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= psy14762
         (136 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 = 71.2 bits (173), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 40/109 (36%), Positives = 59/109 (54%), Gaps = 3/109 (2%)

Query: 28  VKLGLLSTPYFEDNATTHFLSSLTAGAIATTMTQPLDVLKTRAMNATPGQFNSM-WALVT 86
           +K  LL      D+   HF S+  AG   T +  P+DV+KTR MN+  GQ++S     +T
Sbjct: 188 IKDTLLKANLMTDDLPCHFTSAFGAGFCTTVIASPVDVVKTRYMNSALGQYHSAGHCALT 247

Query: 87  YTAKLGPAGFFKGYFPAFVRLAPQTILTFVFLEQLR--LNFGFIKEESP 133
              K GP  F+KG+ P+F+RL    ++ FV  EQL+  L   +   E+P
Sbjct: 248 MLRKEGPRAFYKGFMPSFLRLGSWNVVMFVTYEQLKRALMAAYQSREAP 296



 Score = 32.0 bits (71), Expect = 0.10,   Method: Compositional matrix adjust.
 Identities = 37/148 (25%), Positives = 63/148 (42%), Gaps = 16/148 (10%)

Query: 1   MKRLQGEYDEFKQSVEQLKEQLKQCKTVKLGLL-STPYFEDNATTH------FLSSLTAG 53
           M R +G    +   V  L+ Q+    +V++GL  S   F    + H       L+  T G
Sbjct: 57  MVRTEGPRSLYNGLVAGLQRQMS-FASVRIGLYDSVKQFYTKGSEHAGIGSRLLAGSTTG 115

Query: 54  AIATTMTQPLDVLKTR---AMNATPGQF--NSMWALVTYTAKLGPAGFFKGYFPAFVRLA 108
           A+A  + QP DV+K R      A  G+   +++ A  T   + G  G +KG  P   R A
Sbjct: 116 ALAVAVAQPTDVVKVRFQAQARAGGGRRYQSTVEAYKTIAREEGIRGLWKGTSPNVARNA 175

Query: 109 ---PQTILTFVFLEQLRLNFGFIKEESP 133
                 ++T+  ++   L    + ++ P
Sbjct: 176 IVNCAELVTYDLIKDTLLKANLMTDDLP 203


>pdb|2GBB|A Chain A, Crystal Structure Of Secreted Chorismate Mutase From
           Yersinia Pestis
 pdb|2GBB|B Chain B, Crystal Structure Of Secreted Chorismate Mutase From
           Yersinia Pestis
 pdb|2GBB|C Chain C, Crystal Structure Of Secreted Chorismate Mutase From
           Yersinia Pestis
 pdb|2GBB|D Chain D, Crystal Structure Of Secreted Chorismate Mutase From
           Yersinia Pestis
          Length = 156

 Score = 27.7 bits (60), Expect = 2.1,   Method: Compositional matrix adjust.
 Identities = 16/47 (34%), Positives = 24/47 (51%), Gaps = 2/47 (4%)

Query: 15  VEQLKEQLKQCKTVKLGLLSTPYFEDNATTHFLSSLTAGAIATTMTQ 61
           +EQ+ E+LK CK  + G     +F +    H L+S    AI +T  Q
Sbjct: 108 LEQIAEELKTCKPAEXG--DKAHFINTIRQHNLTSADVEAIFSTFNQ 152


>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 = 27.3 bits (59), Expect = 2.5,   Method: Composition-based stats.
 Identities = 20/61 (32%), Positives = 27/61 (44%), Gaps = 13/61 (21%)

Query: 65  VLKTRAMNATP-----GQFNSMWAL-------VTYTAKLGPAGFFKG-YFPAFVRLAPQT 111
           +LK  A+N  P          +WAL         YTA++   GFF G   PAF+ +A   
Sbjct: 117 ILKWPALNEDPITKTIAALIILWALALTQFGGTKYTARIAKVGFFAGILLPAFILIALAA 176

Query: 112 I 112
           I
Sbjct: 177 I 177


>pdb|1RH5|B Chain B, The Structure Of A Protein Conducting Channel
 pdb|1RHZ|B Chain B, The Structure Of A Protein Conducting Channel
 pdb|2YXQ|B Chain B, The Plug Domain Of The Secy Protein Stablizes The Closed
          State Of The Translocation Channel And Maintains A
          Membrane Seal
 pdb|2YXR|B Chain B, The Plug Domain Of The Secy Protein Stablizes The Closed
          State Of The Translocation Channel And Maintains A
          Membrane Seal
          Length = 74

 Score = 26.9 bits (58), Expect = 3.9,   Method: Compositional matrix adjust.
 Identities = 11/23 (47%), Positives = 17/23 (73%)

Query: 10 EFKQSVEQLKEQLKQCKTVKLGL 32
          +F Q +EQLKE +++C+ V L L
Sbjct: 4  DFNQKIEQLKEFIEECRRVWLVL 26


>pdb|3DKN|B Chain B, Sec61 In The Canine Ribosome-Channel Complex From The
          Endoplasmic Reticulum
          Length = 65

 Score = 26.6 bits (57), Expect = 4.2,   Method: Compositional matrix adjust.
 Identities = 11/23 (47%), Positives = 17/23 (73%)

Query: 10 EFKQSVEQLKEQLKQCKTVKLGL 32
          +F Q +EQLKE +++C+ V L L
Sbjct: 2  DFNQKIEQLKEFIEECRRVWLVL 24


  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
   0.321    0.134    0.388 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,820,234
Number of Sequences: 62578
Number of extensions: 136174
Number of successful extensions: 299
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: 293
Number of HSP's gapped (non-prelim): 7
length of query: 136
length of database: 14,973,337
effective HSP length: 88
effective length of query: 48
effective length of database: 9,466,473
effective search space: 454390704
effective search space used: 454390704
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 46 (22.3 bits)