RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1412
(504 letters)
>gnl|CDD|215685 pfam00060, Lig_chan, Ligand-gated ion channel. This family
includes the four transmembrane regions of the
ionotropic glutamate receptors and NMDA receptors.
Length = 268
Score = 192 bits (491), Expect = 5e-58
Identities = 104/258 (40%), Positives = 136/258 (52%), Gaps = 41/258 (15%)
Query: 266 EIWLYVLAAYLLVSFTLFVMARFSPYEWSNPHPCLAESPIVENQFSVSNSFWFITGTFLR 325
E+WL +LAAYLLV LF++ RFSPYEW P P NQF++SNS WF G ++
Sbjct: 1 EVWLCILAAYLLVGVVLFLLERFSPYEWRGP-------PEEPNQFTLSNSLWFSFGALVQ 53
Query: 326 QGSGLNPKVLQQGSSRTLD--------------TA-LDS--KIEIYQKMWRYMESKKCIL 368
QG P+ L S R L TA L + +E Q + +E
Sbjct: 54 QGHRELPRSL---SGRILVGVWWFFALILLSSYTANLAAFLTVERMQSPIQSLED----- 105
Query: 369 FLGGQGDETFVTIDLSQRADSKIEIYQKMWRYMESK----RPSVFVSDYEEGVKRVLEG- 423
L Q + T+ + E +R M + V V YEEGV+RV +G
Sbjct: 106 -LAKQNKIGYGTLRGGSTFEFFKESKNPTYRRMWEYMISFKGEVNVESYEEGVQRVRKGN 164
Query: 424 -DYAFLMESTMLDYEVQRN-CNLTQIGGLLDSKGYGIATPKGSPWRDRISLAILELQEKG 481
YAFLMES L+YEV R+ C LT +G + +KGYGIA PKGSP RD++S AILEL+E G
Sbjct: 165 GLYAFLMESAYLEYEVARDPCKLTTVGEVFGTKGYGIAFPKGSPLRDKLSRAILELRESG 224
Query: 482 TIQMLYDKWWKNTGDVCN 499
+Q L +KWWK G+ C+
Sbjct: 225 ELQKLENKWWKKKGE-CS 241
>gnl|CDD|197504 smart00079, PBPe, Eukaryotic homologues of bacterial periplasmic
substrate binding proteins. Prokaryotic homologues are
represented by a separate alignment: PBPb.
Length = 133
Score = 158 bits (402), Expect = 1e-46
Identities = 57/106 (53%), Positives = 70/106 (66%), Gaps = 2/106 (1%)
Query: 388 DSKIEIYQKMWRYMESKRPSVFVSDYEEGVKRVLEGDYAFLMESTMLDYEVQRNCNLTQI 447
S Y +MW YM K P VFV Y EGV+RV +YAF+MES LDYE+ RNC+L +
Sbjct: 30 RSGNPEYSRMWPYM--KSPEVFVKSYAEGVQRVRVSNYAFIMESPYLDYELSRNCDLMTV 87
Query: 448 GGLLDSKGYGIATPKGSPWRDRISLAILELQEKGTIQMLYDKWWKN 493
G KGYGIA PKGSP RD +S AIL+L E G ++ L +KWWK+
Sbjct: 88 GEEFGRKGYGIAFPKGSPLRDDLSRAILKLSESGELEKLRNKWWKD 133
>gnl|CDD|204533 pfam10613, Lig_chan-Glu_bd, Ligated ion channel L-glutamate- and
glycine-binding site. This region, sometimes called the
S1 domain, is the luminal domain just upstream of the
first, M1, transmembrane region of transmembrane
ion-channel proteins, and it binds L-glutamate and
glycine. It is found in association with Lig_chan,
pfam00060.
