BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 005894
(671 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1YDY|A Chain A, Crystal Structure Of Periplasmic Glycerophosphodiester
Phosphodiesterase From Escherichia Coli
pdb|1YDY|B Chain B, Crystal Structure Of Periplasmic Glycerophosphodiester
Phosphodiesterase From Escherichia Coli
Length = 356
Score = 37.7 bits (86), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 37/133 (27%), Positives = 57/133 (42%), Gaps = 13/133 (9%)
Query: 271 LIITHNGASGVYAGCTDLAYQQAVDDGADIIDCTVQMSKEGVAFCLESPDLIGKTTAATV 330
++I H GASG T A A GAD ++ + M+K+ L L T A
Sbjct: 32 IVIAHRGASGYLPEHTLPAKAMAYAQGADYLEQDLVMTKDDNLVVLHDHYLDRVTDVADR 91
Query: 331 FMSKATSVPEIQKERGIFSFDLTWTEIQSLKPQISSPFDKSNPPII-----RNPEAKNKG 385
F +A +K+ ++ D T EI+SLK + FD N + R P K+
Sbjct: 92 FPDRA------RKDGRYYAIDFTLDEIKSLK--FTEGFDIENGKKVQTYPGRFPMGKSDF 143
Query: 386 KFVTLDGFLEFAK 398
+ T + +EF +
Sbjct: 144 RVHTFEEEIEFVQ 156
>pdb|1T8Q|A Chain A, Structural Genomics, Crystal Structure Of
Glycerophosphoryl Diester Phosphodiesterase From E. Coli
pdb|1T8Q|B Chain B, Structural Genomics, Crystal Structure Of
Glycerophosphoryl Diester Phosphodiesterase From E. Coli
pdb|1T8Q|C Chain C, Structural Genomics, Crystal Structure Of
Glycerophosphoryl Diester Phosphodiesterase From E. Coli
pdb|1T8Q|D Chain D, Structural Genomics, Crystal Structure Of
Glycerophosphoryl Diester Phosphodiesterase From E. Coli
Length = 336
Score = 35.4 bits (80), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 36/133 (27%), Positives = 56/133 (42%), Gaps = 13/133 (9%)
Query: 271 LIITHNGASGVYAGCTDLAYQQAVDDGADIIDCTVQMSKEGVAFCLESPDLIGKTTAATV 330
++I H GASG T A A GAD ++ + +K+ L L T A
Sbjct: 10 IVIAHRGASGYLPEHTLPAKAXAYAQGADYLEQDLVXTKDDNLVVLHDHYLDRVTDVADR 69
Query: 331 FMSKATSVPEIQKERGIFSFDLTWTEIQSLKPQISSPFDKSNPPII-----RNPEAKNKG 385
F +A +K+ ++ D T EI+SLK + FD N + R P K+
Sbjct: 70 FPDRA------RKDGRYYAIDFTLDEIKSLK--FTEGFDIENGKKVQTYPGRFPXGKSDF 121
Query: 386 KFVTLDGFLEFAK 398
+ T + +EF +
Sbjct: 122 RVHTFEEEIEFVQ 134
>pdb|2PZ0|A Chain A, Crystal Structure Of Glycerophosphodiester
Phosphodiesterase (Gdpd) From T. Tengcongensis
pdb|2PZ0|B Chain B, Crystal Structure Of Glycerophosphodiester
Phosphodiesterase (Gdpd) From T. Tengcongensis
Length = 252
Score = 34.3 bits (77), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 42/75 (56%), Gaps = 2/75 (2%)
Query: 269 RPLIITHNGASGVYAGCTDLAYQQAVDDGADIIDCTVQMSKEGVAFCLESPDLIGKTTAA 328
+ L+I H G S T A+++A++ GAD I+ VQ++K+G + + + +TT
Sbjct: 11 KTLVIAHRGDSKNVPENTIAAFKRAMELGADGIELDVQLTKDGHLVVIHD-ETVDRTTNG 69
Query: 329 TVFMSKATSVPEIQK 343
F+ K ++ EI+K
Sbjct: 70 EGFV-KDFTLEEIKK 83
>pdb|1O1Z|A Chain A, Crystal Structure Of Glycerophosphodiester
Phosphodiesterase (Gdpd) (Tm1621) From Thermotoga
Maritima At 1.60 A Resolution
Length = 234
Score = 32.7 bits (73), Expect = 0.60, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 28/51 (54%)
Query: 271 LIITHNGASGVYAGCTDLAYQQAVDDGADIIDCTVQMSKEGVAFCLESPDL 321
+++ H G S Y T A+ +A++ GA+ ++ V++SK+G DL
Sbjct: 14 IVLGHRGYSAKYLENTLEAFMKAIEAGANGVELDVRLSKDGKVVVSHDEDL 64
>pdb|1P1W|A Chain A, Crystal Structure Of The Glur2 Ligand-Binding Core (S1s2j)
With The L483y And L650t Mutations And In Complex With
Ampa
pdb|1P1W|B Chain B, Crystal Structure Of The Glur2 Ligand-Binding Core (S1s2j)
With The L483y And L650t Mutations And In Complex With
Ampa
Length = 263
Score = 29.3 bits (64), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 30/122 (24%), Positives = 55/122 (45%), Gaps = 10/122 (8%)
Query: 316 LESPDLIGKTTAATVFMSKATSVPEIQKERGIFSFDLTWTEIQSLKPQISSPFDKSNPPI 375
+ES + + K T + + S E + I FD WT ++S +P +
