RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5955
(134 letters)
>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 = 40.5 bits (95), Expect = 9e-05
Identities = 19/62 (30%), Positives = 33/62 (53%), Gaps = 3/62 (4%)
Query: 3 CVKQEPGGLGARCVFITDAK--QPPFSPSSPTYAPLLAK-DLLYNVYRAGTWGSMRHILL 59
++EP RC+F+++ + P + Y + K + NVY++G+WG RH+LL
Sbjct: 145 YFREEPQLKLIRCLFVSNLNSQKEPIIRNGKVYYERVKKNSNIKNVYKSGSWGDFRHLLL 204
Query: 60 DT 61
D
Sbjct: 205 DL 206
>gnl|CDD|219059 pfam06491, Disulph_isomer, Disulphide isomerase. This family of
proteins has disulphide isomerase activity, EC:5.3.4.1.
It has a similar fold to thioredoxin, with an
alpha-beta-alpha-beta-alpha-beta-beta-alpha topology. It
has a conserved CGC motif in the loop immediately
downstream of the first beta strand. This motif is
essential for activity.
Length = 136
Score = 25.3 bits (56), Expect = 9.1
Identities = 8/24 (33%), Positives = 14/24 (58%)
Query: 24 PPFSPSSPTYAPLLAKDLLYNVYR 47
+ PSSP+ A L +L++ + R
Sbjct: 90 EGYPPSSPSMALLKDGELVHMIER 113
>gnl|CDD|220028 pfam08811, DUF1800, Protein of unknown function (DUF1800). This is
a family of large bacterial proteins of unknown
function.
Length = 463
Score = 25.7 bits (57), Expect = 9.4
Identities = 9/20 (45%), Positives = 10/20 (50%)
Query: 23 QPPFSPSSPTYAPLLAKDLL 42
QPPF P SP P A +
Sbjct: 356 QPPFRPPSPDGYPDGAAGWV 375
>gnl|CDD|238724 cd01447, Polysulfide_ST, Polysulfide-sulfurtransferase -
Rhodanese Homology Domain. This domain is believed to
serve as a polysulfide binding and transferase domain
in anaerobic gram-negative bacteria, functioning in
oxidative phosphorylation with polysulfide-sulfur as a
terminal electron acceptor. The active site contains
the same conserved cysteine that is the catalytic
residue in other Rhodanese Homology Domain proteins.
Length = 103
Score = 25.1 bits (55), Expect = 9.6
Identities = 10/26 (38%), Positives = 13/26 (50%)
Query: 28 PSSPTYAPLLAKDLLYNVYRAGTWGS 53
P SP + P A+D + Y A W S
Sbjct: 49 PDSPYHKPAFAEDKPFVFYCASGWRS 74
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
0.320 0.137 0.428
Gapped
Lambda K H
0.267 0.0775 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,782,408
Number of extensions: 580244
Number of successful extensions: 426
Number of sequences better than 10.0: 1
Number of HSP's gapped: 425
Number of HSP's successfully gapped: 9
Length of query: 134
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 48
Effective length of database: 7,123,158
Effective search space: 341911584
Effective search space used: 341911584
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: 54 (24.5 bits)