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= psy9211
         (226 letters)

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

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



>pdb|4B4T|V Chain V, Near-Atomic Resolution Structural Model Of The Yeast 26s
           Proteasome
          Length = 306

 Score = 30.8 bits (68), Expect = 0.58,   Method: Compositional matrix adjust.
 Identities = 18/68 (26%), Positives = 34/68 (50%), Gaps = 1/68 (1%)

Query: 1   MMRRLRRVNVDHYHVGWYQSS-DVANFISLPLIESQFHYQISIEEAVVLIYDTQKTSRGF 59
           MM  L++   D   VGWY S      ++S   + +Q  ++     AV ++ D  ++ +G 
Sbjct: 91  MMDMLKQTGRDQMVVGWYHSHPGFGCWLSSVDVNTQKSFEQLNSRAVAVVVDPIQSVKGK 150

Query: 60  LTLKAYRL 67
           + + A+RL
Sbjct: 151 VVIDAFRL 158


>pdb|3LD1|A Chain A, Crystal Structure Of Ibv Nsp2a
          Length = 359

 Score = 28.1 bits (61), Expect = 4.5,   Method: Compositional matrix adjust.
 Identities = 20/50 (40%), Positives = 27/50 (54%), Gaps = 1/50 (2%)

Query: 93  ENLLLEVPVKIRNSPLT-NVLLSEVDGLVSPAEGNNFLDLGTAFQQQVVR 141
           E L L+V  KI+ S +    L+ EV   V  A G+N   L   F+QQ+VR
Sbjct: 130 EILWLQVAAKIQVSAMAMRRLVGEVTAKVMDALGSNMSALFQIFKQQIVR 179


>pdb|2PMZ|A Chain A, Archaeal Rna Polymerase From Sulfolobus Solfataricus
 pdb|2PMZ|Q Chain Q, Archaeal Rna Polymerase From Sulfolobus Solfataricus
 pdb|3HKZ|A Chain A, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
 pdb|3HKZ|I Chain I, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
          Length = 880

 Score = 27.3 bits (59), Expect = 6.2,   Method: Compositional matrix adjust.
 Identities = 13/35 (37%), Positives = 20/35 (57%)

Query: 72  IQMYKEGEFTPEALRAIKVGFENLLLEVPVKIRNS 106
           IQ YK GE  P   R ++   EN +L+   K+R++
Sbjct: 676 IQKYKNGELEPIPGRTLEESLENYILDTLDKLRST 710


>pdb|2WAQ|A Chain A, The Complete Structure Of The Archaeal 13-Subunit Dna-
           Directed Rna Polymerase
 pdb|2WB1|A Chain A, The Complete Structure Of The Archaeal 13-Subunit Dna-
           Directed Rna Polymerase
 pdb|2WB1|W Chain W, The Complete Structure Of The Archaeal 13-Subunit Dna-
           Directed Rna Polymerase
 pdb|2Y0S|A Chain A, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
           P21 Space Group
 pdb|2Y0S|W Chain W, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
           P21 Space Group
 pdb|4AYB|A Chain A, Rnap At 3.2ang
 pdb|4B1O|A Chain A, Archaeal Rnap-Dna Binary Complex At 4.32ang
 pdb|4B1P|W Chain W, Archaeal Rnap-Dna Binary Complex At 4.32ang
          Length = 880

 Score = 27.3 bits (59), Expect = 6.3,   Method: Compositional matrix adjust.
 Identities = 13/35 (37%), Positives = 20/35 (57%)

Query: 72  IQMYKEGEFTPEALRAIKVGFENLLLEVPVKIRNS 106
           IQ YK GE  P   R ++   EN +L+   K+R++
Sbjct: 676 IQKYKNGELEPIPGRTLEESLENYILDTLDKLRST 710


  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
   0.319    0.132    0.373 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,897,047
Number of Sequences: 62578
Number of extensions: 214774
Number of successful extensions: 554
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 552
Number of HSP's gapped (non-prelim): 6
length of query: 226
length of database: 14,973,337
effective HSP length: 95
effective length of query: 131
effective length of database: 9,028,427
effective search space: 1182723937
effective search space used: 1182723937
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: 50 (23.9 bits)