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= 003442
         (819 letters)

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

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



>pdb|1FA0|A Chain A, Structure Of Yeast Poly(A) Polymerase Bound To Manganate
           And 3'-Datp
 pdb|1FA0|B Chain B, Structure Of Yeast Poly(A) Polymerase Bound To Manganate
           And 3'-Datp
 pdb|3C66|A Chain A, Yeast Poly(A) Polymerase In Complex With Fip1 Residues
           80-105
 pdb|3C66|B Chain B, Yeast Poly(A) Polymerase In Complex With Fip1 Residues
           80-105
          Length = 537

 Score = 32.0 bits (71), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 12/33 (36%), Positives = 19/33 (57%)

Query: 11  VPCSSFTCLCRSASKLYGEVKVSGLGFGVERAF 43
           +PC+ F  LCRS ++ YG+ KV  L     + +
Sbjct: 483 IPCTEFVNLCRSFNEDYGDHKVFNLALRFVKGY 515


>pdb|2O1P|A Chain A, Structure Of Yeast Poly(A) Polymerase In A Somewhat Closed
           State
 pdb|2O1P|B Chain B, Structure Of Yeast Poly(A) Polymerase In A Somewhat Closed
           State
          Length = 546

 Score = 32.0 bits (71), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 12/33 (36%), Positives = 19/33 (57%)

Query: 11  VPCSSFTCLCRSASKLYGEVKVSGLGFGVERAF 43
           +PC+ F  LCRS ++ YG+ KV  L     + +
Sbjct: 483 IPCTEFVNLCRSFNEDYGDHKVFNLALRFVKGY 515


>pdb|2Q66|A Chain A, Structure Of Yeast Poly(A) Polymerase With Atp And
           Oligo(A)
          Length = 525

 Score = 32.0 bits (71), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 12/33 (36%), Positives = 19/33 (57%)

Query: 11  VPCSSFTCLCRSASKLYGEVKVSGLGFGVERAF 43
           +PC+ F  LCRS ++ YG+ KV  L     + +
Sbjct: 479 IPCTEFVNLCRSFNEDYGDHKVFNLALRFVKGY 511


>pdb|2HHP|A Chain A, Structure Of Yeast Poly(A) Polymerase In A Closed
           Conformation
          Length = 530

 Score = 32.0 bits (71), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 12/33 (36%), Positives = 19/33 (57%)

Query: 11  VPCSSFTCLCRSASKLYGEVKVSGLGFGVERAF 43
           +PC+ F  LCRS ++ YG+ KV  L     + +
Sbjct: 483 IPCTEFVNLCRSFNEDYGDHKVFNLALRFVKGY 515


>pdb|3EQ1|A Chain A, The Crystal Structure Of Human Porphobilinogen Deaminase
           At 2.8a Resolution
 pdb|3EQ1|B Chain B, The Crystal Structure Of Human Porphobilinogen Deaminase
           At 2.8a Resolution
          Length = 361

 Score = 30.0 bits (66), Expect = 5.5,   Method: Compositional matrix adjust.
 Identities = 17/57 (29%), Positives = 29/57 (50%), Gaps = 5/57 (8%)

Query: 100 EKDEIVKSVMDLKRAEIEEGYTMDAFMSRQDVLMDVRDKLLFEPEYAGNIRENIPPK 156
           E D +V S+ DL    +  G+T+ A   R++      D ++F P++ G   E +P K
Sbjct: 89  EVDLVVHSLKDLPTV-LPPGFTIGAICKRENP----HDAVVFHPKFVGKTLETLPEK 140


>pdb|3ECR|A Chain A, Structure Of Human Porphobilinogen Deaminase
 pdb|3ECR|B Chain B, Structure Of Human Porphobilinogen Deaminase
          Length = 364

 Score = 30.0 bits (66), Expect = 5.5,   Method: Compositional matrix adjust.
 Identities = 17/57 (29%), Positives = 29/57 (50%), Gaps = 5/57 (8%)

Query: 100 EKDEIVKSVMDLKRAEIEEGYTMDAFMSRQDVLMDVRDKLLFEPEYAGNIRENIPPK 156
           E D +V S+ DL    +  G+T+ A   R++      D ++F P++ G   E +P K
Sbjct: 92  EVDLVVHSLKDLPTV-LPPGFTIGAICKRENP----HDAVVFHPKFVGKTLETLPEK 143


  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
   0.318    0.131    0.385 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 20,788,026
Number of Sequences: 62578
Number of extensions: 760573
Number of successful extensions: 1714
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1706
Number of HSP's gapped (non-prelim): 11
length of query: 819
length of database: 14,973,337
effective HSP length: 107
effective length of query: 712
effective length of database: 8,277,491
effective search space: 5893573592
effective search space used: 5893573592
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 56 (26.2 bits)