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= psy3545
         (130 letters)

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

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



>pdb|3ESF|A Chain A, Crystal Structure Of The Enzyme Fe-Superoxide Dismutase
           Tbsodb2 From Trypanosoma Brucei
 pdb|3ESF|B Chain B, Crystal Structure Of The Enzyme Fe-Superoxide Dismutase
           Tbsodb2 From Trypanosoma Brucei
 pdb|3ESF|C Chain C, Crystal Structure Of The Enzyme Fe-Superoxide Dismutase
           Tbsodb2 From Trypanosoma Brucei
 pdb|3ESF|D Chain D, Crystal Structure Of The Enzyme Fe-Superoxide Dismutase
           Tbsodb2 From Trypanosoma Brucei
          Length = 197

 Score = 28.1 bits (61), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 15/43 (34%), Positives = 22/43 (51%), Gaps = 4/43 (9%)

Query: 13  PVHNHNLKKILMCS----SSNIKYFCNVSVYEQSFLNIVTYDH 51
           P+   +LK IL C     +  I Y  +   Y Q+F N+V +DH
Sbjct: 148 PLTEADLKPILTCDVWEHAYYIDYKNDRPAYVQTFWNVVNWDH 190


>pdb|2BIH|A Chain A, Crystal Structure Of The Molybdenum-containing Nitrate
           Reducing Fragment Of Pichia Angusta Assimilatory Nitrate
           Reductase
          Length = 474

 Score = 27.7 bits (60), Expect = 1.7,   Method: Composition-based stats.
 Identities = 10/25 (40%), Positives = 15/25 (60%), Gaps = 5/25 (20%)

Query: 92  YWVISNQFETSLLNHWWYQSKFTRQ 116
           YW +     TS+LN+WWY+    R+
Sbjct: 411 YWNV-----TSMLNNWWYRVAIIRE 430


>pdb|2BII|A Chain A, Crystal Structure Of Nitrate-Reducing Fragment Of
           Assimilatory Nitrate Reductase From Pichia Angusta
 pdb|2BII|B Chain B, Crystal Structure Of Nitrate-Reducing Fragment Of
           Assimilatory Nitrate Reductase From Pichia Angusta
          Length = 424

 Score = 27.7 bits (60), Expect = 1.9,   Method: Composition-based stats.
 Identities = 10/25 (40%), Positives = 15/25 (60%), Gaps = 5/25 (20%)

Query: 92  YWVISNQFETSLLNHWWYQSKFTRQ 116
           YW +     TS+LN+WWY+    R+
Sbjct: 361 YWNV-----TSMLNNWWYRVAIIRE 380


>pdb|2JOX|A Chain A, Embryonic Neural Inducing Factor Churchill Is Not A Dna-
          Binding Zinc Finger Protein: Solution Structure Reveals
          A Solvent-Exposed Beta-Sheet And Zinc Binuclear Cluster
          Length = 106

 Score = 26.6 bits (57), Expect = 4.0,   Method: Compositional matrix adjust.
 Identities = 13/35 (37%), Positives = 17/35 (48%)

Query: 18 NLKKILMCSSSNIKYFCNVSVYEQSFLNIVTYDHL 52
          N     +CS  +     N S+ E+    IVTYDHL
Sbjct: 25 NFTGCAVCSKRDFMLITNKSLKEEDGEEIVTYDHL 59


>pdb|1UFA|A Chain A, Crystal Structure Of Tt1467 From Thermus Thermophilus Hb8
          Length = 520

 Score = 25.4 bits (54), Expect = 8.3,   Method: Composition-based stats.
 Identities = 7/17 (41%), Positives = 11/17 (64%)

Query: 94  VISNQFETSLLNHWWYQ 110
           VI + ++  L  HWWY+
Sbjct: 347 VILSPYDAELFGHWWYE 363


>pdb|3P0B|A Chain A, Thermus Thermophilus Family Gh57 Branching Enzyme: Crystal
           Structure, Mechanism Of Action And Products Formed
          Length = 540

 Score = 25.4 bits (54), Expect = 8.3,   Method: Composition-based stats.
 Identities = 7/17 (41%), Positives = 11/17 (64%)

Query: 94  VISNQFETSLLNHWWYQ 110
           VI + ++  L  HWWY+
Sbjct: 367 VILSPYDAELFGHWWYE 383


  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
   0.325    0.135    0.443 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,406,168
Number of Sequences: 62578
Number of extensions: 100055
Number of successful extensions: 191
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 185
Number of HSP's gapped (non-prelim): 7
length of query: 130
length of database: 14,973,337
effective HSP length: 88
effective length of query: 42
effective length of database: 9,466,473
effective search space: 397591866
effective search space used: 397591866
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 45 (21.9 bits)