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= psy4871
         (494 letters)

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

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



>pdb|4GBY|A Chain A, The Structure Of The Mfs (Major Facilitator Superfamily)
           Proton:xylose Symporter Xyle Bound To D-Xylose
 pdb|4GBZ|A Chain A, The Structure Of The Mfs (Major Facilitator Superfamily)
           Proton:xylose Symporter Xyle Bound To D-Glucose
 pdb|4GC0|A Chain A, The Structure Of The Mfs (Major Facilitator Superfamily)
           Proton:xylose Symporter Xyle Bound To
           6-Bromo-6-Deoxy-D-Glucose
          Length = 491

 Score = 63.9 bits (154), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 70/297 (23%), Positives = 135/297 (45%), Gaps = 34/297 (11%)

Query: 147 VMRTLQGFSMAAIYVISPMYLGEISETSIRGTIGTLFQISCHLGILYTYVLG------SE 200
           + R + G  +    ++SPMY+ E++   IRG + +  Q +   G L  Y +        +
Sbjct: 131 IYRIIGGIGVGLASMLSPMYIAELAPAHIRGKLVSFNQFAIIFGQLLVYCVNYFIARSGD 190

Query: 201 LSYMN-----YLTYSLIIP-IIFTVTFMFMPESPYFYAIKNQEGKAIESL-KWLRNKTAD 253
            S++N     Y+  S  IP ++F +    +PESP +   + ++ +A   L K + N  A 
Sbjct: 191 ASWLNTDGWRYMFASECIPALLFLMLLYTVPESPRWLMSRGKQEQAEGILRKIMGNTLAT 250

Query: 254 QVQSELQIIKQNTSKNVERTNFREFMGRSNMKAFVFMAFLAVFRAFTGVQSIIAYANTIF 313
           Q   E+    +++  +  +T  R  M    +   V    L++F+ F G+  ++ YA  +F
Sbjct: 251 QAVQEI----KHSLDHGRKTGGRLLM--FGVGVIVIGVMLSIFQQFVGINVVLYYAPEVF 304

Query: 314 ----ASSETFLPSDYISILFAIILLVSIFPSTYYIDRAGRRVLFLVSSAGCSLFSFIAGL 369
               AS++  L     +I+  +I L     +   +D+ GR+ L ++ + G ++  F  G 
Sbjct: 305 KTLGASTDIALLQ---TIIVGVINLTFTVLAIMTVDKFGRKPLQIIGALGMAIGMFSLGT 361

Query: 370 YYYVTIELQYEIPYTSWVPFLSISLLGVFFNLGFGPLFTPLLSEYFSSNMKAVSCAV 426
            +Y       + P    V  LS+      F + +GP+   LLSE F + ++  + A+
Sbjct: 362 AFYT------QAPGI--VALLSMLFYVAAFAMSWGPVCWVLLSEIFPNAIRGKALAI 410


>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 = 34.3 bits (77), Expect = 0.18,   Method: Compositional matrix adjust.
 Identities = 22/71 (30%), Positives = 38/71 (53%)

Query: 109 AGMLVNRIGRKWSLLMTGPITTASWIIAMYSRSVLGLYVMRTLQGFSMAAIYVISPMYLG 168
           A +++NRIG K +LL+ G I +   I + ++ S L + +++TL  F +  + V S  Y+ 
Sbjct: 279 APLIINRIGGKNALLLAGTIMSVRIIGSSFATSALEVVILKTLHMFEVPFLLVGSFKYIT 338

Query: 169 EISETSIRGTI 179
              E     TI
Sbjct: 339 SQFEVRFSATI 349


>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 = 33.1 bits (74), Expect = 0.35,   Method: Compositional matrix adjust.
 Identities = 21/71 (29%), Positives = 37/71 (52%)

Query: 109 AGMLVNRIGRKWSLLMTGPITTASWIIAMYSRSVLGLYVMRTLQGFSMAAIYVISPMYLG 168
           A +++NRIG K +LL+ G I +   I + ++ S L + +++TL  F +  + V    Y+ 
Sbjct: 279 APLIINRIGGKNALLLAGTIMSVRIIGSSFATSALEVVILKTLHMFEVPFLLVGCFKYIT 338

Query: 169 EISETSIRGTI 179
              E     TI
Sbjct: 339 SQFEVRFSATI 349


>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 = 33.1 bits (74), Expect = 0.39,   Method: Compositional matrix adjust.
 Identities = 21/71 (29%), Positives = 37/71 (52%)

Query: 109 AGMLVNRIGRKWSLLMTGPITTASWIIAMYSRSVLGLYVMRTLQGFSMAAIYVISPMYLG 168
           A +++NRIG K +LL+ G I +   I + ++ S L + +++TL  F +  + V    Y+ 
Sbjct: 279 APLIINRIGGKNALLLAGTIMSVRIIGSSFATSALEVVILKTLHMFEVPFLLVGCFKYIT 338

Query: 169 EISETSIRGTI 179
              E     TI
Sbjct: 339 SQFEVRFSATI 349


  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
   0.325    0.138    0.411 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,393,035
Number of Sequences: 62578
Number of extensions: 530897
Number of successful extensions: 1184
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1178
Number of HSP's gapped (non-prelim): 7
length of query: 494
length of database: 14,973,337
effective HSP length: 103
effective length of query: 391
effective length of database: 8,527,803
effective search space: 3334370973
effective search space used: 3334370973
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (25.0 bits)