Length = 65
Score = 89.2 bits (222), Expect = 4e-22
Identities = 36/66 (54%), Positives = 47/66 (71%), Gaps = 2/66 (3%)
Query: 147 PYVMVK-NDANLTGNAMFEGFCIDLLKSIAAQVGFHFVLRLVPDHTYGVYDHETKEWNGI 205
PYVM+K N NLTGN FEG+CIDLL +A +GF++ + LVPD YG D +T EWNG+
Sbjct: 1 PYVMLKENGENLTGNERFEGYCIDLLDELAKILGFNYEIYLVPDGKYGSED-KTGEWNGM 59
Query: 206 VKELMD 211
+ EL+
Sbjct: 60 IGELIR 65
>gnl|CDD|214911 smart00918, Lig_chan-Glu_bd, Ligated ion channel L-glutamate- and
glycine-binding site. This region, sometimes called the
S1 domain, is the luminal domain just upstream of the
first, M1, transmembrane region of transmembrane
ion-channel proteins, and it binds L-glutamate and
glycine. It is found in association with Lig_chan.
Length = 62
Score = 78.4 bits (194), Expect = 2e-18
Identities = 31/64 (48%), Positives = 40/64 (62%), Gaps = 2/64 (3%)
Query: 147 PYVMVKNDANLTGNAMFEGFCIDLLKSIAAQVGFHFVLRLVPDHTYGVYDHETKEWNGIV 206
PYVM+K GN FEG+CIDLLK +A ++GF + + LVPD YG WNG+V
Sbjct: 1 PYVMLKES-PDGGNDRFEGYCIDLLKELAKKLGFTYEIILVPDGKYGARL-PNGSWNGMV 58
Query: 207 KELM 210
EL+
Sbjct: 59 GELV 62
>gnl|CDD|215950 pfam00497, SBP_bac_3, Bacterial extracellular solute-binding
proteins, family 3.
Length = 220
Score = 66.9 bits (164), Expect = 1e-12
Identities = 26/101 (25%), Positives = 44/101 (43%), Gaps = 19/101 (18%)
Query: 147 PYVMVKNDANLTGNAMFEGFCIDLLKSIAAQVGFHFVLRLVPDHTYGVYDHETKEWNGIV 206
P+ V + L G F +DL K+IA ++G V W+G++
Sbjct: 11 PFSYVDENGKLVG------FDVDLAKAIAKRLGVKVEFVPVS-------------WDGLI 51
Query: 207 KELMDKKADLAVASMTINYARESVIDFTKPFMNLGIGILFK 247
L K D+ +A MTI R+ +DF+ P+ G ++ +
Sbjct: 52 PALKSGKVDIIIAGMTITPERKKQVDFSDPYYYSGQVLVVR 92
Score = 54.2 bits (131), Expect = 3e-08
Identities = 28/102 (27%), Positives = 49/102 (48%), Gaps = 4/102 (3%)
Query: 393 IYQKMWRYMESKRPSVFVSDYEEGVKRVLEGDY-AFLMESTMLDYEVQRN--CNLTQIGG 449
+ + + + V D E ++ + G A + +S +L Y +++N NL +
Sbjct: 116 TAEDLLKELLPGAEIVLYDDLAEALQALAAGRVDAVVADSPVLAYLIKKNPGLNLVVVDE 175
Query: 450 LLDSKGYGIATPKGSP-WRDRISLAILELQEKGTIQMLYDKW 490
L + YGIA KG P ++ A+ EL+ GT+ LY+KW
Sbjct: 176 PLSGEPYGIAVRKGDPELLAALNKALAELKADGTLAKLYEKW 217
>gnl|CDD|238078 cd00134, PBPb, Bacterial periplasmic transport systems use
membrane-bound complexes and substrate-bound,
membrane-associated, periplasmic binding proteins (PBPs)
to transport a wide variety of substrates, such as,
amino acids, peptides, sugars, vitamins and inorganic
ions. PBPs have two cell-membrane translocation
functions: bind substrate, and interact with the
membrane bound complex. A diverse group of periplasmic
transport receptors for lysine/arginine/ornithine (LAO),
glutamine, histidine, sulfate, phosphate, molybdate, and
methanol are included in the PBPb CD.
