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= 017691
         (367 letters)

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

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



>pdb|3HGT|A Chain A, Structural And Functional Studies Of The Yeast Class Ii
           Hda1 Hdac Complex
 pdb|3HGT|B Chain B, Structural And Functional Studies Of The Yeast Class Ii
           Hda1 Hdac Complex
          Length = 328

 Score = 31.2 bits (69), Expect = 0.90,   Method: Compositional matrix adjust.
 Identities = 20/75 (26%), Positives = 35/75 (46%), Gaps = 8/75 (10%)

Query: 160 TLDSGQNDLQFWLESMREEQ--------VKASIPNIIDHFALAIEKLYQEGARKFWIHNT 211
           T+D+ Q D+Q+ L+  RE +        V+    N IDH  L   K + + +R++  + T
Sbjct: 203 TVDTSQKDIQYLLQYKRERKGLERYAPIVRLVAINSIDHCRLFFGKKFDKNSREYLENVT 262

Query: 212 GPIGCLPSMVIKYPP 226
             +  L   +   PP
Sbjct: 263 AAMVILRDRLGTLPP 277


>pdb|3HGQ|A Chain A, Structural And Functional Studies Of The Yeast Class Ii
           Hda1 Hdac Complex
 pdb|3HGQ|B Chain B, Structural And Functional Studies Of The Yeast Class Ii
           Hda1 Hdac Complex
 pdb|3HGQ|C Chain C, Structural And Functional Studies Of The Yeast Class Ii
           Hda1 Hdac Complex
 pdb|3HGQ|D Chain D, Structural And Functional Studies Of The Yeast Class Ii
           Hda1 Hdac Complex
          Length = 328

 Score = 30.4 bits (67), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 20/75 (26%), Positives = 34/75 (45%), Gaps = 8/75 (10%)

Query: 160 TLDSGQNDLQFWLESMREEQ--------VKASIPNIIDHFALAIEKLYQEGARKFWIHNT 211
           T+D+ Q D+Q+ L+  RE +        V+    N IDH  L   K + + +R++  + T
Sbjct: 203 TVDTSQKDIQYLLQYKRERKGLERYAPIVRLVAINSIDHCRLFFGKKFDKNSREYLENVT 262

Query: 212 GPIGCLPSMVIKYPP 226
                L   +   PP
Sbjct: 263 AAXVILRDRLGTLPP 277


>pdb|1QUS|A Chain A, 1.7 A Resolution Structure Of The Soluble Lytic
           Transglycosylase Slt35 From Escherichia Coli
 pdb|1QUT|A Chain A, The Soluble Lytic Transglycosylase Slt35 From Escherichia
           Coli In Complex With N-Acetylglucosamine
 pdb|1QDR|A Chain A, 2.1 A Resolution Structure Of Escherichia Coli Lytic
           Transglycosylase Slt35
 pdb|1QDT|A Chain A, 2.1 A Resolution Structure Of Escherichia Coli Lytic
           Transglycoyslase Slt35 In Complex With Calcium
 pdb|1D0K|A Chain A, The Escherichia Coli Lytic Transglycosylase Slt35 In
           Complex With Two Murodipeptides
           (Glcnac-Murnac-L-Ala-D-Glu)
 pdb|1D0L|A Chain A, The Escherichia Coli Lytic Transglycosylase Slt35 In
           Complex With Bulgecin A
 pdb|1D0M|A Chain A, The Escherichia Coli Lytic Transglycosylase Slt35 In
           Complex With Bulgecin A And (Glcnac)2
          Length = 322

 Score = 30.4 bits (67), Expect = 1.6,   Method: Compositional matrix adjust.
 Identities = 32/110 (29%), Positives = 48/110 (43%), Gaps = 11/110 (10%)

Query: 88  FQHGANFAASGSTIQPVDGKLFGAGFNPLSLNIQLSQFEQLKERSTELYNQAKTSQIKSN 147
            Q G +FA + +  Q +D  +   GF+   L   LSQ ++L      + NQA T+ +K  
Sbjct: 9   MQMGGDFANNPNAQQFIDKMVNKHGFDRQQLQEILSQAKRLDSVLRLMDNQAPTTSVKP- 67

Query: 148 LPRPED-----FSKALYTLDSGQNDLQFWLESM----REEQVKASIPNII 188
            P   +     + K   T D+ QN + FW +      R  QV    P II
Sbjct: 68  -PSGPNGAWLRYRKKFITPDNVQNGVVFWNQYEDALNRAWQVYGVPPEII 116


>pdb|1LTM|A Chain A, Accelerated X-ray Structure Elucidation Of A 36 Kda
           Muramidase/transglycosylase Using Warp
          Length = 320

 Score = 30.4 bits (67), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 32/110 (29%), Positives = 48/110 (43%), Gaps = 11/110 (10%)

Query: 88  FQHGANFAASGSTIQPVDGKLFGAGFNPLSLNIQLSQFEQLKERSTELYNQAKTSQIKSN 147
            Q G +FA + +  Q +D  +   GF+   L   LSQ ++L      + NQA T+ +K  
Sbjct: 7   MQMGGDFANNPNAQQFIDKMVNKHGFDRQQLQEILSQAKRLDSVLRLMDNQAPTTSVKP- 65

Query: 148 LPRPED-----FSKALYTLDSGQNDLQFWLESM----REEQVKASIPNII 188
            P   +     + K   T D+ QN + FW +      R  QV    P II
Sbjct: 66  -PSGPNGAWLRYRKKFITPDNVQNGVVFWNQYEDALNRAWQVYGVPPEII 114


  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
   0.320    0.137    0.426 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,054,080
Number of Sequences: 62578
Number of extensions: 530115
Number of successful extensions: 1241
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1241
Number of HSP's gapped (non-prelim): 4
length of query: 367
length of database: 14,973,337
effective HSP length: 100
effective length of query: 267
effective length of database: 8,715,537
effective search space: 2327048379
effective search space used: 2327048379
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 bits)