RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12591
(144 letters)
>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 = 156 bits (397), Expect = 1e-46
Identities = 55/110 (50%), Positives = 72/110 (65%), Gaps = 5/110 (4%)
Query: 1 VSFWSTSPELSNKQRFEYFTRTIPSDHHQVKAMVEIVKKLGWSYVSIIYEESNYGVKAFE 60
+S+ STSPELS+K R++YF+RT+P D Q +AMV+IVK W+YVS + E NYG K E
Sbjct: 131 ISYASTSPELSDKTRYDYFSRTVPPDSFQAQAMVDIVKAFNWTYVSTVASEGNYGEKGIE 190
Query: 61 ELEVLLAKYSICIAIKEKLVKDSGVAEETAYDDIVLKLLTKPRARG--LF 108
E L A+ ICIA EK+ A E +D+I+ KLL+KP AR LF
Sbjct: 191 AFEKLAAERGICIAGSEKIPSS---ATEEEFDNIIRKLLSKPNARVVVLF 237
>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 = 107 bits (269), Expect = 7e-29
Identities = 41/123 (33%), Positives = 60/123 (48%), Gaps = 14/123 (11%)
Query: 1 VSFWSTSPELSNKQRFEYFTRTIPSDHHQVKAMVEIVKKLGWSYVSIIYEESNYGVKAFE 60
+S+ +TSP LS+K +F F RT+PSD Q A+V ++K GW++V ++Y + +YG
Sbjct: 119 ISYGATSPLLSDKLQFPSFFRTVPSDTSQALAIVALLKHFGWTWVGLVYSDDDYGRSGLS 178
Query: 61 ELEVLLAKYSICIAIKEKLVKDSGVAEETAYDDIVLKLLTKPR-----------ARGLFK 109
+LE L K ICIA E + S E I+ KL + A LF
Sbjct: 179 DLEEELEKNGICIAFVEAIPPSS---TEEDIKRILKKLKSSTARVIVVFGDEDDALRLFC 235
Query: 110 RLK 112
Sbjct: 236 EAY 238
>gnl|CDD|107370 cd06375, PBP1_mGluR_groupII, Ligand binding domain of the group II
metabotropic glutamate receptor. Ligand binding domain
of the group II metabotropic glutamate receptor, a
family that contains mGlu2R and mGlu3R, all of which
inhibit adenylyl cyclase. The metabotropic glutamate
receptor is a member of the family C of
G-protein-coupled receptors that transduce extracellular
signals into G-protein activation and ultimately into
intracellular responses. The mGluRs are classified into
three groups which comprise eight subtypes.
Length = 458
Score = 106 bits (265), Expect = 9e-28
Identities = 48/112 (42%), Positives = 67/112 (59%), Gaps = 5/112 (4%)
Query: 1 VSFWSTSPELSNKQRFEYFTRTIPSDHHQVKAMVEIVKKLGWSYVSIIYEESNYGVKAFE 60
+S+ STS +LS+K R++YF RT+P D +Q KAM EI++ W+YVS + E +YG E
Sbjct: 133 ISYASTSAKLSDKSRYDYFARTVPPDFYQAKAMAEILRFFNWTYVSTVASEGDYGETGIE 192
Query: 61 ELEVLLAKYSICIAIKEKLVKDSGVAEETAYDDIVLKLLTKPRARG--LFKR 110
E +ICIA EK+ A+ +YD ++ KLL KP AR LF R
Sbjct: 193 AFEQEARLRNICIATSEKV---GRSADRKSYDSVIRKLLQKPNARVVVLFTR 241
>gnl|CDD|107369 cd06374, PBP1_mGluR_groupI, Ligand binding domain of the group I
metabotropic glutamate receptor. Ligand binding domain
of the group I metabotropic glutamate receptor, a family
containing mGlu1R and mGlu5R, all of which stimulate
phospholipase C (PLC) hydrolysis. The metabotropic
glutamate receptor is a member of the family C of
G-protein-coupled receptors that transduce extracellular
signals into G-protein activation and ultimately into
intracellular responses. The mGluRs are classified into
three groups which comprise eight subtypes.
Length = 472
Score = 103 bits (257), Expect = 1e-26
Identities = 45/131 (34%), Positives = 73/131 (55%), Gaps = 16/131 (12%)
Query: 1 VSFWSTSPELSNKQRFEYFTRTIPSDHHQVKAMVEIVKKLGWSYVSIIYEESNYGVKAFE 60
+++ +TS +LS+K F+YF R +PSD Q +AM++IVK+ W+YVS ++ E NYG E
Sbjct: 145 IAYSATSIDLSDKTLFKYFLRVVPSDTLQARAMLDIVKRYNWTYVSAVHTEGNYGESGME 204
Query: 61 ELEVLLAKYSICIAIKEKLVKDSGVAEETAYDDIVLKL---LTKPRA----------RGL 107
+ L A +CIA +K+ ++G E ++D ++ KL L K R RGL
Sbjct: 205 AFKELAAHEGLCIAHSDKIYSNAG---EQSFDRLLRKLRSRLPKARVVVCFCEGMTVRGL 261
Query: 108 FKRLKLVKDSG 118
++ + G
Sbjct: 262 LMAMRRLGVGG 272
>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 = 91.0 bits (226), Expect = 6e-23
Identities = 34/83 (40%), Positives = 55/83 (66%)
Query: 1 VSFWSTSPELSNKQRFEYFTRTIPSDHHQVKAMVEIVKKLGWSYVSIIYEESNYGVKAFE 60
+S+ +TSP LS+K++F F RT+PSD Q +A+V+++K GW++V ++Y + +YG + E
Sbjct: 99 ISYSATSPLLSDKEQFPSFLRTVPSDSSQAQAIVDLLKHFGWTWVGLVYSDDDYGRRLLE 158
Query: 61 ELEVLLAKYSICIAIKEKLVKDS 83
LE L K IC+A E + S
Sbjct: 159 LLEEELEKNGICVAFVESIPDGS 181
>gnl|CDD|107371 cd06376, PBP1_mGluR_groupIII, Ligand-binding domain of the group
III metabotropic glutamate receptor. Ligand-binding
domain of the group III metabotropic glutamate receptor,
a family which contains mGlu4R, mGluR6R, mGluR7, and
mGluR8; all of which inhibit adenylyl cyclase. The
metabotropic glutamate receptor is a member of the
family C of G-protein-coupled receptors that transduce
extracellular signals into G-protein activation and
ultimately into intracellular responses. The mGluRs are
classified into three groups which comprise eight
subtypes.
