RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17241
(93 letters)
>gnl|CDD|219687 pfam07993, NAD_binding_4, Male sterility protein. This family
represents the C-terminal region of the male sterility
protein in a number of arabidopsis and drosophila. A
sequence-related jojoba acyl CoA reductase is also
included.
Length = 245
Score = 86.5 bits (215), Expect = 2e-22
Identities = 30/78 (38%), Positives = 43/78 (55%), Gaps = 5/78 (6%)
Query: 10 IFDKLKQEQPGFLSKVTIICGDCSKKKLGISDENLKLLQTNVNVIFHTAAIVNFEASLAQ 69
+FD+LK L ++ + GD S+ LG+SDE+ + L V+VI H AA VNF +
Sbjct: 50 LFDRLKA-----LERIIPVAGDLSEPNLGLSDEDFQELAEEVDVIIHNAATVNFVEPYSD 104
Query: 70 AVLSNVCATKEFLELATS 87
+NV T+E L LA
Sbjct: 105 LRATNVLGTREVLRLAKQ 122
>gnl|CDD|187547 cd05236, FAR-N_SDR_e, fatty acyl CoA reductases (FARs), extended
(e) SDRs. SDRs are Rossmann-fold NAD(P)H-binding
proteins, many of which may function as fatty acyl CoA
reductases (FAR), acting on medium and long chain fatty
acids, and have been reported to be involved in diverse
processes such as biosynthesis of insect pheromones,
plant cuticular wax production, and mammalian wax
biosynthesis. In Arabidopsis thaliana, proteins with
this particular architecture have also been identified
as the MALE STERILITY 2 (MS2) gene product, which is
implicated in male gametogenesis. Mutations in MS2
inhibit the synthesis of exine (sporopollenin),
rendering plants unable to reduce pollen wall fatty
acids to corresponding alcohols. This N-terminal domain
shares the catalytic triad (but not the upstream Asn)
and characteristic NADP-binding motif of the extended
SDR family. 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 = 320
Score = 81.2 bits (201), Expect = 5e-20
Identities = 34/75 (45%), Positives = 45/75 (60%)
Query: 11 FDKLKQEQPGFLSKVTIICGDCSKKKLGISDENLKLLQTNVNVIFHTAAIVNFEASLAQA 70
FD+ + P F SK+ I GD S+ LG+SDE+L+ L VN+I H AA V F+ L +A
Sbjct: 55 FDRGRNLNPLFESKIVPIEGDLSEPNLGLSDEDLQTLIEEVNIIIHCAATVTFDERLDEA 114
Query: 71 VLSNVCATKEFLELA 85
+ NV T LELA
Sbjct: 115 LSINVLGTLRLLELA 129
>gnl|CDD|187546 cd05235, SDR_e1, extended (e) SDRs, subgroup 1. This family
consists of an SDR module of multidomain proteins
identified as putative polyketide sythases fatty acid
synthases (FAS), and nonribosomal peptide synthases,
among others. However, unlike the usual ketoreductase
modules of FAS and polyketide synthase, these domains
are related to the extended SDRs, and have canonical
NAD(P)-binding motifs and an active site tetrad.
Extended SDRs are distinct from classical SDRs. In
addition to the Rossmann fold (alpha/beta folding
pattern with a central beta-sheet) core region typical
of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 290
Score = 60.4 bits (147), Expect = 2e-12
Identities = 28/80 (35%), Positives = 43/80 (53%)
Query: 8 NMIFDKLKQEQPGFLSKVTIICGDCSKKKLGISDENLKLLQTNVNVIFHTAAIVNFEASL 67
N+ L LS++ ++ GD SK LG+SD++ + L V+VI H A VN+
Sbjct: 47 NLKEYGLNLWDELELSRIKVVVGDLSKPNLGLSDDDYQELAEEVDVIIHNGANVNWVYPY 106
Query: 68 AQAVLSNVCATKEFLELATS 87
+ +NV TKE L+LA +
Sbjct: 107 EELKPANVLGTKELLKLAAT 126
>gnl|CDD|233557 TIGR01746, Thioester-redct, thioester reductase domain. This model
includes the terminal domain from the fungal alpha
aminoadipate reductase enzyme (also known as
aminoadipate semialdehyde dehydrogenase) which is
involved in the biosynthesis of lysine , as well as the
reductase-containing component of the myxochelin
biosynthetic gene cluster, MxcG. The mechanism of
reduction involves activation of the substrate by
adenylation and transfer to a covalently-linked
pantetheine cofactor as a thioester. This thioester is
then reduced to give an aldehyde (thus releasing the
product) and a regenerated pantetheine thiol. (In
myxochelin biosynthesis this aldehyde is further reduced
to an alcohol or converted to an amine by an
aminotransferase.) This is a fundamentally different
reaction than beta-ketoreductase domains of polyketide
synthases which act at a carbonyl two carbons removed
from the thioester and forms an alcohol as a product.
