RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17128
(124 letters)
>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 = 101 bits (253), Expect = 6e-27
Identities = 36/103 (34%), Positives = 53/103 (51%), Gaps = 19/103 (18%)
Query: 23 MCRQLQNGVQALFGPSDALLGPHVQSICEALDVPHMESRLDLELNSKE-FSVNLYPSQKL 81
+C LQ GV A+FGPS + VQSIC+A ++PH+++R D E S F++NLYPS
Sbjct: 56 VCDLLQQGVAAIFGPSSSEASSIVQSICDAKEIPHIQTRWDPEPKSNRQFTINLYPSN-- 113
Query: 82 LNAAFKDVIRFLNWTKKLLNAAFKDVIRFLNWTKVAIVYEEDN 124
L+ A+ D+++ NW I+YE
Sbjct: 114 ----------------ADLSRAYADIVKSFNWKSFTIIYESAE 140
>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 = 91.6 bits (228), Expect = 2e-23
Identities = 32/102 (31%), Positives = 50/102 (49%), Gaps = 18/102 (17%)
Query: 23 MCRQLQNGVQALFGPSDALLGPHVQSICEALDVPHMESRLDLELNSKEFSVNLYPSQKLL 82
C L GV A+FGPS + VQSIC+AL++PH+ + ++F++NLYPS
Sbjct: 55 ACDLLSQGVAAIFGPSSSSSANTVQSICDALEIPHITTSWSPNPKPRQFTINLYPSM--- 111
Query: 83 NAAFKDVIRFLNWTKKLLNAAFKDVIRFLNWTKVAIVYEEDN 124
+ L+ A D+I++ W K +Y+ D
Sbjct: 112 ---------------RDLSDALLDLIKYFGWRKFVYIYDSDE 138
>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 = 65.8 bits (160), Expect = 8e-14
Identities = 35/77 (45%), Positives = 44/77 (57%), Gaps = 8/77 (10%)
Query: 24 CRQLQNGVQALFGPSDALLGPHVQSICEALDVPHMESR-----LDLELNSKEFSVNLYPS 78
C QL GV A+FGPS VQSIC AL+VPH++ R LD N F VNLYP
Sbjct: 66 CDQLALGVVAIFGPSQGSCTNAVQSICNALEVPHIQLRWKHHPLD---NKDTFYVNLYPD 122
Query: 79 QKLLNAAFKDVIRFLNW 95
L+ A D++++L W
Sbjct: 123 YASLSHAILDLVQYLKW 139
>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 = 64.5 bits (157), Expect = 3e-13
Identities = 33/107 (30%), Positives = 50/107 (46%), Gaps = 23/107 (21%)
Query: 23 MCRQLQN-GVQALFGPSDALLGPHVQSICEALDVPH----MESRLDLELNSKEFSVNLYP 77
+C L + GV A+FGP+ + VQSIC+AL++PH S + ++ LYP
Sbjct: 55 VCDLLVSQGVAAIFGPTSSESASAVQSICDALEIPHISISGGSEGLSDKEESSTTLQLYP 114
Query: 78 SQKLLNAAFKDVIRFLNWTKKLLNAAFKDVIRFLNWTKVAIVYEEDN 124
S + L A D++ + NWTK AI+Y+ D
Sbjct: 115 SL------------------EDLADALLDLLEYYNWTKFAIIYDSDE 143
>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 = 50.5 bits (121), Expect = 2e-08
Identities = 22/107 (20%), Positives = 38/107 (35%), Gaps = 22/107 (20%)
Query: 22 VMCRQLQNGVQALFGPSDALLGPHVQSICEALDVPHME-SRLDLELNSKE---FSVNLYP 77
C GV A+ GPS + + V + A +P + EL+ K P
Sbjct: 42 AACLLKSKGVVAVIGPSCSSVAIAVARLAGAFGIPMISYGATSPELSDKTRYPTFARTVP 101
Query: 78 SQKLLNAAFKDVIRFLNWTKKLLNAAFKDVIRFLNWTKVAIVYEEDN 124
S A D+++ W + VA++Y++D+
Sbjct: 102 SDSKQARAIADILKHFGWKR------------------VAVIYDDDD 130
>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 = 47.1 bits (112), Expect = 3e-07
Identities = 27/107 (25%), Positives = 40/107 (37%), Gaps = 24/107 (22%)
Query: 23 MCRQL--QNGVQALFGPSDALLGPHVQSICEALDVPHME-SRLDLELNSKE---FSVNLY 76
+C L GV A+ GPS + V S+ AL +P + S L+ KE +
Sbjct: 62 LCSLLEKSRGVVAVIGPSSSSSAEAVASLLGALHIPQISYSATSPLLSDKEQFPSFLRTV 121
Query: 77 PSQKLLNAAFKDVIRFLNWTKKLLNAAFKDVIRFLNWTKVAIVYEED 123
PS A D+++ WT V +VY +D
Sbjct: 122 PS------------------DSSQAQAIVDLLKHFGWTWVGLVYSDD 150
>gnl|CDD|107389 cd06394, PBP1_iGluR_Kainate_KA1_2, N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the KA1 and KA2 subunits of Kainate receptor.