Length = 463
Score = 90.3 bits (224), Expect = 4e-22
Identities = 42/108 (38%), Positives = 66/108 (61%), Gaps = 4/108 (3%)
Query: 1 VSFWSTSPELSNKQRFEYFTRTIPSDHHQVKAMVEIVKKLGWSYVSIIYEESNYGVKAFE 60
+S+ ST+PELS+ +R+++F+R +P D Q +AMV+IVK LGW+YVS + E NYG E
Sbjct: 131 ISYASTAPELSDDRRYDFFSRVVPPDSFQAQAMVDIVKALGWNYVSTLASEGNYGESGVE 190
Query: 61 E-LEVLLAKYSICIAIKEKLVKDSGVAEETAYDDIVLKLLTKPRARGL 107
++ +CIA K+ ++ E +D I+ +LL P AR +
Sbjct: 191 AFTQISREAGGVCIAQSIKIPREPRPGE---FDKIIKRLLETPNARAV 235
>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 = 88.7 bits (220), Expect = 7e-22
Identities = 36/106 (33%), Positives = 60/106 (56%), Gaps = 5/106 (4%)
Query: 1 VSFWSTSPELSNKQRFEYFTRTIPSDHHQVKAMVEIVKKLGWSYVSIIYEESNYGVKAFE 60
+S+ +TSPELS+K R+ F RT+PSD Q +A+ +I+K GW V++IY++ +YG E
Sbjct: 78 ISYGATSPELSDKTRYPTFARTVPSDSKQARAIADILKHFGWKRVAVIYDDDDYGEGGLE 137
Query: 61 ELEVLLAKYSICIAIKEKLVKDSGVAEETAYDDIVLKL-LTKPRAR 105
LE L + + V +A + + ++ +L K +AR
Sbjct: 138 ALEDALRE----AGLNVVAVASEVIASDDDFTALLKELKDIKSKAR 179
>gnl|CDD|107358 cd06363, PBP1_Taste_receptor, Ligand-binding domain of the T1R
taste receptor. Ligand-binding domain of the T1R taste
receptor. The T1R is a member of the family C receptors
within the G-protein coupled receptor superfamily, which
also includes the metabotropic glutamate receptors,
GABAb receptors, the calcium-sensing receptor (CaSR),
the V2R pheromone receptors, and a small group of
uncharacterized orphan receptors.
Length = 410
Score = 81.2 bits (201), Expect = 5e-19
Identities = 32/98 (32%), Positives = 59/98 (60%), Gaps = 2/98 (2%)
Query: 1 VSFWSTSPELSNKQRFEYFTRTIPSDHHQVKAMVEIVKKLGWSYVSIIYEESNYGVKAFE 60
+S+ ++S LSNK+ + F RT+PSD Q++AMV+++++ GW++V+ + + YG +
Sbjct: 135 ISYGASSEVLSNKELYPSFLRTVPSDKDQIEAMVQLLQEFGWNWVAFLGSDDEYGRDGLQ 194
Query: 61 ELEVLLAKYSICIAIKEKLVKDSGVAEETAYDDIVLKL 98
L+A ICIA + + D+ ET Y I+ ++
Sbjct: 195 LFSELIANTGICIAYQGLIPLDT--DPETDYQQILKQI 230
>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 = 80.4 bits (199), Expect = 9e-19
Identities = 35/102 (34%), Positives = 53/102 (51%), Gaps = 3/102 (2%)
Query: 1 VSFWSTSPELSNKQRFEYFTRTIPSDHHQVKAMVEIVKKLGWSYVSIIYEESNYGVKAFE 60
+SF +TSP LS++ ++ YF RT PSD Q A+ ++KK GW V+ IYE+ +YG
Sbjct: 94 LSFAATSPSLSSRLQYPYFFRTTPSDSSQNPAIAALLKKFGWRRVATIYEDDDYGSGGLP 153
Query: 61 ELEVLLAKYSICIAIKEKLVKDSGVAEETAYDDIVLKLLTKP 102
+L L + I I+ + A + D + KL K
Sbjct: 154 DLVDALQEAGIEISYRAAF---PPSANDDDITDALKKLKEKD 192
>gnl|CDD|107356 cd06361, PBP1_GPC6A_like, Ligand-binding domain of the promiscuous
L-alpha-amino acid receptor GPRC6A which is a
broad-spectrum amino acid-sensing receptor. This family
includes the ligand-binding domain of the promiscuous
L-alpha-amino acid receptor GPRC6A which is a
broad-spectrum amino acid-sensing receptor, and its fish
homolog, the 5.24 chemoreceptor. GPRC6A is a member of
the family C of G-protein-coupled receptors that
transduce extracellular signals into G-protein
activation and ultimately into cellular responses.
