ + S +L V++ KG+G DL+L+
Sbjct: 178 IGTVVGTCSSR-----SAELNKKLGADHFIDYDAHSGVKLLKPVLENVKGQGKFDLILDC 232
Query: 646 LAEEKLQAS----VRCLAQGGRFLEI-G--KFDLAN---NNMLGMEVFMRET-------S 688
+ L ++ ++ G ++ I G K + N+ R+ S
Sbjct: 233 VGGYDLFPHINSILKPKSKNGHYVTIVGDYKANYKKDTFNSWDNPSANARKLFGSLGLWS 292
Query: 689 FHGVMLDNFFFAEQEWKMSLQKALQKAIDAGAVQPLVRTIFPEDKVEEAFRYMAAGKHIG 748
++ +W + L I G V+P + +++P + +EAF + + + G
Sbjct: 293 YNYQFF--LLDPNADW-IEKCAEL---IADGKVKPPIDSVYPFEDYKEAFERLKSNRAKG 346
Query: 749 KVIIKI 754
KV+IK+
Sbjct: 347 KVVIKV 352
>gnl|CDD|187594 cd05333, BKR_SDR_c, beta-Keto acyl carrier protein reductase (BKR),
involved in Type II FAS, classical (c) SDRs. This
subgroup includes the Escherichai coli K12 BKR, FabG.
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
structurally conserved Rossmann fold (alpha/beta folding
pattern with a central beta-sheet) 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: TGxxxGxG in classical SDRs. 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 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. 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-151 and
Lys-155, and well as Asn-111 (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 = 240
Score = 52.9 bits (128), Expect = 3e-07
Identities = 40/153 (26%), Positives = 63/153 (41%), Gaps = 7/153 (4%)
Query: 782 KSYIICGGLGGFGLELADWLVLRGARKLVLTSRSGVKNGYQALRIKIWKSYDVQVLISTD 841
K ++ G G G +A L GA K+ +T RS + +I K+
Sbjct: 1 KVALVTGASRGIGRAIALRLAAEGA-KVAVTDRS--EEAAAETVEEI-KALGGNAAALEA 56
Query: 842 DITTEAGVVNLLTEA-NKLGPVDGIFNLAVVLKDALFENQTPEDFNASLGPKANATKYFD 900
D++ V L+ + + GPVD + N A + +D L + ED++A +
Sbjct: 57 DVSDREAVEALVEKVEAEFGPVDILVNNAGITRDNLLMRMSEEDWDAVINVNLTGVFNVT 116
Query: 901 K-YSRTMCPT-LGQFVVFSSVSCGRGNAGQTNY 931
+ R M G+ + SSV GN GQ NY
Sbjct: 117 QAVIRAMIKRRSGRIINISSVVGLIGNPGQANY 149
>gnl|CDD|182701 PRK10754, PRK10754, quinone oxidoreductase, NADPH-dependent;
Provisional.
Length = 327
Score = 54.0 bits (130), Expect = 3e-07
Identities = 37/140 (26%), Positives = 67/140 (47%), Gaps = 14/140 (10%)
Query: 534 IPDQWTLEDAATVPCVYATAVYAMFICGQMQKGESILIHAGSGGVGQAAINLARYMDAEI 593
+PD + E AA T Y + +++ E L HA +GGVG A A+ + A++
Sbjct: 109 LPDAISFEQAAASFLKGLTVYYLLRKTYEIKPDEQFLFHAAAGGVGLIACQWAKALGAKL 168
Query: 594 FTTVGTPEKREFIRKTFPFIKEENIG-----NSRDTSFEQLVMKRTKGRGVDLVLNSLAE 648
TVG+ +K + + + G N R+ + + V + T G+ V +V +S+ +
Sbjct: 169 IGTVGSAQKAQ---------RAKKAGAWQVINYREENIVERVKEITGGKKVRVVYDSVGK 219
Query: 649 EKLQASVRCLAQGGRFLEIG 668
+ +AS+ CL + G + G
Sbjct: 220 DTWEASLDCLQRRGLMVSFG 239
>gnl|CDD|235546 PRK05653, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Validated.
Length = 246
Score = 52.9 bits (128), Expect = 3e-07
Identities = 45/164 (27%), Positives = 73/164 (44%), Gaps = 19/164 (11%)
Query: 780 SNKSYIICGGLGGFGLELADWLVLRGARKLVLTSRSGVKNGYQALRIKIWKSYDVQVLIS 839
K+ ++ G G G +A L GA+ V+ S + +AL ++ ++ + +
Sbjct: 4 QGKTALVTGASRGIGRAIALRLAADGAK--VVIYDSNEEAA-EALAAEL-RAAGGEARVL 59
Query: 840 TDDITTEAGVVNLLTEANK-LGPVDGIFNLAVVLKDALFENQTPEDFNASLGPKANATKY 898
D++ EA V L+ A + G +D + N A + +DAL + ED++ + N T
Sbjct: 60 VFDVSDEAAVRALIEAAVEAFGALDILVNNAGITRDALLPRMSEEDWDRVID--VNLTGT 117
Query: 899 FDKYSRTMCPTL--------GQFVVFSSVSCGRGNAGQTNYGMA 934
F + L G+ V SSVS GN GQTNY A
Sbjct: 118 F----NVVRAALPPMIKARYGRIVNISSVSGVTGNPGQTNYSAA 157
>gnl|CDD|176207 cd08245, CAD, Cinnamyl alcohol dehydrogenases (CAD) and related
proteins. Cinnamyl alcohol dehydrogenases (CAD),
members of the medium chain dehydrogenase/reductase
family, reduce cinnamaldehydes to cinnamyl alcohols in
the last step of monolignal metabolism in plant cells
walls. CAD binds 2 zinc ions and is NADPH- dependent.
CAD family members are also found in non-plant species,
e.g. in yeast where they have an aldehyde reductase
activity. The medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes, or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 330
Score = 53.5 bits (129), Expect = 4e-07
Identities = 57/223 (25%), Positives = 97/223 (43%), Gaps = 28/223 (12%)
Query: 534 IPDQWTLEDAATVPCVYATAVYAMFICGQMQKGESILIHAGSGGVGQAAINLARYMDAEI 593
+PD L AA + C T VY+ + GE + + G GG+G A+ AR M E
Sbjct: 132 LPDGLPLAQAAPLLCAGIT-VYSALRDAGPRPGERVAV-LGIGGLGHLAVQYARAMGFET 189
Query: 594 FTTVGTPEKREFIRKTFPFIKEENIGNSRDTSFEQLVMKRTKGRGVDLVLN-SLAEEKLQ 652
+P+KRE RK +E + +S +L + G G D++L ++ +
Sbjct: 190 VAITRSPDKRELARKLGA---DEVV-DSG----AELDEQAAAG-GADVILVTVVSGAAAE 240
Query: 653 ASVRCLAQGGRFLEIGKFDLANNNMLGMEVFMRETSFHGVMLDNFFFAEQEWKMSLQKAL 712
A++ L +GGR + +G + + + M+ S G + L
Sbjct: 241 AALGGLRRGGRIVLVGLPESPPFSPDIFPLIMKRQSIAGSTHGG------------RADL 288
Query: 713 QKAID---AGAVQPLVRTIFPEDKVEEAFRYMAAGKHIGKVII 752
Q+A+D G V+P++ T FP D+ EA+ M G + ++
Sbjct: 289 QEALDFAAEGKVKPMIET-FPLDQANEAYERMEKGDVRFRFVL 330
>gnl|CDD|176188 cd05285, sorbitol_DH, Sorbitol dehydrogenase. Sorbitol and aldose
reductase are NAD(+) binding proteins of the polyol
pathway, which interconverts glucose and fructose.
Sorbitol dehydrogenase is tetrameric and has a single
catalytic zinc per subunit. Aldose reductase catalyzes
the NADP(H)-dependent conversion of glucose to sorbital,
and SDH uses NAD(H) in the conversion of sorbitol to
fructose. NAD(P)(H)-dependent oxidoreductases are the
major enzymes in the interconversion of alcohols and
aldehydes, or ketones. The medium chain alcohol
dehydrogenase family (MDR) have a NAD(P)(H)-binding
domain in a Rossmann fold of a beta-alpha form. The
N-terminal region typically has an all-beta catalytic
domain. These proteins typically form dimers (typically
higher plants, mammals) or tetramers (yeast, bacteria),
and have 2 tightly bound zinc atoms per subunit.
Length = 343
Score = 53.3 bits (129), Expect = 5e-07
Identities = 55/237 (23%), Positives = 99/237 (41%), Gaps = 42/237 (17%)
Query: 534 IPDQWTLEDAATVPCVYATAVYAMFIC--GQMQKGESILIHAGSGGVGQAAINLARYMDA 591
+PD +LE+ A V + + V+A C ++ G+++L+ G+G +G +A+ A
Sbjct: 133 LPDNVSLEEGALVEPL-SVGVHA---CRRAGVRPGDTVLV-FGAGPIGLLTAAVAKAFGA 187
Query: 592 EIFTTVGT---PEKREFIRK---TFPFIKEENIGNSRDTSFEQLVMKRTKGRGVDLVLN- 644
V T P + EF ++ T N+ + + + G+G D+V+
Sbjct: 188 --TKVVVTDIDPSRLEFAKELGATHTV----NVRTEDTPESAEKIAELLGGKGPDVVIEC 241
Query: 645 SLAEEKLQASVRCLAQGGRFLEIG------KFDLANNNMLGMEVFMRETSFHGVMLDNFF 698
+ AE +Q ++ GG + +G L +RE GV F
Sbjct: 242 TGAESCIQTAIYATRPGGTVVLVGMGKPEVTLPL-------SAASLREIDIRGV----FR 290
Query: 699 FAEQEWKMSLQKALQKAIDAGAVQPLVRTIFPEDKVEEAFRYMAAGKHIG-KVIIKI 754
+A + +++ +D V+PL+ FP + EAF A GK KV+I+
Sbjct: 291 YANT-YPTAIELLASGKVD---VKPLITHRFPLEDAVEAFETAAKGKKGVIKVVIEG 343
>gnl|CDD|237218 PRK12825, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 249
Score = 51.8 bits (125), Expect = 8e-07
Identities = 32/164 (19%), Positives = 67/164 (40%), Gaps = 18/164 (10%)
Query: 780 SNKSYIICGGLGGFGLELADWLVLRGARKLVLTSRSGVKNGYQALRIKIWKSYDVQVLIS 839
+ ++ G G G +A L GA +V+ RS + + L + ++ +
Sbjct: 5 MGRVALVTGAARGLGRAIALRLARAGAD-VVVHYRSD-EEAAEELV-EAVEALGRRAQAV 61
Query: 840 TDDITTEAGVVNLLTEA-NKLGPVDGIFNLAVVLKDALFENQTPEDFNASLGPKANATKY 898
D+T +A + + A + G +D + N A + +D + + ++++ + N +
Sbjct: 62 QADVTDKAALEAAVAAAVERFGRIDILVNNAGIFEDKPLADMSDDEWDEVID--VNLSGV 119
Query: 899 FDKYSRTMCPTL--------GQFVVFSSVSCGRGNAGQTNYGMA 934
F + + G+ V SSV+ G G++NY A
Sbjct: 120 F----HLLRAVVPPMRKQRGGRIVNISSVAGLPGWPGRSNYAAA 159
>gnl|CDD|176219 cd08258, Zn_ADH4, Alcohol dehydrogenases of the MDR family. This
group shares the zinc coordination sites of the
zinc-dependent alcohol dehydrogenases. The medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, which contains the
zinc-dependent alcohol dehydrogenase (ADH-Zn) and
related proteins, is a diverse group of proteins related
to the first identified member, class I mammalian ADH.
MDRs display a broad range of activities and are
distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P)-binding Rossmann fold domain of an
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 306
Score = 51.5 bits (124), Expect = 1e-06
Identities = 43/172 (25%), Positives = 81/172 (47%), Gaps = 14/172 (8%)
Query: 504 LRDSGKRVMGLTSGRSLANCCETDVEMAWEIPDQWTLEDAA-TVPCVYATAVYAMFICGQ 562
++ +G + A E E+P+ +LE AA T P A AV+A+
Sbjct: 104 NLCPHRKGIGTQADGGFAEYVLVPEESLHELPENLSLEAAALTEPL--AVAVHAVAERSG 161
Query: 563 MQKGESILIHAGSGGVGQAAINLARYMDAEIFTTVGTPEKREFIRKTFPFIKEENIGNSR 622
++ G+++++ G G +G A +A+ A + VGT + + + +E ++
Sbjct: 162 IRPGDTVVV-FGPGPIGLLAAQVAKLQGATV-VVVGTEKDEVRLD-----VAKELGADAV 214
Query: 623 DTSFE---QLVMKRTKGRGVDLVLN-SLAEEKLQASVRCLAQGGRFLEIGKF 670
+ E +LV + T G G D+V+ S A L+ ++ L +GGR +++G F
Sbjct: 215 NGGEEDLAELVNEITDGDGADVVIECSGAVPALEQALELLRKGGRIVQVGIF 266
>gnl|CDD|234022 TIGR02813, omega_3_PfaA, polyketide-type polyunsaturated fatty acid
synthase PfaA. Members of the seed for this alignment
are involved in omega-3 polyunsaturated fatty acid
biosynthesis, such as the protein PfaA from the
eicosapentaenoic acid biosynthesis operon in
Photobacterium profundum strain SS9. PfaA is encoded
together with PfaB, PfaC, and PfaD, and the functions of
the individual polypeptides have not yet been described.
More distant homologs of PfaA, also included with the
reach of this model, appear to be involved in
polyketide-like biosynthetic mechanisms of
polyunsaturated fatty acid biosynthesis, an alternative
to the more familiar iterated mechanism of chain
extension and desaturation, and in most cases are encoded
near genes for homologs of PfaB, PfaC, and/or PfaD.
Length = 2582
Score = 53.1 bits (127), Expect = 1e-06
Identities = 29/99 (29%), Positives = 47/99 (47%), Gaps = 2/99 (2%)
Query: 842 DITTEAGVVNLLTEANKLGPVDGIFNLAVVLKDALFENQTPEDFNASLGPKANATKYFDK 901
D+T V + NK + GI + A VL D +++T E+FNA G K +
Sbjct: 2102 DVTNSVSVAATVQPLNKTLQITGIIHGAGVLADKHIQDKTLEEFNAVYGTKVDGLLSL-- 2159
Query: 902 YSRTMCPTLGQFVVFSSVSCGRGNAGQTNYGMANSIMER 940
+ + +FSS + GN GQ++Y M+N I+ +
Sbjct: 2160 LAALNAENIKLLALFSSAAGFYGNTGQSDYAMSNDILNK 2198
>gnl|CDD|223990 COG1062, AdhC, Zn-dependent alcohol dehydrogenases, class III
[Energy production and conversion].
Length = 366
Score = 51.5 bits (124), Expect = 2e-06
Identities = 54/237 (22%), Positives = 86/237 (36%), Gaps = 43/237 (18%)
Query: 534 IPDQWTLEDAATVPCVYATAVYAMFICGQMQKGESILIHAGSGGVGQAAINLARYMDAEI 593
I LE A + C T + A+ +++ G+++ + G GGVG AAI A+ A
Sbjct: 154 IDPDAPLEKACLLGCGVTTGIGAVVNTAKVEPGDTVAV-FGLGGVGLAAIQGAKAAGAGR 212
Query: 594 FTTVGT-PEKREFIRK-----TFPFIKEENIGNSRDTSFEQLVMKRTKGRGVDLVLNSLA 647
V PEK E +K N ++ + G D +
Sbjct: 213 IIAVDINPEKLELAKKFGATHFV---------NPKEVDDVVEAIVELTDGGADYAFECVG 263
Query: 648 E-EKLQASVRCLAQGGRFLEIGKFDLANNNMLGMEVFMRETSFHGVMLDNFFFAEQEWKM 706
E ++ ++ +GG + IG +A G E+ R + WK
Sbjct: 264 NVEVMRQALEATHRGGTSVIIG---VAG---AGQEISTRPFQL---------VTGRVWKG 308
Query: 707 SL------QKALQKAID---AG--AVQPLVRTIFPEDKVEEAFRYMAAGKHIGKVII 752
S + + + +D AG + LV P + + EAF M GK I VI
Sbjct: 309 SAFGGARPRSDIPRLVDLYMAGKLPLDRLVTHTIPLEDINEAFDLMHEGKSIRSVIR 365
>gnl|CDD|187535 cd02266, SDR, Short-chain dehydrogenases/reductases (SDR). 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 prostaglandin
dehydrogenase (PGDH) numbering). In addition to the Tyr
and Lys, there is often an upstream Ser (Ser-138, PGDH
numbering) and/or an Asn (Asn-107, 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 (KR) domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type KRs 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 = 186
Score = 49.4 bits (118), Expect = 2e-06
Identities = 45/208 (21%), Positives = 74/208 (35%), Gaps = 55/208 (26%)
Query: 785 IICGGLGGFGLELADWLVLRGARKLVLTSRSGVKNGYQALRIKIWKSYDVQVLISTDDIT 844
++ GG GG G +A WL RG+ K+++ SR V A+ D +++ T
Sbjct: 2 LVTGGSGGIGGAIARWLASRGSPKVLVVSRRDVVVHNAAI------LDDGRLIDLTGSRI 55
Query: 845 TEAGVVNLLTEANKLGPVDGIFNLAVVLKDALFENQTPEDFNASLGPKANATKYFDKYSR 904
A N++ G L A + K R
Sbjct: 56 ERAIRANVV----------GTRRLL------------------------EAARELMKAKR 81
Query: 905 TMCPTLGQFVVFSSVSCGRGNAGQTNYGMANSIMERICEARRAE----GLPGLAVEWGAV 960
LG+F++ SSV+ G G Y + + ++ + + +E GLP AV G
Sbjct: 82 -----LGRFILISSVAGLFGAPGLGGYAASKAALDGLAQQWASEGWGNGLPATAVACGTW 136
Query: 961 GEVGLVADMAEDNL--EVVIGGTLQQRI 986
G MA+ + E ++G
Sbjct: 137 AGSG----MAKGPVAPEEILGNRRHGVR 160
>gnl|CDD|215989 pfam00550, PP-binding, Phosphopantetheine attachment site. A
4'-phosphopantetheine prosthetic group is attached
through a serine. This prosthetic group acts as a a
'swinging arm' for the attachment of activated fatty acid
and amino-acid groups. This domain forms a four helix
bundle. This family includes members not included in
Prosite. The inclusion of these members is supported by
sequence analysis and functional evidence. The related
domain of Vibrio anguillarum angR has the attachment
serine replaced by an alanine.
Length = 66
Score = 44.5 bits (106), Expect = 7e-06
Identities = 21/65 (32%), Positives = 35/65 (53%), Gaps = 4/65 (6%)
Query: 1022 IVDAVINILGLRDLKTVSLHSTLAELGMDSMMAVEIKQTLEREFEVFLTPQDIRGLTFAK 1081
+ + V +LG+ D + L +LG+DS++AVE+ LE EF V + P D+
Sbjct: 3 LREIVAEVLGIPD--EIDPDDDLFDLGLDSLLAVELLARLEEEFGVEIPPSDL--FEHPT 58
Query: 1082 LQDIA 1086
L ++A
Sbjct: 59 LGELA 63
>gnl|CDD|176240 cd08279, Zn_ADH_class_III, Class III alcohol dehydrogenase.
Glutathione-dependent formaldehyde dehydrogenases (FDHs,
Class III ADH) are members of the zinc-dependent/medium
chain alcohol dehydrogenase family. FDH converts
formaldehyde and NAD(P) to formate and NAD(P)H. The
initial step in this process the spontaneous formation
of a S-(hydroxymethyl)glutathione adduct from
formaldehyde and glutathione, followed by FDH-mediated
oxidation (and detoxification) of the adduct to
S-formylglutathione. NAD(P)(H)-dependent oxidoreductases
are the major enzymes in the interconversion of alcohols
and aldehydes or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. Class III ADH are also known as
glutathione-dependent formaldehyde dehydrogenase (FDH),
which convert aldehydes to corresponding carboxylic acid
and alcohol. ADH is a member of the medium chain
alcohol dehydrogenase family (MDR), which has a
NAD(P)(H)-binding domain in a Rossmann fold of an
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES. These
proteins typically form dimers (typically higher plants,
mammals) or tetramers (yeast, bacteria), and have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site and a structural zinc in a lobe of
the catalytic domain. NAD(H) binding occurs in the
cleft between the catalytic and coenzyme-binding
domains at the active site, and coenzyme binding induces
a conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
Length = 363
Score = 49.5 bits (119), Expect = 8e-06
Identities = 55/226 (24%), Positives = 95/226 (42%), Gaps = 20/226 (8%)
Query: 534 IPDQWTLEDAATVPCVYATAVYAMFICGQMQKGESILIHAGSGGVGQAAINLARYMDAEI 593
I D L+ AA + C T V A+ +++ G+++ + G GGVG AI AR A
Sbjct: 151 IDDDIPLDRAALLGCGVTTGVGAVVNTARVRPGDTVAV-IGCGGVGLNAIQGARIAGASR 209
Query: 594 FTTVGT-PEKREFIRK---TFPFIKEENIGNSRDTSFEQLVMKRTKGRGVDLVLNSLAE- 648
V PEK E R+ T N+ + + V T GRG D ++
Sbjct: 210 IIAVDPVPEKLELARRFGATHTV-------NASEDDAVEAVRDLTDGRGADYAFEAVGRA 262
Query: 649 EKLQASVRCLAQGGRFLEIGKFDLANN-NMLGMEVFMRETSFHGVML-DNFFFAEQEWKM 706
++ ++ +GG + +G ++ +E+F+ E G + + +
Sbjct: 263 ATIRQALAMTRKGGTAVVVGMGPPGETVSLPALELFLSEKRLQGSLYGSANPRRDIPRLL 322
Query: 707 SLQKALQKAIDAGAVQPLVRTIFPEDKVEEAFRYMAAGKHIGKVII 752
L +A + +D LV + D++ EAF M AG++ VI+
Sbjct: 323 DLYRAGRLKLDE-----LVTRRYSLDEINEAFADMLAGENARGVIV 363
>gnl|CDD|176184 cd05281, TDH, Threonine dehydrogenase. L-threonine dehydrogenase
(TDH) catalyzes the zinc-dependent formation of
2-amino-3-ketobutyrate from L-threonine via NAD(H)-
dependent oxidation. THD is a member of the
zinc-requiring, medium chain NAD(H)-dependent alcohol
dehydrogenase family (MDR). MDRs have a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. NAD(P)(H)-dependent oxidoreductases are
the major enzymes in the interconversion of alcohols and
aldehydes, or ketones. The N-terminal region typically
has an all-beta catalytic domain. These proteins
typically form dimers (typically higher plants, mammals)
or tetramers (yeast, bacteria) and have 2 tightly bound
zinc atoms per subunit. Sorbitol and aldose reductase
are NAD(+) binding proteins of the polyol pathway, which
interconverts glucose and fructose.