This domain is invariably found at the C-terminus of the
proteins which contain it (presumably because it results
in the release of the product). The majority of hits to
this model are non-ribosomal peptide synthetases in
which this domain is similarly located proximal to a
thiolation domain (pfam00550). In some cases this domain
is found at the end of a polyketide synthetase enzyme,
but is unlike ketoreductase domains which are found
before the thiolase domains. Exceptions to this observed
relationship with the thiolase domain include three
proteins which consist of stand-alone reductase domains
(GP|466833 from M. leprae, GP|435954 from Anabaena and
OMNI|NTL02SC1199 from Strep. coelicolor) and one protein
(OMNI|NTL01NS2636 from Nostoc) which contains N-terminal
homology with a small group of hypothetical proteins but
no evidence of a thiolation domain next to the putative
reductase domain. Below the noise cutoff to this model
are proteins containing more distantly related
ketoreductase and dehydratase/epimerase domains. It has
been suggested that a NADP-binding motif can be found in
the N-terminal portion of this domain that may form a
Rossman-type fold.
Length = 367
Score = 54.3 bits (131), Expect = 4e-10
Identities = 23/65 (35%), Positives = 38/65 (58%)
Query: 23 SKVTIICGDCSKKKLGISDENLKLLQTNVNVIFHTAAIVNFEASLAQAVLSNVCATKEFL 82
++ ++ GD S+ +LG+SD + L NV+ I H A+VN+ ++ +NV T+E L
Sbjct: 61 ERIEVVAGDLSEPRLGLSDAEWERLAENVDTIVHNGALVNWVYPYSELRGANVLGTREVL 120
Query: 83 ELATS 87
LA S
Sbjct: 121 RLAAS 125
>gnl|CDD|187573 cd05263, MupV_like_SDR_e, Pseudomonas fluorescens MupV-like,
extended (e) SDRs. This subgroup of extended SDR family
domains have the characteristic active site tetrad and a
well-conserved NAD(P)-binding motif. This subgroup is
not well characterized, its members are annotated as
having a variety of putative functions. One
characterized member is Pseudomonas fluorescens MupV a
protein involved in the biosynthesis of Mupirocin, a
polyketide-derived antibiotic. 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 = 293
Score = 50.4 bits (121), Expect = 7e-09
Identities = 21/75 (28%), Positives = 37/75 (49%)
Query: 13 KLKQEQPGFLSKVTIICGDCSKKKLGISDENLKLLQTNVNVIFHTAAIVNFEASLAQAVL 72
+ +E +V ++ GD ++ LG+S + L V+ + H AA +F+A A
Sbjct: 39 ERIEEAGLEADRVRVLEGDLTQPNLGLSAAASRELAGKVDHVIHCAASYDFQAPNEDAWR 98
Query: 73 SNVCATKEFLELATS 87
+N+ T+ LELA
Sbjct: 99 TNIDGTEHVLELAAR 113
>gnl|CDD|234212 TIGR03443, alpha_am_amid, L-aminoadipate-semialdehyde dehydrogenase.
Members of this protein family are
L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31),
product of the LYS2 gene. It is also called
alpha-aminoadipate reductase. In fungi, lysine is
synthesized via aminoadipate. Currently, all members of
this family are fungal.
