RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8573
(123 letters)
>gnl|CDD|107368 cd06373, PBP1_NPR_like, Ligand binding domain of natriuretic
peptide receptor (NPR) family. Ligand binding domain of
natriuretic peptide receptor (NPR) family which consists
of three different subtypes: type A natriuretic peptide
receptor (NPR-A, or GC-A), type B natriuretic peptide
receptors (NPR-B, or GC-B), and type C natriuretic
peptide receptor (NPR-C). There are three types of
natriuretic peptide (NP) ligands specific to the
receptors: atrial NP (ANP), brain or B-type NP (BNP),
and C-type NP (CNP). The NP family is thought to have
arisen through gene duplication during evolution and
plays an essential role in cardiovascular and body fluid
homeostasis. ANP and BNP bind mainly to NPR-A, while CNP
binds specifically to NPR-B. Both NPR-A and NPR-B have
guanylyl cyclase catalytic activity and produces
intracellular secondary messenger cGMP in response to
peptide-ligand binding. Consequently, the NPR-A
activation results in vasodilation and inhibition of
vascular smooth muscle cell proliferation. NPR-C acts as
the receptor for all the three members of NP family, and
functions as a clearance receptor. Unlike NPR-A and -B,
NPR-C lacks an intracellular guanylyl cyclase domain and
is thought to exert biological actions by sequestration
of released natriuretic peptides and/or inhibition of
adenylyl cyclase.
Length = 396
Score = 118 bits (299), Expect = 3e-33
Identities = 43/88 (48%), Positives = 59/88 (67%), Gaps = 3/88 (3%)
Query: 8 VVVLCANPQTVREILLAAEELNMIDSGEYVFFNIELFSSMNAASLTPWYVHNDTDVRNER 67
VV++CA+P TVREI+LAA L + SGEYVFFNI+LF S W+ D +E+
Sbjct: 204 VVIMCASPDTVREIMLAAHRLGLT-SGEYVFFNIDLFGSSLYGGGPWWW--ERGDEDDEK 260
Query: 68 ARKAYTALLTVTARTPNNEAYRNFSSEL 95
A++AY AL+T+T R P+N Y+ FS E+
Sbjct: 261 AKEAYQALMTITLREPDNPEYKEFSLEV 288
>gnl|CDD|107347 cd06352, PBP1_NPR_GC_like, Ligand-binding domain of membrane
guanylyl-cyclase receptors. Ligand-binding domain of
membrane guanylyl-cyclase receptors. Membrane guanylyl
cyclases (GC) have a single membrane-spanning region and
are activated by endogenous and exogenous peptides. This
family can be divided into three major subfamilies: the
natriuretic peptide receptors (NPRs), sensory
organ-specific membrane GCs, and the
enterotoxin/guanylin receptors. The binding of peptide
ligands to the receptor results in the activation of the
cytosolic catalytic domain. Three types of NPRs have
been cloned from mammalian tissues: NPR-A/GC-A, NPR-B/
GC-B, and NPR-C. In addition, two of the GCs, GC-D and
GC-G, appear to be pseudogenes in humans. Atrial
natriuretic peptide (ANP) and brain natriuretic peptide
(BNP) are produced in the heart, and both bind to the
NPR-A. NPR-C, also termed the clearance receptor, binds
each of the natriuretic peptides and can alter
circulating levels of these peptides. The ligand binding
domain of the NPRs exhibits strong structural similarity
to the type I periplasmic binding fold protein family.
Length = 389
Score = 90.8 bits (226), Expect = 8e-23
Identities = 34/92 (36%), Positives = 54/92 (58%), Gaps = 3/92 (3%)
Query: 8 VVVLCANPQTVREILLAAEELNMIDSGEYVFFNIELFSSMNAASLTPWYVHNDTDVRNER 67
++++C + + VRE+LLAA +L + G+YVF I+LF+ Y D +E+
Sbjct: 197 IIIMCGSSEDVRELLLAAHDLGLTS-GDYVFILIDLFNYSLPYQ--NSYPWERGDGDDEK 253
Query: 68 ARKAYTALLTVTARTPNNEAYRNFSSELLSAV 99
A++AY A+LT+T R P+N Y FS E+ A
Sbjct: 254 AKEAYDAVLTITLRPPDNPEYEEFSEEVKEAA 285
>gnl|CDD|107381 cd06386, PBP1_NPR_C_like, Ligand-binding domain of type C
natriuretic peptide receptor. Ligand-binding domain of
type C natriuretic peptide receptor (NPR-C). NPR-C is
found in atrial, mesentery, placenta, lung, kidney,
venous tissue, aortic smooth muscle, and aortic
endothelial cells. The affinity of NPR-C for natriuretic
peptides is ANP>CNP>BNP. The extracellular domain of
NPR-C is about 30% identical to NPR-A and NPR-B.
However, unlike the cyclase-linked receptors, it
contains only 37 intracellular amino acids and no
guanylyl cyclase activity. Major function of NPR-C is to
clear natriuretic peptides from the circulation or
extracellular surroundings through constitutive
receptor-mediated internalization and degradation.