Length = 341
Score = 49.2 bits (118), Expect = 9e-06
Identities = 50/195 (25%), Positives = 83/195 (42%), Gaps = 27/195 (13%)
Query: 566 GESILIHAGSGGVGQAAINLARYMDAE-IFTTVGTPEKREFIRKTFPFIKEENIGNSRDT 624
G+S+LI G G +G AI +A+ A + + P + E +K + + + N R+
Sbjct: 164 GKSVLI-TGCGPIGLMAIAVAKAAGASLVIASDPNPYRLELAKK----MGADVVINPREE 218
Query: 625 SFEQLVMKRTKGRGVDLVLN-SLAEEKLQASVRCLAQGGRFLEIG------KFDLANNNM 677
+ V T G GVD+VL S + ++ ++ L GGR +G DL N
Sbjct: 219 DVVE-VKSVTDGTGVDVVLEMSGNPKAIEQGLKALTPGGRVSILGLPPGPVDIDLNN--- 274
Query: 678 LGMEVFMRETSFHGVMLDNFFFAEQEWKMSLQKALQKAIDAGAVQPLVRTIFPEDKVEEA 737
V + + G+ F + W +D + P++ P + EEA
Sbjct: 275 ---LVIFKGLTVQGITGRKMF---ETWYQVSALLKSGKVD---LSPVITHKLPLEDFEEA 325
Query: 738 FRYMAAGKHIGKVII 752
F M +GK GKV++
Sbjct: 326 FELMRSGK-CGKVVL 339
>gnl|CDD|212493 cd08932, HetN_like_SDR_c, HetN oxidoreductase-like, classical (c)
SDR. This subgroup includes Anabaena sp. strain PCC
7120 HetN, a putative oxidoreductase involved in
heterocyst differentiation, and related proteins. 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 = 223
Score = 47.7 bits (114), Expect = 1e-05
Identities = 35/174 (20%), Positives = 62/174 (35%), Gaps = 17/174 (9%)
Query: 785 IICGGLGGFGLELADWLVLRGARKLVLTSRSGVKNGYQALRIKIWKSYDVQVL-ISTDDI 843
++ G G G+E+A L G R + L R+ + DV+ + D
Sbjct: 4 LVTGASRGIGIEIARALARDGYR-VSLGLRNPEDLAALSASG-----GDVEAVPYDARDP 57
Query: 844 TTEAGVVNLLTEANKLGPVDGIFNLAVVLKDALFENQTPEDFNASLGPKANATKYFDKYS 903
+V+ L + G +D + + A + + + + A A +
Sbjct: 58 EDARALVDALRDRF--GRIDVLVHNAGIGRPTTLREGSDAELEAHFSINVIAPAEL---T 112
Query: 904 RTMCPTL-----GQFVVFSSVSCGRGNAGQTNYGMANSIMERICEARRAEGLPG 952
R + P L G+ V +S+S R AG Y + + + A R EG
Sbjct: 113 RALLPALREAGSGRVVFLNSLSGKRVLAGNAGYSASKFALRALAHALRQEGWDH 166
>gnl|CDD|183773 PRK12824, PRK12824, acetoacetyl-CoA reductase; Provisional.
Length = 245
Score = 46.3 bits (110), Expect = 4e-05
Identities = 43/181 (23%), Positives = 77/181 (42%), Gaps = 24/181 (13%)
Query: 781 NKSYIICGGLGGFGLELADWLVLRGARKLVLTSRSGV--------KNGYQALRIKIWKSY 832
K ++ G G G +A L+ G +++ T SG + G+ ++++ K
Sbjct: 2 KKIALVTGAKRGIGSAIARELLNDG-YRVIATYFSGNDCAKDWFEEYGFTEDQVRL-KEL 59
Query: 833 DVQVLISTDDITTEAGVVNLLTEANKLGPVDGIFNLAVVLKDALFENQTPEDFNASLGPK 892
DV TD + + E GPVD + N A + +D++F+ + +++N +
Sbjct: 60 DV-----TDTEECAEALAEIEEE---EGPVDILVNNAGITRDSVFKRMSHQEWNDVIN-- 109
Query: 893 ANATKYFDKYSRTMCPTL----GQFVVFSSVSCGRGNAGQTNYGMANSIMERICEARRAE 948
N F+ G+ + SSV+ +G GQTNY A + M +A +E
Sbjct: 110 TNLNSVFNVTQPLFAAMCEQGYGRIINISSVNGLKGQFGQTNYSAAKAGMIGFTKALASE 169
Query: 949 G 949
G
Sbjct: 170 G 170
>gnl|CDD|187643 cd08939, KDSR-like_SDR_c, 3-ketodihydrosphingosine reductase (KDSR)
and related proteins, classical (c) SDR. These proteins
include members identified as KDSR, ribitol type
dehydrogenase, and others. The group shows strong
conservation of the active site tetrad and glycine rich
NAD-binding motif of the classical SDRs. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold (alpha/beta folding pattern with a central
beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRs are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes catalyze a
wide range of activities including the metabolism of
steroids, cofactors, carbohydrates, lipids, aromatic
compounds, and amino acids, and act in redox sensing.
Classical SDRs have an TGXXX[AG]XG cofactor binding
motif and a YXXXK active site motif, with the Tyr
residue of the active site motif serving as a critical
catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 239
Score = 45.3 bits (108), Expect = 9e-05
Identities = 46/176 (26%), Positives = 71/176 (40%), Gaps = 15/176 (8%)
Query: 785 IICGGLGGFGLELADWLVLRGARKLVLTSRSGVKNGYQALRIKIWKSYDVQ-VLISTDDI 843
+I GG G G LA LV GA +++ +RS K I+ + Q V + D+
Sbjct: 5 LITGGSSGIGKALAKELVKEGA-NVIIVARSESKLEEAVEEIEAEANASGQKVSYISADL 63
Query: 844 TTEAGVVNLLTEA-NKLGPVDGIFNLAVVLKDALFENQTPEDFNASLGPKANATKYFDKY 902
+ V +A K GP D + N A + LFE+ T E+F + YF
Sbjct: 64 SDYEEVEQAFAQAVEKGGPPDLVVNCAGISIPGLFEDLTAEEFERGM-----DVNYFGSL 118
Query: 903 --SRTMCPTL-----GQFVVFSSVSCGRGNAGQTNYGMANSIMERICEARRAEGLP 951
+ + P + G V SS + G G + Y + + + E+ R E P
Sbjct: 119 NVAHAVLPLMKEQRPGHIVFVSSQAALVGIYGYSAYCPSKFALRGLAESLRQELKP 174
>gnl|CDD|212497 cd11731, Lin1944_like_SDR_c, Lin1944 and related proteins,
classical (c) SDRs. Lin1944 protein from Listeria
Innocua is a classical SDR, it contains a glycine-rich
motif similar to the canonical motif of the SDR
NAD(P)-binding site. However, the typical SDR active
site residues are absent in this subgroup of proteins of
undetermined function. 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 prostaglandin dehydrogenase
(PGDH) numbering). In addition to the Tyr and Lys, there
is often an upstream Ser (Ser-138, PGDH numbering)
and/or an Asn (Asn-107, 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 = 198
Score = 44.1 bits (105), Expect = 1e-04
Identities = 38/159 (23%), Positives = 52/159 (32%), Gaps = 32/159 (20%)
Query: 785 IICGGLGGFGLELADWLVLRGARKLVLTSRSGVKNGYQALRIKIWKSYDVQVLISTDDIT 844
I+ G G GL +A L G +++ RS S D QV DIT
Sbjct: 2 IVIGATGTIGLAVAQLLSAHGH-EVITAGRS---------------SGDYQV-----DIT 40
Query: 845 TEAGVVNLLTEANKLGPVDGIFNLAVVLKDALFENQTPEDFNASLGPK----ANATKYFD 900
EA + L + G D I + A + A T DF L K N ++
Sbjct: 41 DEASIKALFEKV---GHFDAIVSTAGDAEFAPLAELTDADFQRGLNSKLLGQINLVRHGL 97
Query: 901 KYSRTMCPTLGQFVVFSSVSCGRGNAGQTNYGMANSIME 939
Y G + S + R G N +E
Sbjct: 98 PYLN----DGGSITLTSGILAQRPIPGGAAAATVNGALE 132
>gnl|CDD|176250 cd08290, ETR, 2-enoyl thioester reductase (ETR). 2-enoyl thioester
reductase (ETR) catalyzes the NADPH-dependent conversion
of trans-2-enoyl acyl carrier protein/coenzyme A
(ACP/CoA) to acyl-(ACP/CoA) in fatty acid synthesis.
2-enoyl thioester reductase activity has been linked in
Candida tropicalis as essential in maintaining
mitiochondrial respiratory function. This ETR family is
a part of the medium chain dehydrogenase/reductase
family, but lack the zinc coordination sites
characteristic of the alcohol dehydrogenases in this
family. NAD(P)(H)-dependent oxidoreductases are the
major enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which has a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. The N-terminal catalytic domain has a
distant homology to GroES. These proteins typically form
dimers (typically higher plants, mammals) or tetramers
(yeast, bacteria), and have 2 tightly bound zinc atoms
per subunit, a catalytic zinc at the active site, and a
structural zinc in a lobe of the catalytic domain.
NAD(H) binding occurs in the cleft between the catalytic
and coenzyme-binding domains, at the active site, and
coenzyme binding induces a conformational closing of
this cleft. Coenzyme binding typically precedes and
contributes to substrate binding. Candida tropicalis
enoyl thioester reductase (Etr1p) catalyzes the
NADPH-dependent reduction of trans-2-enoyl thioesters in
mitochondrial fatty acid synthesis. Etr1p forms
homodimers, with each subunit containing a
nucleotide-binding Rossmann fold domain and a catalytic
domain.
Length = 341
Score = 45.3 bits (108), Expect = 1e-04
Identities = 52/248 (20%), Positives = 95/248 (38%), Gaps = 48/248 (19%)
Query: 534 IPDQWTLEDAATV---PCVYATAVYAM---FICGQMQKGESILIHAGSGGVGQAAINLAR 587
+P+ E AAT+ PC TA Y + F ++Q G+ ++ + + VGQA I LA+
Sbjct: 115 VPNDVDPEQAATLSVNPC---TA-YRLLEDF--VKLQPGDWVIQNGANSAVGQAVIQLAK 168
Query: 588 YMDAEIFTTV----GTPEKREFIRKT--FPFIKEENIGNSRDTSFEQLVMKRTKGRGVDL 641
+ + V E +E ++ + EE + + T ++K G L
Sbjct: 169 LLGIKTINVVRDRPDLEELKERLKALGADHVLTEEELRSLLATE----LLKSAPGGRPKL 224
Query: 642 VLNSLAEEKLQASVRCLAQGGRFLEIGKFDLANNNMLGM----------EVFMRETSFHG 691
LN + + R L+ GG + G GM + ++ + G
Sbjct: 225 ALNCVGGKSATELARLLSPGGTMVTYG----------GMSGQPVTVPTSLLIFKDITLRG 274
Query: 692 VML-DNFFFAEQEWKMSLQKALQKAIDAGAVQP---LVRTIFPEDKVEEAF-RYMAAGKH 746
L A E K + + L + I G ++ T P ++ ++A + G
Sbjct: 275 FWLTRWLKRANPEEKEDMLEELAELIREGKLKAPPVEKVTDDPLEEFKDALANALKGGGG 334
Query: 747 IGKVIIKI 754
GK ++ +
Sbjct: 335 -GKQVLVM 341
>gnl|CDD|237220 PRK12828, PRK12828, short chain dehydrogenase; Provisional.
Length = 239
Score = 43.6 bits (103), Expect = 3e-04
Identities = 42/181 (23%), Positives = 63/181 (34%), Gaps = 25/181 (13%)
Query: 782 KSYIICGGLGGFGLELADWLVLRGARKLVLTSR-----SGVKNGYQALRIKIWKSYDVQV 836
K I GG GG G A WL RGAR + L R S G A ++I
Sbjct: 8 KVVAITGGFGGLGRATAAWLAARGAR-VALIGRGAAPLSQTLPGVPADALRIGGI----- 61
Query: 837 LISTDDITTEAGVVNLLTE-ANKLGPVDGIFNLAVVLKDALFENQTPEDFNASLGPKANA 895
D+ + E + G +D + N+A + + ++ G
Sbjct: 62 -----DLVDPQAARRAVDEVNRQFGRLDALVNIAGAFVWGTIADGDADTWDRMYGVNVKT 116
Query: 896 TKYFDKYSRTMCPTL-----GQFVVFSSVSCGRGNAGQTNYGMANSIMERICEARRAEGL 950
T S+ P L G+ V + + + G Y A + + R+ EA AE L
Sbjct: 117 TLNA---SKAALPALTASGGGRIVNIGAGAALKAGPGMGAYAAAKAGVARLTEALAAELL 173
Query: 951 P 951
Sbjct: 174 D 174
>gnl|CDD|176214 cd08252, AL_MDR, Arginate lyase and other MDR family members. This
group contains a structure identified as an arginate
lyase. Other members are identified quinone reductases,
alginate lyases, and other proteins related to the
zinc-dependent dehydrogenases/reductases. QOR catalyzes
the conversion of a quinone and NAD(P)H to a
hydroquinone and NAD(P+. Quinones are cyclic diones
derived from aromatic compounds. Membrane bound QOR acts
in the respiratory chains of bacteria and mitochondria,
while soluble QOR acts to protect from toxic quinones
(e.g. DT-diaphorase) or as a soluble eye-lens protein in
some vertebrates (e.g. zeta-crystalin). QOR reduces
quinones through a semi-quinone intermediate via a
NAD(P)H-dependent single electron transfer. QOR is a
member of the medium chain dehydrogenase/reductase
family, but lacks the zinc-binding sites of the
prototypical alcohol dehydrogenases of this group.
Alcohol dehydrogenase in the liver converts ethanol and
NAD+ to acetaldehyde and NADH, while in yeast and some
other microorganisms ADH catalyzes the conversion
acetaldehyde to ethanol in alcoholic fermentation. ADH
is a member of the medium chain alcohol dehydrogenase
family (MDR), which has a NAD(P)(H)-binding domain in a
Rossmann fold of a beta-alpha form. The NAD(H)-binding
region is comprised of 2 structurally similar halves,
each of which contacts a mononucleotide. The N-terminal
catalytic domain has a distant homology to GroES. These
proteins typically form dimers (typically higher plants,
mammals) or tetramers (yeast, bacteria), and have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site and a structural zinc in a lobe of
the catalytic domain. NAD(H) binding occurs in the cleft
between the catalytic and coenzyme-binding domains at
the active site, and coenzyme binding induces a
conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
In human ADH catalysis, the zinc ion helps coordinate
the alcohol, followed by deprotonation of a histidine,
the ribose of NAD, a serine, then the alcohol, which
allows the transfer of a hydride to NAD+, creating NADH
and a zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 336
Score = 44.1 bits (105), Expect = 4e-04
Identities = 23/82 (28%), Positives = 40/82 (48%), Gaps = 6/82 (7%)
Query: 533 EIPDQWTLEDAATVPCVYATAVYAMFICGQMQ-----KGESILIHAGSGGVGQAAINLAR 587
P + +AA +P TA A+F + +G+++LI G+GGVG AI LA+
Sbjct: 112 HKPKSLSFAEAAALPLTSLTAWEALFDRLGISEDAENEGKTLLIIGGAGGVGSIAIQLAK 171
Query: 588 YM-DAEIFTTVGTPEKREFIRK 608
+ + T PE ++++
Sbjct: 172 QLTGLTVIATASRPESIAWVKE 193
>gnl|CDD|176256 cd08296, CAD_like, Cinnamyl alcohol dehydrogenases (CAD). Cinnamyl
alcohol dehydrogenases (CAD), members of the medium
chain dehydrogenase/reductase family, reduce
cinnamaldehydes to cinnamyl alcohols in the last step of
monolignal metabolism in plant cells walls. CAD binds 2
zinc ions and is NADPH- dependent. CAD family members
are also found in non-plant species, e.g. in yeast where
they have an aldehyde reductase activity. The medium
chain dehydrogenases/reductase (MDR)/zinc-dependent
alcohol dehydrogenase-like family, which contains the
zinc-dependent alcohol dehydrogenase (ADH-Zn) and
related proteins, is a diverse group of proteins related
to the first identified member, class I mammalian ADH.
MDRs display a broad range of activities and are
distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADHs), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 333
Score = 43.4 bits (103), Expect = 5e-04
Identities = 66/265 (24%), Positives = 98/265 (36%), Gaps = 45/265 (16%)
Query: 488 RRLYQHCVIGFEYSGRLRDSGKRVMGLTSGRSLANCCETDVEMAWEIPDQWTLEDAATVP 547
R + HC G + +G RD G A E IPD +AA +
Sbjct: 99 RGDFVHCENG-KVTGVTRDGG-----------YAEYMLAPAEALARIPDDLDAAEAAPLL 146
Query: 548 CVYATAVYAMFICGQMQKGESILIHAGSGGVGQAAINLARYMDAEIFTTVGTPEKREFIR 607
C T A+ G + G+ + + G GG+G A+ A M +K + R
Sbjct: 147 CAGVTTFNALRNSG-AKPGDLVAVQ-GIGGLGHLAVQYAAKMGFRTVAISRGSDKADLAR 204
Query: 608 K--TFPFIKEENIGNSRDTSFEQLVMKRTKGRGVDLVLNSLAEEK-LQASVRCLAQGGRF 664
K +I DTS E + + G L+L + K + A V LA G+
Sbjct: 205 KLGAHHYI---------DTSKEDVAEALQELGGAKLILATAPNAKAISALVGGLAPRGKL 255
Query: 665 LEIGKFDLANNNMLGMEVFMRETSFH----GVMLDNFFFAEQEWKMSLQKALQKAIDAGA 720
L +G + M S H G LD+ + L+ + G
Sbjct: 256 LILGAAGEPVAVSPLQLI-MGRKSIHGWPSGTALDS------------EDTLKFSALHG- 301
Query: 721 VQPLVRTIFPEDKVEEAFRYMAAGK 745
V+P+V T FP +K EA+ M +GK
Sbjct: 302 VRPMVET-FPLEKANEAYDRMMSGK 325
>gnl|CDD|176217 cd08255, 2-desacetyl-2-hydroxyethyl_bacteriochlorophyllide_like,
2-desacetyl-2-hydroxyethyl bacteriochlorophyllide and
other MDR family members. This subgroup of the medium
chain dehydrogenases/reductase (MDR)/zinc-dependent
alcohol dehydrogenase-like family has members identified
as 2-desacetyl-2-hydroxyethyl bacteriochlorophyllide A
dehydrogenase and alcohol dehydrogenases. The medium
chain dehydrogenases/reductase (MDR)/zinc-dependent
alcohol dehydrogenase-like family, which contains the
zinc-dependent alcohol dehydrogenase (ADH-Zn) and
related proteins, is a diverse group of proteins related
to the first identified member, class I mammalian ADH.
MDRs display a broad range of activities and are
distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability.
Length = 277
Score = 43.0 bits (102), Expect = 7e-04
Identities = 60/287 (20%), Positives = 100/287 (34%), Gaps = 45/287 (15%)
Query: 487 SRRLYQHCVIGFEYSGRLRDSGKRVMGLTSGR------SLANCCETDVEMAWEIPDQWTL 540
+ +L G+ GR+ + G V G G A + +PD
Sbjct: 15 TEKLPLPLPPGYSSVGRVVEVGSGVTGFKPGDRVFCFGPHAERVVVPANLLVPLPDGLPP 74
Query: 541 EDAATVPCVYATAVYAMFICGQMQKGESILIHAGSGGVGQAAINLARYMDAEIFTTVGT- 599
E AA + ATA+ + + GE + + G G VG A LA+ A VG
Sbjct: 75 ERAALTA-LAATALNG-VRDAEPRLGERVAV-VGLGLVGLLAAQLAKAAGAR--EVVGVD 129
Query: 600 --PEKREFIRKTFPFIKEENIGNSRDTSFEQLVMKRTKGRGVDLVLN-SLAEEKLQASVR 656
+RE P GRG D+V+ S + L+ ++R
Sbjct: 130 PDAARRELAEALGPADPV-----------AADTADEIGGRGADVVIEASGSPSALETALR 178
Query: 657 CLAQGGRFLEIGKFDLANNNMLG-------MEVFMRETSFHGVMLDNFFFAEQEWKMSLQ 709
L GR + +G + L LG + + + G + E
Sbjct: 179 LLRDRGRVVLVGWYGLKPLL-LGEEFHFKRLPIRSSQVYGIGRYDRPRRWTE-------A 230
Query: 710 KALQKAID---AGAVQPLVRTIFPEDKVEEAFRYMAAGKHIG-KVII 752
+ L++A+D G ++ L+ P + EA+R + KV++
Sbjct: 231 RNLEEALDLLAEGRLEALITHRVPFEDAPEAYRLLFEDPPECLKVVL 277
>gnl|CDD|188169 TIGR01829, AcAcCoA_reduct, acetoacetyl-CoA reductase. This model
represent acetoacetyl-CoA reductase, a member of the
family short-chain-alcohol dehydrogenases. Note that,
despite the precision implied by the enzyme name, the
reaction of EC 1.1.1.36 is defined more generally as
(R)-3-hydroxyacyl-CoA + NADP+ = 3-oxoacyl-CoA + NADPH.
Members of this family may act in the biosynthesis of
poly-beta-hydroxybutyrate (e.g. Rhizobium meliloti) and
related poly-beta-hydroxyalkanoates. Note that the
member of this family from Azospirillum brasilense,
designated NodG, appears to lack acetoacetyl-CoA
reductase activity and to act instead in the production
of nodulation factor. This family is downgraded to
subfamily for this NodG. Other proteins designated NodG,
as from Rhizobium, belong to related but distinct
protein families.
