RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy18061
(60 letters)
>gnl|CDD|213044 cd12097, DD_RI_PKA, Dimerization/Docking domain of the Type I
Regulatory subunit of cAMP-dependent protein kinase.
cAMP-dependent protein kinase (PKA) is a
serine/threonine kinase (STK), catalyzing the transfer
of the gamma-phosphoryl group from ATP to
serine/threonine residues on protein substrates. The
inactive PKA holoenzyme is a heterotetramer composed of
two phosphorylated and active catalytic subunits with a
dimer of regulatory (R) subunits. Activation is
achieved through the binding of the important second
messenger cAMP to the R subunits, which leads to the
dissociation of PKA into the R dimer and two active
subunits. There are two classes of R subunits, RI and
RII; each exists as two isoforms (alpha and beta) from
distinct genes. These functionally non-redundant R
isoforms allow for specificity in PKA signaling. RI
subunits are pseudo-substrates as they do not contain a
phosphorylation site in their inhibitory site unlike
RII subunits. RIalpha function is required for normal
development as its deletion is embryonically lethal.
RIbeta is expressed highly in the brain and is
associated with hippocampal function. The R subunit
contains an N-terminal dimerization/docking (D/D)
domain, a linker with an inhibitory sequence, and two
c-AMP binding domains. The D/D domain dimerizes to form
a four-helix bundle that serves as a docking site for
A-kinase-anchoring proteins (AKAPs), which facilitates
the localization of PKA to specific sites in the cell.
PKA is present ubiquitously in cells and interacts with
many different downstream targets. It plays a role in
the regulation of diverse processes such as growth,
development, memory, metabolism, gene expression,
immunity, and lipolysis.
Length = 44
Score = 78.5 bits (194), Expect = 7e-22
Identities = 29/43 (67%), Positives = 40/43 (93%)
Query: 14 CEEYVQQHNVQQMLKDCIVQLCVTKPDNPISFLREYFQKLERF 56
CE YVQ+HN+QQ+LKD IVQLC+++P+NP++FLREYF+KLE+
Sbjct: 1 CEAYVQKHNIQQLLKDAIVQLCISRPENPVAFLREYFEKLEKE 43
>gnl|CDD|213048 cd12101, DD_RIalpha_PKA, Dimerization/Docking domain of the Type
I alpha Regulatory subunit of cAMP-dependent protein
kinase. cAMP-dependent protein kinase (PKA) is a
serine/threonine kinase (STK), catalyzing the transfer
of the gamma-phosphoryl group from ATP to
serine/threonine residues on protein substrates. The
inactive PKA holoenzyme is a heterotetramer composed of
two phosphorylated and active catalytic subunits with a
dimer of regulatory (R) subunits. Activation is
achieved through the binding of the important second
messenger cAMP to the R subunits, which leads to the
dissociation of PKA into the R dimer and two active
subunits. There are two classes of R subunits, RI and
RII; each exists as two isoforms (alpha and beta) from
distinct genes. These functionally non-redundant R
isoforms allow for specificity in PKA signaling. RI
subunits are pseudo-substrates as they do not contain a
phosphorylation site in their inhibitory site unlike
RII subunits. RIalpha is the key regulatory subunit
responsible for maintaining cAMP control of the
catalytic subunit. RIalpha function is required for
normal development as its deletion is embryonically
lethal due to failed cardiac morphogenesis. The R
subunit contains an N-terminal dimerization/docking
(D/D) domain, a linker with an inhibitory sequence, and
two c-AMP binding domains. The D/D domain dimerizes to
form a four-helix bundle that serves as a docking site
for A-kinase-anchoring proteins (AKAPs), which
facilitates the localization of PKA to specific sites
in the cell. PKA is present ubiquitously in cells and
interacts with many different downstream targets. It
plays a role in the regulation of diverse processes
such as growth, development, memory, metabolism, gene
expression, immunity, and lipolysis.