Length = 387
Score = 60.6 bits (147), Expect = 6e-12
Identities = 43/112 (38%), Positives = 58/112 (51%), Gaps = 11/112 (9%)
Query: 5 SVAVVVLCANPQTVREILLAAEELNMIDSGEYVFFNIELF--SSMNAASLTPWYVHNDTD 62
S VV++CA T+R I+LAA + SG+Y+FFNIELF SS S W D
Sbjct: 194 SERVVIMCAGADTIRSIMLAAHRRGLT-SGDYIFFNIELFNSSSYGDGS---W---KRGD 246
Query: 63 VRNERARKAYTALLTVT-ARTPNNEAYRNFSSELLSAVLPILDHAKVASAKM 113
+ A++AY++L TVT RT E + FS E+ S+V D M
Sbjct: 247 KHDFEAKQAYSSLNTVTLLRTVKPE-FEKFSMEVKSSVEKAGDLNDCDYVNM 297
>gnl|CDD|216296 pfam01094, ANF_receptor, Receptor family ligand binding region.
This family includes extracellular ligand binding
domains of a wide range of receptors. This family also
includes the bacterial amino acid binding proteins of
known structure.
Length = 343
Score = 58.2 bits (141), Expect = 4e-11
Identities = 25/88 (28%), Positives = 44/88 (50%), Gaps = 14/88 (15%)
Query: 8 VVVLCANPQTVREILLAAEELNMIDSGEYVFFNIELFSSMNAASLTPWYVHNDTDVRNER 67
V+V+C + +R+IL A EL + SG YV+ +L+S D+ N++
Sbjct: 180 VIVVCGSSDDLRQILRQARELGL-MSGGYVWILTDLWSD-------------SLDIDNDK 225
Query: 68 ARKAYTALLTVTARTPNNEAYRNFSSEL 95
AR+A +L T + P++ ++ F L
Sbjct: 226 AREAAKGVLGFTLKPPDSPGFQEFVERL 253
>gnl|CDD|107380 cd06385, PBP1_NPR_A, Ligand-binding domain of type A natriuretic
peptide receptor. Ligand-binding domain of type A
natriuretic peptide receptor (NPR-A). NPR-A is one of
three known single membrane-spanning natriuretic peptide
receptors that regulate blood volume, blood pressure,
ventricular hypertrophy, pulmonary hypertension, fat
metabolism, and long bone growth. In mammals there are
three natriuretic peptides: ANP, BNP, and CNP. NPR-A is
highly expressed in kidney, adrenal, terminal ileum,
adipose, aortic, and lung tissues. The rank order of
NPR-A activation by natriuretic peptides is
ANP>BNP>>CNP. Single allele-inactivating mutations in
the promoter of human NPR-A are associated with
hypertension and heart failure.
Length = 405
Score = 49.3 bits (118), Expect = 6e-08
Identities = 31/94 (32%), Positives = 47/94 (50%), Gaps = 14/94 (14%)
Query: 8 VVVLCANPQTVREILLAAEELNMIDSGEYVFFNIELFSSMNAASLT------PWYVHNDT 61
V+ +C +P R ++L + S +YVFF I+LF ASL PWY D
Sbjct: 205 VIYVCCSPDIFRRLMLQFWREGL-PSEDYVFFYIDLF----GASLQGPDPKRPWY-RGDA 258
Query: 62 DVRNERARKAYTALLTVTARTPNNEAYRNFSSEL 95
D AR+A+ ++ +T + P N Y+ F S+L
Sbjct: 259 DDAA--AREAFQSVKILTYKEPQNPEYKEFLSDL 290
>gnl|CDD|107379 cd06384, PBP1_NPR_B, Ligand-binding domain of type B natriuretic
peptide receptor. Ligand-binding domain of type B
natriuretic peptide receptor (NPR-B). NPR-B is one of
three known single membrane-spanning natriuretic peptide
receptors that have been identified. Natriuretic
peptides are family of structurally related but
genetically distinct hormones/paracrine factors that
regulate blood volume, blood pressure, ventricular
hypertrophy, pulmonary hypertension, fat metabolism, and
long bone growth. In mammals there are three natriuretic
peptides: ANP, BNP, and CNP. Like NPR-A (or GC-A), NPR-B
(or GC-B) is a transmembrane guanylyl cyclase, an enzyme
that catalyzes the synthesis of cGMP. NPR-B is the
predominant natriuretic peptide receptor in the brain.
The rank of order activation of NPR-B by natriuretic
peptides is CNP>>ANP>BNP. Homozygous inactivating
mutations in human NPR-B cause a form of short-limbed
dwarfism known as acromesomelic dysplasia type
Maroteaux.