Length = 242
Score = 42.8 bits (101), Expect = 7e-04
Identities = 54/219 (24%), Positives = 87/219 (39%), Gaps = 31/219 (14%)
Query: 785 IICGGLGGFGLELADWLVLRGARKLVLTSRSGVKNGY--QALRIKIW----KSYDVQVLI 838
++ GG+GG G + L G R V R + W + +
Sbjct: 4 LVTGGMGGIGTAICQRLAKDGYR---------VAANCGPNEERAEAWLQEQGALGFDFRV 54
Query: 839 STDDIT----TEAGVVNLLTEANKLGPVDGIFNLAVVLKDALFENQTPEDFNASLGPKAN 894
D++ +A V + E LGP+D + N A + +DA F+ T E ++A + N
Sbjct: 55 VEGDVSSFESCKAAVAKVEAE---LGPIDVLVNNAGITRDATFKKMTYEQWSAVID--TN 109
Query: 895 ATKYFD---KYSRTMCP-TLGQFVVFSSVSCGRGNAGQTNYGMANSIMERICEARRAEGL 950
F+ M G+ + SSV+ +G GQTNY A + M +A EG
Sbjct: 110 LNSVFNVTQPVIDGMRERGWGRIINISSVNGQKGQFGQTNYSAAKAGMIGFTKALAQEGA 169
Query: 951 P-GLAVEWGAVGEVG--LVADMAEDNLEVVIGGTLQQRI 986
G+ V + G + +V M ED L ++ R+
Sbjct: 170 TKGVTVNTISPGYIATDMVMAMREDVLNSIVAQIPVGRL 208
>gnl|CDD|176245 cd08285, NADP_ADH, NADP(H)-dependent alcohol dehydrogenases. This
group is predominated by atypical alcohol
dehydrogenases; they exist as tetramers and exhibit
specificity for NADP(H) as a cofactor in the
interconversion of alcohols and aldehydes, or ketones.
Like other zinc-dependent alcohol dehydrogenases (ADH)
of the medium chain alcohol dehydrogenase/reductase
family (MDR), tetrameric ADHs have a catalytic zinc that
resides between the catalytic and NAD(H)binding domains;
however, they do not have and a structural zinc in a
lobe of the catalytic domain. The medium chain alcohol
dehydrogenase family (MDR) has a NAD(P)(H)-binding
domain in a Rossmann fold of a beta-alpha form. The
N-terminal region typically has an all-beta catalytic
domain. These proteins typically form dimers (typically
higher plants, mammals) or tetramers (yeast, bacteria),
and have 2 tightly bound zinc atoms per subunit.
Length = 351
Score = 43.0 bits (102), Expect = 9e-04
Identities = 34/147 (23%), Positives = 67/147 (45%), Gaps = 14/147 (9%)
Query: 534 IPDQWTLEDAATVPCVYATAVYAMFICGQMQKGESILIHAGSGGVGQAAINLARYMDAEI 593
+PD T E A +P + +T + ++ G+++ + G G VG A+ AR A
Sbjct: 136 LPDGLTDEQAVMLPDMMSTGFHG-AELANIKLGDTVAVF-GIGPVGLMAVAGARLRGAGR 193
Query: 594 FTTVGTPEKREFIRKTFPFIKEENIGNSRDTSFEQLVMKRTKGRGVDLVLNSL-AEEKLQ 652
VG+ R + K + +I + ++ + ++K T G+GVD V+ + ++ +
Sbjct: 194 IIAVGSRPNRVELAKEY---GATDIVDYKNGDVVEQILKLTGGKGVDAVIIAGGGQDTFE 250
Query: 653 ASVRCLAQGGRFLEIGKFDLANNNMLG 679
+++ L GG ++N N G
Sbjct: 251 QALKVLKPGGT--------ISNVNYYG 269
>gnl|CDD|176183 cd05280, MDR_yhdh_yhfp, Yhdh and yhfp-like putative quinone
oxidoreductases. Yhdh and yhfp-like putative quinone
oxidoreductases (QOR). QOR catalyzes the conversion of a
quinone + NAD(P)H to a hydroquinone + NAD(P)+. Quinones
are cyclic diones derived from aromatic compounds.
Membrane bound QOR actin the respiratory chains of
bacteria and mitochondria, while soluble QOR acts to
protect from toxic quinones (e.g. DT-diaphorase) or as a
soluble eye-lens protein in some vertebrates (e.g.
zeta-crystalin). QOR reduces quinones through a
semi-quinone intermediate via a NAD(P)H-dependent single
electron transfer. QOR is a member of the medium chain
dehydrogenase/reductase family, but lacks the
zinc-binding sites of the prototypical alcohol
dehydrogenases of this group. NAD(P)(H)-dependent
oxidoreductases are the major enzymes in the
interconversion of alcohols and aldehydes, or ketones.
Alcohol dehydrogenase in the liver converts ethanol and
NAD+ to acetaldehyde and NADH, while in yeast and some
other microorganisms ADH catalyzes the conversion
acetaldehyde to ethanol in alcoholic fermentation. ADH
is a member of the medium chain alcohol dehydrogenase
family (MDR), which has a NAD(P)(H)-binding domain in a
Rossmann fold of a beta-alpha form. The NAD(H)-binding
region is comprised of 2 structurally similar halves,
each of which contacts a mononucleotide. A GxGxxG motif
after the first mononucleotide contact half allows the
close contact of the coenzyme with the ADH backbone.
The N-terminal catalytic domain has a distant homology
to GroES. These proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and have 2 tightly bound zinc atoms per
subunit, a catalytic zinc at the active site and a
structural zinc in a lobe of the catalytic domain.
NAD(H) binding occurs in the cleft between the catalytic
and coenzyme-binding domains at the active site, and
coenzyme binding induces a conformational closing of
this cleft. Coenzyme binding typically precedes and
contributes to substrate binding. In human ADH
catalysis, the zinc ion helps coordinate the alcohol,
followed by deprotonation of a histidine, the ribose of
NAD, a serine, then the alcohol, which allows the
transfer of a hydride to NAD+, creating NADH and a
zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 325
Score = 41.8 bits (99), Expect = 0.002
Identities = 66/329 (20%), Positives = 122/329 (37%), Gaps = 72/329 (21%)
Query: 462 QIYYSSINFRDIMLTTAKLAPEVIESRRLYQHCVIGFEYSGRLRDS-------GKRVMGL 514
+++YSS+N++D + T V R Y H G + +G + S G V
Sbjct: 33 RVHYSSLNYKDALAATGN--GGVT---RNYPH-TPGIDAAGTVVSSDDPRFREGDEV--- 83
Query: 515 TSGRSLANCCE----TD--------VEMAW--EIPDQWTLEDAATVPCVYATA------- 553
L + TD V W +P+ +L +A + TA
Sbjct: 84 -----LVTGYDLGMNTDGGFAEYVRVPADWVVPLPEGLSLREAM----ILGTAGFTAALS 134
Query: 554 VYAMFICGQMQKGESILIHAGSGGVGQAAINLARYMDAEIFTTVGTPEKREFIRKTFPFI 613
V+ + GQ + +L+ +GGVG A+ + + + G E+ ++++
Sbjct: 135 VHRLEDNGQTPEDGPVLVTGATGGVGSIAVAILAKLGYTVVALTGKEEQADYLKS----- 189
Query: 614 KEENIGNS----RDTSFEQLVMKRTKGRGVDLVLNSLAEEKLQASVRCLAQGGRFLEIGK 669
+G S R+ ++ K R ++++ + L ++ GG G
Sbjct: 190 ----LGASEVLDREDLLDESKKPLLKAR-WAGAIDTVGGDVLANLLKQTKYGGVVASCGN 244
Query: 670 FDLANNNMLGMEVFMRETSFHGVMLDNFFFAEQEWKMSLQKA----LQKAIDAGAVQPLV 725
+ +R S G+ D+ M L+K L ++ +V
Sbjct: 245 AAGPELTTTVLPFILRGVSLLGI--DS-----VNCPMELRKQVWQKLATEWKPDLLEIVV 297
Query: 726 RTIFPEDKVEEAFRYMAAGKHIGKVIIKI 754
R I E+ + EA + AGKH G+ ++KI
Sbjct: 298 REISLEE-LPEAIDRLLAGKHRGRTVVKI 325
>gnl|CDD|176244 cd08284, FDH_like_2, Glutathione-dependent formaldehyde
dehydrogenase related proteins, child 2.
Glutathione-dependent formaldehyde dehydrogenases (FDHs)
are members of the zinc-dependent/medium chain alcohol
dehydrogenase family. Formaldehyde dehydrogenase (FDH)
is a member of the zinc-dependent/medium chain alcohol
dehydrogenase family. FDH converts formaldehyde and NAD
to formate and NADH. The initial step in this process
the spontaneous formation of a
S-(hydroxymethyl)glutathione adduct from formaldehyde
and glutathione, followed by FDH-mediated oxidation (and
detoxification) of the adduct to S-formylglutathione.
These tetrameric FDHs have a catalytic zinc that resides
between the catalytic and NAD(H)binding domains and a
structural zinc in a lobe of the catalytic domain. The
medium chain alcohol dehydrogenase family (MDR) has a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The N-terminal region typically has an
all-beta catalytic domain. These proteins typically form
dimers (typically higher plants, mammals) or tetramers
(yeast, bacteria), and have 2 tightly bound zinc atoms
per subunit.
Length = 344
Score = 41.9 bits (99), Expect = 0.002
Identities = 47/227 (20%), Positives = 90/227 (39%), Gaps = 21/227 (9%)
Query: 531 AWEIPDQWTLEDAATVPCVYATAVYAMFICGQMQKGESILIHAGSGGVGQAAINLARYMD 590
++PD + E A + + T + Q++ G+++ + G G VG A+ A+ +
Sbjct: 134 LLKLPDGLSDEAALLLGDILPTGYFGA-KRAQVRPGDTVAV-IGCGPVGLCAVLSAQVLG 191
Query: 591 AE-IFTTVGTPEKREFIRKTFPFIKEENIGNSRDTSFEQLVMKRTKGRGVDLVLNSL-AE 648
A +F PE+ E + E I N D + V + T+GRG D+VL ++
Sbjct: 192 AARVFAVDPVPERLERAAA----LGAEPI-NFEDAEPVERVREATEGRGADVVLEAVGGA 246
Query: 649 EKLQASVRCLAQGGRFLEIGKFDLANNNMLGMEVFMRETSFHGVMLDNFFFAEQEWKMSL 708
L + + GG +G G++ + + + SL
Sbjct: 247 AALDLAFDLVRPGGVISSVGVHTAEEFPFPGLDAYNKNLTLRFGRCP---------VRSL 297
Query: 709 QKALQKAIDAGAVQP--LVRTIFPEDKVEEAFRYMAAGKHIGKVIIK 753
L +++G + L+ P ++ EA+R K + KV++
Sbjct: 298 FPELLPLLESGRLDLEFLIDHRMPLEEAPEAYRLFDKRK-VLKVVLD 343
>gnl|CDD|187602 cd05344, BKR_like_SDR_like, putative beta-ketoacyl acyl carrier
protein [ACP] reductase (BKR)-like, SDR. This subgroup
resembles the SDR family, but does not have a perfect
match to the NAD-binding motif or the catalytic tetrad
characteristic of the SDRs. It includes the SDRs, Q9HYA2
from Pseudomonas aeruginosa PAO1 and APE0912 from
Aeropyrum pernix K1. 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 = 253
Score = 41.1 bits (97), Expect = 0.002
Identities = 27/108 (25%), Positives = 43/108 (39%), Gaps = 9/108 (8%)
Query: 781 NKSYIICGGLGGFGLELADWLVLRGARKLVLTSRSG--VKNGYQALRIKIWKSYDVQVLI 838
K ++ G GL +A L GAR + + +R+ ++ LR VL
Sbjct: 1 GKVALVTAASSGIGLAIARALAREGAR-VAICARNRENLERAASELRA-----GGAGVLA 54
Query: 839 STDDITTEAGVVNLLTEA-NKLGPVDGIFNLAVVLKDALFENQTPEDF 885
D+T + L+ +A + G VD + N A F T ED+
Sbjct: 55 VVADLTDPEDIDRLVEKAGDAFGRVDILVNNAGGPPPGPFAELTDEDW 102
>gnl|CDD|176186 cd05283, CAD1, Cinnamyl alcohol dehydrogenases (CAD). Cinnamyl
alcohol dehydrogenases (CAD), members of the medium
chain dehydrogenase/reductase family, reduce
cinnamaldehydes to cinnamyl alcohols in the last step of
monolignal metabolism in plant cells walls. CAD binds 2
zinc ions and is NADPH- dependent. CAD family members
are also found in non-plant species, e.g. in yeast where
they have an aldehyde reductase activity. The medium
chain dehydrogenases/reductase (MDR)/zinc-dependent
alcohol dehydrogenase-like family, which contains the
zinc-dependent alcohol dehydrogenase (ADH-Zn) and
related proteins, is a diverse group of proteins related
to the first identified member, class I mammalian ADH.
MDRs display a broad range of activities and are
distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases
(ADHs) catalyze the NAD(P)(H)-dependent interconversion
of alcohols to aldehydes or ketones. Active site zinc
has a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 337
Score = 41.3 bits (98), Expect = 0.003
Identities = 47/220 (21%), Positives = 87/220 (39%), Gaps = 37/220 (16%)
Query: 534 IPDQWTLEDAATVPCVYATAVYAMFICGQMQKGESILIHAGSGGVGQAAINLARYMDAEI 593
IP+ AA + C T VY+ + G+ + + G GG+G A+ A+ + AE+
Sbjct: 139 IPEGLDSAAAAPLLCAGIT-VYSPLKRNGVGPGKRVGV-VGIGGLGHLAVKFAKALGAEV 196
Query: 594 --FTTVGTPEKREFIRKTFPFIKEENIG-----NSRDTSFEQLVMKRTKGRGVDLVLNSL 646
F+ +P K+E K +G ++D MK+ G +DL+++++
Sbjct: 197 TAFSR--SPSKKEDALK---------LGADEFIATKDPEA----MKKAAGS-LDLIIDTV 240
Query: 647 AEEK-LQASVRCLAQGGRFLEIGKFDLANNNMLGMEVFMRETSFHGVMLDNFFFAEQEWK 705
+ L + L GG + +G + + S G ++ +
Sbjct: 241 SASHDLDPYLSLLKPGGTLVLVG-APEEPLPVPPFPLIFGRKSVAGSLIGG--------R 291
Query: 706 MSLQKALQKAIDAGAVQPLVRTIFPEDKVEEAFRYMAAGK 745
Q+ L A + G ++P V P D + EA + G
Sbjct: 292 KETQEMLDFAAEHG-IKPWVEV-IPMDGINEALERLEKGD 329
>gnl|CDD|180462 PRK06198, PRK06198, short chain dehydrogenase; Provisional.
Length = 260
Score = 40.8 bits (96), Expect = 0.003
Identities = 24/108 (22%), Positives = 44/108 (40%), Gaps = 4/108 (3%)
Query: 781 NKSYIICGGLGGFGLELADWLVLRGARKLVLTSRSGVKNGYQALRIKIWKSYDVQVLIST 840
K ++ GG G G +A RGA LV+ R+ K QA + ++ + +
Sbjct: 6 GKVALVTGGTQGLGAAIARAFAERGAAGLVICGRNAEKGEAQAAEL---EALGAKAVFVQ 62
Query: 841 DDITTEAGVVNLLTEA-NKLGPVDGIFNLAVVLKDALFENQTPEDFNA 887
D++ ++ A G +D + N A + + +PE F+
Sbjct: 63 ADLSDVEDCRRVVAAADEAFGRLDALVNAAGLTDRGTILDTSPELFDR 110
>gnl|CDD|236099 PRK07791, PRK07791, short chain dehydrogenase; Provisional.
Length = 286
Score = 40.4 bits (95), Expect = 0.004
Identities = 27/109 (24%), Positives = 49/109 (44%), Gaps = 9/109 (8%)
Query: 835 QVLISTDDITTEAGVVNLLTEA-NKLGPVDGIFNLAVVLKDALFENQTPEDFNASL---- 889
+ + + DDI G NL+ A G +D + N A +L+D + N + E+++A +
Sbjct: 65 EAVANGDDIADWDGAANLVDAAVETFGGLDVLVNNAGILRDRMIANMSEEEWDAVIAVHL 124
Query: 890 ----GPKANATKYFDKYSRTMCPTLGQFVVFSSVSCGRGNAGQTNYGMA 934
+A Y+ S+ + + SS + +G+ GQ NY A
Sbjct: 125 KGHFATLRHAAAYWRAESKAGRAVDARIINTSSGAGLQGSVGQGNYSAA 173
>gnl|CDD|187622 cd05364, SDR_c11, classical (c) SDR, subgroup 11. 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 = 253
Score = 40.1 bits (94), Expect = 0.005
Identities = 42/159 (26%), Positives = 66/159 (41%), Gaps = 3/159 (1%)
Query: 780 SNKSYIICGGLGGFGLELADWLVLRGARKLVLTSRSGVKNGYQALRIKIWKSYDVQVLIS 839
S K II G G G A GAR L LT R + + ++L+
Sbjct: 2 SGKVAIITGSSSGIGAGTAILFARLGAR-LALTGRDAERLEETRQSCLQAGVSEKKILLV 60
Query: 840 TDDITTEAGVVNLLTEA-NKLGPVDGIFNLAVVLKDALFENQTPEDFNASLGPKANATKY 898
D+T E G +++ K G +D + N A +L E+Q E+++ + A Y
Sbjct: 61 VADLTEEEGQDRIISTTLAKFGRLDILVNNAGILAKGGGEDQDIEEYDKVMNLNLRAVIY 120
Query: 899 FDKYSRT-MCPTLGQFVVFSSVSCGRGNAGQTNYGMANS 936
K + + T G+ V SSV+ GR G Y ++ +
Sbjct: 121 LTKLAVPHLIKTKGEIVNVSSVAGGRSFPGVLYYCISKA 159
>gnl|CDD|176251 cd08291, ETR_like_1, 2-enoyl thioester reductase (ETR) like
proteins, child 1. 2-enoyl thioester reductase (ETR)
like proteins. ETR catalyzes the NADPH-dependent
conversion of trans-2-enoyl acyl carrier
protein/coenzyme A (ACP/CoA) to acyl-(ACP/CoA) in fatty
acid synthesis. 2-enoyl thioester reductase activity has
been linked in Candida tropicalis as essential in
maintaining mitiochondrial respiratory function. This
ETR family is a part of the medium chain
dehydrogenase/reductase family, but lack the zinc
coordination sites characteristic of the 2-enoyl
thioester reductase (ETR) like proteins. ETR catalyzes
the NADPH-dependent dependent conversion of
trans-2-enoyl acyl carrier protein/coenzyme A (ACP/CoA)
to acyl-(ACP/CoA) in fatty acid synthesis. 2-enoyl
thioester reductase activity has been linked in Candida
tropicalis as essential in maintaining mitiochondrial
respiratory function. This ETR family is a part of the
medium chain dehydrogenase/reductase family, but lack
the zinc coordination sites characteristic of the
alcohol dehydrogenases in this family.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which has a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. The N-terminal catalytic domain has a
distant homology to GroES. These proteins typically
form dimers (typically higher plants, mammals) or
tetramers (yeast, bacteria), and have 2 tightly bound
zinc atoms per subunit, a catalytic zinc at the active
site and a structural zinc in a lobe of the catalytic
domain. NAD(H) binding occurs in the cleft between the
catalytic and coenzyme-binding domains at the active
site, and coenzyme binding induces a conformational
closing of this cleft. Coenzyme binding typically
precedes and contributes to substrate binding. Candida
tropicalis enoyl thioester reductase (Etr1p) catalyzes
the NADPH-dependent reduction of trans-2-enoyl
thioesters in mitochondrial fatty acid synthesis. Etr1p
forms homodimers, with each subunit containing a
nucleotide-binding Rossmann fold domain and a catalytic
domain.
Length = 324
Score = 40.7 bits (96), Expect = 0.005
Identities = 51/319 (15%), Positives = 106/319 (33%), Gaps = 53/319 (16%)
Query: 460 IAQIYYSSINFRDIML-----TTAKLAPEVIESRRLYQHCVIGFEYSGRLRDS------- 507
+ ++ + IN D+ + K P GFE SG + +
Sbjct: 34 LIKVEAAPINPSDLGFLKGQYGSTKALP-----------VPPGFEGSGTVVAAGGGPLAQ 82
Query: 508 ---GKRVMGLTSGR-SLANCCETDVEMAWEIPDQWTLEDAATVPCVYA---TAVYAMFIC 560
GKRV L + A D + +PD + E A + TA+ M
Sbjct: 83 SLIGKRVAFLAGSYGTYAEYAVADAQQCLPLPDGVSFEQGA---SSFVNPLTAL-GMLET 138
Query: 561 GQMQKGESILIHAGSGGVGQAAINLARYMDAEIFTTVGTPEKREFIRKTFPFIKEENIGN 620
+ + ++++ A + +G+ + L + ++ V E+ + ++K I E + N
Sbjct: 139 AREEGAKAVVHTAAASALGRMLVRLCKADGIKVINIVRRKEQVDLLKK----IGAEYVLN 194
Query: 621 SRDTSFEQLVMKRTKGRGVDLVLNSLAEEKLQASVRCLAQGGRFLEIGKFDLANNNM--L 678
S D F + + + + +++ + + G G +
Sbjct: 195 SSDPDFLEDLKELIAKLNATIFFDAVGGGLTGQILLAMPYGSTLYVYGYLSGKLDEPIDP 254
Query: 679 GMEVFMRETSFHGVMLDNFFFAEQEWKMSLQKALQKAIDAGAVQPLVRTIF----PEDKV 734
+F ++ ++ F+ W L + K + L +T F P
Sbjct: 255 VDLIFKNKS------IEGFWLT--TWLQKLGPEVVKKLKKLVKTEL-KTTFASRYPLALT 305
Query: 735 EEAFRYMAAGKHIGKVIIK 753
EA + + GK ++
Sbjct: 306 LEAIAFYSKNMSTGKKLLI 324
>gnl|CDD|131872 TIGR02825, B4_12hDH, leukotriene B4
12-hydroxydehydrogenase/15-oxo-prostaglandin
13-reductase. Leukotriene B4 12-hydroxydehydrogenase is
an NADP-dependent enzyme of arachidonic acid metabolism,
responsible for converting leukotriene B4 to the much
less active metabolite 12-oxo-leukotriene B4. The BRENDA
database lists leukotriene B4 12-hydroxydehydrogenase as
one of the synonyms of 2-alkenal reductase (EC
1.3.1.74), while 1.3.1.48 is 15-oxoprostaglandin
13-reductase.