Length = 1389
Score = 45.8 bits (109), Expect = 3e-07
Identities = 22/67 (32%), Positives = 36/67 (53%)
Query: 21 FLSKVTIICGDCSKKKLGISDENLKLLQTNVNVIFHTAAIVNFEASLAQAVLSNVCATKE 80
+ S++ ++ GD SK+K G+SDE L V+VI H A+V++ ++ +NV T
Sbjct: 1032 WASRIEVVLGDLSKEKFGLSDEKWSDLTNEVDVIIHNGALVHWVYPYSKLRDANVIGTIN 1091
Query: 81 FLELATS 87
L L
Sbjct: 1092 VLNLCAE 1098
>gnl|CDD|225857 COG3320, COG3320, Putative dehydrogenase domain of multifunctional
non-ribosomal peptide synthetases and related enzymes
[Secondary metabolites biosynthesis, transport, and
catabolism].
Length = 382
Score = 45.1 bits (107), Expect = 5e-07
Identities = 22/63 (34%), Positives = 36/63 (57%)
Query: 23 SKVTIICGDCSKKKLGISDENLKLLQTNVNVIFHTAAIVNFEASLAQAVLSNVCATKEFL 82
+V ++ GD ++ LG+S+ + L NV++I H AA+VN ++ +NV T E L
Sbjct: 60 DRVEVVAGDLAEPDLGLSERTWQELAENVDLIIHNAALVNHVFPYSELRGANVLGTAEVL 119
Query: 83 ELA 85
LA
Sbjct: 120 RLA 122
>gnl|CDD|235962 PRK07201, PRK07201, short chain dehydrogenase; Provisional.
Length = 657
Score = 41.9 bits (99), Expect = 7e-06
Identities = 18/62 (29%), Positives = 34/62 (54%), Gaps = 1/62 (1%)
Query: 24 KVTIICGDCSKKKLGISDENLKLLQTNVNVIFHTAAIVNFEASLAQAVLSNVCATKEFLE 83
+V + GD ++ LG+S+ ++ L +++ + H AAI + A +NV T+ +E
Sbjct: 52 RVVPLVGDLTEPGLGLSEADIAEL-GDIDHVVHLAAIYDLTADEEAQRAANVDGTRNVVE 110
Query: 84 LA 85
LA
Sbjct: 111 LA 112
>gnl|CDD|215538 PLN02996, PLN02996, fatty acyl-CoA reductase.
Length = 491
Score = 34.3 bits (79), Expect = 0.004
Identities = 16/46 (34%), Positives = 27/46 (58%), Gaps = 2/46 (4%)
Query: 21 FLS-KVTIICGDCSKKKLGISDENLK-LLQTNVNVIFHTAAIVNFE 64
+S KVT + GD S LG+ D NL+ + ++++ + AA NF+
Sbjct: 81 LISEKVTPVPGDISYDDLGVKDSNLREEMWKEIDIVVNLAATTNFD 126
>gnl|CDD|212494 cd08946, SDR_e, extended (e) SDRs. Extended SDRs are distinct
from classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids. Extended SDRs are a diverse collection
of proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and
their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 200
Score = 31.9 bits (73), Expect = 0.027
Identities = 14/44 (31%), Positives = 18/44 (40%), Gaps = 3/44 (6%)
Query: 49 TNVNVIFHTAAIVNFEASLAQAVLS---NVCATKEFLELATSFG 89
++V+ H AA+V AS NV T LE A G
Sbjct: 29 DRLDVVVHLAALVGVPASWDNPDEDFETNVVGTLNLLEAARKAG 72
>gnl|CDD|223528 COG0451, WcaG, Nucleoside-diphosphate-sugar epimerases [Cell
envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 314
Score = 31.1 bits (70), Expect = 0.061
Identities = 20/82 (24%), Positives = 32/82 (39%), Gaps = 13/82 (15%)
Query: 10 IFDKLKQEQPGFLSKVTIICGDCSKKKLGISDENL--KLLQTNVNVIFHTAAIVNFEASL 67
D+L+ LS V + D ++D +L +L + + + H AA + S
Sbjct: 29 GLDRLRDGLDPLLSGVEFVVLD-------LTDRDLVDELAKGVPDAVIHLAAQSSVPDSN 81
Query: 68 AQA----VLSNVCATKEFLELA 85
A + NV T LE A
Sbjct: 82 ASDPAEFLDVNVDGTLNLLEAA 103
>gnl|CDD|187671 cd09811, 3b-HSD_HSDB1_like_SDR_e, human 3beta-HSD (hydroxysteroid
dehydrogenase) and HSD3B1(delta 5-delta
4-isomerase)-like, extended (e) SDRs. This extended-SDR
subgroup includes human 3 beta-HSD/HSD3B1 and C(27)
3beta-HSD/ [3beta-hydroxy-delta(5)-C(27)-steroid
oxidoreductase; HSD3B7], and related proteins. These
proteins have the characteristic active site tetrad and
