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= psy15227
         (515 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 = 66.2 bits (160), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 89/377 (23%), Positives = 167/377 (44%), Gaps = 43/377 (11%)

Query: 113 IARLFIGISKGVAYTAMPIFIGEISEHNIRGALGSIPSGFQMVGTLAILLIGNHVSYNS- 171
           I R+  GI  G+A    P++I E++  +IRG L S      + G L +  +   ++ +  
Sbjct: 131 IYRIIGGIGVGLASMLSPMYIAELAPAHIRGKLVSFNQFAIIFGQLLVYCVNYFIARSGD 190

Query: 172 ---LN-------IALSILPVIFFILFSF-VPETPHFHAAKNNLKKTEKSLKWYRGN--KK 218
              LN        A   +P + F++  + VPE+P +  ++   ++ E  L+   GN    
Sbjct: 191 ASWLNTDGWRYMFASECIPALLFLMLLYTVPESPRWLMSRGKQEQAEGILRKIMGNTLAT 250

Query: 219 DVMEEMNSIMDKTQEDLKSKTGYLELLTNKSNRRAFTLVMAASLFQRLGGITSMITYSST 278
             ++E+   +D  +     KTG   L+          + +  S+FQ+  GI  ++ Y+  
Sbjct: 251 QAVQEIKHSLDHGR-----KTGGRLLMFGVG---VIVIGVMLSIFQQFVGINVVLYYAPE 302

Query: 279 LLPKLDNAYFGPDQCILVFMIIMFLS---NFLQAPLMDILGRKPLSCFSAALGCLLTFST 335
           +   L  +    D  +L  +I+  ++     L    +D  GRKPL    A    +  FS 
Sbjct: 303 VFKTLGAS---TDIALLQTIIVGVINLTFTVLAIMTVDKFGRKPLQIIGALGMAIGMFSL 359

Query: 336 GLFYLYQGELPNFQYIPYITTLLYAASY---YGIGCLPNILVSELFPINVRCQASSCASV 392
           G  +  Q   P    +  ++ L Y A++   +G  C   +L+SE+FP  +R +A + A  
Sbjct: 360 GTAFYTQA--PGI--VALLSMLFYVAAFAMSWGPVCW--VLLSEIFPNAIRGKALAIAVA 413

Query: 393 ALAFGS-FITTKFHILITKS-LGQH----VIFFIYSSVHFCSVVFNYFYLMETKQKTLAE 446
           A    + F++  F ++   S L  H      ++IY  +   + +F + ++ ETK KTL E
Sbjct: 414 AQWLANYFVSWTFPMMDKNSWLVAHFHNGFSYWIYGCMGVLAALFMWKFVPETKGKTLEE 473

Query: 447 IQESIMNSHKQLRREKT 463
           ++       K+ ++  T
Sbjct: 474 LEALWEPETKKTQQTAT 490


>pdb|3RKO|A Chain A, Crystal Structure Of The Membrane Domain Of Respiratory
           Complex I From E. Coli At 3.0 Angstrom Resolution
 pdb|3RKO|E Chain E, Crystal Structure Of The Membrane Domain Of Respiratory
           Complex I From E. Coli At 3.0 Angstrom Resolution
          Length = 147

 Score = 42.4 bits (98), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 17/43 (39%), Positives = 25/43 (58%)

Query: 460 REKTSPFECGFDPISKPRISYSLHFFSIALIFLIFDIEITLIF 502
           R K  PFE G D +   R+  S  F+ +A+ F+IFD+E   +F
Sbjct: 44  RSKNVPFESGIDSVGSARLRLSAKFYLVAMFFVIFDVEALYLF 86


>pdb|4HE8|A Chain A, Crystal Structure Of The Membrane Domain Of Respiratory
           Complex I From Thermus Thermophilus
 pdb|4HE8|B Chain B, Crystal Structure Of The Membrane Domain Of Respiratory
           Complex I From Thermus Thermophilus
 pdb|4HEA|A Chain A, Crystal Structure Of The Entire Respiratory Complex I From
           Thermus Thermophilus
 pdb|4HEA|P Chain P, Crystal Structure Of The Entire Respiratory Complex I From
           Thermus Thermophilus
          Length = 119

 Score = 41.2 bits (95), Expect = 0.001,   Method: Composition-based stats.
 Identities = 16/48 (33%), Positives = 32/48 (66%), Gaps = 1/48 (2%)

Query: 456 KQLRREKTSPFECGFDPISKPRISYSLHFFSIALIFLIFDIEITLIFP 503
           K+  R K  P+E G DP  + +  + +HF+ +A++F++FD+E+  ++P
Sbjct: 34  KKPGRAKLMPYESGNDPAGEVK-RFPVHFYVVAMLFILFDVEVAFLWP 80


>pdb|2QOR|A Chain A, Crystal Structure Of Plasmodium Vivax Guanylate Kinase
          Length = 204

 Score = 28.9 bits (63), Expect = 6.6,   Method: Compositional matrix adjust.
 Identities = 13/32 (40%), Positives = 21/32 (65%)

Query: 428 SVVFNYFYLMETKQKTLAEIQESIMNSHKQLR 459
            V FNYF + +   +T AE++E ++ S+ QLR
Sbjct: 171 KVGFNYFIVNDDLARTYAELREYLLGSYPQLR 202


  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    0.141    0.420 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,342,931
Number of Sequences: 62578
Number of extensions: 502159
Number of successful extensions: 1211
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 1204
Number of HSP's gapped (non-prelim): 4
length of query: 515
length of database: 14,973,337
effective HSP length: 103
effective length of query: 412
effective length of database: 8,527,803
effective search space: 3513454836
effective search space used: 3513454836
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: 54 (25.4 bits)