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= 014334
         (426 letters)

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

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



>pdb|3S6I|A Chain A, Schizosaccaromyces Pombe 3-Methyladenine Dna Glycosylase
           (Mag1) In Complex With Abasic-Dna.
 pdb|3S6I|D Chain D, Schizosaccaromyces Pombe 3-Methyladenine Dna Glycosylase
           (Mag1) In Complex With Abasic-Dna
          Length = 228

 Score = 40.8 bits (94), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 40/141 (28%), Positives = 66/141 (46%), Gaps = 15/141 (10%)

Query: 250 GNFPSPRELANLDESFLAKRCNLGYRAGRILK-LARGIVDGQIQLR-ELEDMCNEASLTA 307
           G FP+P E+ ++D   + + C    R    LK +A   + G I  + E E + NE     
Sbjct: 82  GQFPTPEEIRDMDFEIM-RACGFSARKIDSLKSIAEATISGLIPTKEEAERLSNE----- 135

Query: 308 YVKLAEQLSQINGFGPFTRNNVLV-CIGFYHVIPTDSETIRH-LKQVHARNCTSKTVQMI 365
             +L E+L+QI G G +T   +L+  +    V+P D  +IR+  + +H        + ++
Sbjct: 136 --ELIERLTQIKGIGRWTVEMLLIFSLNRDDVMPADDLSIRNGYRYLHRLPKIPTKMYVL 193

Query: 366 AESIYGKYAPFQFLAYWSELW 386
             S     APF+  A W  LW
Sbjct: 194 KHSEIC--APFRTAAAWY-LW 211


>pdb|3CBD|A Chain A, Directed Evolution Of Cytochrome P450 Bm3, To Octane
           Monoxygenase 139-3
 pdb|3CBD|B Chain B, Directed Evolution Of Cytochrome P450 Bm3, To Octane
           Monoxygenase 139-3
          Length = 455

 Score = 31.6 bits (70), Expect = 0.97,   Method: Compositional matrix adjust.
 Identities = 31/94 (32%), Positives = 43/94 (45%), Gaps = 25/94 (26%)

Query: 125 EDMVKCML----LCNCQW-----------PRTLSMARALCELQWELQHCSPSISEDFIPQ 169
           EDM +  L    LC   +           P  +SM RAL E+  +LQ  +P         
Sbjct: 143 EDMTRLTLDTIGLCGFNYRFNSFYRDQPHPFIISMIRALDEVMNKLQRANPD-------- 194

Query: 170 TPAGKESKRR-QKVSKVASKLTSR-IAESKASSE 201
            PA  E+KR+ Q+  KV + L  + IA+ KAS E
Sbjct: 195 DPAYDENKRQFQEDIKVMNDLVDKIIADRKASGE 228


>pdb|2O8E|A Chain A, Human Mutsalpha (Msh2MSH6) BOUND TO A G T MISPAIR, WITH
           ADP BOUND TO Msh2 Only
          Length = 934

 Score = 29.3 bits (64), Expect = 4.3,   Method: Compositional matrix adjust.
 Identities = 22/72 (30%), Positives = 32/72 (44%), Gaps = 4/72 (5%)

Query: 278 RILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRNNVLVCIGFYH 337
           R+LK  +G       L E+E+    +SL+A +K  E LS  + FG F     L    F  
Sbjct: 243 RLLKGKKGEQMNSAVLPEMENQVAVSSLSAVIKFLELLSDDSNFGQFE----LTTFDFSQ 298

Query: 338 VIPTDSETIRHL 349
            +  D   +R L
Sbjct: 299 YMKLDIAAVRAL 310


>pdb|2O8B|A Chain A, Human Mutsalpha (Msh2MSH6) BOUND TO ADP AND A G T MISPAIR
 pdb|2O8C|A Chain A, Human Mutsalpha (msh2/msh6) Bound To Adp And An
           O6-methyl-guanine T Mispair
 pdb|2O8D|A Chain A, Human Mutsalpha (Msh2MSH6) BOUND TO ADP AND A G DU MISPAIR
 pdb|2O8F|A Chain A, Human Mutsalpha (Msh2MSH6) BOUND TO DNA WITH A SINGLE BASE
           T INSERT
 pdb|3THW|A Chain A, Human Mutsbeta Complexed With An Idl Of 4 Bases (Loop4)
           And Adp
 pdb|3THX|A Chain A, Human Mutsbeta Complexed With An Idl Of 3 Bases (Loop3)
           And Adp
 pdb|3THY|A Chain A, Human Mutsbeta Complexed With An Idl Of 2 Bases (Loop2)
           And Adp
 pdb|3THZ|A Chain A, Human Mutsbeta Complexed With An Idl Of 6 Bases (Loop6)
           And Adp
          Length = 934

 Score = 29.3 bits (64), Expect = 4.3,   Method: Compositional matrix adjust.
 Identities = 22/72 (30%), Positives = 32/72 (44%), Gaps = 4/72 (5%)

Query: 278 RILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRNNVLVCIGFYH 337
           R+LK  +G       L E+E+    +SL+A +K  E LS  + FG F     L    F  
Sbjct: 243 RLLKGKKGEQMNSAVLPEMENQVAVSSLSAVIKFLELLSDDSNFGQFE----LTTFDFSQ 298

Query: 338 VIPTDSETIRHL 349
            +  D   +R L
Sbjct: 299 YMKLDIAAVRAL 310


  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    0.132    0.389 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,219,498
Number of Sequences: 62578
Number of extensions: 424822
Number of successful extensions: 864
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: 862
Number of HSP's gapped (non-prelim): 6
length of query: 426
length of database: 14,973,337
effective HSP length: 102
effective length of query: 324
effective length of database: 8,590,381
effective search space: 2783283444
effective search space used: 2783283444
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: 53 (25.0 bits)