RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9254
(167 letters)
>gnl|CDD|218202 pfam04669, Polysacc_synt_4, Polysaccharide biosynthesis. This
family of proteins plays a role in xylan biosynthesis in
plant cell walls. Its precise role in xylan biosynthesis
is unknown. Its function in other organisms is unknown.
Length = 134
Score = 161 bits (410), Expect = 6e-52
Identities = 60/130 (46%), Positives = 78/130 (60%), Gaps = 8/130 (6%)
Query: 33 VEAMWVSKAVDHAEVYFNILCSV-DPKILRLTAHDDEILKSFRADFPDL-------KVDV 84
+E W KAV+HAE Y N+L P LRLTA +D I + FR FP+L + V
Sbjct: 1 IEMQWAVKAVEHAEPYCNLLVFGLGPSSLRLTALNDGIYEKFRKAFPELEAYHVAYRTKV 60
Query: 85 LNEEEMKSPEGKAKWREFCEKFKDMIEDYNFGTLLRLDAKGEYSEANTMLSTRIQFYAIE 144
L+ +E+KS K KWR F + + +EDYN GTL R DA Y+ NT+ R+QF IE
Sbjct: 61 LDADELKSAAYKEKWRIFVDAPEGYVEDYNAGTLARSDASKGYTPENTVFVHRVQFLCIE 120
Query: 145 LARNKEGLND 154
+ARN+EGLND
Sbjct: 121 IARNREGLND 130
>gnl|CDD|236979 PRK11779, sbcB, exonuclease I; Provisional.
Length = 476
Score = 30.2 bits (69), Expect = 0.50
Identities = 27/109 (24%), Positives = 45/109 (41%), Gaps = 20/109 (18%)
Query: 49 FNILCSVDP---KILRLTAHD---DEILKSFRA-DFPDLKVDVLNEEEMKSPEGKAKWRE 101
I+ +P L LT D +E+L +RA +FP+ L++EE + +W E
Sbjct: 378 MEIIRETEPENLAALDLTFDDPRLEELLFRYRARNFPET----LDDEE------QQRWLE 427
Query: 102 FCEK--FKDMIEDYNFGTLLRLDAKGEYSEANTMLSTRIQFYAIELARN 148
+ + ++ Y L +L + E E L + YA EL
Sbjct: 428 HRRQRLTPERLQQYAA-ELEQLAQEYEDDEEKQALLKALYDYAEELVPT 475
>gnl|CDD|240625 cd05300, 2-Hacid_dh_1, Putative D-isomer specific 2-hydroxyacid
dehydrogenase. 2-Hydroxyacid dehydrogenases catalyze
the conversion of a wide variety of D-2-hydroxy acids
to their corresponding keto acids. The general
mechanism is (R)-lactate + acceptor to pyruvate +
reduced acceptor. Formate/glycerate and related
dehydrogenases of the D-specific 2-hydroxyacid
dehydrogenase superfamily include groups such as
formate dehydrogenase, glycerate dehydrogenase,
L-alanine dehydrogenase, and S-adenosylhomocysteine
hydrolase. Despite often low sequence identity, these
proteins typically have a characteristic arrangement of
2 similar subdomains of the alpha/beta Rossmann fold
NAD+ binding form. The NAD+ binding domain is inserted
within the linear sequence of the mostly N-terminal
catalytic domain, which has a similar domain structure
to the internal NAD binding domain. Structurally, these
domains are connected by extended alpha helices and
create a cleft in which NAD is bound, primarily to the
C-terminal portion of the 2nd (internal) domain. Some
related proteins have similar structural subdomains but
with a tandem arrangement of the catalytic and
NAD-binding subdomains in the linear sequence. While
many members of this family are dimeric, alanine DH is
hexameric and phosphoglycerate DH is tetrameric.
Formate dehydrogenase (FDH) catalyzes the
NAD+-dependent oxidation of formate ion to carbon
dioxide with the concomitant reduction of NAD+ to NADH.
FDHs of this family contain no metal ions or prosthetic
groups. Catalysis occurs though direct transfer of the
hydride ion to NAD+ without the stages of acid-base
catalysis typically found in related dehydrogenases.
FDHs are found in all methylotrophic microorganisms in
energy production and in the stress responses of
plants.