Length = 50
Score = 68.5 bits (167), Expect = 8e-18
Identities = 32/46 (69%), Positives = 42/46 (91%)
Query: 10 SLRECEEYVQQHNVQQMLKDCIVQLCVTKPDNPISFLREYFQKLER 55
SLRECE YVQ+HN+QQ+LKDCIVQLC +P+ P++FLREYF++LE+
Sbjct: 1 SLRECELYVQKHNIQQLLKDCIVQLCTARPERPMAFLREYFERLEK 46
>gnl|CDD|213049 cd12102, DD_RIbeta_PKA, Dimerization/Docking domain of the Type I
beta Regulatory subunit of cAMP-dependent protein
kinase. cAMP-dependent protein kinase (PKA) is a
serine/threonine kinase (STK), catalyzing the transfer
of the gamma-phosphoryl group from ATP to
serine/threonine residues on protein substrates. The
inactive PKA holoenzyme is a heterotetramer composed of
two phosphorylated and active catalytic subunits with a
dimer of regulatory (R) subunits. Activation is
achieved through the binding of the important second
messenger cAMP to the R subunits, which leads to the
dissociation of PKA into the R dimer and two active
subunits. There are two classes of R subunits, RI and
RII; each exists as two isoforms (alpha and beta) from
distinct genes. These functionally non-redundant R
isoforms allow for specificity in PKA signaling. RI
subunits are pseudo-substrates as they do not contain a
phosphorylation site in their inhibitory site unlike
RII subunits. RIbeta is expressed highly in the brain
and is associated with hippocampal function. The R
subunit contains an N-terminal dimerization/docking
(D/D) domain, a linker with an inhibitory sequence, and
two c-AMP binding domains. The D/D domain dimerizes to
form a four-helix bundle that serves as a docking site
for A-kinase-anchoring proteins (AKAPs), which
facilitates the localization of PKA to specific sites
in the cell. PKA is present ubiquitously in cells and
interacts with many different downstream targets. It
plays a role in the regulation of diverse processes
such as growth, development, memory, metabolism, gene
expression, immunity, and lipolysis.
Length = 54
Score = 67.3 bits (164), Expect = 2e-17
Identities = 30/49 (61%), Positives = 43/49 (87%)
Query: 7 EEQSLRECEEYVQQHNVQQMLKDCIVQLCVTKPDNPISFLREYFQKLER 55
E++SL+ CE YVQ+HN+QQ+LK+CIV LC+ KP+ P+ FLRE+F+KLE+
Sbjct: 1 EDESLKGCELYVQKHNIQQILKECIVNLCIAKPERPMKFLREHFEKLEK 49
>gnl|CDD|213043 cd12084, DD_R_PKA, Dimerization/Docking domain of the Regulatory
subunit of cAMP-dependent protein kinase and similar
domains. cAMP-dependent protein kinase (PKA) is a
serine/threonine kinase (STK), catalyzing the transfer
of the gamma-phosphoryl group from ATP to
serine/threonine residues on protein substrates. The
inactive PKA holoenzyme is a heterotetramer composed of
two phosphorylated and active catalytic subunits with a
dimer of regulatory (R) subunits. Activation is
achieved through the binding of the important second
messenger cAMP to the R subunits, which leads to the
dissociation of PKA into the R dimer and two active
subunits. There are two classes of R subunits, RI and
RII; each exists as two isoforms (alpha and beta) from
distinct genes. These functionally non-redundant R
isoforms allow for specificity in PKA signaling. The R
subunit contains an N-terminal dimerization/docking
(D/D) domain, a linker with an inhibitory sequence
(IS), and two c-AMP binding domains. RI and RII
subunits are distinguished by their IS; RII subunits
contain a phosphorylation site and are both substrates
and inhibitors while RI subunits are pseudo-substrates.
RI subunits require ATP and Mg ions to form a stable
holoenzyme while RII subunits do not. The D/D domain
dimerizes to form a four-helix bundle that serves as a
docking site for A-kinase-anchoring proteins (AKAPs),
which facilitates the localization of PKA to specific
sites in the cell. PKA is present ubiquitously in cells
and interacts with many different downstream targets.
It plays a role in the regulation of diverse processes
such as growth, development, memory, metabolism, gene
expression, immunity, and lipolysis.
Length = 37
Score = 42.6 bits (101), Expect = 7e-08
Identities = 11/35 (31%), Positives = 21/35 (60%)
Query: 21 HNVQQMLKDCIVQLCVTKPDNPISFLREYFQKLER 55
H ++LKD ++ +P++ + F EYF+KL +
Sbjct: 1 HGFPELLKDYTREVLRAQPEDILQFAAEYFEKLAK 35
>gnl|CDD|202148 pfam02197, RIIa, Regulatory subunit of type II PKA R-subunit.