Length = 218
Score = 57.4 bits (139), Expect = 2e-09
Identities = 26/83 (31%), Positives = 36/83 (43%), Gaps = 13/83 (15%)
Query: 163 FEGFCIDLLKSIAAQVGFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMT 222
GF +DL K+IA ++G V W+G++ L K DL A MT
Sbjct: 21 LTGFDVDLAKAIAKELGVKVKFVEVD-------------WDGLITALKSGKVDLIAAGMT 67
Query: 223 INYARESVIDFTKPFMNLGIGIL 245
I R +DF+ P+ G IL
Sbjct: 68 ITPERAKQVDFSDPYYKSGQVIL 90
Score = 47.0 bits (112), Expect = 7e-06
Identities = 21/103 (20%), Positives = 46/103 (44%), Gaps = 5/103 (4%)
Query: 394 YQKMWRYMESKRPSVFVSDYEEGVKRVLEGDY-AFLMESTMLDYEVQRNCNLTQIGGL-- 450
+K + + V D E + + G A +++ L ++++ +I G
Sbjct: 116 AEKYLKKALPEAKVVSYDDNAEALAALENGRADAVIVDEIALAALLKKHPPELKIVGPSI 175
Query: 451 -LDSKGYGIATPKGSP-WRDRISLAILELQEKGTIQMLYDKWW 491
L+ G+G+A K + D ++ A+ EL+ G ++ + KW+
Sbjct: 176 DLEPLGFGVAVGKDNKELLDAVNKALKELRADGELKKISKKWF 218
>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 = 55.8 bits (134), Expect = 2e-08
Identities = 29/117 (24%), Positives = 49/117 (41%), Gaps = 26/117 (22%)
Query: 30 LEVPWRDGLSLYNYINTAEPALMYDSVHVLAAGLALLDKSSVIKTSNLSCDLEVPWRDGL 89
L+ + L + + + AL+YD+VH+++ ++ + ++L C WR G
Sbjct: 271 LQAAPKPETGLLDGVMMTDAALLYDAVHMVSVCY---QRAPQMTVNSLQCHRHKAWRFGG 327
Query: 90 SLYNYINT-----------------------LDLLKLKREELRKVGHWTPAEGINIT 123
N+I LD++ LK + L KVG W P G+NIT
Sbjct: 328 RFMNFIKEAQWEGLTGRIVFNKTSGLRTDFDLDIISLKEDGLEKVGVWNPNTGLNIT 384
>gnl|CDD|223904 COG0834, HisJ, ABC-type amino acid transport/signal transduction
systems, periplasmic component/domain [Amino acid
transport and metabolism / Signal transduction
mechanisms].
Length = 275
Score = 55.0 bits (132), Expect = 3e-08
Identities = 24/90 (26%), Positives = 39/90 (43%), Gaps = 11/90 (12%)
Query: 158 TGNAMFEGFCIDLLKSIAAQVGFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLA 217
GF +DL K+IA ++G + W+G++ L K D+
Sbjct: 53 AKGGKLVGFDVDLAKAIAKRLG-----------GDKKVEFVPVAWDGLIPALKAGKVDII 101
Query: 218 VASMTINYARESVIDFTKPFMNLGIGILFK 247
+A MTI R+ +DF+ P+ G +L K
Sbjct: 102 IAGMTITPERKKKVDFSDPYYYSGQVLLVK 131
Score = 36.9 bits (85), Expect = 0.019
Identities = 21/92 (22%), Positives = 38/92 (41%), Gaps = 7/92 (7%)
Query: 408 VFVSDYEEGVKRVLEG--DYAFLMESTMLDYEVQ-RNCNLTQIGG--LLDSKGYGIATPK 462
V E + + G D + + ++ +N L + L + GIA K
Sbjct: 173 VAYDSNAEALLALKNGRADAVVSDSAVLAGLKLLKKNPGLYVLLVFPGLSVEYLGIALRK 232
Query: 463 GSP--WRDRISLAILELQEKGTIQMLYDKWWK 492
G + ++ A+ EL+ GT+Q + DKW+
Sbjct: 233 GDDPELLEAVNKALKELKADGTLQKISDKWFG 264
>gnl|CDD|214497 smart00062, PBPb, Bacterial periplasmic substrate-binding proteins.
bacterial proteins, eukaryotic ones are in PBPe.