Length = 313
Score = 28.6 bits (65), Expect = 1.4
Identities = 14/33 (42%), Positives = 19/33 (57%)
Query: 57 PKILRLTAHDDEILKSFRADFPDLKVDVLNEEE 89
KIL L+ DDE L+ RA P ++ V+ EE
Sbjct: 1 MKILVLSPLDDEHLERLRAAAPGAELRVVTAEE 33
>gnl|CDD|241449 cd13295, PH_EFA6, Exchange Factor for ARF6 Pleckstrin homology (PH)
domain. EFA6 (also called PSD/pleckstrin and Sec7
domain containing) is an guanine nucleotide exchange
factor for ADP ribosylation factor 6 (ARF6), which is
involved in membrane recycling. EFA6 has four
structurally related polypeptides: EFA6A, EFA6B, EFA6C
and EFA6D. It consists of a N-terminal proline rich
region (PR), a SEC7 domain, a PH domain, a PR, a
coiled-coil region, and a C-terminal PR. The EFA6 PH
domain regulates its association with the plasma
membrane. EFA6 activates Arf6 through its Sec7 catalytic
domain and modulates this activity through its
C-terminal domain, which rearranges the actin
cytoskeleton in fibroblastic cell lines. PH domains have
diverse functions, but in general are involved in
targeting proteins to the appropriate cellular location
or in the interaction with a binding partner. They share
little sequence conservation, but all have a common
fold, which is electrostatically polarized. Less than
10% of PH domains bind phosphoinositide phosphates
(PIPs) with high affinity and specificity. PH domains
are distinguished from other PIP-binding domains by
their specific high-affinity binding to PIPs with two
vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2
or PtdIns(3,4,5)P3 which results in targeting some PH
domain proteins to the plasma membrane. A few display
strong specificity in lipid binding. Any specificity is
usually determined by loop regions or insertions in the
N-terminus of the domain, which are not conserved across
all PH domains. PH domains are found in cellular
signaling proteins such as serine/threonine kinase,
tyrosine kinases, regulators of G-proteins, endocytotic
GTPases, adaptors, as well as cytoskeletal associated
molecules and in lipid associated enzymes.
Length = 126
Score = 26.9 bits (60), Expect = 3.1
Identities = 7/20 (35%), Positives = 11/20 (55%)
Query: 91 KSPEGKAKWREFCEKFKDMI 110
K+P GK W+ F K ++
Sbjct: 24 KTPRGKRGWKMFYATLKGLV 43
>gnl|CDD|226683 COG4230, COG4230, Delta 1-pyrroline-5-carboxylate dehydrogenase
[Energy production and conversion].
Length = 769
Score = 27.7 bits (62), Expect = 3.3
Identities = 12/24 (50%), Positives = 16/24 (66%), Gaps = 5/24 (20%)
Query: 3 QISADLGAGELVAGASVLSRPAEE 26
QI+A L AG SVL++PAE+
Sbjct: 256 QIAA-----ALAAGNSVLAKPAEQ 274
>gnl|CDD|178716 PLN03172, PLN03172, chalcone synthase family protein; Provisional.
Length = 393
Score = 27.7 bits (61), Expect = 3.5
Identities = 12/33 (36%), Positives = 18/33 (54%), Gaps = 2/33 (6%)
Query: 73 FRADFPDLKVDVLNEEEMKSPEGKAKWREFCEK 105
+AD+PD + N E M E K K++ C+K
Sbjct: 32 SQADYPDYYFRITNSEHMT--ELKEKFKRMCDK 62
>gnl|CDD|217516 pfam03367, zf-ZPR1, ZPR1 zinc-finger domain. The zinc-finger
protein ZPR1 is ubiquitous among eukaryotes. It is
indeed known to be an essential protein in yeast. In
quiescent cells, ZPR1 is localised to the cytoplasm. But
in proliferating cells treated with EGF or with other
mitogens, ZPR1 accumulates in the nucleolus. ZPR1
interacts with the cytoplasmic domain of the inactive
EGF receptor (EGFR) and is thought to inhibit the basal
protein tyrosine kinase activity of EGFR. This
interaction is disrupted when cells are treated with
EGF, though by themselves, inactive EGFRs are not
sufficient to sequester ZPR1 to the cytoplasm. Upon
stimulation by EGF, ZPR1 directly binds the eukaryotic
translation elongation factor-1alpha (eEF-1alpha) to
form ZPR1/eEF-1alpha complexes. These move into the
nucleus, localising particularly at the nucleolus.