NAD(P)-binding motif of extended SDRs. 3 beta-HSD
catalyzes the oxidative conversion of delta 5-3
beta-hydroxysteroids to the delta 4-3-keto
configuration; this activity is essential for the
biosynthesis of all classes of hormonal steroids. C(27)
3beta-HSD is a membrane-bound enzyme of the endoplasmic
reticulum, it catalyzes the isomerization and oxidation
of 7alpha-hydroxylated sterol intermediates, an early
step in bile acid biosynthesis. Mutations in the human
gene encoding C(27) 3beta-HSD underlie a rare autosomal
recessive form of neonatal cholestasis. 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 sythase 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 = 354
Score = 28.6 bits (64), Expect = 0.36
Identities = 26/85 (30%), Positives = 34/85 (40%), Gaps = 13/85 (15%)
Query: 3 IATGANMIFDKLKQEQPGFLSKVTIICGDCSKKKLGISDEN-LKLLQTNVNVIFHTAAIV 61
A G +I K + + VT I GD I D + L V+V+ HTAAIV
Sbjct: 34 KAFGPELIEHFEKSQGK---TYVTDIEGD-------IKDLSFLFRACQGVSVVIHTAAIV 83
Query: 62 NFEASLAQAVLS--NVCATKEFLEL 84
+ L NV T+ LE
Sbjct: 84 DVFGPPNYEELEEVNVNGTQAVLEA 108
>gnl|CDD|234359 TIGR03802, Asp_Ala_antiprt, aspartate-alanine antiporter. All
members of the seed alignment for this model are
asparate-alanine anti-transporters (AspT) encoded next
to the gene for aspartate 4-decarboxylase (AspD), which
converts asparate to alanine, releasing CO2. The
exchange of Asp for Ala is electrogenic, so the
AspD/AspT system confers a proton-motive force. This
transporter contains two copies of the AspT/YidE/YbjL
antiporter duplication domain (TIGR01625).
Length = 562
Score = 28.0 bits (63), Expect = 0.61
Identities = 12/43 (27%), Positives = 19/43 (44%), Gaps = 6/43 (13%)
Query: 36 KLGISDENLKLLQTNVNV------IFHTAAIVNFEASLAQAVL 72
KLG+S E Q NV V IF T ++ ++ ++
Sbjct: 142 KLGLSPEQKTAYQGNVAVAYAVTYIFGTIGVIIVLVNILPWLM 184
>gnl|CDD|187539 cd05228, AR_FR_like_1_SDR_e, uncharacterized subgroup of aldehyde
reductase and flavonoid reductase related proteins,
extended (e) SDRs. This subgroup contains proteins of
unknown function related to aldehyde reductase and
flavonoid reductase of the extended SDR-type. Aldehyde
reductase I (aka carbonyl reductase) is an NADP-binding
SDR; it has an NADP-binding motif consensus that is
slightly different from the canonical SDR form and
lacks the Asn of the extended SDR active site tetrad.
Aldehyde reductase I catalyzes the NADP-dependent
reduction of ethyl 4-chloro-3-oxobutanoate to ethyl
(R)-4-chloro-3-hydroxybutanoate. The related flavonoid
reductases act in the NADP-dependent reduction of
flavonoids, ketone-containing plant secondary
metabolites. 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 = 318
Score = 27.6 bits (62), Expect = 0.75
Identities = 10/37 (27%), Positives = 17/37 (45%), Gaps = 1/37 (2%)
Query: 50 NVNVIFHTAAIVNFEASLAQAVLS-NVCATKEFLELA 85
+ +FH AA + A + + NV T+ L+ A
Sbjct: 62 GCDRVFHLAAFTSLWAKDRKELYRTNVEGTRNVLDAA 98
>gnl|CDD|129627 TIGR00536, hemK_fam, HemK family putative methylases. The gene
hemK from E. coli was found to contribute to heme
biosynthesis and originally suggested to be
protoporphyrinogen oxidase (Medline 95189105).
