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= 032675
         (136 letters)

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

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



>pdb|4AQ5|E Chain E, Gating Movement In Acetylcholine Receptor Analysed By
           Time- Resolved Electron Cryo-Microscopy (Closed Class)
 pdb|4AQ9|E Chain E, Gating Movement In Acetylcholine Receptor Analysed By
           Time-Resolved Electron Cryo-Microscopy (Open Class)
          Length = 488

 Score = 28.1 bits (61), Expect = 1.8,   Method: Composition-based stats.
 Identities = 9/29 (31%), Positives = 18/29 (62%)

Query: 9   PRRAHKERAQPQSRKKFGLLEKHKDYVVR 37
           P     E+ QP+ R  FG++ K ++Y+++
Sbjct: 338 PSEETPEKPQPRRRSSFGIMIKAEEYILK 366


>pdb|1OED|E Chain E, Structure Of Acetylcholine Receptor Pore From Electron
           Images
          Length = 260

 Score = 27.7 bits (60), Expect = 2.0,   Method: Compositional matrix adjust.
 Identities = 9/29 (31%), Positives = 18/29 (62%)

Query: 9   PRRAHKERAQPQSRKKFGLLEKHKDYVVR 37
           P     E+ QP+ R  FG++ K ++Y+++
Sbjct: 121 PSEETPEKPQPRRRSSFGIMIKAEEYILK 149


>pdb|3ZGQ|A Chain A, Crystal Structure Of Human Interferon-induced Protein
           Ifit5
 pdb|4HOR|A Chain A, Crystal Structure Of Full-length Human Ifit5 With
           5`-triphosphate Oligocytidine
 pdb|4HOS|A Chain A, Crystal Structure Of Full-length Human Ifit5 With
           5`-triphosphate Oligouridine
 pdb|4HOT|A Chain A, Crystal Structure Of Full-length Human Ifit5 With
           5`-triphosphate Oligoadenine
 pdb|4J0U|A Chain A, Crystal Structure Of Ifit5/isg58
          Length = 482

 Score = 25.8 bits (55), Expect = 8.6,   Method: Compositional matrix adjust.
 Identities = 16/44 (36%), Positives = 23/44 (52%), Gaps = 1/44 (2%)

Query: 54  KAAFRNPDEFYLKMIKTKIVDGVHRLESEANKYTQEELILMKTQ 97
           KA   NPD  Y+K+     +  VH  E+E  KY +E L  + +Q
Sbjct: 206 KAVTLNPDNSYIKVFLALKLQDVHA-EAEGEKYIEEILDQISSQ 248


>pdb|4HOQ|A Chain A, Crystal Structure Of Full-length Human Ifit5
          Length = 482

 Score = 25.8 bits (55), Expect = 8.9,   Method: Compositional matrix adjust.
 Identities = 16/44 (36%), Positives = 23/44 (52%), Gaps = 1/44 (2%)

Query: 54  KAAFRNPDEFYLKMIKTKIVDGVHRLESEANKYTQEELILMKTQ 97
           KA   NPD  Y+K+     +  VH  E+E  KY +E L  + +Q
Sbjct: 206 KAVTLNPDNSYIKVFLALKLQDVHA-EAEGEKYIEEILDQISSQ 248


  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    0.137    0.380 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,395,196
Number of Sequences: 62578
Number of extensions: 119361
Number of successful extensions: 543
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 540
Number of HSP's gapped (non-prelim): 9
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: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 46 (22.3 bits)