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= 006615
         (638 letters)

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

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



>pdb|3SPA|A Chain A, Crystal Structure Of Human Mitochondrial Rna Polymerase
          Length = 1134

 Score = 34.7 bits (78), Expect = 0.18,   Method: Compositional matrix adjust.
 Identities = 22/72 (30%), Positives = 35/72 (48%), Gaps = 4/72 (5%)

Query: 164 RQRAKLLSTESYNIVMSVYAKTGKNFEAVETFRQVIDEGAIPNSRTYTVMIEHL----VN 219
           RQ+ KLL+ + YN VM  +A+ G   E V     V D G  P+  +Y   ++ +     +
Sbjct: 157 RQKRKLLTLDMYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAALQCMGRQDQD 216

Query: 220 LGKLDSALEVFS 231
            G ++  LE  S
Sbjct: 217 AGTIERCLEQMS 228


>pdb|3FEW|X Chain X, Structure And Function Of Colicin S4, A Colicin With A
           Duplicated Receptor Binding Domain
          Length = 505

 Score = 30.0 bits (66), Expect = 4.1,   Method: Compositional matrix adjust.
 Identities = 28/110 (25%), Positives = 53/110 (48%), Gaps = 16/110 (14%)

Query: 83  DSALSIMEALKSNPNFSHNQSTLHALATVLAKSQRNHELKTLIGDISSS-KFLNVSVNFM 141
           D A++ +  + SNP F  N++   ALA V  +S    ++   +G+IS + KF +V +   
Sbjct: 352 DDAMASLNKVLSNPGFKFNRADSDALANVW-RSIDAQDMANKLGNISKAFKFADVVMKVE 410

Query: 142 NL----MQWYSTS--GDLELVLSTWNEYRQRAKLLSTESYNIVMSVYAKT 185
            +    ++ Y T   G L L + +W        +LS  +  + + V++ T
Sbjct: 411 KVREKSIEGYETGNWGPLMLEVESW--------VLSGIASAVALGVFSAT 452


  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    0.396 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,816,324
Number of Sequences: 62578
Number of extensions: 565996
Number of successful extensions: 1481
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 1478
Number of HSP's gapped (non-prelim): 16
length of query: 638
length of database: 14,973,337
effective HSP length: 105
effective length of query: 533
effective length of database: 8,402,647
effective search space: 4478610851
effective search space used: 4478610851
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 55 (25.8 bits)