RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy17442
(90 letters)
>3kg2_A Glutamate receptor 2; ION channel, membrane protein, cell membrane,
glycoprotein, transport, membrane, postsynaptic cell
membrane, editing; HET: ZK1 NAG BMA; 3.60A {Rattus
norvegicus}
Length = 823
Score = 72.9 bits (178), Expect = 6e-17
Identities = 16/60 (26%), Positives = 26/60 (43%), Gaps = 1/60 (1%)
Query: 18 KKLMAFIWDSSRLDFEAAQ-DCELVTAGELFGRSGYAIGLQKGSPWADAVTLAILDFHES 76
K A++ +S+ ++ + C+ + G GY I KGS V LA+L E
Sbjct: 688 KGKYAYLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSSLGTPVNLAVLKLSEQ 747
>1yae_A Glutamate receptor, ionotropic kainate 2; kainate receptor,
membrane protein; HET: NAG FUC DOQ; 3.11A {Rattus
norvegicus} SCOP: c.94.1.1
Length = 312
Score = 65.2 bits (158), Expect = 2e-14
Identities = 20/55 (36%), Positives = 31/55 (56%)
Query: 22 AFIWDSSRLDFEAAQDCELVTAGELFGRSGYAIGLQKGSPWADAVTLAILDFHES 76
AF+ +S+ ++F ++C L G L GY +G GSP+ D +T+AIL E
Sbjct: 221 AFLMESTTIEFVTQRNCNLTQIGGLIDSKGYGVGTPMGSPYRDKITIAILQLQEE 275
>3g3k_A Glutamate receptor, ionotropic kainate 2; membrane protein, cell
junction, cell membrane, glycoprotein, ION transport,
ionic channel, membrane; HET: GLU IPA; 1.24A {Rattus
norvegicus} PDB: 3g3j_A* 3g3i_A* 2i0b_A* 3g3h_A* 3g3g_A*
3g3f_A* 1s7y_A* 1s9t_A* 1sd3_A* 1tt1_A* 1s50_A* 2xxr_A*
2xxt_A* 2xxx_A* 2xxw_A* 2xxy_A* 2xxu_A* 2xxv_A* 3qxm_A*
2i0c_A* ...
Length = 259
Score = 63.1 bits (153), Expect = 1e-13
Identities = 21/55 (38%), Positives = 31/55 (56%)
Query: 22 AFIWDSSRLDFEAAQDCELVTAGELFGRSGYAIGLQKGSPWADAVTLAILDFHES 76
AF+ +S+ ++F ++C L G L GY +G GSP+ D +TLAIL E
Sbjct: 187 AFLMESTTIEFVTQRNCNLTQIGGLIDSKGYGVGTPMGSPYRDKITLAILKLQEQ 241
>1pb7_A N-methyl-D-aspartate receptor subunit 1; ligand binding receptor,
NR1, ligand binding protein; 1.35A {Rattus norvegicus}
SCOP: c.94.1.1 PDB: 1pbq_A* 1y1m_A 1y1z_A 1y20_A 2a5t_A*
1pb8_A 1pb9_A
Length = 292
Score = 60.8 bits (147), Expect = 7e-13
Identities = 36/60 (60%), Positives = 46/60 (76%)
Query: 17 TKKLMAFIWDSSRLDFEAAQDCELVTAGELFGRSGYAIGLQKGSPWADAVTLAILDFHES 76
KL AFIWDS+ L+FEA+Q C+LVT GELF RSG+ IG++K SPW V+L+IL HE+
Sbjct: 215 DNKLHAFIWDSAVLEFEASQKCDLVTTGELFFRSGFGIGMRKDSPWKQNVSLSILKSHEN 274
>2v3u_A Glutamate receptor delta-2 subunit; postsynaptic membrane,
ionotropic glutamate receptors, transmembrane, membrane
protein; 1.74A {Rattus norvegicus} PDB: 2v3t_A
Length = 265
Score = 57.0 bits (137), Expect = 2e-11
Identities = 22/57 (38%), Positives = 31/57 (54%), Gaps = 2/57 (3%)
Query: 22 AFIWDSSRLDFEAAQ--DCELVTAGELFGRSGYAIGLQKGSPWADAVTLAILDFHES 76
AF+WD++ L++ A DC T G GY I LQ GSP+ D + IL+ +S
Sbjct: 190 AFVWDAAVLEYVAINDPDCSFYTVGNTVADRGYGIALQHGSPYRDVFSQRILELQQS 246