Length = 403
Score = 79.5 bits (196), Expect = 2e-18
Identities = 36/79 (45%), Positives = 49/79 (62%)
Query: 1 VSFWSTSPELSNKQRFEYFTRTIPSDHHQVKAMVEIVKKLGWSYVSIIYEESNYGVKAFE 60
VS+ ST+ LS+K RF F RT+PSD +Q KAM ++KK GW++V II + +YG A E
Sbjct: 131 VSYASTAEILSDKIRFPSFLRTVPSDFYQTKAMAHLIKKSGWNWVGIIITDDDYGRSALE 190
Query: 61 ELEVLLAKYSICIAIKEKL 79
+ +CIA KE L
Sbjct: 191 TFIIQAEANGVCIAFKEIL 209
>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 = 66.7 bits (163), Expect = 5e-14
Identities = 27/105 (25%), Positives = 52/105 (49%), Gaps = 6/105 (5%)
Query: 1 VSFWSTSPELSNKQRFEYFTRTIPSDHHQVKAMVEIVKKLGWSYVSIIYEESNYGVKAFE 60
+S +T+P L++K+ + Y RT PSD Q +A+ + +K+ W V+I+Y++ +YG E
Sbjct: 95 ISPGATAPGLTDKKGYPYLFRTGPSDEQQAEALADYIKEYNWKKVAILYDDDSYGRGLLE 154
Query: 61 ELEVLLAKYSICIAIKEKLVKDSGVAEETAYDDIVLKLL-TKPRA 104
+ K + + ++ T + ++ KL KP
Sbjct: 155 AFKAAFKKKGGTV-----VGEEYYPLGTTDFTSLLQKLKAAKPDV 194
>gnl|CDD|107359 cd06364, PBP1_CaSR, Ligand-binding domain of the CaSR
calcium-sensing receptor, which is a member of the
family C receptors within the G-protein coupled receptor
superfamily. Ligand-binding domain of the CaSR
calcium-sensing receptor, which is a member of the
family C receptors within the G-protein coupled receptor
superfamily. CaSR provides feedback control of
extracellular calcium homeostasis by responding
sensitively to acute fluctuations in extracellular
ionized Ca2+ concentration. This ligand-binding domain
has homology to the bacterial leucine-isoleucine-valine
binding protein (LIVBP) and a leucine binding protein
(LBP). CaSR is widely expressed in mammalian tissues and
is active in tissues that are not directly involved in
extracellular calcium homeostasis. Moreover, CaSR
responds to aromatic, aliphatic, and polar amino acids,
but not to positively charged or branched chain amino
acids, which suggests that changes in plasma amino acid
levels are likely to modulate whole body calcium
metabolism. Additionally, the family C GPCRs includes at
least two receptors with broad-spectrum amino
acid-sensing properties: GPRC6A which recognizes basic
and various aliphatic amino acids, its gold-fish homolog
the 5.24 chemoreceptor, and a specific taste receptor
(T1R) which responds to aliphatic, polar, charged, and
branched amino acids, but not to aromatic amino acids.
Length = 510
Score = 64.3 bits (156), Expect = 6e-13
Identities = 32/87 (36%), Positives = 48/87 (55%)
Query: 1 VSFWSTSPELSNKQRFEYFTRTIPSDHHQVKAMVEIVKKLGWSYVSIIYEESNYGVKAFE 60
VS+ S+S LSNK +F+ F RTIP+D HQ AM +I++ W++V I + +YG E
Sbjct: 146 VSYASSSRLLSNKNQFKSFLRTIPNDEHQATAMADIIEYFRWNWVGTIAADDDYGRPGIE 205
Query: 61 ELEVLLAKYSICIAIKEKLVKDSGVAE 87
+ + ICI E + + S E
Sbjct: 206 KFREEAEERDICIDFSELISQYSDEEE 232
>gnl|CDD|107341 cd06346, PBP1_ABC_ligand_binding_like_11, Type I periplasmic
ligand-binding domain of uncharacterized ABC (Atpase
Binding Cassette)-type active transport systems that are
predicted to be involved in uptake of amino acids,
peptides, or inorganic ions. This subgroup includes the
type I periplasmic ligand-binding domain of
uncharacterized ABC (Atpase Binding Cassette)-type
active transport systems that are predicted to be
involved in uptake of amino acids, peptides, or
inorganic ions. This subgroup has high sequence
similarity to members of the family of hydrophobic amino
acid transporters (HAAT), such as
leucine/isoleucine/valine binding protein (LIVBP);
however its ligand specificity has not been determined
experimentally.
