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= psy14075
         (414 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 = 34.3 bits (77), Expect = 0.14,   Method: Compositional matrix adjust.
 Identities = 19/51 (37%), Positives = 30/51 (58%), Gaps = 3/51 (5%)

Query: 33 GVMFGSKAFVQLLANPLVGILTHRVG---YSLPMFTGFVIMFLSTLIFAFG 80
          G++F + +   LL  PL G+L+ ++G   Y L + TG ++MF    IF FG
Sbjct: 46 GIIFAAISLFSLLFQPLFGLLSDKLGLRKYLLWIITGMLVMFAPFFIFIFG 96



 Score = 29.3 bits (64), Expect = 3.7,   Method: Compositional matrix adjust.
 Identities = 15/44 (34%), Positives = 21/44 (47%)

Query: 213 PSLPIWMMDTMGADKWQQGVSFLPASISYLIGTNLFGPLGHRMG 256
           P  PIW+ D     K   G+ F   S+  L+   LFG L  ++G
Sbjct: 28  PFFPIWLHDINHISKSDTGIIFAAISLFSLLFQPLFGLLSDKLG 71


>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 = 34.3 bits (77), Expect = 0.15,   Method: Compositional matrix adjust.
 Identities = 19/51 (37%), Positives = 30/51 (58%), Gaps = 3/51 (5%)

Query: 33 GVMFGSKAFVQLLANPLVGILTHRVG---YSLPMFTGFVIMFLSTLIFAFG 80
          G++F + +   LL  PL G+L+ ++G   Y L + TG ++MF    IF FG
Sbjct: 46 GIIFAAISLFSLLFQPLFGLLSDKLGLRKYLLWIITGMLVMFAPFFIFIFG 96



 Score = 29.3 bits (64), Expect = 3.9,   Method: Compositional matrix adjust.
 Identities = 15/44 (34%), Positives = 21/44 (47%)

Query: 213 PSLPIWMMDTMGADKWQQGVSFLPASISYLIGTNLFGPLGHRMG 256
           P  PIW+ D     K   G+ F   S+  L+   LFG L  ++G
Sbjct: 28  PFFPIWLHDINHISKSDTGIIFAAISLFSLLFQPLFGLLSDKLG 71


>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 = 33.9 bits (76), Expect = 0.16,   Method: Compositional matrix adjust.
 Identities = 19/51 (37%), Positives = 30/51 (58%), Gaps = 3/51 (5%)

Query: 33 GVMFGSKAFVQLLANPLVGILTHRVG---YSLPMFTGFVIMFLSTLIFAFG 80
          G++F + +   LL  PL G+L+ ++G   Y L + TG ++MF    IF FG
Sbjct: 46 GIIFAAISLFSLLFQPLFGLLSDKLGLRKYLLWIITGMLVMFAPFFIFIFG 96



 Score = 29.3 bits (64), Expect = 4.1,   Method: Compositional matrix adjust.
 Identities = 15/44 (34%), Positives = 21/44 (47%)

Query: 213 PSLPIWMMDTMGADKWQQGVSFLPASISYLIGTNLFGPLGHRMG 256
           P  PIW+ D     K   G+ F   S+  L+   LFG L  ++G
Sbjct: 28  PFFPIWLHDINHISKSDTGIIFAAISLFSLLFQPLFGLLSDKLG 71


>pdb|1KHB|A Chain A, Pepck Complex With Nonhydrolyzable Gtp Analog, Native Data
 pdb|1KHF|A Chain A, Pepck Complex With Pep
 pdb|1KHG|A Chain A, Pepck
 pdb|1M51|A Chain A, Pepck Complex With A Gtp-Competitive Inhibitor
 pdb|1NHX|A Chain A, Pepck Complex With A Gtp-Competitive Inhibitor
 pdb|2GMV|A Chain A, Pepck Complex With A Gtp-Competitive Inhibitor
 pdb|2GMV|B Chain B, Pepck Complex With A Gtp-Competitive Inhibitor
          Length = 625

 Score = 29.3 bits (64), Expect = 4.8,   Method: Compositional matrix adjust.
 Identities = 13/32 (40%), Positives = 18/32 (56%)

Query: 195 LIAAGAITFANTGIAMLEPSLPIWMMDTMGAD 226
           L AA       T +AM+ PSLP W ++ +G D
Sbjct: 283 LAAAFPSACGKTNLAMMNPSLPGWKVECVGDD 314


  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
   0.324    0.141    0.423 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,393,368
Number of Sequences: 62578
Number of extensions: 367129
Number of successful extensions: 514
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 504
Number of HSP's gapped (non-prelim): 18
length of query: 414
length of database: 14,973,337
effective HSP length: 101
effective length of query: 313
effective length of database: 8,652,959
effective search space: 2708376167
effective search space used: 2708376167
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 53 (25.0 bits)