Functional analysis of the nearest homolog in
Saccharomyces cerevisiae, YNL063w, finds it is not
protoporphyrinogen oxidase and sequence analysis
suggests that HemK homologs have
S-adenosyl-methionine-dependent methyltransferase
activity (Medline 99237242). Homologs are found, usually
in a single copy, in nearly all completed genomes, but
varying somewhat in apparent domain architecture. Both
E. coli and H. influenzae have two members rather than
one. The members from the Mycoplasmas have an additional
C-terminal domain [Protein fate, Protein modification
and repair].
Length = 284
Score = 27.3 bits (61), Expect = 1.0
Identities = 9/31 (29%), Positives = 14/31 (45%)
Query: 26 TIICGDCSKKKLGISDENLKLLQTNVNVIFH 56
+I D S L +++EN + Q V F
Sbjct: 140 EVIAVDISPDALAVAEENAEKNQLEHRVEFI 170
>gnl|CDD|187549 cd05238, Gne_like_SDR_e, Escherichia coli Gne (a
nucleoside-diphosphate-sugar 4-epimerase)-like, extended
(e) SDRs. Nucleoside-diphosphate-sugar 4-epimerase has
the characteristic active site tetrad and NAD-binding
motif of the extended SDR, and is related to more
specifically defined epimerases such as UDP-glucose 4
epimerase (aka UDP-galactose-4-epimerase), which
catalyzes the NAD-dependent conversion of UDP-galactose
to UDP-glucose, the final step in Leloir galactose
synthesis. This subgroup includes Escherichia coli
055:H7 Gne, a UDP-GlcNAc 4-epimerase, essential for O55
antigen synthesis. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately 100
amino acids. Extended SDRs are a diverse collection of
proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 305
Score = 26.6 bits (59), Expect = 1.6
Identities = 25/76 (32%), Positives = 33/76 (43%), Gaps = 11/76 (14%)
Query: 12 DKLKQEQPGFLSKVTIICGDCSKKKLGISDENLKLLQTNVNVIFHTAAIVNFEA----SL 67
D + + P +VT I GD + L E L +V+FH AAIV+ A L
Sbjct: 33 DVVSPKAPSGAPRVTQIAGDLAVPAL---IE--ALANGRPDVVFHLAAIVSGGAEADFDL 87
Query: 68 AQAVLSNVCATKEFLE 83
V NV T+ LE
Sbjct: 88 GYRV--NVDGTRNLLE 101
>gnl|CDD|181958 PRK09564, PRK09564, coenzyme A disulfide reductase; Reviewed.
Length = 444
Score = 26.9 bits (60), Expect = 1.7
Identities = 15/60 (25%), Positives = 24/60 (40%), Gaps = 7/60 (11%)
Query: 3 IATGAN----MIFDKL---KQEQPGFLSKVTIICGDCSKKKLGISDENLKLLQTNVNVIF 55
+AT AN M+ + L G L I D + G+++E K L + +F
Sbjct: 299 LATTANKLGRMVGENLAGRHVSFKGTLGSACIKVLDLEAARTGLTEEEAKKLGIDYKTVF 358
>gnl|CDD|132852 cd07213, Pat17_PNPLA8_PNPLA9_like1, Patatin-like phospholipase.
Patatin is a storage protein of the potato tuber that
shows Phospholipase A2 activity (PLA2; EC 3.1.1.4).
Patatin catalyzes the nonspecific hydrolysis of
phospholipids, glycolipids, sulfolipids, and mono- and
diacylglycerols, thereby showing lipid acyl hydrolase
activity. The active site includes an oxyanion hole
with a conserved GGxR motif; it is found in almost all
the members of this family. The catalytic dyad is
formed by a serine and an aspartate. Patatin belongs to
the alpha-beta hydrolase family which is identified by
a characteristic nucleophile elbow with a consensus
sequence of Sm-X-Nu-Sm (Sm = small residue, X = any
residue and Nu = nucleophile). Members of this family
have been found also in vertebrates. This family
includes subfamily of PNPLA8 (iPLA2-gamma) and PNPLA9
(iPLA2-beta) like phospholipases from human as well as
the Pat17 isozyme from Solanum cardiophyllum.