Length = 312
Score = 56.9 bits (138), Expect = 2e-10
Identities = 24/65 (36%), Positives = 34/65 (52%), Gaps = 7/65 (10%)
Query: 5 STSPELSNKQRFEYFTRTIPSDHHQVKAMVEIVKKLGWSYVSIIYEESNYGV-------K 57
STSP L+ F RT PSD Q +A+ ++ + G+ V+ Y ++YGV K
Sbjct: 100 STSPTLTTLDDNGLFFRTAPSDALQGQALAQLAAERGYKSVATTYINNDYGVGLADAFTK 159
Query: 58 AFEEL 62
AFE L
Sbjct: 160 AFEAL 164
>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 = 51.9 bits (125), Expect = 1e-08
Identities = 22/106 (20%), Positives = 50/106 (47%), Gaps = 6/106 (5%)
Query: 1 VSFWSTSPELSNKQRFEYFTRTIPSDHHQVKAMVEIVKKLGWSYVSIIY-EESNYGVKAF 59
+S+ + LS+K + TRT+P +A++ +++ W ++Y ++S
Sbjct: 96 ISWGCVALSLSDKSEYPTLTRTLPPARKLGEAVLALLRWFNWHVAVVVYSDDSENCFFTL 155
Query: 60 EELEVLLAKYSICIAIKEKLVKDSGVAEETAYDDIVLKLLTKPRAR 105
E LE L ++++ ++ + +SG + +I+ K R+R
Sbjct: 156 EALEAALREFNLTVSHVVFMEDNSGAED---LLEILQD--IKRRSR 196
>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 = 51.8 bits (124), Expect = 1e-08
Identities = 25/109 (22%), Positives = 48/109 (44%), Gaps = 8/109 (7%)
Query: 1 VSFWSTSPELSNKQRFEYFTRTIPSDHHQVKAMVEIVKKLGWSYVSIIYE-ESNYGVKAF 59
VS +T+P+L+ + Y R P + +A E + + GW V++IY + YG +
Sbjct: 86 VSLDATAPDLT---GYPYVFRVGPDNEQAGEAAAEYLAEKGWKRVALIYGDDGAYGRERL 142
Query: 60 EELEVLLAKYSICIAIKEKLVKDSGVAEETAYDDIVLKLLTKPRARGLF 108
E + L K I + ++ + E + ++ L P+ +F
Sbjct: 143 EGFKAALKKAGIEVV----AIEYGDLDTEKGFQALLQLLKAAPKPDAIF 187
>gnl|CDD|107360 cd06365, PBP1_Pheromone_receptor, Ligand-binding domain of the V2R
phermone receptor, a member of the family C receptors
within the G-protein coupled receptor superfamily.
Ligand-binding domain of the V2R phermone receptor, a
member of the family C receptors within the G-protein
coupled receptor superfamily, which also includes the
metabotropic glutamate receptor, the GABAb receptor, the
calcium-sensing receptor (CaSR), the T1R taste receptor,
and a small group of uncharacterized orphan receptors.
Length = 469
Score = 45.7 bits (109), Expect = 1e-06
Identities = 17/79 (21%), Positives = 38/79 (48%)
Query: 1 VSFWSTSPELSNKQRFEYFTRTIPSDHHQVKAMVEIVKKLGWSYVSIIYEESNYGVKAFE 60
+++ P LS++ +F + P D MV ++ W++V ++ + + G +
Sbjct: 131 LTYGPFDPLLSDRVQFPSLYQMAPKDTSLPLGMVSLMLHFSWTWVGLVISDDDRGEQFLS 190
Query: 61 ELEVLLAKYSICIAIKEKL 79
+L + + IC+A EK+
Sbjct: 191 DLREEMQRNGICLAFVEKI 209
>gnl|CDD|107263 cd06268, PBP1_ABC_transporter_LIVBP_like, Periplasmic binding
domain of ATP-binding cassette transporter-like systems
that belong to the type I periplasmic binding fold
protein superfamily. Periplasmic binding domain of
ATP-binding cassette transporter-like systems that
belong to the type I periplasmic binding fold protein
superfamily. They are mostly present in archaea and
eubacteria, and are primarily involved in scavenging
solutes from the environment. ABC-type transporters
couple ATP hydrolysis with the uptake and efflux of a
wide range of substrates across bacterial membranes,
including amino acids, peptides, lipids and sterols, and
various drugs. These systems are comprised of
transmembrane domains, nucleotide binding domains, and
in most bacterial uptake systems, periplasmic binding
proteins (PBPs) which transfer the ligand to the
extracellular gate of the transmembrane domains. These
PBPs bind their substrates selectively and with high
affinity. Members of this group include ABC-type
Leucine-Isoleucine-Valine-Binding Proteins (LIVBP),
which are homologous to the aliphatic amidase
transcriptional repressor, AmiC, of Pseudomonas
aeruginosa. The uncharacterized periplasmic components
of various ABC-type transport systems are included in
this group.
Length = 298
Score = 45.5 bits (108), Expect = 2e-06
Identities = 24/65 (36%), Positives = 34/65 (52%), Gaps = 5/65 (7%)
Query: 1 VSFWSTSPELSNKQRFEYFTRTIPSDHHQVKAMVE-IVKKLGWSYVSIIYEESNYGV--- 56
+S +TSP L+ K Y RT PSD Q A+ + + +K V+IIY++ YG
Sbjct: 94 ISPGATSPALTGKGN-PYVFRTAPSDAQQAAALADYLAEKGKVKKVAIIYDDYAYGRGLA 152
Query: 57 KAFEE 61
AF E
Sbjct: 153 AAFRE 157
>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 = 42.3 bits (100), Expect = 2e-05
Identities = 19/73 (26%), Positives = 37/73 (50%)
Query: 1 VSFWSTSPELSNKQRFEYFTRTIPSDHHQVKAMVEIVKKLGWSYVSIIYEESNYGVKAFE 60
+S+ +S+K ++ F RT+P VK+++ ++K W+ S++YE + FE
Sbjct: 95 ISYKCDEEPVSDKSKYPTFARTVPPSIQVVKSVIALLKHFNWNKFSVVYENDSKYSSVFE 154
Query: 61 ELEVLLAKYSICI 73
L+ +I I
Sbjct: 155 TLKEEAELRNITI 167
>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 = 41.0 bits (96), Expect = 6e-05
Identities = 16/62 (25%), Positives = 32/62 (51%), Gaps = 1/62 (1%)
Query: 1 VSFWSTSPELSNKQRFEYFTRTIPSDHHQVKAMVEIVKKLGWSYVSIIYEESNYGVKAFE 60
+S S LS+K+ + PS A++++++ W+ +IIY +S+ G+ +
Sbjct: 91 ISISGGSEGLSDKEESSTTLQLYPSLEDLADALLDLLEYYNWTKFAIIY-DSDEGLSRLQ 149
Query: 61 EL 62
EL
Sbjct: 150 EL 151
>gnl|CDD|107335 cd06340, PBP1_ABC_ligand_binding_like_6, Type I periplasmic
ligand-binding domain of uncharacterized ABC (ATPase
Binding Cassette)-type active transport systems that are
predicted to be involved in transport of amino acids,
peptides, or inorganic ions. This subgroup includes the
type I periplasmic ligand-binding domain of
uncharacterized ABC (ATPase Binding Cassette)-type
active transport systems that are predicted to be
involved in transport of amino acids, peptides, or
inorganic ions. This subgroup has high sequence
similarity to members of the family of hydrophobic amino
acid transporters (HAAT), such as
leucine-isoleucine-valine-binding protein (LIVBP);
however their ligand specificity has not been determined
experimentally.