Length = 325
Score = 40.4 bits (94), Expect = 0.006
Identities = 51/228 (22%), Positives = 96/228 (42%), Gaps = 14/228 (6%)
Query: 533 EIPDQWTLEDA-ATVPCVYATAVYAMF-ICGQMQKGESILIHAGSGGVGQAAINLARYMD 590
E PD L A TV TA + + ICG ++ GE+++++A +G VG +A+
Sbjct: 105 EWPDTLPLSLALGTVGMPGLTAYFGLLEICG-VKGGETVMVNAAAGAVGSVVGQIAKLKG 163
Query: 591 AEIFTTVGTPEKREFIRKTFPFIKEENIGNSRDTSFEQLVMKRTKGRGVDLVLNSLAEEK 650
++ G+ EK +++K + + N + + +K+ G D +++ E
Sbjct: 164 CKVVGAAGSDEKVAYLKK----LGFDVAFNYKTVKSLEETLKKASPDGYDCYFDNVGGEF 219
Query: 651 LQASVRCLAQGGRFLEIGKFDLANNN-MLGMEVFMRETSFHGVMLDNFFFAEQEWKMSL- 708
+ + + GR G N L + + ++ F W+ +
Sbjct: 220 SNTVIGQMKKFGRIAICGAISTYNRTGPLPPGPPPEIVIYQELRMEGFIV--NRWQGEVR 277
Query: 709 QKALQ---KAIDAGAVQPLVRTIFPEDKVEEAFRYMAAGKHIGKVIIK 753
QKAL+ K + G +Q I + + AF M G+++GK I+K
Sbjct: 278 QKALKELLKWVLEGKIQYKEYVIEGFENMPAAFMGMLKGENLGKTIVK 325
>gnl|CDD|176225 cd08264, Zn_ADH_like2, Alcohol dehydrogenases of the MDR family.
This group resembles the zinc-dependent alcohol
dehydrogenases of the medium chain dehydrogenase family.
However, this subgroup does not contain the
characteristic catalytic zinc site. Also, it contains an
atypical structural zinc-binding pattern:
DxxCxxCxxxxxxxC. NAD(P)(H)-dependent oxidoreductases are
the major enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which has a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES. These
proteins typically form dimers (typically higher plants,
mammals) or tetramers (yeast, bacteria), and have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site and a structural zinc in a lobe of
the catalytic domain. NAD(H)-binding occurs in the cleft
between the catalytic and coenzyme-binding domains at
the active site, and coenzyme binding induces a
conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
In human ADH catalysis, the zinc ion helps coordinate
the alcohol, followed by deprotonation of a histidine,
the ribose of NAD, a serine, then the alcohol, which
allows the transfer of a hydride to NAD+, creating NADH
and a zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 325
Score = 40.4 bits (95), Expect = 0.006
Identities = 37/136 (27%), Positives = 61/136 (44%), Gaps = 15/136 (11%)
Query: 534 IPDQWTLEDAATVPCVYATAVYAMFICGQMQKGESILIHAGSGGVGQAAINLARYMDAEI 593
IPD + E AA++P TA +A+ G GE++++ SG G A+ LA+ M AE+
Sbjct: 132 IPDSISDELAASLPVAALTAYHALKTAGL-GPGETVVVFGASGNTGIFAVQLAKMMGAEV 190
Query: 594 FTTVGTPEKREFIRKTFPFIKEENIGNSRDTSFEQLVMKRTKG-RGVDLVLNSLAEEKLQ 652
+EF G ++++ K + + D+V+NSL
Sbjct: 191 IAVSRKDWLKEF-------------GADEVVDYDEVEEKVKEITKMADVVINSLGSSFWD 237
Query: 653 ASVRCLAQGGRFLEIG 668
S+ L +GGR + G
Sbjct: 238 LSLSVLGRGGRLVTFG 253
>gnl|CDD|176187 cd05284, arabinose_DH_like, D-arabinose dehydrogenase. This group
contains arabinose dehydrogenase (AraDH) and related
alcohol dehydrogenases. AraDH is a member of the medium
chain dehydrogenase/reductase family and catalyzes the
NAD(P)-dependent oxidation of D-arabinose and other
pentoses, the initial step in the metabolism of
d-arabinose into 2-oxoglutarate. Like the alcohol
dehydrogenases, AraDH binds a zinc in the catalytic
cleft as well as a distal structural zinc. AraDH forms
homotetramers as a dimer of dimers. AraDH replaces a
conserved catalytic His with replace with Arg, compared
to the canonical ADH site. NAD(P)(H)-dependent
oxidoreductases are the major enzymes in the
interconversion of alcohols and aldehydes, or ketones.
Alcohol dehydrogenase in the liver converts ethanol and
NAD+ to acetaldehyde and NADH, while in yeast and some
other microorganisms ADH catalyzes the conversion
acetaldehyde to ethanol in alcoholic fermentation. ADH
is a member of the medium chain alcohol dehydrogenase
family (MDR), which has a NAD(P)(H)-binding domain in a
Rossmann fold of a beta-alpha form. The NAD(H)-binding
region is comprised of 2 structurally similar halves,
each of which contacts a mononucleotide. A GxGxxG motif
after the first mononucleotide contact half allows the
close contact of the coenzyme with the ADH backbone.
The N-terminal catalytic domain has a distant homology
to GroES. These proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and have 2 tightly bound zinc atoms per
subunit, a catalytic zinc at the active site and a
structural zinc in a lobe of the catalytic domain.
NAD(H) binding occurs in the cleft between the catalytic
and coenzyme-binding domains at the active site, and
coenzyme binding induces a conformational closing of
this cleft. Coenzyme binding typically precedes and
contributes to substrate binding. In human ADH
catalysis, the zinc ion helps coordinate the alcohol,
followed by deprotonation of a histidine, the ribose of
NAD, a serine, then the alcohol, which allows the
transfer of a hydride to NAD+, creating NADH and a
zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 340
Score = 40.2 bits (95), Expect = 0.006
Identities = 44/197 (22%), Positives = 89/197 (45%), Gaps = 36/197 (18%)
Query: 566 GESILIHAGSGGVGQAAINLARYM-DAEIFTTVGTPEKREFIRKTFPFIKEENIG----- 619
G ++++ G GG+G A+ + R + A + + E + + +G
Sbjct: 168 GSTVVV-IGVGGLGHIAVQILRALTPATVIAVDRSEEALKLAER---------LGADHVL 217
Query: 620 NSRDTSFEQLVMKRTKGRGVDLVLNSL-AEEKLQASVRCLAQGGRFLEIG---KFDLANN 675
N+ D E+ V + T GRG D V++ + ++E L + + LA+GGR++ +G L +
Sbjct: 218 NASDDVVEE-VRELTGGRGADAVIDFVGSDETLALAAKLLAKGGRYVIVGYGGHGRLPTS 276
Query: 676 NMLGMEVFMRETSFHGVMLDNFFFAEQEWKMSLQKALQKAIDAGAVQPLVRTIFPEDKVE 735
+++ E+ + S G AE ++L + +G V+ + T FP +
Sbjct: 277 DLVPTEISVI-GSLWGTR------AELVEVVALAE-------SGKVKVEI-TKFPLEDAN 321
Query: 736 EAFRYMAAGKHIGKVII 752
EA + G+ G+ ++
Sbjct: 322 EALDRLREGRVTGRAVL 338
>gnl|CDD|171822 PRK12938, PRK12938, acetyacetyl-CoA reductase; Provisional.
Length = 246
Score = 39.2 bits (91), Expect = 0.009
Identities = 34/136 (25%), Positives = 63/136 (46%), Gaps = 9/136 (6%)
Query: 858 KLGPVDGIFNLAVVLKDALFENQTPEDFNASLGPKANATKYFDKYSRTMCPTL----GQF 913
++G +D + N A + +D +F T ED+ A + N T F+ + + + G+
Sbjct: 78 EVGEIDVLVNNAGITRDVVFRKMTREDWTAVID--TNLTSLFNVTKQVIDGMVERGWGRI 135
Query: 914 VVFSSVSCGRGNAGQTNYGMANSIMERICEARRAE-GLPGLAVEWGAVGEVG--LVADMA 970
+ SSV+ +G GQTNY A + + + E G+ V + G +G +V +
Sbjct: 136 INISSVNGQKGQFGQTNYSTAKAGIHGFTMSLAQEVATKGVTVNTVSPGYIGTDMVKAIR 195
Query: 971 EDNLEVVIGGTLQQRI 986
D LE ++ +R+
Sbjct: 196 PDVLEKIVATIPVRRL 211
>gnl|CDD|221718 pfam12695, Abhydrolase_5, Alpha/beta hydrolase family. This family
contains a diverse range of alpha/beta hydrolase enzymes.
Length = 145
Score = 37.7 bits (88), Expect = 0.010
Identities = 25/116 (21%), Positives = 43/116 (37%), Gaps = 11/116 (9%)
Query: 1159 TIFMVPGIEGIATVLEPLAKNINAQ-VLVFQFDH-TNPPDTIPEMADSLLPHFKKRLVHG 1216
+ ++ G G PLA+ + ++ V D+ + A+++L
Sbjct: 1 LVVLLHGAGGDPEAYAPLARALASRGYNVVAVDYPGHGASLGAPDAEAVL----ADAPLD 56
Query: 1217 TDEIKLVGFSFGGMVALELAIKLEQLGTKCHLYLVDSAPDYVLTSLRKLPDWNAKL 1272
+ I LVG S GG VAL LA + ++ V A +L L +
Sbjct: 57 PERIVLVGHSLGGGVALLLAARDPRVKA-----AVVLAAGDPPDALDDLAKLTVPV 107
>gnl|CDD|176196 cd08234, threonine_DH_like, L-threonine dehydrogenase. L-threonine
dehydrogenase (TDH) catalyzes the zinc-dependent
formation of 2-amino-3-ketobutyrate from L-threonine,
via NAD(H)-dependent oxidation. THD is a member of the
zinc-requiring, medium chain NAD(H)-dependent alcohol
dehydrogenase family (MDR). MDRs have a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. NAD(P)(H)-dependent oxidoreductases are
the major enzymes in the interconversion of alcohols and
aldehydes, or ketones. The N-terminal region typically
has an all-beta catalytic domain. These proteins
typically form dimers (typically higher plants, mammals)
or tetramers (yeast, bacteria), and have 2 tightly
bound zinc atoms per subunit. Sorbitol and aldose
reductase are NAD(+) binding proteins of the polyol
pathway, which interconverts glucose and fructose.
Length = 334
Score = 39.4 bits (93), Expect = 0.010
Identities = 52/229 (22%), Positives = 98/229 (42%), Gaps = 33/229 (14%)
Query: 534 IPDQWTLEDAATV-PCVYATAVYAMFICGQMQKGESILIHAGSGGVGQAAINLARYMDAE 592
IPD + E+AA P + AV+ + + G ++ G+S+L+ G+G +G L + A
Sbjct: 130 IPDNLSFEEAALAEPL--SCAVHGLDLLG-IKPGDSVLVF-GAGPIGLLLAQLLKLNGAS 185
Query: 593 IFTTVG-TPEKREFIRKTFPFIKEENIGNSRDTSFEQLVMKRTKGRGVDLVLNSL-AEEK 650
T EK E +K E + SR+ + K G D+V+ + +
Sbjct: 186 RVTVAEPNEEKLELAKKLG---ATETVDPSRE---DPEAQKEDNPYGFDVVIEATGVPKT 239
Query: 651 LQASVRCLAQGGRFLEIGKFDLANNN----MLGMEVFMRETSFHGVMLDNFFFAEQEWKM 706
L+ ++ +GG L F + + + E+F +E + G ++ + F
Sbjct: 240 LEQAIEYARRGGTVL---VFGVYAPDARVSISPFEIFQKELTIIGSFINPYTF------- 289
Query: 707 SLQKALQKAIDAGAVQ--PLVRTIFPEDKVEEAFRYMAAGKHIGKVIIK 753
+A+ +++G + LV P ++V EA M +G KV++
Sbjct: 290 --PRAI-ALLESGKIDVKGLVSHRLPLEEVPEALEGMRSGG-ALKVVVV 334
>gnl|CDD|187616 cd05358, GlcDH_SDR_c, glucose 1 dehydrogenase (GlcDH), classical
(c) SDRs. GlcDH, is a tetrameric member of the SDR
family, it catalyzes the NAD(P)-dependent oxidation of
beta-D-glucose to D-glucono-delta-lactone. GlcDH has a
typical NAD-binding site glycine-rich pattern as well as
the canonical active site tetrad (YXXXK motif plus
upstream Ser and Asn). 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 = 253
Score = 38.9 bits (91), Expect = 0.011
Identities = 29/107 (27%), Positives = 45/107 (42%), Gaps = 4/107 (3%)
Query: 781 NKSYIICGGLGGFGLELADWLVLRGARKLVLTSRSGVKNGYQALRIKIWKSYDVQVLIST 840
K ++ G G G +A L GA +V+ RS + + K+ + +
Sbjct: 3 GKVALVTGASSGIGKAIAIRLATAGA-NVVVNYRSKEDAAEEVVEEI--KAVGGKAIAVQ 59
Query: 841 DDITTEAGVVNLLTEANK-LGPVDGIFNLAVVLKDALFENQTPEDFN 886
D++ E VV L A K G +D + N A + DA T ED+N
Sbjct: 60 ADVSKEEDVVALFQSAIKEFGTLDILVNNAGLQGDASSHEMTLEDWN 106
>gnl|CDD|181297 PRK08217, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 253
Score = 39.2 bits (92), Expect = 0.011
Identities = 38/167 (22%), Positives = 71/167 (42%), Gaps = 24/167 (14%)
Query: 781 NKSYIICGGLGGFGLELADWLVLRGAR-KLVLTSRSGVKNGYQALRIKIWKSYDVQVLIS 839
+K +I GG G G +A++L +GA+ L+ ++ ++ + +V
Sbjct: 5 DKVIVITGGAQGLGRAMAEYLAQKGAKLALIDLNQEKLEEAVAECG-----ALGTEVRGY 59
Query: 840 TDDITTEAGVVNLLTEANK-LGPVDGIFNLAVVLKDALF---------ENQTPEDFNASL 889
++T E V + + G ++G+ N A +L+D L + E F + +
Sbjct: 60 AANVTDEEDVEATFAQIAEDFGQLNGLINNAGILRDGLLVKAKDGKVTSKMSLEQFQSVI 119
Query: 890 GPKANATKYF---DKYSRTMCPTLGQFVV--FSSVSCGRGNAGQTNY 931
N T F + + M + + V+ SS++ GN GQTNY
Sbjct: 120 --DVNLTGVFLCGREAAAKMIESGSKGVIINISSIARA-GNMGQTNY 163
>gnl|CDD|221720 pfam12697, Abhydrolase_6, Alpha/beta hydrolase family. This family
contains alpha/beta hydrolase enzymes of diverse
specificity.
Length = 187
Score = 37.8 bits (88), Expect = 0.015
Identities = 22/88 (25%), Positives = 30/88 (34%), Gaps = 16/88 (18%)
Query: 1160 IFMVPGI----EGIATVLEPLAKNINAQVLVFQF-------DHTNPPDTIPEMADSLLPH 1208
+ ++ G E + E LA VL P ++ + A L
Sbjct: 1 VVLLHGAGGSAESWRPLAEALAAGYR--VLAPDLPGHGDSDGPPRTPYSLEDDAADLA-A 57
Query: 1209 FKKRLVHGTDEIKLVGFSFGGMVALELA 1236
L G + LVG S GG VAL A
Sbjct: 58 LLDAL--GLGPVVLVGHSLGGAVALAAA 83
>gnl|CDD|132492 TIGR03451, mycoS_dep_FDH, S-(hydroxymethyl)mycothiol dehydrogenase.
Members of this protein family are mycothiol-dependent
formaldehyde dehydrogenase (EC 1.2.1.66). This protein
is found, so far, only in the Actinobacteria
(Mycobacterium sp., Streptomyces sp., Corynebacterium
sp., and related species), where mycothione replaces
glutathione [Cellular processes, Detoxification].
Length = 358
Score = 38.6 bits (90), Expect = 0.021
Identities = 53/200 (26%), Positives = 87/200 (43%), Gaps = 22/200 (11%)
Query: 561 GQMQKGESILIHAGSGGVGQAAINLARYMDAEIFTTVGTPEKREFIRKTFPFIKEENIGN 620
G +++G+S+ + G GGVG AAI A A V +++ + F + N
Sbjct: 172 GGVKRGDSVAV-IGCGGVGDAAIAGAALAGASKIIAVDIDDRKLEWAREF---GATHTVN 227
Query: 621 SRDTSFEQLVMKRTKGRGVDLVLNSLA--EEKLQA-SVRCLAQGGRFLEIGKFDLANN-N 676
S T + + T G G D+V++++ E QA R LA G + +G
Sbjct: 228 SSGTDPVEAIRALTGGFGADVVIDAVGRPETYKQAFYARDLA--GTVVLVGVPTPDMTLE 285
Query: 677 MLGMEVFMR----ETSFHGVMLDNFFFAEQEWKMSLQKALQKAIDAGAVQPLVRTIFPED 732
+ ++VF R ++S++G L E+++ M + LQ + A V D
Sbjct: 286 LPLLDVFGRGGALKSSWYGDCL-----PERDFPMLVDLYLQGRLPLDA---FVTERIGLD 337
Query: 733 KVEEAFRYMAAGKHIGKVII 752
VEEAF M AG + V+
Sbjct: 338 DVEEAFDKMHAGDVLRSVVE 357
>gnl|CDD|215606 PLN03154, PLN03154, putative allyl alcohol dehydrogenase;
Provisional.
Length = 348
Score = 38.3 bits (89), Expect = 0.023
Identities = 28/111 (25%), Positives = 52/111 (46%), Gaps = 6/111 (5%)
Query: 555 YAMF--ICGQMQKGESILIHAGSGGVGQAAINLARYMDAEIFTTVGTPEKREFIRKTFPF 612
YA F +C +KG+S+ + A SG VGQ LA+ + + G+ +K + ++ F
Sbjct: 147 YAGFYEVCSP-KKGDSVFVSAASGAVGQLVGQLAKLHGCYVVGSAGSSQKVDLLKNKLGF 205
Query: 613 IKEENIGNSRDTSFEQLVMKRTKGRGVDLVLNSLAEEKLQASVRCLAQGGR 663
+ N D +KR G+D+ +++ + L A++ + GR
Sbjct: 206 DEAFNYKEEPDLD---AALKRYFPEGIDIYFDNVGGDMLDAALLNMKIHGR 253
>gnl|CDD|223669 COG0596, MhpC, Predicted hydrolases or acyltransferases (alpha/beta
hydrolase superfamily) [General function prediction
only].
Length = 282
Score = 38.1 bits (87), Expect = 0.027
Identities = 33/167 (19%), Positives = 56/167 (33%), Gaps = 18/167 (10%)
Query: 1159 TIFMVPGIEGIATVLEPLAKNINA-----QVLVFQF----DHTNPPDTIPEMADSLLPHF 1209
+ ++ G G ++V P+ K + A +V+ ++ AD L
Sbjct: 23 PLVLLHGFPGSSSVWRPVFKVLPALAARYRVIAPDLRGHGRSDPAGYSLSAYADDLAALL 82
Query: 1210 KKRLVHGTDEIKLVGFSFGGMVALELAIKLEQLGTKCHLYLVDSA--PDYVLTSLRKLPD 1267
G +++ LVG S GG VAL LA++ L L+ A P + +LR+
Sbjct: 83 DA---LGLEKVVLVGHSMGGAVALALALRHPDR--VRGLVLIGPAPPPGLLEAALRQPAG 137
Query: 1268 WNAKLNY--FLDLMPEDATHSRTYQRNLAHAAYKRITSILKYTDPKH 1312
L + A + L A + L
Sbjct: 138 AAPLAALADLLLGLDAAAFAALLAALGLLAALAAAARAGLAEALRAP 184
>gnl|CDD|187610 cd05352, MDH-like_SDR_c, mannitol dehydrogenase (MDH)-like,
classical (c) SDRs. NADP-mannitol dehydrogenase
catalyzes the conversion of fructose to mannitol, an
acyclic 6-carbon sugar. MDH is a tetrameric member of
the SDR family. This subgroup also includes various
other tetrameric SDRs, including Pichia stipitis
D-arabinitol dehydrogenase (aka polyol dehydrogenase),
Candida albicans Sou1p, a sorbose reductase, and Candida
parapsilosis (S)-specific carbonyl reductase (SCR, aka
S-specific alcohol dehydrogenase) which catalyzes the
enantioselective reduction of 2-hydroxyacetophenone into
(S)-1-phenyl-1,2-ethanediol. 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).
Length = 252
Score = 37.7 bits (88), Expect = 0.028
Identities = 37/186 (19%), Positives = 66/186 (35%), Gaps = 22/186 (11%)
Query: 780 SNKSYIICGGLGGFGLELADWLVLRGARKLVLTSRSGVKNGYQALRIKIWKSYDVQVLIS 839
K I+ GG G GL +A L GA + + S + +A + K Y V+
Sbjct: 7 KGKVAIVTGGSRGIGLAIARALAEAGA-DVAIIYNSAPRAEEKAEELA--KKYGVKTKAY 63
Query: 840 TDDITTEAGVVNLLTEANK-LGPVDGIFNLAVVLKDALFENQTPEDFNASLGPKANATKY 898
D++++ V + K G +D + A + + T E +N + N
Sbjct: 64 KCDVSSQESVEKTFKQIQKDFGKIDILIANAGITVHKPALDYTYEQWNKVIDVNLNGVFN 123
Query: 899 FDKYSRTMCPTL-----GQFVVFSSVSCGRGNAGQTN--YGMANSIMERICEARRAEGLP 951
++ G ++ +S+S N Q Y + + + +
Sbjct: 124 ---CAQAAAKIFKKQGKGSLIITASMSGTIVNRPQPQAAYNASKAAVIHLA--------K 172
Query: 952 GLAVEW 957
LAVEW
Sbjct: 173 SLAVEW 178
>gnl|CDD|131865 TIGR02818, adh_III_F_hyde, S-(hydroxymethyl)glutathione
dehydrogenase/class III alcohol dehydrogenase. The
members of this protein family show dual function.