Length = 38
Score = 42.7 bits (101), Expect = 7e-08
Identities = 13/35 (37%), Positives = 23/35 (65%)
Query: 21 HNVQQMLKDCIVQLCVTKPDNPISFLREYFQKLER 55
H +Q +L+D V++ +P +P+ F +YF+KLE
Sbjct: 1 HGLQALLEDLTVEVLRAQPSDPVQFAADYFEKLEE 35
>gnl|CDD|197697 smart00394, RIIa, RIIalpha, Regulatory subunit portion of type II
PKA R-subunit. RIIalpha, Regulatory subunit portion of
type II PKA R-subunit. Contains dimerisation interface
and binding site for A-kinase-anchoring proteins
(AKAPs).
Length = 38
Score = 42.7 bits (101), Expect = 8e-08
Identities = 12/35 (34%), Positives = 22/35 (62%)
Query: 21 HNVQQMLKDCIVQLCVTKPDNPISFLREYFQKLER 55
H +Q +L+D V++ +P + + F +YF+KLE
Sbjct: 1 HGLQALLEDLTVEVLRAQPSDLVQFAADYFEKLEE 35
>gnl|CDD|147395 pfam05186, Dpy-30, Dpy-30 motif. This motif is found in a wide
variety of domain contexts. It is found in the Dpy-30
proteins hence the motifs name. It is about 40 residues
long and is probably fomed of two alpha-helices. It may
be a dimerisation motif analogous to pfam02197 (Bateman
A pers obs).
Length = 42
Score = 29.5 bits (67), Expect = 0.015
Identities = 11/36 (30%), Positives = 17/36 (47%), Gaps = 1/36 (2%)
Query: 17 YVQQHNVQQMLKDCIVQLCVTKPDNPISFLREYFQK 52
Y+ +L+ L +P++PI FL EY K
Sbjct: 5 YLNDTVAPILLQGLTE-LAKERPEDPIEFLAEYLLK 39
>gnl|CDD|227346 COG5013, NarG, Nitrate reductase alpha subunit [Energy production
and conversion].
Length = 1227
Score = 27.4 bits (61), Expect = 0.34
Identities = 12/46 (26%), Positives = 18/46 (39%), Gaps = 1/46 (2%)
Query: 5 LEEEQSLRECEEYVQQHNVQQMLKDCIVQLCVTKPDNPISFLREYF 50
L+ + VQQ LK ++ + PDNP + R F
Sbjct: 664 LDIADEAEAAGLDPVDYVVQQ-LKSGKLRFAIEDPDNPENHPRNLF 708
>gnl|CDD|180319 PRK05945, sdhA, succinate dehydrogenase flavoprotein subunit;
Reviewed.
Length = 575
Score = 27.0 bits (60), Expect = 0.54
Identities = 11/65 (16%), Positives = 32/65 (49%), Gaps = 14/65 (21%)
Query: 3 SNLEEEQSLRECEEYVQQ----------HNVQQMLKDCIVQLC-VTKPDNPISFLREYFQ 51
++E++ L+E ++ +Q + ++Q +DC+ C V + + ++E +
Sbjct: 419 PEVDEQRYLKEAKQRIQALLDQSGTYRINQLRQQFQDCMTDHCGVFRTE---EIMQEGLE 475
Query: 52 KLERF 56
K+++
Sbjct: 476 KIQQL 480
>gnl|CDD|213296 cd05930, A_NRPS, The adenylation domain of nonribosomal peptide
synthetases (NRPS). The adenylation (A) domain of NRPS
recognizes a specific amino acid or hydroxy acid and
activates it as an (amino) acyl adenylate by hydrolysis
of ATP. The activated acyl moiety then forms a
thioester bond to the enzyme-bound cofactor
phosphopantetheine of a peptidyl carrier protein
domain. NRPSs are large multifunctional enzymes which
synthesize many therapeutically useful peptides in
bacteria and fungi via a template-directed, nucleic
acid independent nonribosomal mechanism. These natural
products include antibiotics, immunosuppressants, plant
and animal toxins, and enzyme inhibitors. NRPS has a
distinct modular structure in which each module is
responsible for the recognition, activation, and in
some cases, modification of a single amino acid residue
of the final peptide product. The modules can be
subdivided into domains that catalyze specific
biochemical reactions.