Length = 219
Score = 53.9 bits (130), Expect = 3e-08
Identities = 31/110 (28%), Positives = 45/110 (40%), Gaps = 20/110 (18%)
Query: 137 TLIVMTREE-KPYVMVKNDANLTGNAMFEGFCIDLLKSIAAQVGFHFVLRLVPDHTYGVY 195
TL V T + P+ D LTG F +DL K+IA ++G V
Sbjct: 1 TLRVGTNGDYPPFSFADEDGELTG------FDVDLAKAIAKELGLKVEFVEV-------- 46
Query: 196 DHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIGIL 245
++ ++ L K D+ A MTI R +DF+ P+ G IL
Sbjct: 47 -----SFDSLLTALKSGKIDVVAAGMTITPERAKQVDFSDPYYRSGQVIL 91
Score = 43.5 bits (103), Expect = 9e-05
Identities = 23/88 (26%), Positives = 41/88 (46%), Gaps = 5/88 (5%)
Query: 408 VFVSDYEEGVKRVLEGDY-AFLMESTMLDYEVQRNCNLT-QIGGLLDSK--GYGIATPKG 463
V E + + G A + ++ +L V+++ +I GY IA KG
Sbjct: 131 VSYDSNAEALAALKAGRADAAVADAPLLAALVKQHGLPELKIVPDPLDTPEGYAIAVRKG 190
Query: 464 SP-WRDRISLAILELQEKGTIQMLYDKW 490
P D+I+ A+ EL+ GT++ + +KW
Sbjct: 191 DPELLDKINKALKELKADGTLKKISEKW 218
>gnl|CDD|236540 PRK09495, glnH, glutamine ABC transporter periplasmic protein;
Reviewed.
Length = 247
Score = 47.4 bits (113), Expect = 5e-06
Identities = 24/84 (28%), Positives = 42/84 (50%), Gaps = 13/84 (15%)
Query: 165 GFCIDLLKSIAAQVGFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTIN 224
GF IDL +IA ++ + L+ + +++GI+ L K DLA+A +TI
Sbjct: 48 GFDIDLWAAIAKELKLDYTLKPM-------------DFSGIIPALQTKNVDLALAGITIT 94
Query: 225 YARESVIDFTKPFMNLGIGILFKV 248
R+ IDF+ + G+ ++ K
Sbjct: 95 DERKKAIDFSDGYYKSGLLVMVKA 118
Score = 42.4 bits (100), Expect = 2e-04
Identities = 19/45 (42%), Positives = 31/45 (68%)
Query: 447 IGGLLDSKGYGIATPKGSPWRDRISLAILELQEKGTIQMLYDKWW 491
+G L+++ YGIA PKGS R++++ A+ L+E GT +Y KW+
Sbjct: 198 VGDSLEAQQYGIAFPKGSELREKVNGALKTLKENGTYAEIYKKWF 242
>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 = 41.9 bits (99), Expect = 6e-04
Identities = 34/112 (30%), Positives = 51/112 (45%), Gaps = 22/112 (19%)
Query: 11 GLALLDKSSVIKTSNLSCDLEVPWRDGLSLYNYIN-TAEPALMYDSVHVLAAGLALLDKS 69
G L+D S + LE+ W +G + T E ALMYD+V++ GL +
Sbjct: 237 GFRLVDPDSPEVKEVIR-SLELSWDEGCRILPSTGVTTESALMYDAVYLF--GL-----T 288
Query: 70 SVIKTSNLSCDLEVPWRDGLSLYNYINTLDLLKLKREELRKVGHWTPAEGIN 121
I+ + G N+ TLD+++L LRKVG W +EG+N
Sbjct: 289 GRIEFDS----------SGQR-SNF--TLDVIELTESGLRKVGTWNSSEGLN 327
>gnl|CDD|233269 TIGR01096, 3A0103s03R, lysine-arginine-ornithine-binding
periplasmic protein. [Transport and binding proteins,
Amino acids, peptides and amines].