N-terminal leucine/isoleucine/valine-binding protein
(LIVBP)-like domain of the KA1 and KA2 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 AMPA 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 = 333
Score = 40.2 bits (94), Expect = 9e-05
Identities = 24/84 (28%), Positives = 39/84 (46%), Gaps = 6/84 (7%)
Query: 18 EEESVMCRQLQNGVQALFGPSDA-LLGPHVQSICEALDVPHM----ESRLDLELNSKEFS 72
E MC+ L GV ++ GPS + V IC ++PH E L+ + S
Sbjct: 53 ETTDTMCQILPKGVVSVLGPSSSPASSSIVSHICGEKEIPHFKVGPEETPKLQY-LRFAS 111
Query: 73 VNLYPSQKLLNAAFKDVIRFLNWT 96
VNL+PS + ++ A ++ N+
Sbjct: 112 VNLHPSNEDISVAVAGILNSFNYP 135
>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 = 37.1 bits (86), Expect = 0.001
Identities = 24/121 (19%), Positives = 42/121 (34%), Gaps = 27/121 (22%)
Query: 12 VNTGLEEEESVMCRQL---QNGVQALFGPSDALLGPHVQSICEALDVPHM-----ESRLD 63
+ + ++ + Q GV AL GP + + V + EAL +P + L
Sbjct: 46 YDDQSDPARALAAARRLCQQEGVDALVGPVSSGVALAVAPVAEALKIPLISPGATAPGLT 105
Query: 64 LELNSKEFSVNLYPSQKLLNAAFKDVIRFLNWTKKLLNAAFKDVIRFLNWTKVAIVYEED 123
+ ++ A D I+ NW KVAI+Y++D
Sbjct: 106 DKKGYPYLFRTGPSDEQQAEALA-------------------DYIKEYNWKKVAILYDDD 146
Query: 124 N 124
+
Sbjct: 147 S 147
>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 = 34.6 bits (80), Expect = 0.006
Identities = 27/105 (25%), Positives = 37/105 (35%), Gaps = 27/105 (25%)
Query: 24 CRQLQNGVQALFGPSDALLGPHVQSICEALDVPH----MESRLDLELNSKEFSVNLYPSQ 79
C QL GV A+FG D + S +AL VP + + N F + + PS
Sbjct: 56 CSQLSRGVFAIFGSYDKSSVNTLTSYSDALHVPFITPSFPTNDLDDGNQ--FVLQMRPS- 112
Query: 80 KLLNAAFKDVIRFLNWTKKLLNAAFKDVIRFLNWTKVAIVYEEDN 124
L A D+I W KV +Y+ D
Sbjct: 113 --------------------LIQALVDLIEHYGWRKVVYLYDSDR 137
>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 = 32.2 bits (74), Expect = 0.044
Identities = 8/19 (42%), Positives = 12/19 (63%)
Query: 106 DVIRFLNWTKVAIVYEEDN 124
D+++ NWT V+ V E N
Sbjct: 165 DIVKAFNWTYVSTVASEGN 183
>gnl|CDD|107376 cd06381, PBP1_iGluR_delta_like, N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of an orphan family of delta receptors,
GluRdelta1 and GluRdelta2. This CD represents the
N-terminal leucine/isoleucine/valine-binding protein
(LIVBP)-like domain of an orphan family of delta
receptors, GluRdelta1 and GluRdelta2. 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. Although the delta receptors are a member
of the ionotropic glutamate receptor family, they cannot
be activated by AMPA, kainate, NMDA, glutamate, or any
other ligands. Phylogenetic analysis shows that both
GluRdelta1 and GluRalpha2 are more homologous to
non-NMDA receptors. GluRdelta2 was shown to function as
an AMPA-like receptor by mutation analysis. Moreover,
targeted disruption of GluRdelta2 gene caused motor
coordination impairment, Purkinje cell maturation, and
long-term depression of synaptic transmission. It has
been suggested that GluRdelta2 is the receptor for
cerebellin 1, a glycoprotein of the Clq, and the tumor
necrosis factor family which is secreted from cerebellar
granule cells. Furthermore, recent studies have shown
that the orphan GluRdelta1 plays an essential role in
high-frequency hearing and ionic homeostasis in the
basal cochlea and that the locus encoding GluRdelta1 may
be involved in congenial or acquired high-frequency
hearing loss in humans.