Length = 445
Score = 26.6 bits (60), Expect = 0.61
Identities = 7/20 (35%), Positives = 12/20 (60%)
Query: 23 VQQMLKDCIVQLCVTKPDNP 42
+ ML+D +L +T PD+
Sbjct: 76 LAYMLEDSGAKLLLTDPDDL 95
>gnl|CDD|213046 cd12099, DD_RII_PKA, Dimerization/Docking domain of the Type II
Regulatory subunit of cAMP-dependent protein kinase.
cAMP-dependent protein kinase (PKA) is a
serine/threonine kinase (STK), catalyzing the transfer
of the gamma-phosphoryl group from ATP to
serine/threonine residues on protein substrates. The
inactive PKA holoenzyme is a heterotetramer composed of
two phosphorylated and active catalytic subunits with a
dimer of regulatory (R) subunits. Activation is
achieved through the binding of the important second
messenger cAMP to the R subunits, which leads to the
dissociation of PKA into the R dimer and two active
subunits. There are two classes of R subunits, RI and
RII; each exists as two isoforms (alpha and beta) from
distinct genes. These functionally non-redundant R
isoforms allow for specificity in PKA signaling. RII
subunits contain a phosphorylation site in their
inhibitory site and are both substrates and inhibitors.
RIIalpha plays a role in the association and
dissociation of PKA with the centrosome during
interphase and mitosis, respectively. RIIbeta plays an
important role in adipocytes and neuronal tissues. The
R subunit contains an N-terminal dimerization/docking
(D/D) domain, a linker with an inhibitory sequence, and
two c-AMP binding domains. The D/D domain dimerizes to
form a four-helix bundle that serves as a docking site
for A-kinase-anchoring proteins (AKAPs), which
facilitates the localization of PKA to specific sites
in the cell. PKA is present ubiquitously in cells and
interacts with many different downstream targets. It
plays a role in the regulation of diverse processes
such as growth, development, memory, metabolism, gene
expression, immunity, and lipolysis.
Length = 39
Score = 25.3 bits (56), Expect = 0.67
Identities = 10/33 (30%), Positives = 18/33 (54%)
Query: 24 QQMLKDCIVQLCVTKPDNPISFLREYFQKLERF 56
++L+D V++ +P + + F EYF KL
Sbjct: 6 TELLQDFTVEVLREQPSDLVDFAAEYFTKLREE 38
>gnl|CDD|226987 COG4640, COG4640, Predicted membrane protein [Function unknown].
Length = 465
Score = 26.0 bits (57), Expect = 0.97
Identities = 5/29 (17%), Positives = 9/29 (31%)
Query: 22 NVQQMLKDCIVQLCVTKPDNPISFLREYF 50
Q+ I N ++F + Y
Sbjct: 347 EENQLKNKYIEFKAEAVNTNNMAFNQSYL 375
>gnl|CDD|131795 TIGR02748, GerC3_HepT, heptaprenyl diphosphate synthase component
II. Members of this family are component II of the
heterodimeric heptaprenyl diphosphate synthase. The
trusted cutoff was set such that all members identified
are encoded near to a recognizable gene for component I
(in Pfam family pfam07307). This enzyme acts in
menaquinone-7 isoprenoid side chain biosynthesis
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Menaquinone and ubiquinone].
Length = 319
Score = 25.1 bits (55), Expect = 2.2
Identities = 11/49 (22%), Positives = 22/49 (44%), Gaps = 6/49 (12%)
Query: 13 ECEEYVQQHNVQQMLKDCIVQLCVTKPD------NPISFLREYFQKLER 55
E ++ Q+L IV++C + + N LR Y ++++R
Sbjct: 120 ETMTEIKDPRAHQILSHTIVEVCRGEIEQIKDKYNFDQNLRTYLRRIKR 168
>gnl|CDD|197503 smart00076, IFabd, Interferon alpha, beta and delta. Interferons
produce antiviral and antiproliferative responses in
cells. They are classified into five groups, all of
them related but gamma-interferon.
Length = 117
Score = 23.4 bits (51), Expect = 7.8
Identities = 8/38 (21%), Positives = 20/38 (52%)
Query: 19 QQHNVQQMLKDCIVQLCVTKPDNPISFLREYFQKLERF 56
Q ++++ LK + + N L++YFQ+++ +
Sbjct: 58 QLNHLEACLKQQMGEEETPLTRNTHLALKKYFQRIQLY 95
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
0.322 0.135 0.396
Gapped
Lambda K H
0.267 0.0718 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 2,995,548
Number of extensions: 199510
Number of successful extensions: 231
Number of sequences better than 10.0: 1
Number of HSP's gapped: 231
Number of HSP's successfully gapped: 17
Length of query: 60
Length of database: 10,937,602
Length adjustment: 31
Effective length of query: 29
Effective length of database: 9,562,628
Effective search space: 277316212
Effective search space used: 277316212
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 (21.9 bits)
S2: 53 (24.2 bits)