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= 016441
         (389 letters)

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

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



>pdb|3TJ1|A Chain A, Crystal Structure Of Rna Polymerase I Transcription
           Initiation Factor Rrn3
 pdb|3TJ1|B Chain B, Crystal Structure Of Rna Polymerase I Transcription
           Initiation Factor Rrn3
          Length = 649

 Score = 32.0 bits (71), Expect = 0.61,   Method: Compositional matrix adjust.
 Identities = 21/53 (39%), Positives = 31/53 (58%), Gaps = 5/53 (9%)

Query: 322 IYDDCSSNANDTLKRFENNVGYPLGESLISYERYMVEAPGRTLNSYIYLIDQL 374
           + D  SSN N    R E++ G  L +S+I++E++  E P  TL+ YIY I  L
Sbjct: 118 LLDILSSNIN----RIESSRGTFLIQSIINFEKWW-ELPPHTLSKYIYFIKIL 165


>pdb|3MPD|A Chain A, Crystal Structure Of Nucleoside Diphosphate Kinase From
           Encephalitozoon Cuniculi, Cubic Form, Apo
 pdb|3MPD|B Chain B, Crystal Structure Of Nucleoside Diphosphate Kinase From
           Encephalitozoon Cuniculi, Cubic Form, Apo
          Length = 151

 Score = 29.6 bits (65), Expect = 2.8,   Method: Compositional matrix adjust.
 Identities = 20/95 (21%), Positives = 42/95 (44%), Gaps = 18/95 (18%)

Query: 87  VDATTMELHPD-LRTRKFDRIIFNFPHAGFYGKEDNHLLIEMHRSLVRDFFRNSSGMLRD 145
           ++ T + + PD ++ R   RII  F   G Y      ++ +                 R+
Sbjct: 5   MERTFIMIKPDAIKRRLISRIIQRFEEKGLYLAASKCVIPK-----------------RE 47

Query: 146 GGEVHVSHKTTVPFSNWNIKELAIGSSLSLIWCSE 180
             E H SH +++PF +  ++++  G  L+++W  +
Sbjct: 48  VLETHYSHLSSMPFFSEMVEDMMSGMVLAMVWVGK 82


>pdb|3CMD|A Chain A, Crystal Structure Of Peptide Deformylase From
           Vre-E.Faecium
 pdb|3CMD|B Chain B, Crystal Structure Of Peptide Deformylase From
           Vre-E.Faecium
          Length = 196

 Score = 29.6 bits (65), Expect = 3.1,   Method: Compositional matrix adjust.
 Identities = 17/45 (37%), Positives = 20/45 (44%), Gaps = 1/45 (2%)

Query: 315 FPGGHYRI-YDDCSSNANDTLKRFENNVGYPLGESLISYERYMVE 358
            PG H  I  DD     N TL+     V  PL E  IS  + M+E
Sbjct: 4   VPGRHMMITMDDIIREGNPTLREVAKEVSLPLSEEDISLGKEMLE 48


  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
   0.321    0.138    0.427 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,704,051
Number of Sequences: 62578
Number of extensions: 570181
Number of successful extensions: 1043
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 1042
Number of HSP's gapped (non-prelim): 3
length of query: 389
length of database: 14,973,337
effective HSP length: 101
effective length of query: 288
effective length of database: 8,652,959
effective search space: 2492052192
effective search space used: 2492052192
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: 52 (24.6 bits)