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= 038665
         (171 letters)

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

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



>pdb|1RQ8|A Chain A, Solution Structure Of The Hypothetical Protein Sav1595
           From Staphylococcus Aureus, A Putative Rna Binding
           Protein
          Length = 104

 Score = 50.8 bits (120), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 28/88 (31%), Positives = 51/88 (57%), Gaps = 3/88 (3%)

Query: 30  TVKEKKELASYAHSLGKKLKCQLVGKSGVTDGVVTSFIETLEANELLKIKIHRTCPGELE 89
           T K+K+ L S AH++    +   +GK G+ + ++    +TLE  EL+K+ + +    + +
Sbjct: 3   TGKQKRYLRSLAHNIDPIFQ---IGKGGINENMIKQIDDTLENRELIKVHVLQNNFDDKK 59

Query: 90  DVVKQLEEATGSAVVSQIGQTVIIYRPS 117
           ++ + L EAT S +V  IG  ++IYR S
Sbjct: 60  ELAETLSEATRSELVQVIGSMIVIYRES 87


>pdb|1LN4|A Chain A, Crystal Structure Of E. Coli Yhby
          Length = 104

 Score = 47.0 bits (110), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 31/94 (32%), Positives = 53/94 (56%), Gaps = 15/94 (15%)

Query: 30  TVKEKKELASYAHSLGKKLKCQLVGKSGVTDGVVTSFIETLEANELLKIKIHRTCPGELE 89
           + K+K+ L   AH L   +   L+G +G+T+GV+    + LE +EL+K+KI        E
Sbjct: 4   STKQKQHLKGLAHPLKPVV---LLGSNGLTEGVLAEIEQALEHHELIKVKI------ATE 54

Query: 90  D------VVKQLEEATGSAVVSQIGQTVIIYRPS 117
           D      +V+ +   TG+  V  IG+T+++YRP+
Sbjct: 55  DRETKTLIVEAIVRETGACNVQVIGKTLVLYRPT 88


>pdb|1JO0|A Chain A, Structure Of Hi1333, A Hypothetical Protein From
           Haemophilus Influenzae With Structural Similarity To
           Rna-binding Proteins
 pdb|1JO0|B Chain B, Structure Of Hi1333, A Hypothetical Protein From
           Haemophilus Influenzae With Structural Similarity To
           Rna-binding Proteins
          Length = 98

 Score = 41.6 bits (96), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 30/103 (29%), Positives = 51/103 (49%), Gaps = 9/103 (8%)

Query: 30  TVKEKKELASYAHSLGKKLKCQLVGKSGVTDGVVTSFIETLEANELLKIKIHRTCPGELE 89
           + K+K+ L   AH L       ++G +G+T+GV+      L  +EL+K+K+        +
Sbjct: 4   STKQKQFLKGLAHHLNP---VVMLGGNGLTEGVLAEIENALNHHELIKVKVAGADRETKQ 60

Query: 90  DVVKQLEEATGSAVVSQIGQTVIIYRPSLTRMKLEEKKQQARR 132
            ++  +   T +A V  IG  +++YRPS      EE K Q  R
Sbjct: 61  LIINAIVRETKAAQVQTIGHILVLYRPS------EEAKIQLPR 97


  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
   0.310    0.128    0.331 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,239,867
Number of Sequences: 62578
Number of extensions: 109740
Number of successful extensions: 266
Number of sequences better than 100.0: 28
Number of HSP's better than 100.0 without gapping: 22
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 241
Number of HSP's gapped (non-prelim): 29
length of query: 171
length of database: 14,973,337
effective HSP length: 92
effective length of query: 79
effective length of database: 9,216,161
effective search space: 728076719
effective search space used: 728076719
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 48 (23.1 bits)