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= psy4254
         (114 letters)

Database: pdbaa 
           62,578 sequences; 14,973,337 total letters

Searching..................................................done



>pdb|2ZIY|A Chain A, Crystal Structure Of Squid Rhodopsin
          Length = 372

 Score = 51.2 bits (121), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 22/52 (42%), Positives = 36/52 (69%)

Query: 51  NSAVRTAQILLMLVICFLLAWTPYAVITFIGQFGDASLITPWVSATPAIFAK 102
           N+ +R A+I +++V  FLL+W+PYAV+  + QFG    +TP+ +  P +FAK
Sbjct: 253 NAEMRLAKISIVIVSQFLLSWSPYAVVALLAQFGPLEWVTPYAAQLPVMFAK 304


>pdb|2Z73|A Chain A, Crystal Structure Of Squid Rhodopsin
 pdb|2Z73|B Chain B, Crystal Structure Of Squid Rhodopsin
 pdb|3AYM|A Chain A, Crystal Structure Of The Batho Intermediate Of Squid
           Rhodopsin
 pdb|3AYM|B Chain B, Crystal Structure Of The Batho Intermediate Of Squid
           Rhodopsin
 pdb|3AYN|A Chain A, Crystal Structure Of Squid Isorhodopsin
 pdb|3AYN|B Chain B, Crystal Structure Of Squid Isorhodopsin
          Length = 448

 Score = 51.2 bits (121), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 22/52 (42%), Positives = 36/52 (69%)

Query: 51  NSAVRTAQILLMLVICFLLAWTPYAVITFIGQFGDASLITPWVSATPAIFAK 102
           N+ +R A+I +++V  FLL+W+PYAV+  + QFG    +TP+ +  P +FAK
Sbjct: 254 NAEMRLAKISIVIVSQFLLSWSPYAVVALLAQFGPLEWVTPYAAQLPVMFAK 305


>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 = 35.8 bits (81), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 25/83 (30%), Positives = 37/83 (44%), Gaps = 1/83 (1%)

Query: 20  PLTKICDCGGVVTNYTLAYKLAMPIHRATPLNSAVRTAQILLMLVICFLLAWTPYAVITF 79
           PL  I  C G +  +T+    A     AT   +     ++++++VI FL+ W PYA + F
Sbjct: 216 PLIVIFFCYGQLV-FTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAF 274

Query: 80  IGQFGDASLITPWVSATPAIFAK 102
                  S   P     PA FAK
Sbjct: 275 YIFTHQGSCFGPIFMTIPAFFAK 297


>pdb|3C9M|A Chain A, Structure Of A Mutant Bovine Rhodopsin In Hexagonal
           Crystal Form
          Length = 348

 Score = 35.8 bits (81), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 25/83 (30%), Positives = 37/83 (44%), Gaps = 1/83 (1%)

Query: 20  PLTKICDCGGVVTNYTLAYKLAMPIHRATPLNSAVRTAQILLMLVICFLLAWTPYAVITF 79
           PL  I  C G +  +T+    A     AT   +     ++++++VI FL+ W PYA + F
Sbjct: 215 PLIVIFFCYGQLV-FTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAF 273

Query: 80  IGQFGDASLITPWVSATPAIFAK 102
                  S   P     PA FAK
Sbjct: 274 YIFTHQGSCFGPIFMTIPAFFAK 296


>pdb|2X72|A Chain A, Crystal Structure Of The Constitutively Active E113q,N2c,
           D282c Rhodopsin Mutant With Bound Galphact Peptide
          Length = 349

 Score = 35.8 bits (81), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 25/83 (30%), Positives = 37/83 (44%), Gaps = 1/83 (1%)

Query: 20  PLTKICDCGGVVTNYTLAYKLAMPIHRATPLNSAVRTAQILLMLVICFLLAWTPYAVITF 79
           PL  I  C G +  +T+    A     AT   +     ++++++VI FL+ W PYA + F
Sbjct: 216 PLIVIFFCYGQLV-FTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAF 274

Query: 80  IGQFGDASLITPWVSATPAIFAK 102
                  S   P     PA FAK
Sbjct: 275 YIFTHQGSCFGPIFMTIPAFFAK 297


>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 = 35.0 bits (79), Expect = 0.009,   Method: Compositional matrix adjust.
 Identities = 25/83 (30%), Positives = 37/83 (44%), Gaps = 1/83 (1%)

Query: 20  PLTKICDCGGVVTNYTLAYKLAMPIHRATPLNSAVRTAQILLMLVICFLLAWTPYAVITF 79
           PL  I  C G +  +T+    A     AT   +     ++++++VI FL+ W PYA + F
Sbjct: 216 PLIVIFFCYGQLV-FTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAF 274

Query: 80  IGQFGDASLITPWVSATPAIFAK 102
                  S   P     PA FAK
Sbjct: 275 YIFTHQGSDFGPIFMTIPAFFAK 297


>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 = 35.0 bits (79), Expect = 0.009,   Method: Compositional matrix adjust.
 Identities = 25/83 (30%), Positives = 37/83 (44%), Gaps = 1/83 (1%)