Length = 399
Score = 47.1 bits (112), Expect = 4e-07
Identities = 25/90 (27%), Positives = 43/90 (47%), Gaps = 3/90 (3%)
Query: 8 VVVLCANPQTVREILLAAEELNMIDSGEYVFFNIELFS-SMNAASLTPWYVHNDTDVRNE 66
+V +C +T EI+L A+ + G+YVFF +++F S+ S Y
Sbjct: 205 IVYICGPLETFLEIMLQAQREGL-TPGDYVFFYLDVFGESLRVKSPRESY-KQMNHSSWT 262
Query: 67 RARKAYTALLTVTARTPNNEAYRNFSSELL 96
++A+ ++ +T R P N Y+ F EL
Sbjct: 263 VLKEAFKSVFVITYREPENPEYKEFQRELH 292
>gnl|CDD|107366 cd06371, PBP1_sensory_GC_DEF_like, Ligand-binding domain of
membrane guanylyl cyclases (GC-D, GC-E, and GC-F) that
are specifically expressed in sensory tissues. This
group includes the ligand-binding domain of membrane
guanylyl cyclases (GC-D, GC-E, and GC-F) that are
specifically expressed in sensory tissues. They share a
similar topology with an N-terminal extracellular
ligand-binding domain, a single transmembrane domain,
and a C-terminal cytosolic region that contains
kinase-like and catalytic domains. GC-D is specifically
expressed in a subpopulation of olfactory sensory
neurons. GC-E and GC-F are colocalized within the same
photoreceptor cells of the retina and have important
roles in phototransduction. Unlike the other family
members, GC-E and GC-F have no known extracellular
ligands. Instead, they are activated under low calcium
conditions by guanylyl cyclase activating proteins
called GCAPs. GC-D expressing neurons have been
implicated in pheromone detection and GC-D is
phylogenetically more similar to the Ca2+-regulated GC-E
and GC-F than to receptor GC-A, -B and -C which are
activated by peptide ligands. Moreover, these olfactory
GCs and retinal GCs share characteristic sequence
similarity in a regulatory domain that is involved in
the binding of GCAPs, suggesting GC-D activity may be
regulated by an unknown extracellular ligand and
intracellular Ca2+. Rodent GC-D-expressing neurons have
been implicated in pheromone detection and were recently
shown to respond to atmospheric CO2 which is an
olfactory stimulus for many invertebrates and regulates
some insect innate behavior, such as the location of
food and hosts.
Length = 382
Score = 37.6 bits (88), Expect = 6e-04
Identities = 28/98 (28%), Positives = 49/98 (50%), Gaps = 25/98 (25%)
Query: 6 VAVVVLCANP-----QTVREILLAAEELNMIDSGEYVF--FNIELFS----SMNAASLTP 54
V VV++C + + R +L A E+ M D G YVF ++ L+S +++ +L
Sbjct: 189 VRVVIMCMHSVLIGGEEQRLLLETALEMGMTD-GRYVFIPYDTLLYSLPYRNVSYPALR- 246
Query: 55 WYVHNDTDVRNERARKAYTALLTVTARTPN---NEAYR 89
N++ + R+AY A+LT+T + EA+R
Sbjct: 247 ----NNS-----KLRRAYDAVLTITMDSGEQSFYEAFR 275
>gnl|CDD|153137 cd06269, PBP1_glutamate_receptors_like, Family C G-protein couples
receptors (GPCRs), membrane bound guanylyl cyclases such
as the family of natriuretic peptide receptors (NPRs),
and the N-terminal leucine/isoleucine/valine- binding
protein (LIVBP)-like domain of the ionotropic glutamate
receptors. This CD represents the ligand-binding domain
of the family C G-protein couples receptors (GPCRs),
membrane bound guanylyl cyclases such as the family of
natriuretic peptide receptors (NPRs), and the N-terminal
leucine/isoleucine/valine- binding protein (LIVBP)-like
domain of the ionotropic glutamate receptors, all of
which are structurally similar and related to the
periplasmic-binding fold type I family. The family C
GPCRs consist of metabotropic glutamate receptor (mGluR)
receptors, a calcium-sensing receptor (CaSR),
gamma-aminobutyric receptors (GABAb), the promiscuous
L-alpha-amino acid receptor GPR6A, families of taste and
pheromone receptors, and orphan receptors. Truncated
splicing variants of the orphan receptors are not
included in this CD. The family C GPCRs are activated by
endogenous agonists such as amino acids, ions, and sugar
based molecules. Their amino terminal ligand-binding
region is homologous to the bacterial
leucine-isoleucine-valine binding protein (LIVBP) and a
leucine binding protein (LBP). The ionotropic glutamate
receptors (iGluRs) have an integral ion channel and are
subdivided into three major groups based on their
pharmacology and structural similarities: NMDA
receptors, AMPA receptors, and kainate receptors. The
family of membrane bound guanylyl cyclases is further
divided into three subfamilies: the ANP receptor
(GC-A)/C-type natriuretic peptide receptor (GC-B), the
heat-stable enterotoxin receptor (GC-C)/sensory organ
specific membrane GCs such as retinal receptors (GC-E,
GC-F), and olfactory receptors (GC-D and GC-G).
