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= psy2422
         (305 letters)

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

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



>pdb|2DSK|A Chain A, Crystal Structure Of Catalytic Domain Of
          Hyperthermophilic Chitinase From Pyrococcus Furiosus
 pdb|2DSK|B Chain B, Crystal Structure Of Catalytic Domain Of
          Hyperthermophilic Chitinase From Pyrococcus Furiosus
          Length = 311

 Score = 31.2 bits (69), Expect = 0.85,   Method: Compositional matrix adjust.
 Identities = 18/58 (31%), Positives = 29/58 (50%), Gaps = 9/58 (15%)

Query: 19 YLIEKIIRARIYDSKYWKEECFALSAELLVDKAMELRYIGG----VFGGNIKPTPFLC 72
          + +  I+ + +Y+   W     ++  E  VD+  ELR IGG     FGG +   P+LC
Sbjct: 38 FTLAFILYSSVYNGPAWAG---SIPLEKFVDEVRELREIGGEVIIAFGGAVG--PYLC 90


>pdb|3A4W|A Chain A, Crystal Structures Of Catalytic Site Mutants Of Active
          Domain 2 Of Thermostable Chitinase From Pyrococcus
          Furiosus Complexed With Chito- Oligosaccharides
 pdb|3A4W|B Chain B, Crystal Structures Of Catalytic Site Mutants Of Active
          Domain 2 Of Thermostable Chitinase From Pyrococcus
          Furiosus Complexed With Chito- Oligosaccharides
          Length = 311

 Score = 30.8 bits (68), Expect = 0.87,   Method: Compositional matrix adjust.
 Identities = 18/58 (31%), Positives = 29/58 (50%), Gaps = 9/58 (15%)

Query: 19 YLIEKIIRARIYDSKYWKEECFALSAELLVDKAMELRYIGG----VFGGNIKPTPFLC 72
          + +  I+ + +Y+   W     ++  E  VD+  ELR IGG     FGG +   P+LC
Sbjct: 38 FTLAFILYSSVYNGPAWAG---SIPLEKFVDEVRELREIGGEVIIAFGGAVG--PYLC 90


>pdb|3A4X|A Chain A, Crystal Structures Of Catalytic Site Mutants Of Active
          Domain 2 Of Thermostable Chitinase From Pyrococcus
          Furiosus Complexed With Chito- Oligosaccharides
 pdb|3A4X|B Chain B, Crystal Structures Of Catalytic Site Mutants Of Active
          Domain 2 Of Thermostable Chitinase From Pyrococcus
          Furiosus Complexed With Chito- Oligosaccharides
 pdb|3AFB|A Chain A, Crystal Structures Of Catalytic Site Mutants Of Active
          Domain 2 Of Chitinase From Pyrococcus Furiosus
 pdb|3AFB|B Chain B, Crystal Structures Of Catalytic Site Mutants Of Active
          Domain 2 Of Chitinase From Pyrococcus Furiosus
          Length = 311

 Score = 30.8 bits (68), Expect = 0.88,   Method: Compositional matrix adjust.
 Identities = 18/58 (31%), Positives = 29/58 (50%), Gaps = 9/58 (15%)

Query: 19 YLIEKIIRARIYDSKYWKEECFALSAELLVDKAMELRYIGG----VFGGNIKPTPFLC 72
          + +  I+ + +Y+   W     ++  E  VD+  ELR IGG     FGG +   P+LC
Sbjct: 38 FTLAFILYSSVYNGPAWAG---SIPLEKFVDEVRELREIGGEVIIAFGGAVG--PYLC 90


>pdb|4G4S|P Chain P, Structure Of Proteasome-Pba1-Pba2 Complex
          Length = 269

 Score = 28.9 bits (63), Expect = 3.6,   Method: Compositional matrix adjust.
 Identities = 21/115 (18%), Positives = 52/115 (45%), Gaps = 11/115 (9%)

Query: 69  PFLCLILKMLQIQPEKDIVVEFIKNE---EFKYVRALGAYYM--------RLTGSSVDCY 117
           P  CL+L ++ +     + ++++ N    E++Y+ AL + Y+        R    S   Y
Sbjct: 2   PMSCLVLPLVSVGNIPQLSIDWLLNSQANEWEYLEALDSKYLVEFVGPLDRPEDGSDSLY 61

Query: 118 KYLEPLFADSRKLRFQNRQGAFEVIHMDEYIDQLLREERMCDVILPRIQKRHVLE 172
           K  +  ++ + ++ +  ++G F +      +        + ++ILP + K ++ E
Sbjct: 62  KDADMKYSSALEVFYNKKRGLFAIQQRTPLVSVNYLNNFIVEIILPFLSKYNISE 116


>pdb|3OU5|A Chain A, Human Mitochondrial Serine Hydroxymethyltransferase 2
          Length = 490

 Score = 27.7 bits (60), Expect = 7.6,   Method: Compositional matrix adjust.
 Identities = 15/44 (34%), Positives = 22/44 (50%), Gaps = 4/44 (9%)

Query: 27  ARIYDSKYWKEECFALSAELLVDKAMELRYIGGVFGGNIKPTPF 70
           AR+ D    +E C  + A LL D A    +I G+    + P+PF
Sbjct: 215 ARLIDYARMREVCDEVKAHLLADMA----HISGLVAAKVIPSPF 254


  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    0.139    0.412 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,542,018
Number of Sequences: 62578
Number of extensions: 231778
Number of successful extensions: 429
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 429
Number of HSP's gapped (non-prelim): 5
length of query: 305
length of database: 14,973,337
effective HSP length: 98
effective length of query: 207
effective length of database: 8,840,693
effective search space: 1830023451
effective search space used: 1830023451
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 51 (24.3 bits)