Length = 347
Score = 40.3 bits (95), Expect = 1e-04
Identities = 14/80 (17%), Positives = 33/80 (41%), Gaps = 7/80 (8%)
Query: 5 STSPELSNKQRFEYFTRTIPSDHHQVKAMVEIVKKLGWSY------VSIIYEESNYGVKA 58
+ S ++ ++ F+Y R P D + M + +K L V++++E++ +G
Sbjct: 102 AVSDSIT-ERGFKYTFRITPHDGMFTRDMFDFLKDLNEKTGKPLKTVALVHEDTEFGTSV 160
Query: 59 FEELEVLLAKYSICIAIKEK 78
E ++ + I
Sbjct: 161 AEAIKKFAKERGFEIVEDIS 180
>gnl|CDD|107339 cd06344, PBP1_ABC_ligand_binding_like_9, Type I periplasmic
ligand-binding domain of uncharacterized ABC (ATPase
Binding Cassette)-type active transport systems that are
predicted to be involved in uptake of amino acids,
peptides, or inorganic ions. This subgroup includes the
type I periplasmic ligand-binding domain of
uncharacterized ABC (ATPase Binding Cassette)-type
active transport systems that are predicted to be
involved in uptake of amino acids, peptides, or
inorganic ions. Members of this group are
sequence-similar to members of the family of ABC-type
hydrophobic amino acid transporters, such as
leucine/isoleucine/valine binding protein (LIVBP);
however their ligand specificity has not been determined
experimentally.
Length = 332
Score = 40.4 bits (95), Expect = 1e-04
Identities = 22/67 (32%), Positives = 32/67 (47%), Gaps = 4/67 (5%)
Query: 5 STSPELSNKQRFEYFTRTIPSDHHQVKAMVEIVKKLGWSY-VSIIY-EESNYGVKAFEEL 62
STS +LSN YF RT+PS+ +A+ + +KK V+I Y S Y +E
Sbjct: 98 STSVKLSNP--GPYFFRTVPSNAVAARALAKYLKKKNKIKKVAIFYNSTSPYSQSLKQEF 155
Query: 63 EVLLAKY 69
L +
Sbjct: 156 TSALLER 162
>gnl|CDD|223755 COG0683, LivK, ABC-type branched-chain amino acid transport
systems, periplasmic component [Amino acid transport and
metabolism].
Length = 366
Score = 37.8 bits (88), Expect = 9e-04
Identities = 24/100 (24%), Positives = 46/100 (46%), Gaps = 6/100 (6%)
Query: 1 VSFWSTSPELSNKQRFEYFTRTIPSDHHQVKAMVE-IVKKLGWSYVSIIYEESNYGVKAF 59
+S +T+P+L+ + RT P+D+ Q A + +VKK G V+II ++ YG
Sbjct: 106 ISPSATAPQLTGRGLKPNVFRTGPTDNQQAAAAADYLVKKGGKKRVAIIGDDYAYGEGLA 165
Query: 60 EELEVLLAKYSICIAIKEKLVKDSGVAEETAYDDIVLKLL 99
+ + L + ++E +T + +V K+
Sbjct: 166 DAFKAALKALGGEVVVEEVY-----APGDTDFSALVAKIK 200
>gnl|CDD|107374 cd06379, PBP1_iGluR_NMDA_NR1, N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the NR1, an essential channel-forming subunit
of the NMDA receptor. N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the NR1, an essential channel-forming subunit
of the NMDA receptor. The ionotropic N-methyl-d-asparate
(NMDA) subtype of glutamate receptor serves critical
functions in neuronal development, functioning, and
degeneration in the mammalian central nervous system.
The functional NMDA receptor is a heterotetramer
ccomposed of two NR1 and two NR2 (A, B, C, and D) or of
NR3 (A and B) subunits. The receptor controls a cation
channel that is highly permeable to monovalent ions and
calcium and exhibits voltage-dependent inhibition by
magnesium. Dual agonists, glutamate and glycine, are
required for efficient activation of the NMDA receptor.
When co-expressed with NR1, the NR3 subunits form
receptors that are activated by glycine alone and
therefore can be classified as excitatory glycine
receptors. NR1/NR3 receptors are calcium-impermeable and
unaffected by ligands acting at the NR2
glutamate-binding site.