Length = 298
Score = 33.6 bits (77), Expect = 0.016
Identities = 10/51 (19%), Positives = 21/51 (41%), Gaps = 2/51 (3%)
Query: 8 VVVLCANPQTVREILLAAEELNMIDSGEYVFFNIELFSSMNAASLTPWYVH 58
V+V+ ++ + +L A EL M+ Y + +L+ + Y
Sbjct: 198 VIVVFSSEEDALRLLEEAVELGMM--TGYHWIITDLWLTSCLDLELLEYFP 246
>gnl|CDD|107346 cd06351, PBP1_iGluR_N_LIVBP_like, N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the NMDA, AMPA, and kainate receptor subtypes
of ionotropic glutamate receptors (iGluRs). N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the NMDA, AMPA, and kainate receptor subtypes
of ionotropic glutamate receptors (iGluRs). While this
N-terminal domain belongs to the periplasmic-binding
fold type I superfamily, the glutamate-binding domain of
the iGluR is structurally homologous to the
periplasmic-binding fold type II. The LIVBP-like domain
of iGluRs is thought to play a role in the initial
assembly of iGluR subunits, but it is not well
understood how this domain is arranged and functions in
intact iGluR. Glutamate mediates the majority of
excitatory synaptic transmission in the central nervous
system via two broad classes of ionotropic receptors
characterized by their response to glutamate agonists:
N-methyl-aspartate (NMDA) and non-NMDA receptors. NMDA
receptors have intrinsically slow kinetics, are highly
permeable to Ca2+, and are blocked by extracellular Mg2+
in a voltage-dependent manner. On the other hand,
non-NMDA receptors have faster kinetics, are weakly
permeable to Ca2+, and are not blocked by extracellular
Mg2+. While non-NMDA receptors typically mediate
excitatory synaptic responses at resting membrane
potentials, NMDA receptors contribute to several forms
of synaptic plasticity and are suggested to play an
important role in the development of synaptic pathways.
Length = 328
Score = 32.1 bits (73), Expect = 0.047
Identities = 11/36 (30%), Positives = 20/36 (55%), Gaps = 1/36 (2%)
Query: 8 VVVLCANPQTVREILLAAEELNMIDSGEYVFFNIEL 43
+++ C++ + +EIL A EL M+ G Y + L
Sbjct: 189 IILDCSSEEEAKEILEQAVELGMMGYG-YHWILTNL 223
>gnl|CDD|107367 cd06372, PBP1_GC_G_like, Ligand-binding domain of membrane guanylyl
cyclase G. This group includes the ligand-binding
domain of membrane guanylyl cyclase G (GC-G) which is a
sperm surface receptor and might function, similar to
its sea urchin counterpart, in the early signaling event
that regulates the Ca2+ influx/efflux and subsequent
motility response in sperm. GC-G appears to be a
pseudogene in human. Furthermore, in contrast to the
other orphan receptor GCs, GC-G has a broad tissue
distribution in rat, including lung, intestine, kidney,
and skeletal muscle.
Length = 391
Score = 31.8 bits (72), Expect = 0.077
Identities = 16/41 (39%), Positives = 27/41 (65%), Gaps = 2/41 (4%)
Query: 5 SVA-VVVLCANPQTVREILLAAEELNMIDSGEYVFFNIELF 44
SVA V++L + + + IL AAE+L + G++VFF ++ F
Sbjct: 195 SVARVIILICSSEDAKAILQAAEKLGL-MKGKFVFFLLQQF 234
>gnl|CDD|107261 cd04509, PBP1_ABC_transporter_GCPR_C_like, Family C of G-protein
coupled receptors and their close homologs, the type I
periplasmic-binding proteins of ATP-binding cassette
transporter-like systems. This CD includes members of
the family C of G-protein coupled receptors and their
close homologs, the type I periplasmic-binding proteins
of ATP-binding cassette transporter-like systems. The
family C GPCR includes glutamate/glycine-gated ion
channels such as the NMDA receptor, G-protein-coupled
receptors, metabotropic glutamate, GABA-B, calcium
sensing, phermone receptors, and atrial natriuretic
peptide-guanylate cyclase receptors. The glutamate
receptors that form cation-selective ion channels,
iGluR, can be classified into three different subgroups
according to their binding-affinity for the agonists
NMDA (N-methyl-D-asparate), AMPA
(alpha-amino-3-dihydro-5-methyl-3-oxo-4-
isoxazolepropionic acid), and kainate. L-glutamate is a
major neurotransmitter in the brain of vertebrates and
acts through either mGluRs or iGluRs. mGluRs subunits
possess seven transmembrane segments and a large
N-terminal extracellular domain. ABC-type
leucine-isoleucine-valine-binding protein (LIVBP) is a
bacterial periplasmic binding protein that has homology
with the amino-terminal domain of the glutamate-receptor
ion channels (iGluRs). The extracellular regions of
iGluRs are made of two PBP-like domains in tandem, a
LIVBP-like domain that constitutes the N terminus -
which is included in this CD - followed by a domain
related to lysine-arginine-ornithine-binding protein
(LAOBP) that belongs to the type II periplasmic binding
fold protein superfamily. The uncharacterized
periplasmic components of various ABC-type transport
systems are included in this group.
