RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13446
(121 letters)
>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 = 86.6 bits (215), Expect = 2e-21
Identities = 34/108 (31%), Positives = 48/108 (44%), Gaps = 10/108 (9%)
Query: 11 GVHFDTSSASLVQGISTAIKVYAYGVEDYMSDSSNANLSLNTQLSCDGVGESRWKTGDRF 70
GV DT SL + A+ + A E + D ++C R +G
Sbjct: 248 GVGLDTWY-SLEARVRDAVAIVARAAESLLRDKGAL---PEPPVNCYDTANKRESSGQYL 303
Query: 71 YRYLRNVSVEGDTGKPNVEFTADGVLKAAELKIMNLRPNLGSQLKWEE 118
R+L NV+ +G+TG +V F DG L +L I+NLR N KWE
Sbjct: 304 ARFLMNVTFDGETG--DVSFNEDGYLSNPKLVIINLRRN----RKWER 345
>gnl|CDD|107373 cd06378, PBP1_iGluR_NMDA_NR2, N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the NR2 subunit of NMDA receptor family.
N-terminal leucine/isoleucine/valine-binding protein
(LIVBP)-like domain of the NR2 subunit of NMDA receptor
family. 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 composed 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. 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 = 85.1 bits (211), Expect = 9e-21
Identities = 23/108 (21%), Positives = 36/108 (33%), Gaps = 11/108 (10%)
Query: 11 GVHFDTSSASLVQGISTAIKVYAYGVEDYMSDSSNANLSLNTQLSCDGVGESRWKTGDRF 70
V +D SL + + + A G + + SC G E R D
Sbjct: 248 SVSYDGWRYSLRARVRDGVAIIATGASAMLRQHGFI---PEAKGSCYGQAEKR----DLP 300
Query: 71 YRYLRNVSVEGDTGKPNVEFTADGVLKAAELKIMNLRPNLGSQLKWEE 118
L + ++ FT DG L +L +++L WEE
Sbjct: 301 PNTLHRYMMNVTWEGRDLSFTEDGYLVNPKLVVISLNKERV----WEE 344
>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 = 43.6 bits (103), Expect = 5e-06
Identities = 21/53 (39%), Positives = 27/53 (50%), Gaps = 3/53 (5%)
Query: 55 SCDGVGESRWKTGDRFYRYLRNVSVEGDTGKPNVEFTADGVLKAAELKIMNLR 107
C G W+TG F R L + G+TG+ VEF DG K A IMN++
Sbjct: 302 ECVGNTVI-WETGPLFKRALMSSKYPGETGR--VEFNDDGDRKFANYDIMNIQ 351
>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 = 31.4 bits (72), Expect = 0.069
Identities = 24/75 (32%), Positives = 32/75 (42%), Gaps = 9/75 (12%)
Query: 20 SLVQGISTAIKVYAYGVEDYMSDSSNANLSLNTQLSCDGVGESRWKTGDRFYRYLRNVSV 79
S VQ + A+ A+ + + D L T CD + G + YLRNVS
Sbjct: 353 SKVQFVIDAVYAMAHALHNMHRD-----LCPGTTGLCD---AMKPIDGRKLLFYLRNVSF 404
Query: 80 EGDTGKPNVEFTADG 94
G G P V F A+G
Sbjct: 405 SGLAGGP-VRFDANG 418
>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 = 30.5 bits (69), Expect = 0.16
Identities = 24/103 (23%), Positives = 38/103 (36%), Gaps = 20/103 (19%)
Query: 8 KKKGVHFDTSSASLVQGIST----AIKVYAYGVEDYMSDSSNANLSLNTQLSCDGVGESR 63
KK + + G + A+ + A+ + + + D N L
Sbjct: 254 KKLANRCTPALDTEPNGYALLAYDAVYLLAHALNEALRDDPNITRGLWVD---------- 303
Query: 64 WKTGDRFYRYLRNVSVEGDTGKPNVEFTA-DGVLKAAELKIMN 105
G + YLRNV+ EG TG V+F G L+I+N
Sbjct: 304 ---GSQLLEYLRNVNFEGLTG--PVQFDDNGGRRPDYSLEILN 341
>gnl|CDD|171770 PRK12851, groEL, chaperonin GroEL; Reviewed.
Length = 541
Score = 28.9 bits (65), Expect = 0.54
Identities = 14/40 (35%), Positives = 24/40 (60%), Gaps = 2/40 (5%)
Query: 75 RNVSVEGDTGKPNVEFTADGVLKAAELKIMNLRPNLGSQL 114
RNV ++ G P + T DGV A E+++ + N+G+Q+
Sbjct: 36 RNVVIDKSFGAPTI--TNDGVTIAKEIELEDKFENMGAQM 73
>gnl|CDD|237231 PRK12850, groEL, chaperonin GroEL; Reviewed.
