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= 004804
         (729 letters)

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

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



>pdb|3R2P|A Chain A, 2.2 Angstrom Crystal Structure Of C Terminal Truncated
           Human Apolipoprotein A-I Reveals The Assembly Of Hdl By
           Dimerization
          Length = 185

 Score = 31.2 bits (69), Expect = 1.9,   Method: Composition-based stats.
 Identities = 23/95 (24%), Positives = 47/95 (49%), Gaps = 5/95 (5%)

Query: 90  ESYETTFLKVAEEGGECEQEYFRRLDDEFNKVDKFYRTKVKEVIAEAQSL-----SQQMD 144
           +S  +TF K+ E+ G   QE++  L+ E   + +     ++EV A+ Q        +  +
Sbjct: 52  DSVTSTFSKLREQLGPVTQEFWDNLEKETEGLRQEMSKDLEEVKAKVQPYLDDFQKKWQE 111

Query: 145 ALIAFRIKVEKLQGVLQDSTQSEPVEQKQETTSSG 179
            +  +R KVE L+  LQ+  + +  E +++ +  G
Sbjct: 112 EMELYRQKVEPLRAELQEGARQKLHELQEKLSPLG 146


>pdb|3J00|0 Chain 0, Structure Of The Ribosome-Secye Complex In The Membrane
           Environment
 pdb|3J00|1 Chain 1, Structure Of The Ribosome-Secye Complex In The Membrane
           Environment
          Length = 200

 Score = 30.8 bits (68), Expect = 2.7,   Method: Composition-based stats.
 Identities = 23/95 (24%), Positives = 47/95 (49%), Gaps = 5/95 (5%)

Query: 90  ESYETTFLKVAEEGGECEQEYFRRLDDEFNKVDKFYRTKVKEVIAEAQSL-----SQQMD 144
           +S  +TF K+ E+ G   QE++  L+ E   + +     ++EV A+ Q        +  +
Sbjct: 8   DSVTSTFSKLREQLGPVTQEFWDNLEKETEGLRQEMSKDLEEVKAKVQPYLDDFQKKWQE 67

Query: 145 ALIAFRIKVEKLQGVLQDSTQSEPVEQKQETTSSG 179
            +  +R KVE L+  LQ+  + +  E +++ +  G
Sbjct: 68  EMELYRQKVEPLRAELQEGARQKLHELQEKLSPLG 102


>pdb|1AV1|A Chain A, Crystal Structure Of Human Apolipoprotein A-I
 pdb|1AV1|B Chain B, Crystal Structure Of Human Apolipoprotein A-I
 pdb|1AV1|C Chain C, Crystal Structure Of Human Apolipoprotein A-I
 pdb|1AV1|D Chain D, Crystal Structure Of Human Apolipoprotein A-I
          Length = 201

 Score = 30.8 bits (68), Expect = 2.7,   Method: Composition-based stats.
 Identities = 23/95 (24%), Positives = 47/95 (49%), Gaps = 5/95 (5%)

Query: 90  ESYETTFLKVAEEGGECEQEYFRRLDDEFNKVDKFYRTKVKEVIAEAQSL-----SQQMD 144
           +S  +TF K+ E+ G   QE++  L+ E   + +     ++EV A+ Q        +  +
Sbjct: 9   DSVTSTFSKLREQLGPVTQEFWDNLEKETEGLRQEMSKDLEEVKAKVQPYLDDFQKKWQE 68

Query: 145 ALIAFRIKVEKLQGVLQDSTQSEPVEQKQETTSSG 179
            +  +R KVE L+  LQ+  + +  E +++ +  G
Sbjct: 69  EMELYRQKVEPLRAELQEGARQKLHELQEKLSPLG 103


  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    0.136    0.404 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 18,615,304
Number of Sequences: 62578
Number of extensions: 692003
Number of successful extensions: 1511
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 1511
Number of HSP's gapped (non-prelim): 7
length of query: 729
length of database: 14,973,337
effective HSP length: 106
effective length of query: 623
effective length of database: 8,340,069
effective search space: 5195862987
effective search space used: 5195862987
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 55 (25.8 bits)