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= 022845
         (291 letters)

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

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



>pdb|1T94|A Chain A, Crystal Structure Of The Catalytic Core Of Human Dna
           Polymerase Kappa
 pdb|1T94|B Chain B, Crystal Structure Of The Catalytic Core Of Human Dna
           Polymerase Kappa
          Length = 459

 Score = 35.0 bits (79), Expect = 0.046,   Method: Compositional matrix adjust.
 Identities = 23/67 (34%), Positives = 33/67 (49%), Gaps = 3/67 (4%)

Query: 107 PLAEQTNKILSSTNNDATIYKDCYTAMPADIKKKSCAQLGDFITPPGSSRYLLSDAGFID 166
           P+A  +  +LS++N  A  +     AMP  I K+ C QL   I PP   +Y        +
Sbjct: 60  PIAVGSMSMLSTSNYHARRF-GVRAAMPGFIAKRLCPQL--IIVPPNFDKYRAVSKEVKE 116

Query: 167 GLSDYDP 173
            L+DYDP
Sbjct: 117 ILADYDP 123


>pdb|3PZP|A Chain A, Human Dna Polymerase Kappa Extending Opposite A Cis-Syn
           Thymine Dimer
 pdb|3PZP|B Chain B, Human Dna Polymerase Kappa Extending Opposite A Cis-Syn
           Thymine Dimer
          Length = 517

 Score = 35.0 bits (79), Expect = 0.048,   Method: Compositional matrix adjust.
 Identities = 23/67 (34%), Positives = 33/67 (49%), Gaps = 3/67 (4%)

Query: 107 PLAEQTNKILSSTNNDATIYKDCYTAMPADIKKKSCAQLGDFITPPGSSRYLLSDAGFID 166
           P+A  +  +LS++N  A  +     AMP  I K+ C QL   I PP   +Y        +
Sbjct: 116 PIAVGSMSMLSTSNYHARRF-GVRAAMPGFIAKRLCPQL--IIVPPNFDKYRAVSKEVKE 172

Query: 167 GLSDYDP 173
            L+DYDP
Sbjct: 173 ILADYDP 179


>pdb|2OH2|A Chain A, Ternary Complex Of Human Dna Polymerase
 pdb|2OH2|B Chain B, Ternary Complex Of Human Dna Polymerase
 pdb|2W7O|A Chain A, Structure And Activity Of Bypass Synthesis By Human Dna
           Polymerase Kappa Opposite The 7,8-Dihydro-8-
           Oxodeoxyguanosine Adduct
 pdb|2W7O|B Chain B, Structure And Activity Of Bypass Synthesis By Human Dna
           Polymerase Kappa Opposite The 7,8-Dihydro-8-
           Oxodeoxyguanosine Adduct
 pdb|2W7P|A Chain A, Structure And Activity Of Bypass Synthesis By Human Dna
           Polymerase Kappa Opposite The 7,8-Dihydro-8-
           Oxodeoxyguanosine Adduct
 pdb|2W7P|B Chain B, Structure And Activity Of Bypass Synthesis By Human Dna
           Polymerase Kappa Opposite The 7,8-Dihydro-8-
           Oxodeoxyguanosine Adduct
 pdb|3IN5|A Chain A, Structure Of Human Dna Polymerase Kappa Inserting Datp
           Opposite An 8-Oxog Dna Lesion
 pdb|3IN5|B Chain B, Structure Of Human Dna Polymerase Kappa Inserting Datp
           Opposite An 8-Oxog Dna Lesion
          Length = 508

 Score = 35.0 bits (79), Expect = 0.052,   Method: Compositional matrix adjust.
 Identities = 23/67 (34%), Positives = 33/67 (49%), Gaps = 3/67 (4%)

Query: 107 PLAEQTNKILSSTNNDATIYKDCYTAMPADIKKKSCAQLGDFITPPGSSRYLLSDAGFID 166
           P+A  +  +LS++N  A  +     AMP  I K+ C QL   I PP   +Y        +
Sbjct: 109 PIAVGSMSMLSTSNYHARRF-GVRAAMPGFIAKRLCPQL--IIVPPNFDKYRAVSKEVKE 165

Query: 167 GLSDYDP 173
            L+DYDP
Sbjct: 166 ILADYDP 172


  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
   0.316    0.132    0.395 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,763,850
Number of Sequences: 62578
Number of extensions: 221059
Number of successful extensions: 434
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 434
Number of HSP's gapped (non-prelim): 3
length of query: 291
length of database: 14,973,337
effective HSP length: 98
effective length of query: 193
effective length of database: 8,840,693
effective search space: 1706253749
effective search space used: 1706253749
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (24.3 bits)