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= psy11010
         (256 letters)

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

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



>pdb|2V8N|A Chain A, Wild-Type Structure Of Lactose Permease
 pdb|2V8N|B Chain B, Wild-Type Structure Of Lactose Permease
          Length = 417

 Score = 35.8 bits (81), Expect = 0.024,   Method: Compositional matrix adjust.
 Identities = 19/51 (37%), Positives = 30/51 (58%), Gaps = 3/51 (5%)

Query: 99  GVMFGSKAFVQLLANPLVGILTHRVG---YSLPMFTGFVIMFLSTLIFAFG 146
           G++F + +   LL  PL G+L+ ++G   Y L + TG ++MF    IF FG
Sbjct: 46  GIIFAAISLFSLLFQPLFGLLSDKLGLRKYLLWIITGMLVMFAPFFIFIFG 96


>pdb|1PV6|A Chain A, Crystal Structure Of Lactose Permease
 pdb|1PV6|B Chain B, Crystal Structure Of Lactose Permease
 pdb|1PV7|A Chain A, Crystal Structure Of Lactose Permease With Tdg
 pdb|1PV7|B Chain B, Crystal Structure Of Lactose Permease With Tdg
 pdb|2CFP|A Chain A, Sugar Free Lactose Permease At Acidic Ph
 pdb|2CFQ|A Chain A, Sugar Free Lactose Permease At Neutral Ph
          Length = 417

 Score = 35.8 bits (81), Expect = 0.024,   Method: Compositional matrix adjust.
 Identities = 19/51 (37%), Positives = 30/51 (58%), Gaps = 3/51 (5%)

Query: 99  GVMFGSKAFVQLLANPLVGILTHRVG---YSLPMFTGFVIMFLSTLIFAFG 146
           G++F + +   LL  PL G+L+ ++G   Y L + TG ++MF    IF FG
Sbjct: 46  GIIFAAISLFSLLFQPLFGLLSDKLGLRKYLLWIITGMLVMFAPFFIFIFG 96


>pdb|2Y5Y|A Chain A, Crystal Structure Of Lacy In Complex With An Affinity
           Inactivator
 pdb|2Y5Y|B Chain B, Crystal Structure Of Lacy In Complex With An Affinity
           Inactivator
          Length = 423

 Score = 35.4 bits (80), Expect = 0.027,   Method: Compositional matrix adjust.
 Identities = 19/51 (37%), Positives = 30/51 (58%), Gaps = 3/51 (5%)

Query: 99  GVMFGSKAFVQLLANPLVGILTHRVG---YSLPMFTGFVIMFLSTLIFAFG 146
           G++F + +   LL  PL G+L+ ++G   Y L + TG ++MF    IF FG
Sbjct: 46  GIIFAAISLFSLLFQPLFGLLSDKLGLRKYLLWIITGMLVMFAPFFIFIFG 96


>pdb|1KQ3|A Chain A, Crystal Structure Of A Glycerol Dehydrogenase (Tm0423)
           From Thermotoga Maritima At 1.5 A Resolution
          Length = 376

 Score = 27.3 bits (59), Expect = 8.0,   Method: Compositional matrix adjust.
 Identities = 11/17 (64%), Positives = 13/17 (76%)

Query: 85  ENRHKYLMGETKAVGVM 101
           EN HKYL GE  A+GV+
Sbjct: 274 ENTHKYLHGEKVAIGVL 290


  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
   0.327    0.140    0.419 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,395,132
Number of Sequences: 62578
Number of extensions: 155451
Number of successful extensions: 225
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 218
Number of HSP's gapped (non-prelim): 8
length of query: 256
length of database: 14,973,337
effective HSP length: 97
effective length of query: 159
effective length of database: 8,903,271
effective search space: 1415620089
effective search space used: 1415620089
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 50 (23.9 bits)