Length = 250
Score = 39.6 bits (93), Expect = 0.002
Identities = 23/90 (25%), Positives = 40/90 (44%), Gaps = 13/90 (14%)
Query: 158 TGNAMFEGFCIDLLKSIAAQVGFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLA 217
N GF +DL K++ R+ + + ++G++ L KK D
Sbjct: 41 DANGKLVGFDVDLAKALCK--------RMKAKCKF-----VEQNFDGLIPSLKAKKVDAI 87
Query: 218 VASMTINYARESVIDFTKPFMNLGIGILFK 247
+A+M+I R+ IDF+ P+ G G + K
Sbjct: 88 MATMSITPKRQKQIDFSDPYYATGQGFVVK 117
Score = 32.3 bits (74), Expect = 0.44
Identities = 12/38 (31%), Positives = 18/38 (47%), Gaps = 1/38 (2%)
Query: 454 KGYGIATPKGSP-WRDRISLAILELQEKGTIQMLYDKW 490
GYGI KG + + A+ ++ GT Q + KW
Sbjct: 212 DGYGIGLRKGDTELKAAFNKALAAIRADGTYQKISKKW 249
>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 = 38.0 bits (89), Expect = 0.008
Identities = 25/74 (33%), Positives = 34/74 (45%), Gaps = 22/74 (29%)
Query: 48 EPALMYDSVHVLAAGLALLDKSSVIKTSNLSCDLEVPWRDGLSLYNYINTLDLLKLKREE 107
E AL YD+V + T + D +G N+ TLD+L+LK
Sbjct: 273 ESALTYDAVLLF--------------TGRIQFD-----ENGQR-SNF--TLDILELKEGG 310
Query: 108 LRKVGHWTPAEGIN 121
LRKVG W P +G+N
Sbjct: 311 LRKVGTWNPEDGLN 324
>gnl|CDD|183061 PRK11260, PRK11260, cystine transporter subunit; Provisional.
Length = 266
Score = 36.6 bits (85), Expect = 0.018
Identities = 25/101 (24%), Positives = 44/101 (43%), Gaps = 19/101 (18%)
Query: 147 PYVMVKNDANLTGNAMFEGFCIDLLKSIAAQVGFHFVLRLVPDHTYGVYDHETKEWNGIV 206
P+ D LTG FE ++ +++A +G L+ W+G++
Sbjct: 53 PFSFQGEDGKLTG---FE---VEFAEALAKHLGVKASLKPTK-------------WDGML 93
Query: 207 KELMDKKADLAVASMTINYARESVIDFTKPFMNLGIGILFK 247
L K+ D+ + +TI+ R+ DF+ P+ GI L K
Sbjct: 94 ASLDSKRIDVVINQVTISDERKKKYDFSTPYTVSGIQALVK 134
Score = 28.5 bits (64), Expect = 7.7
Identities = 14/36 (38%), Positives = 24/36 (66%), Gaps = 1/36 (2%)
Query: 457 GIATPKGSP-WRDRISLAILELQEKGTIQMLYDKWW 491
G+A KG+P ++ AI E+Q+ GT++ L +KW+
Sbjct: 225 GVALRKGNPDLLKAVNQAIAEMQKDGTLKALSEKWF 260
>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 = 36.9 bits (86), Expect = 0.020
Identities = 29/107 (27%), Positives = 39/107 (36%), Gaps = 37/107 (34%)
Query: 48 EPALMYDSVHVLAAGLALL-----DKSSVIKTSNLS----CD--LEVPWR---------- 86
AL +D+V V+A L I S C VPW
Sbjct: 276 TAALAHDAVLVMAEAFRSLRRQRGSGRHRIDISRRGNGGDCLANPAVPWEHGIDIERALK 335
Query: 87 ----DGLSLY----------NYINTLDLLKLKREELRKVGHWTPAEG 119
+GL+ NY TLD+++LK LRKVG+W +G
Sbjct: 336 KVQFEGLTGNVQFDEFGQRTNY--TLDVVELKTRGLRKVGYWNEDDG 380
>gnl|CDD|132040 TIGR02995, ectoine_ehuB, ectoine/hydroxyectoine ABC transporter
solute-binding protein. Members of this family are the
extracellular solute-binding proteins of ABC
transporters that closely resemble amino acid
transporters. The member from Sinorhizobium meliloti is
involved in ectoine uptake, both for osmoprotection and
for catabolism. All other members of the seed alignment
are found associated with ectoine catabolic genes
[Transport and binding proteins, Amino acids, peptides
and amines].