Length = 363
Score = 30.9 bits (70), Expect = 0.12
Identities = 18/112 (16%), Positives = 37/112 (33%), Gaps = 31/112 (27%)
Query: 24 CRQLQNGVQALFGPSDALLGPHVQSICEALDVPHM------------ESRLDLELNSKEF 71
C + G+ AL + +QS+ +A+ +PH+ L+ +++
Sbjct: 56 CDLMNQGILALVTSTGCASAIALQSLTDAMHIPHLFIQRGYGGSPRTACGLNPSPRGQQY 115
Query: 72 SVNLYPSQKLLNAAFKDVIRFLNWTKKLLNAAFKDVIRFLNWTKVAIVYEED 123
++ L P + LN ++ W K Y+ D
Sbjct: 116 TLALRPPVR-------------------LNDVMLRLVTEWRWQKFVYFYDND 148
>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 = 30.4 bits (68), Expect = 0.23
Identities = 19/74 (25%), Positives = 27/74 (36%), Gaps = 4/74 (5%)
Query: 24 CRQLQNGVQALFGPSDALLGPHVQSICEALDVPHMESRLDLELNSKEFSVNLYPSQKLLN 83
C Q GV A+FG D + S C L V + + F + + P L
Sbjct: 51 CSQFSRGVYAIFGFYDKKSVNTITSFCGTLHVSFITPSFPTDGT-HPFVIQMRPD---LK 106
Query: 84 AAFKDVIRFLNWTK 97
A +I + W K
Sbjct: 107 GALLSLIEYYQWDK 120
>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 = 29.5 bits (67), Expect = 0.32
Identities = 8/24 (33%), Positives = 15/24 (62%)
Query: 101 NAAFKDVIRFLNWTKVAIVYEEDN 124
N A +++ W +VA +YE+D+
Sbjct: 123 NPAIAALLKKFGWRRVATIYEDDD 146
>gnl|CDD|107378 cd06383, PBP1_iGluR_AMPA_Like, N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of uncharacterized AMPA-like receptors.
N-terminal leucine/isoleucine/valine-binding protein
(LIVBP)-like domain of uncharacterized AMPA-like
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. 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 = 368
Score = 29.8 bits (67), Expect = 0.34
Identities = 8/22 (36%), Positives = 15/22 (68%)
Query: 103 AFKDVIRFLNWTKVAIVYEEDN 124
A +D++ + N T AI+Y++D
Sbjct: 123 AIRDIVSYYNITNAAILYDDDF 144
Score = 27.8 bits (62), Expect = 1.6
Identities = 9/35 (25%), Positives = 16/35 (45%), Gaps = 4/35 (11%)
Query: 70 EFSVNLYPSQKLLNAAFKDVIRFLNWTKKLLNAAF 104
+ + L P + A +D++ + N T NAA
Sbjct: 108 PYLIQLMPPADDIVEAIRDIVSYYNIT----NAAI 138
>gnl|CDD|107385 cd06390, PBP1_iGluR_AMPA_GluR1, N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the GluR1 subunit of the AMPA receptor.