Length = 299
Score = 31.3 bits (71), Expect = 0.086
Identities = 13/41 (31%), Positives = 18/41 (43%), Gaps = 2/41 (4%)
Query: 8 VVVLCANPQTVREILLAAEELNMIDSGEYVFFNIELFSSMN 48
V+VLC + + IL A E + +G Y I L S
Sbjct: 194 VIVLCGSGEDAATILKQAAEAGL--TGGYPILGITLGLSDV 232
>gnl|CDD|107361 cd06366, PBP1_GABAb_receptor, Ligand-binding domain of GABAb
receptors, which are metabotropic transmembrane
receptors for gamma-aminobutyric acid (GABA).
Ligand-binding domain of GABAb receptors, which are
metabotropic transmembrane receptors for
gamma-aminobutyric acid (GABA). GABA is the major
inhibitory neurotransmitter in the mammalian CNS and,
like glutamate and other transmitters, acts via both
ligand gated ion channels (GABAa receptors) and
G-protein coupled receptors (GABAb). GABAa receptors are
members of the ionotropic receptor superfamily which
includes alpha-adrenergic and glycine receptors. The
GABAb receptor is a member of a receptor superfamily
which includes the mGlu receptors. The GABAb receptor is
coupled to G alpha_i proteins, and activation causes a
decrease in calcium, an increase in potassium membrane
conductance, and inhibition of cAMP formation. The
response is thus inhibitory and leads to
hyperpolarization and decreased neurotransmitter
release, for example.
Length = 350
Score = 31.1 bits (71), Expect = 0.11
Identities = 22/94 (23%), Positives = 38/94 (40%), Gaps = 17/94 (18%)
Query: 8 VVVLCANPQTVREILLAAEELNMIDSGEYVFFNIELFSSMNAASLTPWYVHN---DTDVR 64
V+V+ +P R + A +L M+ G YV+ LT W N +D
Sbjct: 195 VIVVHFSPDLARRVFCEAYKLGMMGKG-YVWI------------LTDWLSSNWWSSSDCT 241
Query: 65 NERARKAYTALLTVTARTPN-NEAYRNFSSELLS 97
+E +A ++ V + PN + + F+S
Sbjct: 242 DEEMLEAMQGVIGVRSYVPNSSMTLQEFTSRWRK 275
>gnl|CDD|223315 COG0237, CoaE, Dephospho-CoA kinase [Coenzyme metabolism].
Length = 201
Score = 29.2 bits (66), Expect = 0.39
Identities = 11/55 (20%), Positives = 17/55 (30%), Gaps = 5/55 (9%)
Query: 18 VREILLAAEELNMIDSGEYVFFNIELFSSMNAASLTP--WYVHNDTDVRNERARK 70
+R + + S YV I L V+ ++R ER K
Sbjct: 92 IRAEIKVVIDG--ARSP-YVVLEIPLLFEAGGEKYFDKVIVVYAPPEIRLERLMK 143
>gnl|CDD|107365 cd06370, PBP1_Speract_GC_like, Ligand-binding domain of membrane
bound guanylyl cyclases. Ligand-binding domain of
membrane bound guanylyl cyclases (GCs), which are known
to be activated by sperm-activating peptides (SAPs),
such as speract or resact. These ligand peptides are
released by a range of invertebrates to stimulate the
metabolism and motility of spermatozoa and are also
potent chemoattractants. These GCs contain a single
transmembrane segment, an extracellular ligand binding
domain, and intracellular protein kinase-like and
cyclase catalytic domains. GCs of insect and nematodes,
which exhibit high sequence similarity to the speract
receptor are also included in this model.
Length = 404
Score = 29.6 bits (67), Expect = 0.39
Identities = 17/81 (20%), Positives = 40/81 (49%), Gaps = 8/81 (9%)
Query: 18 VREILLAAEELNMIDSGEY--VFFNIELFSSMNAASLTPWYVHNDTDVRN----ERARKA 71
+R+ L++ + +++SG+Y + +IE + + + + + N E+A +A
Sbjct: 210 LRQFLMSMLDEGLLESGDYMVLGVDIEYYDRDSQDYYS-LHRGFQSREYNRSDDEKALEA 268
Query: 72 YTALLTVTARTPNNEAYRNFS 92
++L + TP + Y +FS
Sbjct: 269 MKSVLIIVP-TPVSPDYDSFS 288
>gnl|CDD|119353 cd02874, GH18_CFLE_spore_hydrolase, Cortical fragment-lytic enzyme
(CFLE) is a peptidoglycan hydrolase involved in
bacterial endospore germination. CFLE is expressed as
an inactive preprotein (called SleB) in the forespore
compartment of sporulating cells. SleB translocates
across the forespore inner membrane and is deposited as
a mature enzyme in the cortex layer of the spore. As
part of a sensory mechanism capable of initiating
germination, CFLE degrades a spore-specific
peptidoglycan constituent called muramic-acid
delta-lactam that comprises the outer cortex. CFLE has
a C-terminal glycosyl hydrolase family 18 (GH18)
catalytic domain as well as two N-terminal LysM
peptidoglycan-binding domains. In addition to SleB,
this family includes YaaH, YdhD, and YvbX from Bacillus
subtilis.