Indeed, the interaction between ZPR1 and eEF-1alpha has
been shown to be essential for normal cellular
proliferation, and ZPR1 is thought to be involved in
pre-ribosomal RNA expression. The ZPR1 domain consists
of an elongation initiation factor 2-like zinc finger
and a double-stranded beta helix with a helical hairpin
insertion. ZPR1 binds preferentially to GDP-bound eEF1A
but does not directly influence the kinetics of
nucleotide exchange or GTP hydrolysis. The alignment for
this family shows a domain of which there are two copies
in ZPR1 proteins. This family also includes several
hypothetical archaeal proteins (from both Crenarchaeota
and Euryarchaeota), which only contain one copy of the
aligned region. This similarity between ZPR1 and
archaeal proteins was not previously noted.
Length = 160
Score = 27.2 bits (61), Expect = 3.5
Identities = 12/33 (36%), Positives = 15/33 (45%), Gaps = 1/33 (3%)
Query: 79 DLKVDVLNEEEMKSPEGKAKWREFCEKFKDMIE 111
L D + E K K EF EK K++IE
Sbjct: 109 GLSQDQEKRDSED-EETKKKIDEFLEKLKELIE 140
>gnl|CDD|187604 cd05346, SDR_c5, classical (c) SDR, subgroup 5. These proteins are
members of the classical SDR family, with a canonical
active site tetrad and a typical Gly-rich NAD-binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold (alpha/beta folding
pattern with a central beta-sheet), an NAD(P)(H)-binding
region, and a structurally diverse C-terminal region.
Classical SDRs are typically about 250 residues long,
while extended SDRs are approximately 350 residues.
Sequence identity between different SDR enzymes are
typically in the 15-30% range, but the enzymes share the
Rossmann fold NAD-binding motif and characteristic
NAD-binding and catalytic sequence patterns. These
enzymes catalyze a wide range of activities including
the metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 249
Score = 27.2 bits (61), Expect = 3.9
Identities = 20/85 (23%), Positives = 29/85 (34%), Gaps = 16/85 (18%)
Query: 61 RLTAHDDEILKSFRADFPDLKVDVLNEEEMKSPEGKAKWREFCEKFKDMIEDY-----NF 115
RL DE+ F L++DV + E ++ E + D N
Sbjct: 36 RLQELADELGAKFPVKVLPLQLDVSDRESIE---------AALENLPEEFRDIDILVNNA 86
Query: 116 GTLLRLDAKGEYSE--ANTMLSTRI 138
G L LD E TM+ T +
Sbjct: 87 GLALGLDPAQEADLEDWETMIDTNV 111
>gnl|CDD|177643 PHA03415, PHA03415, putative internal virion protein; Provisional.
Length = 1019
Score = 27.3 bits (60), Expect = 5.5
Identities = 19/52 (36%), Positives = 29/52 (55%), Gaps = 6/52 (11%)
Query: 97 AKWREFCEKFKDMIEDYNFGTL-LRLDAKGEYSEANTMLSTRIQFYAIELAR 147
A W + EK ++ + FGT ++LDA G Y++A L ++ A ELAR
Sbjct: 317 AAWDDGLEK--EIAKREGFGTAQIKLDASGRYADAKDALERKV---ADELAR 363
>gnl|CDD|224133 COG1212, KdsB, CMP-2-keto-3-deoxyoctulosonic acid synthetase [Cell
envelope biogenesis, outer membrane].
Length = 247
Score = 26.9 bits (60), Expect = 5.7
Identities = 13/40 (32%), Positives = 23/40 (57%), Gaps = 3/40 (7%)
Query: 55 VDPKILRLTAHDDEILKSFRADFPDLKVDVLNEEEMKSPE 94
++P+++R A E L++ AD L V + +EEE +P
Sbjct: 105 IEPEVIRAVA---ENLENSNADMATLAVKITDEEEAFNPN 141
>gnl|CDD|128949 smart00709, Zpr1, Duplicated domain in the epidermal growth factor-
and elongation factor-1alpha-binding protein Zpr1. Also
present in archaeal proteins.