First, they remove formaldehyde, a toxic metabolite, by
acting as S-(hydroxymethyl)glutathione dehydrogenase
(1.1.1.284). S-(hydroxymethyl)glutathione can form
spontaneously from formaldehyde and glutathione, and so
this enzyme previously was designated
glutathione-dependent formaldehyde dehydrogenase. These
same proteins are also designated alcohol dehydrogenase
(EC 1.1.1.1) of class III, for activities that do not
require glutathione; they tend to show poor activity for
ethanol among their various substrate alcohols [Cellular
processes, Detoxification, Energy metabolism,
Fermentation].
Length = 368
Score = 38.3 bits (89), Expect = 0.028
Identities = 52/235 (22%), Positives = 94/235 (40%), Gaps = 37/235 (15%)
Query: 533 EIPDQWTLEDAATVPCVYATAVYAMFICGQMQKGESILIHAGSGGVGQAAINLARYMDAE 592
+I LE+ + C T + A+ ++++G+++ + G GG+G + I AR A
Sbjct: 153 KINPAAPLEEVCLLGCGVTTGIGAVLNTAKVEEGDTVAVF-GLGGIGLSVIQGARMAKAS 211
Query: 593 IFTTVGT-PEKREFIRK--TFPFIKEENIGNSRDTSFEQLVMKRTKGRGVDLVLNSLAE- 648
+ P K E +K + N D ++++++ T G GVD +
Sbjct: 212 RIIAIDINPAKFELAKKLGATDCVNP----NDYDKPIQEVIVEITDG-GVDYSFECIGNV 266
Query: 649 EKLQASVRCLAQG-GRFLEIG-----------KFDLANNNMLGMEVFMRETSFHGVMLDN 696
++A++ C +G G + IG F L + R ++F GV
Sbjct: 267 NVMRAALECCHKGWGESIIIGVAGAGQEISTRPFQLVTGRV------WRGSAFGGVK--- 317
Query: 697 FFFAEQEWKMSLQKALQKAIDAGAVQPLVRTIFPEDKVEEAFRYMAAGKHIGKVI 751
E +++ ++ I A+ V P + + EAF M GK I VI
Sbjct: 318 ---GRTELPGIVEQYMKGEI---ALDDFVTHTMPLEDINEAFDLMHEGKSIRTVI 366
>gnl|CDD|234024 TIGR02817, adh_fam_1, zinc-binding alcohol dehydrogenase family
protein. Members of this model form a distinct subset
of the larger family of oxidoreductases that includes
zinc-binding alcohol dehydrogenases and NADPH:quinone
reductases (pfam00107). While some current members of
this family carry designations as putative alginate
lyase, it seems no sequence with a direct
characterization as such is detected by this model
[Energy metabolism, Fermentation].
Length = 336
Score = 37.8 bits (88), Expect = 0.033
Identities = 22/80 (27%), Positives = 35/80 (43%), Gaps = 6/80 (7%)
Query: 535 PDQWTLEDAATVPCVYATAVYAMF-----ICGQMQKGESILIHAGSGGVGQAAINLARYM 589
P + +AA +P TA +F ++LI G+GGVG I LAR +
Sbjct: 113 PKSLSFAEAAALPLTSITAWELLFDRLGINDPVAGDKRALLIIGGAGGVGSILIQLARQL 172
Query: 590 -DAEIFTTVGTPEKREFIRK 608
+ T PE +E++ +
Sbjct: 173 TGLTVIATASRPESQEWVLE 192
>gnl|CDD|129775 TIGR00692, tdh, L-threonine 3-dehydrogenase. This protein is a
tetrameric, zinc-binding, NAD-dependent enzyme of
threonine catabolism. Closely related proteins include
sorbitol dehydrogenase, xylitol dehydrogenase, and
benzyl alcohol dehydrogenase. Eukaryotic examples of
this enzyme have been demonstrated experimentally but do
not appear in database search results.E. coli His-90
modulates substrate specificity and is believed part of
the active site [Energy metabolism, Amino acids and
amines].
Length = 340
Score = 37.9 bits (88), Expect = 0.034
Identities = 51/223 (22%), Positives = 94/223 (42%), Gaps = 15/223 (6%)
Query: 531 AWEIPDQWTLEDAATVPCVYATAVYAMFICGQMQKGESILIHAGSGGVGQAAINLARYMD 590
W+ P + AT+ AV+ + + G + G+S+L+ G+G +G AI +A+
Sbjct: 130 IWKNPKSIP-PEYATIQEPLGNAVHTV-LAGPIS-GKSVLV-TGAGPIGLMAIAVAKASG 185
Query: 591 AEIFTTVGTPEKREFIRKTFPFIKEENIGNSRDTSFEQLVMKRTKGRGVDLVLN-SLAEE 649
A V + E+ + + + N + V T G GVD+ L S A +
Sbjct: 186 A---YPVIVSDPNEYRLELAKKMGATYVVNPFKEDVVKEVADLTDGEGVDVFLEMSGAPK 242
Query: 650 KLQASVRCLAQGGRFLEIGKFDLANNNMLGMEVFMRETSFHGVMLDNFFFAEQEWKMSLQ 709
L+ ++ + GGR +G +V + + +G+ + F + W +
Sbjct: 243 ALEQGLQAVTPGGRVSLLGLPPGKVTIDFTNKVIFKGLTIYGITGRHMF---ETWYTVSR 299
Query: 710 KALQKAIDAGAVQPLVRTIFPEDKVEEAFRYMAAGKHIGKVII 752
+D + P++ F DK E+ F M +G+ GKVI+
Sbjct: 300 LIQSGKLD---LDPIITHKFKFDKFEKGFELMRSGQ-TGKVIL 338
>gnl|CDD|176255 cd08295, double_bond_reductase_like, Arabidopsis alkenal double
bond reductase and leukotriene B4
12-hydroxydehydrogenase. This group includes proteins
identified as the Arabidopsis alkenal double bond
reductase and leukotriene B4 12-hydroxydehydrogenase.
The Arabidopsis enzyme, a member of the medium chain
dehydrogenase/reductase family, catalyzes the reduction
of 7-8-double bond of phenylpropanal substrates as a
plant defense mechanism. Prostaglandins and related
eicosanoids (lipid mediators involved in host defense
and inflamation) are metabolized by the oxidation of the
15(S)-hydroxyl group of the NAD+-dependent (type I
15-PGDH) 15-prostaglandin dehydrogenase (15-PGDH)
followed by reduction by NADPH/NADH-dependent (type II
15-PGDH) delta-13 15-prostaglandin reductase (13-PGR) to
15-keto-13,14,-dihydroprostaglandins. 13-PGR is a
bifunctional enzyme, since it also has leukotriene B(4)
12-hydroxydehydrogenase activity. Leukotriene B4 (LTB4)
can be metabolized by LTB4 20-hydroxylase in inflamatory
cells, and in other cells by bifunctional LTB4
12-HD/PGR. These 15-PGDH and related enzymes are members
of the medium chain dehydrogenase/reductase family. The
medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of an
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES.
Length = 338
Score = 37.7 bits (88), Expect = 0.035
Identities = 47/247 (19%), Positives = 90/247 (36%), Gaps = 61/247 (24%)
Query: 542 DAATVPCVYATAVYAM---------FICGQMQKGESILIHAGSGGVGQAAINLARYMDAE 592
D VP Y + M + + +KGE++ + A SG VGQ LA+
Sbjct: 119 DHTDVPLSYYLGLLGMPGLTAYAGFYEVCKPKKGETVFVSAASGAVGQLVGQLAKLKGCY 178
Query: 593 IFTTVGTPEKREFIRKTFPF-----IKEENIGNSRDTSFEQLVMKRTKGRGVDLVLNSLA 647
+ + G+ EK + ++ F KEE ++ +KR G+D+ +++
Sbjct: 179 VVGSAGSDEKVDLLKNKLGFDDAFNYKEEPDLDA--------ALKRYFPNGIDIYFDNVG 230
Query: 648 EEKLQASVRCLAQGGR---------FLEIGKFDLANN-NMLG----MEVFM------RET 687
+ L A + + GR + + N N++ ++ F+ R
Sbjct: 231 GKMLDAVLLNMNLHGRIAACGMISQYNLEWPEGVRNLLNIIYKRVKIQGFLVGDYLHRYP 290
Query: 688 SFHGVMLDNFFFAEQEWKMSLQKALQKAIDAGAVQPLVRTIFPEDKVEEAFRYMAAGKHI 747
F M +E K+ + + + + EAF + G +I
Sbjct: 291 EFLEEMSGYI----KEGKLKYVEDIADGL---------------ESAPEAFVGLFTGSNI 331
Query: 748 GKVIIKI 754
GK ++K+
Sbjct: 332 GKQVVKV 338
>gnl|CDD|187611 cd05353, hydroxyacyl-CoA-like_DH_SDR_c-like, (3R)-hydroxyacyl-CoA
dehydrogenase-like, classical(c)-like SDRs. Beta
oxidation of fatty acids in eukaryotes occurs by a
four-reaction cycle, that may take place in mitochondria
or in peroxisomes. (3R)-hydroxyacyl-CoA dehydrogenase is
part of rat peroxisomal multifunctional MFE-2, it is a
member of the NAD-dependent SDRs, but contains an
additional small C-terminal domain that completes the
active site pocket and participates in dimerization. The
atypical, additional C-terminal extension allows for
more extensive dimerization contact than other SDRs.
MFE-2 catalyzes the second and third reactions of the
peroxisomal beta oxidation cycle. Proteins in this
subgroup have a typical catalytic triad, but have a His
in place of the usual upstream Asn. This subgroup also
contains members identified as 17-beta-hydroxysteroid
dehydrogenases, including human peroxisomal
17-beta-hydroxysteroid dehydrogenase type 4 (17beta-HSD
type 4, aka MFE-2, encoded by HSD17B4 gene) which is
involved in fatty acid beta-oxidation and steroid
metabolism. This subgroup also includes two SDR domains
of the Neurospora crassa and Saccharomyces cerevisiae
multifunctional beta-oxidation protein (MFP, aka Fox2).
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 = 250
Score = 37.3 bits (87), Expect = 0.041
Identities = 38/165 (23%), Positives = 65/165 (39%), Gaps = 17/165 (10%)
Query: 781 NKSYIICGGLGGFGLELADWLVLRGARKLV------LTSRSGVKNGYQALRIKIWKSYDV 834
+ ++ G GG G A RGA+ +V + + +I +
Sbjct: 5 GRVVLVTGAGGGLGRAYALAFAERGAKVVVNDLGGDRKGSGKSSSAADKVVDEIKAAGGK 64
Query: 835 QVLISTDDITTEAGVVNLLTEANKLGPVDGIFNLAVVLKDALFENQTPEDFNASLGPKAN 894
V + D + +V T + G VD + N A +L+D F + ED++ + + +
Sbjct: 65 AV-ANYDSVEDGEKIVK--TAIDAFGRVDILVNNAGILRDRSFAKMSEEDWDLVM--RVH 119
Query: 895 ATKYFDKYSRTMCPTL-----GQFVVFSSVSCGRGNAGQTNYGMA 934
F K +R P + G+ + SS + GN GQ NY A
Sbjct: 120 LKGSF-KVTRAAWPYMRKQKFGRIINTSSAAGLYGNFGQANYSAA 163
>gnl|CDD|214835 smart00824, PKS_TE, Thioesterase. Peptide synthetases are involved
in the non-ribosomal synthesis of peptide antibiotics.
Next to the operons encoding these enzymes, in almost all
cases, are genes that encode proteins that have
similarity to the type II fatty acid thioesterases of
vertebrates. There are also modules within the peptide
synthetases that also share this similarity. With respect
to antibiotic production, thioesterases are required for
the addition of the last amino acid to the peptide
antibiotic, thereby forming a cyclic antibiotic.
Thioesterases (non-integrated) have molecular masses of
25-29 kDa.
Length = 212
Score = 36.8 bits (86), Expect = 0.045
Identities = 35/142 (24%), Positives = 53/142 (37%), Gaps = 15/142 (10%)
Query: 1222 LVGFSFGGMVALELAIKLEQLGTKCH-LYLVDS-APDYVLTSLRKLPDWNAKLNYFLDLM 1279
LVG S GG++A +A +LE G + L+D+ P W +L +
Sbjct: 68 LVGHSSGGLLAHAVAARLEARGIPPAAVVLLDTYPPGD-----PAPEGWLPELLRGV-FE 121
Query: 1280 PEDATHSRTYQRNLAHAAYKRITSILKYTDPKHKAFGGNITLLRPTE--QALPTAEDYGL 1337
ED+ R A AY R+ L+R +E P + G
Sbjct: 122 REDSFVPMDDARLTAMGAYLRLF-----GGWTPGPVAAPTLLVRASEPLAEWPDEDPDGW 176
Query: 1338 SKVCKKPVKVHFVDGNHFTVLD 1359
P V V G+HFT+++
Sbjct: 177 RAHWPLPHTVVDVPGDHFTMME 198
>gnl|CDD|225749 COG3208, GrsT, Predicted thioesterase involved in non-ribosomal
peptide biosynthesis [Secondary metabolites biosynthesis,
transport, and catabolism].
Length = 244
Score = 36.9 bits (86), Expect = 0.047
Identities = 22/77 (28%), Positives = 31/77 (40%), Gaps = 5/77 (6%)
Query: 1194 PPDTIPEMADSLLPHFKKRLVHGTDEIKLVGFSFGGMVALELAIKLEQLGTKC-HLYLVD 1252
I +AD L L+ L G S G M+A E+A +LE+ G L++
Sbjct: 52 LLTDIESLADELANELLPPLLD--APFALFGHSMGAMLAFEVARRLERAGLPPRALFISG 109
Query: 1253 S-APDYVL-TSLRKLPD 1267
AP Y + L D
Sbjct: 110 CRAPHYDRGKQIHHLDD 126
>gnl|CDD|236057 PRK07578, PRK07578, short chain dehydrogenase; Provisional.
Length = 199
Score = 35.9 bits (84), Expect = 0.077
Identities = 23/63 (36%), Positives = 28/63 (44%), Gaps = 8/63 (12%)
Query: 830 KSYDVQVLISTDDITTEAGVVNLLTEANKLGPVDGIFNLAVVLKDALFENQTPEDFNASL 889
S DVQV DIT A + L K+G VD + + A + A T EDFN L
Sbjct: 32 SSGDVQV-----DITDPASIRALF---EKVGKVDAVVSAAGKVHFAPLAEMTDEDFNVGL 83
Query: 890 GPK 892
K
Sbjct: 84 QSK 86
>gnl|CDD|180054 PRK05396, tdh, L-threonine 3-dehydrogenase; Validated.
Length = 341
Score = 36.3 bits (85), Expect = 0.086
Identities = 49/201 (24%), Positives = 80/201 (39%), Gaps = 42/201 (20%)
Query: 566 GESILIHAGSGGVGQAAINLARYMDAE-IFTTVGTPEKREFIRKTFPFIKEENIG----- 619
GE +LI G+G +G A +A+++ A + T + E RK +G
Sbjct: 164 GEDVLI-TGAGPIGIMAAAVAKHVGARHVVITDVNEYRLELARK---------MGATRAV 213
Query: 620 NSRDTSFEQLVMKRTKGRGVDLVLN-SLAEEKLQASVRCLAQGGRFLEIGKFDLANNNML 678
N ++ + G D+ L S A + + + GGR ML
Sbjct: 214 NVAKEDLRDVMAELGMTEGFDVGLEMSGAPSAFRQMLDNMNHGGRI-----------AML 262
Query: 679 G-----MEVFMRETSFHGVMLDNFFFAE--QEW-KMSLQKALQKAIDAGAVQPLVRTIFP 730
G M + + F G+ + + E + W KMS LQ +D + P++ FP
Sbjct: 263 GIPPGDMAIDWNKVIFKGLTIKGIYGREMFETWYKMS--ALLQSGLD---LSPIITHRFP 317
Query: 731 EDKVEEAFRYMAAGKHIGKVI 751
D ++ F M +G+ GKVI
Sbjct: 318 IDDFQKGFEAMRSGQS-GKVI 337
>gnl|CDD|181609 PRK09009, PRK09009, C factor cell-cell signaling protein;
Provisional.
Length = 235
Score = 35.8 bits (83), Expect = 0.10
Identities = 15/30 (50%), Positives = 19/30 (63%), Gaps = 2/30 (6%)
Query: 569 ILIHAGSGGVGQAAIN--LARYMDAEIFTT 596
ILI GSGG+G+A + L RY DA + T
Sbjct: 3 ILIVGGSGGIGKAMVKQLLERYPDATVHAT 32
>gnl|CDD|187625 cd05367, SPR-like_SDR_c, sepiapterin reductase (SPR)-like,
classical (c) SDRs. Human SPR, a member of the SDR
family, catalyzes the NADP-dependent reduction of
sepiaptern to 7,8-dihydrobiopterin (BH2). In addition to
SPRs, this subgroup also contains Bacillus cereus yueD,
a benzil reductase, which catalyzes the stereospecific
reduction of benzil to (S)-benzoin. 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 = 241
Score = 35.7 bits (83), Expect = 0.11
Identities = 28/93 (30%), Positives = 43/93 (46%), Gaps = 6/93 (6%)
Query: 784 YIICGGLGGFGLELADWLVLRGAR-KLVLTSRSGVKNGYQALRIKIWKSYDVQVLISTDD 842
I+ G G G LA+ L+ RG+ +VL +RS + Q L+ ++ ++V D
Sbjct: 2 IILTGASRGIGRALAEELLKRGSPSVVVLLARS--EEPLQELKEEL--RPGLRVTTVKAD 57
Query: 843 ITTEAGVVNLLTEANKLGP-VDGIFNLAVVLKD 874
++ AGV LL KL D + N A L
Sbjct: 58 LSDAAGVEQLLEAIRKLDGERDLLINNAGSLGP 90
>gnl|CDD|235506 PRK05565, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 247
Score = 35.6 bits (83), Expect = 0.11
Identities = 26/108 (24%), Positives = 48/108 (44%), Gaps = 4/108 (3%)
Query: 780 SNKSYIICGGLGGFGLELADWLVLRGARKLVLTSRSGVKNGYQALRIKIWKSYDVQVLIS 839
K I+ G GG G +A+ L GA K+V+ + + ++ K +
Sbjct: 4 MGKVAIVTGASGGIGRAIAELLAKEGA-KVVIAYDINEEAAQE--LLEEIKEEGGDAIAV 60
Query: 840 TDDITTEAGVVNLLTEA-NKLGPVDGIFNLAVVLKDALFENQTPEDFN 886
D+++E V NL+ + K G +D + N A + L + T E+++
Sbjct: 61 KADVSSEEDVENLVEQIVEKFGKIDILVNNAGISNFGLVTDMTDEEWD 108
>gnl|CDD|187593 cd05332, 11beta-HSD1_like_SDR_c, 11beta-hydroxysteroid
dehydrogenase type 1 (11beta-HSD1)-like, classical (c)
SDRs. Human 11beta_HSD1 catalyzes the NADP(H)-dependent
interconversion of cortisone and cortisol. This subgroup
also includes human dehydrogenase/reductase SDR family
member 7C (DHRS7C) and DHRS7B. These proteins have the
GxxxGxG nucleotide binding motif and S-Y-K catalytic
triad characteristic of the SDRs, but have an atypical
C-terminal domain that contributes to homodimerization
contacts. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold (alpha/beta folding
pattern with a central beta-sheet), an NAD(P)(H)-binding
region, and a structurally diverse C-terminal region.
Classical SDRs are typically about 250 residues long,
while extended SDRs are approximately 350 residues.
Sequence identity between different SDR enzymes are
typically in the 15-30% range, but the enzymes share the
Rossmann fold NAD-binding motif and characteristic
NAD-binding and catalytic sequence patterns. These
enzymes catalyze a wide range of activities including
the metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 257
Score = 35.3 bits (82), Expect = 0.15
Identities = 37/151 (24%), Positives = 59/151 (39%), Gaps = 22/151 (14%)
Query: 781 NKSYIICGGLGGFGLELADWLVLRGARKLVLTSRSGVKNGYQALRIKIWKSYDVQVLIST 840
K II G G G ELA L GAR LVL++R + + ++ + + +
Sbjct: 3 GKVVIITGASSGIGEELAYHLARLGAR-LVLSARR--EERLEEVKSECLELGAPSPHVVP 59
Query: 841 DDITTEAGVVNLLTEA-NKLGPVDGIFNLAVVLKDALFENQTPEDFNAS-----LGPKAN 894
D++ ++ EA G +D + N A + +LF + + + GP
Sbjct: 60 LDMSDLEDAEQVVEEALKLFGGLDILINNAGISMRSLFHDTSIDVDRKIMEVNYFGP-VA 118
Query: 895 ATKYFDKYSRTMCPTL-----GQFVVFSSVS 920
TK P L G VV SS++
Sbjct: 119 LTKAA-------LPHLIERSQGSIVVVSSIA 142
>gnl|CDD|176239 cd08278, benzyl_alcohol_DH, Benzyl alcohol dehydrogenase. Benzyl
alcohol dehydrogenase is similar to liver alcohol
dehydrogenase, but has some amino acid substitutions
near the active site, which may determine the enzyme's
specificity of oxidizing aromatic substrates. Also
known as aryl-alcohol dehydrogenases, they catalyze the
conversion of an aromatic alcohol + NAD+ to an aromatic
aldehyde + NADH + H+. NAD(P)(H)-dependent
oxidoreductases are the major enzymes in the
interconversion of alcohols and aldehydes, or ketones.
Alcohol dehydrogenase in the liver converts ethanol and
NAD+ to acetaldehyde and NADH, while in yeast and some
other microorganisms ADH catalyzes the conversion
acetaldehyde to ethanol in alcoholic fermentation. ADH
is a member of the medium chain alcohol dehydrogenase
family (MDR), which has a NAD(P)(H)-binding domain in a
Rossmann fold of a beta-alpha form. The NAD(H)-binding
region is comprised of 2 structurally similar halves,
each of which contacts a mononucleotide. A GxGxxG motif
after the first mononucleotide contact half allows the
close contact of the coenzyme with the ADH backbone.
The N-terminal catalytic domain has a distant homology
to GroES. These proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and have 2 tightly bound zinc atoms per
subunit, a catalytic zinc at the active site and a
structural zinc in a lobe of the catalytic domain.
