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= 033178
         (125 letters)

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

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



>pdb|2DGY|A Chain A, Solution Structure Of The Eukaryotic Initiation Factor
          1a In Mgc11102 Protein
          Length = 111

 Score = 35.8 bits (81), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 19/47 (40%), Positives = 27/47 (57%), Gaps = 6/47 (12%)

Query: 17 GSFVVVDESGKEKAIKDGSKVACIVTKVLFYEQVRALQKSTEWPEIF 63
          G F++VD       I++G KV   ++ VL  + VR+LQK   WPE F
Sbjct: 57 GDFLIVD------PIEEGEKVKAEISFVLCKDHVRSLQKEGFWPEAF 97


>pdb|2O8B|B Chain B, Human Mutsalpha (Msh2MSH6) BOUND TO ADP AND A G T MISPAIR
 pdb|2O8C|B Chain B, Human Mutsalpha (msh2/msh6) Bound To Adp And An
           O6-methyl-guanine T Mispair
 pdb|2O8D|B Chain B, Human Mutsalpha (Msh2MSH6) BOUND TO ADP AND A G DU MISPAIR
 pdb|2O8E|B Chain B, Human Mutsalpha (Msh2MSH6) BOUND TO A G T MISPAIR, WITH
           ADP BOUND TO Msh2 Only
 pdb|2O8F|B Chain B, Human Mutsalpha (Msh2MSH6) BOUND TO DNA WITH A SINGLE BASE
           T INSERT
          Length = 1022

 Score = 27.7 bits (60), Expect = 1.9,   Method: Compositional matrix adjust.
 Identities = 15/35 (42%), Positives = 20/35 (57%)

Query: 11  LVFNCAGSFVVVDESGKEKAIKDGSKVACIVTKVL 45
           L+   A S V+VDE G+  A  DG+ +A  V K L
Sbjct: 863 LMHATAHSLVLVDELGRGTATFDGTAIANAVVKEL 897


>pdb|3CVJ|A Chain A, Crystal Structure Of A Putative Phosphoheptose Isomerase
           (Bh3325) From Bacillus Halodurans C-125 At 2.00 A
           Resolution
 pdb|3CVJ|B Chain B, Crystal Structure Of A Putative Phosphoheptose Isomerase
           (Bh3325) From Bacillus Halodurans C-125 At 2.00 A
           Resolution
 pdb|3CVJ|C Chain C, Crystal Structure Of A Putative Phosphoheptose Isomerase
           (Bh3325) From Bacillus Halodurans C-125 At 2.00 A
           Resolution
 pdb|3CVJ|D Chain D, Crystal Structure Of A Putative Phosphoheptose Isomerase
           (Bh3325) From Bacillus Halodurans C-125 At 2.00 A
           Resolution
          Length = 243

 Score = 26.2 bits (56), Expect = 4.6,   Method: Compositional matrix adjust.
 Identities = 11/36 (30%), Positives = 19/36 (52%)

Query: 37  VACIVTKVLFYEQVRALQKSTEWPEIFKSTNSDDAN 72
           + C + + L  E +  L +    P +FKS+N D A+
Sbjct: 195 IGCFLAQALIVETLHLLVQQGFEPPVFKSSNVDGAD 230


>pdb|3JU2|A Chain A, Crystal Structure Of Protein Smc04130 From Sinorhizobium
          Meliloti 1021
          Length = 284

 Score = 26.2 bits (56), Expect = 5.4,   Method: Compositional matrix adjust.
 Identities = 14/31 (45%), Positives = 17/31 (54%), Gaps = 1/31 (3%)

Query: 7  NDIKLVFNCAGSFVVV-DESGKEKAIKDGSK 36
          N +KL   C G F    D SG+EKAI D  +
Sbjct: 58 NGLKLTGLCRGGFFPAPDASGREKAIDDNRR 88


>pdb|3QC0|A Chain A, Crystal Structure Of A Sugar Isomerase (Smc04130) From
          Sinorhizobium Meliloti 1021 At 1.45 A Resolution
          Length = 275

 Score = 25.8 bits (55), Expect = 6.0,   Method: Compositional matrix adjust.
 Identities = 14/28 (50%), Positives = 16/28 (57%), Gaps = 1/28 (3%)

Query: 7  NDIKLVFNCAGSFVVV-DESGKEKAIKD 33
          N +KL   C G F    D SG+EKAI D
Sbjct: 57 NGLKLTGLCRGGFFPAPDASGREKAIDD 84


  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
   0.315    0.131    0.382 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,750,497
Number of Sequences: 62578
Number of extensions: 82496
Number of successful extensions: 158
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 155
Number of HSP's gapped (non-prelim): 6
length of query: 125
length of database: 14,973,337
effective HSP length: 86
effective length of query: 39
effective length of database: 9,591,629
effective search space: 374073531
effective search space used: 374073531
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: 45 (21.9 bits)