Length = 544
Score = 28.5 bits (64), Expect = 0.75
Identities = 15/40 (37%), Positives = 24/40 (60%), Gaps = 2/40 (5%)
Query: 75 RNVSVEGDTGKPNVEFTADGVLKAAELKIMNLRPNLGSQL 114
RNV +E G P + T DGV A E+++ + N+G+Q+
Sbjct: 36 RNVVLEKSFGAPRI--TKDGVTVAKEIELEDKFENMGAQM 73
>gnl|CDD|177123 MTH00048, COX1, cytochrome c oxidase subunit I; Provisional.
Length = 511
Score = 28.5 bits (64), Expect = 0.83
Identities = 14/41 (34%), Positives = 22/41 (53%), Gaps = 5/41 (12%)
Query: 9 KKGVHFDTSSASLVQGISTAIKVYAYGVEDYMSDSSNANLS 49
K V F SS +++ G+ T IKV+++ YM +S S
Sbjct: 298 KTAVFF--SSVTMIIGVPTGIKVFSW---LYMLLNSRVRKS 333
>gnl|CDD|233828 TIGR02348, GroEL, chaperonin GroL. This family consists of GroEL,
the larger subunit of the GroEL/GroES cytosolic
chaperonin. It is found in bacteria, organelles derived
from bacteria, and occasionally in the Archaea. The
bacterial GroEL/GroES group I chaperonin is replaced a
group II chaperonin, usually called the thermosome in
the Archaeota and CCT (chaperone-containing TCP) in the
Eukaryota. GroEL, thermosome subunits, and CCT subunits
all fall under the scope of pfam00118 [Protein fate,
Protein folding and stabilization].
Length = 524
Score = 28.4 bits (64), Expect = 0.83
Identities = 16/40 (40%), Positives = 24/40 (60%), Gaps = 2/40 (5%)
Query: 75 RNVSVEGDTGKPNVEFTADGVLKAAELKIMNLRPNLGSQL 114
RNV +E G P + T DGV A E+++ + N+G+QL
Sbjct: 34 RNVVLEKSFGAPTI--TKDGVTVAKEIELEDKFENMGAQL 71
>gnl|CDD|235620 PRK05841, flgE, flagellar hook protein FlgE; Validated.
Length = 603
Score = 27.9 bits (62), Expect = 1.3
Identities = 18/95 (18%), Positives = 34/95 (35%), Gaps = 2/95 (2%)
Query: 9 KKGVHFDTSSASLVQGISTAIKVYAYGVEDYMSDSSNANLSLNTQLSCDGVGESRWKTGD 68
KKG+ D+ + + ST +++Y + Y+ S + S + W+
Sbjct: 343 KKGISRDSVAIK-IPSYSTEVEIYDKAGDKYLLQSEYYMTNSGDPTSSPRKNQ-TWEVKS 400
Query: 69 RFYRYLRNVSVEGDTGKPNVEFTADGVLKAAELKI 103
+ D V F A +KAA + +
Sbjct: 401 YIVDPKNKTPINTDPTWEIVGFDATHKMKAAPMTL 435
>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 = 27.9 bits (62), Expect = 1.3
Identities = 11/35 (31%), Positives = 14/35 (40%), Gaps = 2/35 (5%)
Query: 87 NVEFTADGVLKAAELKIMNLRPNLGSQ--LKWEES 119
V F DGV L I+ L + G + W S
Sbjct: 289 TVSFDEDGVRSNFTLDIIELNRSRGWRKVGTWNGS 323
>gnl|CDD|237232 PRK12852, groEL, chaperonin GroEL; Reviewed.
Length = 545
Score = 27.5 bits (61), Expect = 2.0
Identities = 15/40 (37%), Positives = 24/40 (60%), Gaps = 2/40 (5%)
Query: 75 RNVSVEGDTGKPNVEFTADGVLKAAELKIMNLRPNLGSQL 114
RNV +E G P + T DGV A E+++ + N+G+Q+
Sbjct: 36 RNVVIEKSFGAPRI--TKDGVTVAKEIELEDKFENMGAQM 73
>gnl|CDD|107375 cd06380, PBP1_iGluR_AMPA, N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the AMPA receptor. N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the AMPA
(alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic
acid) receptor, a member of the glutamate-receptor ion
channels (iGluRs). AMPA receptors are the major
mediators of excitatory synaptic transmission in the
central nervous system. 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. AMPA
receptors consist of four types of subunits (GluR1,
GluR2, GluR3, and GluR4) which combine to form a
tetramer and play an important roles in mediating the
rapid excitatory synaptic current.
Length = 382
Score = 27.3 bits (61), Expect = 2.4
Identities = 18/64 (28%), Positives = 25/64 (39%), Gaps = 3/64 (4%)
Query: 56 CDGVGESRWKTGDRFYRYLRNVSVEGDTGKPNVEFTADGVLKAAELKIMNLRPNLGSQ-L 114
C W+ G R L+ V EG TG NV+F G L ++ L+ +
Sbjct: 316 CLANPAVPWEHGIDIERALKKVQFEGLTG--NVQFDEFGQRTNYTLDVVELKTRGLRKVG 373
Query: 115 KWEE 118
W E
Sbjct: 374 YWNE 377
>gnl|CDD|107384 cd06389, PBP1_iGluR_AMPA_GluR2, N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the GluR2 subunit of the AMPA receptor.