Length = 313
Score = 28.8 bits (65), Expect = 0.73
Identities = 14/42 (33%), Positives = 17/42 (40%), Gaps = 5/42 (11%)
Query: 59 NDTDVRNERARKAYTALLTVTARTPNNEAYRNFSSELLSAVL 100
D + R+ LL +T N NF SEL AVL
Sbjct: 46 PDERLIEAAKRRGVKPLLVIT-----NLTNGNFDSELAHAVL 82
>gnl|CDD|179909 PRK04984, PRK04984, fatty acid metabolism regulator; Provisional.
Length = 239
Score = 28.3 bits (64), Expect = 0.82
Identities = 17/45 (37%), Positives = 23/45 (51%), Gaps = 3/45 (6%)
Query: 14 NPQTVREILLAAEELNMIDSGE-YVFFNIELFSSMNAASLTPWYV 57
NP+ E+L AEEL D+ E + F+ LF + AS P Y
Sbjct: 120 NPEKALEVLATAEELE--DTAEAFAEFDYNLFRGLAFASGNPIYG 162
>gnl|CDD|163028 TIGR02812, fadR_gamma, fatty acid metabolism transcriptional
regulator FadR. Members of this family are FadR, a
transcriptional regulator of fatty acid metabolism,
including both biosynthesis and beta-oxidation. It is
found exclusively in a subset of Gammaproteobacteria,
with strictly one copy per genome. It has an N-terminal
DNA-binding domain and a less well conserved C-terminal
long chain acyl-CoA-binding domain. FadR from this
family heterologously expressed in Escherichia coli show
differences in regulatory response and fatty acid
binding profiles. The family is nevertheless designated
equivalog, as all member proteins have at least
nominally the same function [Fatty acid and phospholipid
metabolism, Biosynthesis, Fatty acid and phospholipid
metabolism, Degradation, Regulatory functions, DNA
interactions].
Length = 235
Score = 28.1 bits (63), Expect = 0.95
Identities = 16/45 (35%), Positives = 23/45 (51%), Gaps = 3/45 (6%)
Query: 14 NPQTVREILLAAEELNMIDSGE-YVFFNIELFSSMNAASLTPWYV 57
NP+ E+L A EL D+ E + F+ +LF + AS P Y
Sbjct: 119 NPEKALEVLANANELE--DTAEAFTEFDYQLFRGLAFASGNPIYG 161
>gnl|CDD|116452 pfam07840, FadR_C, FadR C-terminal domain. This family contains
sequences that are similar to the fatty acid metabolism
regulator protein (FadR). This functions as a dimer,
with each monomer being composed of an N-terminal
DNA-binding domain and a regulatory C-terminal domain.
A linker comprising two short alpha helices joins the
two domains. In the C-terminal domain, an antiparallel
array of six alpha helices forms a barrel-like
structure, while a seventh alpha helix forms a 'lid' at
the end closest to the N-terminal domain. This
structure was found to be similar to that of the
C-terminal domain of the Tet repressor. Long-chain
acyl-CoA thioesters interact directly and reversibly
with the C-terminal domain, and this interaction
affects the structure and therefore the DNA binding
properties of the N-terminal domain.
Length = 164
Score = 27.5 bits (62), Expect = 1.3
Identities = 15/44 (34%), Positives = 22/44 (50%), Gaps = 1/44 (2%)
Query: 14 NPQTVREILLAAEELNMIDSGEYVFFNIELFSSMNAASLTPWYV 57
NP+ EIL +EL + + F+ +LF + AS P YV
Sbjct: 49 NPEKSAEILAQLDELED-TAEAFAEFDYQLFHGLAFASGNPIYV 91
>gnl|CDD|153138 cd06350, PBP1_GPCR_family_C_like, Ligand-binding domain of
membrane-bound glutamate receptors that mediate
excitatory transmission on the cellular surface through
initial binding of glutamate and are categorized into
ionotropic glutamate receptors (iGluRs) and metabotropic
glutamate receptors (mGluRs). Ligand-binding domain of
membrane-bound glutamate receptors that mediate
excitatory transmission on the cellular surface through
initial binding of glutamate and are categorized into
ionotropic glutamate receptors (iGluRs) and metabotropic
glutamate receptors (mGluRs). The metabotropic glutamate
receptors (mGluR) are key receptors in the modulation of
excitatory synaptic transmission in the central nervous
system. The mGluRs are coupled to G proteins and are
thus distinct from the iGluRs which internally contain
ligand-gated ion channels. The mGluR structure is
divided into three regions: the extracellular region,
the seven-spanning transmembrane region and the
cytoplasmic region. The extracellular region is further
devided into the ligand-binding domain (LBD) and the
cysteine-rich domain. The LBD has sequence similarity to
the LIVBP, which is a bacterial periplasmic protein
(PBP), as well as to the extracellular region of both
iGluR and the gamma-aminobutyric acid (GABA)b receptor.
iGluRs are divided into three main subtypes based on
pharmacological profile: NMDA, AMPA, and kainate
receptors. All family C GPCRs have a large extracellular
N terminus that contain a domain with homology to
bacterial periplasmic amino acid-binding proteins.
