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= psy17635
         (103 letters)

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

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



>pdb|3JYB|A Chain A, Crystal Structure Of The Rets Periplasmic Domain
 pdb|3JYB|B Chain B, Crystal Structure Of The Rets Periplasmic Domain
          Length = 145

 Score = 27.3 bits (59), Expect = 2.0,   Method: Compositional matrix adjust.
 Identities = 12/33 (36%), Positives = 18/33 (54%)

Query: 63  YSQPLDGKPRTRSSMSSEKHPVESDTDSMAEYG 95
           +S P+DGKP T     +  HP+ +  D + E G
Sbjct: 108 FSLPVDGKPXTLYVRXTSNHPLXAWFDQIDEAG 140


>pdb|2XBZ|A Chain A, Multiple Oligomeric Forms Of The Pseudomonas Aeruginosa
           Rets Sensor Domain Modulate Accessibility To The Ligand-
           Binding Site
 pdb|2XBZ|B Chain B, Multiple Oligomeric Forms Of The Pseudomonas Aeruginosa
           Rets Sensor Domain Modulate Accessibility To The Ligand-
           Binding Site
          Length = 171

 Score = 27.3 bits (59), Expect = 2.1,   Method: Compositional matrix adjust.
 Identities = 12/33 (36%), Positives = 18/33 (54%)

Query: 63  YSQPLDGKPRTRSSMSSEKHPVESDTDSMAEYG 95
           +S P+DGKP T     +  HP+ +  D + E G
Sbjct: 134 FSLPVDGKPXTLYVRXTSNHPLXAWFDQIDEAG 166


>pdb|3VR8|A Chain A, Mitochondrial Rhodoquinol-Fumarate Reductase From The
           Parasitic Nematode Ascaris Suum
 pdb|3VR8|E Chain E, Mitochondrial Rhodoquinol-Fumarate Reductase From The
           Parasitic Nematode Ascaris Suum
 pdb|3VRB|A Chain A, Mitochondrial Rhodoquinol-Fumarate Reductase From The
           Parasitic Nematode Ascaris Suum With The Specific
           Inhibitor Flutolanil And Substrate Fumarate
 pdb|3VRB|E Chain E, Mitochondrial Rhodoquinol-Fumarate Reductase From The
           Parasitic Nematode Ascaris Suum With The Specific
           Inhibitor Flutolanil And Substrate Fumarate
          Length = 645

 Score = 26.2 bits (56), Expect = 4.4,   Method: Compositional matrix adjust.
 Identities = 10/29 (34%), Positives = 18/29 (62%)

Query: 44  EREAAHGRHDYPEEPGFNEYSQPLDGKPR 72
           E   AH R D+P+     +YS+P++G+ +
Sbjct: 568 ESRGAHARDDFPKREDEYDYSKPIEGQTK 596


>pdb|3IKL|A Chain A, Crystal Structure Of Pol Gb Delta-I4.
 pdb|3IKL|B Chain B, Crystal Structure Of Pol Gb Delta-I4
          Length = 459

 Score = 25.8 bits (55), Expect = 7.4,   Method: Composition-based stats.
 Identities = 16/53 (30%), Positives = 23/53 (43%), Gaps = 2/53 (3%)

Query: 36 RGGKYAVHEREAAHGRHDYPEEPGFNEYSQPLDGKPRTRSSMSSEKHPVESDT 88
          +GG    H     +G H  PE PG  E S+ L    + R  +S  K  +  D+
Sbjct: 40 KGGHVKSHAELEGNGEH--PEAPGSGEGSEALLEICQRRHFLSGSKQQLSRDS 90


>pdb|2G4C|A Chain A, Crystal Structure Of Human Dna Polymerase Gamma
          Accessory Subunit
 pdb|2G4C|B Chain B, Crystal Structure Of Human Dna Polymerase Gamma
          Accessory Subunit
 pdb|2G4C|C Chain C, Crystal Structure Of Human Dna Polymerase Gamma
          Accessory Subunit
 pdb|2G4C|D Chain D, Crystal Structure Of Human Dna Polymerase Gamma
          Accessory Subunit
          Length = 474

 Score = 25.4 bits (54), Expect = 8.1,   Method: Composition-based stats.
 Identities = 16/53 (30%), Positives = 23/53 (43%), Gaps = 2/53 (3%)

Query: 36 RGGKYAVHEREAAHGRHDYPEEPGFNEYSQPLDGKPRTRSSMSSEKHPVESDT 88
          +GG    H     +G H  PE PG  E S+ L    + R  +S  K  +  D+
Sbjct: 29 KGGHVKSHAELEGNGEH--PEAPGSGEGSEALLEICQRRHFLSGSKQQLSRDS 79


  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
   0.308    0.128    0.386 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,049,853
Number of Sequences: 62578
Number of extensions: 109885
Number of successful extensions: 100
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 92
Number of HSP's gapped (non-prelim): 10
length of query: 103
length of database: 14,973,337
effective HSP length: 68
effective length of query: 35
effective length of database: 10,718,033
effective search space: 375131155
effective search space used: 375131155
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.6 bits)
S2: 45 (21.9 bits)