Length = 160
Score = 26.5 bits (59), Expect = 6.1
Identities = 11/19 (57%), Positives = 13/19 (68%)
Query: 93 PEGKAKWREFCEKFKDMIE 111
PE K K EF EK K++IE
Sbjct: 122 PETKEKIDEFLEKLKELIE 140
>gnl|CDD|176106 cd08414, PBP2_LTTR_aromatics_like, The C-terminal substrate
binding domain of LysR-type transcriptional regulators
involved in the catabolism of aromatic compounds and
that of other related regulators, contains type 2
periplasmic binding fold. This CD includes the
C-terminal substrate binding domain of LTTRs involved
in degradation of aromatic compounds, such as CbnR,
BenM, CatM, ClcR and TfdR, as well as that of other
transcriptional regulators clustered together in
phylogenetic trees, including XapR, HcaR, MprR, IlvR,
BudR, AlsR, LysR, and OccR. The structural topology of
this substrate-binding domain is most similar to that
of the type 2 periplasmic binding proteins (PBP2),
which are responsible for the uptake of a variety of
substrates such as phosphate, sulfate, polysaccharides,
lysine/arginine/ornithine, and histidine. The PBP2 bind
their ligand in the cleft between these domains in a
manner resembling a Venus flytrap. After binding their
specific ligand with high affinity, they can interact
with a cognate membrane transport complex comprised of
two integral membrane domains and two cytoplasmically
located ATPase domains. This interaction triggers the
ligand translocation across the cytoplasmic membrane
energized by ATP hydrolysis. Besides transport
proteins, the PBP2 superfamily includes the
substrate-binding domains from ionotropic glutamate
receptors, LysR-like transcriptional regulators, and
unorthodox sensor proteins involved in signal
transduction.
Length = 197
Score = 26.3 bits (59), Expect = 7.1
Identities = 9/27 (33%), Positives = 18/27 (66%), Gaps = 3/27 (11%)
Query: 68 EILKSFRADFPDLKVDVLNEEEMKSPE 94
+L+ FRA +PD+++++ EM + E
Sbjct: 17 RLLRRFRARYPDVELEL---REMTTAE 40
>gnl|CDD|176113 cd08421, PBP2_LTTR_like_1, The C-terminal substrate binding
domain of an uncharacterized LysR-type transcriptional
regulator, contains the type 2 periplasmic binding
fold. LysR-transcriptional regulators comprise the
largest family of prokaryotic transcription factor.
Homologs of some of LTTRs with similar domain
organizations are also found in the archaea and
eukaryotic organisms. The LTTRs are composed of two
functional domains joined by a linker helix involved in
oligomerization: an N-terminal HTH (helix-turn-helix)
domain, which is responsible for the DNA-binding
specificity, and a C-terminal substrate-binding domain,
which is structurally homologous to the type 2
periplasmic binding proteins. As also observed in the
periplasmic binding proteins, the C-terminal domain of
the bacterial transcriptional repressor undergoes a
conformational change upon substrate binding which in
turn changes the DNA binding affinity of the repressor.
The genes controlled by the LTTRs have diverse
functional roles including amino acid biosynthesis, CO2
fixation, antibiotic resistance, degradation of
aromatic compounds, nodule formation of nitrogen-fixing
bacteria, and synthesis of virulence factors, to a name
a few. This substrate-binding domain shows significant
homology to the type 2 periplasmic binding proteins
(PBP2), which are responsible for the uptake of a
variety of substrates such as phosphate, sulfate,
polysaccharides, lysine/arginine/ornithine, and
histidine. The PBP2 bind their ligand in the cleft
between these domains in a manner resembling a Venus
flytrap. After binding their specific ligand with high
affinity, they can interact with a cognate membrane
transport complex comprised of two integral membrane
domains and two cytoplasmically located ATPase domains.
This interaction triggers the ligand translocation
across the cytoplasmic membrane energized by ATP
hydrolysis.
Length = 198
Score = 26.3 bits (59), Expect = 7.2
Identities = 11/27 (40%), Positives = 16/27 (59%), Gaps = 3/27 (11%)
Query: 68 EILKSFRADFPDLKVDVLNEEEMKSPE 94
E L SF A PD+++D+ EE S +
Sbjct: 17 EDLASFLAAHPDVRIDL---EERLSAD 40
>gnl|CDD|176139 cd08448, PBP2_LTTR_aromatics_like_2, The C-terminal substrate
binding domain of an uncharacterized LysR-type
transcriptional regulator similar to regulators
involved in the catabolism of aromatic compounds,
contains type 2 periplasmic binding fold. This CD
represents the substrate binding domain of an
uncharacterized LysR-type regulator similar to CbnR
which is involved in the regulation of chlorocatechol
breakdown. The transcription of the genes encoding
enzymes involved in such degradation is regulated and
expression of these enzymes is enhanced by inducers,
which are either an intermediate in the metabolic
pathway or compounds to be degraded. This
substrate-binding domain shows significant homology to
the type 2 periplasmic binding proteins (PBP2), which
are responsible for the uptake of a variety of
substrates such as phosphate, sulfate, polysaccharides,
lysine/arginine/ornithine, and histidine. The PBP2 bind
their ligand in the cleft between these domains in a
manner resembling a Venus flytrap. After binding their
specific ligand with high affinity, they can interact
with a cognate membrane transport complex comprised of
two integral membrane domains and two cytoplasmically
located ATPase domains. This interaction triggers the
ligand translocation across the cytoplasmic membrane
energized by ATP hydrolysis.