Length = 275
Score = 32.6 bits (74), Expect = 0.43
Identities = 24/118 (20%), Positives = 43/118 (36%), Gaps = 20/118 (16%)
Query: 142 TREEKPYVMVKNDANLTGNAMFEGFCIDLLKSIAAQVGFHFVLRLVPDHTYGVYDHETKE 201
E P+ V D ++G A D+ ++I ++G V + E
Sbjct: 39 IANEPPFTYVGADGKVSGAAP------DVARAIFKRLGIADVNASI------------TE 80
Query: 202 WNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIGILFKVPTSQPTRLFSF 259
+ ++ L + D A + I R + FT+P + +L V P L S+
Sbjct: 81 YGALIPGLQAGRFDAIAAGLFIKPERCKQVAFTQPILCDAEALL--VKKGNPKGLKSY 136
>gnl|CDD|184969 PRK15007, PRK15007, putative ABC transporter arginine-biding
protein; Provisional.
Length = 243
Score = 31.2 bits (70), Expect = 1.1
Identities = 29/141 (20%), Positives = 63/141 (44%), Gaps = 24/141 (17%)
Query: 368 LFLGGQGDETFVTIDLSQRADSKIEIYQKMWRYMESKRPSVFVSDYEEGVKRVLE----- 422
LF+G QG + ++D + ++ +++ K P + Y+ L+
Sbjct: 110 LFVGQQG--KYTSVDQLKGKKVGVQNGTTHQKFIMDKHPEITTVPYDSYQNAKLDLQNGR 167
Query: 423 -----GDYAFLMESTMLDYEVQRNCNLTQIGGLLDSKGY-----GIATPKG-SPWRDRIS 471
GD A + E ++ N L +G + K Y GIA +G + + +++
Sbjct: 168 IDAVFGDTAVVTEW------LKDNPKLAAVGDKVTDKDYFGTGLGIAVRQGNTELQQKLN 221
Query: 472 LAILELQEKGTIQMLYDKWWK 492
A+ ++++ GT + +Y+KW++
Sbjct: 222 TALEKVKKDGTYETIYNKWFQ 242
>gnl|CDD|100079 cd06158, S2P-M50_like_1, Uncharacterized homologs of Site-2
protease (S2P), zinc metalloproteases (MEROPS family
M50) which cleave transmembrane domains of substrate
proteins, regulating intramembrane proteolysis (RIP) of
diverse signal transduction mechanisms. Members of the
S2P/M50 family of RIP proteases use proteolytic activity
within the membrane to transfer information across
membranes to integrate gene expression with physiologic
stresses occurring in another cellular compartment. In
eukaryotic cells they regulate such processes as sterol
and lipid metabolism, and endoplasmic reticulum stress
responses. In prokaryotes they regulate such processes
as sporulation, cell division, stress response, and cell
differentiation. This group includes bacterial,
eukaryotic, and Archaeal S2P/M50s homologs with a
minimal core protein and no PDZ domains.
Length = 181
Score = 29.4 bits (67), Expect = 2.8
Identities = 12/49 (24%), Positives = 20/49 (40%), Gaps = 4/49 (8%)
Query: 236 PFMNLGIGILFKVPTSQPTRLFSFMNPLAVEIWLYVLAAYLLVSFTLFV 284
P NL + +LF + RL + +LA +L++ L V
Sbjct: 89 PLSNLLLALLFALLL----RLLPAFGGVVASFLFLMLAYGVLINLVLAV 133
>gnl|CDD|211985 TIGR04262, orph_peri_GRRM, extracellular substrate-binding orphan
protein, GRRM family. This subfamily belongs to
bacterial extracellular solute-binding protein family 3
(pfam00497). In that family, most members are ABC
transporter periplasmic substrate-binding proteins.