N-terminal leucine/isoleucine/valine-binding protein
(LIVBP)-like domain of the GluR1 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 = 364
Score = 29.1 bits (65), Expect = 0.53
Identities = 27/93 (29%), Positives = 38/93 (40%), Gaps = 5/93 (5%)
Query: 5 PSLVEVNVNTGLEEEESVMCRQLQNGVQALFGPSDALLGPHVQSICEALDVPHMESRLDL 64
P + VN++ E + C Q GV A+FG D + S C AL V + +
Sbjct: 32 PQIDIVNISDSFEMTYT-FCSQFSKGVYAIFGFYDRKTVNMLTSFCGALHVCFITPSFPV 90
Query: 65 ELNSKEFSVNLYPSQKLLNAAFKDVIRFLNWTK 97
+ S +F + L P L A VI W K
Sbjct: 91 D-TSNQFVLQLRPE---LQDALISVIEHYKWQK 119
>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 = 1.8
Identities = 19/132 (14%), Positives = 42/132 (31%), Gaps = 13/132 (9%)
Query: 6 SLVEVNVNTGLEEEESVMCRQLQNGVQALFGPSDALLGPHVQSICEALDVPHME-SRLDL 64
++ + + E + +Q GV + GP + V + A +P +
Sbjct: 34 EVILADSQSDPERALEALRDLIQQGVDGIIGPPSSSSALAVVELAAAAGIPVVSLDATAP 93
Query: 65 ELNSKEFSVNLYPSQKLLNAAFKDVIRFLNWTK------------KLLNAAFKDVIRFLN 112
+L + + P + A + + W + + FK ++
Sbjct: 94 DLTGYPYVFRVGPDNEQAGEAAAEYLAEKGWKRVALIYGDDGAYGRERLEGFKAALKKAG 153
Query: 113 WTKVAIVYEEDN 124
VAI Y + +
Sbjct: 154 IEVVAIEYGDLD 165
>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 = 27.4 bits (61), Expect = 2.0
Identities = 9/20 (45%), Positives = 13/20 (65%)
Query: 103 AFKDVIRFLNWTKVAIVYEE 122
A +++RF NWT V+ V E
Sbjct: 164 AMAEILRFFNWTYVSTVASE 183
>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 = 27.2 bits (60), Expect = 2.3
Identities = 21/95 (22%), Positives = 42/95 (44%), Gaps = 16/95 (16%)
Query: 31 VQALFGPSDALLGPHVQSICEALDVPHME-SRLDLELNSKEFSVNLYPSQKLLNAAFKDV 89
+ + GP + + VQ++ + ++P + S ++L+ K FK
Sbjct: 118 IVGVIGPGSSSVAIQVQNLLQLFNIPQIAYSATSIDLSDKTL--------------FKYF 163
Query: 90 IRFLNWTKKLLNAAFKDVIRFLNWTKVAIVYEEDN 124
+R + + L A D+++ NWT V+ V+ E N
Sbjct: 164 LRVVP-SDTLQARAMLDIVKRYNWTYVSAVHTEGN 197
>gnl|CDD|238745 cd01468, trunk_domain, trunk domain. COPII-coated vesicles carry
proteins from the endoplasmic reticulum to the Golgi
complex. This vesicular transport can be reconstituted
by using three cytosolic components containing five
proteins: the small GTPase Sar1p, the Sec23p/24p
complex, and the Sec13p/Sec31p complex. This domain is
known as the trunk domain and has an alpha/beta vWA fold
and forms the dimer interface. Some members of this
family possess a partial MIDAS motif that is a
characteristic feature of most vWA domain proteins.
Length = 239
Score = 26.8 bits (60), Expect = 3.3
Identities = 17/94 (18%), Positives = 33/94 (35%), Gaps = 15/94 (15%)
Query: 7 LVEVNVNTGLEEEESVMCRQLQNGVQALFGPSDALLG-------PHVQSICEALDVPHME 59
+++V+ E + L + L G A +G H ++ L P M
Sbjct: 9 VIDVSYEAIKEGLLQALKESLLASLDLLPGDPRARVGLITYDSTVHFYNLSSDLAQPKMY 68
Query: 60 SRLDLE------LNSKEFSVNLYPSQKLLNAAFK 87
DL+ + F V L +K+++ +
Sbjct: 69 VVSDLKDVFLPLPDR--FLVPLSECKKVIHDLLE 100
>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 = 26.6 bits (59), Expect = 3.3
Identities = 23/103 (22%), Positives = 32/103 (31%), Gaps = 19/103 (18%)
Query: 25 RQL-QNGVQALFGP--SDALLGPHVQSICEALDVPHMESRLDLELNSKEFSVNLYPSQKL 81
R+L +GV A+ GP S L + E VP S S L
Sbjct: 60 RELVDDGVDAVIGPLSSGVALA--AAPVAEEAGVPL-------------ISPGA-TSPAL 103
Query: 82 LNAAFKDVIRFLNWTKKLLNAAFKDVIRFLNWTKVAIVYEEDN 124
V R + A + KVAI+Y++
Sbjct: 104 TGKGNPYVFRTAPSDAQQAAALADYLAEKGKVKKVAIIYDDYA 146
>gnl|CDD|139075 PRK12568, PRK12568, glycogen branching enzyme; Provisional.