N-terminal leucine/isoleucine/valine-binding protein
(LIVBP)-like domain of the GluR2 subunit of the AMPA
(alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic
acid) receptor. The AMPA receptor is a member of the
glutamate-receptor ion channels (iGluRs) which are the
major mediators of excitatory synaptic transmission in
the central nervous system. AMPA receptors are composed
of four types of subunits (GluR1, GluR2, GluR3, and
GluR4) which combine to form a tetramer and play an
important role in mediating the rapid excitatory
synaptic current. Furthermore, this N-terminal domain of
the iGluRs has homology with LIVBP, a bacterial
periplasmic binding protein, as well as with the
structurally related glutamate-binding domain of the
G-protein-coupled metabotropic receptors (mGluRs).
Length = 370
Score = 26.5 bits (58), Expect = 3.9
Identities = 16/46 (34%), Positives = 23/46 (50%), Gaps = 2/46 (4%)
Query: 64 WKTGDRFYRYLRNVSVEGDTGKPNVEFTADGVLKAAELKIMNLRPN 109
W G R L+ V VEG TG N++F +G + +M L+ N
Sbjct: 311 WGQGVEIERALKQVQVEGLTG--NIKFDQNGKRINYTINVMELKSN 354
>gnl|CDD|234344 TIGR03754, conj_TOL_TraD, conjugative coupling factor TraD, TOL
family. Members of this protein are assigned by
homology to the TraD family of conjugative coupling
factor. This particular clade serves as a marker for an
extended gene region that occurs occasionally on
plasmids, including the toluene catabolism TOL plasmid.
More commonly, the gene region is chromosomal, flanked
by various markers of conjugative transfer and
insertion.
Length = 643
Score = 26.2 bits (58), Expect = 5.0
Identities = 10/37 (27%), Positives = 17/37 (45%)
Query: 25 ISTAIKVYAYGVEDYMSDSSNANLSLNTQLSCDGVGE 61
+S A +Y +G++D + D+ L CD E
Sbjct: 467 VSVAGHIYKFGIDDGLPDAKYTEQKPPINLHCDEFNE 503
>gnl|CDD|223941 COG1009, NuoL, NADH:ubiquinone oxidoreductase subunit 5 (chain
L)/Multisubunit Na+/H+ antiporter, MnhA subunit [Energy
production and conversion / Inorganic ion transport and
metabolism].
Length = 606
Score = 26.1 bits (58), Expect = 6.4
Identities = 13/35 (37%), Positives = 17/35 (48%), Gaps = 6/35 (17%)
Query: 11 GVHFDTSS---ASLVQGISTAIKVYAYGVEDYMSD 42
G+ D S A LV G+ I +Y+ G YMS
Sbjct: 69 GLRIDGLSLLMALLVTGVGFLIHLYSIG---YMSH 100
>gnl|CDD|172594 PRK14104, PRK14104, chaperonin GroEL; Provisional.
Length = 546
Score = 25.8 bits (56), Expect = 7.8
Identities = 14/40 (35%), Positives = 24/40 (60%), Gaps = 2/40 (5%)
Query: 75 RNVSVEGDTGKPNVEFTADGVLKAAELKIMNLRPNLGSQL 114
RNV ++ G P + T DGV A E+++ + N+G+Q+
Sbjct: 36 RNVVLDKSFGAPRI--TKDGVTVAKEIELEDKFENMGAQM 73
>gnl|CDD|178331 PLN02730, PLN02730, enoyl-[acyl-carrier-protein] reductase.
Length = 303
Score = 25.5 bits (56), Expect = 9.7
Identities = 19/55 (34%), Positives = 27/55 (49%), Gaps = 4/55 (7%)
Query: 8 KKKGVHFDTSSASLVQGISTAIKVYAYGVEDYMSDSSNANLSLNTQLSCDGVGES 62
+K + +T SA + S A K A G D M + S AN L +L+ D VG +
Sbjct: 213 RKYKIRVNTISAGPLG--SRAAK--AIGFIDDMIEYSYANAPLQKELTADEVGNA 263
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
0.311 0.129 0.363
Gapped
Lambda K H
0.267 0.0743 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,711,616
Number of extensions: 458932
Number of successful extensions: 291
Number of sequences better than 10.0: 1
Number of HSP's gapped: 286
Number of HSP's successfully gapped: 24
Length of query: 121
Length of database: 10,937,602
Length adjustment: 84
Effective length of query: 37
Effective length of database: 7,211,866
Effective search space: 266839042
Effective search space used: 266839042
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 53 (24.2 bits)