Length = 348
Score = 27.7 bits (62), Expect = 1.5
Identities = 9/51 (17%), Positives = 19/51 (37%), Gaps = 2/51 (3%)
Query: 8 VVVLCANPQTVREILLAAEELNMIDSGEYVFFNIELFSSMNAASLTPWYVH 58
V+V+ + + A +L M +G+Y + + +S T
Sbjct: 220 VIVVFGDEDDALRLFCEAYKLGM--TGKYWIISTDWDTSTCLLLFTLDAFQ 268
>gnl|CDD|107248 cd01391, Periplasmic_Binding_Protein_Type_1, Type 1 periplasmic
binding fold superfamily. Type 1 periplasmic binding
fold superfamily. This model and hierarchy represent the
ligand binding domains of the LacI family of
transcriptional regulators, periplasmic binding proteins
of the ABC-type transport systems, the family C
G-protein couples receptors (GPCRs), membrane bound
guanylyl cyclases including the family of natriuretic
peptide receptors (NPRs), and the N-terminal
leucine/isoleucine/valine- binding protein (LIVBP)-like
domains of the ionotropic glutamate receptors (iGluRs).
In LacI-like transcriptional regulator and the bacterial
periplasmic binding proteins the ligands are
monosaccharides including lactose, ribose, fructose,
xylose, arabinose, galactose/glucose, and other sugars,
with a few exceptions. Periplasmic sugar binding
proteins are one of the components of ABC transporters
and are involved in the active transport of
water-soluble ligands. The LacI family of proteins
consists of transcriptional regulators related to the
lac repressor. In this case, the sugar binding domain
binds a sugar which changes the DNA binding activity of
the repressor domain. The periplasmic binding proteins
are the primary receptors for chemotaxis and transport
of many sugar based solutes. The core structures of
periplasmic binding proteins are classified into two
types, and they differ in number and order of beta
strands: type 1 has six beta strands, while type 2 has
five beta strands per sub-domain. These two structural
folds are thought to be distantly related via a common
ancestor. Notably, while the N-terminal LIVBP-like
domain of iGluRs belongs to the type 1
periplasmic-binding fold protein superfamily, the
glutamate-binding domain of the iGluR is structurally
similar to the type 2 periplasmic-binding fold.
Length = 269
Score = 27.5 bits (61), Expect = 2.0
Identities = 12/77 (15%), Positives = 24/77 (31%), Gaps = 10/77 (12%)
Query: 9 VVLCANPQTVREILLAAEELNMIDSGEYVFFNIELFSSMN---------AASLTPWYVHN 59
+ N + L AA E + G+ + + ++ + +
Sbjct: 185 AIFACNDEMAAGALKAAREAGL-TPGDISIIGFDGSPAALLAAGEAGPGLTTVAQPFPGD 243
Query: 60 DTDVRNERARKAYTALL 76
D D + A Y A+L
Sbjct: 244 DPDQPDYPAALGYDAVL 260
>gnl|CDD|233315 TIGR01213, pseudo_Pus10arc, tRNA pseudouridine(54/55) synthase.
Members of this family show twilight-zone similarity to
several predicted RNA pseudouridine synthases. All
trusted members of this family are archaeal. Several
eukaryotic homologs lack N-terminal homology including
two CXXC motifs [Hypothetical proteins, Conserved].
Length = 388
Score = 27.4 bits (61), Expect = 2.1
Identities = 18/72 (25%), Positives = 30/72 (41%), Gaps = 14/72 (19%)
Query: 9 VVLCANPQTVREILL--AAEELNMIDSGEYVFFNIELFSSMNAASLTPWYVHNDTDVRNE 66
V+ P+ R+I L EE+N G+ ++ F++ V+ E
Sbjct: 226 VLEVKEPR-YRKIDLDPLEEEINTSGKGKVEVEGLK-FATREEVEE----------VKEE 273
Query: 67 RARKAYTALLTV 78
+ RK Y AL+ V
Sbjct: 274 KHRKVYRALVEV 285
>gnl|CDD|107357 cd06362, PBP1_mGluR, Ligand binding domain of the metabotropic
glutamate receptors (mGluR). Ligand binding domain of
the metabotropic glutamate receptors (mGluR), which are
members of the family C of G-protein-coupled receptors
that transduce extracellular signals into G-protein
activation and ultimately into cellular responses.
mGluRs bind to glutamate and function as an excitatory
neurotransmitter; they are involved in learning, memory,
anxiety, and the perception of pain. Eight subtypes of
mGluRs have been cloned so far, and are classified into
three groups according to their sequence similarities,
transduction mechanisms, and pharmacological profiles.