Query: 20  PLTKICDCGGVVTNYTLAYKLAMPIHRATPLNSAVRTAQILLMLVICFLLAWTPYAVITF 79
           PL  I  C G +  +T+    A     AT   +     ++++++VI FL+ W PYA + F
Sbjct: 215 PLIVIFFCYGQLV-FTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAF 273

Query: 80  IGQFGDASLITPWVSATPAIFAK 102
                  S   P     PA FAK
Sbjct: 274 YIFTHQGSDFGPIFMTIPAFFAK 296


>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 = 34.7 bits (78), Expect = 0.013,   Method: Compositional matrix adjust.
 Identities = 25/83 (30%), Positives = 36/83 (43%), Gaps = 1/83 (1%)

Query: 20  PLTKICDCGGVVTNYTLAYKLAMPIHRATPLNSAVRTAQILLMLVICFLLAWTPYAVITF 79
           PL  I  C G +  +T+    A     AT   +     +++++ VI FL+ W PYA + F
Sbjct: 216 PLIVIFFCYGQLV-FTVKEAAAQQQESATTQKAEKEVTRMVIIYVIAFLICWLPYAGVAF 274

Query: 80  IGQFGDASLITPWVSATPAIFAK 102
                  S   P     PA FAK
Sbjct: 275 YIFTHQGSCFGPIFMTIPAFFAK 297


>pdb|4DAJ|A Chain A, Structure Of The M3 Muscarinic Acetylcholine Receptor
 pdb|4DAJ|B Chain B, Structure Of The M3 Muscarinic Acetylcholine Receptor
 pdb|4DAJ|C Chain C, Structure Of The M3 Muscarinic Acetylcholine Receptor
 pdb|4DAJ|D Chain D, Structure Of The M3 Muscarinic Acetylcholine Receptor
          Length = 479

 Score = 30.4 bits (67), Expect = 0.26,   Method: Compositional matrix adjust.
 Identities = 10/34 (29%), Positives = 21/34 (61%)

Query: 55  RTAQILLMLVICFLLAWTPYAVITFIGQFGDASL 88
           + AQ L  +++ F++ WTPY ++  +  F D+ +
Sbjct: 371 KAAQTLSAILLAFIITWTPYNIMVLVNTFCDSCI 404


>pdb|2QE7|D Chain D, Crystal Structure Of The F1-Atpase From The
           Thermoalkaliphilic Bacterium Bacillus Sp. Ta2.A1
 pdb|2QE7|E Chain E, Crystal Structure Of The F1-Atpase From The
           Thermoalkaliphilic Bacterium Bacillus Sp. Ta2.A1
 pdb|2QE7|F Chain F, Crystal Structure Of The F1-Atpase From The
           Thermoalkaliphilic Bacterium Bacillus Sp. Ta2.A1
          Length = 462

 Score = 26.6 bits (57), Expect = 3.8,   Method: Composition-based stats.
 Identities = 17/46 (36%), Positives = 21/46 (45%)

Query: 43  PIHRATPLNSAVRTAQILLMLVICFLLAWTPYAVITFIGQFGDASL 88
           PIHR  P    + TA  +L   I  +    PYA    IG FG A +
Sbjct: 110 PIHRPAPEFEELSTADEILETGIKVIDLLAPYAKGGKIGLFGGAGV 155


>pdb|2I3B|A Chain A, Solution Structure Of A Human Cancer-Related Nucleoside
           Triphosphatase
          Length = 189

 Score = 26.6 bits (57), Expect = 3.8,   Method: Compositional matrix adjust.
 Identities = 14/45 (31%), Positives = 21/45 (46%)

Query: 9   GPRRRYQVRSPPLTKICDCGGVVTNYTLAYKLAMPIHRATPLNSA 53
           GP  R  +  PP  + C  G  V + T   +LA+P+ R    +S 
Sbjct: 59  GPLSRVGLEPPPGKRECRVGQYVVDLTSFEQLALPVLRNADCSSG 103


>pdb|3UON|A Chain A, Structure Of The Human M2 Muscarinic Acetylcholine
           Receptor Bound To An Antagonist
          Length = 467

 Score = 25.4 bits (54), Expect = 8.7,   Method: Compositional matrix adjust.
 Identities = 8/29 (27%), Positives = 17/29 (58%)

Query: 55  RTAQILLMLVICFLLAWTPYAVITFIGQF 83
           +  + +L +++ F++ W PY V+  I  F
Sbjct: 385 KVTRTILAILLAFIITWAPYNVMVLINTF 413


  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
   0.330    0.143    0.450 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,999,564
Number of Sequences: 62578
Number of extensions: 90038
Number of successful extensions: 252
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 238
Number of HSP's gapped (non-prelim): 16
length of query: 114
length of database: 14,973,337
effective HSP length: 77
effective length of query: 37
effective length of database: 10,154,831
effective search space: 375728747
effective search space used: 375728747
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 45 (21.9 bits)