Sbjct: 121 IESAEDLSKQTEIAYGTTDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVAR 180
Query: 376 IRNPEAKNKGKFV-----TLDGFLEFAKTKAVSGVLININNAAY-LASKKGLGVVDAVTK 429
+R K+KGK+ T++ ++E K V N+++ Y +A+ KG + +AV
Sbjct: 181 VR----KSKGKYAYLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSSLGNAVNL 236
Query: 430 AL 431
A+
Sbjct: 237 AV 238
>pdb|1P1N|A Chain A, Glur2 Ligand Binding Core (S1s2j) Mutant L650t In Complex
With Kainate
pdb|1P1O|A Chain A, Crystal Structure Of The Glur2 Ligand-Binding Core (S1s2j)
Mutant L650t In Complex With Quisqualate
pdb|1P1Q|A Chain A, Crystal Structure Of The Glur2 Ligand Binding Core (S1s2j)
L650t Mutant In Complex With Ampa
pdb|1P1Q|B Chain B, Crystal Structure Of The Glur2 Ligand Binding Core (S1s2j)
L650t Mutant In Complex With Ampa
pdb|1P1Q|C Chain C, Crystal Structure Of The Glur2 Ligand Binding Core (S1s2j)
L650t Mutant In Complex With Ampa
pdb|1P1U|A Chain A, Crystal Structure Of The Glur2 Ligand-Binding Core (S1s2j)
L650t Mutant In Complex With Ampa (Ammonium Sulfate
Crystal Form)
pdb|1P1U|B Chain B, Crystal Structure Of The Glur2 Ligand-Binding Core (S1s2j)
L650t Mutant In Complex With Ampa (Ammonium Sulfate
Crystal Form)
Length = 263
Score = 28.9 bits (63), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 30/122 (24%), Positives = 55/122 (45%), Gaps = 10/122 (8%)
Query: 316 LESPDLIGKTTAATVFMSKATSVPEIQKERGIFSFDLTWTEIQSLKPQISSPFDKSNPPI 375
+ES + + K T + + S E + I FD WT ++S +P +
Sbjct: 121 IESAEDLSKQTEIAYGTTDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVAR 180
Query: 376 IRNPEAKNKGKFV-----TLDGFLEFAKTKAVSGVLININNAAY-LASKKGLGVVDAVTK 429
+R K+KGK+ T++ ++E K V N+++ Y +A+ KG + +AV
Sbjct: 181 VR----KSKGKYAYLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSSLGNAVNL 236
Query: 430 AL 431
A+
Sbjct: 237 AV 238
>pdb|2I3V|A Chain A, Measurement Of Conformational Changes Accompanying
Desensitization In An Ionotropic Glutamate Receptor:
Structure Of G725c Mutant
pdb|2I3V|B Chain B, Measurement Of Conformational Changes Accompanying
Desensitization In An Ionotropic Glutamate Receptor:
Structure Of G725c Mutant
pdb|2I3V|C Chain C, Measurement Of Conformational Changes Accompanying
Desensitization In An Ionotropic Glutamate Receptor:
Structure Of G725c Mutant
pdb|2I3V|D Chain D, Measurement Of Conformational Changes Accompanying
Desensitization In An Ionotropic Glutamate Receptor:
Structure Of G725c Mutant
Length = 259
Score = 28.9 bits (63), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 30/122 (24%), Positives = 54/122 (44%), Gaps = 10/122 (8%)
Query: 316 LESPDLIGKTTAATVFMSKATSVPEIQKERGIFSFDLTWTEIQSLKPQISSPFDKSNPPI 375
+ES + + K T + S E + I FD WT ++S +P +
Sbjct: 119 IESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVAR 178
Query: 376 IRNPEAKNKGKFV-----TLDGFLEFAKTKAVSGVLININNAAY-LASKKGLGVVDAVTK 429
+R K+KGK+ T++ ++E K V N+++ Y +A+ KG + +AV
Sbjct: 179 VR----KSKGKYAYLLESTMNEYIEQRKPCDTMKVGCNLDSKGYGIATPKGSSLGNAVNL 234
Query: 430 AL 431
A+
Sbjct: 235 AV 236
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.317 0.133 0.379
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 18,527,422
Number of Sequences: 62578
Number of extensions: 764403
Number of successful extensions: 2126
Number of sequences better than 100.0: 44
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 41
Number of HSP's that attempted gapping in prelim test: 2116
Number of HSP's gapped (non-prelim): 51
length of query: 671
length of database: 14,973,337
effective HSP length: 105
effective length of query: 566
effective length of database: 8,402,647
effective search space: 4755898202
effective search space used: 4755898202
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 55 (25.8 bits)