Length = 288
Score = 26.5 bits (59), Expect = 2.1
Identities = 6/21 (28%), Positives = 12/21 (57%)
Query: 10 IFDKLKQEQPGFLSKVTIICG 30
+ +L +E P FL ++ + G
Sbjct: 20 LLKRLAEEFPSFLDQIDLFAG 40
>gnl|CDD|187543 cd05232, UDP_G4E_4_SDR_e, UDP-glucose 4 epimerase, subgroup 4,
extended (e) SDRs. UDP-glucose 4 epimerase (aka
UDP-galactose-4-epimerase), is a homodimeric extended
SDR. It catalyzes the NAD-dependent conversion of
UDP-galactose to UDP-glucose, the final step in Leloir
galactose synthesis. This subgroup is comprised of
bacterial proteins, and includes the Staphylococcus
aureus capsular polysaccharide Cap5N, which may have a
role in the synthesis of UDP-N-acetyl-d-fucosamine.
This subgroup has the characteristic active site tetrad
and NAD-binding motif of the extended SDRs. Extended
SDRs are distinct from classical SDRs. In addition to
the Rossmann fold (alpha/beta folding pattern with a
central beta-sheet) core region typical of all SDRs,
extended SDRs have a less conserved C-terminal
extension of approximately 100 amino acids. Extended
SDRs are a diverse collection of proteins, and include
isomerases, epimerases, oxidoreductases, and lyases;
they typically have a TGXXGXXG cofactor binding motif.
SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving
as a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton
relay involving the conserved Tyr and Lys, a water
molecule stabilized by Asn, and nicotinamide. Atypical
SDRs generally lack the catalytic residues
characteristic of the SDRs, and their glycine-rich
NAD(P)-binding motif is often different from the forms
normally seen in classical or extended SDRs. Complex
(multidomain) SDRs such as ketoreductase domains of
fatty acid synthase have a GGXGXXG NAD(P)-binding motif
and an altered active site motif (YXXXN). Fungal type
ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding
motif.
Length = 303
Score = 25.8 bits (57), Expect = 4.2
Identities = 10/41 (24%), Positives = 14/41 (34%), Gaps = 5/41 (12%)
Query: 50 NVNVIFHTAAIVNFEASLAQAVLS-----NVCATKEFLELA 85
V+ + H AA V+ LS N T+ A
Sbjct: 57 GVDAVVHLAARVHVMNDQGADPLSDYRKVNTELTRRLARAA 97
>gnl|CDD|187566 cd05256, UDP_AE_SDR_e, UDP-N-acetylglucosamine 4-epimerase,
extended (e) SDRs. This subgroup contains
UDP-N-acetylglucosamine 4-epimerase of Pseudomonas
aeruginosa, WbpP, an extended SDR, that catalyzes the
NAD+ dependent conversion of UDP-GlcNAc and UDPGalNA to
UDP-Glc and UDP-Gal. This subgroup has the
characteristic active site tetrad and NAD-binding motif
of the extended SDRs. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately 100
amino acids. Extended SDRs are a diverse collection of
proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 304
Score = 25.6 bits (57), Expect = 4.4
Identities = 21/75 (28%), Positives = 28/75 (37%), Gaps = 11/75 (14%)
Query: 19 PGFLSKVTIICGDCSKKKLGISD-ENLKLLQTNVNVIFHTAAIVNFEASLAQAVLS---N 74
P V I GD I D E ++ V+ +FH AA + S+ + N
Sbjct: 41 PEVKPNVKFIEGD-------IRDDELVEFAFEGVDYVFHQAAQASVPRSIEDPIKDHEVN 93
Query: 75 VCATKEFLELATSFG 89
V T LE A G
Sbjct: 94 VLGTLNLLEAARKAG 108
>gnl|CDD|172522 PRK14028, PRK14028, pyruvate ferredoxin oxidoreductase subunit
gamma/delta; Provisional.
