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= psy3203
         (110 letters)

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

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



>pdb|2LCK|A Chain A, Structure Of The Mitochondrial Uncoupling Protein 2
           Determined By Nmr Molecular Fragment Replacement
          Length = 303

 Score = 72.4 bits (176), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 40/110 (36%), Positives = 60/110 (54%), Gaps = 3/110 (2%)

Query: 1   MVKLGLLSTPYFEDNATTHFLSSLTAGAIATTMTQPLDVLKTRAMNATPGQFNSM-WALV 59
           ++K  LL      D+   HF S+  AG   T +  P+DV+KTR MN+  GQ++S     +
Sbjct: 187 LIKDTLLKANLMTDDLPCHFTSAFGAGFCTTVIASPVDVVKTRYMNSALGQYHSAGHCAL 246

Query: 60  TYTAKLGPAGFFKGYFPAFVRLAPQTILTFVFLEQLR--LNFGFIKEESP 107
           T   K GP  F+KG+ P+F+RL    ++ FV  EQL+  L   +   E+P
Sbjct: 247 TMLRKEGPRAFYKGFMPSFLRLGSWNVVMFVTYEQLKRALMAAYQSREAP 296



 Score = 30.0 bits (66), Expect = 0.33,   Method: Compositional matrix adjust.
 Identities = 31/121 (25%), Positives = 52/121 (42%), Gaps = 15/121 (12%)

Query: 2   VKLGLL-STPYFEDNATTH------FLSSLTAGAIATTMTQPLDVLKTR---AMNATPGQ 51
           V++GL  S   F    + H       L+  T GA+A  + QP DV+K R      A  G+
Sbjct: 83  VRIGLYDSVKQFYTKGSEHAGIGSRLLAGSTTGALAVAVAQPTDVVKVRFQAQARAGGGR 142

Query: 52  F--NSMWALVTYTAKLGPAGFFKGYFPAFVRLA---PQTILTFVFLEQLRLNFGFIKEES 106
              +++ A  T   + G  G +KG  P   R A      ++T+  ++   L    + ++ 
Sbjct: 143 RYQSTVEAYKTIAREEGIRGLWKGTSPNVARNAIVNCAELVTYDLIKDTLLKANLMTDDL 202

Query: 107 P 107
           P
Sbjct: 203 P 203


>pdb|2WKN|A Chain A, Gamma Lactamase From Delftia Acidovorans
 pdb|2WKN|B Chain B, Gamma Lactamase From Delftia Acidovorans
 pdb|2WKN|C Chain C, Gamma Lactamase From Delftia Acidovorans
 pdb|2WKN|D Chain D, Gamma Lactamase From Delftia Acidovorans
 pdb|2WKN|E Chain E, Gamma Lactamase From Delftia Acidovorans
 pdb|2WKN|F Chain F, Gamma Lactamase From Delftia Acidovorans
 pdb|2WKN|G Chain G, Gamma Lactamase From Delftia Acidovorans
 pdb|2WKN|H Chain H, Gamma Lactamase From Delftia Acidovorans
          Length = 409

 Score = 29.6 bits (65), Expect = 0.51,   Method: Composition-based stats.
 Identities = 21/76 (27%), Positives = 35/76 (46%), Gaps = 9/76 (11%)

Query: 14  DNATTHFLSSLTAGAIATTMTQPLDVLKTRAMNATPGQFNSMWALVTYTAKLGPAGFFKG 73
           D +T HFLS    G +     +P D+L    ++    + +S+W    + +K    GF   
Sbjct: 65  DLSTVHFLS----GPVGVKGAEPGDLLVVDLLD-IGARDDSLWGFNGFFSKQNGGGFLDE 119

Query: 74  YFPAFVRLAPQTILTF 89
           +FP    LA ++I  F
Sbjct: 120 HFP----LAQKSIWDF 131


>pdb|4DJI|A Chain A, Structure Of Glutamate-Gaba Antiporter Gadc
 pdb|4DJI|B Chain B, Structure Of Glutamate-Gaba Antiporter Gadc
 pdb|4DJK|A Chain A, Structure Of Glutamate-Gaba Antiporter Gadc
 pdb|4DJK|B Chain B, Structure Of Glutamate-Gaba Antiporter Gadc
          Length = 511

 Score = 26.9 bits (58), Expect = 2.8,   Method: Compositional matrix adjust.
 Identities = 20/61 (32%), Positives = 27/61 (44%), Gaps = 13/61 (21%)

Query: 39  VLKTRAMNATP-----GQFNSMWALV-------TYTAKLGPAGFFKGY-FPAFVRLAPQT 85
           +LK  A+N  P          +WAL         YTA++   GFF G   PAF+ +A   
Sbjct: 117 ILKWPALNEDPITKTIAALIILWALALTQFGGTKYTARIAKVGFFAGILLPAFILIALAA 176

Query: 86  I 86
           I
Sbjct: 177 I 177


>pdb|1EWR|A Chain A, Crystal Structure Of Taq Muts
 pdb|1EWR|B Chain B, Crystal Structure Of Taq Muts
          Length = 649

 Score = 25.4 bits (54), Expect = 7.6,   Method: Composition-based stats.
 Identities = 12/32 (37%), Positives = 18/32 (56%)

Query: 76  PAFVRLAPQTILTFVFLEQLRLNFGFIKEESP 107
           PA V LAP+ +    FL++ R  F  +  E+P
Sbjct: 59  PAEVLLAPELLENGAFLDEFRKRFPVMLSEAP 90


  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
   0.323    0.135    0.401 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,125,405
Number of Sequences: 62578
Number of extensions: 108092
Number of successful extensions: 202
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 196
Number of HSP's gapped (non-prelim): 7
length of query: 110
length of database: 14,973,337
effective HSP length: 74
effective length of query: 36
effective length of database: 10,342,565
effective search space: 372332340
effective search space used: 372332340
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 45 (21.9 bits)