Length = 730
Score = 26.8 bits (59), Expect = 3.4
Identities = 12/30 (40%), Positives = 17/30 (56%)
Query: 19 EESVMCRQLQNGVQALFGPSDALLGPHVQS 48
E+VM + LQ L + A+LGPH Q+
Sbjct: 7 SEAVMSQTLQALADGLPADAFAVLGPHPQA 36
>gnl|CDD|133037 cd04194, GT8_A4GalT_like, A4GalT_like proteins catalyze the
addition of galactose or glucose residues to the
lipooligosaccharide (LOS) or lipopolysaccharide (LPS) of
the bacterial cell surface. The members of this family
of glycosyltransferases catalyze the addition of
galactose or glucose residues to the lipooligosaccharide
(LOS) or lipopolysaccharide (LPS) of the bacterial cell
surface. The enzymes exhibit broad substrate
specificities. The known functions found in this family
include: Alpha-1,4-galactosyltransferase,
LOS-alpha-1,3-D-galactosyltransferase,
UDP-glucose:(galactosyl) LPS
alpha1,2-glucosyltransferase, UDP-galactose: (glucosyl)
LPS alpha1,2-galactosyltransferase, and
UDP-glucose:(glucosyl) LPS alpha1,2-glucosyltransferase.
Alpha-1,4-galactosyltransferase from N. meningitidis
adds an alpha-galactose from UDP-Gal (the donor) to a
terminal lactose (the acceptor) of the LOS structure of
outer membrane. LOSs are virulence factors that enable
the organism to evade the immune system of host cells.
In E. coli, the three alpha-1,2-glycosyltransferases,
that are involved in the synthesis of the outer core
region of the LPS, are all members of this family. The
three enzymes share 40 % of sequence identity, but have
different sugar donor or acceptor specificities,
representing the structural diversity of LPS.
Length = 248
Score = 26.8 bits (60), Expect = 3.5
Identities = 14/38 (36%), Positives = 21/38 (55%), Gaps = 1/38 (2%)
Query: 57 HMESRLDLELNSKEFSVNLYPSQKLLNAAFKDVIRFLN 94
++ +L LEL + +YP Q +LNA KD I +L
Sbjct: 168 NITEKL-LELIKEYGGRLIYPDQDILNAVLKDKILYLP 204
>gnl|CDD|152128 pfam11692, DUF3289, Protein of unknown function (DUF3289). This
family of proteins with unknown function appears to be
restricted to Proteobacteria.
Length = 277
Score = 26.6 bits (59), Expect = 3.9
Identities = 14/42 (33%), Positives = 20/42 (47%), Gaps = 2/42 (4%)
Query: 81 LLNAAFKDVIRFLNWTKKLLNAAFKDVI-RFLNWTKVAIVYE 121
LLNAA K+VI + T K ++ R ++W K Y
Sbjct: 126 LLNAALKEVI-LGDKTNNSSLLVIKAILDRGIDWDKKIFPYN 166
>gnl|CDD|213328 cd04519, RasGAP, Ras GTPase Activating Domain. RasGAP functions as
an enhancer of the hydrolysis of GTP that is bound to
Ras-GTPases. Proteins having a RasGAP domain include
p120GAP, IQGAP, Rab5-activating protein 6, and
Neurofibromin, among others. Although the Rho (Ras
homolog) GTPases are most closely related to members of
the Ras family, RhoGAP and RasGAP exhibit no similarity
at their amino acid sequence level. RasGTPases function
as molecular switches in a large number of signaling
pathways. They are in the on state when bound to GTP,
and in the off state when bound to GDP. The RasGAP
domain speeds up the hydrolysis of GTP in Ras-like
proteins acting as a negative regulator.