>2rc8_A Glutamate [NMDA] receptor subunit 3A; membrane protein, cell
junction, glycoprotein, ION transport channel,
magnesium; 1.45A {Rattus norvegicus} PDB: 2rc7_A 2rc9_A
2rca_A 2rcb_A
Length = 294
Score = 55.8 bits (134), Expect = 4e-11
Identities = 23/63 (36%), Positives = 33/63 (52%), Gaps = 2/63 (3%)
Query: 16 GTKKLMAFIWDSSRLDFEAAQ--DCELVTAGELFGRSGYAIGLQKGSPWADAVTLAILDF 73
+KL AFI D + LD+E + DC+L+T G+ F GY IGL SP ++ I +
Sbjct: 214 DPEKLDAFIMDKALLDYEVSIDADCKLLTVGKPFAIEGYGIGLPPNSPLTSNISELISQY 273
Query: 74 HES 76
Sbjct: 274 KSH 276
>1mqi_A Glutamate receptor 2; GLUR2, ligand binding core, S1S2, partial
agonist, WILLARDIINES, fluoro-WILLARDIINE, membrane
protein; HET: FWD; 1.35A {Rattus norvegicus} SCOP:
c.94.1.1 PDB: 1ftj_A* 1ftl_A* 1fto_A 1fw0_A* 1m5b_A*
1ftm_A* 1m5c_A* 1mm6_A* 1mm7_A* 1mqg_A* 1m5e_A* 1mqj_A*
1ms7_A* 1mxu_A* 1mxv_A 1mxw_A 1mxx_A 1mxy_A 1mxz_A
1my0_A ...
Length = 263
Score = 51.6 bits (123), Expect = 2e-09
Identities = 16/56 (28%), Positives = 28/56 (50%), Gaps = 1/56 (1%)
Query: 22 AFIWDSSRLDFEAAQ-DCELVTAGELFGRSGYAIGLQKGSPWADAVTLAILDFHES 76
A++ +S+ ++ + C+ + G GY I KGS +AV LA+L +E
Sbjct: 189 AYLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSSLGNAVNLAVLKLNEQ 244
>2a5s_A N-methyl-D-aspartate receptor nmdar2A subunit, NMDA receptor
nmdar2A; protein-ligand complex, metal
transport,membrane protein; HET: GLU; 1.70A {Rattus
norvegicus} SCOP: c.94.1.1 PDB: 2a5t_B* 3oen_A* 3oel_A*
3oem_A* 3oek_A*
Length = 284
Score = 49.6 bits (118), Expect = 7e-09
Identities = 32/79 (40%), Positives = 48/79 (60%), Gaps = 4/79 (5%)
Query: 2 RFDVKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQ--DCELVT--AGELFGRSGYAIGLQ 57
RF+ + +V T KL AFI+D++ L+++A + C+LVT +G +F +GY I LQ
Sbjct: 189 RFNQRGVEDALVSLKTGKLDAFIYDAAVLNYKAGRDEGCKLVTIGSGYIFATTGYGIALQ 248
Query: 58 KGSPWADAVTLAILDFHES 76
KGSPW + LA+L F
Sbjct: 249 KGSPWKRQIDLALLQFVGD 267
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 33.9 bits (77), Expect = 0.004
Identities = 16/59 (27%), Positives = 22/59 (37%), Gaps = 7/59 (11%)
Query: 33 EAAQDCELVTAGELFGR-SGYAIGL---QKGSPWADAVTLAILDFHESTVCYLFMAKVH 87
A D E T EL G+ GY L K + + L + +F YL +H
Sbjct: 47 GFAADDEPTTPAELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENC---YLEGNDIH 102
>2pyy_A Ionotropic glutamate receptor bacterial homologue; GLUR0 ligand
binding domain, transport protein; HET: GLU; 2.10A
{Nostoc punctiforme}
Length = 228
Score = 31.8 bits (73), Expect = 0.014
Identities = 15/57 (26%), Positives = 26/57 (45%), Gaps = 2/57 (3%)
Query: 22 AFIWDSSRLDFEAAQ--DCELVTAGELFGRSGYAIGLQKGSPWADAVTLAILDFHES 76
A ++D+ L F AA ++ G + Y I L SP+ + A+L+ E+