Length = 377
Score = 35.5 bits (82), Expect = 0.005
Identities = 22/74 (29%), Positives = 37/74 (50%), Gaps = 1/74 (1%)
Query: 9 ELSNKQRFEYFTRTIPSDHHQVKAMVEIVKKLGWSYVSIIYEESNYGVKAFEELEVLLAK 68
S+K F RT+P HQ +E+++ W+ V ++ + + G A + E LL +
Sbjct: 121 IFSDKNIHLSFLRTVPPYSHQADVWLEMLRSFKWNKVILLVSDDHEGRAAQKRFETLLEE 180
Query: 69 YSICIAIK-EKLVK 81
I IK EK+V+
Sbjct: 181 REIEFKIKVEKVVE 194
>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 = 34.1 bits (79), Expect = 0.016
Identities = 10/54 (18%), Positives = 25/54 (46%)
Query: 1 VSFWSTSPELSNKQRFEYFTRTIPSDHHQVKAMVEIVKKLGWSYVSIIYEESNY 54
++ + + S+K + TRT PS + ++ + + WS +++Y +
Sbjct: 101 LTAGAPAAGFSDKSEYSTLTRTGPSYTKLGEFVLALHEHFNWSRAALLYHDDKN 154
>gnl|CDD|107388 cd06393, PBP1_iGluR_Kainate_GluR5_7, N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the GluR5-7 subunits of Kainate receptor.
N-terminal leucine/isoleucine/valine-binding protein
(LIVBP)-like domain of the GluR5-7 subunits of Kainate
receptor. 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. There are five types of
kainate receptors, 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 = 384
Score = 33.8 bits (77), Expect = 0.023
Identities = 17/70 (24%), Positives = 37/70 (52%), Gaps = 3/70 (4%)
Query: 8 PELSNKQRFEYFTRTIPSDHHQVKAMVEIVKKLGWSYVSIIYEESNYGVKAFEELEVLLA 67
L NK F + P A++++V+ L W +++Y++S G+ +EL + +
Sbjct: 107 HPLDNKDTF--YVNLYPDYASLSHAILDLVQYLKWRSATVVYDDST-GLIRLQELIMAPS 163
Query: 68 KYSICIAIKE 77
+Y+I + I++
Sbjct: 164 RYNIRLKIRQ 173
>gnl|CDD|107362 cd06367, PBP1_iGluR_NMDA, N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the ionotropic N-methyl-d-asparate (NMDA)
subtype of glutamate receptors. N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the ionotropic N-methyl-d-asparate (NMDA)
subtype of glutamate receptors. 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. The function
of the NMDA subtype receptor serves critical functions
in neuronal development, functioning, and degeneration
in the mammalian central nervous system. The functional
NMDA receptor is a heterotetramer comprising two NR1 and
two NR2 (A, B, C, and D) or NR3 (A and B) subunits. The
receptor controls a cation channel that is highly
permeable to monovalent ions and calcium and exhibits
voltage-dependent inhibition by magnesium. Dual
agonists, glutamate and glycine, are required for
efficient activation of the NMDA receptor. Among NMDA
receptor subtypes, the NR2B subunit containing receptors
appear particularly important for pain perception; thus
NR2B-selective antagonists may be useful in the
treatment of chronic pain.
Length = 362
Score = 33.0 bits (76), Expect = 0.038
Identities = 24/98 (24%), Positives = 40/98 (40%), Gaps = 4/98 (4%)
Query: 7 SPELSNKQRFEYFTRTIPSDHHQVKAMVEIVKKLGWSYVSIIYEESNY-GVKAFEE-LEV 64
S +S+K F +T PS Q M+EI+++ W S++ S G + F + +E
Sbjct: 101 SIFMSDKNIHSLFLQTGPSLEQQADVMLEILEEYDWHQFSVVT--SRDPGYRDFLDRVET 158
Query: 65 LLAKYSICIAIKEKLVKDSGVAEETAYDDIVLKLLTKP 102
L + + + L D + A LK L
Sbjct: 159 TLEESFVGWEFQLVLTLDLSDDDGDARLLRQLKKLESR 196
>gnl|CDD|107328 cd06333, PBP1_ABC-type_HAAT_like, Type I periplasmic binding
component of ABC (ATPase Binding Cassette)-type
transport systems that are predicted to be involved in
uptake of amino acids. This subgroup includes the type
I periplasmic binding component of ABC (ATPase Binding
Cassette)-type transport systems that are predicted to
be involved in uptake of amino acids. Members of this
subgroup are sequence-similar to members of the family
of ABC-type hydrophobic amino acid transporters (HAAT),
such as leucine-isoleucine-valine-binding protein
(LIVBP); their ligand specificity has not been
determined experimentally, however.
Length = 312
Score = 31.8 bits (73), Expect = 0.096
Identities = 25/86 (29%), Positives = 40/86 (46%), Gaps = 8/86 (9%)
Query: 21 RTIPSDHHQVKAMVEIVKKLGWSYVSIIYEESNYGVKAFEELEVLLAKYSICIAIKEKL- 79
+T +D +A++ +KK G V+ I YG +EL+ L KY I + E+
Sbjct: 112 KTPQNDRLMAEAILADMKKRGVKTVAFIGFSDAYGESGLKELKALAPKYGIEVVADERYG 171
Query: 80 VKDSGVAEETAYDDIVLKLL-TKPRA 104
D+ V TA +LK+ +P A
Sbjct: 172 RTDTSV---TA---QLLKIRAARPDA 191
>gnl|CDD|107325 cd06330, PBP1_Arsenic_SBP_like, Periplasmic solute-binding domain
of active transport proteins. Periplasmic
solute-binding domain of active transport proteins found
in bacteria and Archaea that is predicted to be involved
in the efflux of toxic compounds. Members of this
subgroup include proteins from Herminiimonas
arsenicoxydans, which is resistant to arsenic and
various heavy metals such as cadmium and zinc. Moreover,
they show significant sequence similarity to the cluster
of AmiC and active transport systems for short-chain
amides and urea (FmdDEF), and thus are likely to exhibit
a ligand-binding mode similar to that of the amide
sensor protein AmiC from Pseudomonas aeruginosa.