However, members of the present subfamily are orphans in
the sense of being adjacent to neither ABC transporter
ATP-binding proteins or permease subunits. Instead, most
members are encoded next to the two signature proteins
of the proposed Glycine-Rich Repeat Modification (GRRM)
system, a radical SAM/SPASM protein GrrM (TIGR04261) and
the Gly-rich repeat protein itself GrrA (TIGR04260).
Length = 257
Score = 29.6 bits (67), Expect = 3.0
Identities = 21/104 (20%), Positives = 41/104 (39%), Gaps = 14/104 (13%)
Query: 144 EEKPYVMVKNDANLTGNAMFEGFCIDLLKSIAAQVGFHFVLRLVPDHTYGVYDHETKEWN 203
+ P K+DA ++G D+L+ I Q+ + + +
Sbjct: 10 DVLPLYQ-KDDAG------YDGLSFDVLELIRDQLQ-AELGKPITIQFV-----VVNSVQ 56
Query: 204 GIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIGILFK 247
+ +L KAD+A + + R+ +D++ PF GI +L
Sbjct: 57 EGLPKLRSGKADIA-CGVAFTWERQMFVDYSLPFAVSGIRLLAP 99
>gnl|CDD|223246 COG0168, TrkG, Trk-type K+ transport systems, membrane components
[Inorganic ion transport and metabolism].
Length = 499
Score = 30.0 bits (68), Expect = 3.4
Identities = 14/78 (17%), Positives = 29/78 (37%), Gaps = 2/78 (2%)
Query: 207 KELMDKKADLAVASMTINYARESVIDFTKP-FMNLGIGILFKVPTSQPTRLFSFMNPLAV 265
L+ + V ++ Y + ++ F + L IG+L +P +
Sbjct: 12 LLLLLFSLLMLVPALVALYYEDGLLAFAITILIGLLIGLLLSLPFRHEPDELRDGFLIVA 71
Query: 266 EIWLYVLAAYLLVSFTLF 283
WL V +++ + FT
Sbjct: 72 LFWL-VASSFGALPFTAS 88
>gnl|CDD|236796 PRK10922, PRK10922, 3-octaprenyl-4-hydroxybenzoate decarboxylase;
Provisional.
Length = 497
Score = 29.9 bits (67), Expect = 3.5
Identities = 18/41 (43%), Positives = 21/41 (51%), Gaps = 2/41 (4%)
Query: 10 AGLALLDKSSVIKTSNLSCDLEVPWRDGLSLYNYINTAEPA 50
AGL K+ V+K LS DLEVP + L YI E A
Sbjct: 245 AGLLRGTKTEVVKC--LSNDLEVPASAEIVLEGYIEPGEMA 283
>gnl|CDD|111216 pfam02300, Fumarate_red_C, Fumarate reductase subunit C. Fumarate
reductase is a membrane-bound flavoenzyme consisting of
four subunits, A-B. A and B comprise the
membrane-extrinsic catalytic domain and C and D link the
catalytic centres to the electron-transport chain. This
family consists of the 15kD hydrophobic subunit C.
Length = 128
Score = 28.4 bits (64), Expect = 4.5
Identities = 13/30 (43%), Positives = 19/30 (63%), Gaps = 1/30 (3%)
Query: 258 SFM-NPLAVEIWLYVLAAYLLVSFTLFVMA 286
SF+ NP+ V + + LAA LL + T F +A
Sbjct: 61 SFLQNPVVVILNIIALAAALLHTKTWFSLA 90
>gnl|CDD|215689 pfam00067, p450, Cytochrome P450. Cytochrome P450s are
haem-thiolate proteins involved in the oxidative
degradation of various compounds. They are particularly
well known for their role in the degradation of
environmental toxins and mutagens. They can be divided
into 4 classes, according to the method by which
electrons from NAD(P)H are delivered to the catalytic
site. Sequence conservation is relatively low within the
family - there are only 3 absolutely conserved residues
- but their general topography and structural fold are
highly conserved. The conserved core is composed of a
coil termed the 'meander', a four-helix bundle, helices
J and K, and two sets of beta-sheets. These constitute
the haem-binding loop (with an absolutely conserved
cysteine that serves as the 5th ligand for the haem
iron), the proton-transfer groove and the absolutely
conserved EXXR motif in helix K. While prokaryotic P450s
are soluble proteins, most eukaryotic P450s are
associated with microsomal membranes. their general
enzymatic function is to catalyze regiospecific and
stereospecific oxidation of non-activated hydrocarbons
at physiological temperatures.