Sbjct: 154 AVVFDAPVLLFYAANEGKGKVEIVGSILREESYGIILPNNSPYRKPINQALLNLKEN 210
>2v25_A Major cell-binding factor; antigen, adhesin, aspartate, glutamate,
transport, ABC transport, virulence factor, receptor;
1.49A {Campylobacter jejuni}
Length = 259
Score = 31.9 bits (73), Expect = 0.015
Identities = 13/50 (26%), Positives = 19/50 (38%), Gaps = 3/50 (6%)
Query: 22 AFIWDSSRLDFEAAQDCELVTAGELFGRSGYAIGLQKGSP-WADAVTLAI 70
AF D S L E++ + F Y I +K P +A V +
Sbjct: 196 AFSVDKSILLGYVDDKSEIL--PDSFEPQSYGIVTKKDDPAFAKYVDDFV 243
>4dz1_A DALS D-alanine transporter; D-alanine binding, periplasmic,
transport protein; 1.90A {Salmonella enterica} PDB:
3r39_A 4f3s_A
Length = 259
Score = 30.8 bits (70), Expect = 0.037
Identities = 8/50 (16%), Positives = 15/50 (30%), Gaps = 1/50 (2%)
Query: 22 AFIWDS-SRLDFEAAQDCELVTAGELFGRSGYAIGLQKGSPWADAVTLAI 70
+ F+ + + + I +KGSP D L +
Sbjct: 187 LAFIEEPVYFTFKNKKKMPIESRYVFKNVDQLGIAFKKGSPVRDDFNLWL 236
>1ii5_A SLR1257 protein; membrane protein; HET: GLU; 1.60A {Synechocystis
SP} SCOP: c.94.1.1 PDB: 1iit_A 1iiw_A
Length = 233
Score = 30.3 bits (69), Expect = 0.055
Identities = 11/57 (19%), Positives = 21/57 (36%), Gaps = 2/57 (3%)
Query: 22 AFIWDSSRLDFEAAQ--DCELVTAGELFGRSGYAIGLQKGSPWADAVTLAILDFHES 76
A ++D L + Q + L Y L++ SP + + +L+ S
Sbjct: 158 AVMFDRPALIYYTRQNPNLNLEVTEIRVSLEPYGFVLKENSPLQKTINVEMLNLLYS 214
>1xt8_A Putative amino-acid transporter periplasmic solut protein; ABC
transport, cysteine uptake; 2.00A {Campylobacter jejuni}
SCOP: c.94.1.1
Length = 292
Score = 30.0 bits (68), Expect = 0.066
Identities = 9/57 (15%), Positives = 20/57 (35%), Gaps = 2/57 (3%)
Query: 22 AFIWDSSRLDFEAAQDCEL-VTAGELFGRSGYAIGLQKGSP-WADAVTLAILDFHES 76
A D++ L + + EL + A ++KG + + I+ +
Sbjct: 197 ALSHDNTLLFAWVKDHPDFKMGIKELGNKDVIAPAVKKGDKELKEFIDNLIIKLGQE 253
>3k4u_A Binding component of ABC transporter; structural genomics, protein
structure INI NEW YORK structural genomix research
consortium, nysgxrc; HET: LYS; 2.62A {Wolinella
succinogenes}
Length = 245
Score = 29.2 bits (66), Expect = 0.14
Identities = 10/58 (17%), Positives = 17/58 (29%), Gaps = 3/58 (5%)
Query: 22 AFIWDSSRLDFEAAQ--DCELVTAGELFGRSGYAIGLQKGSP-WADAVTLAILDFHES 76
FI+D AQ LV ++KG P + + + +
Sbjct: 159 MFIFDLPFNVAFMAQKGQGYLVHLDTSLTYEPLGWAIKKGDPDFLNWLNHFLAQIKHD 216
>4f3p_A Glutamine-binding periplasmic protein; ssgcid, structural genomics,
GLUT seattle structural genomics center for infectious
disease; 2.40A {Burkholderia pseudomallei}
Length = 249
Score = 28.8 bits (65), Expect = 0.19
Identities = 13/47 (27%), Positives = 17/47 (36%), Gaps = 2/47 (4%)
Query: 22 AFIWDSSRLDFEAAQ--DCELVTAGELFGRSGYAIGLQKGSPWADAV 66
A + D+ + F + AG Y IG KGSP V
Sbjct: 174 AAMHDTPNVLFFVNNEGKGRVKVAGAPVSGDKYGIGFPKGSPLVAKV 220