NAD(H) binding occurs in the cleft between the catalytic
and coenzyme-binding domains at the active site, and
coenzyme binding induces a conformational closing of
this cleft. Coenzyme binding typically precedes and
contributes to substrate binding. In human ADH
catalysis, the zinc ion helps coordinate the alcohol,
followed by deprotonation of a histidine, the ribose of
NAD, a serine, then the alcohol, which allows the
transfer of a hydride to NAD+, creating NADH and a
zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 365
Score = 35.6 bits (83), Expect = 0.16
Identities = 47/234 (20%), Positives = 86/234 (36%), Gaps = 49/234 (20%)
Query: 540 LEDAATVPCVYATAVYAMFICGQMQKGESILIHAGSGGVGQAAINLARYMDAEIFTTVGT 599
LE A + C T A+ + + G SI + G+G VG AA+ A+ V
Sbjct: 161 LELLAPLGCGIQTGAGAVLNVLKPRPGSSIAV-FGAGAVGLAAVMAAKIAGCTTIIAVDI 219
Query: 600 -PEKREFIRKTFPFIKEENIG-----NSRDTSFEQLVMKRTKGRGVDLVLNSLAEEK-LQ 652
+ E ++ +G N ++ + + T G GVD L++ ++
Sbjct: 220 VDSRLELAKE---------LGATHVINPKEEDLVAAIREIT-GGGVDYALDTTGVPAVIE 269
Query: 653 ASVRCLAQGGRFLEIG--------KFDLANNNMLGMEVFMRETSFHGVMLDNFFFAEQEW 704
+V LA G +G D+ + + G + GV+ E
Sbjct: 270 QAVDALAPRGTLALVGAPPPGAEVTLDVNDLLVSGKTI-------RGVI---------EG 313
Query: 705 KMSLQKALQKAID---AGA--VQPLVRTIFPEDKVEEAFRYMAAGKHIGKVIIK 753
Q+ + + I+ G LV +P + + +A +GK I K +++
Sbjct: 314 DSVPQEFIPRLIELYRQGKFPFDKLVTF-YPFEDINQAIADSESGKVI-KPVLR 365
>gnl|CDD|181120 PRK07792, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 306
Score = 35.5 bits (82), Expect = 0.18
Identities = 30/102 (29%), Positives = 45/102 (44%), Gaps = 9/102 (8%)
Query: 842 DITTEAGVVNLLTEANKLGPVDGIFNLAVVLKDALFENQTPEDFNASLGPKA-------- 893
DI+ A L+ A LG +D + N A + +D + N + E+++A +
Sbjct: 70 DISQRATADELVATAVGLGGLDIVVNNAGITRDRMLFNMSDEEWDAVIAVHLRGHFLLTR 129
Query: 894 NATKYF-DKYSRTMCPTLGQFVVFSSVSCGRGNAGQTNYGMA 934
NA Y+ K P G+ V SS + G GQ NYG A
Sbjct: 130 NAAAYWRAKAKAAGGPVYGRIVNTSSEAGLVGPVGQANYGAA 171
>gnl|CDD|129685 TIGR00597, rad10, DNA repair protein rad10. All proteins in this
family for which functions are known are components in a
multiprotein endonuclease complex (usually made up of
Rad1 and Rad10 homologs). This complex is used primarily
for nucleotide excision repair but also for some aspects
of recombination repair. This family is based on the
phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
Stanford University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 112
Score = 32.9 bits (75), Expect = 0.28
Identities = 13/34 (38%), Positives = 19/34 (55%)
Query: 1169 IATVLEPLAKNINAQVLVFQFDHTNPPDTIPEMA 1202
I L+ L KN N ++L+ Q D NP + E+A
Sbjct: 55 IHRRLQSLGKNFNLRILLVQVDVKNPQQALKELA 88
>gnl|CDD|237219 PRK12827, PRK12827, short chain dehydrogenase; Provisional.
Length = 249
Score = 34.3 bits (79), Expect = 0.29
Identities = 39/157 (24%), Positives = 62/157 (39%), Gaps = 18/157 (11%)
Query: 786 ICGGLGGFGLELADWLVLRGARKLVL-----TSRSGVKNGYQALRIKIWKSYDVQVLIST 840
I GG GG G +A L GA +VL R+ + K+ +
Sbjct: 11 ITGGSGGLGRAIAVRLAADGADVIVLDIHPMRGRAEADAVAAGIEAAGGKALGLAF---- 66
Query: 841 DDITTEAGVVNLL-TEANKLGPVDGIFNLAVVLKDALFENQTPEDFNASLGPKANATKYF 899
D+ A L + G +D + N A + DA F + E+++ + N +F
Sbjct: 67 -DVRDFAATRAALDAGVEEFGRLDILVNNAGIATDAAFAELSIEEWDDVID--VNLDGFF 123
Query: 900 DKYSRTMCPTL-----GQFVVFSSVSCGRGNAGQTNY 931
+ + P + G+ V +SV+ RGN GQ NY
Sbjct: 124 NVTQAALPPMIRARRGGRIVNIASVAGVRGNRGQVNY 160
>gnl|CDD|171820 PRK12936, PRK12936, 3-ketoacyl-(acyl-carrier-protein) reductase
NodG; Reviewed.
Length = 245
Score = 34.5 bits (79), Expect = 0.30
Identities = 26/84 (30%), Positives = 39/84 (46%), Gaps = 6/84 (7%)
Query: 859 LGPVDGIFNLAVVLKDALFENQTPEDFNASLGPKANATKYFDKYSRTMCPTL----GQFV 914
L VD + N A + KD LF + ED+++ L + N T F P + G+ +
Sbjct: 78 LEGVDILVNNAGITKDGLFVRMSDEDWDSVL--EVNLTATFRLTRELTHPMMRRRYGRII 135
Query: 915 VFSSVSCGRGNAGQTNYGMANSIM 938
+SV GN GQ NY + + M
Sbjct: 136 NITSVVGVTGNPGQANYCASKAGM 159
>gnl|CDD|143453 cd07135, ALDH_F14-YMR110C, Saccharomyces cerevisiae aldehyde
dehydrogenase family 14 and related proteins. Aldehyde
dehydrogenase family 14 (ALDH14), isolated mainly from
the mitochondrial outer membrane of Saccharomyces
cerevisiae (YMR110C) and most closely related to the
plant and animal ALDHs and fatty ALDHs family 3 members,
and similar fungal sequences, are present in this CD.
Length = 436
Score = 34.9 bits (81), Expect = 0.33
Identities = 18/56 (32%), Positives = 25/56 (44%), Gaps = 1/56 (1%)
Query: 1254 APDYVLTSLRKLPDWNAKLNYFLDLM-PEDATHSRTYQRNLAHAAYKRITSILKYT 1308
APDYVL ++ +L LD P A S Y R + + R+ S+L T
Sbjct: 250 APDYVLVDPSVYDEFVEELKKVLDEFYPGGANASPDYTRIVNPRHFNRLKSLLDTT 305
>gnl|CDD|187548 cd05237, UDP_invert_4-6DH_SDR_e, UDP-Glcnac (UDP-linked
N-acetylglucosamine) inverting 4,6-dehydratase, extended
(e) SDRs. UDP-Glcnac inverting 4,6-dehydratase was
identified in Helicobacter pylori as the hexameric flaA1
gene product (FlaA1). FlaA1 is hexameric, possesses
UDP-GlcNAc-inverting 4,6-dehydratase activity, and
catalyzes the first step in the creation of a
pseudaminic acid derivative in protein glycosylation.
Although this subgroup has the NADP-binding motif
characteristic of extended SDRs, its members tend to
have a Met substituted for the active site Tyr found in
most SDR families. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately 100
amino acids. Extended SDRs are a diverse collection of
proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 287
Score = 34.5 bits (80), Expect = 0.34
Identities = 21/91 (23%), Positives = 37/91 (40%), Gaps = 7/91 (7%)
Query: 780 SNKSYIICGGLGGFGLELADWLVLRGARKLVLTSRSGVKNGYQALRIKIWKSYDVQVLIS 839
K+ ++ GG G G EL ++ G +KL++ R +N L ++ + L
Sbjct: 1 KGKTILVTGGAGSIGSELVRQILKFGPKKLIVFDRD--ENKLHELVRELRSRFPHDKLRF 58
Query: 840 TD-DITTEAGVVNLLTEANKLGPVDGIFNLA 869
D+ + L A K D +F+ A
Sbjct: 59 IIGDVRDKE----RLRRAFKERGPDIVFHAA 85
>gnl|CDD|176246 cd08286, FDH_like_ADH2, formaldehyde dehydrogenase (FDH)-like.
This group is related to formaldehyde dehydrogenase
(FDH), which is a member of the zinc-dependent/medium
chain alcohol dehydrogenase family. This family uses
NAD(H) as a cofactor in the interconversion of alcohols
and aldehydes, or ketones. Another member is identified
as a dihydroxyacetone reductase. Like the zinc-dependent
alcohol dehydrogenases (ADH) of the medium chain alcohol
dehydrogenase/reductase family (MDR), tetrameric FDHs
have a catalytic zinc that resides between the catalytic
and NAD(H)binding domains and a structural zinc in a
lobe of the catalytic domain. Unlike ADH, where
NAD(P)(H) acts as a cofactor, NADH in FDH is a tightly
bound redox cofactor (similar to nicotinamide proteins).
The medium chain alcohol dehydrogenase family (MDR) has
a NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The N-terminal region typically has an
all-beta catalytic domain. These proteins typically form
dimers (typically higher plants, mammals) or tetramers
(yeast, bacteria), and have 2 tightly bound zinc atoms
per subunit.
Length = 345
Score = 34.5 bits (80), Expect = 0.35
Identities = 24/84 (28%), Positives = 41/84 (48%), Gaps = 6/84 (7%)
Query: 561 GQMQKGESILIHAGSGGVGQAAINLARYMDAEIFTTVGTPEKR-EFIRKTFPFIKEENIG 619
G+++ G+++ I G+G VG AA+ A+ V + R E +K +
Sbjct: 162 GKVKPGDTVAI-VGAGPVGLAALLTAQLYSPSKIIMVDLDDNRLEVAKK---LGATHTV- 216
Query: 620 NSRDTSFEQLVMKRTKGRGVDLVL 643
NS + V++ T GRGVD+V+
Sbjct: 217 NSAKGDAIEQVLELTDGRGVDVVI 240
>gnl|CDD|223314 COG0236, AcpP, Acyl carrier protein [Lipid metabolism / Secondary
metabolites biosynthesis, transport, and catabolism].
Length = 80
Score = 31.9 bits (73), Expect = 0.36
Identities = 16/67 (23%), Positives = 34/67 (50%), Gaps = 4/67 (5%)
Query: 1021 NIVDAVINILGLRDLKTVSLHSTLAE-LGMDSMMAVEIKQTLEREFEVFLTPQDIRGLTF 1079
+ D + LG+ D + ++ ++ E LG+DS+ VE+ LE EF + + +++
Sbjct: 9 RVKDIIAEQLGV-DEEEITTEASFVEDLGLDSLDLVELVMALEEEFGIEIPDEEL--ENI 65
Query: 1080 AKLQDIA 1086
+ D+
Sbjct: 66 KTVGDLV 72
>gnl|CDD|176243 cd08283, FDH_like_1, Glutathione-dependent formaldehyde
dehydrogenase related proteins, child 1. Members
identified as glutathione-dependent formaldehyde
dehydrogenase(FDH), a member of the
zinc-dependent/medium chain alcohol dehydrogenase
family. FDH converts formaldehyde and NAD(P) to formate
and NAD(P)H. The initial step in this process the
spontaneous formation of a S-(hydroxymethyl)glutathione
adduct from formaldehyde and glutathione, followed by
FDH-mediated oxidation (and detoxification) of the
adduct to S-formylglutathione. MDH family uses NAD(H)
as a cofactor in the interconversion of alcohols and
aldehydes, or ketones. Like many zinc-dependent alcohol
dehydrogenases (ADH) of the medium chain alcohol
dehydrogenase/reductase family (MDR), these FDHs form
dimers, with 4 zinc ions per dimer. The medium chain
alcohol dehydrogenase family (MDR) has a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The N-terminal region typically has an
all-beta catalytic domain. These proteins typically form
dimers (typically higher plants, mammals) or tetramers
(yeast, bacteria), and have 2 tightly bound zinc atoms
per subunit.
Length = 386
Score = 33.7 bits (78), Expect = 0.62
Identities = 26/116 (22%), Positives = 50/116 (43%), Gaps = 16/116 (13%)
Query: 534 IPDQWTLEDAATVPCVYATAVYAMFICGQMQKGESILIHAGSGGVGQAAINLARYMDAE- 592
IPD + E A + + T +A + ++ G+++ + G G VG A A+ + AE
Sbjct: 154 IPDDLSDEKALFLSDILPTGYHAAELAE-VKPGDTVAVW-GCGPVGLFAARSAKLLGAER 211
Query: 593 IFTTVGTPEKREFIRKTFP-----FIKEENIGNSRDTSFEQLVMKRTKGRGVDLVL 643
+ PE+ E R F + +++ + + + T GRG D+ +
Sbjct: 212 VIAIDRVPERLEMARSHLGAETINFEEVDDVVEA--------LRELTGGRGPDVCI 259
>gnl|CDD|187624 cd05366, meso-BDH-like_SDR_c, meso-2,3-butanediol
dehydrogenase-like, classical (c) SDRs. 2,3-butanediol
dehydrogenases (BDHs) catalyze the NAD+ dependent
conversion of 2,3-butanediol to acetonin; BDHs are
classified into types according to their
stereospecificity as to substrates and products.
Included in this subgroup are Klebsiella pneumonia
meso-BDH which catalyzes meso-2,3-butanediol to
D(-)-acetonin, and Corynebacterium glutamicum L-BDH
which catalyzes lX+)-2,3-butanediol to L(+)-acetonin.
This subgroup is comprised of classical SDRs with the
characteristic catalytic triad and 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 = 33.5 bits (77), Expect = 0.68
Identities = 35/163 (21%), Positives = 56/163 (34%), Gaps = 19/163 (11%)
Query: 780 SNKSYIICGGLGGFGLELADWLVLRGARKLVLTSRSGVKNGYQALRIKIWKSYDVQVLIS 839
+K II G G G +A+ L G +VL + + I+ +
Sbjct: 1 MSKVAIITGAAQGIGRAIAERLAADGF-NIVLADLNLEEAAKST--IQEISEAGYNAVAV 57
Query: 840 TDDITTEAGVVNLLTEA-NKLGPVDGIFNLAVVLKDALFENQTPEDFNASL--------- 889
D+T + V L+ +A K G D + N A + T ED
Sbjct: 58 GADVTDKDDVEALIDQAVEKFGSFDVMVNNAGIAPITPLLTITEEDLKKVYAVNVFGVLF 117
Query: 890 GPKANATKYFDKYSRTMCPTLGQFVVFSSVSCGRGNAGQTNYG 932
G +A A + F K G+ + SS++ +G Y
Sbjct: 118 GIQA-AARQFKKLGHG-----GKIINASSIAGVQGFPNLGAYS 154
>gnl|CDD|236074 PRK07666, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 239
Score = 33.1 bits (76), Expect = 0.79
Identities = 38/173 (21%), Positives = 72/173 (41%), Gaps = 23/173 (13%)
Query: 781 NKSYIICGGLGGFGLELADWLVLRGAR-KLVLTSRSGVKNGYQALRIKIWKSYDVQVLIS 839
K+ +I G G G +A L G L+ + +K + + ++Y V+V+I+
Sbjct: 7 GKNALITGAGRGIGRAVAIALAKEGVNVGLLARTEENLKAVAEEV-----EAYGVKVVIA 61
Query: 840 TDDITTEAGVVNLLTE-ANKLGPVDGIFNLAVVLKDALFENQTPEDFNASLGPKANATKY 898
T D++ V + + N+LG +D + N A + K F P ++ + Y
Sbjct: 62 TADVSDYEEVTAAIEQLKNELGSIDILINNAGISKFGKFLELDPAEWEKIIQVNLMGVYY 121
Query: 899 FDKYSRTMCPTL-----GQFVVFSSVSCGRGNAGQTNY--------GMANSIM 938
+R + P++ G + SS + +G A + Y G+ S+M
Sbjct: 122 A---TRAVLPSMIERQSGDIINISSTAGQKGAAVTSAYSASKFGVLGLTESLM 171
>gnl|CDD|183832 PRK12935, PRK12935, acetoacetyl-CoA reductase; Provisional.
Length = 247
Score = 33.1 bits (75), Expect = 0.81
Identities = 43/164 (26%), Positives = 68/164 (41%), Gaps = 14/164 (8%)
Query: 782 KSYIICGGLGGFGLELADWLVLRGARKLVL--TSRSGVKNGYQALRIKIWKSYDVQVLIS 839
K I+ GG G G + L GA+ ++ +S+ +N L + Y VQ
Sbjct: 7 KVAIVTGGAKGIGKAITVALAQEGAKVVINYNSSKEAAENLVNELGKEGHDVYAVQA--- 63
Query: 840 TDDITTEAGVVNLLTEA-NKLGPVDGIFNLAVVLKDALFENQTPEDFNASLGPKANATKY 898
D++ L+ EA N G VD + N A + +D F+ ED+ + N +
Sbjct: 64 --DVSKVEDANRLVEEAVNHFGKVDILVNNAGITRDRTFKKLNREDWERVI--DVNLSSV 119
Query: 899 FDKYSRTMCPTL----GQFVVFSSVSCGRGNAGQTNYGMANSIM 938
F+ S + G+ + SS+ G GQTNY A + M
Sbjct: 120 FNTTSAVLPYITEAEEGRIISISSIIGQAGGFGQTNYSAAKAGM 163
>gnl|CDD|233393 TIGR01392, homoserO_Ac_trn, homoserine O-acetyltransferase. This
family describes homoserine-O-acetyltransferase, an
enzyme of methionine biosynthesis. This model has been
rebuilt to identify sequences more broadly, including a
number of sequences suggested to be homoserine
O-acetyltransferase based on proximity to other Met
biosynthesis genes [Amino acid biosynthesis, Aspartate
family].
Length = 351
Score = 33.0 bits (76), Expect = 0.96
Identities = 19/48 (39%), Positives = 23/48 (47%), Gaps = 10/48 (20%)
Query: 1194 PPDTIPEMADS---LLPHFKKRLVHGTDEIKLV-GFSFGGMVALELAI 1237
P TI + + LL H G ++I V G S GGM ALE AI
Sbjct: 105 PLITIRDDVKAQKLLLDHL------GIEQIAAVVGGSMGGMQALEWAI 146
>gnl|CDD|181585 PRK08936, PRK08936, glucose-1-dehydrogenase; Provisional.
Length = 261
Score = 32.8 bits (75), Expect = 1.0
Identities = 41/140 (29%), Positives = 61/140 (43%), Gaps = 27/140 (19%)
Query: 777 YAD-SNKSYIICGGLGGFGLELADWLVLRGARKLVLTSRSGVKNGYQALRIKIWKSYDVQ 835
Y+D K +I GG G G +A A K+V+ RS + +I K+ +
Sbjct: 2 YSDLEGKVVVITGGSTGLGRAMAVRFGKEKA-KVVINYRSDEEEANDVAE-EIKKA-GGE 58
Query: 836 VLISTDDITTEAGVVNLLTEA-NKLGPVDGIFNLAVVLKDALFENQTP------EDFN-- 886
+ D+T E+ VVNL+ A + G +D V++ +A EN P ED+N
Sbjct: 59 AIAVKGDVTVESDVVNLIQTAVKEFGTLD------VMINNAGIENAVPSHEMSLEDWNKV 112
Query: 887 -------ASLGPKANATKYF 899
A LG + A KYF
Sbjct: 113 INTNLTGAFLGSRE-AIKYF 131
>gnl|CDD|183778 PRK12829, PRK12829, short chain dehydrogenase; Provisional.
Length = 264
Score = 32.7 bits (75), Expect = 1.0
Identities = 37/163 (22%), Positives = 56/163 (34%), Gaps = 19/163 (11%)
Query: 779 DSNKSYIICGGLGGFGLELADWLVLRGARKLVLTSRSGVKNGYQALRIKIWKSYDVQVLI 838
++ GG G G +A+ GAR V A +
Sbjct: 9 LDGLRVLVTGGASGIGRAIAEAFAEAGARVHVCDVSEAALAATAAR-------LPGAKVT 61
Query: 839 STD-DITTEAGVVNLL-TEANKLGPVDGIFNLA-VVLKDALFENQTPEDFNASLGPKANA 895
+T D+ A V + T + G +D + N A + + TPE + +L N
Sbjct: 62 ATVADVADPAQVERVFDTAVERFGGLDVLVNNAGIAGPTGGIDEITPEQWEQTLAVNLNG 121
Query: 896 TKYFDKYSRTMCPTL-----GQFVVFSSVSCGR-GNAGQTNYG 932
YF +R P L G ++ S GR G G+T Y
Sbjct: 122 QFYF---ARAAVPLLKASGHGGVIIALSSVAGRLGYPGRTPYA 161
>gnl|CDD|187629 cd05371, HSD10-like_SDR_c, 17hydroxysteroid dehydrogenase type 10
(HSD10)-like, classical (c) SDRs. HSD10, also known as
amyloid-peptide-binding alcohol dehydrogenase (ABAD),
was previously identified as a L-3-hydroxyacyl-CoA
dehydrogenase, HADH2. In fatty acid metabolism, HADH2
catalyzes the third step of beta-oxidation, the
conversion of a hydroxyl to a keto group in the
NAD-dependent oxidation of L-3-hydroxyacyl CoA. In
addition to alcohol dehydrogenase and HADH2 activites,
HSD10 has steroid dehydrogenase activity. Although the
mechanism is unclear, HSD10 is implicated in the
formation of amyloid beta-petide in the brain (which is
linked to the development of Alzheimer's disease).