Length = 256
Score = 26.3 bits (58), Expect = 5.1
Identities = 16/104 (15%), Positives = 32/104 (30%), Gaps = 19/104 (18%)
Query: 23 MCRQLQNGVQALFGPSDALLGPHVQS-------ICEALDVPHMESRLDLELNSKEFSVNL 75
+ + L+ + F P + S IC A+ P + + E + +
Sbjct: 153 VFKILREFLAERF-PEEPDEAYQAVSGFLFLRFICPAIVSPELFGLVPDEPSEQARRNLT 211
Query: 76 YPSQKLLNAAF-----------KDVIRFLNWTKKLLNAAFKDVI 108
S+ L + A K + F+ K L ++
Sbjct: 212 LISKVLQSLANGVEFGDKEPFMKPLNDFIKSNKPKLKQFLDELS 255
>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 = 26.1 bits (58), Expect = 6.1
Identities = 7/12 (58%), Positives = 9/12 (75%)
Query: 112 NWTKVAIVYEED 123
NW K ++VYE D
Sbjct: 135 NWNKFSVVYEND 146
>gnl|CDD|107383 cd06388, PBP1_iGluR_AMPA_GluR4, N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the GluR4 subunit of the AMPA receptor.
N-terminal leucine/isoleucine/valine-binding protein
(LIVBP)-like domain of the GluR4 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 = 371
Score = 26.1 bits (57), Expect = 6.2
Identities = 21/77 (27%), Positives = 31/77 (40%), Gaps = 4/77 (5%)
Query: 21 SVMCRQLQNGVQALFGPSDALLGPHVQSICEALDVPHMESRLDLELNSKEFSVNLYPSQK 80
+ C Q GV A+FG D + S C AL + + E S +F + L PS
Sbjct: 54 NAFCSQYSRGVFAIFGLYDKRSVHTLTSFCSALHISLITPSFPTEGES-QFVLQLRPS-- 110
Query: 81 LLNAAFKDVIRFLNWTK 97
L A ++ W +
Sbjct: 111 -LRGALLSLLDHYEWNR 126
>gnl|CDD|178003 PLN02375, PLN02375, molybderin biosynthesis protein CNX3.
Length = 270
Score = 25.9 bits (56), Expect = 6.6
Identities = 14/46 (30%), Positives = 26/46 (56%), Gaps = 2/46 (4%)
Query: 30 GVQALFGPSDALLGPHVQSICEALDVPHMESRLDLELNSKEFSVNL 75
GV + G + A + +C + + H+ R+DL LN ++FSV++
Sbjct: 168 GVAKIAGINGAKQTSSLIPLCHNIALTHV--RVDLRLNPEDFSVDI 211
>gnl|CDD|200471 cd11332, AmyAc_OligoGlu_TS, Alpha amylase catalytic domain found in
oligo-1,6-glucosidase (also called isomaltase;
sucrase-isomaltase; alpha-limit dextrinase), trehalose
synthase (also called maltose
alpha-D-glucosyltransferase), and related proteins.
Oligo-1,6-glucosidase (EC 3.2.1.10) hydrolyzes the
alpha-1,6-glucosidic linkage of
isomaltooligosaccharides, pannose, and dextran. Unlike
alpha-1,4-glucosidases (EC 3.2.1.20), it fails to
hydrolyze the alpha-1,4-glucosidic bonds of
maltosaccharides. Trehalose synthase (EC 5.4.99.16)
catalyzes the isomerization of maltose to produce
trehalulose. The Alpha-amylase family comprises the
largest family of glycoside hydrolases (GH), with the
majority of enzymes acting on starch, glycogen, and
related oligo- and polysaccharides. These proteins
catalyze the transformation of alpha-1,4 and alpha-1,6
glucosidic linkages with retention of the anomeric
center. The protein is described as having 3 domains: A,
B, C. A is a (beta/alpha) 8-barrel; B is a loop between
the beta 3 strand and alpha 3 helix of A; C is the
C-terminal extension characterized by a Greek key. The
majority of the enzymes have an active site cleft found
between domains A and B where a triad of catalytic
residues (Asp, Glu and Asp) performs catalysis. Other
members of this family have lost the catalytic activity
as in the case of the human 4F2hc, or only have 2
residues that serve as the catalytic nucleophile and the
acid/base, such as Thermus A4 beta-galactosidase with 2
Glu residues (GH42) and human alpha-galactosidase with 2
Asp residues (GH31). The family members are quite
extensive and include: alpha amylase,
maltosyltransferase, cyclodextrin glycotransferase,
maltogenic amylase, neopullulanase, isoamylase,
1,4-alpha-D-glucan maltotetrahydrolase,
4-alpha-glucotransferase, oligo-1,6-glucosidase,
amylosucrase, sucrose phosphorylase, and amylomaltase.