>2yjp_A Putative ABC transporter, periplasmic binding Pro amino acid;
transport protein, solute-binding protein; 2.26A
{Neisseria gonorrhoeae}
Length = 291
Score = 28.5 bits (64), Expect = 0.21
Identities = 13/57 (22%), Positives = 21/57 (36%), Gaps = 2/57 (3%)
Query: 22 AFIWDSSRLDFEAAQDCEL-VTAGELFGRSGYAIGLQKGSP-WADAVTLAILDFHES 76
A D++ L A ++ V G L A +QKG+ + V I +
Sbjct: 208 ALAHDNALLWAWAKENPNFEVAIGNLGPAEFIAPAVQKGNADLLNWVNGEIAAMKKD 264
>2o1m_A Probable amino-acid ABC transporter extracellular-binding protein
YTMK; NESG X-RAY O34852 YTMK_bacsu, structural genomics,
PSI-2; 2.00A {Bacillus subtilis}
Length = 258
Score = 26.5 bits (59), Expect = 1.2
Identities = 7/41 (17%), Positives = 12/41 (29%), Gaps = 1/41 (2%)
Query: 22 AFIWDSSRLDFEAAQ-DCELVTAGELFGRSGYAIGLQKGSP 61
A I +DF+ + T G + + K
Sbjct: 174 ATISTPFAVDFQNKTSTIKEKTVGNVLSNAKVYFMFNKNEQ 214
>2d69_A Ribulose bisphosphate carboxylase; alpha/beta barrel, structural
genomics, NPPSFA, national Pro protein structural and
functional analyses; 1.90A {Pyrococcus horikoshii} SCOP:
c.1.14.1 d.58.9.1 PDB: 2cxe_A 2cwx_A
Length = 430
Score = 26.2 bits (57), Expect = 1.5
Identities = 8/26 (30%), Positives = 12/26 (46%), Gaps = 1/26 (3%)
Query: 33 EAAQDC-ELVTAGELFGRSGYAIGLQ 57
E A+ EL + G S +G+Q
Sbjct: 404 EKAKSSPELKKSLREVGLSKAKVGVQ 429
>3epo_A Thiamine biosynthesis protein THIC; alpha-beta barrel, SAM
superfamily, biosynthetic protein; HET: MP5; 2.10A
{Caulobacter crescentus} PDB: 3epm_A* 3epn_A*
Length = 612
Score = 25.5 bits (56), Expect = 2.8
Identities = 15/48 (31%), Positives = 21/48 (43%), Gaps = 10/48 (20%)
Query: 2 RFDVKFSPSTVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTAGELFGR 49
+DV FS +R G+ D++ + AQ EL T GEL
Sbjct: 365 AYDVSFSLGDGLRPGS------TADAN----DEAQFSELRTLGELTKV 402
>2q0o_A Probable transcriptional activator protein TRAR; helix-turn-helix,
two-helix coiled coil; HET: LAE; 2.00A {Rhizobium SP}
Length = 236
Score = 25.4 bits (55), Expect = 2.9
Identities = 10/60 (16%), Positives = 18/60 (30%), Gaps = 2/60 (3%)
Query: 12 VVRHGTKKLMAFIWDSSRLDFEAAQDC-ELVTAGELFG-RSGYAIGLQKGSPWADAVTLA 69
V+ ++ F W + + G R G I ++ A +T A
Sbjct: 74 VLAEAKRRRDVFFWTADAWPARGSSPLRRFRDEAISHGIRCGVTIPVEGSYGSAMMLTFA 133
>1wdn_A GLNBP, glutamine binding protein; closed form, complex, peptide,
complex (binding protein/peptide); 1.94A {Escherichia
coli} SCOP: c.94.1.1 PDB: 1ggg_A
Length = 226
Score = 25.2 bits (56), Expect = 3.3
Identities = 6/25 (24%), Positives = 9/25 (36%)
Query: 37 DCELVTAGELFGRSGYAIGLQKGSP 61
+ + G+ Y I KGS
Sbjct: 170 NGQFKAVGDSLEAQQYGIAFPKGSD 194
>2pvu_A ARTJ; basic amino acid binding protein, ABC transport system, THER
bacterium, transport protein; HET: LYS; 1.79A