Length = 197
Score = 26.1 bits (58), Expect = 7.7
Identities = 11/28 (39%), Positives = 18/28 (64%), Gaps = 3/28 (10%)
Query: 67 DEILKSFRADFPDLKVDVLNEEEMKSPE 94
IL++FRA++P ++V + EM S E
Sbjct: 16 PRILRAFRAEYPGIEVAL---HEMSSAE 40
>gnl|CDD|176163 cd08474, PBP2_CrgA_like_5, The C-terminal substrate binding
domain of an uncharacterized LysR-type transcriptional
regulator CrgA-like, contains the type 2 periplasmic
binding fold. This CD represents the substrate binding
domain of an uncharacterized LysR-type transcriptional
regulator (LTTR) CrgA-like 5. The LTTRs are acting as
both auto-repressors and activators of target
promoters, controlling operons involved in a wide
variety of cellular processes such as amino acid
biosynthesis, CO2 fixation, antibiotic resistance,
degradation of aromatic compounds, nodule formation of
nitrogen-fixing bacteria, and synthesis of virulence
factors, to name a few. In contrast to the tetrameric
form of other LTTRs, CrgA from Neisseria meningitides
assembles into an octameric ring, which can bind up to
four 63-bp DNA oligonucleotides. Phylogenetic cluster
analysis showed that the CrgA-like regulators form a
subclass of the LTTRs that function as octamers. The
CrgA is an auto-repressor of its own gene and activates
the expression of the mdaB gene which coding for an
NADPH-quinone reductase and that its action is
increased by MBL (alpha-methylene-gamma-butyrolactone),
an inducer of NADPH-quinone oxidoreductase. The
structural topology of this substrate-binding domain is
most similar to that of the type 2 periplasmic binding
proteins (PBP2), which are responsible for the uptake
of a variety of substrates such as phosphate, sulfate,
polysaccharides, lysine/arginine/ornithine, and
histidine. The PBP2 bind their ligand in the cleft
between these domains in a manner resembling a Venus
flytrap. After binding their specific ligand with high
affinity, they can interact with a cognate membrane
transport complex comprised of two integral membrane
domains and two cytoplasmically located ATPase domains.
This interaction triggers the ligand translocation
across the cytoplasmic membrane energized by ATP
hydrolysis.
Length = 202
Score = 26.3 bits (59), Expect = 8.3
Identities = 8/38 (21%), Positives = 20/38 (52%), Gaps = 7/38 (18%)
Query: 60 LRLTAHDD-------EILKSFRADFPDLKVDVLNEEEM 90
LR+ A +L F A +PD++++++ ++ +
Sbjct: 5 LRINAPRVAARLLLAPLLARFLARYPDIRLELVVDDGL 42
>gnl|CDD|237018 PRK11905, PRK11905, bifunctional proline
dehydrogenase/pyrroline-5-carboxylate dehydrogenase;
Reviewed.
Length = 1208
Score = 26.4 bits (59), Expect = 8.9
Identities = 12/24 (50%), Positives = 17/24 (70%), Gaps = 5/24 (20%)
Query: 3 QISADLGAGELVAGASVLSRPAEE 26
QI+A LVAG +VL++PAE+
Sbjct: 696 QIAA-----ALVAGNTVLAKPAEQ 714
>gnl|CDD|235766 PRK06276, PRK06276, acetolactate synthase catalytic subunit;
Reviewed.
Length = 586
Score = 26.3 bits (58), Expect = 9.1
Identities = 19/58 (32%), Positives = 28/58 (48%), Gaps = 6/58 (10%)
Query: 56 DPKILRLTAHDDEILKSFRADFP---DLKV---DVLNEEEMKSPEGKAKWREFCEKFK 107
+ KI+ + EI K+ R D P D K D+L E K + K++W E +K K
Sbjct: 294 NAKIIHIDIDPAEIGKNVRVDVPIVGDAKNVLRDLLAELMKKEIKNKSEWLERVKKLK 351
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.316 0.132 0.378
Gapped
Lambda K H
0.267 0.0752 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,571,421
Number of extensions: 790010
Number of successful extensions: 828
Number of sequences better than 10.0: 1
Number of HSP's gapped: 826
Number of HSP's successfully gapped: 42
Length of query: 167
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 77
Effective length of database: 6,945,742
Effective search space: 534822134
Effective search space used: 534822134
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 55 (24.9 bits)