Although HSD10 is normally concentrated in the
mitochondria, in the presence of amyloid beta-peptide it
translocates into the plasma membrane, where it's action
may generate cytotoxic aldehydes and may lower estrogen
levels through its use of 17-beta-estradiol as a
substrate. HSD10 is a member of the SRD family, but
differs from other SDRs by the presence of two
insertions of unknown function. 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 = 252
Score = 32.3 bits (74), Expect = 1.4
Identities = 27/113 (23%), Positives = 44/113 (38%), Gaps = 15/113 (13%)
Query: 781 NKSYIICGGLGGFGLELADWLVLRGARKLVLTSRSGVKNGYQALRIKIWKSYDVQVLIST 840
++ GG G GL + L+ +GA+ ++L + G ++
Sbjct: 2 GLVAVVTGGASGLGLATVERLLAQGAKVVILDLPN--SPGETVAKLGD------NCRFVP 53
Query: 841 DDITTEAGVVNLLTEA-NKLGPVDGIFN---LAVVLKDALFENQTP---EDFN 886
D+T+E V L A K G +D + N +AV K + Q P E F
Sbjct: 54 VDVTSEKDVKAALALAKAKFGRLDIVVNCAGIAVAAKTYNKKGQQPHSLELFQ 106
>gnl|CDD|132409 TIGR03366, HpnZ_proposed, putative phosphonate catabolism
associated alcohol dehydrogenase. This clade of
zinc-binding alcohol dehydrogenases (members of
pfam00107) are repeatedly associated with genes proposed
to be involved with the catabolism of phosphonate
compounds.
Length = 280
Score = 32.5 bits (74), Expect = 1.4
Identities = 34/134 (25%), Positives = 53/134 (39%), Gaps = 16/134 (11%)
Query: 534 IPDQWTLEDAATVPCVYATAVYAMFICGQMQKGESILIHAGSGGVGQAAINLARYMDA-E 592
+PD AA C AT + A+ G + KG +L+ G+G +G A A A
Sbjct: 90 VPDDLPDAVAAPAGCATATVMAALEAAGDL-KGRRVLV-VGAGMLGLTAAAAAAAAGAAR 147
Query: 593 IFTTVGTPEKREFIRKTFPFIKEENIGNS---RDTSFEQLVMKRTKGRGVDLVLN-SLAE 648
+ +P++RE + G + + GRGVD+ L S A
Sbjct: 148 VVAADPSPDRREL---------ALSFGATALAEPEVLAERQGGLQNGRGVDVALEFSGAT 198
Query: 649 EKLQASVRCLAQGG 662
++A + L GG
Sbjct: 199 AAVRACLESLDVGG 212
>gnl|CDD|236668 PRK10252, entF, enterobactin synthase subunit F; Provisional.
Length = 1296
Score = 33.1 bits (76), Expect = 1.5
Identities = 25/108 (23%), Positives = 48/108 (44%), Gaps = 9/108 (8%)
Query: 1155 GNNNTIFMVPGIEGIATVLEPLAKNINAQVLVFQFDHTNP------PDTIPEMADSLLPH 1208
G+ T+F G A L++ ++ Q ++ P ++ E+ ++ L
Sbjct: 1066 GDGPTLFCFHPASGFAWQFSVLSRYLDPQWSIYGIQSPRPDGPMQTATSLDEVCEAHLAT 1125
Query: 1209 FKKRLVHGTDEIKLVGFSFGGMVALELAIKLEQLGTKC-HLYLVDSAP 1255
++ HG L+G+S GG +A +A +L G + L L+D+ P
Sbjct: 1126 LLEQQPHG--PYHLLGYSLGGTLAQGIAARLRARGEEVAFLGLLDTWP 1171
>gnl|CDD|235726 PRK06181, PRK06181, short chain dehydrogenase; Provisional.
Length = 263
Score = 32.3 bits (74), Expect = 1.6
Identities = 40/187 (21%), Positives = 68/187 (36%), Gaps = 39/187 (20%)
Query: 781 NKSYIICGGLGGFGLELADWLVLRGARKLVLTSRSGVKNGYQALRIKIWKSYDVQVLIST 840
K II G G G LA L GA+ LVL +R+ + +L ++ + + L+
Sbjct: 1 GKVVIITGASEGIGRALAVRLARAGAQ-LVLAARNETR--LASLAQEL-ADHGGEALVVP 56
Query: 841 DDITTEAGVVNLLTEA-NKLGPVDGIFNLAVVLKDALFENQTPEDFNASLGPKANATKYF 899
D++ L+ A + G +D + N A + + F+
Sbjct: 57 TDVSDAEACERLIEAAVARFGGIDILVNNAGITMWSRFD----------------ELTDL 100
Query: 900 DKYSRTM---------C-----PTL----GQFVVFSSVSCGRGNAGQTNYGMANSIMERI 941
+ R M C P L GQ VV SS++ G ++ Y + +
Sbjct: 101 SVFERVMRVNYLGAVYCTHAALPHLKASRGQIVVVSSLAGLTGVPTRSGYAASKHALHGF 160
Query: 942 CEARRAE 948
++ R E
Sbjct: 161 FDSLRIE 167
>gnl|CDD|235914 PRK07041, PRK07041, short chain dehydrogenase; Provisional.
Length = 230
Score = 31.9 bits (73), Expect = 1.9
Identities = 27/93 (29%), Positives = 34/93 (36%), Gaps = 8/93 (8%)
Query: 785 IICGGLGGFGLELADWLVLRGARKLVLTSRSGVKNGYQALRIKIWKSYDVQVLISTDDIT 844
++ GG G GL LA GAR + + SRS + A + L DIT
Sbjct: 1 LVVGGSSGIGLALARAFAAEGAR-VTIASRSRDRLAAAARALGGGAPVRTAAL----DIT 55
Query: 845 TEAGVVNLLTEANKLGPVDGIFNLAVVLKDALF 877
EA V EA GP D + A
Sbjct: 56 DEAAVDAFFAEA---GPFDHVVITAADTPGGPV 85
>gnl|CDD|135637 PRK05876, PRK05876, short chain dehydrogenase; Provisional.
Length = 275
Score = 31.8 bits (72), Expect = 2.1
Identities = 54/196 (27%), Positives = 86/196 (43%), Gaps = 21/196 (10%)
Query: 785 IICGGLGGFGLELADWLVLRGARKLVLT--SRSGVKNGYQALRIKIWKSYDVQVLISTDD 842
+I GG G GL RGAR +VL + G++ LR + +DV ++ D
Sbjct: 10 VITGGASGIGLATGTEFARRGAR-VVLGDVDKPGLRQAVNHLR---AEGFDVHGVMC--D 63
Query: 843 ITTEAGVVNLLTEANK-LGPVDGIFNLAVVLKDALFENQTPEDF----NASLGPKANATK 897
+ V +L EA + LG VD +F+ A ++ T +D+ + L + +
Sbjct: 64 VRHREEVTHLADEAFRLLGHVDVVFSNAGIVVGGPIVEMTHDDWRWVIDVDLWGSIHTVE 123
Query: 898 YFDKYSRTMCPTLGQFVVFSSVSCGR-GNAGQTNYGMAN----SIMERICEARRAEGLPG 952
F R + G VVF++ G NAG YG+A + E + A+G+ G
Sbjct: 124 AF--LPRLLEQGTGGHVVFTASFAGLVPNAGLGAYGVAKYGVVGLAETLAREVTADGI-G 180
Query: 953 LAVEWGAVGEVGLVAD 968
++V V E LVA+
Sbjct: 181 VSVLCPMVVETNLVAN 196
>gnl|CDD|176241 cd08281, liver_ADH_like1, Zinc-dependent alcohol dehydrogenases
(ADH) and class III ADG (AKA formaldehyde
dehydrogenase). NAD(P)(H)-dependent oxidoreductases are
the major enzymes in the interconversion of alcohols and
aldehydes or ketones. This group contains members
identified as zinc dependent alcohol dehydrogenases
(ADH), and class III ADG (aka formaldehyde
dehydrogenase, FDH). Alcohol dehydrogenase in the liver
converts ethanol and NAD+ to acetaldehyde and NADH,
while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. NAD(P)(H)-dependent
oxidoreductases are the major enzymes in the
interconversion of alcohols and aldehydes or ketones.
Alcohol dehydrogenase in the liver converts ethanol and
NAD+ to acetaldehyde and NADH, while in yeast and some
other microorganisms ADH catalyzes the conversion
acetaldehyde to ethanol in alcoholic fermentation.
Class III ADH are also know as glutathione-dependent
formaldehyde dehydrogenase (FDH), which convert
aldehydes to the corresponding carboxylic acid and
alcohol. ADH is a member of the medium chain alcohol
dehydrogenase family (MDR), which have a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES. These
proteins typically form dimers (typically higher plants,
mammals) or tetramers (yeast, bacteria), and have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site and a structural zinc in a lobe of
the catalytic domain. NAD(H) binding occurs in the
cleft between the catalytic and coenzyme-binding domains
at the active site, and coenzyme binding induces a
conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
In human ADH catalysis, the zinc ion helps coordinate
the alcohol, followed by deprotonation of a histidine,
the ribose of NAD, a serine, then the alcohol, which
allows the transfer of a hydride to NAD+, creating NADH
and a zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 371
Score = 32.0 bits (73), Expect = 2.1
Identities = 32/131 (24%), Positives = 53/131 (40%), Gaps = 8/131 (6%)
Query: 540 LEDAATVPCVYATAVYAMFICGQMQKGESILIHAGSGGVGQAAINLARYMDA-EIFTTVG 598
LE AA C T V A+ ++ G+S+ + G GGVG +A+ A A ++
Sbjct: 166 LEIAALFGCAVLTGVGAVVNTAGVRPGQSVAV-VGLGGVGLSALLGAVAAGASQVVAVDL 224
Query: 599 TPEKREFIRKTFPFIKEENIGNSRDTSFEQLVMKRTKGRGVDLVLNSLAEEK-LQASVRC 657
+K R+ + N+ D + + V + T G GVD L+ +
Sbjct: 225 NEDKLALARE----LGATATVNAGDPNAVEQVRELTGG-GVDYAFEMAGSVPALETAYEI 279
Query: 658 LAQGGRFLEIG 668
+GG + G
Sbjct: 280 TRRGGTTVTAG 290
>gnl|CDD|187586 cd05325, carb_red_sniffer_like_SDR_c, carbonyl reductase
sniffer-like, classical (c) SDRs. Sniffer is an
NADPH-dependent carbonyl reductase of the classical SDR
family. Studies in Drosophila melanogaster implicate
Sniffer in the prevention of neurodegeneration due to
aging and oxidative-stress. This subgroup also includes
Rhodococcus sp. AD45 IsoH, which is an NAD-dependent
1-hydroxy-2-glutathionyl-2-methyl-3-butene dehydrogenase
involved in isoprene metabolism, Aspergillus nidulans
StcE encoded by a gene which is part of a proposed
sterigmatocystin biosynthesis gene cluster, Bacillus
circulans SANK 72073 BtrF encoded by a gene found in the
butirosin biosynthesis gene cluster, and Aspergillus
parasiticus nor-1 involved in the biosynthesis of
aflatoxins. 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 = 233
Score = 31.5 bits (72), Expect = 2.2
Identities = 24/113 (21%), Positives = 38/113 (33%), Gaps = 6/113 (5%)
Query: 784 YIICGGLGGFGLELADWLVLRGARKLVLTSRSGVKNGYQALRIKIWKSYDVQVLISTDDI 843
+I G G GLEL L+ RG ++ T R + L + S+ ++ D
Sbjct: 1 VLITGASRGIGLELVRQLLARGNNTVIATCRD--PSAATELA-ALGASHSRLHILELDVT 57
Query: 844 TTEAGVVNLLTEANKLGPVDGIFNLAVVL-KDALFENQTPEDFNASLGPKANA 895
A + E +D + N A +L ED + N
Sbjct: 58 DEIAESAEAVAERLGDAGLDVLINNAGILHSYGPASEVDSEDLLEVF--QVNV 108
>gnl|CDD|187618 cd05360, SDR_c3, classical (c) SDR, subgroup 3. These proteins are
members of the classical SDR family, with a canonical
active site triad (and also active site Asn) 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 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 = 233
Score = 31.6 bits (72), Expect = 2.3
Identities = 29/102 (28%), Positives = 42/102 (41%), Gaps = 5/102 (4%)
Query: 785 IICGGLGGFGLELADWLVLRGARKLVLTSRSGVKNGYQALRIKIWKSYDVQVLISTDDIT 844
+I G G G A RGA K+VL +RS L ++ + + + D+
Sbjct: 4 VITGASSGIGRATALAFAERGA-KVVLAARS--AEALHELAREV-RELGGEAIAVVADVA 59
Query: 845 TEAGVVNLL-TEANKLGPVDGIFNLAVVLKDALFENQTPEDF 885
A V T + G +D N A V FE+ TPE+F
Sbjct: 60 DAAQVERAADTAVERFGRIDTWVNNAGVAVFGRFEDVTPEEF 101
>gnl|CDD|224932 COG2021, MET2, Homoserine acetyltransferase [Amino acid transport and
metabolism].
Length = 368
Score = 31.9 bits (73), Expect = 2.4
Identities = 17/47 (36%), Positives = 24/47 (51%), Gaps = 8/47 (17%)
Query: 1194 PPDTIPEMADSLLPHFKKRLVH--GTDEIK-LVGFSFGGMVALELAI 1237
P TI +M ++ L+ G ++ +VG S GGM ALE AI
Sbjct: 125 PVITIRDMV-----RAQRLLLDALGIKKLAAVVGGSMGGMQALEWAI 166
>gnl|CDD|201306 pfam00561, Abhydrolase_1, alpha/beta hydrolase fold. This catalytic
domain is found in a very wide range of enzymes.
Length = 226
Score = 31.3 bits (71), Expect = 2.5
Identities = 16/48 (33%), Positives = 24/48 (50%), Gaps = 4/48 (8%)
Query: 1215 HGTDEIKLVGFSFGGMVALELAIKLEQLGTKC-HLYLVDSAPDYVLTS 1261
G D++ LVG S GG++AL A + + L LV + L+S
Sbjct: 39 LGLDKVNLVGHSMGGLIALAYA---AKYPDRVKALVLVGTVHPAGLSS 83
>gnl|CDD|181295 PRK08213, PRK08213, gluconate 5-dehydrogenase; Provisional.
Length = 259
Score = 31.5 bits (72), Expect = 2.6
Identities = 26/91 (28%), Positives = 44/91 (48%), Gaps = 5/91 (5%)
Query: 780 SNKSYIICGGLGGFGLELADWLVLRGARKLVLTSRSGVKNGYQALRIKIWKSYDVQVLIS 839
S K+ ++ GG G GL++A+ L GAR +VL++R + + ++ + L
Sbjct: 11 SGKTALVTGGSRGLGLQIAEALGEAGAR-VVLSARK--AEELEEAAAHL-EALGIDALWI 66
Query: 840 TDDITTEAGVVNLLTEA-NKLGPVDGIFNLA 869
D+ EA + L E + G VD + N A
Sbjct: 67 AADVADEADIERLAEETLERFGHVDILVNNA 97
>gnl|CDD|224001 COG1075, LipA, Predicted acetyltransferases and hydrolases with the
alpha/beta hydrolase fold [General function prediction
only].
Length = 336
Score = 31.7 bits (72), Expect = 2.8
Identities = 22/133 (16%), Positives = 46/133 (34%), Gaps = 10/133 (7%)
Query: 1109 ALSVEDIPDVGIQY-LMRTIGDEILANKPVIRLPSLKNNGSTVEEPVGNNNTIFMVPGIE 1167
A ++ +Y + +G + V +L S I +V G+
Sbjct: 12 AYALHTWATNNGKYNIANKLGLPLALRLLV--YVALAAALSASAAEARAKEPIVLVHGLG 69
Query: 1168 GIATVLEPLAKNINAQ----VLVFQFDHT--NPPDTIPEMADSLLPHFKKRLVH-GTDEI 1220
G PL + V+ F+ + + ++ + L + + L G ++
Sbjct: 70 GGYGNFLPLDYRLAILGWLTNGVYAFELSGGDGTYSLAVRGEQLFAYVDEVLAKTGAKKV 129
Query: 1221 KLVGFSFGGMVAL 1233
L+G S GG+ +
Sbjct: 130 NLIGHSMGGLDSR 142
>gnl|CDD|237011 PRK11892, PRK11892, pyruvate dehydrogenase subunit beta; Provisional.
Length = 464
Score = 31.8 bits (73), Expect = 2.8
Identities = 17/47 (36%), Positives = 27/47 (57%), Gaps = 2/47 (4%)
Query: 1198 IPEMADSLLPHFKKRLVH-GTDEIKLVGFSFGGMVALELAIKLEQLG 1243
+P++ D +LP K R+ G D + +V FS G AL+ A +L + G
Sbjct: 321 VPKLDDFVLPIGKARIHREGKD-VTIVSFSIGMTYALKAAEELAKEG 366
>gnl|CDD|176226 cd08265, Zn_ADH3, Alcohol dehydrogenases of the MDR family. This
group resembles the zinc-dependent alcohol dehydrogenase
and has the catalytic and structural zinc-binding sites
characteristic of this group. The medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, which contains the
zinc-dependent alcohol dehydrogenase (ADH-Zn) and
related proteins, is a diverse group of proteins related
to the first identified member, class I mammalian ADH.
MDRs display a broad range of activities and are
distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines. Other MDR members have only a catalytic zinc,
and some contain no coordinated zinc.
Length = 384
Score = 31.7 bits (72), Expect = 2.9
Identities = 34/137 (24%), Positives = 58/137 (42%), Gaps = 8/137 (5%)
Query: 512 MGLTSGRSLANCCETDVEMAWEIPD------QWTLEDAATVPCVYATAVYAMFI-CGQMQ 564
+G ++ + A + AWEI + + +A + + A +FI G +
Sbjct: 143 LGFSADGAFAEYIAVNARYAWEINELREIYSEDKAFEAGALVEPTSVAYNGLFIRGGGFR 202
Query: 565 KGESILIHAGSGGVGQAAINLARYMDAEIFTTVGTPEKREFIRKTFPFIKEENIGNSRDT 624
G ++++ G+G +G AAI LA+ A E+R + K N RD
Sbjct: 203 PGAYVVVY-GAGPIGLAAIALAKAAGASKVIAFEISEERRNLAKEMGADYVFNPTKMRDC 261
Query: 625 SFEQLVMKRTKGRGVDL 641
+ VM+ TKG G D+
Sbjct: 262 LSGEKVMEVTKGWGADI 278
>gnl|CDD|187620 cd05362, THN_reductase-like_SDR_c,
tetrahydroxynaphthalene/trihydroxynaphthalene
reductase-like, classical (c) SDRs.
1,3,6,8-tetrahydroxynaphthalene reductase (4HNR) of
Magnaporthe grisea and the related
1,3,8-trihydroxynaphthalene reductase (3HNR) are typical
members of the SDR family containing the canonical
glycine rich NAD(P)-binding site and active site tetrad,
and function in fungal melanin biosynthesis. This
subgroup also includes an SDR from Norway spruce that
may function to protect against both biotic and abitoic
stress. 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 = 243
Score = 31.1 bits (71), Expect = 3.5
Identities = 23/111 (20%), Positives = 45/111 (40%), Gaps = 8/111 (7%)
Query: 780 SNKSYIICGGLGGFGLELADWLVLRGARKLV--LTSRSGVKNGYQALRIKIWKSYDVQVL 837
+ K ++ G G G +A L GA +V +S++ + + ++ + +
Sbjct: 2 AGKVALVTGASRGIGRAIAKRLARDGASVVVNYASSKAAAEEVVAEI-----EAAGGKAI 56
Query: 838 ISTDDITTEAGVVNLLTEANK-LGPVDGIFNLAVVLKDALFENQTPEDFNA 887
D++ + V L A K G VD + N A V+ + E+F+
Sbjct: 57 AVQADVSDPSQVARLFDAAEKAFGGVDILVNNAGVMLKKPIAETSEEEFDR 107
>gnl|CDD|218074 pfam04413, Glycos_transf_N, 3-Deoxy-D-manno-octulosonic-acid
transferase (kdotransferase). Members of this family
transfer activated sugars to a variety of substrates,
including glycogen, fructose-6-phosphate and
lipopolysaccharides. Members of the family transfer UDP,
ADP, GDP or CMP linked sugars. The Glycos_transf_N
region is flanked at the N-terminus by a signal peptide
and at the C-terminus by Glycos_transf_1 (pfam00534).
The eukaryotic glycogen synthases may be distant members
of this bacterial family.
Length = 186
Score = 30.6 bits (70), Expect = 4.1
Identities = 20/52 (38%), Positives = 22/52 (42%), Gaps = 5/52 (9%)
Query: 565 KGESILIHAGSGGVGQAAINL-----ARYMDAEIFTTVGTPEKREFIRKTFP 611
G I +HA S G AA+ L ARY I T TP E RK P
Sbjct: 20 GGPLIWLHAASVGEVLAALPLIEALKARYPGLRILVTTTTPTGAELARKLLP 71
>gnl|CDD|236843 PRK11092, PRK11092, bifunctional (p)ppGpp synthetase II/
guanosine-3',5'-bis pyrophosphate
3'-pyrophosphohydrolase; Provisional.
Length = 702
Score = 31.2 bits (71), Expect = 4.7
Identities = 17/61 (27%), Positives = 28/61 (45%), Gaps = 11/61 (18%)
Query: 1032 LRDLKTVSLHSTLAELGMDSMMAVEIKQTLEREFEVFLTPQD------IRG-----LTFA 1080
L +K +L LAE+G+ + M+V + + L + T I+G +TFA
Sbjct: 512 LDRMKLATLDDLLAEIGLGNAMSVVVAKNLLGDDAELPTATSSHGKLPIKGADGVLITFA 571
Query: 1081 K 1081
K
Sbjct: 572 K 572
>gnl|CDD|236399 PRK09186, PRK09186, flagellin modification protein A; Provisional.
Length = 256
Score = 30.7 bits (70), Expect = 5.1
Identities = 27/116 (23%), Positives = 46/116 (39%), Gaps = 8/116 (6%)
Query: 780 SNKSYIICGGLGGFGLELADWLVLRGARKLVLTSRSGVKNGYQALRIKIWKSYDVQVLIS 839
K+ +I G G G L ++ G ++ K L + K + + L
Sbjct: 3 KGKTILITGAGGLIGSALVKAILEAGGI-VIAADID--KEALNELLESLGKEFKSKKLSL 59
Query: 840 TD-DITTEAGVVNLLTE-ANKLGPVDGIFNLAVVLKD---ALFENQTPEDFNASLG 890
+ DIT + + L++ A K G +DG N A F + + +DFN +L
Sbjct: 60 VELDITDQESLEEFLSKSAEKYGKIDGAVNCAYPRNKDYGKKFFDVSLDDFNENLS 115
>gnl|CDD|184896 PRK14903, PRK14903, 16S rRNA methyltransferase B; Provisional.