Length = 312
Score = 25.7 bits (56), Expect = 4.4
Identities = 12/23 (52%), Positives = 14/23 (60%)
Query: 63 FEASLAQAVLSNVCATKEFLELA 85
FE L +AV N ATKE E+A
Sbjct: 159 FETQLGKAVEENFAATKEAYEVA 181
>gnl|CDD|218765 pfam05820, DUF845, Baculovirus protein of unknown function
(DUF845). This family consists of several highly
related Baculovirus proteins of unknown function.
Length = 119
Score = 24.9 bits (55), Expect = 4.6
Identities = 13/39 (33%), Positives = 20/39 (51%), Gaps = 8/39 (20%)
Query: 20 GFLSKVTIICGDCSKKKLG--ISDENLKLLQTNVNVIFH 56
G L KV ++C +C KK+L + EN + N+ F
Sbjct: 78 GTLIKVLVLCDECCKKELRDFVEGEN------SFNIAFK 110
>gnl|CDD|227898 COG5611, COG5611, Predicted nucleic-acid-binding protein,
contains PIN domain [General function prediction only].
Length = 130
Score = 24.9 bits (54), Expect = 5.9
Identities = 7/27 (25%), Positives = 15/27 (55%)
Query: 2 RIATGANMIFDKLKQEQPGFLSKVTII 28
++ T A F++L Q+ F+ + +I
Sbjct: 18 KVQTKAEQFFEELSQKGKLFIPEEVLI 44
>gnl|CDD|215279 PLN02503, PLN02503, fatty acyl-CoA reductase 2.
Length = 605
Score = 25.2 bits (55), Expect = 6.3
Identities = 19/88 (21%), Positives = 37/88 (42%), Gaps = 5/88 (5%)
Query: 10 IFDKLKQE-----QPGFLSKVTIICGDCSKKKLGISDENLKLLQTNVNVIFHTAAIVNFE 64
+F L++ Q LSK+ + G+ + LG+ + + V+VI ++AA F+
Sbjct: 174 LFKCLQETHGKSYQSFMLSKLVPVVGNVCESNLGLEPDLADEIAKEVDVIINSAANTTFD 233
Query: 65 ASLAQAVLSNVCATKEFLELATSFGELE 92
A+ N + A +L+
Sbjct: 234 ERYDVAIDINTRGPCHLMSFAKKCKKLK 261
>gnl|CDD|148159 pfam06385, Baculo_LEF-11, Baculovirus LEF-11 protein. This
family consists of several Baculovirus LEF-11 proteins.
The exact function of this family is unknown although
it has been shown that LEF-11 is required for viral DNA
replication during the infection cycle.
Length = 95
Score = 24.5 bits (54), Expect = 7.2
Identities = 10/16 (62%), Positives = 12/16 (75%)
Query: 22 LSKVTIICGDCSKKKL 37
L K II GDCSKK++
Sbjct: 47 LDKAFIIVGDCSKKRV 62
>gnl|CDD|216283 pfam01073, 3Beta_HSD, 3-beta hydroxysteroid
dehydrogenase/isomerase family. The enzyme 3
beta-hydroxysteroid dehydrogenase/5-ene-4-ene isomerase
(3 beta-HSD) catalyzes the oxidation and isomerisation
of 5-ene-3 beta-hydroxypregnene and
5-ene-hydroxyandrostene steroid precursors into the
corresponding 4-ene-ketosteroids necessary for the
formation of all classes of steroid hormones.
Length = 280
Score = 24.6 bits (54), Expect = 8.3
Identities = 13/38 (34%), Positives = 19/38 (50%), Gaps = 8/38 (21%)
Query: 25 VTIICGD-CSKKKLGISDENLKLLQTNVNVIFHTAAIV 61
+T I GD K+ L L+ +V+ HTAAI+
Sbjct: 47 ITYIEGDVTDKQDL---RRALQ----GSDVVIHTAAII 77
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 0.133 0.365
Gapped
Lambda K H
0.267 0.0778 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,390,858
Number of extensions: 340102
Number of successful extensions: 291
Number of sequences better than 10.0: 1
Number of HSP's gapped: 289
Number of HSP's successfully gapped: 34
Length of query: 93
Length of database: 10,937,602
Length adjustment: 60
Effective length of query: 33
Effective length of database: 8,276,362
Effective search space: 273119946
Effective search space used: 273119946
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 (21.8 bits)
S2: 53 (24.1 bits)