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= 036242
         (330 letters)

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

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



>pdb|2YIU|A Chain A, X-Ray Structure Of The Dimeric Cytochrome Bc1 Complex From
           The Soil Bacterium Paracoccus Denitrificans At 2.7
           Angstrom Resolution
 pdb|2YIU|D Chain D, X-Ray Structure Of The Dimeric Cytochrome Bc1 Complex From
           The Soil Bacterium Paracoccus Denitrificans At 2.7
           Angstrom Resolution
          Length = 450

 Score = 29.3 bits (64), Expect = 3.6,   Method: Compositional matrix adjust.
 Identities = 45/188 (23%), Positives = 80/188 (42%), Gaps = 37/188 (19%)

Query: 131 DSRQRKRNFHQFLSILMPMGAMMARYLKVFRFGNPAWFYL-------HVACQVSAYIIGV 183
           D  + K  F ++L   +P+ +++   L +    N  W+++        +  Q++  I+ V
Sbjct: 7   DHYEPKTGFERWLHRRLPIVSLVYDTLMIPTPKNLNWWWIWGIVLAFCLVLQIATGIVLV 66

Query: 184 AGWATGIDLS-SGISSLNRD--------YIHRNIGIALFFLATVQVFALLLRPKPDHKYR 234
             +   +DL+ + +  + RD        Y+H N G +LFFLA              H +R
Sbjct: 67  MHYTPHVDLAFASVEHIMRDVNGGYMLRYLHAN-GASLFFLAVYI-----------HIFR 114

Query: 235 -LYWNIYH------WAVGYAIIVTSVFNVLKGLSLLDPEIQWWHAYIVTAISSGIISAAL 287
            LY+  Y       W VG  I +  +     G  L   ++ +W A ++T +  G I    
Sbjct: 115 GLYYGSYKAPREVTWIVGMLIYLMMMGTAFMGYVLPWGQMSFWGATVITGL-FGAIPGVG 173

Query: 288 EAI-TWTI 294
           EAI TW +
Sbjct: 174 EAIQTWLL 181


>pdb|3C0K|A Chain A, Crystal Structure Of A Ribosomal Rna Methyltranferase
 pdb|3C0K|B Chain B, Crystal Structure Of A Ribosomal Rna Methyltranferase
          Length = 396

 Score = 28.5 bits (62), Expect = 5.5,   Method: Compositional matrix adjust.
 Identities = 13/34 (38%), Positives = 19/34 (55%), Gaps = 3/34 (8%)

Query: 5  WTYDPSTNVVDLAF--RRSTPSSQWVTWALNPSG 36
          WT+DPS + +D+AF  RR   + +W  W     G
Sbjct: 66 WTFDPSES-IDIAFFSRRLQQAQKWRDWLAQKDG 98


  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    0.423 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,938,663
Number of Sequences: 62578
Number of extensions: 402647
Number of successful extensions: 633
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 631
Number of HSP's gapped (non-prelim): 12
length of query: 330
length of database: 14,973,337
effective HSP length: 99
effective length of query: 231
effective length of database: 8,778,115
effective search space: 2027744565
effective search space used: 2027744565
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: 52 (24.6 bits)