Group I is composed of mGlu1R and mGlu5R that both
stimulate PLC hydrolysis. Group II includes mGlu2R and
mGlu3R, which inhibit adenylyl cyclase, as do mGlu4R,
mGlu6R, mGlu7R, and mGlu8R, which form group III.
Length = 452
Score = 26.8 bits (60), Expect = 3.2
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 8 VVVLCANPQTVREILLAAEELN 29
VVVL +R +L AA+ LN
Sbjct: 233 VVVLFCREDDIRGLLAAAKRLN 254
>gnl|CDD|182334 PRK10251, PRK10251, phosphopantetheinyltransferase component of
enterobactin synthase multienzyme complex; Provisional.
Length = 207
Score = 26.7 bits (59), Expect = 3.4
Identities = 14/69 (20%), Positives = 25/69 (36%), Gaps = 5/69 (7%)
Query: 42 ELFSSMNAASLTPWYVHNDTDVRNERARKAYTALLTVTARTPNNEAYRNFSSELLSAVLP 101
E+FS+ A LT + R A+ LT+ A + A++ + L
Sbjct: 113 EIFSAQTATELTDNIITPAEHERLADCGLAFPLALTL-AFSAKESAFKASEIQ----TLA 167
Query: 102 ILDHAKVAS 110
++ S
Sbjct: 168 GFLDYQIIS 176
>gnl|CDD|221641 pfam12569, NARP1, NMDA receptor-regulated protein 1. This domain
family is found in eukaryotes, and is approximately 40
amino acids in length. The family is found in
association with pfam07719, pfam00515. There is a single
completely conserved residue L that may be functionally
important. NARP1 is the mammalian homologue of a yeast
N-terminal acetyltransferase that regulates entry into
the G(0) phase of the cell cycle.
Length = 516
Score = 26.4 bits (59), Expect = 4.7
Identities = 13/49 (26%), Positives = 17/49 (34%), Gaps = 6/49 (12%)
Query: 64 RNERARKAYTALLTVTARTPNNEAYRNFSSELLSAVLPILDHAKVASAK 112
R E A Y ALL R P N Y L A+ + + +
Sbjct: 53 RKEEAEATYRALL---DRNPENYDYYE---GLQKALGLEISSGDIEALL 95
>gnl|CDD|220855 pfam10711, DUF2513, Hypothetical protein (DUF2513). This family
is found in bacteria. The function is not known.
Length = 102
Score = 25.0 bits (55), Expect = 7.9
Identities = 8/17 (47%), Positives = 10/17 (58%)
Query: 18 VREILLAAEELNMIDSG 34
+R+ILLA EEL
Sbjct: 7 IRDILLALEELLKPGEA 23
>gnl|CDD|107377 cd06382, PBP1_iGluR_Kainate, N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the kainate receptors. N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the kainate receptors, non-NMDA ionotropic
receptors which respond to the neurotransmitter
glutamate. While this N-terminal domain belongs to the
periplasmic-binding fold type I superfamily, the
glutamate-binding domain of the iGluR is structurally
homologous to the periplasmic-binding fold type II. The
LIVBP-like domain of iGluRs is thought to play a role in
the initial assembly of iGluR subunits, but it is not
well understood how this domain is arranged and
functions in intact iGluR. Kainate receptors have five
subunits, GluR5, GluR6, GluR7, KA1, and KA2, which are
structurally similar to AMPA and NMDA subunits of
ionotropic glutamate receptors. KA1 and KA2 subunits can
only form functional receptors with one of the GluR5-7
subunits. Moreover, GluR5-7 can also form functional
homomeric receptor channels activated by kainate and
glutamate when expressed in heterologous systems.
Kainate receptors are involved in excitatory
neurotransmission by activating postsynaptic receptors
and in inhibitory neurotransmission by modulating
release of the inhibitory neurotransmitter GABA through
a presynaptic mechanism. Kainate receptors are closely
related to AMAP receptors. In contrast of AMPA
receptors, kainate receptors play only a minor role in
signaling at synapses and their function is not well
defined.
Length = 327
Score = 25.3 bits (56), Expect = 9.1
Identities = 7/38 (18%), Positives = 21/38 (55%), Gaps = 1/38 (2%)
Query: 9 VVLCANPQTVREILLAAEELNMIDS-GEYVFFNIELFS 45
+++ + + E+L A+++ M+ Y+ N++L +
Sbjct: 185 IIIDCSADILIELLKQAQQVGMMSEYYHYIITNLDLHT 222
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 0.130 0.371
Gapped
Lambda K H
0.267 0.0766 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,064,749
Number of extensions: 509883
Number of successful extensions: 439
Number of sequences better than 10.0: 1
Number of HSP's gapped: 426
Number of HSP's successfully gapped: 36
Length of query: 123
Length of database: 10,937,602
Length adjustment: 85
Effective length of query: 38
Effective length of database: 7,167,512
Effective search space: 272365456
Effective search space used: 272365456
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 (24.1 bits)