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= 042605
(209 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3OAX|A Chain A, Crystal Structure Of Bovine Rhodopsin With Beta-Ionone
pdb|3OAX|B Chain B, Crystal Structure Of Bovine Rhodopsin With Beta-Ionone
pdb|1GZM|A Chain A, Structure Of Bovine Rhodopsin In A Trigonal Crystal Form
pdb|1GZM|B Chain B, Structure Of Bovine Rhodopsin In A Trigonal Crystal Form
pdb|1HZX|A Chain A, Crystal Structure Of Bovine Rhodopsin
pdb|1HZX|B Chain B, Crystal Structure Of Bovine Rhodopsin
pdb|2I36|A Chain A, Crystal Structure Of Trigonal Crystal Form Of Ground-State
Rhodopsin
pdb|2I36|B Chain B, Crystal Structure Of Trigonal Crystal Form Of Ground-State
Rhodopsin
pdb|2I36|C Chain C, Crystal Structure Of Trigonal Crystal Form Of Ground-State
Rhodopsin
pdb|2I35|A Chain A, Crystal Structure Of Rhombohedral Crystal Form Of
Ground-State Rhodopsin
pdb|2I37|A Chain A, Crystal Structure Of A Photoactivated Rhodopsin
pdb|2I37|B Chain B, Crystal Structure Of A Photoactivated Rhodopsin
pdb|2I37|C Chain C, Crystal Structure Of A Photoactivated Rhodopsin
pdb|2HPY|A Chain A, Crystallographic Model Of Lumirhodopsin
pdb|2HPY|B Chain B, Crystallographic Model Of Lumirhodopsin
pdb|2PED|A Chain A, Crystallographic Model Of 9-Cis-Rhodopsin
pdb|2PED|B Chain B, Crystallographic Model Of 9-Cis-Rhodopsin
pdb|2G87|A Chain A, Crystallographic Model Of Bathorhodopsin
pdb|2G87|B Chain B, Crystallographic Model Of Bathorhodopsin
pdb|1L9H|A Chain A, Crystal Structure Of Bovine Rhodopsin At 2.6 Angstroms
Resolution
pdb|1L9H|B Chain B, Crystal Structure Of Bovine Rhodopsin At 2.6 Angstroms
Resolution
pdb|1U19|A Chain A, Crystal Structure Of Bovine Rhodopsin At 2.2 Angstroms
Resolution
pdb|1U19|B Chain B, Crystal Structure Of Bovine Rhodopsin At 2.2 Angstroms
Resolution
Length = 349
Score = 31.2 bits (69), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 17/68 (25%), Positives = 31/68 (45%), Gaps = 4/68 (5%)
Query: 67 VIWYSECLLRYSNVSFF----SAMDTKPFFYTSSTQNSTSRRLFEQQVWSLMNEALNRAL 122
VI + C L Y+ V+F+ D P F T + + ++ ++ +MN+ +
Sbjct: 259 VIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCM 318
Query: 123 STTKCLGQ 130
TT C G+
Sbjct: 319 VTTLCCGK 326
>pdb|1JFP|A Chain A, Structure Of Bovine Rhodopsin (Dark Adapted)
pdb|1LN6|A Chain A, Structure Of Bovine Rhodopsin (Metarhodopsin Ii)
pdb|3CAP|A Chain A, Crystal Structure Of Native Opsin: The G Protein-Coupled
Receptor Rhodopsin In Its Ligand-Free State
pdb|3CAP|B Chain B, Crystal Structure Of Native Opsin: The G Protein-Coupled
Receptor Rhodopsin In Its Ligand-Free State
pdb|3C9L|A Chain A, Structure Of Ground-State Bovine Rhodospin In A Hexagonal
Crystal Form
pdb|1F88|A Chain A, Crystal Structure Of Bovine Rhodopsin
pdb|1F88|B Chain B, Crystal Structure Of Bovine Rhodopsin
pdb|3DQB|A Chain A, Crystal Structure Of The Active G-protein-coupled Receptor
Opsin In Complex With A C-terminal Peptide Derived From
The Galpha Subunit Of Transducin
pdb|3PQR|A Chain A, Crystal Structure Of Metarhodopsin Ii In Complex With A
C-Terminal Peptide Derived From The Galpha Subunit Of
Transducin
pdb|3PXO|A Chain A, Crystal Structure Of Metarhodopsin Ii
Length = 348
Score = 31.2 bits (69), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 17/68 (25%), Positives = 31/68 (45%), Gaps = 4/68 (5%)
Query: 67 VIWYSECLLRYSNVSFF----SAMDTKPFFYTSSTQNSTSRRLFEQQVWSLMNEALNRAL 122
VI + C L Y+ V+F+ D P F T + + ++ ++ +MN+ +
Sbjct: 258 VIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCM 317
Query: 123 STTKCLGQ 130
TT C G+
Sbjct: 318 VTTLCCGK 325
>pdb|1GAX|A Chain A, Crystal Structure Of Thermus Thermophilus Valyl-Trna
Synthetase Complexed With Trna(Val) And Valyl-Adenylate
Analogue
pdb|1GAX|B Chain B, Crystal Structure Of Thermus Thermophilus Valyl-Trna
Synthetase Complexed With Trna(Val) And Valyl-Adenylate
Analogue
pdb|1IVS|A Chain A, Crystal Structure Of Thermus Thermophilus Valyl-Trna
Synthetase Complexed With Trna(Val) And Valyl-Adenylate
Analogue
pdb|1IVS|B Chain B, Crystal Structure Of Thermus Thermophilus Valyl-Trna
Synthetase Complexed With Trna(Val) And Valyl-Adenylate
Analogue
pdb|1IYW|A Chain A, Preliminary Structure Of Thermus Thermophilus Ligand-Free
Valyl-Trna Synthetase
pdb|1IYW|B Chain B, Preliminary Structure Of Thermus Thermophilus Ligand-Free
Valyl-Trna Synthetase
Length = 862
Score = 29.6 bits (65), Expect = 1.3, Method: Composition-based stats.
