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= 028144
         (213 letters)

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

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



>pdb|3SMV|A Chain A, X-Ray Crystal Structure Of L-Azetidine-2-Carboxylate
           Hydrolase
          Length = 240

 Score = 32.0 bits (71), Expect = 0.24,   Method: Compositional matrix adjust.
 Identities = 18/61 (29%), Positives = 27/61 (44%), Gaps = 3/61 (4%)

Query: 113 DELPRPPATSRPPEKRQRVPSAYN---RFIKDEIQRIKAGNPDISHREAFSAAAKNWAHF 169
           DEL      +  P++ +   + Y    R + D I +     PD + RE F  + KNW  F
Sbjct: 42  DELLEVFGRNESPQQTETPGALYQDILRAVYDRIAKEWGLEPDAAEREEFGTSVKNWPAF 101

Query: 170 P 170
           P
Sbjct: 102 P 102


>pdb|3TQ6|A Chain A, Crystal Structure Of Human Mitochondrial Transcription
           Factor A, Tfam Or Mttfa, Bound To The Light Strand
           Promoter Lsp
 pdb|3TQ6|B Chain B, Crystal Structure Of Human Mitochondrial Transcription
           Factor A, Tfam Or Mttfa, Bound To The Light Strand
           Promoter Lsp
          Length = 214

 Score = 29.6 bits (65), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 15/47 (31%), Positives = 21/47 (44%)

Query: 133 SAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLVPD 179
           S+Y RF K+++   KA NPD    E     A+ W   P     +  D
Sbjct: 15  SSYLRFSKEQLPIFKAQNPDAKTTELIRRIAQRWRELPDSKKKIYQD 61


>pdb|3TMM|A Chain A, Tfam Imposes A U-Turn On Mitochondrial Dna
          Length = 238

 Score = 29.3 bits (64), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 15/47 (31%), Positives = 21/47 (44%)

Query: 133 SAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLVPD 179
           S+Y RF K+++   KA NPD    E     A+ W   P     +  D
Sbjct: 47  SSYLRFSKEQLPIFKAQNPDAKTTELIRRIAQRWRELPDSKKKIYQD 93


  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
   0.320    0.134    0.418 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,637,273
Number of Sequences: 62578
Number of extensions: 281838
Number of successful extensions: 600
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 592
Number of HSP's gapped (non-prelim): 12
length of query: 213
length of database: 14,973,337
effective HSP length: 95
effective length of query: 118
effective length of database: 9,028,427
effective search space: 1065354386
effective search space used: 1065354386
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 bits)