Length = 461
Score = 29.6 bits (67), Expect = 4.7
Identities = 17/77 (22%), Positives = 25/77 (32%), Gaps = 16/77 (20%)
Query: 394 YQKMWRYMESKRPSVFVSDYEEGVKRVL--EGDY-AFLMESTMLDYEVQRNCNLTQIGGL 450
Y ++R +P V +S E VK VL +G+ + +
Sbjct: 33 YGPIFRLYLGPKPVVVLSGP-EAVKEVLIKKGEEFSGRPDEPWFATS------------R 79
Query: 451 LDSKGYGIATPKGSPWR 467
G GI G WR
Sbjct: 80 GPFLGKGIVFANGPRWR 96
>gnl|CDD|235327 PRK04987, PRK04987, fumarate reductase subunit C; Provisional.
Length = 130
Score = 28.0 bits (63), Expect = 6.0
Identities = 14/30 (46%), Positives = 19/30 (63%), Gaps = 1/30 (3%)
Query: 258 SFM-NPLAVEIWLYVLAAYLLVSFTLFVMA 286
SF+ NP+ V + + LAA LL + T F MA
Sbjct: 62 SFLQNPIVVILNIITLAAALLHTKTWFEMA 91
>gnl|CDD|153320 cd07636, BAR_GRAF, The Bin/Amphiphysin/Rvs (BAR) domain of GTPase
Regulator Associated with Focal adhesion kinase. BAR
domains are dimerization, lipid binding and curvature
sensing modules found in many different proteins with
diverse functions. GTPase Regulator Associated with
Focal adhesion kinase (GRAF), also called Rho GTPase
activating protein 26 (ARHGAP26), is a GAP with activity
towards RhoA and Cdc42 and is only weakly active towards
Rac1. It influences Rho-mediated cytoskeletal
rearrangements and binds focal adhesion kinase (FAK),
which is a critical component of integrin signaling.
GRAF contains an N-terminal BAR domain, followed by a
Pleckstrin homology (PH) domain, a Rho GAP domain, and a
C-terminal SH3 domain. BAR domains form dimers that bind
to membranes, induce membrane bending and curvature, and
may also be involved in protein-protein interactions.
The BAR domain of GRAF directly interacts with its Rho
GAP domain and inhibits its activity. Autoinhibited GRAF
is capable of binding membranes and tubulating
liposomes, showing that the membrane-tubulation and
GAP-inhibitory functions of the BAR domain can occur
simultaneously.
Length = 207
Score = 28.5 bits (63), Expect = 6.3
Identities = 17/74 (22%), Positives = 37/74 (50%), Gaps = 12/74 (16%)
Query: 195 YDHETKEWNGIVKELMD-----KKADLAVASMTINYARESVIDFTKPFMNLGIGILFKVP 249
YD ET+++ ++++ ++ K++ L A ++ R+ F + + +FKV
Sbjct: 116 YDKETEKYCAVLEKHLNLSSKKKESQLHEADSQVDLVRQH-------FYEVSLEYVFKVQ 168
Query: 250 TSQPTRLFSFMNPL 263
Q ++F F+ PL
Sbjct: 169 EVQERKMFEFVEPL 182
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.320 0.136 0.410
Gapped
Lambda K H
0.267 0.0761 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 25,520,080
Number of extensions: 2466071
Number of successful extensions: 2125
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2107
Number of HSP's successfully gapped: 54
Length of query: 504
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 403
Effective length of database: 6,457,848
Effective search space: 2602512744
Effective search space used: 2602512744
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 (21.8 bits)
S2: 61 (27.2 bits)