Identities = 17/65 (26%), Positives = 28/65 (43%)
Query: 97 TQNSTSRRLFEQQVWSLMNEALNRALSTTKCLGQQTKITQTARRMSAVSSYNIRYELYPF 156
T++ R F ++VW E+ L K LG ++ A M S +RY +
Sbjct: 101 TRHDLGREKFLERVWQWKEESGGTILKQLKRLGASADWSREAFTMDEKRSRAVRYAFSRY 160
Query: 157 YNDTL 161
Y++ L
Sbjct: 161 YHEGL 165
>pdb|1LE6|A Chain A, Carboxylic Ester Hydrolase, P 1 21 1 Space Group
pdb|1LE6|B Chain B, Carboxylic Ester Hydrolase, P 1 21 1 Space Group
pdb|1LE6|C Chain C, Carboxylic Ester Hydrolase, P 1 21 1 Space Group
pdb|1LE7|A Chain A, Carboxylic Ester Hydrolase, C 2 2 21 Space Group
pdb|1LE7|B Chain B, Carboxylic Ester Hydrolase, C 2 2 21 Space Group
Length = 123
Score = 28.5 bits (62), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 16/63 (25%), Positives = 28/63 (44%), Gaps = 1/63 (1%)
Query: 93 YTSSTQNSTSRRLFEQQVWSLMNEALNRALSTTKCLGQQTKITQTARRMSAVSSYNIRYE 152
YT + + S + E+ W +N+++ + KC K Q A + YN++Y
Sbjct: 50 YTRAEEAGCSPKT-ERYSWQCVNQSVLCGPAENKCQELLCKCDQEIANCLAQTEYNLKYL 108
Query: 153 LYP 155
YP
Sbjct: 109 FYP 111
>pdb|4A4M|A Chain A, Crystal Structure Of The Light-Activated Constitutively
Active N2c,M257y,D282c Rhodopsin Mutant In Complex With
A Peptide Resembling The C-Terminus Of The
Galpha-Protein Subunit (Gact)
Length = 349
Score = 27.3 bits (59), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 16/68 (23%), Positives = 30/68 (44%), Gaps = 4/68 (5%)
Query: 67 VIWYSECLLRYSNVSFFSAMDTK----PFFYTSSTQNSTSRRLFEQQVWSLMNEALNRAL 122
VI + C L Y+ V+F+ P F T + + ++ ++ +MN+ +
Sbjct: 259 VIAFLICWLPYAGVAFYIFTHQGSCFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCM 318
Query: 123 STTKCLGQ 130
TT C G+
Sbjct: 319 VTTLCCGK 326
>pdb|2J4Y|A Chain A, Crystal Structure Of A Rhodopsin Stabilizing Mutant
Expressed In Mammalian Cells
pdb|2J4Y|B Chain B, Crystal Structure Of A Rhodopsin Stabilizing Mutant
Expressed In Mammalian Cells
Length = 349
Score = 27.3 bits (59), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 16/68 (23%), Positives = 30/68 (44%), Gaps = 4/68 (5%)
Query: 67 VIWYSECLLRYSNVSFFSAMDTK----PFFYTSSTQNSTSRRLFEQQVWSLMNEALNRAL 122
VI + C L Y+ V+F+ P F T + + ++ ++ +MN+ +
Sbjct: 259 VIAFLICWLPYAGVAFYIFTHQGSCFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCM 318
Query: 123 STTKCLGQ 130
TT C G+
Sbjct: 319 VTTLCCGK 326
>pdb|2X72|A Chain A, Crystal Structure Of The Constitutively Active E113q,N2c,
D282c Rhodopsin Mutant With Bound Galphact Peptide
Length = 349
Score = 27.3 bits (59), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 16/68 (23%), Positives = 30/68 (44%), Gaps = 4/68 (5%)
Query: 67 VIWYSECLLRYSNVSFFSAMDTK----PFFYTSSTQNSTSRRLFEQQVWSLMNEALNRAL 122
VI + C L Y+ V+F+ P F T + + ++ ++ +MN+ +
Sbjct: 259 VIAFLICWLPYAGVAFYIFTHQGSCFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCM 318
Query: 123 STTKCLGQ 130
TT C G+
Sbjct: 319 VTTLCCGK 326
>pdb|3C9M|A Chain A, Structure Of A Mutant Bovine Rhodopsin In Hexagonal
Crystal Form
Length = 348
Score = 27.3 bits (59), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 16/68 (23%), Positives = 30/68 (44%), Gaps = 4/68 (5%)
Query: 67 VIWYSECLLRYSNVSFFSAMDTK----PFFYTSSTQNSTSRRLFEQQVWSLMNEALNRAL 122
VI + C L Y+ V+F+ P F T + + ++ ++ +MN+ +
Sbjct: 258 VIAFLICWLPYAGVAFYIFTHQGSCFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCM 317
Query: 123 STTKCLGQ 130
TT C G+
Sbjct: 318 VTTLCCGK 325
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
0.322 0.130 0.396
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,666,734
Number of Sequences: 62578
Number of extensions: 135012
Number of successful extensions: 240
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 238
Number of HSP's gapped (non-prelim): 8
length of query: 209
length of database: 14,973,337
effective HSP length: 94
effective length of query: 115
effective length of database: 9,091,005
effective search space: 1045465575
effective search space used: 1045465575
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 49 (23.5 bits)