Length = 481
Score = 25.7 bits (57), Expect = 7.1
Identities = 9/18 (50%), Positives = 12/18 (66%)
Query: 93 LNWTKKLLNAAFKDVIRF 110
LNW + A F+DV+RF
Sbjct: 175 LNWDNPEVRAEFEDVLRF 192
>gnl|CDD|233864 TIGR02432, lysidine_TilS_N, tRNA(Ile)-lysidine synthetase,
N-terminal domain. The only examples in which the
wobble position of a tRNA must discriminate between G
and A of mRNA are AUA (Ile) vs. AUG (Met) and UGA
(stop) vs. UGG (Trp). In all bacteria, the wobble
position of the tRNA(Ile) recognizing AUA is lysidine,
a lysine derivative of cytidine. This family describes
a protein domain found, apparently, in all bacteria in
a single copy. Eukaryotic sequences appear to be
organellar. The domain archictecture of this protein
family is variable; some, including characterized
proteins of E. coli and B. subtilis known to be
tRNA(Ile)-lysidine synthetase, include a conserved
50-residue domain that many other members lack. This
protein belongs to the ATP-binding PP-loop family (
pfam01171). It appears in the literature and protein
databases as TilS, YacA, and putative cell cycle
protein MesJ (a misnomer) [Protein synthesis, tRNA and
rRNA base modification].
Length = 189
Score = 25.7 bits (57), Expect = 7.4
Identities = 9/31 (29%), Positives = 17/31 (54%)
Query: 45 HVQSICEALDVPHMESRLDLELNSKEFSVNL 75
VQ C+ L++P ++D++ +K NL
Sbjct: 49 FVQQFCKKLNIPLEIKKVDVKALAKGKKKNL 79
>gnl|CDD|238766 cd01489, Uba2_SUMO, Ubiquitin activating enzyme (E1) subunit UBA2.
UBA2 is part of the heterodimeric activating enzyme
(E1), specific for the SUMO family of ubiquitin-like
proteins (Ubls). E1 enzymes are part of a conjugation
cascade to attach Ub or Ubls, covalently to substrate
proteins consisting of activating (E1), conjugating
(E2), and/or ligating (E3) enzymes. E1 activates
ubiquitin by C-terminal adenylation, and subsequently
forms a highly reactive thioester bond between its
catalytic cysteine and Ubls C-terminus. The E1 also
associates with E2 and promotes ubiquitin transfer to
the E2's catalytic cysteine. Post-translational
modification by SUMO family of ubiquitin-like proteins
(Ublps) is involved in cell division, nuclear transport,
the stress response and signal transduction. UBA2
contains both the nucleotide-binding motif involved in
adenylation and the catalytic cysteine involved in the
thioester intermediate and Ublp transfer to E2.
Length = 312
Score = 25.4 bits (56), Expect = 9.4
Identities = 9/16 (56%), Positives = 11/16 (68%)
Query: 45 HVQSICEALDVPHMES 60
HV +C A DVP +ES
Sbjct: 106 HVNKMCLAADVPLIES 121
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
0.319 0.134 0.396
Gapped
Lambda K H
0.267 0.0663 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,208,068
Number of extensions: 532499
Number of successful extensions: 479
Number of sequences better than 10.0: 1
Number of HSP's gapped: 464
Number of HSP's successfully gapped: 37
Length of query: 124
Length of database: 10,937,602
Length adjustment: 85
Effective length of query: 39
Effective length of database: 7,167,512
Effective search space: 279532968
Effective search space used: 279532968
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 (21.7 bits)
S2: 53 (24.3 bits)