Length = 431
Score = 31.0 bits (70), Expect = 5.5
Identities = 17/91 (18%), Positives = 35/91 (38%), Gaps = 11/91 (12%)
Query: 197 NNWVAFMDNMLQLQILQYDTRGLFVPTSIQKLVINVSDHVNLLSTLDEE---TPEYPVFV 253
N W +F+ L+I++++ L + L I + + +L+ E P +
Sbjct: 140 NYWRSFLPEEAVLRIMEWNQEPLPTMLRVNSLAITREEVIKILAEEGTEAVPGKHSPFSL 199
Query: 254 Y--------KEVEVIKSGGVEIRGLKASAIP 276
+ VIK G ++G + +P
Sbjct: 200 IVRKLGVNMNDSRVIKDGLATVQGESSQIVP 230
>gnl|CDD|166155 PLN02514, PLN02514, cinnamyl-alcohol dehydrogenase.
Length = 357
Score = 30.5 bits (69), Expect = 5.9
Identities = 22/73 (30%), Positives = 31/73 (42%), Gaps = 5/73 (6%)
Query: 534 IPDQWTLEDAATVPCVYATAVYAMFICGQMQKG--ESILIHAGSGGVGQAAINLARYMDA 591
IP+ E AA + C T + G Q G IL G GGVG + +A+ M
Sbjct: 149 IPEGMAPEQAAPLLCAGVTVYSPLSHFGLKQSGLRGGIL---GLGGVGHMGVKIAKAMGH 205
Query: 592 EIFTTVGTPEKRE 604
+ + +KRE
Sbjct: 206 HVTVISSSDKKRE 218
>gnl|CDD|233032 TIGR00580, mfd, transcription-repair coupling factor (mfd). All
proteins in this family for which functions are known
are DNA-dependent ATPases that function in the process
of transcription-coupled DNA repair in which the repair
of the transcribed strand of actively transcribed genes
is repaired at a higher rate than the repair of
non-transcribed regions of the genome and than the
non-transcribed strand of the same gene. This family is
based on the phylogenomic analysis of JA Eisen (1999,
Ph.D. Thesis, Stanford University). This family is
closely related to the RecG and UvrB families [DNA
metabolism, DNA replication, recombination, and repair].
Length = 926
Score = 30.8 bits (70), Expect = 6.2
Identities = 37/228 (16%), Positives = 69/228 (30%), Gaps = 41/228 (17%)
Query: 695 DNFFFAEQEWKMSLQKALQKAIDAGAVQPLVRTIFPEDKVEEAFRYMAAGKHIGKVIIKI 754
+ F A + + L++ +A + R D E AF A
Sbjct: 142 ERFHSAARFLQRELEEFYNALEEAKKLINPPRL--DLDPSELAFEASAISLS-------- 191
Query: 755 RDEEPTKICTPKVKQLLA---VPRYYADSNKSYIICGGLGGFGLELADWLVLRGARKLVL 811
R + + + K + + F EL WL +
Sbjct: 192 RVQLENEHLSLKASEAIEGAQKHSRLEFGEILA--------FKEELFRWLKAGFKITVAA 243
Query: 812 TSRSGVKNGYQALRIK-IWKSYDVQVLISTDDITTEAGVVNLLTEANKLGPVDGIFNLAV 870
S S QA R+K + +D+ + + V ++ A G + LAV
Sbjct: 244 ESES------QAERLKSLLAEHDIAAQVIDESCIIIPAVRYVMIGALSSGFILPTAGLAV 297
Query: 871 VLKDALFENQ---TPEDFNASLGPKANATKYFDKYSRTMCPTLGQFVV 915
+ + LF ++ P+ K+ + ++ G +VV
Sbjct: 298 ITESELFGSRVLRRPKKSRL----KSKPIESLNE------LNPGDYVV 335
>gnl|CDD|187595 cd05334, DHPR_SDR_c_like, dihydropteridine reductase (DHPR),
classical (c) SDRs. Dihydropteridine reductase is an
NAD-binding protein related to the SDRs. It converts
dihydrobiopterin into tetrahydrobiopterin, a cofactor
necessary in catecholamines synthesis. Dihydropteridine
reductase has the YXXXK of these tyrosine-dependent
oxidoreductases, but lacks the typical upstream Asn and
Ser catalytic residues. 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 = 221
Score = 30.0 bits (68), Expect = 6.5
Identities = 31/175 (17%), Positives = 57/175 (32%), Gaps = 26/175 (14%)
Query: 785 IICGGLGGFGLELADWLVLRGARKLVLTSRSGVKNGYQALRIKIWKSYDVQVLISTDDIT 844
++ GG G G + RG + + +A + VL S
Sbjct: 5 LVYGGRGALGSAVVQAFKSRGWWVASI----DLAENEEA-------DASIIVLDSDSFTE 53
Query: 845 TEAGVVNLLTEANKLGPVDGIFNLA------VVLKDALFENQTPEDFNASLGPKANATKY 898
VV + G VD + +A + +N + +L A+
Sbjct: 54 QAKQVVASVAR--LSGKVDALICVAGGWAGGSAKSKSFVKN-WDLMWKQNLWTSFIASHL 110
Query: 899 FDKYSRTMCPTLGQFVVFSSVSCGRGNAGQTNYGMANSIMERICEARRAE--GLP 951
K+ + G V+ + + G YG A + + ++ ++ AE GLP
Sbjct: 111 ATKHLLSG----GLLVLTGAKAALEPTPGMIGYGAAKAAVHQLTQSLAAENSGLP 161
>gnl|CDD|240080 cd04729, NanE, N-acetylmannosamine-6-phosphate epimerase (NanE)
converts N-acetylmannosamine-6-phosphate to
N-acetylglucosamine-6-phosphate. This reaction is part
of the pathway that allows the usage of sialic acid as a
carbohydrate source. Sialic acids are a family of
related sugars that are found as a component of
glycoproteins, gangliosides, and other
sialoglycoconjugates.
Length = 219
Score = 30.2 bits (69), Expect = 6.5
Identities = 16/53 (30%), Positives = 27/53 (50%), Gaps = 5/53 (9%)
Query: 247 PEYPVFV---YKEVEVIKSGGVEIRGLKASAIPRKKPLGEPVLEKYKFIQNEG 296
P+ V++ +EV+ + + G +I L A+ R +P GE + E K I E
Sbjct: 72 PDSEVYITPTIEEVDALAAAGADIIALDATD--RPRPDGETLAELIKRIHEEY 122
>gnl|CDD|216940 pfam02230, Abhydrolase_2, Phospholipase/Carboxylesterase. This
family consists of both phospholipases and
carboxylesterases with broad substrate specificity, and
is structurally related to alpha/beta hydrolases
pfam00561.
Length = 213
Score = 30.0 bits (68), Expect = 7.0
Identities = 10/26 (38%), Positives = 12/26 (46%)
Query: 1216 GTDEIKLVGFSFGGMVALELAIKLEQ 1241
I + GFS G VAL A+ Q
Sbjct: 100 PASRIIIGGFSQGAAVALYTALTSPQ 125
>gnl|CDD|224561 COG1647, COG1647, Esterase/lipase [General function prediction only].
Length = 243
Score = 30.0 bits (68), Expect = 7.0
Identities = 19/48 (39%), Positives = 24/48 (50%), Gaps = 4/48 (8%)
Query: 1189 FDHTNPPDTIPEMADSLLPHFKKRLVHGTDEIKLVGFSFGGMVALELA 1236
F T P D E + K+ G DEI +VG S GG+ AL+LA
Sbjct: 60 FLKTTPRDWW-EDVEDGYRDLKEA---GYDEIAVVGLSMGGVFALKLA 103
>gnl|CDD|177748 PLN00144, PLN00144, acetylornithine transaminase.
Length = 382
Score = 30.4 bits (69), Expect = 7.2
Identities = 18/48 (37%), Positives = 22/48 (45%), Gaps = 4/48 (8%)
Query: 895 ATKYFDKYSRTMCPTLGQFVVFSSVSCGRGNAG----QTNYGMANSIM 938
ATK F + R +C G +VF V CG G G YG+ IM
Sbjct: 185 ATKEFLQGLRALCDEAGALLVFDEVQCGLGRTGYLWAHEAYGVEPDIM 232
>gnl|CDD|187600 cd05341, 3beta-17beta-HSD_like_SDR_c, 3beta17beta hydroxysteroid
dehydrogenase-like, classical (c) SDRs. This subgroup
includes members identified as 3beta17beta
hydroxysteroid dehydrogenase, 20beta hydroxysteroid
dehydrogenase, and R-alcohol dehydrogenase. These
proteins exhibit the canonical active site tetrad and
glycine rich NAD(P)-binding motif of the classical SDRs.
17beta-dehydrogenases are a group of isozymes that
catalyze activation and inactivation of estrogen and
androgens, and include members of the SDR family. 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 = 247
Score = 30.0 bits (68), Expect = 7.3
Identities = 33/109 (30%), Positives = 46/109 (42%), Gaps = 12/109 (11%)
Query: 780 SNKSYIICGGLGGFGLELADWLVLRGARKLVLTSRSGVKNGYQALRIKIWKSYDVQVLIS 839
K I+ GG G GL A LV GA K+VL+ + G A + +
Sbjct: 4 KGKVAIVTGGARGLGLAHARLLVAEGA-KVVLSDILD-EEGQAAAAELGDAARFFHL--- 58
Query: 840 TDDITTEAG---VVNLLTEANKLGPVDGIFNLAVVLKDALFENQTPEDF 885
D+T E G VV+ EA G +D + N A +L E T E++
Sbjct: 59 --DVTDEDGWTAVVDTAREA--FGRLDVLVNNAGILTGGTVETTTLEEW 103
>gnl|CDD|187644 cd08940, HBDH_SDR_c, d-3-hydroxybutyrate dehydrogenase (HBDH),
classical (c) SDRs. DHBDH, an NAD+ -dependent enzyme,
catalyzes the interconversion of D-3-hydroxybutyrate and
acetoacetate. It is a classical SDR, with the canonical
NAD-binding motif and active site tetrad. 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 = 258
Score = 30.1 bits (68), Expect = 7.4
Identities = 27/109 (24%), Positives = 50/109 (45%), Gaps = 3/109 (2%)
Query: 780 SNKSYIICGGLGGFGLELADWLVLRGARKLVLTSRSGVKNGYQALRIKIWKSYDVQVLIS 839
K ++ G G GL +A L GA ++ + G +A+R + + V+VL
Sbjct: 1 KGKVALVTGSTSGIGLGIARALAAAGAN--IVLNGFGDAAEIEAVRAGLAAKHGVKVLYH 58
Query: 840 TDDITTEAGVVNLLTEANK-LGPVDGIFNLAVVLKDALFENQTPEDFNA 887
D++ A + +++ A + G VD + N A + A E+ E ++A
Sbjct: 59 GADLSKPAAIEDMVAYAQRQFGGVDILVNNAGIQHVAPIEDFPTEKWDA 107
>gnl|CDD|239105 cd02425, Peptidase_C39F, A sub-family of peptidase family C39.
Peptidase family C39 mostly contains
bacteriocin-processing endopeptidases from bacteria. The
cysteine peptidases in family C39 cleave the
"double-glycine" leader peptides from the precursors of
various bacteriocins (mostly non-lantibiotic). The
cleavage is mediated by the transporter as part of the
secretion process. Bacteriocins are antibiotic proteins
secreted by some species of bacteria that inhibit the
growth of other bacterial species. The bacteriocin is
synthesized as a precursor with an N-terminal leader
peptide, and processing involves removal of the leader
peptide by cleavage at a Gly-Gly bond, followed by
translocation of the mature bacteriocin across the
cytoplasmic membrane. Most endopeptidases of family C39
are N-terminal domains in larger proteins (ABC
transporters) that serve both functions. The proposed
protease active site is conserved in this sub-family.
Length = 126
Score = 29.2 bits (66), Expect = 7.4
Identities = 23/86 (26%), Positives = 30/86 (34%), Gaps = 30/86 (34%)
Query: 1301 ITSILKYTDPKHKAFGGNITL--LRPTEQALPT----------AEDYGLS-KVCKKPVKV 1347
IL Y FG ++L LR + E+YG KV K K
Sbjct: 17 YAMILNY-------FGYKVSLNELREKYELGRDGLSLSYLKQLLEEYGFKCKVYKISFKK 69
Query: 1348 H----------FVDGNHFTVLDNIKS 1363
+ F + NHF VL+ IK
Sbjct: 70 NLYPLKLPVIIFWNNNHFVVLEKIKK 95
>gnl|CDD|176249 cd08289, MDR_yhfp_like, Yhfp putative quinone oxidoreductases.
yhfp putative quinone oxidoreductases (QOR). QOR
catalyzes the conversion of a quinone + NAD(P)H to a
hydroquinone + NAD(P)+. Quinones are cyclic diones
derived from aromatic compounds. Membrane bound QOR
actin the respiratory chains of bacteria and
mitochondria, while soluble QOR acts to protect from
toxic quinones (e.g. DT-diaphorase) or as a soluble
eye-lens protein in some vertebrates (e.g.
zeta-crystalin). QOR reduces quinones through a
semi-quinone intermediate via a NAD(P)H-dependent single
electron transfer. QOR is a member of the medium chain
dehydrogenase/reductase family, but lacks the
zinc-binding sites of the prototypical alcohol
dehydrogenases of this group. NAD(P)(H)-dependent
oxidoreductases are the major enzymes in the
interconversion of alcohols and aldehydes, or ketones.
Alcohol dehydrogenase in the liver converts ethanol and
NAD+ to acetaldehyde and NADH, while in yeast and some
other microorganisms ADH catalyzes the conversion
acetaldehyde to ethanol in alcoholic fermentation. ADH
is a member of the medium chain alcohol dehydrogenase
family (MDR), which has a NAD(P)(H)-binding domain in a
Rossmann fold of a beta-alpha form. The NAD(H)-binding
region is comprised of 2 structurally similar halves,
each of which contacts a mononucleotide. A GxGxxG motif
after the first mononucleotide contact half allows the
close contact of the coenzyme with the ADH backbone.
The N-terminal catalytic domain has a distant homology
to GroES. These proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and have 2 tightly bound zinc atoms per
subunit, a catalytic zinc at the active site, and a
structural zinc in a lobe of the catalytic domain.
NAD(H) binding occurs in the cleft between the catalytic
and coenzyme-binding domains at the active site, and
coenzyme binding induces a conformational closing of
this cleft. Coenzyme binding typically precedes and
contributes to substrate binding. In human ADH
catalysis, the zinc ion helps coordinate the alcohol,
followed by deprotonation of a histidine, the ribose of
NAD, a serine, then the alcohol, which allows the
transfer of a hydride to NAD+, creating NADH and a
zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 326
Score = 30.4 bits (69), Expect = 7.9
Identities = 16/79 (20%), Positives = 38/79 (48%), Gaps = 3/79 (3%)
Query: 533 EIPDQWTLEDA---ATVPCVYATAVYAMFICGQMQKGESILIHAGSGGVGQAAINLARYM 589
+P TL++A T A +++ + G + +L+ +GGVG A+++ +
Sbjct: 111 PLPKGLTLKEAMILGTAGFTAALSIHRLEENGLTPEQGPVLVTGATGGVGSLAVSILAKL 170
Query: 590 DAEIFTTVGTPEKREFIRK 608
E+ + G + ++++K
Sbjct: 171 GYEVVASTGKADAADYLKK 189
>gnl|CDD|235589 PRK05749, PRK05749, 3-deoxy-D-manno-octulosonic-acid transferase;
Reviewed.
Length = 425
Score = 30.2 bits (69), Expect = 7.9
Identities = 19/52 (36%), Positives = 21/52 (40%), Gaps = 5/52 (9%)
Query: 569 ILIHAGSGGVGQAAINL-----ARYMDAEIFTTVGTPEKREFIRKTFPFIKE 615
I HA S G +AAI L RY D I T TP E + F E
Sbjct: 53 IWFHAVSVGETRAAIPLIRALRKRYPDLPILVTTMTPTGSERAQALFGDDVE 104
>gnl|CDD|187584 cd05323, ADH_SDR_c_like, insect type alcohol dehydrogenase
(ADH)-like, classical (c) SDRs. This subgroup contains
insect type ADH, and 15-hydroxyprostaglandin
dehydrogenase (15-PGDH) type I; these proteins are
classical SDRs. ADH catalyzes the NAD+-dependent
oxidation of alcohols to aldehydes/ketones. This
subgroup is distinct from the zinc-dependent alcohol
dehydrogenases of the medium chain
dehydrogenase/reductase family, and evolved in fruit
flies to allow the digestion of fermenting fruit.
15-PGDH catalyzes the NAD-dependent interconversion of
(5Z,13E)-(15S)-11alpha,15-dihydroxy-9-oxoprost-13-enoate
and (5Z,13E)-11alpha-hydroxy-9,15-dioxoprost-13-enoate,
and has a typical SDR glycine-rich NAD-binding motif,
which is not fully present in ADH. 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 = 244
Score = 30.0 bits (68), Expect = 8.0
Identities = 27/106 (25%), Positives = 42/106 (39%), Gaps = 5/106 (4%)
Query: 782 KSYIICGGLGGFGLELADWLVLRGARKLVLTSRSGVKNGYQALRIKIWKSYDVQVLISTD 841
K II GG G GL A L+ +GA K+ + R+ L+ K V+
Sbjct: 1 KVAIITGGASGIGLATAKLLLKKGA-KVAILDRNENPGAAAELQAINPK---VKATFVQC 56
Query: 842 DITTEAGVVNLLTEA-NKLGPVDGIFNLAVVLKDALFENQTPEDFN 886
D+T+ + +A K G VD + N A +L + +
Sbjct: 57 DVTSWEQLAAAFKKAIEKFGRVDILINNAGILDEKSYLFAGKLPPP 102
>gnl|CDD|130890 TIGR01831, fabG_rel, 3-oxoacyl-(acyl-carrier-protein) reductase,
putative. This model represents a small, very well
conserved family of proteins closely related to the FabG
family, TIGR01830, and possibly equal in function. In
all completed genomes with a member of this family, a
FabG in TIGR01830 is also found [Fatty acid and
phospholipid metabolism, Biosynthesis].
Length = 239
Score = 29.9 bits (67), Expect = 9.2
Identities = 20/78 (25%), Positives = 35/78 (44%), Gaps = 7/78 (8%)
Query: 864 GIFNLAVVLKDALFENQTPEDFNASLGPKANATKYFDKYSRTMCPTL-----GQFVVFSS 918
G+ A + +DA F + ED++ + N +++ P + G+ + +S
Sbjct: 79 GVVLNAGITRDAAFPALSEEDWDIVI--HTNLDGFYNVIHPCTMPMIRARQGGRIITLAS 136
Query: 919 VSCGRGNAGQTNYGMANS 936
VS GN GQ NY A +
Sbjct: 137 VSGVMGNRGQVNYSAAKA 154
>gnl|CDD|181553 PRK08775, PRK08775, homoserine O-acetyltransferase; Provisional.
Length = 343
Score = 30.1 bits (68), Expect = 9.4
Identities = 17/62 (27%), Positives = 27/62 (43%), Gaps = 12/62 (19%)
Query: 1183 QVLVFQF---DHTNP-PDTIPEMADS---LLPHFKKRLVHGTDEIKLVGFSFGGMVALEL 1235
++L F F D + P + AD+ LL +H VG+S+G +V L+
Sbjct: 101 RLLAFDFIGADGSLDVPIDTADQADAIALLLDALGIARLHA-----FVGYSYGALVGLQF 155
Query: 1236 AI 1237
A
Sbjct: 156 AS 157
>gnl|CDD|215378 PLN02702, PLN02702, L-idonate 5-dehydrogenase.
Length = 364
Score = 30.1 bits (68), Expect = 9.6
Identities = 58/242 (23%), Positives = 105/242 (43%), Gaps = 26/242 (10%)
Query: 519 SLANCCETDVEMAWEIPDQWTLEDAATVPCVYATAVYAMFICGQMQKG-ESILIHAGSGG 577
SLAN ++ +++P+ +LE+ A + + V+A C + G E+ ++ G+G
Sbjct: 137 SLANQVVHPADLCFKLPENVSLEEGAMCEPL-SVGVHA---CRRANIGPETNVLVMGAGP 192
Query: 578 VGQAAINLARYMDAEIFTTVGTPEKREFIRKTFPFIKEENI---GNSRDTSFEQLVMKRT 634
+G + AR A V ++R + K +E + N D E +++
Sbjct: 193 IGLVTMLAARAFGAPRIVIVDVDDERLSVAKQLG--ADEIVLVSTNIEDVESEVEEIQKA 250
Query: 635 KGRGVDLVLNSLAEEK-LQASVRCLAQGGRFLEIGKFDLANNNM-LGME-VFMRETSFHG 691
G G+D+ + + K + ++ GG+ +G + +N M + + RE G
Sbjct: 251 MGGGIDVSFDCVGFNKTMSTALEATRAGGKVCLVG---MGHNEMTVPLTPAAAREVDVVG 307
Query: 692 VMLDNFFFAEQEWKMSLQKALQKAIDAGAVQPLV--RTIFPEDKVEEAFRYMAAGKHIGK 749
V F W + L+ ID V+PL+ R F + +VEEAF A G + K
Sbjct: 308 V-----FRYRNTWPLCLEFLRSGKID---VKPLITHRFGFSQKEVEEAFETSARGGNAIK 359
Query: 750 VI 751
V+
Sbjct: 360 VM 361
>gnl|CDD|181335 PRK08264, PRK08264, short chain dehydrogenase; Validated.
Length = 238
Score = 29.5 bits (67), Expect = 9.7
Identities = 10/34 (29%), Positives = 16/34 (47%)
Query: 781 NKSYIICGGLGGFGLELADWLVLRGARKLVLTSR 814
K ++ G G G + L+ RGA K+ +R
Sbjct: 6 GKVVLVTGANRGIGRAFVEQLLARGAAKVYAAAR 39
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
0.319 0.136 0.393
Gapped
Lambda K H
0.267 0.0902 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 71,322,567
Number of extensions: 7250897
Number of successful extensions: 6263
Number of sequences better than 10.0: 1
Number of HSP's gapped: 6079
Number of HSP's successfully gapped: 197
Length of query: 1392
Length of database: 10,937,602
Length adjustment: 109
Effective length of query: 1283
Effective length of database: 6,103,016
Effective search space: 7830169528
Effective search space used: 7830169528
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 65 (28.5 bits)