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= psy1957
         (149 letters)

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

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



>pdb|3RBN|A Chain A, Crystal Structure Of Mutl Protein Homolog 1 Isoform 1
           [homo Sapiens]
 pdb|3RBN|B Chain B, Crystal Structure Of Mutl Protein Homolog 1 Isoform 1
           [homo Sapiens]
          Length = 284

 Score =  139 bits (349), Expect = 7e-34,   Method: Compositional matrix adjust.
 Identities = 68/146 (46%), Positives = 92/146 (63%)

Query: 4   RREIKLSSVRDLRGEIEKQKSSQLCEVFRKLSFVGCATPCMCLIQHETKLYIVNVTYVLE 63
           RR I L+SV  L+ EI +Q    L E     SFVGC  P   L QH+TKLY++N T + E
Sbjct: 31  RRIINLTSVLSLQEEINEQGHEVLREXLHNHSFVGCVNPQWALAQHQTKLYLLNTTKLSE 90

Query: 64  ELFYQLMLHDFGNFGVFRFENPVSIKELLLISLDLPDSGWDPSNGSKSEVAESASQFLLS 123
           ELFYQ++++DF NFGV R   P  + +L  ++LD P+SGW   +G K  +AE   +FL  
Sbjct: 91  ELFYQILIYDFANFGVLRLSEPAPLFDLAXLALDSPESGWTEEDGPKEGLAEYIVEFLKK 150

Query: 124 RADMLTDYFSMEIDTQARLRTLPLLV 149
           +A+ L DYFS+EID +  L  LPLL+
Sbjct: 151 KAEXLADYFSLEIDEEGNLIGLPLLI 176


>pdb|4E4W|A Chain A, Structure Of The C-terminal Domain Of The Saccharomyces
           Cerevisiae Mutl Alpha (mlh1/pms1) Heterodimer
          Length = 285

 Score = 61.6 bits (148), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 39/135 (28%), Positives = 72/135 (53%), Gaps = 7/135 (5%)

Query: 4   RREIKLSSVRDLRGEIEKQKSSQLCEVFRKLSFVGCATP--CMCLIQHETKLYIVNVTYV 61
           R  + L+S++ LR +++     +L ++F  L++VG       +  IQH+ KL++++   V
Sbjct: 22  RVNVNLTSIKKLREKVDDSIHRELTDIFANLNYVGVVDEERRLAAIQHDLKLFLIDYGSV 81

Query: 62  LEELFYQLMLHDFGNFGVFRFENPVSIKELLLISLDLPDSGWDPSNGSKSEVAESASQFL 121
             ELFYQ+ L DF NFG    ++     +++L +L    S +D  N   S+  E     +
Sbjct: 82  CYELFYQIGLTDFANFGKINLQSTNVSDDIVLYNL---LSEFDELNDDASK--EKIISKI 136

Query: 122 LSRADMLTDYFSMEI 136
              + ML +Y+S+E+
Sbjct: 137 WDMSSMLNEYYSIEL 151


>pdb|4FMN|A Chain A, Structure Of The C-terminal Domain Of The Saccharomyces
           Cerevisiae Mutl Alpha (mlh1/pms1) Heterodimer Bound To A
           Fragment Of Ntg2
 pdb|4FMO|A Chain A, Structure Of The C-terminal Domain Of The Saccharomyces
           Cerevisiae Mutl Alpha (mlh1/pms1) Heterodimer Bound To A
           Fragment Of Exo1
          Length = 288

 Score = 61.6 bits (148), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 39/135 (28%), Positives = 72/135 (53%), Gaps = 7/135 (5%)

Query: 4   RREIKLSSVRDLRGEIEKQKSSQLCEVFRKLSFVGCATP--CMCLIQHETKLYIVNVTYV 61
           R  + L+S++ LR +++     +L ++F  L++VG       +  IQH+ KL++++   V
Sbjct: 25  RVNVNLTSIKKLREKVDDSIHRELTDIFANLNYVGVVDEERRLAAIQHDLKLFLIDYGSV 84

Query: 62  LEELFYQLMLHDFGNFGVFRFENPVSIKELLLISLDLPDSGWDPSNGSKSEVAESASQFL 121
             ELFYQ+ L DF NFG    ++     +++L +L    S +D  N   S+  E     +
Sbjct: 85  CYELFYQIGLTDFANFGKINLQSTNVSDDIVLYNL---LSEFDELNDDASK--EKIISKI 139

Query: 122 LSRADMLTDYFSMEI 136
              + ML +Y+S+E+
Sbjct: 140 WDMSSMLNEYYSIEL 154


  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    0.138    0.400 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,766,932
Number of Sequences: 62578
Number of extensions: 132812
Number of successful extensions: 280
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 275
Number of HSP's gapped (non-prelim): 3
length of query: 149
length of database: 14,973,337
effective HSP length: 90
effective length of query: 59
effective length of database: 9,341,317
effective search space: 551137703
effective search space used: 551137703
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 47 (22.7 bits)