{Geobacillus stearothermophilus} PDB: 2q2a_A* 2q2c_A*
Length = 272
Score = 25.0 bits (55), Expect = 3.7
Identities = 7/40 (17%), Positives = 14/40 (35%)
Query: 37 DCELVTAGELFGRSGYAIGLQKGSPWADAVTLAILDFHES 76
+++ + F Y + K S V A+ + S
Sbjct: 211 KLQVIEDPKNFASEYYGMIFPKNSELKAKVDEALKNVINS 250
>3h7m_A Sensor protein; histidine kinase sensor domain, kinase,
phosphoprotein, transferase; 2.40A {Geobacter
sulfurreducens}
Length = 234
Score = 24.5 bits (54), Expect = 5.5
Identities = 4/25 (16%), Positives = 7/25 (28%)
Query: 37 DCELVTAGELFGRSGYAIGLQKGSP 61
LV Y +++G
Sbjct: 178 LTNLVPVARSIAAQRYGYAVRQGDA 202
>2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-PR;
fatty acid synthase, acyl-carrier-protein, beta-ketoacyl
RED beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae}
Length = 1688
Score = 24.5 bits (53), Expect = 6.7
Identities = 17/59 (28%), Positives = 23/59 (38%), Gaps = 8/59 (13%)
Query: 25 WDSSRLDFEAAQDCELVTAG--EL---FGRSGYAIGLQKGSP---WADAVTLAILDFHE 75
W S+R +E E G E+ G Y G KG P W D+ T +D +
Sbjct: 831 WGSARTRWEMEAFGEFSLEGCVEMAWIMGFISYHNGNLKGRPYTGWVDSKTKEPVDDKD 889
>3jsj_A Putative TETR-family transcriptional regulator; DNA-binding,
transcription regulation; 2.10A {Streptomyces
avermitilis ma-4680}
Length = 190
Score = 24.0 bits (52), Expect = 7.9
Identities = 7/18 (38%), Positives = 9/18 (50%)
Query: 40 LVTAGELFGRSGYAIGLQ 57
L A L R G IG++
Sbjct: 15 LEAAAALTYRDGVGIGVE 32
>2hlz_A Ketohexokinase; non-protein kinase, creatine kinase, fructokinase,
isoform A, structural genomics, structural genomics
consortium, SGC transferase; 1.85A {Homo sapiens} PDB:
2hqq_A 2hw1_A* 3nbv_A* 3nbw_A* 3nc2_A* 3nc9_A* 3nca_A*
3q92_A* 3qa2_A* 3qai_A* 3ro4_A* 3b3l_A
Length = 312
Score = 24.1 bits (53), Expect = 8.4
Identities = 13/61 (21%), Positives = 21/61 (34%), Gaps = 4/61 (6%)
Query: 12 VVRHGTKKLMAFIWDSSRLDFEAAQDCELV-T--AGELFGRSGYAIGLQKGSPWADAVTL 68
V + A D L +A +V T AG+ F + L +G +A+
Sbjct: 236 VCAWAEEGADALGPDGKLLHSDAFPPPRVVDTLGAGDTF-NASVIFSLSQGRSVQEALRF 294
Query: 69 A 69
Sbjct: 295 G 295
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.325 0.136 0.424
Gapped
Lambda K H
0.267 0.0750 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,361,104
Number of extensions: 65435
Number of successful extensions: 261
Number of sequences better than 10.0: 1
Number of HSP's gapped: 257
Number of HSP's successfully gapped: 42
Length of query: 90
Length of database: 6,701,793
Length adjustment: 57
Effective length of query: 33
Effective length of database: 5,110,296
Effective search space: 168639768
Effective search space used: 168639768
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 51 (23.4 bits)