Length = 346
Score = 31.5 bits (72), Expect = 0.10
Identities = 14/66 (21%), Positives = 21/66 (31%), Gaps = 11/66 (16%)
Query: 5 STSPELSNKQRFEYFTRTIPSDHHQVKAMVEIVKKLG-----WSYVSIIYEESNYG---V 56
+P L+ + Y RT S A KL W+ ++ Y YG
Sbjct: 99 PGTPRLTEEPDNPYVFRTRNSTIMDAVAGALYAAKLDKKAKTWATINPDYA---YGQDAW 155
Query: 57 KAFEEL 62
F+
Sbjct: 156 ADFKAA 161
>gnl|CDD|107337 cd06342, PBP1_ABC_LIVBP_like, Type I periplasmic ligand-binding
domain of ABC (Atpase Binding Cassette)-type active
transport systems that are involved in the transport of
all three branched chain aliphatic amino acids (leucine,
isoleucine and valine). This subgroup includes the type
I periplasmic ligand-binding domain of ABC (Atpase
Binding Cassette)-type active transport systems that are
involved in the transport of all three branched chain
aliphatic amino acids (leucine, isoleucine and valine).
This subgroup also includes a leucine-specific binding
protein (or LivK), which is very similar in sequence and
structure to leucine-isoleucine-valine binding protein
(LIVBP). ABC-type active transport systems are
transmembrane proteins that function in the transport of
diverse sets of substrates across extra- and
intracellular membranes, including carbohydrates, amino
acids, inorganic ions, dipeptides and oligopeptides,
metabolic products, lipids and sterols, and heme, to
name a few.
Length = 334
Score = 31.4 bits (72), Expect = 0.13
Identities = 14/52 (26%), Positives = 29/52 (55%), Gaps = 2/52 (3%)
Query: 5 STSPELSNKQRFEYFTRTIPSDHHQVKAMVE-IVKKLGWSYVSIIYEESNYG 55
+T+P+L+ ++ ++ R + D Q A + V+ L V+II +++ YG
Sbjct: 98 ATNPKLT-ERGYKNVFRVVARDDQQGPAAAKYAVETLKAKKVAIIDDKTAYG 148
>gnl|CDD|188551 TIGR04036, LLM_CE1758_fam, putative luciferase-like
monooxygenase, FMN-dependent, CE1758 family. This
tightly conserved subfamily of the bacterial
luciferase-like monooxygenase (LLM) family, with
members showing > 60 % pairwise sequence identity,
includes proteins from both species with and species
without the ability to make coenzyme F420. Therefore,
the like cofactor is FMN rather than F420. The presence
of three members in Kineococcus radiotolerans SRS30216
and two in Saccharopolyspora erythraea NRRL 2338
suggest closely related (subfamily) rather than exactly
conserved (equivalog) function. Gene neighborhoods
around members are not conserved [Unknown function,
Enzymes of unknown specificity].
Length = 355
Score = 28.6 bits (64), Expect = 1.2
Identities = 10/20 (50%), Positives = 14/20 (70%)
Query: 20 TRTIPSDHHQVKAMVEIVKK 39
T P++H ++KAMVEI K
Sbjct: 17 TGRTPTEHERIKAMVEIALK 36
>gnl|CDD|107330 cd06335, PBP1_ABC_ligand_binding_like_2, Type I periplasmic
ligand-binding domain of uncharacterized ABC (ATPase
Binding Cassette)-type active transport systems that are
predicted to be involved in transport of amino acids,
peptides, or inorganic ions. This subgroup includes the
type I periplasmic ligand-binding domain of
uncharacterized ABC (ATPase Binding Cassette)-type
active transport systems that are predicted to be
involved in transport of amino acids, peptides, or
inorganic ions. Members of this group are
sequence-similar to members of the family of ABC-type
hydrophobic amino acid transporters, such as
leucine-isoleucine-valine-binding protein (LIVBP);
however their ligand specificity has not been determined
experimentally.
Length = 347
Score = 28.0 bits (63), Expect = 1.7
Identities = 12/52 (23%), Positives = 25/52 (48%), Gaps = 1/52 (1%)
Query: 21 RTIPSDHHQVKAMVE-IVKKLGWSYVSIIYEESNYGVKAFEELEVLLAKYSI 71
R D Q +V+ VK+ G+ V+++ + + +G ++L LA +
Sbjct: 116 RVSADDSIQAPFLVDEAVKRGGFKKVALLLDNTGWGRSNRKDLTAALAARGL 167
>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 = 28.0 bits (63), Expect = 1.8
Identities = 9/24 (37%), Positives = 13/24 (54%)
Query: 31 KAMVEIVKKLGWSYVSIIYEESNY 54
+A +IVK W +IIYE +
Sbjct: 118 RAYADIVKSFNWKSFTIIYESAEG 141
>gnl|CDD|107363 cd06368, PBP1_iGluR_non_NMDA_like, N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the non-NMDA (N-methyl-d-asparate) subtypes of
ionotropic glutamate receptors. N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the non-NMDA (N-methyl-d-asparate) subtypes of
ionotropic glutamate receptors. 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-d -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. Non-NMDA receptors have faster
kinetics, are most often only 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 several forms of synaptic plasticity and are
thought to play an important role in the development of
synaptic pathways. Non-NMDA receptors include
alpha-amino-3-hydroxy-5-methyl-4-isoxazole proprionate
(AMPA) and kainate receptors.
Length = 324
Score = 27.2 bits (61), Expect = 2.8
Identities = 12/41 (29%), Positives = 20/41 (48%), Gaps = 4/41 (9%)
Query: 31 KAMVEIVKKLGWSYVSIIYEESNYGVKAFEELEVLLAKYSI 71
A+++++K GW IY +S+ G L+ LL S
Sbjct: 116 DALLDLIKYFGWRKFVYIY-DSDEG---LLRLQELLDALSP 152
>gnl|CDD|221394 pfam12047, DNMT1-RFD, Cytosine specific DNA methyltransferase
replication foci domain. This domain is part of a
cytosine specific DNA methyltransferase enzyme. It
functions non-catalytically to target the protein
towards replication foci. This allows the DNMT1 protein
to methylate the correct residues. This domain targets
DMAP1 and HDAC2 to the replication foci during the S
phase of mitosis. They are thought to have some
importance in conversion of critical histone lysine
moieties.
Length = 143
Score = 26.5 bits (59), Expect = 3.4
Identities = 6/39 (15%), Positives = 20/39 (51%), Gaps = 1/39 (2%)
Query: 63 EVLLAKYSICIAIKEKLVKDSGVAEETAYDDIVLKLLTK 101
E + K + + + + L ++ V + + +D++ ++L
Sbjct: 106 EPVFEKARVTVEVLKFLKRNPRVPDLS-LEDLLARVLRS 143
>gnl|CDD|234862 PRK00912, PRK00912, ribonuclease P protein component 3;
Provisional.
Length = 237
Score = 26.9 bits (60), Expect = 4.0
Identities = 36/150 (24%), Positives = 52/150 (34%), Gaps = 28/150 (18%)
Query: 21 RTIPSDHHQVKAMVEIVKKLGWSYVSIIYEESNYGVKAFEELEVLLA---KYSICIAIKE 77
+P + V ++ LG+S +++ Y ++ ELE LL + I
Sbjct: 9 HAVPDGYDTVLRLISEASHLGYSGIALSNHSDKYP-ESKPELEDLLGFEIFRGVEIVASN 67
Query: 78 -----KLVK--------------DSGV---AEETAYDDIVLKLLTKPRARGLFKRL-KLV 114
LV D V A E DI+ TK + G+ L K
Sbjct: 68 PSKLRGLVGKFRKKVDVLAVHGGDEKVNRAACENPRVDILSHPYTKRKDSGINHVLAKEA 127
Query: 115 KDSGVAEETAYDDIVLKLLTKPRARAVSEI 144
+ VA E DI LK RAR +S
Sbjct: 128 ARNNVAIEFNLRDI-LKSRGGRRARTLSNF 156
>gnl|CDD|149800 pfam08854, DUF1824, Domain of unknown function (DUF1824). This
uncharacterized family of proteins are principally
found in cyanobacteria.
Length = 125
Score = 26.4 bits (59), Expect = 4.3
Identities = 14/53 (26%), Positives = 20/53 (37%), Gaps = 15/53 (28%)
Query: 6 TSPELSNKQR-------------FEYFTRTI--PSDHHQVKAMVEIVKKLGWS 43
+P+LS QR ++FT I PS + A+ LGW
Sbjct: 12 IAPQLSPAQRKKLRQELVALMDNADWFTIGIMAPSAEEAINALRSYEAALGWP 64
>gnl|CDD|191610 pfam06799, DUF1230, Protein of unknown function (DUF1230). This
family consists of several hypothetical plant and
photosynthetic bacterial proteins of around 160 residues
in length. The function of this family is unknown
although looking at the species distribution the protein
may play a part in photosynthesis.
Length = 145
Score = 26.0 bits (58), Expect = 5.1
Identities = 10/20 (50%), Positives = 12/20 (60%), Gaps = 7/20 (35%)
Query: 40 LGWSYV-------SIIYEES 52
LGWSYV ++ YEES
Sbjct: 85 LGWSYVRKRLLSETVEYEES 104
>gnl|CDD|107340 cd06345, PBP1_ABC_ligand_binding_like_10, Type I periplasmic
ligand-binding domain of uncharacterized ABC (Atpase
Binding Cassette)-type active transport systems that are
predicted to be involved in uptake of amino acids,
peptides, or inorganic ions. This subgroup includes the
type I periplasmic ligand-binding domain of
uncharacterized ABC (Atpase Binding Cassette)-type
active transport systems that are predicted to be
involved in uptake of amino acids, peptides, or
inorganic ions. This subgroup has high sequence
similarity to members of the family of hydrophobic amino
acid transporters (HAAT), such as
leucine/isoleucine/valine binding protein (LIVBP);
however its ligand specificity has not been determined
experimentally.
Length = 344
Score = 26.6 bits (59), Expect = 5.9
Identities = 16/86 (18%), Positives = 42/86 (48%), Gaps = 8/86 (9%)
Query: 5 STSPELS---NKQRFEYFTRTIPSDHHQVKAMVEIVK-----KLGWSYVSIIYEESNYGV 56
+ SPE++ + + ++Y R P++ +++ + +K K G+ +I+ E++ +G
Sbjct: 99 AASPEITTADDYETYKYVFRAGPTNSSYAQSVADALKETLVDKHGFKTAAIVAEDAAWGK 158
Query: 57 KAFEELEVLLAKYSICIAIKEKLVKD 82
++ LL + + + E+ D
Sbjct: 159 GIDAGIKALLPEAGLEVVSVERFSPD 184
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
0.317 0.133 0.371
Gapped
Lambda K H
0.267 0.0714 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,341,228
Number of extensions: 671308
Number of successful extensions: 592
Number of sequences better than 10.0: 1
Number of HSP's gapped: 587
Number of HSP's successfully gapped: 49
Length of query: 144
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 56
Effective length of database: 7,034,450
Effective search space: 393929200
Effective search space used: 393929200
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 (21.7 bits)
S2: 54 (24.6 bits)